Stories tagged Life Science

Apr
01
2013

Broccoli ice cream anyone?: Broccoli is just one of the new flavors of genetically modified ice cream now for sale. Through the GM process, 93 percent of calories have been removed from the new ice cream products.
Broccoli ice cream anyone?: Broccoli is just one of the new flavors of genetically modified ice cream now for sale. Through the GM process, 93 percent of calories have been removed from the new ice cream products.Courtesy Terence Ong
In one of the biggest breakthroughs in food and dietary history, the U.S. Food and Drug Administration has announced today (April 1, 2013), that it is permitting the sale of genetically modified ice cream to the public. The announcement comes on the heals of 16 years of experimenting and testing to come with a healthier version of the dairy food.

"Through the genetic modification (GM) process, we've been able to remove up to 93 percent of the calories you find in traditional ice creams, explained FDA spokesman Herman Guernsey. "And with that breakthrough, we've eliminated 100 percent of the guilt associated with eating ice cream. Now, people will be able to enjoy healthier and happier ice cream."

Of course, such breakthroughs also require some significant changes to the ice cream. The GM process did not work for traditional ice cream flavors like vanilla, chocolate or strawberry. "We did have to turn to some more health-oriented flavorings, but our focus groups seemed to especially like the GM ice cream flavors of broccoli, spinach and tuna," said Guernsey.

Cost is another issue for consumers. In order to push the GM ice cream through this advanced process, the cost right now is about $10 a pint. While public sales start today, GM ice cream may not be available in all grocery stores. But internet orders are being accepted at the website www.gmicecream.com. "We strongly advise anyone making internet orders do do so in the winter time as the ice cream is shipped by U.S. mail," Guernsey added.

He concluded: "We think people will enjoy this new GM ice cream and have a good laugh while reading this blog post."

Feb
25
2013

OMG! Can nothing stop them?: According to a new study, mosquitoes, those buzzing, biting, itch-producing flying pests that make life miserable for many of Earth's inhabitants (mainly we humans), can easily adapt to Deet, one of the commonly used ingredients in insect repellents.
OMG! Can nothing stop them?: According to a new study, mosquitoes, those buzzing, biting, itch-producing flying pests that make life miserable for many of Earth's inhabitants (mainly we humans), can easily adapt to Deet, one of the commonly used ingredients in insect repellents.Courtesy Mark Ryan (with photo help from NASA)

We've all seen them, those great B-films where a giant, vicious monster from under the sea, or invaders from outer space arrive to cause mayhem across our cities and generally mess up our way of life. In the end, it seems no matter who or what it was that was attacking us, be it Mothra, Godzilla, or some race of belligerent extra-terrestrials, we could always count on the military to save our collective behind.

Unfortunately, with mosquitoes, that might now be the case anymore.

Scientists are reporting that Deet, one of the most widely used active ingredients in insect repellents, loses its effectiveness against mosquitoes shortly after those ubiquitous, blood-seeking winged vermin are first exposed to it.

Deet - the common name for N,N-diethyl-meta-toluamide - was developed by the US Army after the Second World War to help combat insects during jungle warfare. It was used extensively in the Korean and Vietnam wars, but mosquitoes seem to be able to adapt quickly to it.

"Mosquitoes are very good at evolving very very quickly", said Dr. James Logan of the London School of Hygiene and Tropical Medicine and co-author of the study. "There is something about being exposed to the chemical that first time that changes their olfactory system - changes their sense of smell - and their ability to smell Deet, which makes it less effective."

So what I want to know is where does that leave us here in Minnesota where the mosquito constantly competes with the Common Loon for the title of State Bird? Maybe it's time to start digging the bunker in the backyard.

SOURCE and LINKS
BBC Science news
Original study at Plos One
The Life Cycle of the Mosquito
All about mosquitoes on NatGeo

Jan
31
2013

Home at last: Our late cat, Ernesto "El Gato Gordo" Hemingway, seen recuperating after somehow managing to find his way back home from across the street in 1997.
Home at last: Our late cat, Ernesto "El Gato Gordo" Hemingway, seen recuperating after somehow managing to find his way back home from across the street in 1997.Courtesy Mark Ryan
A cat in Florida got loose on one side of the state and managed to find its way back home to the other side, baffling both the delighted owners and scientists. Holly, the directionally-savvy 4-year-old tortoiseshell cat traveled from Daytona Beach to within a mile of her owners’ home in West Palm Beach. It took her about 50 days to traverse the 200 mile distance. When found, the poor kitty was weak and emaciated, had a croaky meow, and displayed signs of hoofing it over long distances.

