Saturday, March 18, 2023

Genetic adaptations help Amazonian populations resist Chagas infection

An international study \in which the Institute for Evolutionary Biology (IBE-CSIC-UPF) has participated discovers a genetic variant that confers resistance to Chagas infection in Amazonian populations

Peer-Reviewed Publication

UNIVERSITAT POMPEU FABRA - BARCELONA

High-frequency distribution of the putatively selected PPP3CA allele. 

IMAGE: HIGH-FREQUENCY DISTRIBUTION OF THE PUTATIVELY SELECTED PPP3CA ALLELE. view more 

CREDIT: RESEARCH AUTHORS.

Chagas disease affects approximately 6 million people only in Latin America and is one of the leading causes of death in this region. This infectious disease, also called American Trypanosomiasis, is caused by the parasite Trypanosoma cruzi (T.cruzi). However, despite being in contact with the parasite, Amazonian populations hardly suffer from Chagas infection. This study aimed to find out why.

The research has analysed the genomic data of 118 contemporary individuals from 19 different populations of the Amazon to find traces of genetic adaptation to the Amazon rainforest environment.

“We focused on finding evidence of positive natural selection related to tropical diseases in the Americas.” Points out Tábita Hünemeier, Principal Investigator at the Institute of Evolutionary Biology (IBE-CSIC-UPF) who led the study.

Through the analysis of the genomes, the study found a high-frequency variant of the PPP3CA gene in the inhabitants of Amazonia that could be responsible for this resistance. To verify its effectiveness, functional studies were carried out in the laboratory. In this way, the study discovered that the variant of the PPP3CA gene reduces the risk of infection by the Chagas pathogen.

Functional studies on the immunological action of the PPP3CA gene against the Chagas parasite

The PPP3CA gene codes for a key protein in the activation of immune cells, the innate immune response, and the internalization of the T.cruzi parasite in human cells. This study detected a variant of this gene in a very abundant way in Amazonian populations that is expressed in heart tissue and in immune cells.

The study performed functional studies with heart cell tissue using stem cells, some of which contained the PPP3CA gene variant found in high frequency in Amazonian populations. The results showed that there is less internalization of the parasite in heart cells when they have the gene variant.

“The presence of the PPP3CA gene variant could be the cause of milder disease or less infection in these populations.” Adds David Comas, Professor of Biology in the Department of Medicine and Life Sciences (MELIS) at the UPF, Principal Investigator at IBE (CSIC-Pompeu Fabra University) and co-author of the research.

Positive natural selection in the Amazonian population due to a pathogen

Study results estimate that the natural selection for Chagas disease resistance began 7,500 years ago after the Amazonian population separated from the Andean and Pacific coast populations.

Supported by previous studies with 9,000-year-old samples, the research concludes that the epidemics would have positively selected the individuals with the greatest resistance to tropical diseases, such as Chagas disease, generating a unique resistance in this population.

Behavioral genetic adaptations to life in the jungle

Additionally, the study found genetic adaptations associated with behavioral traits such as "Novelty-seeking behaviors", a genetic trait that determines the search for new experiences. According to the study, this trait could have been crucial to the hunter-gatherer lifestyle of Amazonian populations in the past, as it enabled them to explore new territories and search for resources.

Cardiovascular and metabolic traits

The study also detected cardiovascular and metabolic traits that are consistent with the genetic predominance observed in previous research, since a 66% rate of obesity, diabetes, and coronary heart disease had already been detected in some Amazonian populations.

  

Reduction in PPP3CA levels significantly inhibited iPS-CM T. cruzi infection.

CREDIT

Research authors.

Article

Title: Indigenous people from Amazon show genetic Q1 signatures of pathogen-driven selection

Authors: Cainã M. Couto-Silva1, Kelly Nunes1, Gabriela Venturini, Marcos Araújo Castro e Silva, Lygia V. Pereira, David Comas, Alexandre Pereira, Tábita Hünemeier.

Publication: Science Advances

Research shows success of working from home depends on company health

MU expert in health management shares best practices for working-from-home policies.

