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3 blind mice, see how they… see again!

For the first time ever, blind animals have had their sight restored in a lab.

This revolutionary experiment was carried out in mice, by a group of scientists from the University of California. They used a process known as ‘gene therapy’. A gene – a unit of DNA which can carry the instructions to make a particular protein – was injected into the eye of the mouse.

The gene in question carried instructions for a special protein called a receptor, whose job is to detect light entering the eye, and send signals to the brain.

Injecting the gene into the blind eye provides the eye with the information to make new receptors, which therefore begins to sense light again.

When undergoing tests, the previously-blind mice behaved similarly to normal mice – indicating that they could see again.

This is a significant breakthrough as currently the only option for patients with blindness caused by damage to the retina is an implant connected to a video camera. This provides a resolution of about 100 pixels (compared with millions of pixels in normal vision) and is awkward and expensive.

“To the limits that we can test the mice, you can’t tell the [experimentally] treated mice’s behaviour from the normal mice without special equipment,” John Flannery, a UC Berkeley professor of molecular sight and biology, said in a press release. “It remains to be seen what that translates to in a patient.”

Smell test for Parkinson’s?

brain2

A Scottish woman has the uncanny ability to detect whether a person will develop Parkinson’s disease – by smelling them!

Joy Milne first noticed the smell on her husband, who was diagnosed with Parkinson’s at a later date. She linked the odour to the disease after detecting it on other people with the disease at a support group.

Parkinson’s is a brain disease linked to the death of cells in a particular part of the brain called the substantia nigra. Symptoms include the characteristic tremor and difficulty initiating and regulating movement in the body.

Joy has worked with the University of Manchester and is named in their paper, published in ACS Central Science, as a ‘Super Smeller’. In a test where she was given clothes worn by a set of people with Parkinson’s and clothes worn by people without the disease, she identified an impressive 11 out of 12 correctly.

Researchers aimed to investigate Joy’s ability using a machine called a mass spectrometer. This was used to analyse components of the sebum – an oily substance secreted from the skin – of people with Parkinson’s disease.

Analysis of the sebum samples of Parkinson’s patients revealed a distinct ‘signature’ of compounds including ‘altered levels of perillic aldehyde and eicosane’.

This information could enable earlier diagnosis of the disease, since the odour can be detected years before symptoms occur.

Homing pigeons humans

pigeon

New research suggests humans may detect Earth’s magnetic field in a similar way to some birds and animals. ‘Magnetoreception’ as it is known, is common in a variety of animals, for example pigeons, who use it to help them navigate. An exact explanation for how animals do this has not yet been established.

It has never before been clear whether magnetoreception occurs in humans.
Research was carried out at Caltech and the University of Tokyo and published in the journal eNeuro. The findings indicate that the human brain responds unconsciously to changes in magnetic fields.

The researchers used a special metal cage to shield participants from external radio waves. They then sat participants in the dark, in silence, and monitored their brain waves with electrodes attached to the head. When the magnetic field was moved silently around the chamber, this appeared to be detected by people’s brains.

“Given the known presence of highly evolved geomagnetic navigation systems in species across the animal kingdom, it is perhaps not surprising that we might retain at least some functioning neural components, especially given the nomadic hunter-gatherer lifestyle of our not-too-distant ancestors. The full extent of this inheritance remains to be discovered,” says Joseph Kirschvink of Caltech.

by Molly Andrews

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Zika may be prevented by previous exposure to dengue virus

A recent study, published in Science, has found that previous exposure to the dengue virus could protect against the Zika virus. Both viruses are spread by the same species of mosquito, Aedes aegypti and Aedes albopictus. The dengue virus is genetically similar to the Zika virus and the researchers sought to understand the role of pre-existing dengue immunity in Zika infection.

The team was able to take advantage of an ongoing long-term study of urban slum health to compare results from before and after the 2015 Zika outbreak. During the Brazilian epidemic just under three-quarters of the inhabitants of the studied slum caught the virus. Infection rates varied from as low as 29% in one area to up to 83% in others.

