The idea that scientists could create a defensive shield to protect the United States may sound like science fiction, but it’s real, it was begun in the 1960s—and it’s made of insects.

This insect barrier was designed to protect North America from screwworm flies, whose larvae feast on cows and other livestock, inflicting millions of dollars in damage. A screwworm fly-breeding facility along the narrow strip of land connecting North and South America, jointly operated by the United States and Panama, releases sterile male flies across the isthmus at a rate of millions per week. These sterile males mate with female screwworm flies in the wild, ensuring the females produce no living larvae. Perpetual application of this “sterile insect technique” (SIT)—a pesticide-free, genetic method—prevents screwworm fly populations from making their way north from Colombia, keeping North and Central America almost entirely free of a pest that had once been a significant threat in the US south, Mexico, and Central America.

Sterile insect technique—a genetic approach to pest control

The concept of SIT has been around for a long time. During the 1930s and 1940s, scientists working in the United States, the Soviet Union, and Tanzania independently developed the idea of reducing insect numbers by infiltrating the wild populations with lab-raised insects designed to sabotage their reproduction. A main challenge was how to generate large numbers of sterile animals. Research on the fruit fly Drosophila as early as the 1920s showed that X-ray irradiation provided a fast, efficient way to make flies sterile. This finding prompted USDA scientists to test the effects of irradiation on screwworm flies. They found that screwworm flies irradiated in the pupa stage developed into normal-seeming adults, but when untreated females mated with irradiated males, none of the resulting eggs hatched. Scientists now had a feasible way to generate large numbers of sterile male flies.

Screwworm flies are particularly susceptible to control by SIT because females mate only once during their lifespan. Efforts to use SIT to eradicate the screwworm fly began in Florida as early as 1957, spread to other US states and, by the 1970s, continued southward, reaching the narrow and therefore easily covered border of Panama in 2002. Because screwworm flies still live below this border, the need for SIT is ongoing. Every week, millions of sterile males are released along Panama’s southern border, enough to outcompete any fertile males that might try to make their way up from Colombia. Still, in 2016, a screwworm infestation broke out among deer in the Florida Keys. Thanks to shipments of sterile males from the Panama facility, the Florida outbreak was quickly contained. 

SIT has also been used to control some other insect pests, including for the control of crop pests in southern California, northern Mexico, and the Rio Grande Valley in Texas. But traditional SIT has limitations, and modern molecular genetics tools might offer improvements. 

One goal for improvement of SIT is to develop practical and effective methods for control of mosquitoes that transmit disease. Researchers at the University of California, San Diego are using the gene editing technology CRISPR to create sterile male mosquitoes in a targeted fashion, by knocking out specific genes. A system called “precision-guided sterile insect technique” allows the creation of sabotaged eggs that will either hatch sterile males or not hatch at all. Eggs are much hardier than irradiated adult mosquitoes. The hope is that these eggs can be shipped to a destination, sterile males will hatch and mate with wild females, and the mosquito population in that region will be suppressed. 

A harmless nematode helps researchers study a deadly parasite 

Genetic tools are helping researchers control and understand other threats beyond insects. Soil-transmitted parasitic nematodes infect more than one billion people worldwide, often by penetrating the skin of the feet. But these parasites are difficult to rear in the laboratory because they require a living host for some stages of life. Studies conducted on common research organisms—which are innocuous and easily reared in labs—can provide important supplements to study of pests, parasites, and disease vector species like these. The nematode C. elegans, for example, is a cousin to parasitic nematodes, and as such, offers both a source of information and a testing ground for genetic technologies.

Back in the 1960s, Sydney Brenner selected C. elegans as a research organism because it has certain favorable characteristics: a rapid life cycle, small size, and a simple reproductive cycle. Since then, C. elegans has become widely used in laboratories, and it was the first multicellular organism to have its genome completely sequenced. Researchers have fully mapped the tiny worm’s “connectome,” a wiring diagram that shows all its neurons and how they connect. Over the years, sophisticated genetic methods for studying the nematode nervous system have been developed and optimized.

“We have methods for monitoring neural activity, for silencing neurons, for cell-specific labeling of neurons, and also for knocking out genes in Strongyloides,” says Elissa Hallem of UCLA, who studies the parasitic nematode Strongyloides stercoralis. Researchers study the worms’ neurons to learn how they sense the world around them, looking for any avenue to exploit in the pursuit of repelling or exterminating the pests. It is estimated that 30–100 million people are infected with Strongyloides stercoralis around the world. The nematode enters the body through the skin and can travel through the bloodstream, reproducing in the small intestine. Symptoms of a Strongyloides infection include intermittent rash, abdominal pain, or cough. The disease can be life threatening in people with a compromised immune system. 

Hallem and others study S. stercoralis because it is a worldwide health problem, but also because it’s one of the only parasitic nematodes amenable to genetic manipulation in the lab. Even so, it’s fussy and time consuming to work with. Not only does it require an animal host to reproduce, but it’s difficult to establish a stable transgenic line. When new DNA is injected, the parasite generally silences it after one generation unless it’s integrated into the genome. There are tools to insert a transgene into the genome, Hallem says, but the process is inefficient and uptake is generally low. By contrast, C. elegans will continue expressing extra-chromosomal DNA generation after generation. That’s one reason researchers look to C. elegans to suggest starting points for genetic experiments in Strongyloides. 

One active area of investigation is how the worms detect temperature differences and respond to them. As a parasite, Strongyloides needs to infect a host in order to reproduce. The ability to sense the heat of a warm-blooded animal and move toward it is critical for survival. Although C. elegans doesn’t need to find an animal host, it can detect changes in temperature. “C. elegans and Strongyloides have, for the most part, the same set of neurons in the same position throughout the body, and their behaviors are totally different,” Hallem says. In C. elegans, certain proteins on the surface of a particular type of neuron allow the worm to sense temperature changes. By searching the Strongyloides genome for genes in the same family, Hallem’s lab found related genes in that organism likely to be involved in temperature sensing. 

Once they uncovered the candidate genes in Strongyloides, it still wasn’t a simple matter to test the genes’ function. Technical issues around rearing the little worms make it very difficult to establish breeding populations that contain mutated versions of the genes of interest. Again, C. elegans was there for the assist: researchers in Hallem’s lab engineered C. elegans to express the Strongyloides genes, enabling them to study its effect on the temperature-sensing neurons using cheaper and faster methods than would be needed to study genetically modified Strongyloides. Understanding the molecular process underlying the parasites’ heat-seeking capabilities could suggest ways to thwart the process and prevent infection, Hallem says.

Planarians, all but abandoned as a research organism, make a comeback

Planarians, free-living flatworms, enjoyed a brief heyday as a research organism in the 1960s when many laboratories studied their regenerative properties. By the 1990s, however, their popularity had subsided. “When I got interested in studying them, there were just a handful of labs left,” says Phil Newmark of the Morgridge Institute in Madison, WI. “As a postdoc, I went to the University of Barcelona, the only group I knew about that was actively using molecular biology to understand planarian regeneration.” Now, the little flatworms are making a comeback.

