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Parasites and the microbiome

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In a study of ethnically diverse people from Cameroon, the presence of a parasite infection was closely linked to the make-up of the gastrointestinal microbiome, according to a research team led by Penn scientists

Parasite infections are a constant presence for many people who live in tropical regions, particularly in less industrialized areas. These often chronic conditions are at best unpleasant; more seriously, children with parasite diseases that cause diarrhea can die of malnutrition or dehydration.

In Genome Biology, a study led by University of Pennsylvania scientists investigated the links between parasite infection and the gut microbiome. Using genetic methods to characterize the gastrointestinal microbiome of 575 ethnically diverse Cameroonian people representing populations from nine villages with meaningful differences in lifestyle, the researchers discovered that the presence of parasites was strongly associated with the overall composition of the microbiome.

“We found that we could look at someone’s microbiome and use it to predict whether someone had a gastrointestinal parasite infection,” says Meagan Rubel, who completed her doctorate degree at Penn and is now a postdoc at the University of California, San Diego. “Whether or not it was parasites changing the microbiome or something in the resident microbiota of a person that made them more susceptible to infection, we can’t say, but the association was strong.”

Rubel led the study in collaboration with Penn’s Sarah Tishkoff, a Penn Integrates Knowledge Professor in the Perelman School of Medicine and School of Arts and Sciences, and Frederic Bushman, a microbiologist in the medical school. In addition to the microbiome and parasites, the research also examined markers of immune function, dairy digestion, and pathogen infection, a rich dataset.

The investigation entailed six months of field work, collecting fecal and blood samples from Mbororo Fulani pastoralists, cattle herders with a diet high in meat and dairy; Baka and Bagyeli rainforest hunter-gatherers, who practice a limited amount of farming but also forage for meat and plant-based foods; and Bantu-speaking agropastoralists, who both grow crops and raise livestock. As a comparison group, the study included data from two groups of people living in urban areas of the United States, with a diet heavier in animal fats, proteins, and processed foods.

In the field, the researchers tested for malaria and a number of other pathogens that infect both the blood and gastrointestinal system.

Of the 575 people tested in Cameroon, the researchers found nearly 40% were infected with more than one parasite before receiving an antiparasitic treatment, with hunter-gatherers, on average, most likely to be co-infected with multiple parasites. In particular, the team found that four soil-transmitted gut parasites tended to co-occur at a rate much higher than chance: Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis, or ANTS.

“Gut parasites are a global public health concern,” says Rubel. “And you tend to see several of these parasites together in resource-poor settings where people may not have access to clinical care, piped water, and soap, so there’s more opportunity for them to be transmitted.”

Back in the lab at Penn, the researchers used genomic sequencing tools to take a snapshot of the participants’ gut microbiomes. The composition of the microbiome, they found, could accurately predict a person’s country (U.S. or Cameroon) and lifestyle (urban, pastoralist, agropastoralist, or hunter-gatherer). But after these two variables, the presence of ANTS parasites could be predicted with greater accuracy by the microbiome structure than any other variable the research team studied. Taken together, the microbiome could predict the presence of these four gut parasites with roughly 80% accuracy.

Infection with these parasites also led to upticks in immune system activation, specifically turning on pathways that promote inflammatory responses. Parasite infection was also associated with a greater likelihood of having bacteria from the order Bacteroidales, which are known to play a role in influencing digestion and immune system function.

In a second part of the study, the Penn-led team assessed the relationship between the gut microbiome and milk consumption in the Fulani pastoralist population. Earlier work by Tishkoff and colleagues illuminated how genetic mutations enabling lactose digestion arose in pastoralist communities in Africa, selected through evolution because of the important nutritional benefits of consuming dairy. In looking at the Fulani’s microbiomes, they also tended to have an abundance of bacterial genes capable of breaking down galactose, a component of lactose, and fats, compared to other groups. “This enrichment of genes could help you extract more nutrition from the food you eat,” Rubel says.

The researchers believe their findings, the largest-ever study on the link between gut microbiome composition and parasite infection from sub-Saharan Africa, can open new possibilities for future work. “The kinds of microbiome markers we found could be useful to predict the type of pathogens you have, or to shed light on the interplay between the microbiome and the immune system,” says Rubel.