While immunity to the dengue virus had been shown experimentally to protect against infection from the Zika virus, its influence had not been thoroughly studied in a human population. The results of the current study showed that those who had previously been exposed to the dengue virus had antibodies which protected them from Zika. The researchers hypothesised that the high rates of immunity against Zika caused by infection with either Zika or dengue will likely avoid a similar outbreak to that of 2015.

http://science.sciencemag.org/content/363/6427/607.full

Hachimoji DNA

dnaThe genetic alphabet has just been expanded. DNA is composed of four letters, or bases, but researchers have recently published a system using eight. The new system, introduced in Science is named Hachimoji DNA, hachi meaning eight and moji meaning letter. One of the paper’s authors, Dr. Benner, has reportedly been working on expanding the DNA alphabet since 1985.

But creating new artificial bases that don’t exist in nature was never going to be easy. They have to fit into the double helix structure of DNA and be read by enzymes in order to create proteins. RNA polymerases – enzymes that transcribe the genetic information from DNA – were able to transcribe information from the Hachimoji nucleotides. The authors reported that the eight nucleotide bases – four natural, four synthetic – can be transcribed into RNA and are have therefore been shown to be structurally similar enough to the four traditional bases to fit requirements needed for ‘Darwinian evolution’. RNA acts as a kind of translator between DNA and proteins and enables cells to produce proteins from their DNA “recipes”. In this case the enzyme the researchers used was an engineered T7 RNA polymerase, which was able to translate the new eight letter code into an RNA strand.

Videos, songs and documents have previously been encoded in DNA, and Hachimoji DNA offers the potential to expand this storage opportunity. Expanding the DNA alphabet has other potential advantages; it is currently unknown whether Hachimoji DNA could support life in the same way the four natural bases do, but it could change the way we think about extra-terrestrial lifeforms and what they are made of.

http://science.sciencemag.org/content/363/6429/884

How the zebra got its stripes

zebraA recent study in Plos One has suggested a plausible reason for the stripes on nature’s most recognisable member of the Equidae family. At a horse farm and conservation centre for zebras near Bristol, UK, the researchers filmed horse flies trying to bite the animals. They observed a lower landing rate on zebras than for horses, and that the flies were unable to fly in a controlled manner, which led to fewer bites. The researchers theorized that the fly’s low-resolution vision might be dazzled by the stark black and white stripes.

To control for the different smells of zebras and horses, seven horses were dressed in a zebra-striped coat. The rate of landing on the exposed head of the horse remained the same while decreasing on the body, confirming the initial results.

However, it is worth noting that these experiments were carried out in England and the native species of flies in Africa may behave differently. In the meantime, perhaps we will see some zebra print-wearing horse riders taking advantage of the results of this study.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210831

 

Articles written by Isobel Tibbetts

 

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Meat: Animal versus Lab

Some of you might have heard of the possibility to create meat in the lab. Stem cells, which are cells that can potentially change into any type of cell found in the body, can be harvested from live animals and cultured in the lab. These cell cultures can then be coaxed by various cocktails of hormones and growth factors to grow into fibres, which can then be accumulated into a bulk. Et voila, a chicken nugget. While the technology is still far from main stream, it has obvious exciting implications, including for people concerned with animal welfare or climate change. But a new study on the impact of animal vs lab meat production has now cast some doubt onto the anticipated advantages of lab meat for the climate. The thing is, cows and other live stock are problematic, in part, because they produce methane. While methane does contribute to the greenhouse effect, it only stays in the atmosphere for about 12 years. Carbon dioxide on the other hand can accumulate in the atmosphere for thousands of years, contributing to climate change over a much longer period of time. Considering that most laboratories’ energy needs aren’t covered entirely by renewable energy, the study said, could tip the scales in favour of meat produced by animals. At least regarding the climate impact. The authors note that meat production in the lab is not only a matter of climate change, but other ethical and economical concerns and that it is difficult to discern whether improved methods or reduced carbon emission of laboratories in the future could tip the scales again. So, until lab meat appears in our supermarkets, you might use the time to ponder whether you’re happy to try it once it becomes available.