Over the last decade or so, researchers working with planarians noticed that they share many features of their biology with parasitic flatworms, called schistosomes, which infect some 200 million people worldwide. When the parasites lay their eggs in the body, they trigger an inflammatory reaction that eventually leads to severe organ damage. A schistosome infection can persist for decades, but not because the eggs hatch into new worms inside the body–schistosomes are just extremely long lived. This extraordinary longevity appears to be related to the type of stem cells that give planarians their regenerative ability, Newmark says. “As we started working on them, we really kind of adopted the toolkit from planarian biology to begin to understand how these parasites operate,” he says. “It’s been really rewarding to see the basic biology of planarians used to help us understand new aspects of the biology of these parasites.”

A major hurdle for controlling schistosomes is that only one drug exists, setting the stage for resistance to emerge. To develop more treatments, researchers are investigating schistosome biology to look for weaknesses that could be exploited with new drugs. Recently, researchers discovered that a gene involved in regeneration in planarians is necessary in schistosomes for digesting their blood meal. Understanding this and other genes involved in the organisms’ fundamental biology could lead to new angles for treating schistosome infections. 

Across a variety of species, research organisms provide anchor points that allow us to understand what might be true of related but harmful species. If the adage “know thy enemy” holds true, then the knowledge we gain from their study might one day help us control a broader range of threats in the future.

To learn more about how genetics contributes to the control and study of pests, parasites, and disease vector species, visit any of the links below.

1. National Geographic on SIT in the screwworm

2. World Health Organization on SIT in mosquitoes  

3. Rockefeller Institute on a study of how mosquitoes sense us

4. In G3, publication of the genome of the invasive crop pest Drosophila suzukii

5. In G3, analysis in a pathogenic yeast points to potential drug targets

6. VEuPathDB database of eukaryotic pathogen and host information

7. Importance of Vector control

This article is part of a series of posts outlining the history and impact of research in experimental organisms. The series is developed in collaboration with the GSA Public Communications and Engagement Committee.

By the time Bertrand Might was six months old, it was clear something was amiss. His muscles weren’t developing normally; he was “jiggly” and had little motor control. As he got older, new symptoms emerged, including seizures, sugars in his urine, and an inability to produce tears. Bertrand’s parents spent countless hours consulting with medical specialists to track down the cause of Bertrand’s illness. In 2010, when he was four years old, the Mights enrolled Bertrand in a clinical trial of a then-novel technology: DNA exome sequencing. Sequencing revealed that he had inherited two different nonfunctional copies of a gene called NGLY1.

With that DNA test, Bertrand became a medical and scientific pioneer—the first patient ever diagnosed with NGLY1 deficiency. But because the disease is so rare, there were no therapies that could cure or treat it at its source; doctors could only try to relieve Bertrand’s symptoms as best they could.

To raise awareness, Bertrand’s dad, Matt Might, published a post on his popular computer science blog detailing the family’s diagnostic odyssey. Over time, the Mights connected with dozens of families also coping with the condition. Interestingly, the collection of symptoms varied quite a bit from case to case,
and genetic sequencing helped a number of families finally put a name to their diseases.

Doctors learned more about the disease with every new patient that came forward. But to really understand how the loss of NGLY1 can cause devastating symptoms throughout the body, scientists would have to take a different path: studying NGLY1’s function in the body at a molecular level. They needed to explore the biochemistry of the protein that NGLY1 encodes, find other molecules that interact with it as it performs its functions, and map out the ripple effects of losing the gene. To capture that level of detail requires controlled studies at a huge scale, something only possible in fast-reproducing research organisms, such as fruit flies and nematode worms.

The not-so-lowly worm

Around the time that doctors were beginning to recognize the clinical effects of NGLY1 deficiency in people, a researcher named Nicolas Lehrbach was making his own surprising discovery about NGLY1, in a different context. Now an assistant professor at Fred Hutchinson Cancer Center, Lehrbach first stumbled across NGLY1 while doing his postdoctoral research at Harvard Medical School.

Lehrbach studies how cells take out their molecular trash, or, more specifically, he studies how cells can compensate when their trash-disposal system isn’t working. When we talk about cellular “trash,” generally that means protein molecules that are damaged, misfolded, or otherwise no longer needed. The cellular machine that breaks down these proteins is called the proteasome. Lehrbach studies the proteasome in the tiny nematode C. elegans—colloquially called “the worm” in biology labs.

“If you think about the fundamental machinery needed by every cell, whether it’s in a human or a worm or a fungus or a plant, there are some basic processes that are simply required for life,” Lehrbach explains. “The underlying molecules that do those jobs are almost the same in any living thing.” The proteasome does one of those essential jobs required by every living animal cell. So by figuring out what molecules keep the proteasome humming along in worms, Lehrbach could also learn something about what makes the proteasome tick in humans.

Worms are inexpensive and quick to breed in the lab—a worm matures from embryo to adult in three days, and each worm produces about 300 offspring.This means that researchers can do thousands of experiments at once looking for rare mutations that affect some aspect of the animal’s development or behavior. Suppose you’re trying to understand how the nervous system develops. First, you would feed the worms a chemical that increases the chances of genetic mutations, and then you’d examine thousands and thousands of mutated worms to find the handful whose nerves didn’t develop properly. By analyzing the genes of those animals, you’d discover which genes contained mutations that caused the defect.

Lehrbach applied this approach to studying proteasome function. He designed a genetic screen to hunt for genes that, when mutated, boost the cell’s production of the proteins that make up the proteasome. “If the proteasome is not working well, one of the ways that our cells can cope with that is just to make more proteasomes to compensate,” Lehrbach says. His experiment revealed that the worm relies on a version of NGLY1 for that process.

“The power of that method is that it doesn’t presuppose any model or hypothesis about what kind of genes are going to be involved,” Lehrbach explains. Rather than choosing a gene and seeing whether it does something important, the researchers can do a wide-ranging search and see what turns up. “I would have never in a thousand years—if I were searching in a more targeted, hypothesis-driven way—I would never have thought the NGLY1 gene would have that role,” he says.

Proteasome failure is a hallmark of various human diseases, including neurodegenerative diseases like Parkinson’s and Alzheimer’s, but Lehrbach wasn’t narrowly focused on pathways involved in disease. The worm studies exemplify how expanding our knowledge of basic cellular processes can lead to unanticipated clinical benefits. “When you have a patient with clinical symptoms, but you want to get back to the molecular mechanism, that’s a really hard puzzle to solve,” Lehrbach says. “That clue from genetics, which really came out of the blue from doing a very open experiment, provided an insight that helped accelerate the process of understanding NGLY1 deficiency.”

Of flies and men

After receiving Bertrand’s genetic diagnosis, the Might family started a foundation, NGLY1.org. Through the foundation, they reached out to geneticist Clement Chow at University of Utah Health for help to uncover more information about how the lack of NGLY1 was making their son ill.

Chow’s lab studies protein misfolding and how the cell deals with incorrectly-folded proteins when they build up in a part of the cell called the endoplasmic reticulum. NGLY1 plays a role in clearing those misfolded proteins, and Chow set out to uncover exactly what that role is.

Using the fruit fly Drosophila in the lab, Chow and his colleagues genetically engineered different flies with different NGLY1 mutants, to see what effect each mutation would have on the fly. Some mutations might completely destroy the NGLY1 protein, while others might just make it weaker or less efficient at doing its job. Flies with mutations in NGLY1 had delays in development, and some died in the larval stage. Others matured to adulthood but still died sooner than normal flies.