Eventually, she adds, more research could even illuminate strategies for purposefully modulating the microbiome to reduce the risk of a parasite infection or minimize the harm it causes to the body.

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This research was supported in part by the Lewis and Clark Fund, University of Pennsylvania, Leakey Foundation, Wenner-Gren Foundation, National Institutes of Health (grants AI007532-18, DK104339-01, GM113657-01, GM134957-01, HL113252, HL137063, HL098957, HL087115, and HL115354), National Science Foundation (grants 1540432 and 1317217), American Diabetes Association, Penn Center for AIDS Research, and PennCHOP Microbiome Program.

Rubel, Bushman, and Tishkoff’s coauthors on the paper were Penn Medicine’s Arwa Abbas, Louis J. Taylor, and Andrew Connell; the Children’s Hospital of Philadelphia’s Ceylan Tanes and Kyle Bittinger; the Johns Hopkins Cameroon Program’s Valantine N. Ndze; the Yaoundé Central Hospital’s Julius Y. Fonsah and Alfred K. Njamnshi; the University of Yaoundé’s Eric Ngwang and Charles Fokunang; and the Mbalmayo District Hospital’s André Essiane.

Frederic Bushman is the William Maul Measey Professor in Microbiology in the Perelman School of Medicine at Penn.

Meagan Rubel earned her Ph.D. from Penn and is now a postdoctoral researcher at the University of California, San Diego.

Sarah Tishkoff is the David and Lyn Silfen University Professor and a Penn Integrates Knowledge Professor at Penn, with appointments in the Department of Genetics in the Perelman School of Medicine and the Department of Biology in the School of Arts & Sciences.

Source: https://bioengineer.org/parasites-and-the-microbiome/

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USC Stem Cell study identifies molecular ‘switch’ that turns precursors into kidney cells

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Kidney development is a balancing act between the self-renewal of stem and progenitor cells to maintain and expand their numbers, and the differentiation of these cells into more specialized cell types. In a new study in the journal eLife from Andy McMahon’s laboratory in the Department of Stem Cell Biology and Regenerative Medicine at the Keck School of Medicine of USC, former graduate student Alex Quiyu Guo and a team of scientists demonstrate the importance of a molecule called β-catenin in striking this balance.

β-catenin is a key driver at the end of a complex signaling cascade known as the Wnt pathway. Wnt signaling plays critical roles in the embryonic development of multiple organs including the kidneys. By partnering with other Wnt pathway molecules, β-catenin controls the activity of hundreds to thousands of genes within the cell.

The new study builds on the McMahon Lab’s previous discovery that Wnt/β-catenin can initiate progenitor cells to execute a lengthy and highly orchestrated program of forming structures in the kidney called nephrons. A healthy human kidney contains a million nephrons that balance body fluids and remove soluble waste products. Too few nephrons results in kidney disease.

Previous studies from the UT Southwestern Medical Center laboratory of Thomas Carroll, a former postdoctoral trainee in the McMahon Lab, suggested that Wnt/β-catenin signaling plays opposing roles in ensuring the proper number of nephrons: promoting progenitor maintenance and self-renewal, and stimulating progenitor cell differentiation.

“It sounded like Wnt/β-catenin is doing two things–both maintenance and differentiation–that seem to be opposite operations,” said Guo. “Therefore, the hypothesis was that different levels of Wnt/β-catenin can dictate different fates of the nephron progenitors: when it’s low, it works on maintenance; when it’s high, it directs differentiation.”

In 2015, it became more possible to test this hypothesis when Leif Oxburgh, a scientist at the Rogosin Institute in New York and a co-author of the eLife study, developed a system for growing large numbers of nephron progenitor cells, or NPCs, in a Petri dish.

Relying on this game-changing new system, Guo and his collaborators grew NPCs, added different levels of a chemical that activates β-catenin, and saw their hypothesis play out in the Petri dishes.

