Like humans, amoebae pack a lunch before they travel

Some amoebae do what many people do. Before they travel, they pack a lunch.

In results of a study reported today in the journal Nature, evolutionary biologists Joan Strassmann and David Queller of Rice University show that long-studied social amoebae Dictyostellum discoideum (commonly known as slime molds) increase their odds of survival through a rudimentary form of agriculture. Research by lead author Debra Brock, a graduate student at Rice, found that some amoebae sequester their food--particular strains of bacteria--for later use.

"We now know that primitively social slime molds have genetic variation in their ability to farm beneficial bacteria as a food source," says George Gilchrist, program director in the National Science Foundation's Division of Environmental Biology, which funded the research. "But the catch is that with the benefits of a portable food source, comes the cost of harboring harmful bacteria." After these "farmer" amoebae aggregate into a slug, they migrate in search of nourishment--and form a fruiting body, or a stalk of dead amoebae topped by a sorus, a structure containing fertile spores. Then they release the bacteria-containing spores to the environment as feedstock for continued growth.

The findings run counter to the presumption that all "Dicty" eat everything in sight before they enter the social spore-forming stage. Non-farmer amoebae do eat everything, but farmers were found to leave food uneaten, and their slugs don't travel as far. Perhaps because they don't have to. The advantages of going hungry now to ensure a good food supply later are clear, as farmers are able to thrive in environments in which non-farmers find little food. The researchers found that about a third of wild-collected Dicty are farmers. Instead of consuming all the bacteria they encounter, these amoebae eat less and incorporate bacteria into their migratory systems.

Brock showed that carrying bacteria is a genetic trait by eliminating all living bacteria from four farmers and four non-farmers--the control group--by treating them with antibiotics. All amoebae were grown on dead bacteria; tests confirmed that they were free of live bacteria. When the eight clones were then fed live bacteria, the farmers all regained their abilities to seed bacteria colonies, while the non-farmers did not. Dicty farmers are always farmers; non-farmers never learn.

Rice graduate student Tracy Douglas co-authored the paper with Brock, Queller and Strassmann. She confirmed that farmers and non-farmers belong to the same species and do not form a distinct evolved group. Still, mysteries remain.

The researchers want to know what genetic differences separate farmers from non-farmers. They also wonder why farmer clones don't migrate as far as their counterparts.

It might be a consequence of bacterial interference, they say, or an evolved response, since farmers carry the seeds of their own food supply and don't need to go as far. Also, some seemingly useless or even harmful bacteria are not consumed as food, but may serve an as-yet-undetermined function, Brock says.

That has implications for treating disease as it may, for instance, provide clues to the way tuberculosis bacteria invade cells, says Strassmann, infecting the host while resisting attempts to break them down. The results demonstrate the importance of working in natural environments with wild organisms whose complex ties to their living environment have not been broken.

Source : National Science Foundation

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Your genome in minutes: New technology could slash sequencing time

Scientists from Imperial College London are developing technology that could ultimately sequence a person's genome in mere minutes, at a fraction of the cost of current commercial techniques.

The researchers have patented an early prototype technology that they believe could lead to an ultrafast commercial DNA sequencing tool within ten years. Their work is described in a study published this month in the journal 'Nano Letters' and it is supported by the Wellcome Trust Translational Award and the Corrigan Foundation.

The research suggests that scientists could eventually sequence an entire genome in a single lab procedure, whereas at present it can only be sequenced after being broken into pieces in a highly complex and time-consuming process. Fast and inexpensive genome sequencing could allow ordinary people to unlock the secrets of their own DNA, revealing their personal susceptibility to diseases such as Alzheimer's, diabetes and cancer. Medical professionals are already using genome sequencing to understand population-wide health issues and research ways to tailor individualised treatments or preventions.

Dr Joshua Edel, one of the authors on the study from the Department of Chemistry at Imperial College London, said: "Compared with current technology, this device could lead to much cheaper sequencing: just a few dollars, compared with $1m to sequence an entire genome in 2007. We haven't tried it on a whole genome yet but our initial experiments suggest that you could theoretically do a complete scan of the 3,165 million bases in the human genome within minutes, providing huge benefits for medical tests, or DNA profiles for police and security work. It should be significantly faster and more reliable, and would be easy to scale up to create a device with the capacity to read up to 10 million bases per second, versus the typical 10 bases per second you get with the present day single molecule real-time techniques."