Chow also investigated how the loss of NGLY1 changed the expression of other genes. Genes can be turned on or off, meaning they actively produce their protein or they lie idle. They can also be adjusted up or down, like twisting a volume knob on a stereo, so they produce a little more or less protein. Often, these adjustments are managed via biochemical feedback pathways in the cell. NGLY1 removes sugar molecules called glycans from various proteins, and when that function is lost, the excess of glycans alters the activities of those proteins. These changes can have a cascade of effects that lead to changes ingene expression. For instance, there is a protein called Nrf1 whose job is to turn on several genes that make components of the proteasome, to ramp up new production when it detects proteasome failure. It can do this only after NGLY1 removes a glycan from a key building block molecule in the protein, chemically changing its identity. Without NGLY1 there to strip off the glycan, Nrf1 can’t activate those genes, and the cell can no longer compensate for proteasome failure.

By comparing gene expression between healthy flies and those without NGLY1, Chow discovered that losing NGLY1 caused a drop in the level of a protein that helps make a sugar called GlcNAc. Adding and removing GlcNAc from proteins is one key way the cell directs their activity. Currently, GlcNAc is sold over the counter as a supplement. “What’s exciting about this is that patients had already been thinking about using this particular sugar,” Chow says. Because GlcNAc is easy to get, parents of kids with NGLY1 deficiency had tried it at home. “There had been anecdotes that it was providing relief, especially with tear production,” says Chow. When he gave GlcNAc to the mutant flies, they tended to live longer than those that didn’t receive the supplement. A clinical trial of GlcNAc eye drops in kids with NGLY1 deficiency is getting underway at Mayo Clinic to test how well the supplement performs at increasing tear production in these kids who have NGLY1 deficiency.

The GlcNAc discovery in flies not only helped explain how the supplement was helping kids with NGLY1 deficiency, but it was powerful in another way, as well: it validated the fly as a model of how NGLY1 was working in human cells. “That was kind of our first foray into thinking about NGLY1 and what we can do with the fly,” Chow explains.

The next step for the Chow lab was to understand how other genes interact with NGLY1, creating variation in the disease presentation. Among the patients with NGLY1 deficiency, the severity of symptoms ranged widely; for example,the second NGLY1 patient to be identified, Grace Wilsey, learned to crawl, talk, and follow simple directions, skills that Bertrand Might never acquired. Human NGLY1 patients are too few, and too genetically complex, to support clinical studies of genetic interactions that may provide clues to why disease presentation is so variable. Using fruit flies enables researchers to study thousands of animals from genetically controlled populations.

To look at how variants in NGLY1 interacted with other genes in the genome, Chow’s lab turned to the Drosophila Genetic Reference Panel, a collection of fruit fly lines that all carry slightly different genetic changes. The flies were bred from the same original population, so they mostly share the same genome, and each line’s genome sequence is well-documented. By disabling the NGLY1 gene in each different fly population, then documenting the number and severity of the symptoms, they uncovered a gene called NKCC1.

The fruit fly experiments were invaluable to test a large number of genetic interactions in a short period of time, but to fully characterize how the NGLY1 and NKCC1 proteins interact, Chow turned to mice. Experiments in mouse cells grown in the lab revealed exactly how NGLY1 chemically modifies NKCC1 to keep it working properly. “We started out with this very basic tool that fly genetics labs use all the time, which is a genetic screen, and they brought us all the way to thinking of finding defects in mammalian cells in a pretty quick order,” Chow said. “That tells us that the flies are modeling exactly the same thing we see in mice and humans.”

Studying mammalian cells or even human cells grown in a dish in the lab may sound like a more representative model for human disease, but these lab-grown cells can’t perfectly replicate what’s happening in a live animal. To understand the complex interactions between the many genes and proteins over the course of a life cycle, nothing can replace an intact, living animal, even if it’s a miniscule worm or a fruit fly. “There are certain processes, like communication between different types of cells within an organism, that are impossible to model with a layer of cells in a dish, which are all undifferentiated and more or less identical to one another,” Lehrbach says.

And while a worm or a fly can’t exhibit speech delays or intellectual disability, the genes responsible for these issues in people perform largely the same functions on the cellular level in all creatures. “These are mutations in basic housekeeping genes that every organism needs to have functioning,” Chow said. “While their disease may not perfectly match what we see in humans, the cellular process and the biological process is nearly identical in flies and humans, so that makes it a pretty good model for disease.”

For Bertrand Might, genome sequencing revealed the cause of his disease, marking the end of the family’s diagnostic odyssey. At the same time, the diagnosis was only the beginning of a new odyssey: a quest to find a treatment that could compensate for the loss of NGLY1. Sadly, there’s not yet any cure for
NGLY1 deficiency, nor a treatment that directly addresses the genetic cause of the disease. But ongoing research to understand all the different ways that NGLY1 manages important cellular functions is leading to interventions that can lessen the impact of losing NGLY1. While Bertrand himself died in 2020, the research he inspired—including a Precision Medicine Institute at the University of Alabama at Birmingham, which Matt Might directs—aims to someday help other children with NGLY1 deficiency and other rare disorders to live longer, healthier lives.

To learn more about the ways that model research organisms contribute to the study of rare disease, visit any of the links below.

1. GENETICS: https://academic.oup.com/genetics/article/214/2/233/5930504
2. Undiagnosed Diseases Network: https://undiagnosed.hms.harvard.edu/
3. MARRVEL: http://marrvel.org/
4. ModelMatcher:  https://onlinelibrary.wiley.com/doi/10.1002/humu.24364
5. Rare Diseases Models and Mechanisms Network: http://www.rare-diseases-catalyst-network.ca/
6. The Jackson Laboratory Rare Disease Translation Center: https://www.jax.org/news-and-insights/2022/December/jax-strives-to-advance-rare-disease-research-andreatment-options
7. Zolgensma for Spinal Muscle Atrophy: https://www.pennmedicine.org/news/news-releases/2019/may/zolgensma-based-on-delivery-system-discovered-by-penn-gene-therapy-pioneer
8. Zolgensma for Spinal Muscle Atrophy:   https://www.sheffieldchildrens.nhs.uk/news/edwards-story-the-world-is-his-oyster-after-gene-therapy-treatment/ 
9. Charcot-Marie-Tooth: https://www.jax.org/news-and-insights/2018/August/kathy-morelli-finding-cures-for-rare-diseases 

Ever since Charles Darwin proposed the idea of natural selection in 1858, biologists have been pondering exactly how selection works, somehow driving the evolution from single-celled life to the wide array of complex vertebrates that now populate the planet. As advances in technology have enabled genomic mapping at increasingly finer resolution, the questions have only deepened. How could natural selection, “survival of the fittest,” allow for so much duplication and seemingly unnecessary stretches of DNA seen in vertebrate genomes? Why haven’t the forces of evolution created a lean, sleek genomic masterpiece?