“Her pads on her feet were bleeding,” said Bonnie Richter, who along with her husband, Jacob, are the happy owners (read: service staff) of the migratory feline. “Her claws are worn weird. The front ones are really sharp, the back ones worn down to nothing.

Skeptics might conjecture that the found cat is merely a stray that just looks like the long-lost Holly, and that the distraught owners only think it’s their cat because they miss her so and want to believe it’s her. Well, they couldn’t be more wrong. The scruffy cat in question had an implanted microchip that proves it is indeed Holly.

The Richters’ tale is but one of many incredible stories about lost or separated pets finding their way back home across vast distances. And surprisingly, science doesn’t seem to have any answers as how the animals do it.

“I really believe these stories, but they’re just hard to explain,” said Marc Bekoff, a behavioral ecologist at the University of Colorado. “Maybe being street-smart, maybe reading animal cues, maybe being able to read cars, maybe being a good hunter. I have no data for this.”

SOURCE
New York Times story

Jan
25
2013

Doubling up the double helix: The newly discovered quadruple helix in human DNA could lead to new treatments in cancer.
Doubling up the double helix: The newly discovered quadruple helix in human DNA could lead to new treatments in cancer.Courtesy rijksbandradio (original image) via Flckr; graphic by author.
By now most readers are aware of the double helix, the two intertwined ribbons of genetic information that make up our DNA.

Now researchers at University of Cambridge have announced the discovery of a quadruple helix in the human genome. The four-stranded genetic ribbons are termed G-quadruplexes because they contain high levels of the nucleotide guanine (the other 3 nucleotides are adenine, thymine, and cytosine – together they make up the G, A, T, and C elements of DNA; uracil (U) replaces thymine in RNA). G-quadruplexes mainly appear at the moment of cell replication, when cells divide and multiply. Researchers think this indicates that G-quadruplexes are an essential part of the replication process. The upsurge of G-quadrupleexes was detected using fluorescent biomarkers. The discovery could open up new avenues in the treatment of cancer

"The research indicates that quadruplexes are more likely to occur in genes of cells that are rapidly dividing, such as cancer cells,” said Shankar Balasubramanian, the study’s lead researcher. “For us, it strongly supports a new paradigm to be investigated -- using these four-stranded structures as targets for personalised treatments in the future."

Balasubramanian, a professor at the Department of Chemistry and Cambridge Research Institute, thinks synthetic molecules could one day be used to corral the G-quadruplexes and hinder the out-of-control cell division often prevalent in cancerous cells. In fact, the research team has already been successful in slowing down the replication process by using such molecules. During their experiments, when cell division was blocked, the number of G-quadruplexes decreased.

The research was published in Nature Chemistry. The 'quadruple helix' discovery comes 60 years after the discovery of the double helix in 1953, also at the University of Cambridge.

SOURCES and LINKS
Wired
Science Daily

Jan
24
2013

Sniffing Out Cancer: Amherst chemists develop a way to "smell" cancer cells.
Sniffing Out Cancer: Amherst chemists develop a way to "smell" cancer cells.Courtesy Jeremie63
Chemists from the University of Massachusetts Amherst have developed a way to quickly and accurately detect and identify metastatic cancer cells in living tissue, in much the same way that your nose can detect and identify certain odors.

The smell of a rose, for example, is a unique pattern of molecules, which activates a certain set of receptors in your nose. When these specific receptors are triggered, your brain immediately recognizes it as a rose.

Similarly, each type of cancer has a unique pattern to the proteins that make up its cells. The Amherst chemists just needed a "nose" to recognize these patterns. What they came up with was an array of gold nanoparticle sensors, coupled with green fluorescent proteins (GFP). The researchers took healthy tissue and tumor samples from mice, and trained the nanoparticle-GFP sensors to recognize the bad cells, and for the GFP to fluoresce in the presence of metastatic tissues.

This method is really sensitive to subtle differences, it's quick (can detect cancer cells within minutes), it can differentiate between types of cancers, and is minimally invasive. The researchers haven't tested this method on human tissue samples yet, but it holds some exciting potential.

Jan
11
2013

Nano at home!: Forget those super-sterile clean rooms.  The DIY Nano app lets you explore nanoscale science in the comfort of your own home!
Nano at home!: Forget those super-sterile clean rooms. The DIY Nano app lets you explore nanoscale science in the comfort of your own home!Courtesy NISE Network
When things get really really small (nanoscale small), they behave completely differently! For example, gold at the nanoscale can look purple, orange, or red; static electricity has a greater effect on nanoparticles than gravity; and aluminum (the stuff your benign soda cans are made of) is explosive at the nanoscale!

