PLOS One

Physicists Confirm There’s a Second Layer of Information Hidden in Our DNA

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IN BRIEF

Theoretical physicists have confirmed that it’s not just the information coded in our DNA that shapes who we are—it’s also the way DNA folds itself that controls which genes are expressed inside our bodies.

We all learned in high school how Watson and Crick pieced together the findings of many scientists to come up with a model of deoxyribonucleic acid (DNA). Information in DNA is stored as code sequences made up of nitrogenous bases. Each cell has the same sequence of codes but executes a different function. Code sequences determine the type of protein to be produced in a certain cell, but it is hypothesized that the mechanical properties of the DNA acts as a second layer of information.

Each cell in our body contains around 2 meters of DNA. But since our cells are so tiny, DNA strands have to be tightly wrapped into bundles called nucleosomes in order to fit.

Learn more about DNA and nucleosomes in the video below:

URL”https://youtu.be/4Z4KwuUfh0A

The folding mechanism of DNA is believed to play a large role in how genes are read by the rest of the cell. Biologists have started to isolate mechanical cues that determine how DNA is folded. Now, theoretical physicists from Leiden University in the Netherlands confirmed through computer simulations that these cues are actually coded into our DNA.

Physicist Helmut Schiessel and his group simulated the folding of DNA strands with randomly assigned cues. The team used genomes of baker’s yeast and fission yeast to find correlations between the mechanics and the actual folding structure of DNA in the two organisms.

The results confirm that this second layer of information exists. This led them to conclude that genetic mutations are not just caused by a change in the sequence of codes but also by a change in the way the strands are folded. This simulation may be helpful in hiding unwanted sequences like those that cause diseases.

 Source:PLOS ONE.

Watched chimps change their hunting habits

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Chimpanzees in Uganda may have changed their hunting strategy in response to being watched by scientists.

While studying the animals, researchers documented very different hunting habits of two closely neighbouring chimp “tribes”.

“Sonso” chimps hunt in small groups for colobus monkeys, while those from the “Waibira” troop hunt solo and catch “whatever they can get their hands on”.

The findings show how sensitive chimp society is to human presence.

They are published in the journal PLoS One,

Biologists who have followed and studied these animals for years think that work may have disturbed the group hunting that seems key to chasing and catching colobus monkeys.

Lead researcher Dr Catherine Hobaiter, from the University of St Andrews, said the Waibira group’s behaviour might have changed to a more “opportunistic” strategy because those chimps were much less used to the presence of human scientists.

Speaking to BBC News from Budongo Forest, in Uganda, where she studies both of these chimpanzee groups, Dr Hobaiter said Sonso and Waibira chimps “shared territorial borders”, so she would expect their food sources and prey to be the same.

“The main thing that’s different about them right now is how used to having humans follow them around the forest they are,” Dr Hobaiter said.

“For Sonso – most of the current generation of adults were born with us being there, so they’re really incredibly relaxed about our presence.

“But [for] Waibira – some of the young ones have started to grow up and become very comfortable with us, but some of the adults would be 30-40 years old when we started, and five years of us following them round is a fraction of their lifetime.

“It just takes time with chimpanzees.”

At other sites where researchers had begun a similar habituation and close observation of wild chimp groups, Dr Hobaiter said, a similar “pattern” had emerged.

“They hunt for lots of different species, then later they seem to switch and settle in to hunting colobus.”

Key to this could be the natural tendency of chimpanzees’ groups to be territorial and wary of newcomers.

“I think that makes it that much harder for them to accept our presence as being a part of their lives,” said Dr Hobaiter.

Following our cousins

“Long-term research with wild chimpanzees brings real conservation benefits, but we have to remember that our presence can affect their behaviour.”

Dr Hobaiter said that – as well as conserving endangered primates and the forests they lived in – directly observing and recording chimpanzee behaviour was the best way to understand the origins of human language and social structure.

“But we need to ask – should we be going in there [to follow the chimps]?

