Category Archives: Biology

Biology News

Life, but not as we know it

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Michaela Livingstone


A newly discovered bacterium uses the deadly arsenic to grow and live.


The only organism able to use a different chemical from the accepted fundamental building blocks of life has been found living in a lake in California, substituting phosphorus for the usually poisonous element arsenic, opening up questions on what other forms of life might be possible in the universe.


Until now, all life on Earth has been found to use the same basic building blocks for life, the elements carbon, hydrogen, oxygen, nitrogen, phosphorus and sulphur. These elements make up the various cellular parts and machinery from DNA to proteins and lipids.


The bacterial strain, named the not-so-exotic GFAJ-1, was isolated from mud samples collected from the shores of the briny Mono Lake in California, known to have high levels of arsenic, by NASA researcher Felisa Wolfe-Simon and was reported in a research article in this week’s issue of the journal Science.

Phosphorus is contained in a phosphate form (phosphorus and oxygen) in the backbone of DNA and RNA, as well as energy-carrying molecules such as ATP. There had been suggestions that arsenic in the form of arsenate could be used by life as it is chemically similar to phosphate, which is why it is usually deadly.


The bacterium was shown to have arsenate incorporated in to its DNA and other cellular parts when grown in media lacking phosphorus but containing a relatively high level of arsenic. The organism was however still able to grow faster in the presence of phosphorus.


Some researchers have hailed this as evidence that it is possible for life elsewhere in the universe to use different chemicals as their building blocks, opening up many possibilities for extraterrestrial environments where life could thrive, where before it was thought impossible. It suggests that anything is possible and that alien life may look very different from what we have assumed, if we ever come face to face with it.


Others say it opens up questions as to how, and how many times, life may have evolved here on Earth speculating that life may have evolved in harsh environments with high levels of arsenic such as volcanic vents on sea beds before later incorporating phosphorus.


Clara Chan, a geomicrobiologist from the University of Delaware, Newark was reported by the journal Science as saying that the strongly held belief is that the chemistry of life is so specific that any changes would not be tolerated, “The implication of this work is that life can be quite different from what we know.”


Other scientists are less convinced by the data, withholding belief that the organism really is able to use arsenate in place of phosphate until more data is produced to show that the arsenate isn’t simply being stored in the bacterium.


GFAJ-1 at least shows that is possible for life to exist in the absence of phosphorus. Wolfe-Simon hopes now to find bacteria growing naturally in high-arsenic but low phosphate-containing environments to find proof of life that depends on arsenic.

 

Find the original research article here:

http://www.sciencemag.org/content/early/2010/12/01/science.1197258

 

Plant help signals intercepted by the enemy

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Izzy Dean

A recent talk given at the University of Sheffield by Harro Bouwmeester gave an fascinating insight into the secret life of parasitic  plants. The word parasite commonly brings up images of fleas, ticks and worms but parasitism is also rife in the plant kingdom. Parasitic plants can have a large effect on crops, causing devastating effects particularly in poorer third world farming communities.

 Some plant parasites, such as Witchweed and Broomrape, have evolved to become completely dependent on the plant which they parasitise and these parasites are unable to survive in absence of a host.  Parasite seeds often remain dormant for long periods of time, only germinating if a potential host plant is nearby. The parasite then grows through the soil towards the host plant and attaches to the roots of the plant, before piercing the host root and obtaining nutrients through this attachment.

Scientists, from Wageningen University in the Netherlands, discovered that parasitic plants can recognise certain chemicals released by roots of potential host plants. This group of plant hormones, named strigolactones, allow parasites to detect and locate host plants so they can time germination and the direction of initial growth accurately.

Ironically, Strigolactones are released with the intention to attract assistance from a special group of helpful fungi. These fungi, which also attach to the plant root, provide critical nutrients from the soil in exchange for the carbon they take from the plant. Plants growing in soils which are low in nutrients such as phosphorus have a higher dependency on fungi partnership and so release higher amounts of strigolactones.  

These findings have important implications for regions with low quality soil, such as areas of Africa, where striga is a major problem. Research into the production of strigolactones in plants is ongoing, but it appears that strigolactones may have a secondary function, making suppression of these chemicals in prevention of parasites difficult.

For more information: http://www.plantphysiol.org/cgi/content/short/139/2/920

Seeing shapes, touching shapes… Hearing shapes?

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Maria Panagiotidi

“Can shape be represented by sound artificially?” That is the question that Jung-Kyong Kim  and Robert J. Zatorre posed in their recent study published in October’s Experimental Brain Research Journal.