They observed that high levels of β-catenin triggered a “switch” in part of the Wnt pathway that relies on another family of transcription factors known as TCF/LEF. There are two types of TCF/LEF transcription factors: one type inhibits genes related to differentiation, and the other activates these genes. In response to high levels of β-catenin, the “activating” members of TCF/LEF switched places with the “inhibiting” members, effectively taking charge. This “switch” triggered NPCs to differentiate into more specialized types of kidney cells.

When they looked at low levels of β-catenin, they saw NPCs self-renewing and maintaining their populations, as expected. However, they were surprised to learn that β-catenin was not engaged with any of the known genes related to self-renewal and maintenance.

“β-catenin does something,” said Guo. “That is for sure. But how it does it is kind of mysterious right now.”

After publishing these results in eLife, Guo earned his PhD from USC, and began his postdoctoral training at UCLA. Helena Bugacov, a current PhD student in the McMahon Lab and a co-author of the eLife study, is now taking the lead in continuing the project–which has implications far beyond the kidney field, due to the broad role of Wnt throughout the body.

“Understanding how Wnt regulates these two very distinct cell outcomes of self-renewal and differentiation, which is very important for kidney development, is also important for understanding the development of other organs and adult stem cells, as Wnt signaling plays important roles in almost all developmental systems,” said Bugacov. “There is also a lot of attention from cancer researchers, as this process can go awry in cancer. Many therapeutics are trying to target this process.”

She added, “The more we know about things, the better we can inform work on developing human kidney organoid cultures, which can be more readily used to understand problems in human health, regeneration and development.”

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Additional co-authors of the eLife study include: Albert Kim, Andrew Ransick, Xi Chen, and Nils Lindstrom from USC; Aaron Brown from the Maine Medical Center Research Institute; and Bin Li and Bing Ren from the University of California, San Diego. The research was supported by federal funding from the National Institute of Diabetes and Digestive and Kidney Diseases (grant number R01 DK054364).

https://stemcell.keck.usc.edu/usc-stem-cell-study-identifies-molecular-switch-that-turns-precursors-into-kidney-cells/

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Source: https://bioengineer.org/usc-stem-cell-study-identifies-molecular-switch-that-turns-precursors-into-kidney-cells/

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Evidence of Antarctic glacier’s tipping point confirmed for first time

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Researchers have confirmed for the first time that Pine Island Glacier in West Antarctica could cross tipping points, leading to a rapid and irreversible retreat which would have significant consequences for global sea level

Researchers have confirmed for the first time that Pine Island Glacier in West Antarctica could cross tipping points, leading to a rapid and irreversible retreat which would have significant consequences for global sea level.

Pine Island Glacier is a region of fast-flowing ice draining an area of West Antarctica approximately two thirds the size of the UK. The glacier is a particular cause for concern as it is losing more ice than any other glacier in Antarctica.

Currently, Pine Island Glacier together with its neighbouring Thwaites glacier are responsible for about 10% of the ongoing increase in global sea level.

Scientists have argued for some time that this region of Antarctica could reach a tipping point and undergo an irreversible retreat from which it could not recover. Such a retreat, once started, could lead to the collapse of the entire West Antarctic Ice Sheet, which contains enough ice to raise global sea level by over three metres.

While the general possibility of such a tipping point within ice sheets has been raised before, showing that Pine Island Glacier has the potential to enter unstable retreat is a very different question.

Now, researchers from Northumbria University have shown, for the first time, that this is indeed the case.

Their findings are published in leading journal, The Cryosphere.

Using a state-of-the-art ice flow model developed by Northumbria’s glaciology research group, the team have developed methods that allow tipping points within ice sheets to be identified.

For Pine Island Glacier, their study shows that the glacier has at least three distinct tipping points. The third and final event, triggered by ocean temperatures increasing by 1.2C, leads to an irreversible retreat of the entire glacier.

The researchers say that long-term warming and shoaling trends in Circumpolar Deep Water, in combination with changing wind patterns in the Amundsen Sea, could expose Pine Island Glacier’s ice shelf to warmer waters for longer periods of time, making temperature changes of this magnitude increasingly likely.

The lead author of the study, Dr Sebastian Rosier, is a Vice-Chancellor’s Research Fellow in Northumbria’s Department of Geography and Environmental Sciences. He specialises in the modelling processes controlling ice flow in Antarctica with the goal of understanding how the continent will contribute to future sea level rise.

