‘Alien’ life form is grown in a lab: Scientists add unnatural DNA strands to the genetic code of bacteria to create a new strain

 

  • Researchers at the Scripps Research Institute in La Jolla, California, introduced DNA molecules not found in nature to a common bacterium
  • The E. coli bugs are able to grow and reproduce as normal despite containing two extra letters in their genetic code
  • Research involved overcoming a billion years of evolution to get the expanded genetic alphabet into living bacteria
  • In the future the research could lead to creation of microbes capable of manufacturing entirely new proteins that could be used in medicine
  • Some people are worried that the rapid advance of ‘synthetic biology’ could lead to the worrying prospect of new life-forms escaping from labs

 

From left to right, the structures of A-, B- a...

Continue reading “‘Alien’ life form is grown in a lab: Scientists add unnatural DNA strands to the genetic code of bacteria to create a new strain”

New demographic data show how diversely different species age – biologists cannot explain why

Aging out of bounds

December 08, 2013

Despite aging being one the hottest topic in the media recently, scientists have no coherent explanation for it. New demographic data on humans, animals and plants for the first time unveil such an extraordinary diversity of aging processes that no existing evolutionary theory can account for. Both life spans and mortalities vary from species to species. The fact that the probability of dying rises with age applies to humans, but is not principally true. This is shown by a catalogue of 46 species with their respective mortality and fertility rates, which has now been published in the science journal Nature. It is the result of a long-term data collection project led by scientists at the Max Planck Institute for Demographic Research (MPIDR) in Rostock, Germany, and at the Max-Planck Odense Center on the Biodemography of Aging (MaxO) in Odense, Denmark. Continue reading “New demographic data show how diversely different species age – biologists cannot explain why”

1 in 4 has alarmingly few intestinal bacteria

Contact: Oluf Pedersen oluf@sund.ku.dk 45-52-39-56-50 University of Copenhagen

All people have trillions of bacteria living in their intestines. If you place them on a scale, they weigh around 1.5 kg. Previously, a major part of these ‘blind passengers’ were unknown, as they are difficult or impossible to grow in laboratories. But over the past five years, an EU-funded research team, MetaHIT, coordinated by Professor S. Dusko Ehrlich at the INRA Research Centre of Jouy-en-Josas, France and with experts from Europe and China have used advanced DNA analysis and bioinformatics methods to map human intestinal bacteria.

-The genetic analysis of intestinal bacteria from 292 Danes shows that about a quarter of us have up to 40% less gut bacteria genes and correspondingly fewer bacteria than average. Not only has this quarter fewer intestinal bacteria, but they also have reduced bacterial diversity and they harbour more bacteria causing a low-grade inflammation of the body. This is a representative study sample, and the study results can therefore be generalised to people in the Western world, says Oluf Pedersen, Professor and Scientific Director at the Faculty of Health and Medical Sciences, University of Copenhagen.

Oluf Pedersen and Professor Torben Hansen have headed the Danish part of the MetaHIT project, and the findings are reported in the highly recognised scientific journal Nature.

The gut is like a rainforest

Oluf Pedersen compares the human gut and its bacteria with a tropical rainforest. He explains that we need as much diversity as possible, and – as is the case with the natural tropical rainforests – decreasing diversity is a cause for concern. It appears that the richer and more diverse the composition of our intestinal bacteria, the stronger our health. The bacteria produce vital vitamins, mature and strengthen our immune system and communicate with the many nerve cells and hormone-producing cells in the intestinal system. And, not least, the bacteria produce a wealth of bioactive substances which penetrate into the bloodstream and affect our biology in countless ways.

-Our study shows that people having few and less diverse intestinal bacteria are more obese than the rest. They have a preponderance of bacteria which exhibit the potential to cause mild inflammation in the digestive tract and in the entire body, which is reflected in blood samples that reveal a state of chronic inflammation, which we know from other studies to affect metabolism and increase the risk of type 2 diabetes and cardiovascular diseases, says Oluf Pedersen.

-And we also see that if you belong to the group with less intestinal bacteria and have already developed obesity, you will also gain more weight over a number of years. We don’t know what came first, the chicken or the egg, but one thing is certain: it is a vicious circle that poses a health threat, says the researcher.

