Wednesday, January 11, 2023

Urban lizards share genomic markers not found in forest-dwellers

Studying Anolis cristatellus lizards in Puerto Rican cities and their surrounding forests, researchers find parallel physical differences and genomic signatures in urban populations

Peer-Reviewed Publication

NEW YORK UNIVERSITY

Anolis cristatellus 

IMAGE: ANOLIS CRISTATELLUS LIZARDS—A SMALL-BODIED SPECIES ALSO KNOWN AS THE PUERTO RICAN CRESTED ANOLE—ARE COMMONLY FOUND IN BOTH URBAN AND FORESTED AREAS OF PUERTO RICO. view more 

CREDIT: KRISTIN WINCHELL

Lizards living in different cities have parallel genomic markers when compared to neighboring forest lizards, according to a new study published in the Proceedings of the National Academy of Sciences (PNAS).

 

The genetic variations linked to urbanization underlie physical differences in the urban lizards, including longer limbs and larger toe pads that show how these lizards have evolved to adapt to city environments.

 

Urbanization has dramatically transformed landscapes around the world—changing how animals interact with nature, creating “heat islands” with higher temperatures, and hurting local biodiversity. Yet many organisms survive and even thrive in these urban environments, taking advantage of new types of habitat created by humans. Researchers studying evolutionary changes in urban species have found that some populations, for example, undergo metabolic changes from new diets or develop an increased tolerance of heat.

 

“Urbanization impacts roughly two-thirds of the Earth and is expected to continue to intensify, so it’s important to understand how organisms might be adapting to changing environments,” said Kristin Winchell, assistant professor of biology at NYU and the study’s first author. “In many ways, cities provide us with natural laboratories for studying adaptive change, as we can compare urban populations with their non-urban counterparts to see how they respond to similar stressors and pressures over short periods of time.”

 

Anolis cristatellus lizards—a small-bodied species also known as the Puerto Rican crested anole—are commonly found in both urban and forested areas of Puerto Rico. Prior studies by Winchell and her colleagues found that urban Anolis cristatellus have evolved certain traits to live in cities: they have larger toe pads with more specialized scales that allow them to cling to smooth surfaces like walls and glass, and have longer limbs that help them sprint across open areas.

 

In the PNAS study, the researchers looked at 96 Anolis cristatellus lizards from three regions of Puerto Rico—San Juan, Arecibo, and Mayagüez—comparing lizards living in urban centers with those living in forests surrounding each city. 

 

They first confirmed that the lizard populations in the three regions were genetically distinct from one another, so any similarities they found among lizards across the three cities could be attributed to urbanization. They then measured their toe pads and legs and found that urban lizards had significantly longer limbs and larger toe pads with more specialized scales on their toes, supporting their earlier research that these traits have evolved to enable urban lizards to thrive in cities. 

 

To understand the genetic basis of these trait differencesthe researchers conducted several genomic analyses on exomic DNAthe regions of the genome that code for proteins. They identified a set of 33 genes found in three regions of the lizard genome that were repeatedly associated with urbanization across populations, including genes related to immune function and metabolism.

 

“While we need further analysis of these genes to really know what this finding means, we do have evidence that urban lizards get injured more and have more parasites, so changes to immune function and wound healing would make sense. Similarly, urban anoles eat human food, so it is possible that they could be experiencing changes to their metabolism,” said Winchell.

 

In an additional analysis, they found 93 genes in the urban lizards that are important for limb and skin development, offering a genomic explanation for the increases in their legs and toe pads. 

 

“The physical differences we see in the urban lizards appear to be mirrored at the genomic level,” said Winchell. “If urban populations are evolving with parallel physical and genomic changes, we may even be able to predict how populations will respond to urbanization just by looking at genetic markers.”

 

“Understanding how animals adapt to urban environments can help us focus our conservation efforts on the species that need it the most, and even build urban environments in ways that maintain all species,” added Winchell.

 

Do the differences in urban lizards apply to people living in cities? Not necessarily, according to Winchell, as humans aren’t at the whim of predators like lizards are. But humans are subject to some of the same urban factors, including pollution and higher temperatures, that seem to be contributing to adaptation in other species.