Detecting sepsis

holmesSepsis, a complication of infection, can occur in people of any age, at any time and can have serious consequences, including death. The patient with suspected sepsis needs to be treated with broadband antibiotics, and fast. Every hour of delayed treatment makes death and other serious complications, such as amputations, more likely. But diagnosing sepsis is not easy. There are certain symptoms that you can look out for however: Slurred speech or confusion, extreme shivering or muscle pain, passing no urine all day, severe breathlessness, it feels like you’re going to die and skin mottled or discoloured. To combat this problem researchers at the University of Strathclyde have started to develop a test that could detect sepsis as rapidly as in 2 and a half minutes. The test could potentially be used in hospital or GP settings and detect biomarkers for sepsis, including interleukin 6 (IL-6). More and more biomarkers are being discovered and could greatly improve outcomes for patients in the future if the test goes into clinical trials. The test could aid the choice of antibiotic as well, making the therapy more targeted to the actual infection. While still in its early stages of development, the test could potentially save lives and has been welcomed by sufferers and charities alike.

Bright eyed into the future

eye-scanAMD, or age-related macular degeneration is a problem that affects about 600,000 people in the UK and leads to vision loss. The vision loss is caused by the death of cells that form something called the macular at the back of the eye. Patients experience central vision loss, as well as the ability to see details and AMD is currently the most common cause of blindness in the UK. A new trial, supported by the Welcome Trust, is now injecting gene therapy at the back of the eye in 10 patients with macular degeneration. While the ultimate goal of the therapy is to stop or even avoid any loss of vision in AMD, the current trial is only testing the safety of the procedure. All participants have already lost some of their vision, but if successful, gene therapy could potentially provide a cure for AMD. There have been other trials, including the successful implantation of stem cells at the back of the eye of two patients at Moorfields Eye Hospital in London, restoring their vision. The novelty of the gene therapy approach is that “healthy” DNA is inserted into the macula to fix the underlying cause of AMD. If successful, AMD might be halted in patients before they lose a significant amount of their vision.

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Why Do We Salt Our Roads?

We’ve probably all noticed that it’s a little cold at the moment – in fact, Scotland, England, Wales and Northern Ireland have all experienced their coldest temperatures of this winter so far, dropping as low as -13°C in some places.

However, have we ever stopped to think why we use salt to grit our roads and pavements?

A common misconception of the reason we use salt in cold weather is that it causes the ice to melt. This is in fact not the case! When water and salt are mixed together, the freezing point of the water/salt solution is lowered to well below 0°C. Although how much the freezing point is lowered depends on how much salt is used, the salt solution used in most cities will lower the freezing point to about -9°C.

It is important to note that for the salt to effectively lower the freezing point of water it must be mixed in with liquid water. This is why many cities spray a salt solution on roads and pavements before any ice forms. If salt is put on top of ice, it will rely on the sun or friction from cars driving on the surface to melt the ice to a slush before mixing with the water thus lowering the freezing point.

Boldly Going Where No 3D Printer has Gone Before

3D printers typically build objects by depositing or solidifying material, usually plastic, layer by layer. However, researchers at the University of California, Berkeley have developed a new printer that creates structures by projecting light into a resin that then solidifies as a whole. The 3D printer has been nicknamed the “replicator” as a tribute to the machines in Star Trek that can materialise any inanimate object.

The researchers were inspired by CT scanners. These work by taking x-ray images of patients from many different angles which are then reconstructed to build a 3D model. The researches have applied the same process but in reverse. By using a computer program to produce 2D images at many different angles of a 3D model, they then compiled all the images into a video sequence. Using a resin that solidifies when in contact with specific intensities of light, they projected this video onto the resin while rotating the resin vat to create the object, in this case Rodin’s “The Thinker”.