Take care of your intestinal bacteria

The researchers thus still cannot explain why some people have fewer intestinal bacteria, but the researchers are focusing their attention at dietary components, genetic variation in the human host, exposure to antimicrobial agents during early childhood and the chemistry we encounter daily in the form of preservatives and disinfectants.

A French research team reports a study in the same issue of Nature showing that by maintaining a low-fat diet for just six weeks, a group of overweight individuals with fewer and less diverse intestinal bacteria may, to some extent, increase the growth of intestinal bacteria, both in terms of actual numbers and diversity.

-This indicates that you can repair some of the damage to your gut bacteria simply by changing your dietary habits. Our intestinal bacteria are actually to be considered an organ just like our heart and brain, and the presence of health-promoting bacteria must therefore be cared for in the best way possible. Over the next years, we will be gathering more knowledge of how best to do this,” says Oluf Pedersen, whose research team is studying, among other things, the impact of dietary gluten on gut bacteria composition and gut function.

Towards innovative early diagnostics and treatment options

Obesity and type 2 diabetes are not just a result of unfortunate combinations of intestinal bacteria or lack of health-promoting intestinal bacteria, Oluf Pedersen emphasises. There are likely many causal factors at play. But the MetaHit researchers’ contribution opens a new universe in which we begin to understand how gut bacteria in direct contact with the surrounding environment have a decisive impact on our health and risk of disease.

-At present we cannot do anything about our own DNA, individual variation in which also plays a crucial role in susceptibility for lifestyle diseases. But thanks to the new gut microbiota research, we now can start exploring interactions between host genetics and the gut bacteria- related environment which we may be able to change. That is why it is so exciting for us scientist within this research field– the possibilities are huge, says Oluf Pedersen.

-The long-term dream is to map and characterize any naturally occurring gut bacteria that produce appetite-inhibiting bioactive substances and in this way learn to exploit the body’s own medicine to prevent the obesity epidemic and type 2 diabetes, says Oluf Pedersen.

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Factbox 1: Danish researchers involved

Scientists from a number of Danish research institutions and hospitals have participated in the study: Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen;  Lundbeck Foundation Center for Applied Medical Genomics in Personalised Disease Prediction, Prevention and Care (LuCamp); Center for Biological Sequence Analysis, Technical University of Denmark; Hagedorn Research Institute, Gentofte; Department of Systems Biology, Technical University of Denmark; Department of Biology, Faculty of Science, University of Copenhagen; University of Aarhus; University of Aalborg; University of Southern Denmark; Research Centre for Prevention and Health, Glostrup; Hospital of Vejle.

Factbox 2: The scientific article

In the article in Nature, the MetaHit scientists demonstrate that they by testing for just a few different bacteria species – with 98 % accuracy can distinguish between people with healthy intestinal bacteria and those who lack and have unhealthy bacteria. This provides promising opportunities for predicting diseases associated with an unhealthy bacterial composition in the intestines, for example type 2 diabetes and cardiovascular diseases.

It all started with a bang, but the universe may not be expanding after all

Theoretical physicist Christof Wetterich publishes paper ‘a Universe without expansion’

Heather Saul

Tuesday, 13 August 2013

A theoretical physicist looks set to disrupt textbook concepts of cosmology, after producing a paper outlining his theory that the universe is not expanding after all.

The most widely accepted theory of the universe centres on the notion that the world started with a big bang, and has been expanding ever since.

But Christof Wetterich, a theoretical physicist at the university of Heidelberg, has produced a paper theorising that the universe is not expanding, but the mass of all of its particles are instead increasing.

His theory could potentially help examine the more problematic aspects of the big bang theory, such as the ‘singularity’ present during the big bang.

In his paper: A Universe Without Expansion, Wettrich discusses a cosmological model “where the universe shrinks rather than expands during the radiation and matter dominated periods”.

His paper was published on the arXiv preprint server. In his abstract, he writes: “Only dimensionless ratios as the distance between galaxies divided by the atom radius are observable. The cosmological increase of this ratio can also be attributed to shrinking atoms.”

In the 1920s, astronomers such as Georges Lemaitre and Edwin Hubble analysed the light emitted or absorbed by atoms, which appeared in a spectrum of characteristic colours, or frequencies.

When matter moved away, they discovered that galaxies exhibited a shift to the red, lower frequency part of the spectrum.

After observing that most galaxies exhibit a red shift that became greater for more distant galaxies, they theorised that the universe was expanding.