Dr Rosier is a member of the University’s glaciology research group, led by Professor Hilmar Gudmundsson, which is currently working on a major £4million study to investigate if climate change will drive the Antarctic Ice Sheet towards a tipping point.

Dr Rosier explained: “The potential for this region to cross a tipping point has been raised in the past, but our study is the first to confirm that Pine Island Glacier does indeed cross these critical thresholds.

“Many different computer simulations around the world are attempting to quantify how a changing climate could affect the West Antarctic Ice Sheet but identifying whether a period of retreat in these models is a tipping point is challenging.

“However, it is a crucial question and the methodology we use in this new study makes it much easier to identify potential future tipping points.”

Hilmar Gudmundsson, Professor of Glaciology and Extreme Environments worked with Dr Rosier on the study. He added: “The possibility of Pine Island Glacier entering an unstable retreat has been raised before but this is the first time that this possibility is rigorously established and quantified.

“This is a major forward step in our understanding of the dynamics of this area and I’m thrilled that we have now been able to finally provide firm answers to this important question.

“But the findings of this study also concern me. Should the glacier enter unstable irreversible retreat, the impact on sea level could be measured in metres, and as this study shows, once the retreat starts it might be impossible to halt it.”

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The paper, The tipping points and early warning indicators for Pine island Glacier, West Antarctica, is now available to view in The Cryosphere.

Northumbria is fast becoming the UK’s leading university for research into Antarctic and extreme environments.

As well as the £4m tipping points study, known as TiPPACCs, Northumbria is also the only UK university to play a part in two projects in the £20m International Thwaites Glacier Collaboration – the largest joint project undertaken by the UK and USA in Antarctica for more than 70 years – where Northumbria is leading the PROPHET and GHC projects. This particular study was funded through both TiPPACCs and PROPHET.

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Source: https://bioengineer.org/evidence-of-antarctic-glaciers-tipping-point-confirmed-for-first-time/

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Diversity can prevent failures in large power grids

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Integrated power grids offer benefits, but also pose challenges best addressed by leveraging differences

The recent power outages in Texas brought attention to its power grid being separated from the rest of the country. While it is not immediately clear whether integration with other parts of the national grid would have completely eliminated the need for rolling outages, the state’s inability to import significant amounts of electricity was decisive in the blackout.

A larger power grid has perks, but also has perils that researchers at Northwestern University are hoping to address to expedite integration and improvements to the system.

An obvious challenge in larger grids is that failures can propagate further — in the case of Texas, across state lines. Another is that all power generators need to be kept synchronized to a common frequency in order to transmit energy. The U.S. is served by three “separate” grids: The Eastern interconnection, the Western interconnection and the Texas interconnection, interlinked only by direct-current power lines. Any persistent deviation in frequencies within a region can lead to an outage.

As a result, researchers are searching for ways to stabilize the grid by looking for methods to mitigate deviations in the power generators’ frequencies.

The new Northwestern research shows that counter to assumptions held by some, there are stability benefits to heterogeneity in the power grid. Examining several power grids across the U.S. and Europe, a team led by Northwestern physicist Adilson Motter recently reported that generators operating on different frequencies return to their normal state more quickly when they are damped by “breakers” at different rates than generators around them.

The paper was published March 5 in the journal Nature Communications.

Motter is the Charles E. and Emma H. Morrison Professor in the department of physics and astronomy in the Weinberg College of Arts and Sciences. His research focuses on nonlinear phenomena in complex systems and networks.

Motter compares power grids to a choir: “It’s a little bit like a choir without a conductor. The generators have to listen to others and speak in sync. They react and respond to each other’s frequencies.”

Listen to an out-of-whack frequency, and the result can be a failure. Given the interconnected makeup of the system, a failure can propagate across the network. Historically, these malfunctions have been prevented by using active controllers. However, failures are often caused precisely by control and equipment errors. This points to a need to build additional stability within the design of the system. To achieve that, the team looked into leveraging the natural heterogeneities of the grid.