 

Additional study authors include Shane Campbell-Staton of Princeton University, Jonathan Losos of Washington University in St. Louis, Liam Revell of the University of Massachusetts Boston and Universidad Católica de la Santísima Concepción in Chile, Brian Verrelli of Virginia Commonwealth University, and Anthony Geneva of Rutgers University-Camden. The research was funded in part by the National Science Foundation (DEB 1354044, DEB 1927194, DEB 1701706), and by the University of Massachusetts Boston Bollinger Memorial Research Grant.

Warming oceans have decimated marine parasites — but that’s not a good thing

Peer-Reviewed Publication

UNIVERSITY OF WASHINGTON

Dissecting Sample 

IMAGE: A RESEARCHER HOLDS OPEN A PRESERVED FISH SPECIMEN THAT HAS BEEN INSPECTED FOR PARASITES. THE STUDY INCLUDED EIGHT FISH SPECIES AND 699 FISH SPECIMENS, WHICH YIELDED MORE THAN 17,000 PARASITES. view more 

CREDIT: KATHERINE MASLENIKOV/UW BURKE MUSEUM

More than a century of preserved fish specimens offer a rare glimpse into long-term trends in parasite populations. New research from the University of Washington shows that fish parasites plummeted from 1880 to 2019, a 140-year stretch when Puget Sound — their habitat and the second largest estuary in the mainland U.S. — warmed significantly.

The study, published the week of Jan. 9 in the Proceedings of the National Academy of Sciences, is the world’s largest and longest dataset of wildlife parasite abundance. It suggests that parasites may be especially vulnerable to a changing climate.

“People generally think that climate change will cause parasites to thrive, that we will see an increase in parasite outbreaks as the world warms,” said lead author Chelsea Wood, a UW associate professor of aquatic and fishery sciences. “For some parasite species that may be true, but parasites depend on hosts, and that makes them particularly vulnerable in a changing world where the fate of hosts is being reshuffled.”

While some parasites have a single host species, many parasites travel between host species. Eggs are carried in one host species, the larvae emerge and infect another host and the adult may reach maturity in a third host before laying eggs.

For parasites that rely on three or more host species during their lifecycle — including more than half the parasite species identified in the study’s Puget Sound fish — analysis of historic fish specimens showed an 11% average decline per decade in abundance. Of 10 parasite species that had disappeared completely by 1980, nine relied on three or more hosts.

“Our results show that parasites with one or two host species stayed pretty steady, but parasites with three or more hosts crashed,” Wood said. “The degree of decline was severe. It would trigger conservation action if it occurred in the types of species that people care about, like mammals or birds.”

And while parasites inspire fear or disgust — especially for people who associate them with illness in themselves, their kids or their pets — the result is worrying news for ecosystems, Wood said.

“Parasite ecology is really in its infancy, but what we do know is that these complex-lifecycle parasites probably play an important role in pushing energy through food webs and in supporting top apex predators,” Wood said. She is one of the authors of a 2020 report laying out a conservation plan for parasites.

Wood’s study is among the first to use a new method for resurrecting information on parasite populations of the past. Mammals and birds are preserved with taxidermy, which retains parasites only on skin, feathers or fur. But fish, reptile and amphibian specimens are preserved in fluid, which also preserves any parasites living inside the animal at the time of its death.

The study focused on eight species of fish that are common in the behind-the-scenes collections of natural history museums. Most came from the UW Fish Collection at the Burke Museum of Natural History and Culture. The authors carefully sliced into the preserved fish specimens and then identified and counted the parasites they discovered inside before returning the specimens to the museums.

“It took a long time. It’s certainly not for the faint of heart,” Wood said. “I’d love to stick these fish in a blender and use a genomic technique to detect their parasites’ DNA, but the fish were first preserved with a fluid that shreds DNA. So what we did was just regular old shoe-leather parasitology.”

Among the multi-celled parasites they found were arthropods, or animals with an exoskeleton, including crustaceans, as well as what Wood describes as “unbelievably gorgeous tapeworms:” the Trypanorhyncha, whose heads are armed with hook-covered tentacles. In total, the team counted 17,259 parasites, of 85 types, from 699 fish specimens.