However, Wetterich highlights that this light emitted by atoms is also determined by masses of the elementary particles, and in particular, their electrons.

If the mass of an atom increases, it emits more energetic photons. If the particles were to become lighter, frequencies would become redshifted.

Writing in Nature News, Jon Cartwright explains: “Because the speed of light is finite, when we look at distant galaxies we are looking backwards in time — seeing them as they would have been when they emitted the light that we observe.

“If all masses were once lower, and had been constantly increasing, the colours of old galaxies would look redshifted in comparison to current frequencies, and the amount of redshift would be proportionate to their distances from Earth.

“Thus, the redshift would make galaxies seem to be receding even if they were not.”

For Wetterich, the universe still expands rapidly during a temporary period called inflation, but before this inflation, the big bang no longer contains a ‘singularity’ where the density of the universe would be infinite. Instead, Cartwright continues, “the big bang stretches out in the past over an essentially infinite period of time”.

“The current cosmos could be static or even beginning to contract,” he adds.

Wetterich’s paper has not yet been peer reviewed but has been received with both interest and scepticism by other cosmologists in the field.

“I think it’s fascinating to explore this alternative representation,” Hongsheng Zhao, a cosmologist at the University of St Andrews told Nature News. “His treatment seems rigorous enough to be entertained.”

However, Niayesh Afshordi, an astrophysicist at the Perimeter Institute in Waterloo, Canada told the journal he “remained to be convinced about the advantage, or novelty, of this picture.”

Unfortunately, the plausibility of this concept is currently impossible to test, but Wetterich argues it could be a useful concept to use when considering different cosmological models.

 

http://www.independent.co.uk/news/science/it-all-started-with-a-bang-but-the-universe-may-not-be-expanding-after-all-8759893.html#

Digest This: Cure for Cancer May Live in Our Intestines / People will not die from cancer, if our prediction is true

The discovery of Robo1 protein in the intestinal stem cells (depicted in yellow) leads to tolerance of higher doses of chemoradiation for cancer patients. (Credit: Dr. Wei-Jie Zhou)

July 31, 2013 — Treating a cancerous tumor is like watering a houseplant with a fire hose — too much water kills the plant, just as too much chemotherapy and radiation kills the patient before it kills the tumor.

However, if the patient’s gastrointestinal tract remains healthy and functioning, the patient’s chances of survival increase exponentially, said Jian-Guo Geng, associate professor at the University of Michigan School of Dentistry. Recently, Geng’s lab discovered a biological mechanism that preserves the gastrointestinal tracts in mice who were delivered lethal doses of chemotherapy.

The findings, which will appear in the journal Nature, could revolutionize cancer therapy, Geng said.

“It’s our belief that this could eventually cure later-staged metastasized cancer. People will not die from cancer, if our prediction is true,” said Geng, who emphasized that the findings had not yet been proven in humans. “All tumors from different tissues and organs can be killed by high doses of chemotherapy and radiation, but the current challenge for treating the later-staged metastasized cancer is that you actually kill the patient before you kill the tumor.

“Now you have a way to make a patient tolerate to lethal doses of chemotherapy and radiotherapy. In this way, the later-staged, metastasized cancer can be eradicated by increased doses of chemotherapy and radiation.”

Geng’s lab found that when certain proteins bind with a specific molecule on intestinal stem cells, it revs intestinal stem cells into overdrive for intestinal regeneration and repair. Stem cells naturally heal damaged organs and tissues, but so-called “normal” amounts of stem cells in the intestine simply cannot keep up with the wreckage left behind by the lethal doses of chemotherapy and radiation required to successfully treat late-stage tumors.

However, the phalanx of extra stem cells protect the intestine and gastrointestinal tract, which means the patient can ingest nutrients, the body can perform other critical functions and the bacterial toxins in the intestine are prevented from entering the blood circulation, Geng said.

These factors could give the patient just enough of an extra edge to survive the stronger doses of chemotherapy and radiation, until the tumor or tumors are eradicated.

In the study, 50-to-75 percent of the mice treated with the molecule survived otherwise lethal doses of chemotherapy. All of the mice that did not receive the molecule died, Geng said.

“If you can keep the gut going, you can keep the patient going longer,” Geng said. “Now we have found a way to protect the intestine. The next step is to aim for a 100-percent survival rate in mice who are injected with the molecules and receive lethal doses of chemotherapy and radiation.”