Shape is an inherent property of objects that we encounter in our everyday life. It is thought to be experienced mainly through vision and touch. Previous experiments suggest that sound can also convey visual information by means of image-to-sound coding. This is similar to echolocation, a system that allows species such as bats to navigate and identify objects.  It has also been used as an alternative way to allow people with impaired vision to experience the world.

In this study, scientists from McGill University in Montreal investigated whether sound can code tactile information. They did this by blindfolding sighted participants and training them to recognise spatial information using specially-coded sounds. These sounds represented information of abstract shapes. After the training session, the participants were tested on old (previously learned) and new subjects. It was found that they were able to match auditory input to tactually discern shapes meaning that they could use sounds to “see” shapes. 

The results from this study provide evidence for the hypothesis that the perception of a coherent object or event ultimately occurs at a highly abstract level in a form independent of the sense from which it was perceived. In addition to that, this approach could possibly lead to the development of new methods aiming to aid individuals with impaired vision.

 

Original article: Jung-Kyong Kim, Robert J. Zatorre. Canyou hear shapes you touch?Experimental Brain Research, 2010; 202 (4): 747 DOI: 10.1007/s00221-010-2178-6

Bacterial enzyme reveals novel mechanism of DNA repair

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Arran-Leigh Roberts

Our DNA comes under attack daily from a variety of things in our environment; cigarette smoke, industrial waste and UV radiation from the sun to name a few. This is in addition to natural damage that occurs in our cells from chemical conditions and errors in DNA replication. All this amounts to that in a given cell, up to 1 million bases of DNA are damaged per day. Fortunately, our cells contain a number of molecular repair mechanisms which deal with this damage by restoring the correct DNA sequence.

Researchers at Vanderbilt University, Pennsylvania State University and the University of Pittsburgh have now uncovered a new mechanism by which DNA is repaired when it has undergone damage by a process called alkylation. Alkylation is a common type of DNA damage which is caused by certain industrial toxins, some components of cigarette smoke and even some chemotherapy drugs. These alkylating agents transfer methyl or other alkyl groups onto guanine bases in the DNA – where they do not belong. This causes an alteration in the shape of the DNA molecule itself and stops replication occurring successfully, especially if the damage occurs within a gene-containing region.

Whilst humans only have one enzyme to repair different types of alkylation, namely a glycosylase called AAG, bacteria have several of these, with each targeting specific types of damage. Whilst studying bacterial glycosylases, the researchers discovered the enzyme AlkD, which functions in a novel manner. The enzyme essentially causes the base pair damaged by alkylation to rotate out of the DNA helix. Once outside the helix, it is able to spontaneously detach and AlkD helps to accelerate this process.

Although this research highlights the function of just a single bacterial enzyme, it provides invaluable insight into the process by which enzymes may recognise and deal with DNA damage. This has been previously impossible to pin down with the help of the human enzyme, AAG.

This finding may be particularly relevant to the production of new chemotherapy drugs for cancer treatment. These drugs specifically aim to cause lethal alkylation of the DNA contained in tumour cells. The trouble with current chemotherapy drugs is that they can potentially cause harmful mutations in the DNA of healthy cells. It is hoped that by better understanding the mechanisms of DNA repair, novel chemotherapy drugs can be produced that are able to target their toxic effects to tumour cells only.

New coral reef found off the coast of Israel

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Joey Shepherd

 

A crew of marine researchers, headed by Prof. Zvi Ben-Avraham from the from the Leon H. Charney School of Marine Sciences at the University of Haifa in Israel, set sail on September 6.  In the Nautilus, a research ship owned by famed oceanographer Robert Ballard who discovered the wreck of RMS Titanic, the team set out to research the relatively unknown Mediterranean sea floor off the coast of Israel. At the time, Prof. Aaron Ben-Ze’ev, President of the University of Haifa, was quoted as saying “The future is in the sea and this voyage is a first step towards understanding the mystery of a region that is so close to us yet still so far and unknown”. The researchers didn’t know when they embarked on their voyage that what they would find was a ‘magnificent’ deep-sea coral reef, 30-40km off the coast of Tel Aviv and some 700m deep, in an area of scarce sea life – an oasis of life in the deep sea.

Prof. Zvi Ben-Avraham, who also captained the vessel, headed the scientific team for the two and a half week long expedition aboard the Nautilus – a ship equipped with the technology needed for sea-floor research, including diving robots which ranged to depths of 1.7km down into the Mediterranean during the expedition. “We did not expect, know, or even imagine that we would come across these reefs and certainly not such large ones. It’s like finding a flourishing oasis in the middle of the desert,” said Dr. Yizhaq Makovsky, who directed the University of Haifa control centre for the project. The reefs are the first deep sea coral reefs to be found off the coast of Israel, and their discovery could, amongst other things, aid researchers in unravelling the effects of global climate changes through history.