By combining population genetics with quantitative genetics, Michael Lynch has made remarkable progress toward answering these questions. He’s shown that natural selection is just one of several mechanisms driving evolution, and that much genomic complexity arose “passively” through an accumulation of random changes that nature couldn’t eradicate. His ideas have ruffled more than a few feathers in the evolutionary biology world, but his paper on genetic subfunctionalization, or how duplicated genes acquire new functions, became one of the most-cited GENETICS papers of all time. He authored the seminal text, Origins of Genome Architecture, and now he’s working to found a new field, evolutionary cell biology.

“Michael Lynch is a pretty amazing individual,” said Chris Amemiya of UC Merced. “He’s been a real driver of a lot of science in this country.”

For his accomplishments, Lynch has been awarded the 2022 Thomas Hunt Morgan Medal for lifetime achievement in the field of genetics from the Genetics Society of America.

Comparing proteins, comparing genomes

Lynch started out as an ecologist, but after switching into population genetics and quantitative genetics, he became interested in applying the concepts of these fields to natural populations. “It started out at a pretty crude level,” he recalled, before the widespread availability of DNA sequencing. To identify genetic differences, the team looked for differences in proteins. “We were doing what were called allozyme gels, for protein variants, which was pretty neat. It gave us a first glimpse of variation. But it was a real art form.”

The rise of fast, cheap DNA sequencing enabled scientists to interrogate genomes at the individual level at unimaginable depth. “We could go beyond just speculating,” Lynch says. “I started developing models for understanding how genome complexity evolves, particularly how we can passively evolve in a domain where we have more and more complex genomes, even though that’s not pushed forward by natural selection.”

The common understanding of Darwinian evolution is roughly as follows: random mutations lead to variation within a population, and occasionally a mutation will arise that confers its bearer with a reproductive advantage. Natural selection is the process by which these beneficial mutations outcompete their less-advantageous counterparts. Over millions of years, this process leads to species becoming exquisitely adapted to their particular ecological niches. As so often happens in biology, however, this explanation omits quite a bit.

Genome complexity can arise passively, without selection

Some mutations are mild enough that selection pressure can’t stop them from accumulating, Lynch explains. “The messy genomes of big clunky vertebrates and land plants are not due to the fact that everything’s driven by refinements by natural selection,” he says. “It’s a consequence of the inability of selection to eliminate what would ordinarily be viewed as bad changes in the genome.” Introns are one example of this, he points out. For every additional base pair a chromosome accumulates, the organism has to spend more energy to maintain and replicate that lengthened genome, and yet the genomes of complex organisms are stuffed with sequences that never make it into a finished protein.

“One quite influential piece of work that came out of the very earliest days was our work on gene duplication,” Lynch says. In their groundbreaking paper, Lynch and graduate student Allan Force showed how mutations in different regulatory elements of duplicated genes allow both copies of the gene to be retained and, eventually, lead to divergent gene functions. This contradicted the prevailing idea that when a gene is duplicated, one copy eventually accumulates enough mutations that it either degenerates or, in rare cases, acquires a new function.

“This was 1998. We’d hardly had any genome sequences yet; that was just starting to happen,” Lynch said. “I think we were in the right place at the right time. Prior to that point, people knew genes were duplicating, but we had no idea how common it was.”

Lynch and Force realized that duplicate genes were far too common for every new duplicate to have acquired a completely new function. In their paper, they argued that if the original gene had multiple functions governed by different regulatory elements in different types of cells—for instance, the head and thorax of an insect—that modularity could allow the duplicate gene to diverge via mutations in the regulatory element. “What can happen is one loses its ability to be expressed in head, and the other gets complementary degenerative mutations, and it can’t be expressed in thorax,” said Lynch. “Nothing’s changed dramatically, biologically. But you’ve made a more complex organism.”

The Center for Mechanisms of Evolution

In 2017, Lynch moved to Arizona State University to launch the Biodesign Center for Mechanisms of Evolution. “We’re trying to grow a new center with six new faculty, plus me, all focused on trying to understand evolution at the cellular level,” Lynch says. “We’re trying to integrate biochemistry and biophysics into this mix as well, to come up with a comprehensive view of how cellular features evolve, or don’t evolve. What are the constraints—what prevents cells from going down a certain route?” 

Lynch calls evolutionary cell biology “the last missing link,” pointing out, “There’s an amazing field of cell biology; everything’s done in exquisite detail at the molecular level. But there’s no real evolutionary biology in cell biology.”

“This unique Center promises to diversify the field of evolutionary genetics into new avenues of inquiry,” write Bill Bradshaw and Chris Holzapfel, who nominated Lynch for the medal. “This diversification will lead not only to greater insight into the genetics of evolutionary processes, but also into medically important areas of genetic disorders. Under Lynch’s direction, the Center will produce a new generation of forward-looking geneticists firmly rooted in integrative and transformational research.”

Indeed, Lynch has long championed integrative research, says Amemiya. “He’s got his hand in a lot of things, not only in genetics, but also in developmental biology and ecology. Some of these principles, I think, have been percolating for a long time, and he was able to bring these kinds of ideas into the fore.” Lynch has served as president of multiple scientific societies, including the Society for the Study of Evolution, the American Genetic Association, the Society for Molecular Biology and Evolution, and, of course, the Genetics Society of America. “He’s been an amazing advocate for interdisciplinary science,” Amemiya says.

The Thomas Hunt Morgan Medal recognizes individual GSA members for lifetime achievement in the field of genetics. Recipients have made substantial contributions to genetics throughout their careers and have a strong history as a mentor to fellow geneticists.

Harmit Malik loves conflict—genetic conflict, that is. “I’m really interested in this idea that components of the same genome, or components of different genomes, are constantly doing battle with each other,” says Malik, who heads a lab at the Fred Hutchinson Cancer Research Center.

To understand genetic conflict, Malik focuses on the parts of the genome that are rapidly changing and evolving. By studying these tumultuous regions, Malik has made impactful discoveries, some of which have overturned the conventional wisdom in genetics that the most important elements of the genome are protected from rapid mutation.

For his contributions, Harmit Malik has been awarded the 2022 Edward Novitski Prize, which recognizes an extraordinary level of creativity and intellectual ingenuity in the solution of significant problems in genetics research.

Breaking evolution’s “speed limit”

Some genes evolve quickly, while others haven’t changed much throughout evolutionary history. Immune system genes, for instance, evolve fast to keep up with the relentless onslaught of different pathogens that they need to fight. For these genes, agility provides the organism with a selective advantage.

On the other hand, genes and proteins that are needed for fundamental cellular functions, like mitosis and meiosis, are expected to evolve much more slowly. Mutations in these genes would be detrimental to the organism’s fitness, presumably, and therefore kept to a minimum. It turns out that this isn’t always the case, however. During his postdoc, Malik made the astonishing discovery that centromeres, among the most essential structures in the cell, undergo unexpectedly rapid evolution.

Centromeres are the constricted regions that give chromosomes their “belted” appearance. They ensure that during cell division, both daughter cells inherit a full and correct set of chromosomes. Centromeric DNA is highly repetitive and does not encode genes, and centromeric histones are proteins that bind to these DNA repeats.

“Centromeric DNA, base pair for base pair, is actually one of the fastest evolving components of our genome,” he says, and centromeric proteins also showed a similarly rapid mutation rate. In fact, the researchers found that mutations arise in these regions faster than the random mutation rate would predict, implying an evolutionary pressure driving the rapid change. At the time, this was “a completely heretical idea, and one of the very first instances where an essential gene had been evolving under what we refer to as positive selection—this idea of faster than expected evolution,” Malik says.