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Learning the language of bacteria

Bacteria are among the simplest organisms in nature, but many of them can still talk to each other, using a chemical "language" that is critical to the process of infection. Sending and receiving chemical signals allows bacteria to mind their own business when they are scarce and vulnerable, and then mount an attack after they become numerous enough to overwhelm the host's immune system.

This system, called "quorum sensing," is an interesting example of sophistication among microbes, says Helen Blackwell, an associate professor of chemistry at the University of Wisconsin-Madison. In practical terms, she adds, quorum sensing may provide an alternative therapeutic target as bacteria continue to evolve resistance to antibiotics.

Theoretically, blocking quorum sensing would prevent the bacteria from turning pathogenic and producing the toxins that are an immediate cause of disease in bacterial infections.

Bacteria use simple chemical signals to control quorum sensing, and Blackwell is interested in how these compounds work and in developing new ways to intercept them. In a study just published online in the journal ChemBioChem, Blackwell and colleagues Andrew Palmer, Evan Streng and Kelsea Jewell showed that several species of bacteria can respond to identical signals, suggesting that one drug could battle quorum sensing in several types of bacteria. Many bacteria use a class of molecules called lactones for quorum sensing, and Blackwell's lab has synthesized many non-native lactones, and then tested them in two species of bacteria that use identical native lactone signals. Overall, the organisms responded similarly to the same synthetic molecules, despite the dramatic differences between the species. These results suggest that the same basic chemical sensing mechanism could be common among microbes, Blackwell says. "That tells us that we can use these classes of chemicals to study — and perhaps eventually fight — a much broader range of bacteria."

Finding a broad-spectrum activity for the synthetic lactones is good news, Blackwell adds. "Bacteria come in countless varieties, and the ability to target multiple organisms with one compound could streamline the search for drugs. At the same time, we also have found differences in signal selectivity that may allow us to target some bacteria while ignoring others." That could provide the best of both worlds, Blackwell says. One drug might halt multiple infections, but related drugs might affect only one microbe in a mixture. "The data indicate that it should be possible to design and use compounds that are either selective or broad-spectrum."

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How we come to know our bodies as our own

[PRESS RELEASE, 17 June 2011] By taking advantage of a 'body swap' illusion, researchers at Karolinska Institutet have captured the brain regions involved in one of the most fundamental aspects of self-awareness: how we recognize our bodies as our own, distinct from others and from the outside world. That self-perception is traced to specialized multisensory neurons in various parts of the brain that integrate different sensory inputs across all body parts into a unified view of the body. The findings, reported in the journal Current Biology, may have important medical and industrial applications.

Activity in the brain associated with the illusion of owning a manniquin's body. Credit: Current Biology and the study authors

"When we look down at our body, we immediately experience that it belongs to us," says Valeria Petkova, one of the researchers behind the study. "We do not experience our body as a set of fragmented parts, but rather as a single entity. Our study is the first to tackle the important question of how we come to have the unitary experience of owning an entire body."

Earlier studies showed that the integration of visual, tactile and proprioceptive information (the sense of the relative position of body parts) in multisensory areas constitutes a mechanism for the self-attribution of single limbs, the researchers explained. But how ownership of individual body parts translates into the unitary experience of owning a whole body remained a mystery.

In the current study, the researchers used a 'body-swap' illusion, in which people experienced a mannequin to be their own, in combination with functional magnetic resonance imaging (fMRI). Participants observed touching of the mannequi's body from the point of view of the mannequin's head while feeling identical synchronous touches on his or her own body, which they could not see. Those studies revealed a tight coupling between the experience of full-body ownership and neural responses in brain regions known to represent multisensory processing nodes in the primate brain, specifically the bilateral ventral premotor and left intraparietal cortices and the left putamen.

