Zebrafish – Tiny fish offers big hopes in genome research

Tiny fish offers big hopes in genome research (via AFP)

One of the world’s most popular aquarium fishes on Wednesday joined the rat, the mouse, fruitfly and nematode worm in the roll call of creatures whose DNA has been sequenced to help fight disease among humans. A consortium of researchers unveiled the genome of the zebrafish in the British journal Nature…

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Icy cosmic start for amino acids and DNA ingredients

The Green Bank Telescope and some of the molecules it has discovered. (Credit: Bill Saxton, NRAO/AUI/NSF)

Feb. 28, 2013 — Using new technology at the telescope and in laboratories, researchers have discovered an important pair of prebiotic molecules in interstellar space. The discoveries indicate that some basic chemicals that are key steps on the way to life may have formed on dusty ice grains floating between the stars.

The scientists used the National Science Foundation’s Green Bank Telescope (GBT) in West Virginia to study a giant cloud of gas some 25,000 light-years from Earth, near the center of our Milky Way Galaxy. The chemicals they found in that cloud include a molecule thought to be a precursor to a key component of DNA and another that may have a role in the formation of the amino acid alanine.

One of the newly-discovered molecules, called cyanomethanimine, is one step in the process that chemists believe produces adenine, one of the four nucleobases that form the “rungs” in the ladder-like structure of DNA. The other molecule, called ethanamine, is thought to play a role in forming alanine, one of the twenty amino acids in the genetic code.

“Finding these molecules in an interstellar gas cloud means that important building blocks for DNA and amino acids can ‘seed’ newly-formed planets with the chemical precursors for life,” said Anthony Remijan, of the National Radio Astronomy Observatory (NRAO).

In each case, the newly-discovered interstellar molecules are intermediate stages in multi-step chemical processes leading to the final biological molecule. Details of the processes remain unclear, but the discoveries give new insight on where these processes occur.

Previously, scientists thought such processes took place in the very tenuous gas between the stars. The new discoveries, however, suggest that the chemical formation sequences for these molecules occurred not in gas, but on the surfaces of ice grains in interstellar space.

“We need to do further experiments to better understand how these reactions work, but it could be that some of the first key steps toward biological chemicals occurred on tiny ice grains,” Remijan said.

The discoveries were made possible by new technology that speeds the process of identifying the “fingerprints” of cosmic chemicals. Each molecule has a specific set of rotational states that it can assume. When it changes from one state to another, a specific amount of energy is either emitted or absorbed, often as radio waves at specific frequencies that can be observed with the GBT.

New laboratory techniques have allowed astrochemists to measure the characteristic patterns of such radio frequencies for specific molecules. Armed with that information, they then can match that pattern with the data received by the telescope. Laboratories at the University of Virginia and the Harvard-Smithsonian Center for Astrophysics measured radio emission from cyanomethanimine and ethanamine, and the frequency patterns from those molecules then were matched to publicly-available data produced by a survey done with the GBT from 2008 to 2011.

A team of undergraduate students participating in a special summer research program for minority students at the University of Virginia (U.Va.) conducted some of the experiments leading to the discovery of cyanomethanimine. The students worked under U.Va. professors Brooks Pate and Ed Murphy, and Remijan. The program, funded by the National Science Foundation, brought students from four universities for summer research experiences. They worked in Pate’s astrochemistry laboratory, as well as with the GBT data.

“This is a pretty special discovery and proves that early-career students can do remarkable research,” Pate said.

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Stash of stem cells found in a human parasite

A composite image of a scanning electron micrograph of a pair of male and female Schistosoma mansoni with the outer tegument (skin) of the male worm “peeled back” (digitally) to reveal the stem cells (orange) underneath. (Credit: Jim Collins, Ana Vieira and Phillip Newmark, Howard Hughes Medical Institute and University of Illinois at Urbana-Champaign)

Feb. 22, 2013 — The parasites that cause schistosomiasis, one of the most common parasitic infections in the world, are notoriously long-lived. Researchers have now found stem cells inside the parasite that can regenerate worn-down organs, which may help explain how they can live for years or even decades inside their host.

Schistosomiasis is acquired when people come into contact with water infested with the larval form of the parasitic worm Schistosoma, known as schistosomes. Schistosomes mature in the body and lay eggs that cause inflammation and chronic illness. Schistosomes typically live for five to six years, but there have been reports of patients who still harbor parasites decades after infection.

According to new research from Howard Hughes Medical Institute (HHMI) investigator Phillip Newmark, collections of stem cells that can help repair the worms’ bodies as they age could explain how the worms survive for so many years. The new findings were published online on February 20, 2013, in the journal Nature.

