Category Archives: Research

Researchers Explain How Rotifers Thrive Despite Forgoing Sex

Bdelloid rotifers haven’t had sex for at least thirty million years. Most asexual animals are doomed to extinction. The excellent show, Science Friday, looks at the extraordinary adaptations that allow rotifers to thrive sex-free.

For millions of years, the rotifers have reproduced asexually, flying in the face of an idea known as the Red Queen Hypothesis, which states that without the advantage of sexual reproduction, more-rapidly evolving parasites and predators will eventually doom the asexual species. Now, the researchers studying the tiny organism say that its ability to dry up and blow away to greener pastures may have given the rotifers a hidden tactical edge in this evolutionary war.

The webcast provides a nice overview of the research. Every week Science Friday provides many such interesting reviews of recent scientific research.

What Are Rotifers?

Rotifers are small, mostly freshwater animals, and are amongst the smallest members of the Metazoa — that group of multicellular animals which includes humans, and whose bodies are organized into systems of organs.
Most rotifers are about 0.5mm in length or less, and their bodies have a total of around a thousand cells. This means that their organ systems are a greatly simplified distillation of the organ systems found in the bodies of the higher animals.

A typical rotifer might have a brain of perhaps fifteen cells with associated nerves and ganglia, a stomach of much the same number, an excretory system of only a dozen or so cells, and a similarly fundamental reproductive system. They have no circulatory system. It is an anomaly that despite their complexity, many rotifers are much smaller than common single-celled organisms whose world they share.
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they are able to survive long periods — even perhaps hundreds of years — in a dried or frozen state, and will resume normal behaviour when rehydrated or thawed.
Secondly, they exhibit what biologists call cell constancy — they grow in size not by cell division, but by increase in the size of the cells which they already have.

Researchers Find Switch That Allows Cancer Cells to Spread

Researchers discovered of a specific protein called disabled-2 (Dab2) that switches on the process that releases cancer cells from the original tumor and allows the cells to spread and develop into new tumors in other parts of the body.

The process called epithelial-mesenchymal transdifferientiation (EMT) has been known to play a role in releasing cells (epithelial cells) on the surface of the solid tumor and transforming them into transient mesenchymal cell: cells with the ability to start to grow a new tumor.

This is often the fatal process in breast, ovarian, pancreatic and colon-rectal cancers.

Searching to understand how the EMT process begins, Ge Jin, who has joint appointments at the Case Western Reserve University School of Dental Medicine and the Lerner Research Institute at the Cleveland Clinic, began by working backwards from EMT to find its trigger. The researchers found that a compound called transforming growth factor-ÃŸ (TGF-ÃŸ) triggers the formation of the Dab2 protein. It was this protein, Dab2, that activated the EMT process.

He discovered that when the researchers knocked out Dab2, EMT was not triggered. “This is the major piece in cancer research that has been missing,” Jin said. Most tumors are epithelial in origin and have epithelial markers on their surface. The EMT process takes place when some of those cells dislodge from the surface and undergo a transformation into a fibrous mesenchymal cell maker with the ability to migrate.

“EMT is the most important step in this process,” said Jin. He was part of a six-member research team, led by Philip Howe from the Department of Cancer Biology at the Lerner Research Institute in a National Institute of Cancer-funded study. The research group studied the biological processes that initiated the cancer spread by using cancer cells in animal models.

“If we can understand the signaling pathway for modulating EMT, then we can design drugs to delay or halt EMT cells and control tumor progression,” Jin said. Beyond cancer, Jin said. “The process we discovered may lead to understanding how other diseases progress.”

Slime Mold and Engineers Design Similar Solution

Slime Mold Grows Network Just Like Tokyo Rail System

Talented and dedicated engineers spent countless hours designing Japan’s rail system to be one of the world’s most efficient. Could have just asked a slime mold.

When presented with oat flakes arranged in the pattern of Japanese cities around Tokyo, brainless, single-celled slime molds construct networks of nutrient-channeling tubes that are strikingly similar to the layout of the Japanese rail system, researchers from Japan and England report Jan. 22 in Science. A new model based on the simple rules of the slime mold’s behavior may lead to the design of more efficient, adaptable networks, the team contends.
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The yellow slime mold Physarum polycephalum grows as a single cell that is big enough to be seen with the naked eye. When it encounters numerous food sources separated in space, the slime mold cell surrounds the food and creates tunnels to distribute the nutrients. In the experiment, researchers led by Toshiyuki Nakagaki, of Hokkaido University in Sapporo, Japan, placed oat flakes (a slime mold delicacy) in a pattern that mimicked the way cities are scattered around Tokyo, then set the slime mold loose.
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Initially, the slime mold dispersed evenly around the oat flakes, exploring its new territory. But within hours, the slime mold began to refine its pattern, strengthening the tunnels between oat flakes while the other links gradually disappeared. After about a day, the slime mold had constructed a network of interconnected nutrient-ferrying tubes. Its design looked almost identical to that of the rail system surrounding Tokyo, with a larger number of strong, resilient tunnels connecting centrally located oats. “There is a remarkable degree of overlap between the two systems,” Fricker says.