The sea-bed samples recovered from the expedition are waiting to be examined in detail, however, and as Dr. Makovsky explained, “Our discovery only demonstrates the potential of the many surprises that await us in the depths of this area. An immediate implication of this discovery is that there is an urgent need to classify the area as a deep-sea reserve, as are other coral reef areas around the world”.

As well as finding the coral reefs the team photographed marine life hundreds of metres below the surface in its natural habitat for the first time. They also encountered two shipwrecks, perhaps solving old mysteries whilst discovering new ones.

Inflammation and Diabetes – a Fishy Tale

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Kathryn Vaughan

Researchers investigating the function of a particular G-protein coupled receptor, GPR120, have found potent anti-inflammatory effects to be mediated when stimulated with ingredients of fish oil.

Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are omega-3 fatty acids found in fish oil. These fatty acids have already been shown to have health benefits, e.g. DHA reduces blood triglycerides to decrease the risk of atherosclerosis and heart disease.

Chronic inflammation, mediated by macrophages (white blood cells that enter diseased tissues and mediate an inflammatory response), is linked to decreased sensitivity to insulin in obesity, thus the anti-inflammatory effects mediated upon GPR120 activation may promote insulin sensitisation.

Adipose (fat) tissue and pro-inflammatory tissue macrophages were found to express GPR120, and, in particular, the receptor was highly induced in the obese murine model. Further investigation by the research team found that DHA activation of GPR120 increased the translocation of GLUT4 (Glucose Transporter 4) to the cellular surface and hence transportation of glucose into the cells.

Monocytic cell lines and murine primary intraperitoneal macrophages both containing and lacking the GPR120 receptor were also used in the research. A high-fat diet with or without omega-3 fatty acid supplementation was fed to the mice, and in ordinary mice DHA and EPA mediated anti-inflammatory effects by inhibition of both the TLR (Toll-like Receptor) and TNF (Tumour Necrosis Factor) inflammatory pathways. In the GPR120 knockout mice DHA and EPA had no effect.

The research was led by Jerrold Olefsky, Associate Dean for Scientific Affairs and Professor of Medicine at University of California, San Diego School of Medicine. Speaking in video clips posted on the University of California’s website Prof. Olefsky said that potentially the effects seen in mice may be mediated in humans to treat insulin resistance. However, in experiments they had to give the mice relatively high doses of fatty acids, which would be non-beneficial to humans. Therefore it may be more reasonable to target GPR120 for therapeutic treatment. If they could find a small molecule that mimics the effects of the fatty acids then a reasonable dose may be consumed to mediate anti-inflammatory and anti-insulin resistance effects.

The researchers conclude that GPR120 may be an important signalling molecule in anti-inflammatory and insulin-sensitising responses thus may provide a new approach for the treatment of insulin resistant diseases.

 

Oh et al (2010) GPR120 is an omega-3 fatty acid receptor mediating potent anti-inflammatory and insulin-sensitizing effects. Cell, 142, 687-698.

The paper can be found at:

http://www.cell.com/fulltext/S0092-8674%2810%2900888-3

Secrets of cross-species transmission revealed

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Arran Roberts


Scientists have come up with a new theory on how viruses can cross the species divide. Humans are susceptible to a number of viruses which originate from non-human hosts, for example, the recent swine flu epidemic originated in pigs.  A collaboration of researchers from the University of Georgia, the U.S Centre for Disease Control, the University of Tennessee, Knoxville and Western Michigan University has made a groundbreaking discovery which may explain how viruses are able to jump from host to host.


Viruses pass between species via a phenomenon known as ‘cross-species transmission’ or CST. It was previously thought that viruses were able to cross species due to high rates of genetic mutation, allowing the virus to adapt to whichever species it came into contact with.


This latest piece of research, led by Daniel Streiker of the University of Georgia, suggests that transmission depends on a different factor entirely; evolution. The team investigated the transmission of the rabies virus between different species of bat. It was concluded that the rabies virus was only able to infect a subset of bat species, which were closely related to the original carrier. This implies that this kind of jump depends on the hosts being evolutionarily related. “Although CST events are the source of infectious diseases that kill millions of people each year, the natural reservoirs of viruses in wild animals and how they cross species barriers are poorly known and difficult to observe” said Professor Gary McCracken in the initial press release. This result has finally brought clarity to what it is that determines virus transmission between species.


The research also carries wider implications for our health. At the moment, the World Health Organization which are hard pressed to predict the next human epidemic as a result of a CST event. However, with this new knowledge, it will be significantly easier to follow the pattern of infection and deduce which viruses may eventually jump to a human host.