“We can do amazing things with camera traps, remote microphones and drones – it’s getting much easier to get good quality data.

“Part of our work is to understand what our impact is and to try to minimise it.”

Scientists Discover Method To ‘Expand’ Stem Cells In The Laboratory That Could Lead To New Cancer Treatments

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Stem cells used in cell-based therapies have so far saved countless lives that may have otherwise been lost to cancer or birth defects. But such therapies are always subject to finding sufficient quantities of stem cells from a donor. But now, scientists from the University of Colorado School of Medicine have discovered a novel process that allows them to expand production of stem cells. An article on the research has been published Friday in PLOS ONE.

Stem cell cultivation

Stem cell cultivation Growing stem cells in the laboratory can greatly help in developing interventions for several autoimmune and metabolic conditions.

The scientists have uncovered the molecular code, or the process that regulates how the stem cells differentiate to produce more stem cells and retain their stem-cell characteristics. The discovery has generated great excitement among researchers, who hope the findings will aid in a cure for cancers, inborn immunodeficiency and metabolic conditions, and autoimmune diseases.

Importance of Stem Cells

Stem cells are the internal repair system of the body. Their ability to divide and produce more stem cells enables them to replenish old and worn out tissues with new ones. They also have the unique property of differentiating into specialized cells with specialized functions, such as muscle cells, red blood cells, or brain cells. But such differentiation in organs, like the pancreas or the heart, requires specialized conditions.

Scientists have been trying for years to reproduce these specialized conditions that would allow stem cells to differentiate in the laboratory to be used for regenerative and cell-based therapies.

“Use of stem cells to treat cancer patients who face bone marrow transplants has been a common practice for four decades,” said Yosef Refaeli, lead scientist of the study, in a statement. “The biggest challenge, however, has been finding adequate supplies of stem cells that help patients fight infection after the procedure.”

To overcome this, the team developed protein products that can be directly administered to blood stem cells to encourage them to multiply without permanent genetic modifications. The technology worked on blood stem cells obtained from cord blood, adult bone marrow, or peripheral blood from adults.

“Most of those approaches have been limited by the nature of the resulting cells or the inadequate number of cells produced,” said Gates Stem Cell Center Director Dennis Roop, referring to previous attempts to “grow” stem cells in a lab, which have not always been successful.

“The ability to multiply blood stem cells from any source in a dish will be critical for adoption of this new technology in clinics,” said Brian Turner, one of the lead authors of the study.

The researchers are now attempting to start human clinical trials, which will involve attempting blood stem cell expansion in patients suffering from inborn immunodeficiency conditions, like SCID and sickle cell anemia, to metabolic conditions, like Hurler’s disease or Gaucher syndrome, autoimmune diseases like multiple sclerosis and lupus, or cancers such as lymphoma, myeloma, and other types of solid tumors.

Source: Rafaeli Y, Turner B, et al. PLOS ONE. 2014.

Turning Urine Into Electricity Can Also Kill Pathogens in Wastewater

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Fuel cells with microorganisms that feed on pee and generate electricity already sound like a pretty clever trick. It’s one of the emerging biotechnology solutions in a world that’s moving away from fossil fuels.

But now scientists have taken it a significant step further, showing that not only can you power mobile phones and light globes with urine, but you can also kill pathogens in the wastewater as you do so. This development makes the technology even more attractive for use in the developing world.

 

A research team from the University of the West of England (UWE)  in the UK has already demonstrated that it’s possible to rig a urinal with cheap pee-powered fuel cells to generate enough electricity for the cubicle lighting.

The trial, created in partnership with Oxfam in 2015, showed the potential of this technology for places like disaster zones and refugee camps, where power supply is often lacking and lack of outdoor lighting at night makes people more vulnerable to potential assault.