If you want to experience some of these nanoscale phenomena first-hand, check out whatisnano.org, or download the DIY Nano app. The website and the app were both created by the Nanoscale Informal Science Education Network (NISE Net for short), and have videos and activity guides, complete with instructions and material lists, so you can do some nano experiments at home! The app was a Parents' Choice award winner for 2012, and was featured in Wired Magazine's review of apps. Definitely worth a look!

Have fun exploring nanoscale properties!

Jan
07
2013

A white-throated sparrow: Is its tweeting music to the ears other birds?
A white-throated sparrow: Is its tweeting music to the ears other birds?Courtesy Dave Govoni (Va bene!)
Is birdsong music? Does the tweeting and chirping of our feathered friends elicit the same emotional response in them as one of Chopin’s nocturnes does in us? Do they serve the same purpose? These are questions that have long been argued in scientific circles and elsewhere.

A new study published recently in Frontiers of Evolutionary Neuroscience shows some interesting results in how birds perceive birdsong.

Researcher Sarah Earp and neuroscientist Donna Maney, both of Emory University looked at brain imaging data gathered from studies of human neural responses to music and compared them with similar data from birdsong studies.

Some of the white-throated sparrows were given a boost of hormones (testosterone and estradiol) that made them all a-twitter and ready for love. When a male sparrow stepped up to the microphone and started serenading, the females showed a definite response.

“We found that the same neural reward system is activated in female birds in the breeding state that are listening to male birdsong, and in people listening to music that they like,” said Sarah Earp.

But what was music to the ears of the female sparrows was perceived by their male counterparts as discordant (and probably very annoying) noise from a rival suitor. An awkward third-wheel sort of deal, I suppose.

“Birdsong is a signal,” said Maney. “And the definition of a signal is that it elicits a response in the receiver. Previous studies hadn’t approached the question from that angle, and it’s an important one.”

The females in the sample group showed increased activity in the same region of their bird brains that humans display in their corresponding region when hearing a piece of music they enjoy. The response of the control group females - those not in a breeding state and without any hormonal boost - showed little response to song. Male sparrows treated with testosterone showed an amygdala response not unlike how the human brain responds to scary movie music.*

The brain’s mesolimbic reward pathway has counterparts in both humans and birds. In humans it lies beneath the cerebrum and is involved in emotions, memory, and olfaction. A neurotransmitter called dopamine is produced within the brain’s limbic system and spreads along the limbic pathways to help regulate the brain’s reward and pleasure centers. The chemical messenger also governs movement and emotions.

The study shows that not only does birdsong and music produce similar responses in corresponding brain regions linked to reward but also in areas thought to regulate emotions. And the response also seems to connected to social context in both birds and humans.

“Both birdsong and music elicit responses not only in brain regions associated directly with reward, but also in interconnected regions that are thought to regulate emotion,” Earp said. “That suggests that they both may activate evolutionarily ancient mechanisms that are necessary for reproduction and survival.”

LINKS
Emory University story
Frontiers of Evolutionary Neuroscience
More about dopamine
The intelligence of birds

*Rather than scary, I find composer Bernard Herrmann’s musical score used in Alfred Hitchcock’s PSYCHO very compelling – not sure what that response means. But it’s interesting to note that Herrmann’s music in the movie was also a big influence on record producer George Martin’s string arrangement for the Beatles’ melancholy ballad ELEANOR RIGBY.

Dec
20
2012

C-MORE Group Blog Post

On October 2, 2012, the Center for Microbial Oceanography: Research and Education (C-MORE) hosted the Virtual Workshop on Science Writing as part of the Science Communication module for the Professional Development Training Program for graduate students and post-doctoral researchers. One of the activities for the workshop was to write a 350(+/-)-word blurb about their own research for a broader audience. We are excited to share some of these blog posts. Thanks for reading!
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Life is tough: we live in a dog-eat-dog world, where it is every man for himself and those that prosper seem to be the smartest and the sneakiest. Life in the deep blue sea is similarly challenging: food is scarce, hiding places are few, and predators are always lurking in dark waters in search of a quick meal. However, all marine organisms are connected to one another through a network of feeding interactions called a food web. Marine food webs are whale-eat-plankton, squid-eat-shrimp, shark-eat-tuna kinds of places. All of these diverse organisms are engaged in an on-going arms race for survival.