Geng’s lab has worked with these molecules, called R-spondin1 and Slit2, for more than a decade. These molecules repair tissue in combination with intestinal stem cells residing in the adult intestine.

Black mamba venom makes a great painkiller : Equal to morphine without effecting opioid receptors

  • 03 October 2012
  • Magazine issue 2885.
  • For similar stories, visit the The Human Brain Topic Guide

ONE bite from a black mamba can kill a person within half an hour. Strangely though, venom from what’s arguably the world’s deadliest snake could actually be a painkiller on a par with morphine.

In search of a new analgesic, Anne Baron at the Institute of Molecular and Cellular Pharmacology in Valbonne, France, and her colleagues, hunted through hundreds of compounds for one that blocks acid-sensing ion channels in nerves. These are key in a common pain pathway. The successful compound turned out to be venom from a black mamba.

Baron’s team then identified which proteins in the venom blocked the ion channels, before naming them mambalgins and purifying them to produce a drug.

Mice injected with the drug appeared to be significantly more resilient to pain compared with those given a sham treatment (Nature, DOI: 10.1038/nature11494).

The drug did not affect the opioid receptors that are targeted by morphine but was just as effective in relieving pain.

Anyone taking the new drug might therefore avoid side effects associated with morphine, which include addiction and breathing problems, says Baron

http://www.newscientist.com/article/mg21628855.500-black-mamba-venom-makes-a-great-painkiller.html

Predicting If Scientists Will Be Stars: New Formula Reveals If Young Scientists Will Have Brilliant Future

ScienceDaily (Sep. 12, 2012) — A medical school committee is weighing whether to hire a promising young neuroscientist. Will she have a brilliant future as a researcher, publish in top journals and nab abundant research funds?

If only there were a crystal ball. Wait, now there is!

A new Northwestern Medicine study published Sept. 13 in Nature offers the first formula that accurately predicts a young scientist’s success up to 10 years into the future and could be useful for hiring and funding decisions.

Currently, hiring decisions are made using the instincts and research of search committees. Universities are increasingly complementing this with a measure of the quality and quantity of papers published, called the h index.

But the new formula is more than twice as accurate as the h index for predicting future success for researchers in the life sciences. It considers other important factors that contribute to a scientist’s trajectory including the number of articles written, the current h index, the years since publishing the first article, the number of distinct journals one has published in and the number of articles in high impact journals.

The formula was developed in the lab of Konrad Kording, senior author of the Nature paper and associate professor in physical medicine and rehabilitation at Northwestern University Feinberg School of Medicine and a researcher at the Rehabilitation Institute of Chicago.

“The algorithm could be useful for hiring and tenure decisions as well as funding decisions, particularly at a time when funding agencies and hiring committees are dealing with vast number of applications,” Kording said. “You want to fund someone who will have high impact in the future.”

While the formula won’t replace evaluation by a group of peers who examine scientific contributions and research depth, it could provide a valuable complementary tool, Kording noted. The predictions are targeted to a scientist at the level of assistant professor, someone within five to 15 years of writing his or her first paper as a Ph.D. student.

Kording and colleagues based and tested the formula on data from 3,293 scientists (3,085 neuroscientists, 57 Drosphila scientists and 151 evolutionary scientists) for whom they constructed a publication, citation and funding history.

The paper shows that the number of articles written, the diversity of publication and the number of top articles over time all become increasingly influential predictors of a scientist’s success.

Perhaps publishing in many different journals leads to less overlapping populations of scientists who cite the work, Kording said, which leads to an increased number of citations for already published articles. The number of top journal publications also may give visibility to other papers of a scientist, both past and future.

The ability to predict future success also shows important discoveries are the result of ongoing hard work, not random luck.

“People think scientists sit there and all of a sudden have these strokes of genius that turn them into a superstar,” Kording said. “In reality, people who have important scientific insights usually have been incredibly successful before.”

The lead author of the paper is Daniel E. Acuna, a postdoctoral student in Kording’s lab at Northwestern’s Feinberg School of Medicine and a research affiliate in biomedical engineering at the McCormick School of Engineering and Applied Science.

Try the prediction engine: http://klab.smpp.northwestern.edu/h-index.html

Kording’s research was supported by the National Science Foundation