The stem cells that Newmark’s team found closely resemble stem cells in planaria, free-living relatives of the parasitic worms. Planaria rely on these cells, called neoblasts, to regenerate lost body parts. Whereas most adult stem cells in mammals have a limited set of possible fates—blood stem cells can give rise only to various types of blood cells, for example —planarian neoblasts can turn into any cell in the worm’s body under the right circumstances.

Newmark’s lab at the University of Illinois at Urbana-Champaign has spent years focused on planaria, so they knew many details about planarian neoblasts —what they look like, what genes they express, and how they proliferate. They also knew that in uninjured planarians, neoblasts maintain tissues that undergo normal wear and tear over the worm’s lifetime.

“We began to wonder whether schistosomes have equivalent cells and whether such cells could be partially responsible for their longevity,” says Newmark.

Following this hunch, and using what they knew about planarian neoblasts, post-doctoral fellow Jim Collins, Newmark, and their colleagues hunted for similar cells in Schistosoma mansoni, the most widespread species of human-infecting schistosomes.

Their first step was to look for actively dividing cells in the parasites. To do this, they grew worms in culture and added tags that would label newly replicated DNA as cells prepare to divide; this label could later be visualized by fluorescence. Following this fluorescent tag, they saw a collection of proliferating cells inside the worm’s body, separate from any organs.

The researchers isolated those cells from the schistosomes and studied them individually. They looked like typical stem cells, filled with a large nucleus and a small amount of cytoplasm that left little room for any cell-type-specific functionality. Newmark’s lab observed the cells and found that they often divided to give rise to two different cells: one cell that continued dividing, and another cell that did not.

“One feature of stem cells,” says Newmark, “is that they make more stem cells; furthermore, many stem cells undergo asymmetric division.” The schistosomes cells were behaving like stem cells in these respects. The other characteristic of stem cells is that they can differentiate into other cell types.

To find out whether the schistosome cells could give rise to multiple types of cells, Newmark’s team added the label for dividing cells to mice infected with schistosomes, waited a week, and then harvested the parasites to see where the tag ended up. They could detect labeled cells in the intestines and muscles of the schistosomes, suggesting that stem cells incorporating the labels had developed into both intestinal and muscle cells.

Years of previous study on planarians by many groups paved the way for this type of work on schistosomes, Newmark says.

“The cells we found in the schistosome look remarkably like planarian neoblasts. They aren’t associated with any one organ, but can give rise to multiple cell types. People often wonder why we study the ‘lowly’ planarian, but this work provides an example of how basic biology can lead you, in unanticipated and exciting ways, to findings that are directly relevant to important public health problems.”

Newmark says the stem cells aren’t necessarily the sole reason schistosome parasites survive for so many years, but their ability to replenish multiple cell types likely plays a role. More research is needed to find out how the cells truly affect lifespan, as well as what factors in the mouse or human host spur the parasite’s stem cells to divide, and whether the parasites maintain similar stem cells during other stages of their life cycle.

The researchers hope that with more work, scientists will be able to pinpoint a way to kill off the schistosome stem cells, potentially shortening the worm’s lifespan and treating schistosome infections in people.

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Scientists develop zombie cells | TG Daily

Posted February 23, 2013 – 18:39 by David Konow

With the advent of The Walking Dead, zombies are more popular now than ever before.

Interestingly enough, GiantFreakinRobot and the Huffington Post recently ran a story about biologists developing zombie cells.

No, this is not something out of I Am Legend where a virus gets out and created zombies everywhere, don’t panic, this was an experiment developed in Sandia National Laboratories and the University of New Mexico biology labs where they developed “zombie-like” cells.

As the Post tells us, mammalian cells are coated with silica, and it makes replicas that are nearly perfect to the original. The silica protects the cells, and they can keep living at higher temperatures and pressures than the first living cells. At 400 degrees, the protein of the cell evaporates, but a three-dimensional replica of the “formerly living being” is left behind, thanks to the silica.
The head researcher said, “Our zombie cells bridge chemistry and biology to create forms that not only near-perfectly resemble their past selves, but can do future work.” But as Robot tells us, this is not for the development of creating zombies, thankfully. This is to try and create fossils that we can create fuels from.

“That’s right,” writes Rudie Obias. “Zombie gasoline for cars, boats, and airplanes.” Could this eventually end all energy crises and we’ll never have to go to war with the Middle East over oil again? That would be cool, no? And we thought electric cars and going solar were going to save us.
In other undead news, you read our report on TG about hackers pulling a zombie prank in Montana. The pranksters got onto the local station KRTV, and played an emergency warning that the undead were attacking. This thankfully did not result in wide-spread panic, the TV viewers who saw the warning apparently got the joke, but the FCC didn’t find this very amusing.
In fact, according to Media Bistro, the Federal Communications Commission has been telling TV stations to “take immediate action” and make sure their Emergency Alert Systems are more secure after this zombie hacker prank.”