Peer-Reviewed Publication

UNIVERSITY OF MISSOURI-COLUMBIA

Naresh Khatri 

IMAGE: NARESH KHATRI view more 

CREDIT: UNIVERSITY OF MISSOURI

While more businesses continue to shift to remote work, some well-known CEOs remain steadfast against the movement. Naresh Khatri, an associate professor of health management and informatics in the School of Medicine at the University of Missouri, said the success of shifting to remote work depends on the flexibility of the organization to adjust to individual employees and the technology available to them.

As an expert who has published more than 60 research articles and book chapters about organizational structure and management within health care organizationsKhatri said offering remote work as an option to employees can serve as a powerful recruitment tool and one that can be easily implemented by organizations with the right resources. The key is providing strategic and impactful human resource and information technology departments.

“Regardless of where employees are working, these two departments are vital to a healthy workforce,” said Khatri,who recently co-authored a guest editiorial published in Personnel Review . “Many businesses are embracing this newer option because it opens up the potential for more applicants and workers.”

Additionally, Khatri analyzed several studies and found companies with effective HR and IT departments became even stronger when employees were allowed to work from anywhere because the option offered more flexibility. The end result showed that work completed by employees from home was not statistically different from work produced by employees in the office. In fact, no matter where they were working, employees were able to complete collaborative tasks with a similar level of quality and quantity.

“Past research has shown that the performance of remote and in-person workers were not significantly different, even when employees were working on collaborative tasks that depended upon work from other employees,” he said. “In fact, research has also shown that the people working from home exhibit no decline in their ability to collaborate.”

By supporting HR and IT with funding and labor, businesses are better prepared to face issues such as motivation and technical glitches that employees might encounter while working from home, Khatri said.

“To help prevent burnout and inefficient hours, HR practitioners should tailor their motivational practices to ensure they meet the unique needs of their employees, including employees who need to or would like to work from home,” he said. “That takes time and effort, but prior research shows that this support ultimately leads to mutual gains or benefits for both the employees and the company.”

Research also shows that HR offices that continuously explore new ways to implement innovative practices to inspire employees tend to have more success in creating favorable mindset and attitudes in their employees, which Khatri said could help prevent burnout and uncover best practices for individual employees.

“People are different,” he said. “Some are more efficient when working from home, and some are more efficient being around people in the office. Either way, the workforce is changing. Industries are changing, and if companies are preventing people from working from home, they are missing out on a valuable way to expand their profits, their personnel and company health as a whole.”

Guest Editorial: Work from anywhere: Implications for employees and organizations” was published in Personnel Review.

Ohio EPA and EPA contractors collect soil and air samples

Ohio EPA and EPA contractors collect soil and air samples from the Norfolk Southern train derailment site on March 9, 2023 in East Palestine, Ohio.

 (Photo: Michael Swensen/Getty Images)

East Palestine Soil Contains Dioxin Levels Hundreds of Times Over Cancer Risk Threshold

"I certainly wouldn't be comfortable living there," said one organic chemist.

East Palestine, Ohio residents' concerns about the enduring impact of last month's fiery train derailment are likely to intensify following the release of data showing that levels of dioxin in the soil near the wreck site are far higher than the cancer risk threshold recommended by federal scientists.

Dioxin is a toxic and carcinogenic byproduct of burning vinyl chloride, a hazardous chemical that at least five Norfolk Southern train cars were carrying when they derailed in early February, sparking a full-blown environmental and public health disaster.

Citing a report that Pace Analytical prepared for Ohio's neighbor Indiana, The Guardianreported Friday that "East Palestine soil showed levels of '2,3,7,8 TCDD toxicity equivalence' of 700 parts per trillion (ppt)," potentially stemming from the controlled burn of vinyl chloride in the wake of the crash.

"The level at which the EPA will initiate cleanup action in residential areas is 1,000 ppt," the newspaper explained. "However, the cleanup triggers are much lower in many states—90 ppt in Michigan, and 50 ppt in California... Moreover, EPA scientists in 2010 put the cancer risk threshold for dioxins in residential soil at 3.7 ppt, and the agency recommended lowering the cleanup trigger to 72 ppt."

The Obama administration tanked the EPA scientists' effort to formally lower the federal cleanup threshold, The Guardian noted.