So how do scientists know the structure of the marine food web? Who eats whom? Which organisms are the most important players in the web? What happens if human activity like large-scale fishing or trawling interrupts some of the links in the web? Anela Choy, a Ph.D. student studying Oceanography at the University of Hawaii, is trying to answer some of these very questions in Hawaiian waters. Traditional techniques like looking in the stomachs of marine organisms can be time-consuming, sample-intensive, and downright smelly. However, new biochemical tracers (e.g., stable isotopes, fatty acids and trace metals) are being used by Anela to elucidate food web connectivity. Ultimately, Anela hopes to shed new light in the dark ocean on understudied predator-prey relationships between deeper ocean animals and large marine fishes, many of which are commercially harvested at unsustainable levels.

Predator-prey interactions make up the backbone of a food web. While complex and confusing at times, the transfer of energy through these interactions allows for life to persist in the ocean. For example, without microscopic plankton there would be no large sharks – not because sharks dine regularly at the plankton salad bar but because plankton is food for small crustaceans called zooplankton, which are in turn food for small fishes, which then feed larger fishes that sharks eventually eat themselves. A change or break in any link of the food web ultimately means changes in the other links. A better understanding of marine food webs will provide a basis for ensuring that in an ever-changing ocean, people will still have access to fresh and delicious Hawaiian-caught fish for dinner!

Anela Choy is a Ph.D. graduate student at the University of Hawaii at Manoa. You can read more about her research here.
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On a November morning in Hawai’i, the ocean stretches out like a rippling sheet of glass before me – the surfers are surely disappointed, but it’s a perfect day for SCUBA diving. One hundred feet beneath the boat, colonies of “cauliflower” coral are clearly visible. As the name implies, they bear a striking resemblance to a certain hated vegetable. Once at depth, I’m amazed by the diversity of animals hiding in the reef – a startled octopus that immediately releases a cloud of ink, a moray eel defending his crevice, and even a pair of whitetip reef sharks resting in a shallow cave. But what about the corals themselves? They are as animated as rocks or trees. So, are corals animal, vegetable, or mineral?

The answer is that although corals are technically animals (so props to you if you guessed correctly!), they also have aspects that are “vegetable,” “mineral,” and perhaps most surprisingly, “microbial”. It has long been recognized that the coral harbors symbiotic algae (the “vegetable” part) that perform photosynthesis and pass most of the sugar products to the coral. Likewise, anyone who’s ever cut herself on a reef realizes that corals produce a hard skeleton (the “mineral” part). The “microbial” part of coral, invisible to the naked eye, has only received serious attention within the last decade.

But what a decade it’s been! Microbes on corals, including bacteria, viruses, fungi, and a domain of life known as the Archaea, have been found to play essential roles in both coral health and disease. For instance, certain bacteria are now known to provide nutrients to the coral host. However, other microbial species cause the deadly White Band Disease, which has decimated the elkhorn and staghorn coral populations in the Caribbean. These are only a couple of examples of microbial activities on coral reefs – the fact is, there are hundreds of millions of microbes on each square centimeter of coral and we know next to nothing about them. Scientists have their work cut out for them – so stay tuned for updates from the world of corals and microbes!

Dr. Christine Shulse is a postdoctoral scholar with C-MORE at the University of Hawaii where she studies coral symbioses with marine bacteria. Read more about her research here.
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How did life start on Earth? One idea is that organic molecules, the basic building blocks of life, were delivered to Earth by comet impacts. However, recent research at the University of Hawai’i suggests that organic molecules could be produced much closer to home, in craters at the Moon’s poles, as a natural result of exposing simple ices like water and CO2 to radiation from space.

The craters at the Moon’s poles are never exposed to sunlight, so temperatures in these craters can reach as low as 25 Kelvin (about -248 degrees Celsius), as measured by the Diviner instrument on the Lunar Reconnaissance Orbiter spacecraft. These permanently shadowed regions are cold enough to trap volatile compounds like water, carbon dioxide, ammonia, and more from comets, asteroids, and the solar wind. These simple ices can combine to form complex organic molecules when they’re exposed to radiation—in fact, this is one process used to explain the presence of organic molecules on comets.

The Moon is constantly exposed to radiation from galactic cosmic rays, or energetic charged particles from outside the solar system. The only question is whether the trapped ices at the Moon’s poles are present long enough to acquire the high radiation doses that stimulate organic synthesis on comets, since the Moon’s tilt changes with time and today’s permanently shadowed regions probably weren’t cold enough to trap ices two billion years ago.

