Posts Tagged ‘science’


The way oral bacteria sets up shop in our mouths is not unlike how we humans settle into our cities, a new study has found.

There’s a reason bacteria are said to live in ‘colonies’, and the more we learn about how these tiny architects build their communities, the more familiar their behavior seems to us.

A new study following how multiple individual settlers develop into microcolonies has found growth patterns and dynamics that mirror our own urban inclinations.

“We take this ‘satellite-level’ view, following hundreds of bacteria distributed on a surface from their initial colonisation to biofilm formation,” says Hyun Koo from the University of Pennsylvania.

“And what we see is that, remarkably, the spatial and structural features of their growth are analogous to what we see in urbanisation.”

Just as in nature, bacteria in your mouth live in complex structures known as biofilms. In fact, 99.9 percent of prokaryotes live crammed together with millions of other neighbours in one of these settlements.

Biofilms are everywhere, but if they’re on your teeth, we refer to them as plaque. This dense and sticky deposit is hard to remove, thereby protecting resident microbes from environmental assaults, like toothpaste, floss or even antibiotics.

It builds up when several individual settlers develop into microcolonies, but exactly how this happens remains underexplored.

Using the oral bacterium Streptococcus mutans, researchers have shown that microbial cells settle at random and regardless of the surface type. Nevertheless, only a subset of colonisers actually begin clustering, expanding their scope “by amalgamating neighboring bacteria into densely populated microcolonies.”

“We thought that the majority of the individual bacteria would end up growing,” says Koo. “But the actual number was less than 40 percent, with the rest either dying off or being engulfed by the growth of other microcolonies.”

Once the clusters arise, something really curious happens: they begin to interact with one another, growing and organising into densely populated “micron-scale microcolonies that further expand and merge” to form a biofilm superstructure.

This sort of cooperation is interesting, as previous studies have reported bacterial competition in other species, especially when there was a scarcity of nutrients.

In this case, the nutrients only impacted the actual forming of the colonies. After that, “the individual microcolonies (distant or in close proximity) continued to grow without disruption until merging with each other, and the merged structures behaved and grew like a single new harmonised community,” the researchers write.

Only when more antagonistic foreign species were introduced did it affect that seemingly peaceful unit, and the growth of the microcolonies was lowered.

“These communities (microcolonies) can expand and merge with each other in a collaborative fashion, without competition between adjacent communities,” the authors conclude.

It’s the type of growth that indicates “communal behavior between microorganisms”, and it looks similar to human urbanisation, where some settlers stay static, while others grow into villages that further expand into densely-populated microcolonies or cities, which then merge into microbial megacities.

Of course, there are limits to this idea of bacterial urbanisation. The authors aren’t saying microbes build traffic signs, roads and supply lines, but the general idea is the same and it can not only help us tackle infections better, it might also help us build more sustainably.

“It’s a useful analogy, but it should be taken with a grain of salt,” Koo says. “We’re not saying these bacteria are anthropomorphic. But taking this perspective of biofilm growth gives us a multiscale, multidimensional picture of how they grow that we’ve not seen before.”

The study was published in Nature Communications.

Evidence of a worm-like creature about the size of a grain of rice has been uncovered in South Australia, and researchers believe it is the oldest ancestor on the family tree that includes humans and most animals.

The creature lived 555 million years ago.

It’s considered to be the earliest bilaterian. Bilaterians are organisms with a front, back, two openings on either end and a gut that connects them. They were an evolutionary step forward for early life on Earth.

Some of the oldest life on Earth, including those sponges and algal mats, is referred to as the Ediacaran Biota. This group is based on the earliest fossils ever discovered, providing evidence of complex, multicellular organisms.

But those aren’t directly related to animals living today. And researchers have been trying to find fossilized evidence of the common ancestor of most animals.

Developing bilaterian body structure and organization successfully allowed life to move in specific, purposeful directions. This includes everything from worms and dinosaurs to amphibians and humans.