Chemical experts and former EPA officials expressed alarm over the data while acknowledging it was limited to just two soil samples and more testing is needed.

"The levels are not screaming high, but we have confirmed that dioxins are in East Palestine's soil," Linda Birnbaum, former head of the U.S. National Toxicology Program, told The Guardian. "The EPA must test the soil in the area more broadly."

Carsten Prasse, an organic chemist at Johns Hopkins University, added that the dioxin concentrations in the soil samples examined are "actually concerning."

"My main concern is: is this reflective of the level in the area in East Palestine... and of the levels individuals who live near the rail are exposed to?" Prasse asked. "I certainly wouldn't be comfortable living there."

Despite outside experts' fears, EPA regional administrator Debra Shore insisted that the dioxin levels detected in the Indiana report are "very low."

The Guardian's reporting came days after Ohio's Republican attorney general filed suit against Norfolk Southern, accusing the rail giant of "recklessly endangering" East Palestine residents.

"Ohio shouldn't have to bear the tremendous financial burden of Norfolk Southern's glaring negligence," said AG Dave Yost said. "The fallout from this highly preventable incident may continue for years to come, and there's still so much we don't know about the long-term effects on our air, water, and soil."

In Congress, a bipartisan group of lawmakers is working to build support for legislation that would impose more strict regulations on trains carrying hazardous materials such as vinyl chloride.

During Senate testimony last week, Norfolk Southern CEO Alan Shaw refused to endorse the bill.

"If Norfolk Southern had paid a little more attention to safety and a little less attention to its profits—had cared a little more about the Ohioans along its tracks, and a little less about its executives and shareholders—these accidents would not have been as bad, or might not have happened at all," Sen. Sherrod Brown (D-Ohio), the lead Democratic sponsor of the Railway Safety Act, said during the hearing.

Engineered bacteria find tumors, then alert the authorities

Peer-Reviewed Publication

COLUMBIA UNIVERSITY IRVING MEDICAL CENTER


Nicholas Arpaia 

IMAGE: NICHOLAS ARPAIA, PHD, ASSISTANT PROFESSOR OF MICROBIOLOGY AND IMMUNOLOGY AT COLUMBIA’S VAGELOS COLLEGE OF PHYSICIANS AND SURGEONS view more 

CREDIT: COLUMBIA UNIVERSITY VAGELOS COLLEGE OF PHYSICIANS AND SURGEONS

Combining discoveries in cancer immunology with sophisticated genetic engineering, Columbia University researchers have created a sort of  “bacterial suicide squad” that targets tumors, attracting the host’s own immune cells to the cancer to destroy it. The new work, published today in Science Advances, marks a major step forward in efforts to enlist non-pathogenic bacteria to combat cancer.

Scientists have known for years that some species of bacteria can thrive inside tumors. “It’s been speculated that this is due to the low pH, necrotic and immune-excluded environment … that’s unique to the core of a tumor and supports bacterial growth while preventing clearance of bacteria by immune cells,” says Nicholas Arpaia, PhD, assistant professor of microbiology and immunology at Columbia’s Vagelos College of Physicians and Surgeons and senior author on the new paper. In an ongoing collaboration with Tal Danino, PhD, associate professor of biomedical engineering at Columbia Engineering, Dr. Arpaia has been building an anti-tumor strategy around that phenomenon.

At the core of the approach is a probiotic strain of the bacterium E. coli, engineered with a synchronized lysis circuit. Once the bacterial cells reach a quorum inside a tumor, the circuit triggers, causing most of the bacteria to lyse, or break apart, releasing their contents. Previously, the investigators have added genes to the microbes encoding proteins that block tumor cell growth, or that flag the tumor for digestion by immune cells.

“My graduate student, Thomas [Savage], had the idea of potentially utilizing this platform to deliver chemokines,” says Dr. Arpaia, who is also a member of the Herbert Irving Comprehensive Cancer Center (HICCC) at NewYork-Presbyterian/Columbia University Irving Medical Center.