Researchers at the University of Hawaii used particle physics modeling to calculate the radiation dose received by ices at the lunar poles. In results submitted to the scientific journal Icarus, they discovered that the Moon’s cold traps could accumulate 36 eV per molecule of radiation over their two billion history—compared to only 10 eV per molecule required by chemists to stimulate organic synthesis in experiments.

These results suggest that organic molecules are not a rare resource in the inner solar system, delivered only by wayward comets. Instead, they could be continuously produced in craters on the Moon, Mercury, and asteroids, providing a wealth of ingredients from which life could have formed billions of years ago. If organics really are being produced at the Moon’s poles, it means that, as the closest place to Earth where we can study this process, the Moon would be a great natural laboratory for future robotic and human astrobiology missions to visit!

Sarah T. Crites is a Ph. D. student at the Hawaii Institute for Geophysics and Planetology at the University of Hawaii at Manoa.
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Similar to the way that a meteorologist predicts the weather, I predict the activity of phytoplankton (plant-like micro-organisms, or algae) in the ocean; I like to figure out where, when and how these cell-sized plants grow. I do this using numerical models. Some of these models are statistical (e.g., regression, correlation) or more mechanistic (e.g., fitting data to a specially shaped curve), while others are complex and deterministic (i.e., using fancy partial differential equations calculated over 3-dimensional domains).

Most recently, I have been able to investigate how phytoplankton interact and complement one another using a complex “trait-based model”. With this type of model, I first prescribe simple rules (or parameters) to each phytoplankton type: some types prefer lots of nutrients; some prefer low light conditions, etc. I put all of these different phytoplankton types into a model that simulates the tides and sloshing around of the ocean’s waters, watch the different phytoplankton types interact and compete for resources, and see where they end up (or “emerge”).

It turns out that the types that prefer nutrient-poor waters offshore may ultimately depend on those types that prefer growing in high nutrient coastal waters! All of these phytoplankton types together are called a community. Even though they are single-celled plant-like organisms, they grow and interact with one another in ways that parallel that of human communities. And like people, phytoplankton are complicated, their behaviors vary quite a bit, they come in all shapes and sizes, and sometimes they can be very unpredictable! Despite the challenges of measuring and predicting phytoplankton populations in the ocean, our ecosystem model of the California Coastal System does a great job at capturing seasonal changes in the low productive offshore waters and high productive coastal waters, as shown in this video:

See video

Dr. Nicole Goebel is a post-doctoral researcher at the University of California, Santa Cruz.
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Food webs are all around us: ant caravans carrying food, deer nibbling leaves, bats snapping insects, and squirrels crunching nuts. Open ocean food webs are harder to spot, because in the oceans, all the action is microscopic! Whales, sharks, tuna, and anchovy alike are all ultimately fed by phytoplankton, plants that are too small to see.

Land plants grow by adding leaves or thickening trunks. Phytoplankton have less storage space and can’t just keep growing bigger, so they behave differently. Consider a teabag in water; inside the bag are particles like phytoplankton cells. The tea itself is water and various dissolved compounds, like sugars, proteins, caffeine, and amino acids. During phytoplankton photosynthesis, some of the new organic carbon material they produce from carbon dioxide, using sunlight energy, stays within their cells (growth of particulate stuff, basically making more stuff in the teabag); some of the new material becomes dissolved compounds like sugars, proteins, fats, and amino acids. Just like terrestrial plants, phytoplankton are eaten by other organisms called zooplankton. These zooplankton don’t eat neatly and so some of each cell they try to eat is spilled and adds to the amount of dissolved compounds; we call this “sloppy feeding”. Think of a baby first learning to eat, sometimes as much gets on baby and parent as goes into the child!

We can certainly drink tea and use the dissolved compounds it contains (caffeine!), but many ocean organisms can’t use dissolved material, because they swim in water. If they drank the water to get the compounds dissolved in it, they would be trying to drink the ocean. So, the dissolved stuff from phytoplankton is available only to bacteria, because bacteria are small enough to get the dissolved amino acids, and proteins, and so on without taking in the water as well. The bacteria then turn some of those dissolved compounds back into carbon dioxide as they respire, and some of it they use to build new cell material. That cell material now in the bacteria is then big enough to attract the attention of the zooplankton, and so that dissolved stuff can be recycled back into the food web.