To explain the parasite declines, the authors considered three possible causes: how abundant the host species was in Puget Sound; pollution levels; and temperature at the ocean’s surface. The variable that best explained the decline in parasites was sea surface temperature, which rose by 1 degree Celsius (1.8 degrees Fahrenheit) in Puget Sound from 1950 to 2019.

A parasite that requires multiple hosts is like a delicate Rube Goldberg machine, Wood said. The complex series of steps they face to complete their lifecycle makes them vulnerable to disruption at any point along the way.

“This study demonstrates that major parasite declines have happened in Puget Sound. If this can happen unnoticed in an ecosystem as well studied as this one, where else might it be happening?” Wood said. “I hope our work inspires other ecologists to think about their own focal ecosystems, identify the right museum specimens, and see whether these trends are unique to Puget Sound, or something that is occurring in other places as well.

“Our result draws attention to the fact that parasitic species might be in real danger,” Wood added. “And that could mean bad stuff for us — not just fewer worms, but less of the parasite-driven ecosystem services that we’ve come to depend on.”

The research was funded by the National Science Foundation, the UW-based Cooperative Institute for Climate, Ocean, and Ecosystem Studies, the Alfred P. Sloan Foundation, the University of Washington and the Washington Research Foundation.

These monogenean worms (Microcotyle sebastis) were dissected from the gills of a preserved copper rockfish specimen from the UW Fish Collection at the Burke Museum

CREDIT

Katie Leslie/University of Washington

Co-authors are Rachel Welicky at Pennsylvania’s Neumann University, who did this work as a UW postdoctoral researcher; Whitney Preisser at Georgia’s Kennesaw State University, who did this work as a UW postdoctoral researcher; Katie Leslie, a UW Research Technologist; Natalie Mastick, a UW doctoral student; Katherine Maslenikov, manager of the UW Fish Collection at the Burke Museum of Natural History and Culture; Luke Tornabene and Timothy Essington, faculty members in aquatic and fishery sciences at the UW; Correigh Greene at NOAA’s Northwest Fisheries Science Center; and John M. Kinsella at HelmWest Laboratory in Missoula, Montana.

 

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For more information, contact Wood at chelwood@uw.edu

Forests recovering from logging act as a source of carbon

Peer-Reviewed Publication

IMPERIAL COLLEGE LONDON

Logging 

IMAGE: LOGGING EXTRACTION IN THE BORNEAN RAINFOREST view more 

CREDIT: ZOE G DAVIES

Tropical forests recovering from logging are sources of carbon for years afterwards, contrary to previous assumptions, finds a new study.

Tropical forests that are recovering from having trees removed were thought to be carbon absorbers, as the new trees grow quickly. A new study, led by Imperial College London researchers, turns this on its head, showing that the carbon released by soil and rotting wood outpaces the carbon absorbed by new growth.

The researchers say the result highlights the need for logging practices that minimise collateral damage to improve the sustainability of the industry. The study, which monitored carbon in forests in Malaysian Borneo as part of the Stability of Altered Forest Ecosystem (SAFE) Project, is published today in Proceedings of the National Academy of Sciences.

First author Maria Mills, who began the work at Imperial and completed it at the University of Leicester, said: “Our results show that for the tropical forest we studied, logged areas are a source of carbon even a decade after logging has occurred. This means we need to reassess their role in global carbon budgets – we can no longer apply the blanket assumption that they are carbon sinks.”

Lead researcher Dr Terhi Riutta, now at the University of Exeter, said: “A lot of the carbon released in recovering forests is from collateral damage – trees that have died as a result of damage during the logging operations left to rot, and from disturbed soil. Logged forests still have value – we know they have a unique biodiversity – so making sure they are also not releasing extra carbon through better logging practices will boost their sustainability.”

Many previous studies of recovering forests have focused on measuring tree growth to estimate the amount of carbon taken from the atmosphere. The new study also measured how much carbon was coming from the ground (soil and dead wood) to calculate the carbon budget from the incoming and outgoing carbon flows for logged and unlogged (old-growth) forest.

Logged forest plots in the study had experienced logging at different stages over the prior few decades. The measurements were taken between 2011 and 2017.