Activation in those multisensory areas was stronger when the stimulated body part was attached to a body, as compared with when it was detached, they report, evidence that the integrity between body segments facilitates ownership of the parts. According to the researchers, the findings suggest that the integration of visual, tactile and proprioceptive information in body-part-centered reference frames represents a basic neural mechanism underlying the feeling of ownership of entire bodies.

"Understanding the mechanisms underlying the self-attribution of a body in the healthy brain can help developing better diagnostic and therapeutic strategies to address pathological disturbances of bodily self- perception," says Associate Professor Henrik Ehrsson, who led the study. "In addition, understanding the mechanisms of perceiving an entire body or a body part as belonging to oneself can have important implications for the design and production of mechanical prosthesis or robotic substitutes for paralyzed or amputated body parts."

Publication:

Valeria I. Petkova, Malin Björnsdotter, Giovanni Gentile, Tomas Jonsson, Tie-Qiang Li, H. Henrik Ehrsson

From part to whole body ownership in the multisensory brain

Current Biology, Volume 21; Issue 13, online 16 June 2011

• Journal website

For questions, please contact:

PhD Valeria Petkova

Work:

+46 (0)85248 7989

E-mail:

• valeria.petkova@ki.se

• Department of neuroscience

Associate Professor Henrik Ehrsson

Work:

+46 (0)8 524 87 231

E-mail:

• Henrik.Ehrsson@ki.se

• Contact the press office and download photos

Last modified by: Katarina Sternudd 2011-06-17

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Bacterium engineered with DNA in which thymine is replaced by synthetic building block

The genetic information of all living cells is stored in the DNA composed of the four canonical bases adenine (A), cytosine (C), guanine (G) and thymine (T). An international team of researchers has now succeeded in generating a bacterium possessing a DNA in which thymine is replaced by the synthetic building block 5-chlorouracil (c), a substance toxic for other organisms.The project, coordinated by Rupert Mutzel (Institut für Biologie, Freie Universität Berlin) and Philippe Marlière (Heurisko USA Inc.), involved researchers of the French CEA (Commissariat à l'Energie Atomique et aux Energies Alternatives) and of the Katholieke Universiteit Leuven (Belgium). As described in the latest issue of Angewandte Chemie International Edition, the experimental work was based on a unique technology developed by Marlière and Mutzel enabling the directed evolution of organisms under strictly controlled conditions. Large populations of microbial cells are cultured for prolonged periods in the presence of a toxic chemical -- in this case, 5-chlorouracil -- at sublethal levels, thereby selecting for genetic variants capable of tolerating higher concentrations of the toxic substance.
In response to the appearance of such variants in the cell population the concentration of the toxic chemical in the growth medium is increased, thus keeping the selection pressure constant. This automated procedure of long term evolution was applied to adapt genetically engineered Escherichia coli bacteria unable to synthesize the natural nucleobase thymine to grow on increasing concentrations of 5-chlorouracil. After a culture period of about 1000 generations descendants of the original strain were obtained which used 5-chlorouracil as complete substitute for thymine. Subsequent genome analysis revealed numerous mutations in the DNA of the adapted bacteria. The contribution of these mutations to the adaptation of the cells towards the halogenated base will be the subject of follow-up studies.
Besides the obvious interest of this radical change in the chemistry of living systems for basic research the scientists consider the outcome of their work also to be of importance for "xenobiology," a branch of synthetic biology. This young area of the life sciences aims at the generation of new organisms not found in nature harboring metabolic traits optimized for alternative modes of energy production or for the synthesis of high value chemicals. Like GMOs, such organisms are seen as a potential threat for natural ecosystems when released from their laboratory confinements, either through direct competition with wild type organisms or through diffusion of their "synthetic" DNA.
Scientists have recognized that physical containment cannot in every single case prevent engineered live forms from reaching natural habitats, in the same way as radioactive isotopes can leak into the surroundings of a nuclear power plant. However, synthetic organisms like those evolved by Marlière and Mutzel and their collaborators which depend on the availability of substances for their proliferation not found in nature or which incorporate non-natural building blocks in their genetic material could neither compete nor exchange genetic messages with wild type organisms, but would die in the absence of the xenobioticM I B S I T B T

A man from Alabama first to receive Stem Cell Therapy

A man from Alabama has become the first person in the United States to receive a highly-debated embryonic stem cell transplant. Researchers are hoping the technology will be a game changer for those with debilitating spinal cord injuries.