Intrigued, he set out to find what was driving the rapid evolution of centromeric DNA and proteins. During the process of egg formation, four haploid daughter cells are formed, but only one gets selected to be the egg and the other three are destroyed. “We realized this actually introduced an incredible degree of competition as to which chromosomal variant was going to be inherited as the egg chromosome,” says Malik. This competition set the stage for “selfish” genetic variants to arise. A mutation in the centromeric DNA or proteins that increased the chance of being passed down to the egg would have a selective advantage.

Still, something didn’t add up. “It was actually against the best interests of the genome to have this selfish behavior,” says Malik. If centromeric DNA and proteins evolved together, each boosting the other’s inheritance rate, the selfish elements would quickly take over the population and reduce the genetic diversity of the offspring. “We then realized that, actually, they were probably working in conflict with each other,” Malik says. Malik and his postdoc mentor, Steve Henikoff, proposed the “centromere drive model,” which explains the rapid co-evolution of centromeric proteins and DNA as an effect of genetic conflict. While selfish centromeric DNA evolves to increase its chance of being passed down, the centromeric proteins were evolving to suppress this inequity and increase the random chance of any chromosome surviving to the next generation. “The entire centromere drive hypothesis came about to reconcile how something so fundamental to our cell division process could be subjected to the kind of innovation that we see in the host-pathogen interaction,” Malik explains.

Beyond the centromere

While Malik’s work has uncovered a tremendous amount about the evolution of the centromere, his interest in genetic conflicts has taken him into other uncharted research waters. “I think what most of us do is pick a topic that we’re interested in and then try to figure out how to address it,” says Sue Biggins, director of the Basic Sciences Division at Fred Hutchinson. “He has this opposite way of doing it, which is to say if something’s rapidly evolving, something super interesting is happening. He has this fascinating way of using rapid evolution to open up the questions for him. To me, that is the hallmark of someone really creative.”

For instance, Malik helped pioneer the field of paleovirology, studying the traces of viral genes left behind in host genomes over the course of evolution. Viruses are constantly mutating and evolving, and, correspondingly, defenses arise in the genomes of host organisms to combat them. By studying the DNA evidence of this evolutionary arms race, Malik and others hope to glean information about viral defense strategies that could someday be translated into antiviral therapies.

Malik’s creative enthusiasm makes him invaluable as a mentor and colleague. “Talking science with Harmit is invigorating and joyful, in part because of his openness, his authenticity, and his humility,” says Mia Levine of the University of Pennsylvania, who nominated Malik for the award. “He is a perpetual student, making these conversations feel like one of collaborative discovery. These interactions help you see the gold that you are sitting on and give you the confidence to tell the world about it.”

Creative ideas that challenge existing paradigms often run into resistance from the community, and it can take courage to swim against the current. Malik says that he draws on the fearlessness he learned from his mentors to convey that sense of daring to his early career scientists while also providing honest feedback. “My mentor was super supportive, and he really wanted us to not be afraid of being wrong,” he says. “I’m trying very hard to do the same thing. I want people to recognize that science is not a zero-sum game, that it’s actually possible for you to be successful and yet be a really good colleague.”

The Edward Novitski Prize recognizes an extraordinary level of creativity and intellectual ingenuity in the solution of significant problems in genetics research. The prize honors solid, significant, scientific experimental work—either a single experimental accomplishment or a body of work.

Becoming the president of a world-class university isn’t something that typically happens “by accident,” but that’s exactly how Shirley Tilghman describes it. “I did not intend to be a university president,” Tilghman says. “I probably had the steepest learning curve of any university president ever.”

In 2000, Tilghman was serving as founding director of the Lewis-Sigler Institute for Integrative Genomics at Princeton University. When Princeton’s then-president, Harold Shapiro, announced his departure, Tilghman joined the search committee to ensure that the next president would support the new genomics initiative. “I was going to protect my turf,” she says.

“I was on that committee for about six months. At one point, I left the committee early to teach, and when I came to the next meeting, the chair said, ‘The committee would like you to step down and to become a candidate.’ I thought they were out of their minds,” she recalls. “I think I said to them, ‘I can’t leave you people alone for a minute!’”

Still, Tilghman gave the idea careful consideration. “I decided I had probably done the best science I was going to do by that point,” she recalls. Considering a possible next chapter, she began to get excited about “the opportunity to make an institution that [she] adored—Princeton—better.” In June 2001, she was sworn in as Princeton’s first female president.

Tilghman’s body of research had, indeed, already secured her place in genetics textbooks. In addition, she served as a key advisor to the Human Genome Project, helping to steer the initiative through the capricious winds of government funding and forever transforming the field of genetics. For her outstanding contributions, Tilghman has been awarded the 2022 George W. Beadle Award from the Genetics Society of America, which recognizes individuals who have made outstanding contributions to the community of genetics researchers beyond an exemplary research career.

Genomic imprinting

As a postdoc, Tilghman helped develop a method of cloning mammalian genes. She went on to characterize the mouse beta-globin gene, uncovering a great deal about gene structure and “intervening sequences,” now called introns, that interrupt coding regions. As a faculty member at Princeton in the early 1990s, Tilghman and members of her lab studied a gene called H19, which was very highly expressed in the mouse embryo. The first odd thing they discovered was that the gene contained no open reading frame, indicating it could not encode a protein. “There was no other long noncoding RNA at the time, this was the first,” Tilghman recalls. “At that point, I was given very good advice from many colleagues who said [to] drop it like a hot potato.”

However, tantalized by the high expression levels in the embryo, Tilghman couldn’t let H19 go. Work by Marisa Bartolomei, a postdoc in the lab at the time, showed that H19 was only expressed from the maternal chromosome. “That’s when the floodgates opened,” Tilghman recalls.

H19 was located next to another imprinted gene, IGF2, which was only expressed from the paternal chromosome. This pair of genes provided the first evidence of imprinted gene clusters. Tilghman’s lab produced a number of papers characterizing the promoters and enhancers that lay between the two genes and describing the molecular mechanisms involved in imprinting, including chromatin organization and methylation as a key regulator of expression. Bartolomei, who now heads her own lab at the Perelman School of Medicine at the University of Pennsylvania, recalls that era of rapid discovery. “It was insanely exciting,” she says. “Shirley is definitely one of the more creative people who worked in the imprinting field.”

Human Genome Project and beyond

As one of the founding members of the National Advisory Council of the Human Genome Project, Tilghman helped define the public effort in sequencing the human genome. She advocated for sequencing the genomes of various model organisms in addition to the human genome, a move that conferred two key advantages. First, it allowed for small, incremental victories to maintain high enthusiasm for the project and keep funding flowing over the long timeframe required. Second, it expanded interest in the project and the perception of benefit to a wider range of scientists beyond just the handful studying human genetics. “A genome enthusiast,” she once said, “is a genome critic who just got a hit in their organism’s sequence database.”