Although further work is needed to increase the scale of the objects made and improve the finish of the objects, it took the researcher only a couple of minutes to materialise The Thinker using this method, while using traditional 3D printers would typically take a few hours.

the-thinker
The miniature copy of The Thinker created by the “Replicator” (Credit: Stephen McNally, UC Berkeley)

Alligator Have a Strange Taste for Rocks

The typical alligator’s diet is varied, including many types of mammals, birds and other reptiles, but scientists have long known that alligators also swallow rocks. The likely reasoning behind this was thought to be an aid in digesting their tough-to-process meals, much like birds have been found to do, or just an accident when digging into a live and thrashing dinner.

However, a new study points to a different reason: alligators could be consuming stones on purpose as a way of increasing the time they spend under water on dives.

Researchers looked at seven young American alligators in their lab and measured how long they stayed submerged before and after voluntarily swallowing small (<10mm in diameter) granite stones equivalent to 2.5% of the alligator’s body weight. The scientists found that the average duration of dives increased by 88% and the maximum duration increased by 117%. When swallowing the stones to increase their specific gravity, the alligators compensated by increasing lung volume and therefore dived with larger stores of oxygen.

alligator
Photo by Lance Anderson on Unsplash

Written by Jeanne Kroeger

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Facebook for Chimps

According to the UN environment programme about 3,000 great apes, two thirds of which are chimpanzees, are illegally trafficked around the world every year. The chimpanzees are often offered and sold via social media, including advertisement via Facebook posts. To make catching perpetrators easier, the non-profit Conversation X Labs, in collaboration with computer vision expert Dr Colin McCormick, are now developing a face recognition programme called “ChimpFace”. The software can be used on social media to identify chimpanzees that have previously been rescued or were removed from their wild habitats. It can be surprisingly difficult for a programme to distinguish between a human and a chimpanzee face and to tackle this problem, nine chimpanzee conservation organizations have contributed pictures for the programme to learn from. The database now uses about 3,000 ape face images and about 30 images per chimp to identify an individual. Similar pattern software already exists for lemures, which can identify a lemur with 97% accuracy. Face recognition does not only work for apes and monkeys though and the Zoological Society of London has worked with Google to develop a facial recognition software that can help to track elephants in the wild. With processing times of under a second per picture, illegal online animal trade might soon be a thing of the past.

Life on the Moon

sproutChina’s Chang’e-4 mission set out to explore the dark side of the moon and landed successfully on the moon’s surface on the 3rd of January 2019. On board was an 18 centimetre tall, 3 kilogram heavy cannister, which was designed by a collaboration of 28 Chinese Universities. This container carried cotton and potato seeds, as well as yeast and fruit fly eggs. The idea was to create a self-sustaining, albeit artificial, mini biosphere on the moon. And it worked. The seeds became the first biological matter to ever sprout on the moon. Growing things in space in naturally difficult, and although plants have been successfully grown on the international space station, none have ever been grown on the moon before. The cannister controlled the environment of the plants, in particular the temperature, as it can vary between -173C to +100C on the moon’s surface. While successful at first, the sprouting plant died soon after, as the experiment was only designed to last for about 200 hours, after which the temperature control was disabled and the extreme conditions on the dark side of the moon caught up with the young plants. This experiment shows that it is in theory possible to grow things in space, which could be an important step towards longer journeys through space, e.g. to Mars, where self sufficiency in food and or water supplies could make or break a mission. The often-cited concern over contamination did not pose a great risk on the moon, as human waste had been left behind from the Apollo missions several decades earlier.