But for our common ancestor, they knew that fossils of the tiny, simple creatures they imagined would be nearly impossible to find because of its size and soft body.

Burrows were found in stone that belonged to a tiny creature who lived billions of years ago.

Then, they turned to fossilized burrows, dated to the Ediacaran Period some 555 million years ago, found in Nilpena, South Australia. For 15 years, scientists knew they were created by bilaterians. But there was no evidence of what made the burrows and lived in them.

That is, until researchers decided to take a closer look at the burrows. Geology professor Mary Droser and doctoral graduate Scott Evans, both from the University of California, Riverside, spotted impressions shaped like ovals near the burrows.

A 3-D laser scan revealed the impressions contained evidence of a body shaped and sized like a rice grain, with a noticeable head, tail and even V-shaped grooves suggesting muscles.

Contractions of the muscles would have enabled the creature to move and create the burrows, like the way a worm moves. Patterns of displaced sediment and signs of feeding led the researchers to determine that it had a mouth, gut and posterior opening.

And the size of the creature matched with the size of the burrows they found.

The study published Monday in the journal Proceedings of the National Academy of Sciences.
“We thought these animals should have existed during this interval, but always understood they would be difficult to recognize,” Evans said. “Once we had the 3D scans, we knew that we had made an important discovery.”

A 3D scan revealed the shape and characteristics of the creature that made the burrows.

The researchers involved in the study named the creature Ikaria wariootia. The first name translates to “meeting place” in the Adnyamathanha language. Adnyamathanha is the name of contemporary Indigenous Australian people that live in the area where the fossil was found. And the name of the species is a variation on a waterway in the area, called Warioota Creek.

The fossilized burrows were found beneath the impressions of other fossils in the lowest layer of Nilpena’s Ediacaran Period deposits. During its lifetime, Ikaria searched for the organic matter it fed on by burrowing through layers of sand on the ocean floor. Given that the burrows track through sand that was oxygenated, rather than toxic spots, suggest the creature had basic senses.

“Burrows of Ikaria occur lower than anything else. It’s the oldest fossil we get with this type of complexity,” Droser said. “We knew that we also had lots of little things and thought these might have been the early bilaterians that we were looking for.”

Droser also explained that other, larger fossils belonging to other creatures they found in the past were likely evolutionary dead-ends.

“This is what evolutionary biologists predicted,” Droser said. “It’s really exciting that what we have found lines up so neatly with their prediction.”

By Anette Breindl

The first attempt at using existing drugs to treat patients infected with SARS-CoV-2 has yielded disappointing results.

In 200 hospitalized patients with severe COVID-19, a 14-day regimen of twice-daily treatment with Kaletra/Aluvia (lopinavir/ritonavir, Abbvie Inc.) did not hasten recovery when added to the standard of care. Chinese clinicians led by Bin Cao of the National Clinical Research Center for Respiratory Diseases reported their findings in the March 19, 2020, issue of The New England Journal of Medicine.

Lopinavir is a protease inhibitor, while ritonavir increases the half-life of lopinavir by inhibiting its metabolism. The drug was tested because screening studies had flagged it as having activity against MERS-CoV, which has led to a clinical trial of a combination of Kaletra/Aluvia and interferon-beta for the treatment of MERS-CoV in the Kingdom of Saudi Arabia.

In the COVID-19 trial, 199 patients were treated, split evenly between drug and standard-of-care groups. The study’s primary endpoint, time to improvement, was the same between the two groups, both of which took 16 days to improve. Mortality and viral load at various time points were also not different.

In an editorial published alongside the paper, Lindsey Baden, of Harvard Medical School, and Eric Rubin, of the Harvard TH Chan School of Public Health, wrote that “the results for certain secondary endpoints are intriguing,” but also acknowledged that those results were hard to interpret, due to a mix of trial size, possible differences in illness severity at baseline, and the fact that the trial was randomized but not blinded.