The full research paper appears in the August 6th edition of Science Magazine.

Disease threatens regional extinction of little brown bats

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Claire Tree-Booker

 

White-nose syndrome, a fungal disease affecting hibernating bats, has caused the death of around one million little brown bats in North America, describe scientists in the journal Science.

The disease-causing fungus, known as Geomyces destructans, causes early arousal from hibernation in these bats, which results in them using up their crucial fat reserves. The fungus is thought to thrive in the damp, dark conditions in the caves where little brown bats hibernate.

Many bats hibernate in groups of up to half a million, meaning that the fungus, which grows on the bats’ exposed wings and noses, can spread very easily.

The researchers think that the disease was carried to North America by humans travelling from Europe; Dr Kunz, leading the team, said that the disease was first discovered in a New York cave that was frequently visited by tourists.

Following analysis of data collected from bat colonies over 17 years, the scientists calculated that the fungus kills approximately 73% of bats in a colony once infection has occurred.

They conclude that little brown bats in North America could be extinct within the next 16 years.

This study only investigated the effects of white-nose syndrome in little brown bats, but at least seven species, including the northern long-eared bat and the tri-coloured bat, are affected by the disease.

Dr Kunz said “this is only the tip of the iceberg in terms of what we’re likely to see in the next several years”.

If little brown bats become extinct, it could have a huge impact on ecosystems, as many of these insects are agricultural pests, bats are essential to keep their numbers down. Dr Kunz said “a single bat can eat half its bodyweight in insects in one night”.

The researchers say that this decline of a common bat species highlights the need for increased research and monitoring of wildlife diseases.

 

Original article: An Emerging Disease Causes Regional Population Collapse of a Common North American Bat Species. Winifred F. Frick, Jacob F. Pollock, Alan C. Hicks, Kate E. Langwig, D. Scott Reynolds, Gregory G. Turner, Calvin M. Butchkoski, and Thomas H. Kunz. Science 6 August 2010: 679-682. 

 

A step closer to HIV vaccine

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Helen Phillips

 

An antibody has been discovered which can neutralise the Human Immunodeficiency Virus, the pathogen that causes AIDS. The antibody can fight 90% of HIV-1 strains, the most common form of the virus. Researchers at the NIAID Vaccine Research Center have even been able to establish how the antibody works.

A vaccine to HIV has been difficult to develop as the surface of the virus constantly changes. This antibody is interesting because it attaches to a part of the virus which hardly changes. This is possibly the reason why the antibody has such a broad effect across strains.

The antibody is naturally occurring and has been extracted from an infected patient’s blood. However, not everyone carries these antibodies.  The next important step will be finding a way to stimulate the production of these antibodies in other people.

These findings have recently been published in the journal Science; the discovery of these broadly neutralising antibodies is one of the most significant steps in the quest to find a vaccine.

 

Articles: 

Wu X et al. Rational design of envelope surface identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science. 2010.

Zhou T et al. Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science. 2010.

The Miracle of Birth

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Steph Wagg

 

Pregnancy can be a magical time for women, especially for those who suffer from debilitating chronic illnesses such as rheumatoid arthritis and multiple sclerosis. The severity of the symptoms can reduce or disappear completely for the duration of the pregnancy.

 

Rheumatoid arthritis and multiple sclerosis are both diseases where the immune system tries to attack itself (auto-immune disorder).  So, a team from the University of Michigan have been looking into the changes in immune response during pregnancy.

 

They focused their research on white blood cells (leukocytes), key components of the immune system.  They analysed the blood of pregnant and non-pregnant women as well as women with pre-eclampsia (a common complication during pregnancy).  A significant difference in the amount of one particular enzyme was found.

 

Pyruvate kinase is an enzyme which helps break down glucose into a chemical called pyruvate. The main function of this glycolysis is to release energy, in the form of a molecule called ATP, within cells to fuel more reactions. However, the team found that in the white blood cells of pregnant women the amount of pyruvate kinase is reduced compared to those who were not pregnant. Interestingly they also found that the levels of the enzyme in women suffering from pre-eclampsia were only marginally reduced.

 

There are many questions still remaining about the adaptations the body makes during pregnancy and the reactions going on inside the unborn child. The team seem hopeful that this research could lead to potentially new medications that target the enzyme for sufferers of rheumatoid arthritis or multiple sclerosis or even new methods of diagnosing pre-eclampsia earlier.

 

Original paper: Xu Y, Madsen-Bouterse SA, Romero R, Hassan S, Mittal P, Elfline M, Zhu A, Petty HR. Leukocyte pyruvate kinase expression is reduced in normal human pregnancy but not pre-eclampsia. Am J. Reprod Immunol 2010.