Siftable Modular Computers

Pretty cool. I must admit I don’t really see how this would function outside of specifically designed situation. I can imagine it could be very cool for education, especially of young kids. Siftables act in concert to form a single interface: users physically manipulate them – piling, grouping, sorting – to interact with digital information and media. David Merrill and Jeevan Kalanithi originally created Siftables at the MIT Media Lab and have formed a company to commercialize the product and have received a grant from NSF to continue the work.

Microbes Flourish In Healthy People

Bugs Inside: What Happens When the Microbes That Keep Us Healthy Disappear? by Katherine Harmon

The human body has some 10 trillion human cells—but 10 times that number of microbial cells. So what happens when such an important part of our bodies goes missing?
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“Someone who didn’t have their microbes, they’d be naked,” says Martin Blaser, a professor of microbiology and chair of the Department of Medicine at New York University Langone Medical Center in New York City.
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Even though it is such an apparently integral and ancient aspect of human health, scientists are still grasping for better ways to study human microbiota—before it changes beyond historical recognition. Borrowing models from outside of medicine has helped many in the field gain a better understanding of this living world within us. “The important concept is about extinctions,” Blaser says. “It’s ecology.”
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The first step in understanding these systems is simply taking stock of what archaea, bacteria, fungi, protozoa and viruses are present in healthy individuals. This massive micro undertaking has been ongoing since 2007 through the National Institutes of Health’s (NIH) Human Microbiome Project. So far it has turned up some surprisingly rich data, including genetic sequencing for some 205 of the different genera that live on healthy human skin.

Despite the flood of new data, Foxman laughs when asked if there is any hope for a final report from the Human Microbiome Project any time soon. “This is the very, very beginning,” she says, comparing this project with the NIH’s Human Genome Project, which jump-started a barrage of new genetic research. “There are basic, basic questions that we don’t know the answers to,” she says, such as how different microbiota are between random individuals or family members; how much microbiota change over time; or how related the microbiota are to each other on or inside a person’s body.

Fungus-gardening Ant Species Has Given Up Sex Completely

The complete asexuality of a widespread fungus-gardening ant, the only ant species in the world known to have dispensed with males entirely, has been confirmed by a team of Texas and Brazilian researchers.

photo of christian rabeling excavating ants in Brazil

Graduate student Christian Rabeling excavating fungus-farming ant nests in Brasilia.

Most social insects—the wasps, ants and bees—are relatively used to daily life without males. Their colonies are well run by swarms of sterile sisters lorded over by an egg-laying queen. But, eventually, all social insect species have the ability to produce a crop of males who go forth in the world to fertilize new queens and propagate.

Queens of the ant Mycocepurus smithii reproduce without fertilization and males appear to be completely absent, report Christian Rabeling, Ulrich Mueller and their Brazilian colleagues in open access journal PLoS ONE this week.

“Animals that are completely asexual are relatively rare, which makes this is a very interesting ant,” says Rabeling, an ecology, evolution and behavior graduate student at The University of Texas at Austin. “Asexual species don’t mix their genes through recombination, so you expect harmful mutations to accumulate over time and for the species to go extinct more quickly than others. They don’t generally persist for very long over evolutionary time.”

Previous studies of the ants from Puerto Rico and Panama have pointed toward the ants being completely asexual. One study in particular, by Mueller and former graduate student Anna Himler (now at Arizona State University), showed that the ants reproduced in the lab without males, and that no amount of stress induced the production of males.

Scientists believed that specimens of male ants previously collected in Brazil in the 1960s could be males of M. smithii. If males of the species existed, it would suggest that—at least from time to time—the ants reproduce sexually.

Rabeling analyzed the males in question and discovered that they belonged to another closely related (sexually reproducing) species of fungus-farmer, Mycocepurus obsoletus, thus establishing that no males are known to exist for M. smithii. He also dissected reproducing M. smithii queens from Brazil and found that their sperm storage organs were empty.

Taken together with the previous studies of the ants, Rabeling and his colleagues have concluded that the species is very likely to be totally asexual across its entire range, from Northern Mexico through Central America to Brazil, including some Caribbean islands.