TJ Atchinson hopes he's living the dream of Superman Christopher Reeve -- to become the first human to receive embryonic stem cell therapy. Atchinson was paralyzed following a devastating car accident."I realized I couldn't feel from (the top) down," Atchinson said. "When I got to the hospital, they said I would never walk again."

Atchinson was still accepting the news when doctors told him he'd be a great candidate for the stem cell therapy. Though he was injured just a few days before getting the offer, his body was strong and his will was even stronger. Atchinson agreed to be a laboratory of hope -- the first human with a spinal cord injury to test human embryonic stem cells. 

Doctors began the procedure by opening his wound, then guiding a needle into his body. Doctors injected Atchinson with two million all-purpose stem cells that they hope will transform into new nerve cells and attach to muscles, refiring his central nervous system.
In the laboratory, they've used embryonic stem cells to repair the broken spinal cords of small animals that walked again. The stem cells have the potential to produce unlimited quantities of any type of cell. Atchinson's mother says she knows that people oppose the therapy on religious grounds, but thinks they're unreasonable."There are some people who are against it, but until they've been put in the position I don't think they should judge anybody," Atchinson's mother told ABC News. Atchinson says his role in the procedure was to prove it was safe, but he says he can already start to feel it working. "Right now, I can feel that," Atchinson said while pulling at hair on his leg.

Six months after the procedure, Atchinson says he can feel a sense of weight when he places heavy items onto his lap. As he rubs his leg, Atchinson says, "I can tell that...I can feel that there's something there." Atchinson is holding out hope that he can one day run again like he once did before his accident.

Source: ABC7News, San Francisco, CA

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India's Top 50 Engineering Colleges 2011

Heavily dominated by public institutions, the top-50 listing is a roll call of excellence India's top 50 engineering institutions 2011

Ranking the top colleges is a very difficult task. While it is relatively easy to create clusters of colleges, it is differentiating within clusters that became the most difficult exercise. So for the first time in the country we have used balanced scorecard methodology to arrive at the ranking of the top 50 colleges. Ranking methodology: We scanned the last five year rankings of about 241 colleges and normalised their ranks, by assigning differential weights to subjective and objective ranking. Such a process is used to develop clusters of institutions. The research standing of individual institutions were further used to refine the clusters and remove the odd men out. Individual clusters were ranked serially. In each of these clusters the differences in cut-off marks, wherever possible (like in case of IITs and AIEEE institutes and some States) were used to arrive at individual ranks. Heavily dominated by public institutions, the top-50 listing is a roll call of excellence India's top 50 engineering institutions 2011

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Gut Bacteria can affect Mental Health: Did you know that?

A gut feeling may help you make a quick decision, but one study credits the digestive system for possibly influencing our mental states and behavior as well. The results help scientists understand how inflammatory bowel diseases, irritable bowel syndrome and other digestive problems relate to the psychological issues that often accompany them. Anxiety and depression commonly occur alongside these bowel conditions.

Scientists want to know whether certain gut bacteria influence humans' behavior. If so, doctors may be able to battle the physical and psychological effects of disease-causing bacteria by developing treatments such as probiotics.In the experiment, researchers introduced antimicrobials to mice via drinking water in order to change the ratios of their gut bacteria. The control group received sterile water. Afterward, both groups of mice were placed between two boxes -- one in the dark, one with light, as scientists recorded their behaviors. Mice with altered digestive bacteria showed less apprehension and were less afraid to go into the well-lit box, a common sign the animals are under the influence of drugs or illness.

Scientists then euthanized the mice to study their intestines and brains. They also found out that the hippocampus of the rodents with altered gut bacteria produced more brain-derived neurotrophic factor, also called BDNF, which often increases with stress and mood disorders, according to the U.S. National Library of Medicine. Although more research is needed to extend the findings to humans, the team found that the effects of bacterial imbalance were reversible in mice, meaning there might be a way to do the same thing for humans in the future.