Attracting killer T cells

Immunologists have found that different chemokines, immune system signaling proteins, attract different types of immune cells and stimulate them to respond in specific ways. In the new work, the team included a mutated version of a human chemokine gene that attracts “killer” T cells. “Although T cell responses that are specific to tumor-derived antigens are primed, sometimes what will happen is that despite there being primed anti-tumor T cells, they fail to be recruited into the tumor environment,” says Dr. Arpaia.

To further augment therapeutic efficacy, the researchers added a second bacterial strain expressing another chemokine, this time to attract dendritic cells. “By coupling this with chemokines that drive the infiltration and activation of dendritic cells, a critical innate immune cell type, detection of tumor antigens is increased,” says Dr. Arpaia. Activated dendritic cells eat the tumor cells, then present their antigens to the T cells, which can then recognize the tumor cells better and respond to them more reliably.

The new work involved collaborators from the Department of Pathology and Cell Biology, the HICCC and the Data Science Institute at Columbia, and also built on a long series of previous findings by others. “Through decades of research that’s allowed us to understand how an immune response develops, [we’re] developing therapeutics that specifically target each one of those discrete steps,” says Dr. Arpaia.

In mouse models of cancer, the engineered bacteria induce robust immune responses against tumors that have been injected directly with the bacteria, as well as more distant tumors that weren’t injected. Delivering the bacteria intravenously also works. “What we see is that the bacteria will only colonize the tumor environment, and they only reach a sufficient level of quorum to induce lysis within the tumor, so we can’t detect bacteria in other healthy organs,” says Dr. Arpaia.

The scientists continue to tinker with the system to optimize it, while also laying the groundwork to take it into clinical trials. Dr. Arpaia and some of his collaborators have applied for a patent on the approach, and are part of a company, GenCirq, Inc., to develop the therapy further.

What ‘Chernobyl dogs’ can tell us about survival in contaminated environments

Peer-Reviewed Publication

COLUMBIA UNIVERSITY'S MAILMAN SCHOOL OF PUBLIC HEALTH

March 9, 2023-- In the first step toward understanding how dogs – and perhaps humans – might adapt to intense environmental pressures such as exposure to radiation, heavy metals, or toxic chemicals, researchers at North Carolina State, Columbia University Mailman School of Public Health, University of South Carolina, and the National Institutes of Health found that two groups of dogs living within the Chornobyl Exclusion Zone, one at the site of the former Chornobyl reactors, and another 16.5 km away in Chornobyl City, showed significant genetic differences between them. The results indicate that these are two distinct populations that rarely interbreed. While earlier studies focused on the effects of the Chornobyl Nuclear Power Plant disaster on various species of wildlife, this is the first investigation into the genetic structure of stray dogs living near the Chornobyl nuclear power plant.

The 1986 Chornobyl nuclear power plant disaster displaced more than 300,000 people living nearby and led to  the establishment of an Exclusion Zone, a “no man’s land” of an approximately 30 km radius surrounding the damaged reactor complex, While a massive steam explosion releasing enormous amounts of ionizing radiation into the air, water, and soil was the direct cause of the catastrophe, radiation exposure is not the only environmental hazard resulting from the disaster. Chemicals, toxic metals, pesticides, and organic compounds left behind by years-long cleanup efforts and from abandoned and decaying structures, including the nearby abandoned city of Pripyat and the Duga-1 military base, all contribute to an ecological and environmental disaster.

“Somehow, two small populations of dogs managed to survive in that highly toxic environment,” noted Norman J. Kleiman, PhD, assistant professor of Environmental Health Sciences at Columbia Mailman School of Public Health, and a co-author. “In addition to classifying the population dynamics within these dogs at both locations, we took the first steps towards understanding how chronic exposure to multiple environmental hazards may have impacted these populations.”

“The overarching question here is: does an environmental disaster of this magnitude have a genetic impact on life in the region?” says Matthew Breen, Oscar J. Fletcher Distinguished Professor of Comparative Oncology Genetics at NC State, and a corresponding author. “And we have two populations of dogs living at and near the site of a major environmental disaster that may provide key information to help us answer that question.”

Earlier research by the co-authors, led by collaborators at NIH, used a much smaller set of genetic variants, but a larger number of dogs, to show that the two populations were separate and that each had complicated family structures.  