Tilghman was influential in setting a precedent for data accessibility, starting with the mouse genome, says Tamara Caspary of Emory University, who was a graduate student in Tilghman’s lab. “It was really important to her that those data be publicly available,” Caspary says. “She very clearly highlighted that it needed to be community-driven, in terms of selecting what strains to be sequenced.” By actively involving the genetics community, Tilghman helped sustain a wide enthusiasm for the genome sequencing efforts that carried the project to its ultimate successes. Similarly, as a trustee of the Jackson Laboratory, she strongly supported establishing the Mouse Genome Informatics database. “It’s tremendous,” Caspary says. “The well just gets deeper with the data you can mine out of that website. She made that data accessible worldwide.”

Tilghman has been equally influential on the personal side of science, advocating for reform in the biomedical research pipeline. As ever-increasing numbers of trainees vie for limited resources, it becomes harder for science students and postdocs to envision a viable path to a research career. Tilghman has worked to address what she sees as systemic flaws in the process, including perverse incentives in research funding, problems with the peer review system and obstacles to new investigators obtaining federal grants.

Through all these accomplishments, Tilghman has served as an important role model for a generation of women in science. “She was incredibly fearless in going from one thing to another,” Bartolomei says. “She led by example. The key is that not only is she smart, she’s creative, she gives great talks—she’s the complete package. She taught me how to be a woman in science.”

The George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers. GSA established the award in 1999 in honor of an outstanding scientist and a respected academic, administrator, and public servant—George W. Beadle (1903-1989).

Aspergillus fumigatus isolated from clinical settings is resistant to agricultural fungicides.

Infections have long been a deadly problem for hospital patients. Though modern medicine has an impressive array of antimicrobial drugs at its disposal, pathogens continue to evolve resistance, creating ever more dangerous infections as the microbial “arms race” escalates.

Overprescribing of antibiotics is one source of resistance, but there could be another culprit further afield. In a new publication in G3: Genes|Genomes|Genetics, fungal biologists Michelle Momany and Marin Brewer report their finding that some strains of a pathogenic fungus apparently acquired antifungal resistance in an agricultural setting rather than a clinical one. Genetic analysis revealed that strains of the fungus Aspergillus fumigatus that were resistant to antifungals used in people had also developed resistance to fungicides used only on plants.

Fungal infections endanger both plants and people

Momany and Brewer are part of the Fungal Biology Group at the University of Georgia, one of the largest fungal biology research groups in the world. Fungal diseases are a major problem both clinically and in agriculture, but doctors generally use different compounds to treat people than farmers use to treat crops. A class of antifungals known as azoles, however, is used in both people and plants. Many different azoles are currently available, and though they are considered “moderate” in terms of the risk of fungi developing resistance, azole-resistant strains of the fungus Aspergillus fumigatus have begun turning up more frequently in hospitals.

Unlike drug-resistant bacteria, which can spread from person to person, A. fumigatus is always picked up environmentally. There’s no documented case of anyone getting sick by breathing in Aspergillus exhaled by an infected patient, says Momany. Because of this, fungal researchers suspected A. fumigatus was evolving azole resistance in the field, rather than in patients. Still, there was no way to know for sure that it wasn’t caused by hospital drugs.

From “Big Chicken” to Big Tulip

“The idea came to me when I was reading the book Big Chicken by Maryn McKenna,” says Brewer. In the book, scientists showed that antibiotic-resistant bacteria had moved from chickens to humans – not the other way around – by showing that bacteria isolated from people contained genetic evidence of resistance to compounds used only in chickens. Brewer decided to apply that same logic to Aspergillus. “I thought it would be interesting to look for the signatures for resistance to fungicides only used in agricultural environments,” she says.

The researchers analyzed 700 different isolates of A. fumigatus collected from compost heaps, soil samples, and plant debris from 56 sites around Georgia and Florida. They sequenced and analyzed the genomes of 135 of these isolates. Most of the sites had a history of azole fungicide use, but two were organic sites with no fungicide use for 10 years. They also analyzed publicly available genome data of A. fumigatus samples from the US, the UK, the Netherlands, and India that were resistant to multiple azole compounds. 

They found that A. fumigatus in the environment that carried resistance to azole compounds had often developed resistance to two other classes of fungicides used only in agriculture, benzimidazoles (MBC) and quinone outside inhibitors (QoI). Even more tellingly, A. fumigatus samples collected from patients carried the genetic markers indicating resistance to MBC and QoI.

“Those signatures showed that they were exposed to fungicides in an agricultural environment, and we’re finding them in strains from patients in hospital environments,” says Brewer.

The first hint that agricultural fungicides might be a problem in hospitals came from the Netherlands, the world’s major supplier of tulips and other ornamental flowers. “It turns out a tulip bulb is a wonderful place for fungi to grow,” Momany says. “Nobody wants decorative flowers with mold spots on them. To prepare these for shipping, they’re treated with azoles.” Discarded plant matter from these industrial tulip farms, she says, can spread azoles into the surrounding environment. Strikingly, Momany points out, A. fumigatus isn’t even dangerous to plants. It’s not the intended target of agricultural azole use, but because it’s so widespread, it gets exposed incidentally. “Once those azoles are in the environment, then the A. fumigatus that’s there develops its own resistance,” she says.

People are likely to encounter azole-resistant A. fumigatus in compost or in flower beds. “Compost is definitely a hot spot for Aspergillus that’s azole resistant,” says Brewer. “People who are immunocompromised should be very careful around compost, flower beds, or dusty areas where there can be a lot of fungi.”

This study is one of the first to characterize a fungal pathogen that has picked up antifungal resistance in an agricultural setting and carried that resistance into the clinic. “There could be a lot of others, and people just haven’t looked,” Brewer says.

CITATION:

Evidence for the agricultural origin of resistance to multiple antimicrobials in Aspergillus fumigatus, a fungal pathogen of humans

S. Earl Kang, Leilani G. Sumabat, Tina Melie, Brandon Mangum, Michelle Momany, and Marin T. Brewer

G3: GENES|GENOMES|GENETICS February 2022, jkab427

https://doi.org/10.1093/g3journal/jkab427

Complex multicellular organisms have mastered the art of specialization; embryonic stem cells give rise to a multitude of different cell types that perform specific functions. Later, adult stem cells dedicated to specific tissues maintain and repair many organs in the body throughout life. Some specialized cell types, like skin, blood, lining of the intestine and colon, and sperm are continually replenished, each from their own dedicated adult stem cells. When such adult stem cells divide, they must not only spawn cells able to specialize into the correct cell type(s) but also produce new stem cells to maintain regenerative capacity.

Margaret “Minx” Fuller studies how male germ cells balance self-renewal versus differentiation to both maintain the stem cell population and continually produce sperm cells. Her research has helped uncover chemical signaling pathways and cellular mechanisms that underlie this process. By studying male germ cells within the context of their cellular neighborhood, Fuller showed that signals coming from surrounding cells coordinate with behavior of cytoskeleton components to induce the stem cells to divide asymmetrically. Studying how stem cells replicate and retain their ability to generate specialized cells could have important implications in cancer research as well as regenerative medicine.

For her achievements, Fuller has been awarded the 2022 Genetics Society of America Medal, which recognizes outstanding contributions in the field of genetics in the last 15 years.

“I don’t see many people who so seamlessly go back and forth between understanding of genetics and cell biology and developmental biology,” says Yukiko Yamashita, a Howard Hughes Medical Institute Investigator at MIT and former postdoc in Fuller’s lab. “Always there is clarity in her thinking, and that is her real contribution—that’s why so many people followed to adopt this model system.”