But if this biotech can also kill pathogens in wastewater, that opens up a host of other potential uses, including routine installation in off-grid areas of the world where municipal resources for cleaning waste are in short supply.

urine tricityThe urinal project from 2015 / Credit: UWE Bristol News

The technology runs on microbial fuel cells (MFC) in which microbes feed on organic material such as urine, fuelling their growth and generating a small amount of energy in the process.

“The MFC is in effect a system which taps a portion of that biochemical energy used for microbial growth, and converts that directly into electricity – what we are calling urine-tricity or pee power,” lead researcher Ioannis Ieropoulos explained back in 2015.

Studies have shown that MFCs seem to have some disinfecting properties, likely due to the generation of hydrogen peroxide during the energy generation process. This disinfection happens at a later stage in the fuel cell system, so it doesn’t kill the microbes powering the MFC.

This disinfection potential gave the UWE team an idea to systematically test how MFCs could be used to purify wastewater. For this, they picked one of the most important gastrointestinal pathogens, a strain of the Salmonella bacterium which causes typical food poisoning symptoms.

“This species was introduced into an MFC cascade system treating human urine, to determine the anodic killing efficacy when operating in continuous flow conditions,” the researchers write in the study.

When they checked the outflow at the end of the purification process to measure the remaining pathogen levels, they found just what they had hoped for – greatly reduced Salmonella counts.

“We were really excited with the results – it shows we have a stable biological system in which we can treat waste, generate electricity and stop harmful organisms making it through to the sewerage network,” says Ieropoulos.

In fact, the batteries destroyed these pathogens so effectively, they brought their levels down to what’s considered acceptable in conventional sanitation practices.

“We have reduced the number of pathogenic organisms significantly but we haven’t shown we can bring them down to zero – we will continue the work to test if we can completely eliminate them,” says one of the team, microbiologist John Greenman.

To raise awareness of this project, which is founded by the Bill & Melinda Gates Foundation, the team has also incorporated their tech into a portable toilet that will get some limelight at this year’s Glastonbury music festival in the UK.

Energy generated by the ‘Pee Power’ toilet will be used to power information displays at the festival. The plan is to process over 1,000 litres (264 gallons) of pee a day, using the electricity for a set of ten info panels.

“The festival updates are one way of showing that Pee Power and the MFC technology can be developed for a whole range of uses,” says Ieropoulos.

Source:PLOS ONE.

Extremely Positive People Aren’t as Good at Empathy.

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People with extremely sunny attitudes find it difficult to empathize with people who are recounting a negative experience, according to a study recently published at PLOS ONE. Ironically, positive people also reported being better at empathizing than did people who labelled themselves as slightly less than bubbly.

For the study, participants were shown videos of people telling life stories: two happy and two sad. The viewers were asked to rate, second-by-second, the level of positive or negative emotion they thought the speaker was feeling. Alex Fradera, at the British Psychological Society’s Research Digest, describes the result:

“Participants with a more upbeat personality believed their accuracy on this task to be higher than others. However, the speakers had conducted an identical rating process on their own videos, and it turns out the happier participants were no closer to the true feelings than the more downbeat participants. In fact, happy participants found it harder to judge the emotional tone of a highly negative monologue, in which a participant described the death of a parent.”

Dev Patnaik, author and founder of Jump Associates, argues that empathy is not just a personal quality that we all (are blessed to) have. Empathy, he argues, is an essential business skill that corporations must possess to help their employees innovate and to create a loyal customer base.

Source:http://bigthink.com

 

Stunning scientific discovery finds that gut bacteria control your brain chemistry, altering moods and more.

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Researchers from the University of Exeter Medical School and University of Zaragoza in Spain have uncovered a new way that the community of microorganisms symbiotically living in the human gut may contribute to helping regulate brain chemistry. The remarkable study was published in the journal PLOS ONE.

The human gut alone hosts approximately 100 trillion bacteria and other microbes of many different species, which are collectively known as the gut microbiome or microbiota (our body’s overall microbiome also includes microbes living on the skin and in other parts of the body). Studies have shown that the gut microbiome plays a key role in regulating everything from digestion and metabolism to immune function and even mood, but the mechanisms of this action remain largely a mystery.