Again, people got the joke, but you never know. Without a disclaimer that the whole thing’s in fun, maybe there could be an undead panic down the road, especially if The Walking Dead stays on top in the ratings, and zombie cells becomes the energy source of the future.

Flowers use electrical signals to summon bees | TG Daily

Posted February 22, 2013 – 04:20 by Kate Taylor

Flowers ‘advertise’ the presence of nectar to bees using electrical signals, say University of Bristol researchers, by indicating whether they’ve recently been visited by another bee.

Plants are usually charged negatively and emit weak electric fields; while bees acquire a positive charge as they fly through the air. While sparks don’t actually fly as a charged bee approaches a charged flower, a small electric force builds up that can potentially convey information.

“This novel communication channel reveals how flowers can potentially inform their pollinators about the honest status of their precious nectar and pollen reserves,” says Dr Heather Whitney, a co-author of the study.

By placing electrodes in the stems of petunias, the researchers showed that when a bee lands, the flower’s electrical potential changes and remains so for several minutes. And, they found, bumblebees can detect and distinguish between different floral electric fields, letting them know whether another bee has recently visited.

The team isn’t sure just how the bees detect electric fields – although they speculate that it’s the same electrostatic force that makes your hair stand up after brushing, affecting the bumblebees’ hairy bodies.

The discovery of such electric detection has opened up a whole new understanding of insect perception and flower communication, says lead author Professor Daniel Robert.

“The last thing a flower wants is to attract a bee and then fail to provide nectar: a lesson in honest advertising since bees are good learners and would soon lose interest in such an unrewarding flower,” he says.

“The co-evolution between flowers and bees has a long and beneficial history, so perhaps it’s not entirely surprising that we are still discovering today how remarkably sophisticated their communication is.”

Newt Finding Might Set Back Efforts to Regrow Human Limbs: Scientific American

Unique proteins in these amphibians cast doubt on the existence of any latent potential for limb regeneration

By Zoe Cormier and Nature magazine

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The Eastern, or red-spotted, newt may have evolved the ability to regenerate organs and limbs in relatively recent times Image: Flickr/StoneHorse Studios

The ability of some animals to regenerate tissue is generally considered to be an ancient quality of all multicellular animals. A genetic analysis of newts, however, now suggests that it evolved much more recently.

Tiny and delicate it may be, but the red spotted newt (Notophthalmus viridescens) has tissue-engineering skills that far surpass the most advanced biotechnology labs. The newt can regenerate lost tissue, including heart muscle, components of its central nervous system and even the lens of its eye.

Doctors hope that this skill relies on a basic genetic program that is common — albeit often in latent form — to all animals, including mammals, so that they can harness it in regenerative medicine. Mice, for instance, are able to generate new heart cells after myocardial injury.

The newt study, by Thomas Braun at the Max Planck Institute for Heart and Lung Research in Bad Nauheim, Germany, and his colleagues, suggest that it might not be so simple.

Attempts to analyze the genetics of newts in the same way as for humans, mice and flies have so far been hampered by the enormous size of the newt genome, which is ten times larger than our own. Braun and his colleagues therefore looked at the RNA produced when genes are expressed — known as the transcriptome — and used three analytical techniques to compile their data.

The team compiled the first catalogue of all the RNA transcripts expressed in N. viridescens, looking at both primary and regenerated tissue in the heart, limbs and eyes of both embryos and larvae.

The researchers found more than 120,000 RNA transcripts, of which they estimate 15,000 code for proteins. Of those, 826 were unique to the newt. What is more, several of those sequences were expressed at different levels in regenerated tissue than in primary tissue. Their results are published in Genome Biology.

Modern or ancestral?
The findings add to existing evidence that the ability evolved recently, says Jeremy Brockes of University College London, whose research provided the first evidence that regenerating tissue in salamanders express proteins that are not found in other vertebrates.

“I no longer believe that there is an ancestral program that is waiting to be reawakened,” Brockes says. “However, I absolutely do believe it’s possible to coax mammal tissues into regenerating to a greater degree with the lessons we learn from newts.”

But saying that the trait is either ancestral or recent is probably too “black and white”, says Elly Tanaka of the Center for Regenerative Therapies in Dresden, Germany. The truth, she says, could be somewhere in the middle. “It may in fact be that regeneration is ancestral, but that newts have species-specific adaptations that allow it to have such spectacular regenerative capacities compared with other vertebrates.”

Moreover, Tanaka adds, scientists would do well to look for more grey zones in the potential for harnessing the regenerative capacities of newts (and of other animals, such as fish). Rather than focusing on spectacular, but perhaps unlikely, scenarios in which amputees could regrow entire limbs, researchers should instead focus on more plausible options, such as improving the healing of scars and burns or increasing the speed of organ regeneration.

This article is reproduced with permission from the magazine Nature. The article was first published on February 21, 2013.