To measure the carbon released from the ground, researchers used a portable carbon dioxide monitor to test patches of ground and pieces of deadwood in several plots monthly for several years. The team had also set up a 52-metre-tall tower above the forest canopy to continuously measure the ‘flux’ of carbon into and out of the forest to see whether it was a net source or sink of carbon.

They found that unlogged forested areas are generally carbon neutral, but that moderately and heavily logged tropical forest areas are a carbon source. They estimate an average carbon source of 1.75 +/- 0.94 tonnes of carbon per hectare within moderately logged plots and 5.23 +/- 1.23 tonnes of carbon per hectare in severely degraded plots, with emissions continuing at these rates for at least one decade after logging.

Co-author Professor Rob Ewers, from the Department of Life Sciences at Imperial, said: “The measurements from the tower show us whether the forest area is a source or a sink of carbon, and the soil monitoring tells us why this is. From these measurements, we know logged forests are still a source of carbon up to a decade after they have been logged, and that this primarily comes from organic matter in the soil or from rotting wood.”

The team say carbon monitoring should be conducted in other forests in different regions to build a more accurate picture of how logged forests contribute to global carbon budgets.

Broccoli looks more like cauliflower in a warmer world

Peer-Reviewed Publication

CORNELL UNIVERSITY

ITHACA, N.Y. – As seasoned gardeners know, broccoli heads don’t develop properly and can resemble cauliflower when grown in higher temperatures.

A new study identifies the genetic underpinnings for why broccoli heads become abnormal when it’s hot, providing insight into effects of climate-induced warming for all crops and pointing the way for breeding heat-resistant new varieties.

Broccoli grows best when planted in cool early spring or late summer, into fall. The researchers found that while broccoli grows normally at average temperatures of 61 degrees Fahrenheit, its crowns begin to deform at 72 degrees F and it forms dense cauliflower-like heads (called curds) at 82 degrees F.

The researchers then applied 5-azacytidine, a chemical known to inhibit a process called DNA methylation, where a methyl group – a small molecule – gets added to DNA. Methylation is one mechanism for turning genes on and off; in this case it suppresses a cluster of genes required for normal broccoli head production. When 5-azacytidine was administered, normal broccoli heads grew even at 82 degrees F, suggesting that methylation was behind the abnormal growth in the presence of heat. 

“Once we understand the mechanism better, we should be able to devise ways to develop a new biotechnology, a molecular genetics approach to suppress DNA methylation, in order to breed crops to grow in much warmer temperatures and in wider regions,” said Susheng Gan, Cornell University professor in the College of Agriculture and Life Sciences, and a co-corresponding author of the paper published Dec. 22 in the journal Molecular Horticulture. Liping Chen, a professor of vegetable science at Zhejiang University in Hangzhou, China, is the other corresponding author.    

Warming temperatures impact all aspects of growth and development in plants. Flower development is especially complex and sensitive to temperatures, with heat reducing the quality and yield of vegetables such as broccoli where the complete flower head – including stems, stalks, leaves and flowers – is eaten. Though more study is needed, Gan believes that at higher temperatures, DNA methylation of genes involved in floral development may be conserved across all crops. 

In the study, the researchers profiled broccoli plants (Brassica oleracea) using whole-genome sequencing technologies that identified the plant’s methylome – where in the genome methylation occurred – and its transcriptome – which identifies which genes are turned on. They found that abnormal flower development in broccoli was regulated by sets of floral development cessation-associated genes (FCGs). At 61 degrees F, broccoli heads (its floral bud) developed normally. At 82 degrees F and to a lesser extent at 72 degrees F, methylation of genetic elements that turned on FCGs were suppressed.

When grown at warmer temperatures, floral development becomes restricted to earlier stages of development. So, at 72 degrees F, broccoli buds are restricted to a stage where they look like a cross between a broccoli head and cauliflower curd; and at 82 degrees, they are even further undeveloped, and resemble a cauliflower-like curd.

Future studies will examine the mechanism behind DNA methylation of FCGs at high temperatures.

Zilei Yao and Lu Yuan, both at Zhejiang University, are co-first authors of the study. 

For additional information, see this Cornell Chronicle story.