Image: Stunning scientific discovery finds that gut bacteria control your brain chemistry, altering moods and more

Microbes manipulate serotonin levels

Prior research has shown that a disrupted microbiome may contribute to the development of inflammatory disease, including inflammatory bowel diseases (IBD) such as Crohn’s disease or ulcerative colitis. Research has also confirmed that people with IBD have a different gut microbiome composition than healthy people.

The current study was funded by the Foundation for the Study of Inflammatory Bowel Diseases in Aragón, Spain (ARAINF), in order to further study this connection. The researchers focused their investigations on a protein known as TLR2, which is a key marker of the presence of certain microbes in the intestines. Studies have also suggested that IBD may be triggered by the failure of TLR2 to function correctly.

In experiments conducted in cell cultures and in living mice, the researchers found that TLR2 actually helps regulate levels of the chemical serotonin. Although perhaps most well-known as a neurotransmitter that carries signals for the brain, serotonin also plays a key role in regulating bowel function.

The findings suggest that certain gut microbes can, through the action of TLR2, modulate levels of serotonin and therefore directly influence human physiology and brain chemistry.

Could the gut microbiome also modify serotonin levels to cause changes in mood or brain function? A 2014 review of the evidence into whether gut microbes can influence human emotions and behavior, published in the journal BioEssays, concluded that there is strong theoretical support for the idea but that evidence remains circumstantial. For example, studies suggest that some microbes can release chemicals that change the activity of the vagus nerve, which runs from the gut to the brain. Another study showed a different makeup of gut microbes in people who regularly crave chocolate, regardless of what they had recently eaten.

“Microbes have the capacity to manipulate behavior and mood through altering the neural signals in the vagus nerve, changing taste receptors, producing toxins to make us feel bad, and releasing chemical rewards to make us feel good,” said senior author Athena Aktipis. (RELATED: Find more news about scientific discoveries at Scientific.news.)

Far-reaching effects

A 2015 study published in the journal Nature found another mechanism by which gut microbes might influence human physiology. That study showed that the common industrial food ingredients known as emulsifiers (detergents used to improve food’s texture and shelf life) produce changes in the gut microbiome that lead to more of the inflammation associated with IBD and metabolic syndrome.

Metabolic syndrome is a cluster of physiological symptoms linked with a higher risk of heart disease, diabetes, liver disease and Alzheimer’s disease. It is associated with high levels of systemic inflammation. IBD, in turn, is characterized by abnormal inflammation of the digestive tract. Both conditions have dramatically increased since the time period that saw the widespread adoption of chemical food additives.

Inflammation is an immune response, thus suggesting at least one mechanism by which gut microbes interact directly with the immune system.

Another recent study linked the gut microbiome with the development of Parkinson’s disease, while others have linked a disrupted microbiome with the development of autism.

Sources:

MedicalXpress.com

NaturalNews.com

 

New research could lead to restoring vision for sufferers of retinal disorders

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New research could lead to restoring vision for sufferers of retinal disorders
Fly brain diagram.

Engineers and neuroscientists at the University of Sheffield have demonstrated for the first time that the cells in the retina carry out key processing tasks. This could pave the way for improving retinal implants and therefore the sight of thousands of people suffering from retinal disorders.

 Up to now, it was thought that the function of these retinal cells, or photoreceptors, was mainly to convert light into electrical signals, from which the brain can interpret images.

However, the new research from Sheffield, published in the journal PLOS ONE, shows that in fruit flies, the photoreceptors believed to be involved in motion detection play a key role in providing visual information about the world around us.

The similarities that exist between responses of human cone photoreceptors and fly photoreceptors suggest that the human eye processes visual signals in a similar way.

If this were true, the research could have significant implications for those developing for patients with retinal disorders such as macular degeneration. Age-related macular degeneration is the most common cause of sight loss in the developed world and currently affects more than 600,000 people in the UK.