Bleeding gums and Alzheimer’s

brain-adPorphyromonas gingivalis might not sound familiar, but it is the key bacteria causing chronic gum disease in people. Gum disease affects about one third of the population and worryingly has been connected to the development of Alzehimer’s Disease (AD). Certain proteins, called amyloid plaques and tau tangles, accumulate in the brain of Alzheimer’s patients and have long been thought to be the cause of the disease. This hypothesis has recently been called into question, after it was found that people can have protein plaques without developing dementia and treating the plaques does not lead to a betterment of the disease. Growing evidence actually points towards the reverse, namely that the role of amyloid proteins might be to protect the brain from bacteria.  Bacteria have been found in brains of people with AD, but until recently it wasn’t clear whether this was causal or consequential of the disease. Interestingly, gum disease has been known to be a major predictor for the development of AD and now a possible mechanism of action has been discovered. Research revealed that p. gingivalis invades and inflames the brain regions affected by AD and gum infections have been shown to worsen symptoms in mice that have been genetically engineered to develop AD. P. gingivalis secretes a toxic enzyme called gingipains, which is thought to be the root of the problem. Both, bacteria and gingipains have been found at higher levels in brains of people with more severe AD, as well as in their spinal fluid. The exciting thing is that the presence of p. gingivalis or their toxins could potentially be used as a biomarker for AD and a drug that blocks this main toxin is already entering major clinical trials this year. Studies in mice have already shown that the drug can reduce p. gingivalis infection in the brain, reduce amyloid production, lower brain inflammation and even rescue damaged neurons. The drug is especially exciting because it isn’t an antibiotic and therefore the bacteria are less likely to build up a resistance. The number of people living with AD in the UK is set to hit 1 million in 2025 and while the research is still in its infancy, the possibility of a treatment or even vaccine for AD is an exciting one.

 

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Going down-krill

Increasing ocean temperatures are having a profound effect on a particular species of sea creature.

Populations of Antarctic Krill, a tiny species of crustacean, are moving closer to the Antarctic circle, as a result of warming seas.

Data about the population distribution of the krill has been collected over the past 90 years. The data was published in the journal Nature Climate Change this week.

It shows a clear shift in distribution in recent years. The krill are moving south towards the Antarctic circle where the sea temperature is lower. Not only has the distribution changed, but the total quantity of krill decreased too.

“Our results suggest that over the past 40 years, the amount of krill has, on average, gone down, and also the location of the krill has contracted to much less of the habitat. That suggests all these other animals that eat krill will face much more intense competition with each other for this important food resource,” Simeon Hill from the British Antarctic Survey told BBC News.

Krill are a staple food source of animals such as whales, seals and penguins. If this trend continues, it is likely that populations of these animals will begin to decline too.

New development in Alzheimer’s research

neuronsA protein has been identified which accurately predicts the onset and progression of Alzheimer’s disease.

The research was published in Nature Medicine. Mathias Jucker, who headed up the study, reports that the protein, called ‘Neurofilament [light chain]’, can be detected up to 16 years before the onset of symptoms.

Alzheimer’s is a brain disorder that causes memory problems which worsen over time. At present, there are no effective treatments for the disease. This is because once symptoms appear, the extent of cell death in the brain is too great to be repaired.

When cells die, their contents are released, and can be found in the blood. Normally such molecules quickly breakdown, however the protein in question, Neurofilament, is resistant to breakdown. The study showed that Neurofilament builds up in the blood before any symptoms occur, and can be detected many years before the first signs of the disease appear. Neurofilament can accurately predict the course of the disease when monitored over time.

“It is not the absolute neurofilament concentration, but its temporal evolution, which is meaningful and allows predictions about the future progression of the disease,” says Jucker.

This is an important discovery, as it can be used to test the effect of new drugs on disease progression.

Cerebellum gets social

brainA brain area originally thought to be responsible for movement alone, has another important function. The cerebellum, an area at the back of the brain, has been found to play a role in social interaction.

New research suggests that the cerebellum is linked to another brain area called the Ventral Tegmental Area (VTA), which is known to be involved in reward and reinforcement.

The experiment, published in Science journal, was carried out using mice. Electrodes in the brains of the mice were used to record activity from brain cells in the cerebellum which were linked to brain cells in the VTA.

Researchers noticed that these particular cells were active when the mice were interacting with other mice. When the cells were artificially turned off using lasers, the mice no longer preferred to spend time with other mice rather than spend time alone. This strongly suggests the cells play a role in social behaviours.

Brain disorders such as Autism have been associated with damage to the cerebellum. Social deficits observed in individuals with autism might be explained through this link between the cerebellum, VTA and social behaviours.

 

 

 

 

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Is a universal cancer test possible?