How much new organic material is usually produced? Is it mostly inside cells or outside the cells? As part of my work with the Hawaii Ocean Time-series program, I try to measure how much dissolved material is produced by phytoplankton photosynthesis, what percent of the total photosynthetic production that is, and also how fast the bacteria are growing. I want to know if these production rates change with seasons, or the amount of light, or the amount of nutrients present. I am also interested in how ocean acidification affects the amount of dissolved material produced. As we add more CO2 to the atmosphere and it finds its way into the oceans, does increased CO2 make the phytoplankton produce more organic matter, and if so, will that new material be in the tea or in the teabag?

Donn Viviani is a Ph.D. graduate student at the University of Hawaii at Manoa. You can read more about his research here.
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Leaning over the railing of our 40’ research vessel, I notice a tug on the thick blue rope serving as our fishing line. “I think we’ve got one!” I yell to the crew, "Get the tagging gear ready!” From over 1000 feet below the surface of the ocean, we haul a live, 10-foot sixgill shark onto the boat.

Sixgill sharks live on deep slopes of islands and continents, where divers cannot venture and light hardly penetrates. So, how can we find out anything about them? Well, Kevin Weng and his team at the University of Hawaii tag them with small sensors, which collect data such as depth, temperature, and light. The tags pop off at a preset date, so we don’t have to catch the shark twice to find out where it's been.

Using these tags, we’ve discovered that sixgill sharks cover a lot of "ground"! They are amazing divers, diving over 1000' each day. Horizontally, they can cross hundreds of miles of open ocean. Sixgills could be moving all around the Pacific, or even beyond! This could mean that distant populations of sixgills may be connected by movements and breeding, which might make them less susceptible to local fishing impacts. But even with large-scale geographic movements, sixgill sharks could still be in trouble. Some studies indicate rapid declines in sixgill shark populations over short time scales, potentially associated with fishing pressure. Deep sharks often grow and mature quite slowly, so it might take a long time to replenish a population. Learning where sharks go and how they use their habitat can help us locate important nursery areas, which need to be protected to ensure continued survival of the species.

Returning to the deck of our research vessel, it’s time to tag a shark. On the count of three, we insert the sensor under the tough layer of skin and set the shark free. She points her snout downwards and with two tail beats, is diving back to her dark, cold home far beneath the surface.

Christina Comfort recently completed her M.S. degree in Biological Oceanography this semester at the University of Hawaii at Manoa.
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Each summer in the dark bottom waters off Louisiana, fish and crabs scatter to avoid suffocating in a 20,000 square kilometer dead zone. The Dead Zone is neither adjacent to the Twilight Zone nor crawling with zombies, but it does sit 70 miles southeast of New Orleans in the Gulf of Mexico. Hundreds of kilotons of nitrogen and phosphorous rich fertilizer runoff from the breadbasket of America drain in to the Gulf of Mexico via the Mississippi River, stimulating the growth of tiny aquatic plants (phytoplankton). These plants die and sink to the sea floor where bacteria devour the remains using oxygen in the process. It is this hypoxic (oxygen lacking) area that mobile animals flee from, searching for healthier waters.

What happens when there is no escape? What makes this low-oxygen layer a long-term threat? Don’t all those tiny plants make more than enough oxygen?

The answer to that is stratification: the sun-warmed, freshwater from the river sits on top of the salty, cold ocean water, due to density differences. The physical differences between the two water bodies prohibit movement of gases by creating a physical barrier called a pycnocline that prohibits oxygen from passing from the surface to the bottom. Beneath the pycnocline any oxygen produced is devoured rapidly with every microbial bite.

Yet, something in the dark survives, because the Dead Zone isn’t really “dead.” The Mississippi River’s persistent plunge to the sea has gone on for a thousand years and a hardy community of invertebrates has learned to thrive under these harsh conditions. In 2005, the passage of Hurricane Katrina threw the entire ecosystem for a loop. The physical havoc wreaked on the seafloor opened the door for a whole new set of invertebrates to move in and take over, but they could not adapt to the low oxygen levels ensuring a summer massacre on the sea floor. They just didn’t have the decades of adaptations to sit calmly in the dark and wait out the long rain of dead plants and wait for fall storms to mix oxygen back into the bottom layer.

Climate change is going to impact coastal ecosystems in many unexpected ways. Systems that function admirably under environmental stress can be devastated by the unexpected. The Dead Zone might soon resemble the horrifying corpse-ridden wasteland that its name suggests.

Dr. Clifton Nunnally is a post-doctoral research fellow at the University of Hawaii.
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The wind blowing over the ocean does not only produce surface waves that are enjoyed by surfers, but it also generates waves that propagate from the surface towards the deep ocean. For that reason, this type of wave is called “internal wave” or “internal swell” in an analogy to the surface waves people see on the beach.