 

In this parallel study, the team analyzed the dog DNA samples with four times the number of genetic variants, which provided a closer look at the genomes.  In addition to confirming that the two populations are indeed genetically distinct, the  team were also able to identify 391 outlier regions in the genomes of the dogs that differed between dogs living at the two locations.  “Think of these regions as markers, or signposts, on a highway,” Breen says. “They identify areas within the genome where we should look more closely at nearby genes. Moreover, some of these markers are pointing to genes associated with genetic repair; specifically, with genetic repair after exposures similar to those experienced by the dogs in Chornobyl.” He went on to say “at this stage we cannot say for sure that any genetic alterations are in response to the multigenerational and complex exposures; we have a lot more work to do to determine if that is the case”

“The question we must answer now are why are there striking genetic differences between the two dog populations?” says Megan Dillion, PhD candidate at NC State and a lead author of the published study. “Are the differences just due to genetic drift, or are they due to the unique environmental stressors at each location?”

“The dog is a sentinel species,” Breen says. “By and teasing out whether or not the genetic changes we detected in these dogs are the canine genome’s response to the exposures the populations have faced, we may be able to understand how the dogs survived in such a hostile environment and what that might mean for any population – animal or human – that experiences similar exposures.”

“Though 37 years have passed since the accident, the ~30-year-long half-lives of lingering radioisotopes means the danger posed by radiation exposure is still very much real,” notes Kleiman, who is also director of the Columbia University Radiation Safety Officer Training course. “When radiation exposure is combined with a complex toxic chemical mixture of uncertain composition, there are very real human health concerns raised for the thousands of people who continue to work within the Exclusion Zone on continuing cleanup efforts as well as at two newly constructed nuclear fuel reprocessing plants.”

 “Understanding the genetic and health impacts of these chronic exposures in the dogs will strengthen our broader understanding of how these types of environmental hazards can impact humans and how best to mitigate health risks.”

The research appears in Canine Medicine and Genetics.

Columbia University Mailman School of Public Health

Founded in 1922, the Columbia University Mailman School of Public Health pursues an agenda of research, education, and service to address the critical and complex public health issues affecting New Yorkers, the nation and the world. The Columbia Mailman School is the fourth largest recipient of NIH grants among schools of public health. Its nearly 300 multi-disciplinary faculty members work in more than 100 countries around the world, addressing such issues as preventing infectious and chronic diseases, environmental health, maternal and child health, health policy, climate change and health, and public health preparedness. It is a leader in public health education with more than 1,300 graduate students from 55 nations pursuing a variety of master’s and doctoral degree programs. The Columbia Mailman School is also home to numerous world-renowned research centers, including ICAP and the Center for Infection and Immunity. For more information, please visit www.mailman.columbia.edu.

 


Spanish physicists disagree with the Sleep Society and endorse the time change in the USA

José María Martín-Olalla from the University of Seville and Jorge Mira Pérez from the University of Santiago de Compostela dispute the manifesto issued by the Sleep Research Society advocating permanent adoption of winter time

Peer-Reviewed Publication

UNIVERSITY OF SEVILLE

Putting the clocks forward does not affect the length of the daylight period - a natural phenomenon beyond human control - but rather makes it possible to optimise its use by using early morning light for activities and thus to enjoy more hours of leisure time during the day. This is the crux of the article that José María Martín-Olalla and Jorge Mira Pérez, lecturers at the University of Seville (US) and the University of Santiago de Compostela (USC), have just published in the journal Sleep, where they analyse the naturalness and usefulness of putting the clocks forward, in response to a manifesto of the Sleep Research Society that calls for its abolition in the United States and the adoption of permanent winter time. Regarding the time change due to take place in the United States on 12 March, the researchers believe that “cancelling the time change will not improve the current scenario in the range of latitudes where the United States is located.”

However, they believe that the springtime change occurs too early in the United States, and the autumn time change is too late, which particularly affects people who work earlier in the working day. In the view of the researchers, if it is accepted that the dates of time changes must be adjusted for the benefit of the people, the springtime change should occur after the equinox, in early April, as was the case in the United States until 2007. “Likewise, if the autumn time change were to occur in early October, as it was until 1954, many workers and schoolchildren would no longer suffer the stressful twilight hours of October mornings,” the authors explain in their paper.