Research published in Nature Communications suggests that it might be.

cancer-testScientists, based at the University of Queensland, have discovered something they believe to be common to all cancers – a unique nano-scaled DNA signature.

The scientists used this unique signature to develop a test that might detect cancer from any tissue type, including blood.

Dr Laura Carrascosa, a researcher at the University of Queensland, said: “There’s been a big hunt to find whether there is some distinct DNA signature that is just in the cancer and not in the rest of the body.”

To find this distinct signature the researchers assessed molecular patterns displayed by methyl groups that are usually distributed evenly across a healthy cell’s DNA. Methyl groups serve as signals to control which genes are turned on or off at any given time and are very important to cell function.

The team discovered that in a cancer cell the genome is almost bare, except for intense clusters of methyl groups at specific locations.

This signature, named by the scientists as the cancer ‘methylscape’ appeared in breast, prostate and colorectal cancer cells.

“Virtually every piece of cancerous DNA we examined had this highly predictable pattern,” said Professor Matt Trau, lead researcher at the University of Queensland.

It was then found that these clusters of methyl groups cause cancer DNA fragments to fold into 3-D structures that will stick to gold nanoparticles.

The researchers made use of this curious finding to develop the reported cancer detection method. They used gold nanoparticles that change colour depending on whether the 3D nanostructures associated with cancer DNA are present or not. The resulting test is simple, cheap and can provide results in less than 10 minutes and is believed to potentially be a radical new approach to cancer detection.

“Our technique could be a screening tool to inform clinicians that a patient may have a cancer, but they would require subsequent tests with other techniques to identify the cancer type and stage,” Carrascosa said.

The test has been reported to have a sensitivity of around 90%, so would detect 90 in 100 cases of cancer.

Dr Ged Brady, of the Cancer Research UK Manchester Institute, commented: “This approach represents an exciting step forward in detecting tumour DNA in blood samples and opens up the possibility of a generalised blood-based test to detect cancer. Further clinical studies are required to evaluate the full clinic potential of the method.”

Gene-edited babies – how far is too far?

Claims by scientist He Jiankui last month of the creation of the world’s first gene-edited twins, shocked and appalled the global scientific community.

gene-edited twinsHis experiment still hasn’t been fully substantiated, but the way it was conducted, the implications of his research and the way it was announced, has caused worldwide controversy.

“We heard an unexpected and deeply disturbing claim that human embryos had been edited and implanted, resulting in a pregnancy and the birth of twins,” read a statement released by the organising committee of the Second International Summit on Human Genome Editing in Hong Kong.

“Even if the modifications are verified, the procedure was irresponsible and failed to conform with international norms.”

He Jiankui is an associate professor at the Southern University of Science and Technology in Shenzhen, an institution that denied any knowledge of his research.

Xu Nanping, Vice-Minister for Science and Technology told the Chinese state-owned network CCTV: “The genetically edited infant incident reported by media blatantly violated China’s relevant laws and regulations. It has also violated the ethical bottom line that the academic community adheres to. It is shocking and unacceptable.”

CRISPR is a gene-editing tool, that can be used to control which genes are expressed in an organism. Through its use, it’s possible to delete undesirable traits or add them to an organism’s genome.

It has previously been used in the lab for editing human embryos, but the created embryos have never been implanted and allowed to develop into gene-edited babies. The novel nature of this procedure, the lack of testing and disregard of the proper protocol has raised concerns with many in the science community.

Were the parents properly informed of what was happening? Did they understand the implications fully? Could the technology have unwanted side effects? Is it ethical? These are just a few of the questions currently circulating.

The edited embryos also have germline mutations, meaning that the edited genes of the twins could be passed on to any children that they may have.

The creation of the CRISPR edited twins has shown the potential threat and power of technology that isn’t carefully regulated and monitored. And it serves as a call to action for scientists and regulators across the globe to think more carefully about gene editing technology.

But is the answer simply to suspend gene-editing efforts? Or could this create even more problems with scientists going underground to try out this new tech?

Written by Angharad Baldwin