The ocean can be thought of as composed of an infinite amount of thin layers of same density or temperature (“stratified”). Internal waves displace these layers up and down as they move from the surface to the deep. Because of this, researchers have long recognized breaking internal waves as key factors in controlling the amount of mixing between warmer near-surface waters and colder deeper waters.

The amount of mixing occurring in the interior of the ocean, which depends strongly on the energy of the internal waves, has important implications to Earth’s climate and its understanding remains as one of the biggest conundrums in climate science. For instance, it is still unclear how much of the wind energy is converted to internal waves, let alone how much of the wave’s energy is used for mixing in the deep ocean. Therefore it is important to map and quantify the sources of internal swells.

Similar to surf waves, most of the internal swell energy in the ocean has been known to originate from winter storms near the Westerlies region. However, researchers at the University of Hawaii suggest that powerful internal swells may be regularly generated in the tropics, more specifically off the coast of Central America.

In this region, an atmospheric phenomenon called the Easterly Wave is responsible for blowing strong winds over the ocean, repeating itself every 3 to 7 days with such perfect timing as to generate energetic, near-inertial (because their frequency is close to that of the Earth’s rotation) internal waves. Because of the particularly strong stratification of this part of the ocean, most of this energy inputted by the wind is carried away downward as big internal swells. Thus, the Easterly Wave can be a viable source of energy for mixing in the deep ocean, or for surfers to find the biggest waves yet, if only they could catch internal waves!

Saulo Soares is a Ph.D. graduate student at the University of Hawaii at Manoa.
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With our bodies bent at the waist, leaning dangerously over the rail, we watch in anticipation as the Secchi disk twirls in the purplish blue waters near Easter Island. The round, black-and-white plastic disk has been providing measurements of water clarity since its invention in 1865. The white sections of the disk flicker as sunlight penetrates to an astounding depth of 236 ft. Who lives down below, and how do they live?

Since phytoplankton use sunlight, carbon dioxide, and water to make their cells, one might think that the phytoplankton in this region would be happy campers. But phytoplankton, much like land plants, also need nutrients to make proteins, nucleic acids, and other cell parts for reproduction. Even though the South Pacific Gyre is full of light, it is one of the most “oligotrophic” (low nutrient) waters in the world. My goal during this expedition was to investigate the identities of a group of really small phytoplankton that have adapted to low-nutrient conditions, and to determine whether some species prefer to live in specific light levels at different depths in the ocean.

To obtain a census of the photosynthetic inhabitants of this region, I collect and filter about half a gallon of seawater from different depths onto a small filter membrane. Each filter is barely an inch wide, but contains ~3 million cells of my study organisms. When I'm back on land, the cells on the filter are extracted for DNA, molecules comprising genetic instructions for cell development. A specific gene (18S ribosomal RNA) in this extracted DNA is isolated using coding markers, and is compared to genes from other cells collected around the world. If I find matches, I will know that either the same, or related, phytoplankton species are living in certain regions of the world ocean. I can then piece together a larger picture, linking the types of phytoplankton to their environmental characteristics such as light intensity and nutrient concentrations.

With every expedition, one gene at a time, I am able to zoom into the life of the phytoplankton that make their home in the clearest ocean water on Earth.

Shimi Rii is a Ph.D. graduate student at the University of Hawaii at Manoa. She hosted the C-MORE Virtual Workshop on Science Writing.

Dec
13
2012

Vision evolution: The compound eye of a 390 million-year-old trilobite, Phacops rana milleri.
Vision evolution: The compound eye of a 390 million-year-old trilobite, Phacops rana milleri.Courtesy Striving to a goal
Somewhere, deep in the recesses of animal evolution, a mass of molecules known as opsin mutated from a run-of-the-mill protein into a detector protein with great vision. Not vision in the figurative way, but vision in the literal way. Opsin is the protein in the photopigments of your eye that interacts with light, and allows you to see all the wonderful things visible in the universe. If you’re reading this post, you have the opsins in your eyes to thank.

Here’s how it works. When a particle or wave of light (a photon) enters your eye, the light sensitive opsin traps it using a small chromophore molecule in it architecture called retinal. Normally, retinal’s tail is all twisted and bent, tensed up, and waiting for something to happen. That’s just the way retinal is when it’s chilling out. But when a photon hits it, the light particle interrupts retinal’s naptime, and the molecule reacts by straightening out its tail. The tail’s movement starts a chain reaction of sorts activating the opsin, which in turn, activates a nearby nerve that shoots out a signal that your brain perceives as light.