And if certain endpoints were intriguing, others were discouraging. In particular, viral loads did not differ between the groups, tellingly so, according to Baden and Rubin. “Since the drug is supposed to act as a direct inhibitor of viral replication, the inability to suppress the viral load and the persistent detection of viral nucleic acid strongly suggest that it did not have the activity desired,” they wrote. “Thus, although some effect of the drug is possible, it was not easily observed.”

It is possible that larger trials will yet uncover an effect of Kaletra/Aluvia. But for now, perhaps the best hope is that other drugs will work better – in particular, remdesivir (Gilead Sciences Inc.), which was originally developed for Ebola virus disease, but proved less effective there than several other options.

A paper in the Jan. 10, 2020, issue of Nature Communications investigated the effects of Aluvia on MERS-CoV in mouse experiments, where it showed ho-hum effects. The authors of the Nature Communications paper reported that “prophylactic [Kaletra/Aluvia plus interferon-beta] slightly reduces viral loads without impacting other disease parameters.”

But remdesivir was more effective. “Both prophylactic and therapeutic [remdesivir] improve pulmonary function and reduce lung viral loads and severe lung pathology” in a mouse model of MERS, the authors reported.

Remdesivir is in both an NIH-sponsored clinical trial and a Japanese-Chinese trial as potential COVID-19 treatment, after a January case report of a patient who showed rapid improvement after he was treated with the drug for COVID-19.

Though the Kaletra/Aluvia trial’s results were not as hoped, Baden and Rubin noted that the trial itself was an encouraging bit of news, as well as a “heroic effort…. As we saw during the 2014 Ebola outbreak in West Africa, obtaining high-quality clinical trial data to guide the care of patients is extremely difficult in the face of an epidemic, and the feasibility of a randomized design has been called into question. Yet Cao’s group of determined investigators not only succeeded but ended up enrolling a larger number of patients (199) than originally targeted.”

Dive Brief:

Rheumatoid arthritis drug Kevzara will be used in an international study of patients infected with the new coronavirus and suffering from acute respiratory distress syndrome, Regeneron Pharmaceuticals and Sanofi announced Monday.

The trial will kick off in disease hotspot New York City, expanding to a total of 16 U.S. sites and enrolling 400 patients. The companies aim to study whether Kevzara can reduce fever and the need for supplemental oxygen in patients severely affected by COVID-19, the illness caused by the virus.

Roche’s Actemra, which has a similar mechanism of action, has been tested in Chinese patients and led to a decrease in fever and oxygen use, prompting the country to include it in treatment guidelines. The drug’s use shows the speed with which global public health officials are willing to consider using drugs off-label in order to address the coronavirus pandemic.

Dive Insight:

A vaccine to prevent infections of the novel coronavirus SARS-CoV-2 is likely a year or more away — at best — and treatments specifically designed to fight this virus or its complications are similarly far off.

Possible treatments, however, could already be available in the form of marketed or existing experimental drugs. Global public health officials, eager for a weapon to use in the midst of a global pandemic, are showing a willingness to be flexible in terms of the clinical trials and the evidence needed to prove treatments’ effectiveness.

Earlier this month, China OK’d the use of Actemra in patients with lung complications and high levels of interleukin-6, or IL-6, a protein that mediates inflammatory and immune response. High levels of IL-6 have been associated with a greater risk of death in patients with community-acquired pneumonia.

Actemra and Kevzara both block IL-6 and are prescribed for rheumatoid arthritis, a disorder in which an overactive immune system creates joint-damaging inflammation and pain. Actemra is similarly approved in conjunction with cancer cell therapy, which can sometimes trigger an immune reaction known as cytokine release syndrome.

The U.S.-based Kevzara trial is a two-part design that will initially evaluate fever and oxygen use in patients with acute respiratory distress syndrome, or ARDS. Two different dose levels will be used and compared to a placebo.