From physics to “APOG”

As an undergraduate, Fuller started out studying physics, but summer research in a biology laboratory changed her direction. “Maybe naively, I thought in physics you need a big machine between you and your questions—a neutrino detector or a synchrotron or whatever,” she says. A sophomore year biology class with laboratory revealed to her many fascinating unanswered questions, and her experiences at the bench the following summer sealed the bill. “I got hooked by the fact that in laboratory biology, you can ask and answer questions with your mind, some test tubes, and a water bath,” she says.

After graduation, she studied microbiology at MIT, where she worked on the protein-protein interactions that regulate virus capsid assembly. “The thing that was drilled into us was ‘APOG’—the awesome power of genetics,” Fuller recalls. Coming from physics, she was fascinated by how cells change shape and how protein-based machines build structures inside the cell. Researching what to study next for her postdoc, Fuller attended a conference on the cytoskeleton, where she was startled to discover that in the entire conference only two presentations, both posters, used genetics. “So I said, aha! This field needs genetics,” Fuller recalls. “I’m going to go do genetics on the cytoskeleton.”

During her postdoc at Indiana University, she studied proteins that interact with and regulate the microtubule cytoskeleton in spermatocytes, the cells that give rise to sperm cells. Working with mutants that effect spermatogenesis, Fuller realized that here was a perfect system to apply forward genetic strategies to investigate the questions that had caught her interest as an undergraduate and postdoc: How do cells change shape?  How does the developmental program add layers of regulation on fundamental cellular processes like cell division, transcription and mRNA processing to specify specialized cell types. When she set up her own lab, Fuller shifted to studying spermatogenesis, the process by which stem cells give rise to specialized sperm cells, in its own right. While a lot of labs were working on oogenesis and embryonic development, only a few at the time were studying spermatogenesis.

“She realized the overarching fundamental principles you could learn from studying a tissue where there are stem cells present that continue to divide throughout the whole adult lifespan,” says Julie Brill of the Hospital for Sick Children and University of Toronto, another of Fuller’s former postdocs. “She wasn’t the only one to develop the testis as a model, but Minx is just such a fabulous speaker that she also really brought people into the system.” As an example, Brill says, Fuller organized a “testis workshop” during the Annual Drosophila Research Conference, which helped create a community among researchers who might otherwise see themselves as competitors. “We all met each other and learned what everybody else was doing,” Brill says. “She’s so good at organizing and inspiring others around her.”

Pre-programmed versus environmental

Fuller’s work shed light on the question of whether the daughter cell fates were determined by pre-programming within the stem cell or by chemical signals coming from the “niche,” the environment outside the cell. “One of the major ideas in the field was that there was a niche, a local microenvironment that instructed the stem cells to maintain stem cell identity,” she says. This idea hadn’t been proven, because the standard procedure at the time was to isolate, sort, and transplant cells before evaluating their stem cell potential. “Well, you can’t study the role of the microenvironment if the first thing you do is take the cells out!” Fuller says. “I realized, I have a great system in my hands in my lab for studying the role of the microenvironment in stem cell biology, right here in the fly testis.”

In addition to signals from the microenvironment, Fuller’s work showed that stem cells also have internal mechanisms that bring about asymmetric cell division. The centriole is a microtubule-based structure that organizes the mitotic spindle, and when the cell divides, the two centrioles migrate to opposite poles. By marking the oldest centriole, Yamashita while in Fuller’s lab discovered that the older centriole stays anchored in the stem cell, while the cell that inherits the younger centriole goes on to become differentiated. “This whole mechanism of orienting the spindle and asymmetric division—I think that has been most impactful outside my immediate field,” Fuller says. Now, people studying other types of adult stem cells also look for whether or not the cells undergo asymmetric division, she says, partly inspired by the observations from the testis. Moving down the differentiation lineage, Fuller’s laboratory is now focusing on uncovering the mechanisms that regulate the switch from precursor cell proliferation to turning on expression of the correct cell type specific gene expression program.

Most recently, Fuller contributed to the Fly Cell Atlas project, an ambitious effort to catalog the gene expression profiles of all the cells in Drosophila. “It was during COVID, so we had a big Zoom jamboree of maybe 12 labs that contributed to that paper,” Fuller says. “It’s been a vehicle for open communication among labs that could have been competing, but we’re collaborating and it’s just so much fun.”

Over the years, Fuller says she has gotten great joy from seeing all the projects her trainees have been able to take with them when they leave to start their own labs. “The most gratifying thing to me is that a group of my former postdocs and students got together and wrote a nomination letter,” Fuller says. “I think my most important contribution to science has been all these fantastic people who are now doing their own science.”

The Genetics Society of America Medal honors an individual member of the Society for outstanding contributions to the field of genetics in the last 15 years. GSA established the Medal in 1981 to recognize members who exemplify the ingenuity of the GSA membership through elegant and highly meaningful contributions to modern genetics.

Efforts to diversify an inbred population must take into account the genetic backgrounds of the founders.

The nocturnal flightless parrot known as the kākāpō was once abundant throughout New Zealand. But after the introduction of mammalian predators, the species all but disappeared. Today, every living kākāpō is descended from a tiny handful of island survivors and a single male from the mainland. The entire population of 201 birds is closely watched over by conservationists on a few predator-free island refuges, where they hope the hefty green parrots will continue to breed.

But because their numbers dropped into the double digits, the kākāpō face a genetic bottleneck. Inbreeding can increase rates of genetic disease and contribute to poor health among the population. Geneticists studying the remaining kākāpō have quantified the amount of inbreeding among the birds as one way to understand the health of the species. Their results, reported in a new paper in G3: Genes|Genomes|Genetics, suggest that inbreeding isn’t necessarily hurting chicks’ chances of survival and that introducing additional genetic diversity may not always have the intended effect.

Saved from extinction

“Kākāpō have a really interesting natural history,” says Yasmin Foster, a graduate student at the University of Otago and the study’s lead author. “They were functionally extinct, but then a small population was found on an island in the south of New Zealand.”

“Functionally extinct” in this case meant no more females could be found on the New Zealand mainland; only a few males remained. In 1977, about 50 kākāpō were discovered living on Stewart Island, a large island about 19 miles south of the mainland. Predators such as feral cats roamed Stewart Island, however, so in 1982 conservationists began relocating the birds to several smaller, mammal-free outlying islands.

By then, only one male kākāpō remained on the mainland, and he was taken to a predator-free island refuge along with the Stewart Island population. The Stewart Island kākāpō had diverged from the mainland population around 10,000 years ago, giving the two groups time to develop distinct genetic profiles. Introducing the mainland bird was meant to help boost genetic diversity among a new generation of chicks.

Now, the population has grown to 201 individuals. To help inform conservation strategies, Foster and her colleagues set out to document the amount of inbreeding in the colony. Creating a large, multigenerational pedigree of the wild kākāpō wouldn’t work for a founder population of this type, so the researchers turned to DNA sequence analysis. Thanks to the availability of a high-quality kākāpō reference genome, the team could genotype the birds using genome-wide mapping of single nucleotide polymorphisms (SNPs).