As for the age of the species, the scientists estimate the ants could have first evolved within the last one to two million years, a very young species given that the fungus-farming ants evolved 50 million years ago.

Rabeling says he is using genetic markers to study the evolution and systematics of the fungus-gardening ants and this will help determine the date of the appearance and genetic mechanism of asexual reproduction more precisely in the near future.

Full press release

Sumatran Tiger and Cubs Filmed by Remote Wildlife Monitoring Cameras

Video cameras installed in the Sumatran jungle in Indonesia have captured close-up footage of a tiger and two cubs. This is the first time that the World Wildlife Fund has recorded evidence of tiger breeding in central Sumatra in what should be prime tiger habitat.

The Sumatran Tiger is the smallest of all surviving tiger subspecies. Male Sumatran tigers average 204 cm (6 feet, 8 inches) in length from head to tail and weigh about 136 kg (300 lb).

Analysis of DNA is consistent with the hypothesis that the Sumatran Tigers have been isolated after a rise in sea level at the Pleistocene to Holocene border (about 12,000-6,000 years ago) from other tiger populations. The Sumatran Tiger is genetically isolated from all living mainland tigers.

Wouldn’t it be nice to see the photos those tigers could take with the awesome cat cam?

Printing Bone, Muscle and More

A Pittsburgh-based research team has created and used an innovative ink-jet system to print “bio-ink” patterns that direct muscle-derived stem cells from adult mice to differentiate into both muscle cells and bone cells.

The custom-built ink-jet printer, developed at Carnegie Mellon’s Robotics Institute, can deposit and immobilize growth factors in virtually any design, pattern or concentration, laying down patterns on native extracellular matrix-coated slides (such as fibrin). These slides are then placed in culture dishes and topped with muscle-derived stem cells (MDSCs). Based on pattern, dose or factor printed by the ink-jet, the MDSCs can be directed to differentiate down various cell-fate differentiation pathways (e.g. bone- or muscle-like).

“This system provides an unprecedented means to engineer replacement tissues derived from muscle stem cells,” said Johnny Huard, professor of orthopedic surgery at the University of Pittsburgh School of Medicine and director of the Stem Cell Research Center at Children’s Hospital of UPMC. Huard has long-standing research findings that show how muscle-derived stem cells (MDSCs) from mice can repair muscle in a model for Duchenne Muscular Dystrophy, improve cardiac function following heart failure, and heal large bone and articular cartilage defects.

Weiss and Campbell, along with graduate student Eric Miller, previously demonstrated the use of ink-jet printing to pattern growth factor “bio-inks” to control cell fates. For their current research, they teamed with Phillippi, Huard and biologists of the Stem Cell Research Center at Children’s Hospital to gain experience in using growth factors to control differentiation in populations of MDSCs from mice.

The team envisions the ink-jet technology as potentially useful for engineering stem cell-based therapies for repairing defects where multiple tissues are involved, such as joints where bone, tendon, cartilage and muscle interface. Patients afflicted with conditions like osteoarthritis might benefit from these therapies, which incorporate the needs of multiple tissues and may improve post-treatment clinical outcomes.

The long-term promise of this new technology could be the tailoring of tissue-engineered regenerative therapies. In preparation for preclinical studies, the Pittsburgh researchers are combining the versatile ink-jet system with advanced real-time live cell image analysis developed at the Robotics Institute and Molecular Biosensor and Imaging Center to further understand how stem cells differentiate into bone, muscle and other cell types.

Prion Proteins, Without Genes, Can Evolve

‘Lifeless’ prion proteins are ‘capable of evolution’

scientists transferred prion populations from brain cells to other cells in culture and observed the prions that adapted to the new cellular environment out-competed their brain-adapted counterparts. When returned to the brain cells, the brain-adapted prions again took over the population.

Charles Weissmann, head of Scripps Florida’s department of infectology who led the study, said: “On the face of it, you have exactly the same process of mutation and adaptive change in prions as you see in viruses.

“This means that this pattern of Darwinian evolution appears to be universally active. “In viruses, mutation is linked to changes in nucleic acid sequence that leads to resistance.

“Now, this adaptability has moved one level down- to prions and protein folding – and it’s clear that you do not need nucleic acid (DNA or RNA) for the process of evolution.”
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He said: “The prion protein is not a clone, it is a quasi-species that can create different protein strains even in the same animal. “The abnormal prion proteins multiply by converting normal prion proteins.

“The implication of Charles Weissmann’s work is that it would be better to cut off that supply of normal prion proteins rather than risk the abnormal prion adapting to a drug and evolving into a new more virulent form.

Microcosm by Carl Zimmer

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.