Retinal implants replace damaged or dead cells by converting light into electrical signals that are sent to the brain. The implants do not restore vision completely but can help patients to detect patterns and shapes.

Daniel Coca, lead researcher from Sheffield’s Department of Automatic Control and Systems Engineering, said: “We think that implementing the processing tasks performed by photoreceptors into retinal implants could help the brain accomplish key tasks such as object recognition and motion detection. This could significantly improve the performance of artificial retinas and therefore the sight of thousands of people suffering from macular degeneration.”

Snail study reveals that stress is bad for memory.

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New research on pond snails has revealed that high levels of stress can block memory processes. Researchers from the University of Exeter and the University of Calgary trained snails and found that when they were exposed to multiple stressful events they were unable remember what they had learned. Previous research has shown that stress also affects human ability to remember. This study, published in the journal PLOS ONE, found that experiencing multiple simultaneously has a cumulative detrimental effect on .

Dr Sarah Dalesman, a Leverhulme Trust Early Career Fellow, from the University of Exeter, formally at the University of Calgary, said: “It’s really important to study how different forms of stress interact as this is what animals, including people, frequently experience in real life. By training snails, and then observing their behaviour and brain activity following exposure to , we found that a single stressful event resulted in some impairment of memory but multiple stressful events prevented any memories from being formed.”

The pond snail, Lymnaea stagnalis, has easily observable behaviours linked to memory and large neurons in the brain, both useful benefits when studying . They also respond to stressful events in a similar way to mammals, making them a useful model species to study learning and memory.

In the study, the pond snails were trained to reduce how often they breathed outside water. Usually pond snails breathe underwater and absorb oxygen through their skin. In water with low oxygen levels the snails emerge and inhale air using a basic lung opened to the air via a breathing hole.

To train the snails not to breathe air they were placed in poorly oxygenated water and their breathing holes were gently poked every time they emerged to breathe. Snail memory was tested by observing how many times the snails attempted to breathe air after they had received their training. Memory was considered to be present if there was a reduction in the number of times they opened their breathing holes. The researchers also assessed memory by monitoring neural activity in the brain.

https://i0.wp.com/cdn.physorg.com/newman/gfx/news/2013/stressmakess.jpg

Immediately before training, the snails were exposed to two different stressful experiences, low calcium – which is stressful as calcium is necessary for healthy shells – and overcrowding by other pond snails.

When faced with the stressors individually, the pond snails had reduced ability to form long term memory, but were still able to learn and form short and intermediate term memory lasting from a few minutes to hours. However, when both stressors were experienced at the same time, results showed that they had additive effects on the ‘ ability to form memory and all learning and memory processes were blocked.

Babies can learn their first lullabies in the womb.

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An infant can recognise a lullaby heard in the womb for several months after birth, potentially supporting later speech development. This is indicated in a new study at the University of Helsinki.

The study focused on 24 women during the final trimester of their pregnancies. Half of the women played the melody of Twinkle Twinkle Little Star to their fetuses five days a week for the final stages of their pregnancies. The brains of the babies who heard the melody in utero reacted more strongly to the familiar melody both immediately and four months after birth when compared with the control group. These results show that fetuses can recognise and remember sounds from the outside world.

This is significant for the early rehabilitation, since rehabilitation aims at long-term changes in the brain.

“Even though our earlier research indicated that fetuses could learn minor details of speech, we did not know how long they could retain the information. These results show that babies are capable of learning at a very young age, and that the effects of the learning remain apparent in the brain for a long time,” expounds Eino Partanen, who is currently finishing his dissertation at the Cognitive Brain Research Unit.

“This is the first study to track how long fetal memories remain in the brain. The results are significant, as studying the responses in the brain let us focus on the foundations of fetal memory. The early mechanisms of memory are currently unknown,” points out Dr Minna Huotilainen, principal investigator.