Longer-term, the trial hopes to measure prevention of death, use of ventilation, supplemental oxygen or hospitalization, but the design will be “adaptive” to determine the number of patients that will be followed and the endpoints to be used. ARDS often causes permanent lung damage and can lead to early death.

The trial aims to enroll 400 patients in the U.S. Regeneron’s partner Sanofi will handle international trial sites, naming Italy as one likely location for testing in coronavirus patients.

To get the trial underway quickly, Regeneron and Sanofi worked closely with the Food and Drug Administration and the Biomedical Advanced Research and Development Authority, the division of HHS involved in preparing for natural and man-made biological threats.

by Emily Makowski

Some ants produce natural antibiotic chemicals to defend themselves against fungi and bacteria. Ecologist Joachim Offenberg of Aarhus University in Denmark wondered what effect these compounds had on the health of the plants the ants called home. “We had this thought that if ants produce antibiotics, maybe these antibiotics could have an effect . . . on the diseases of the plants they walk on,” he tells The Scientist.

In a review of studies investigating the effect of ants on plant pathogens, he and fellow Aarhus ecologist Christian Damgaard found that, out of 30 plant species that were commonly inhabited by some kind of ant, 18 showed a decrease in the effects of pathogens. These included reduced bacterial load and increased germination rates enjoyed by plants inhabited by ants compared with plants of the same species that did not host ants.

Data have long confirmed that ants provide protection to their botanical hosts by eating pests, says Andreas Schramm, a microbiologist at Aarhus University who was not involved with the study. “The chemical defense of plants is really another direction that the authors quite convincingly put out here,” he says. Overall, Offenberg and Damgaard estimated that the effects of ants’ antibiotics were comparable to the benefits plants receive from the insects’ consumption of herbivorous pests.

Six of the plant species had increased pathogen incidence with ants, however, and six either had no significant difference between groups or insufficient data. Offenberg notes that a plant that hosts ants may already have a major infection that can’t be controlled with ant-produced antimicrobial compounds. Moreover, the insects can inadvertently disperse pathogens: fungal spores, for example, can cling to their legs.

Adam Castillejo, known in the scientific literature as the London Patient, in London’s East End, March 1, 2020.

By Gina Yu and Amy Woodyatt

he second person ever to be cured of HIV is still free of active virus more than two years on, a study published by medical journal The Lancet HIV revealed on Tuesday.

Two and a half years ago, Adam Castillejo — previously identified as the “London patient” — finished HIV antiretroviral therapy.

He underwent a stem cell transplant to treat lymphoma and his donor carried a mutation known as CCR5-delta 32, which made him resistant to HIV.

Researchers said that in treating his lymphoma, they believe Castillejo, now 41, was cured of HIV.

HIV (human immunodeficiency virus) is a life-long viral infection that attacks the body’s immune system and can have significant health consequences. There is no widely available cure, however, the virus is treatable with a combination of drugs known as antiretroviral therapy that reduces the amount of virus in a person’s blood and it is preventable by using PrEP, which was approved by the US Food and Drug Administration in 2012.

According to UNAids there were 37.9 million people globally living with HIV in 2018.

“Our findings show that the success of stem cell transplantation as a cure for HIV, first reported nine years ago in the Berlin patient, can be replicated,” said Ravindra Gupta, lead author of the study and a professor in University of Cambridge’s clinical microbiology department.

Unlike the Berlin patient — identified later as Timothy Ray Brown — Castillejo underwent only one stem-cell transplantation instead of two and did not have radiotherapy to his entire body as part of his treatment.

Castillejo represents a step toward a less intensive treatment approach, the authors said.
Still, given the invasive nature of the experimental treatment, the authors caution its widespread use.

“It is important to note that this curative treatment is high-risk, and only used as a last resort for patients with HIV who also have life-threatening haematological malignancies,” Gupta said. “Therefore, this is not a treatment that would be offered widely to patients with HIV who are on successful antiretroviral treatment.”