When the frequencies of the power generators are moved away from the synchronous state, they can swing around for a long time and even become more erratic. To mitigate these fluctuations, they came up with something akin to a door mechanism used to close a door the fastest, but without slamming.

“Mathematically, the problem of damping frequency deviations in a power generator is analogous to the problem of optimally damping a door to get it to close the fastest, which has a known solution in the case of a single door,” Motter said. “But it’s not a single door in this analogy. It’s a network of many doors that are coupled with each other, if you can imagine the doors as power generators.”

When creating an “optimal damping” effect, they discovered that rather than making each damper identical, damping the power generators in a way that is suitably different from each other can further optimize their ability to synchronize to the same frequency as quickly as possible. That is, suitably heterogenous damping across the network can lead to improved stability in the power grids studied by the team.

This discovery could have implications for future grid design as developers work to optimize technology and in considerations to further integrate now separated networks.

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The paper is titled “Asymmetry underlies stability in power grids.” Additional co-authors include former postdoctoral researcher Ferenc Molnar and research professor Takashi Nishikawa.

The study was supported by Northwestern University’s Finite Earth Initiative (supported by Leslie and Mac McQuown) and ARPA-E Award No. DE-AR0000702 and also benefited from logistical support from the Northwestern Institute for Sustainability and Energy.

https://news.northwestern.edu/stories/2021/04/diversity-can-prevent-failures-in-large-power-grids/

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Source: https://bioengineer.org/diversity-can-prevent-failures-in-large-power-grids/

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How Fortnite and Zelda can up your surgical game (no joke!)

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Scalpel? Check. Gaming console? Check. Study finds video games can be a new tool on surgical tray for medical students

Video games offer students obvious respite from the stresses of studies and, now, a study from a University of Ottawa medical student has found they could benefit surgical skills training.

Arnav Gupta carries a heavy course load as a third-year student in the Faculty of Medicine, so winding down with a game of Legend of Zelda always provides relief from the rigorous of study. But Zelda may be helping improve his surgical education, too, as Gupta and a team of researchers from the University of Toronto found in a paper they recently published in the medical journal Surgery.

“Given the limited availability of simulators and the high accessibility of video games, medical students interested in surgical specialties should know that video games may be a valuable adjunct training for enhancing their medical education, especially in surgical specialties where it can be critical,” says Gupta, whose findings were deciphered from a systematic review of 16 studies involving 575 participants.

“Particularly, in robotic surgery, being a video gamer was associated with improvements in time to completion, economy of motion, and overall performance. In laparoscopic surgery, video games-based training was associated with improvement in duration on certain tasks, economy of motion, accuracy, and overall performance,” explains Gupta, who has been a gamer since age 8.

This study builds on past reviews and is the first to focus on a specific medical student population where this style of training could be feasibly implemented. Their timely study found some of the most beneficial games for students of robotic surgery and laparoscopy were: Super Monkey Ball, Half Life, Rocket League and Underground. Underground is purposely designed to assist medical students with their robotic surgery training via a video game console.

“While video games can never replace the value of first-hand experience, they do have merit as an adjunctive tool, especially when attempting to replicate important movements to surgery. For example, first-person shooting games require you to translate three dimensional motions onto a two-dimensional screen, which is like the concept of laparoscopic surgery,” says Gupta, whose studies are focused on surgery in ophthalmology, which makes games like Resident Evil 4 or Trauma Center: New Blood fitted for his own ambitions.

“I’m not joking when I say that games such as Fortnite have the potential to enhance those necessary movements, providing stronger motivational components and in a low stakes environment.”

Reports suggest 55 percent of university students are gamers and enjoy proficiency with video consoles. Yet, many medical students don’t admit to owning and using a gaming console.

“I think there definitely is some ambivalence towards video games in medicine,” says Gupta, who is also a fan of Witcher 3. “Given how accessible games have become and how video game technology is advancing, video games definitely are an easy go-to for the students who do love them in some capacity. The hope is that maybe this study can inspire someone to take advantage of video games’ unique capabilities, reduce the general ambivalence towards it, and develop some fun ways to let students engage with surgical education.”

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https://media.uottawa.ca/news/how-fortnite-and-zelda-can-your-surgical-game-no-joke

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