The researchers believe that song and speech are most beneficial for the fetus in terms of speech development. According to the current understanding, the processing of singing and speech in the babies brains are partly based on shared mechanisms, and so hearing a song can support a baby’s speech development. However, little is known about the possible detrimental effects that noise in the workplace can cause to a fetus during the final trimester. An extensive research project on this topic is underway at the Finnish Institute of Occupational Health.

The study was published by the esteemed American scientific journal PLoS ONE. The research was conducted at the Academy of Finland’s Finnish Centre of Excellence in Interdisciplinary Music Research as well as the Cognitive Brain Research Unit at the University of Helsinki Institute of Behavioural Sciences.

Scientists discover another cause of bee deaths.

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So what is with all the dying bees? Scientists have been trying to discover this for years. Meanwhile, bees keep dropping like… well, you know.

Is it mites? Pesticides? Cell phone towers? What is really at the root? Turns out the real issue really scary, because it is more complex and pervasive than thought.

Quartz reports:

Scientists had struggled to find the trigger for so-called Colony Collapse Disorder (CCD) that has wiped out an estimated 10 million beehives, worth $2 billion, over the past six years. Suspects have included pesticides, disease-bearing parasites and poor nutrition. But in a first-of-its-kind study published today in the journal PLOS ONE, scientists at the University of Maryland and the US Department of Agriculture have identified a witch’s brew of pesticides and fungicides contaminating pollen that bees collect to feed their hives. The findings break new ground on why large numbers of bees are dying though they do not identify the specific cause of CCD, where an entire beehive dies at once.
The researchers behind that study in PLOS ONE — Jeffery S. Pettis, Elinor M. Lichtenberg, Michael Andree, Jennie Stitzinger, Robyn Rose, Dennis vanEngelsdorp — collected pollen from hives on the east coast, including cranberry and watermelon crops, and fed it to healthy bees. Those bees had a serious decline in their ability to resist a parasite that causes Colony Collapse Disorder. The pollen they were fed had an average of nine different pesticides and fungicides, though one sample of pollen contained a deadly brew of 21 different chemicals. Further, the researchers discovered that bees that ate pollen with fungicides were three times more likely to be infected by the parasite.

The discovery means that fungicides, thought harmless to bees, is actually a significant part of Colony Collapse Disorder. And that likely means farmers need a whole new set of regulations about how to use fungicides. While neonicotinoids have been linked to mass bee deaths — the same type of chemical at the heart of the massive bumble bee die off in Oregon — this study opens up an entirely new finding that it is more than one group of pesticides, but a combination of many chemicals, which makes the problem far more complex.

And it is not just the types of chemicals used that need to be considered, but also spraying practices. The bees sampled by the authors foraged not from crops, but almost exclusively from weeds and wildflowers, which means bees are more widely exposed to pesticides than thought.

The authors write, “[M]ore attention must be paid to how honey bees are exposed to pesticides outside of the field in which they are placed. We detected 35 different pesticides in the sampled pollen, and found high fungicide loads. The insecticides esfenvalerate and phosmet were at a concentration higher than their median lethal dose in at least one pollen sample. While fungicides are typically seen as fairly safe for honey bees, we found an increased probability of Nosema infection in bees that consumed pollen with a higher fungicide load. Our results highlight a need for research on sub-lethal effects of fungicides and other chemicals that bees placed in an agricultural setting are exposed to.”

While the overarching issue is simple — chemicals used on crops kill bees — the details of the problem are increasingly more complex, including what can be sprayed, where, how, and when to minimize the negative effects on bees and other pollinators while still assisting in crop production. Right now, scientists are still working on discovering the degree to which bees are affected and by what. It will still likely be a long time before solutions are uncovered and put into place. When economics come into play, an outright halt in spraying anything at all anywhere is simply impossible.

Quartz notes, “Bee populations are so low in the US that it now takes 60% of the country’s surviving colonies just to pollinate one California crop, almonds. And that’s not just a west coast problem—California supplies 80% of the world’s almonds, a market worth $4 billion.”