Since Castillejo is only the second reported patient to undergo this experimental treatment successfully, the authors note that he will require continued, but much less frequent, monitoring for re-emergence of the virus.

Sharon Lewin, director of the Peter Doherty Institute for Infection and Immunity at the University of Melbourne, said that the case was an “exciting advance” but should be viewed in context.

“It’s hard to know if this is a cure, only time will tell, but this is looking very promising,” Lewin said in a statement sent to CNN.

“This case is an exciting advance, but we need to also place it in context — curing people of HIV via a bone marrow transplant is just not a viable option on any kind of scale. We need to constantly reiterate the importance of, prevention, early testing and treatment adherence as the pillars of the current global response to HIV/AIDS. And maintain the search for an HIV cure,” she added.

In an interview with the New York Times, Castillejo said that he decided to reveal his identity after years of difficult treatments and moments of despair.

“This is a unique position to be in, a unique and very humbling position,” Castillejo told the newspaper. “I want to be an ambassador of hope.”

Kat Smithson, director of policy at the National AIDS Trust, applauded Castillejo for sharing his experience, adding that there is a stigma around HIV which can make it difficult for some people to seek help.

“His story helps raise much-needed awareness of HIV, but broader than that it’s a story about incredible resilience, determination and hope,” she said in a statement to CNN.

By Rob Picheta

The science is looking pretty unanimous on this one: Drivers of expensive cars are the worst.

A new study has found that drivers of flashy vehicles are less likely to stop and allow pedestrians to cross the road — with the likelihood they’ll slow down decreasing by 3% for every extra $1,000 that their vehicle is worth.

Researchers from the University of Nevada, Las Vegas speculated that the expensive car owners “felt a sense of superiority over other road users” and were less able to empathize with lowly sidewalk-dwellers.

They came to this conclusion after asking volunteers to cross a sidewalk hundreds of times, filming and analyzing the responses by car drivers.

Researchers used one white and one black man, and one white and one black woman — also finding that cars were more likely to yield for the white and female participants. Vehicles stopped 31% of the time for both women and white participants, compared with 24% of the time for men and 25% of the time for black volunteers.

But the best predictor of whether a car would stop was its cost, researchers discovered. “Disengagement and a lower ability to interpret thoughts and feelings of others along with feelings of entitlement and narcissism may lead to a lack of empathy for pedestrians” among costly car owners, they theorized in the study.

And the discovery of a car-value-to-jerkish-behavior correlation isn’t new; the research, published in the Journal of Transport and Health, backed up a Finnish study published last month that found that men who own flashy vehicles are more likely to be “argumentative, stubborn, disagreeable and unempathetic.”

According to that survey of 1,892 drivers by the University of Helsinki, those deemed to have more disagreeable character traits were “more drawn to high-status cars.”

But it also found that conscientious people often favor higher-priced vehicles, too. If you’re reading this while stuck in traffic in your brand new BMW: yes, you’re definitely in that category.

“I had noticed that the ones most likely to run a red light, not give way to pedestrians and generally drive recklessly and too fast were often the ones driving fast German cars,” Helsinki University’s Jan-Erik Lönnqvist said in a press release.

He set out to discover what kind of person is more likely to buy an expensive car, creating a personality test of Finnish car owners.

“The answers were unambiguous: self-centred men who are argumentative, stubborn, disagreeable and unempathetic are much more likely to own a high-status car such as an Audi, BMW or Mercedes,” the press release states.

“These personality traits explain the desire to own high-status products, and the same traits also explain why such people break traffic regulations more frequently than others,” Lönnqvist added.

His study cited previous research that indicated drivers behind the wheel of a costly vehicle are more likely to flout traffic regulations or drive recklessly.

But he also found people with “conscientious” characters seek out pricey models, too.

“People with this type of personality are, as a rule, respectable, ambitious, reliable and well-organised,” the statement said. “They take care of themselves and their health and often perform well at work.”