The researchers go on to argue that modern societies, governed by pre-set schedules, can only seasonally regulate their activities by one hour increments, as with the current change. The temporary disruption, according to experts, is offset by better alignment of when people begin their activities and sunrise. In their paper they point out that, in practice, people do not change their schedules after the changes, which is an indication of the success of the measure, according to Jorge Mira Pérez and José María Martín Olalla. “It is not easy to keep a strict schedule all year round, when sunrise times change from winter to summer, we relieve that need by seasonal time changes, and if we didn’t, we would change working hours seasonally,” they say.

 

Pre-adaptation

The authors stress the fact that in winter days are short, which affects human activity, while summer nights are also shorter, which affects people’s ability to fall asleep, whether or not they change the hour. “We highlight the fact that winter sunrise and summer sunset are twelve hours apart, irrespective of latitude. If human activity begins with the winter sunrise and seasonal time regulation is applied, then the start of human activity in summer and the summer sunset are separated by eleven hours, which is probably sufficient for adequate sleep. Those who start their activities earlier than the winter sunrise time may find that the clock changes are less appropriate in summer. But it is notable that the changes themselves have helped to prevent human activity from taking place before the winter sunrise,” they explain.

“In summer, either you go to bed early, soon after nightfall, or you get up late, long after dawn,” explains Jorge Mira, who was a member of the Spanish Government’s commission to examine the official time. José María Martín Olalla, who researches the social uses of time, with particular emphasis on human adaptation to the seasonal cycle of light and darkness, adds “we know the disadvantages of putting the clocks forward that is, the nuisance of changing the clock twice a year; we forget its benefits and we don’t know the drawbacks of not having done so.”

The greatest concern of the chronobiological and sleep community lies in the risks of putting the clocks forward. Thus, the authors propose preventative adaptation by, for example, changing the alarm clock’s time in the weeks running up to putting the clock forward in spring by four increments of 15 minutes, three of 20 minutes or two of 30 minutes. In Europe, the time change will take place on Sunday, 26 March, while in New Zealand, Australia and Chile it will take place on Sunday, 3 April.

JUST IN TIME FOR MARCH MADNESS

Physics model could optimize basketball player positioning

Reports and Proceedings

CORNELL UNIVERSITY

ITHACA, N.Y. – A physics theory that’s proven useful to predict the crowd behavior of molecules and fruit flies also seems to work on another group – NBA players.

A model based on density functional theory can suggest the best positioning for each player on the basketball court in a given scenario if they want to raise their probability of either scoring or defending successfully.

Boris Barron, a doctoral student working with Tomás Arias, professor of physics presented his work on March 9 at the American Physical Society conference in Las Vegas. He used detailed data of player positions from this season’s NBA games to develop his model.

Using the results, Barron is able to:

  • predict where a particular player may go next;
  • determine which players tend to be in good or bad positions;
  • calculate the probability of success, either offensively or defensively, based on player positioning; and
  • create simulations of how the opposing team will or should respond if a player performs a particular move, such as running across the court.

“We can see precisely where a player should be to help their team, and those few feet can result in as much as a 3% difference (in success),” he said.

“In these high-scoring games, three points out of 100 is a big deal for one player,” said Arias.

The mathematical models that Barron employs are based on Nobel Prize-winning methods originally developed to study large collections of quantum mechanically interacting electrons. The work builds on Arias’ research, which combines mathematical concepts and approaches from density-functional fluctuation theory to study everything from crowd behavior to social phenomena such as migration and segregation.

These methods work when you’re analyzing a game like basketball, Arias said, because the behavior of groups of people is difficult to quantify.

“Our physics techniques come into play because you’re not looking at players individually, but how they are collaborating on the court,” he said. “That’s why you need this higher-level analysis.”

The implications for team sports like basketball are obvious, Barron said. Coaches could input team- or player-specific data for their opponents into this model to develop a strategy to thwart the most common plays.

For additional information, see this Cornell Chronicle story.

Cornell University has dedicated television and audio studios available for media interviews.

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