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U$A

Private equity changes workforce stability in physician-owned medical practices


Study reveals more churn in workforce, greater reliance on physician assistants

Peer-Reviewed Publication

OREGON HEALTH & SCIENCE UNIVERSITY

New research reveals private equity firms that acquire physician-owned medical practices experience greater replacement of the workforce and rely more heavily on advanced practice providers — such as physician assistants and nurse practitioners — rather than physicians.

The study is the first to characterize the shift in workforce composition following private equity acquisition. It was published today in the January issue of the journal Health Affairs by researchers at Oregon Health & Science University, the University of Chicago, Harvard University and Johns Hopkins University.

The impacts come amid well-documented shortages in the overall health care workforce exacerbated by the COVID-19 pandemic.

“We really ought to be paying more attention to how these big-picture practice delivery shifts are affecting physicians,” said senior author Jane Zhu, M.D., assistant professor of medicine (general internal medicine and geriatrics) in the OHSU School of Medicine in Portland. “There is a finite number of us. If the measures we found in this study suggest dissatisfaction among physicians, then ultimately that’s yet another burden on a workforce that is already on the brink of burnout.”

The findings are the latest in a line of research to suggest private equity firms are increasing pressure to maximize profits.

“A lot of the current research on private equity looks at changes in costs, revenue or services following acquisitions. The purpose of this study was to capture private equity in the context of the clinical workforce,” said first author Joseph Dov Bruch, Ph.D., assistant professor of public health sciences at the University of Chicago. “That we observe greater clinician replacement at private equity-acquired practices compared with non-private equity-acquired practices suggests that private equity’s business strategy may differ from that of traditional practice owners.”

Researchers did not specifically examine the effect of the changes in workforce composition on health outcomes or patient care, although the study cites previous research that suggests patient care suffers with a more transitory workforce.

“A more stable workforce is associated with better health outcomes for patients, improved quality metrics, and reduced resource use,” they write.

The study identified 213 private equity-acquired practices in dermatology, ophthalmology and gastroenterology, and compared them with 995 physician-owned practices in those same specialties. They found that physicians in private equity-acquired practices were more likely than their counterparts in physician-owned practices to both enter and leave a practice.

The study also documented growth of advanced practice provider staffing in private equity-acquired practices.

“Private equity maximizes profits by increasing revenues or cutting costs,” Zhu said. “Shifting toward ancillary service providers and advanced practice providers is one way to accomplish both of those things.”

In addition to Zhu and Bruch, co-authors include Canyon Foot of OHSU; Yashaswini Singh, M.P.A., and Daniel Polsky, Ph.D., M.P.P., of Johns Hopkins; and Zirui Song, M.D., Ph.D., of Harvard.

This study was supported by the National Institute for Health Care Management (NIHCM) Foundation (to Jane Zhu). The funders had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Families with food insecurity have greater health care expenditures

Peer-Reviewed Publication

ATRIUM HEALTH WAKE FOREST BAPTIST

Deepak Palakshappa, MD 

IMAGE: DEEPAK PALAKSHAPPA, M.D., ASSOCIATE PROFESSOR OF GENERAL INTERNAL MEDICINE AT WAKE FOREST UNIVERSITY SCHOOL OF MEDICINE view more 

CREDIT: WAKE FOREST UNIVERSITY SCHOOL OF MEDICINE

WINSTON-SALEM, N.C. – Jan. 9, 2023 – Food insecurity, which is the limited or uncertain availability of nutritionally adequate and safe food, impacts about 10.2% of U.S. households, according to the U.S. Department of Agriculture Economic Research Service. In families with children in the home, food insecurity is even higher, at 12.5%.

Previous studies have shown an association between food insecurity and individual health care expenditures, but there is little research on how food insecurity impacts families’ health care use.

Now, researchers at Wake Forest University School of Medicine are reporting the results of a new study that shows food-insecure families have higher health care expenditures than families that are food secure.

The study was released today in the January issue of Health Affairs.

“We know that food insecurity has a negative impact on individual health outcomes,” said Deepak Palakshappa, M.D., associate professor of general internal medicine at Wake Forest University School of Medicine and principal investigator of the study. “But we need a better understanding of the financial implications on families and health care expenditures.”