Source: U.S. National Library of Medicine

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Astrocytes now can be grown in lab

The most common brain cell, called the astrocyte, is often overlooked in the face of its cousin, the neuron. Researchers are finally realizing their importance and have, for the first time, been able to grow them in the lab.

"Not a lot of attention has been paid to these cells because human astrocytes have been hard to get," study researcher Su-Chun Zhang, at the University of Wisconsin-Madison. "But we can make billions or trillions of them from a single stem cell." Astrocytes are small, star-shaped cells in the brain that act like the neuron's bodyguards, and because of that they play an important role in diseases of the central nervous system, including dementia. They are more common than neurons but have been hard to grow in the lab. Being able to study them could help researchers understand their role in normal brain functioning, and help find new treatments for disease.

"Without the astrocyte, neurons can't function," Zhang said in a statement. "Astrocytes wrap around nerve cells to protect them and keep them healthy. They participate in virtually every function or disorder of the brain." They protect neurons by performing basic housekeeping functions, like regulating blood flow, cleaning up excess neurotransmitters (the communication molecules used by neurons), and playing a key role in controlling the blood-brain barrier, which keeps toxic substances out of the brain.

Zhang created the cells from both embryonic and adult stem cells by treating them with special proteins to get them to grow into astrocytes. These cells could also be useful as a transplant, to treat diseases like Lou Gehrig's disease (also called amyotrophic lateral sclerosis), in which the neurons are overworked. Transplanting healthy astrocytes could rescue the injured neurons.

Source: University of Wisconsin-Madison

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Anxiety may be in your gut rather than in your head

For the first time, researchers at McMaster University have conclusive evidence that bacteria residing in the gut influence brain chemistry and behaviour.The findings are important because several common types of gastrointestinal disease, including irritable bowel syndrome, are frequently associated with anxiety or depression. In addition there has been speculation that some psychiatric disorders, such as late onset autism, may be associated with an abnormal bacterial content in the gut.
"The exciting results provide stimulus for further investigating a microbial component to the causation of behavioural illnesses," said Stephen Collins, professor of medicine and associate dean research, Michael G. DeGroote School of Medicine. Collins and Premysl Bercik, assistant professor of medicine, undertook the research in the Farncombe Family Digestive Health Research Institute.The research appears in the online edition of the journal Gastroenterology.
For each person, the gut is home to about 1,000 trillium bacteria with which we live in harmony. These bacteria perform a number of functions vital to health: They harvest energy from the diet, protect against infections and provide nutrition to cells in the gut. Any disruption can result in life-threatening conditions, such as antibiotic-induced colitis from infection with the "superbug" Clostridium difficile.Working with healthy adult mice, the researchers showed that disrupting the normal bacterial content of the gut with antibiotics produced changes in behaviour; the mice became less cautious or anxious. This change was accompanied by an increase in brain derived neurotrophic factor (BDNF), which has been linked, to depression and anxiety.
When oral antibiotics were discontinued, bacteria in the gut returned to normal. "This was accompanied by restoration of normal behaviour and brain chemistry," Collins said.To confirm that bacteria can influence behaviour, the researchers colonized germ-free mice with bacteria taken from mice with a different behavioural pattern. They found that when germ-free mice with a genetic background associated with passive behaviour were colonized with bacteria from mice with higher exploratory behaviour, they became more active and daring. Similarly, normally active mice became more passive after receiving bacteria from mice whose genetic background is associated with passive behaviour.
While previous research has focused on the role bacteria play in brain development early in life, Collins said this latest research indicates that while many factors determine behaviour, the nature and stability of bacteria in the gut appear to influence behaviour and any disruption , from antibiotics or infection, might produce changes in behaviour. Bercik said that these results lay the foundation for investigating the therapeutic potential of probiotic bacteria and their products in the treatment of behavioural disorders, particularly those associated with gastrointestinal conditions such as irritable bowel syndrome.

Source: Mcmaster University
 

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