Three types of opsin can exist in the eye: R-opsins (rhabdomeric), C-opsins (ciliary, and Go/RGR-opsins (Go-coupled/retinal G protein-coupled receptor). The R and C opsins, depending what type of animal you are (e.g. vertebrate or jellyfish), are used for detecting light. Go/RGR-opsins don’t detect light but are used instead to help regenerate retinal cells and regulate an animal’s inner clock or biological rhythms. Scientists have known about opsins since the 19th century, but haven’t known much on how they evolved, or how they became designated light detectors.

In a recent study published in the journal PNAS, Roberto Feuda of the Department of Biology, National University of Ireland Maynooth, and colleagues reported on their detailed examination of the genetic trail of opsins in all kinds of animal life, from sponges and jellyfish to reptiles, birds and mammals. And while their results warrant further study, they did add new knowledge to our understanding how the eye evolved.

The study negated a long-held idea among scientists that only certain light-designated opsins were present in certain animal types. Generally, C-opsins were thought to be present only in vertebrates, and R-opsins only in invertebrates. But the study showed otherwise. It postulated that all three forms of opsins probably existed in the earliest common ancestor right from the beginning. Later, somewhere along their respective evolutionary lines each group designated the C or R opsins for light detection. The leftover opsins (whether C or R) were used for other non-visual purposes such as setting biological rhythms.

It also pushed the origins of light-sensitive organs back a couple hundred million years from about half a billion years ago to three-quarters of a billion years ago, a time not long after sponges had diverged from other animals and before they split into Bilateria and Cnidaria. Within that evolutionary timeline opsins were found in the gene sequence of the tiny and transparent shape-shifting microorganisms called placozoa. However, because the genome lacks a critical retinal-binding amino acid - lysine 296– it’s unlikely these opsins were able to detect light. (It should be noted that placozoan phylogeny is still under debate). But somewhere along the evolutionary line, these non-visual opsins mutated into a light sensing protein. After just two more gene duplications the three opsins, R, C, and Go/RGR we find in our eye’s photopigments today, were already present in the genome.

Why or when opsins developed into part of the eye’s photopigment is anyone’s guess. This research doesn’t solve all the mysteries surrounding them, particularly their non-visual functions but it does fill in some of the gaps in our understanding of key components of vision evolution.

SOURCES

The Conversation article
Scientific American article
Intro to phyologeny

Oct
08
2012

Crystal Palace dinosaurs: These out-dated depictions of dinosaurs were created by artist Benjamin Waterhouse Hawkins with scientific input from Sir Richard Owen - the comparative anatomist who coined the term "dinosaur". The sculptures, built in 1854, still grace the old grounds of the Crystal Palace in south London today (in Sydenham Park) and were some of the very first images of dinosaurs presented to the general public. More than a 150 years later International Dinosaur Month is celebrated now each October.
Crystal Palace dinosaurs: These out-dated depictions of dinosaurs were created by artist Benjamin Waterhouse Hawkins with scientific input from Sir Richard Owen - the comparative anatomist who coined the term "dinosaur". The sculptures, built in 1854, still grace the old grounds of the Crystal Palace in south London today (in Sydenham Park) and were some of the very first images of dinosaurs presented to the general public. More than a 150 years later International Dinosaur Month is celebrated now each October.Courtesy Mark Ryan
I don’t have a clue who or what entity officially proclaimed October as International Dinosaur Month (and there doesn’t seem to be any official site online), but whoever it was, it’s a great idea! This means not only do we get to celebrate Earth Science Week (October 14-20), and National Fossil Day (October 17*) this month but we also get to celebrate everyone’s favorite prehistoric beasts! A quick Internet search brought up a couple teacher sites here, here and here each offering some interesting ideas on how to celebrate the great Mesozoic monsters this month. There's also this International Dinosaur Month site on Pinterest , and another Pinterest site (mine) featuring dinosaur postcards. Or you could go view some dinosaurs at a local or nearby museum. Below, I’ve included a few museum links to dinosaur-related exhibits, and a site that lists dinosaur exhibitions around the world. If you or your classes are celebrating dinosaurs this month or have other suggestions on how to do so, please let us know.

*The Science Museum of Minnesota will celebrate National Fossil Day on Saturday, October 20 this year.

Smithsonian NMNH
American Museum of Natural History
Dinosaur National Monument
Where to see dinosaurs around the world