In the retrospective study, Palakshappa’s team sought to determine the association between a family’s food insecurity over the course of one year and their health care expenditures throughout the following year. Researchers analyzed data from the 2016 and 2017 Medical Expenditure Panel Survey, a large-scale survey conducted annually by the Agency for Healthcare Research and Quality that is representative of the U.S. population. The survey collects information from U.S. medical providers about health care services, health insurance, expenditures and sociodemographic characteristics.

The team collected data on 14,666 individuals from 6,621 families and found that food-insecure families had 20% greater total health care expenditures than food-secure families, an annual difference of about $2,456.

“We found that food insecurity in 2016 was associated with increased care expenditures in 2017 among families regardless of insurance coverage type,” Palakshappa said.

The results also have significant implications for any potential programs or policies aimed at addressing food insecurity.

“Interventions that address food insecurity in one or more specific family members may also provide benefits to others in the home,” Palakshappa said. “And there’s a potential financial benefit for insurers to invest in these programs.”

Palakshappa’s team also found that 1 in 5 families had more than one insurance plan, making it challenging to determine the full financial benefit of food insecurity interventions in households with mixed insurance coverage.

“More parents are enrolling their children in Medicaid or CHIP instead of their employer-sponsored health insurance because of increased out-of-pocket expenses,” Palakshappa said. “However, the expansion of public subsidies such as the Supplemental Nutrition Assistance Program or child tax credits can alleviate food insecurity.”

Palakshappa said additional research is needed to evaluate how addressing food insecurity at an individual patient visit may affect the health outcomes and health care utilization of other family members.

UK

Mobility specialists looking to quit profession


Study reveals a third of orthotists working privately and in NHS seek a way out


Peer-Reviewed Publication

ANGLIA RUSKIN UNIVERSITY

More than a third of orthotists, specialists who improve quality of life for people with long term conditions and disabilities, would leave the profession if they could, according to a new study.

Orthotists provide gait analysis to patients and design and fit external devices. These include insoles, braces and splints, to support and improve posture, function and mobility and manage pain and deformity.

However, new research by Anglia Ruskin University (ARU) has found that 37% of orthotists working with NHS and private patients would leave the orthotic profession if they could, suggesting a potential retention crisis. The figure was roughly the same among those employed by the NHS and those employed by private companies.

Around 70% of orthotists in the UK work in NHS settings but are employed by private companies. The research found that the leading reason for orthotists wanting to leave the profession was treatment by their employer. Many respondents also reported they did not have enough time with patients during appointments, and that facilities were inadequate. Privately employed orthotists reported that their working conditions were significantly lower than those employed by the NHS.

Orthotic services provide financial value to the NHS. A previous report by the NHS Purchasing and Supply Agency found that the health service could save £4 for every £1 spent on improving orthotics services, because patients who access these services suffer fewer falls and require less pain relief or surgical interventions.

Orthotics services provide treatment options for people with a wide range of conditions and orthotists work closely with a number of clinical specialties within the NHS including diabetes care, elderly medicine, neurology, orthopaedics, paediatrics, stroke and trauma teams.

Dr Nebil Achour, co-author of the paper and Associate Professor in Disaster Mitigation at Anglia Ruskin University (ARU), said: “This study highlights the substantial challenges facing the orthotic profession in terms of staff satisfaction and retention. The perception among orthotists that they were treated poorly by their employer appears to be the catalyst for a significant number wishing to leave not just their job but the profession overall. This is a vulnerability in our healthcare sector and needs to be addressed urgently.

“A resilient healthcare sector requires all professions and capabilities to be ready to respond effectively during times of adversities.”

Lead author Katie Prosser, who carried out the research while studying for a Masters Degree in Healthcare Management at ARU, said: “These are concerning results with clear and considerable implications for the future of the orthotic workforce, as well as patients requiring their services. Usually if people are dissatisfied with an NHS post they can look to move into private roles. However, in this profession it appears there is little to be gained in terms of job satisfaction or conditions by doing this, which may lead orthotists to want to do something else entirely.”

The peer-reviewed study is published today in the British Journal of Healthcare Management.