Comparing measures of inbreeding

“We had this unique founding population with 50 Stewart Island birds and one mainland male,” says Foster. “From the inbreeding metrics I looked at, we found that they’re both inbred, but in different ways.” She says the study raises an interesting point about how combining two inbred populations in an attempt to increase genetic diversity can actually introduce more deleterious alleles.

Comparing multiple inbreeding metrics helped Foster get a robust view of the birds’ genome, and also to evaluate the accuracy of each one. “Some people just use one or another, but what I found was that some of them give a different story,” she says.

She started by calculating the coefficient of inbreeding, or F_H, which is the probability of an individual inheriting two copies of the same allele from the same ancestor on both sides. She compared this with a newer method of measurement, called “runs of homozygosity” or F_ROH, which looks for long sections of the genome where both copies are the same.

A third method, using pairwise analysis to construct a genomic-relatedness matrix, turned out to be the weakest of the metrics, Foster says. “Other people have found that when you have a small group of individuals that are a lot different to the larger group, they skew the outcome maybe a bit too much,” she says. “Their genetic information is more rare, and the way the maths compute this inbreeding metric, it gives more power to those rare alleles.”

‘Hybrid vigor’ – or not

In addition, they compared levels of inbreeding with survival in chicks. When the mainland male was added to the Stewart Island population, the expectation was that he would infuse genetic diversity into a new generation of chicks, boosting their health. But that turned out not to be the case: decreased inbreeding did not correspond to improved survival, partly because the less-inbred chicks had unexpectedly high levels of mortality.

“That was probably down to the mainland individuals also being reduced to a small population for a long period of time,” says Foster. The mainland male apparently brought in quite a few detrimental mutations that had been lost from the island population over the years.

The inbreeding study and others like it could help guide conservation strategies moving forward. Kākāpō have a lek mating system, which means that the males all congregate and compete to entice the females. The most popular male will produce the most offspring, and this can tighten the genetic bottleneck even more.

“One male kākāpō had fathered 22 chicks, which is really significant when there’s only 200 left,” says Foster. “Obviously his genetic material spread across the population. He was so successful, we had to translocate him to another island to give some of the other males a chance.”

CITATION

Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō

Yasmin Foster, Ludovic Dutoit, Stefanie Grosser, Nicolas Dussex, Brodie J. Foster, Ken G. Dodds, Rudiger Brauning, Tracey Van Stijn, Fiona Robertson, John C. McEwan, Jeanne M. E. Jacobs, and Bruce C. Robertson

G3 Genes|Genomes|Genetics 2021; jkab307

https://doi.org/10.1093/g3journal/jkab307

Yeast screens explore the therapeutic potential of chemical rescue.

Anyone who’s worked in a lab knows that sinking feeling of discovering that the temperature of an incubator, carefully set the night before, has crept up high enough to ruin the experiment. While such a mishap usually spells disaster, occasionally, it can lead to an unexpected discovery.

One such revelation was prompted by an uncooperative incubator in the lab of Michael McMurray, a cell biologist at University of Colorado’s Anschutz Medical Campus. McMurray studies the septin family of cytoskeletal proteins, and inside the incubator were plates of yeast with temperature-sensitive septin mutations. The mutant yeast could survive only at mild temperatures, so the incubator was set to a comfortable 27°C.

For this experiment, a chemical called guanidine hydrochloride had been added to some of the plates, to test whether it would stop the mutants from growing at the permissive temperature. When the incubator was found roasting away at more than 30°C, however, all of the yeast should have been dead.

“Amazingly, one of the mutants actually grew,” says McMurray. “The guanidine restored its viability.”

That discovery launched an investigation of how, exactly, guanidine had protected the mutant from normally lethal conditions. In a paper in the September issue of G3: Genes|Genomes|Genetics, Hassell et al. report several mutants that can be rescued by guanidine. They also show that another naturally occurring small molecule can correct an even broader range of mutants.

Guanidine can stand in for a lost arginine

Guanidine’s molecular structure mimics the side chain of the amino acid arginine. Researchers had previously shown that guanidine could restore function to an enzyme that had been mutated to lack an arginine in its active site. But all of this work had been done in vitro. This piqued McMurray’s interest even more. “Arginine is the most commonly mutated amino acid in human disease,” he says. “If guanidine can restore function to arginine mutant proteins, why has no one explored this in living cells?”

McMurray’s team began by testing enzymes in which a single arginine mutation disabled the enzyme enough to cause disease, such as ornithine transcarbamylase (OTC). OTC deficiency is an inherited metabolic disease that leads to a buildup of toxic ammonia in the body. The researchers created yeast with the same OTC arginine mutation that causes the human disease, making the yeast unable to grow without nutritional supplementation. Adding guanidine hydrochloride to the growth media restored some of the lost enzyme function.

“The effect was pretty small,” McMurray says. “It wasn’t a full rescue, but it was something.”

Next, the researchers decided to broaden their investigation. Instead of testing candidate enzymes, they screened hundreds of yeast mutants to see if guanidine restored function to any of them. “We decided to let the cells tell us what would work best,” McMurray says. “That’s when things started to get interesting.”

The screen uncovered 11 new candidates, the most interesting of which was an arginine mutant of actin, another cytoskeletal protein. “It just so happens that arginine is also mutated in human cardiac beta actin, and that mutation causes disease,” McMurray says.

As an ATPase, actin is technically an enzyme, but the arginine mutation is far from the active site, and guanidine isn’t restoring catalytic activity per se. Instead, McMurray says, it’s helping the protein fold into its proper 3D shape. “All proteins have to fold,” McMurray says. Protein folding results from chemical interactions between the side chains of various amino acids. “To rescue the mutant, the guanidine just has to be able to fix what’s missing and restore the folding.”

The idea of rescuing mutants by restoring proper protein folding led them to investigate other chemicals that can influence protein folding. “From a biological perspective, what are other cases in nature in which organisms have to deal with alterations in protein folding?” McMurray says. “Then we thought of sea creatures — sharks and rays.”

Moving beyond guanidine

Because they live in saltwater, sharks maintain high concentrations of urea in their bodies to keep from losing water through osmosis. Urea, however, is toxic to proteins, and causes them to unfold. To counteract the urea, these animals also have high levels of a chemical called trimethylamine oxide (TMAO), which promotes protein folding.

Does the shark’s protein protection trick work in other contexts? To follow up, research assistant Daniel Hassell screened yeast mutants using TMAO. He turned up hundreds of mutants that were rescued by the molecule. The genes and mutant types were all very different from each other, suggesting that TMAO has a more general stabilizing effect rather than specifically replacing a particular amino acid. This broad effect suggests a potential role for the molecule in synthetic biology, as a way to design proteins with an on/off switch system.

For its part, guanidine is already FDA-approved as a treatment for an inherited autoimmune disorder called Lambert-Eaton myasthenic syndrome. McMurray remains curious about whether it has the potential to treat other genetic diseases.

“That would be my ultimate hope, that someone would be inspired by our work to try it in an animal model or the clinic,” McMurray says.

CITATION

Chemical rescue of mutant proteins in living Saccharomyces cerevisiae cells by naturally occurring small molecules
Daniel S Hassell, Marc G Steingeisser, Ashley S Denney, Courtney R Johnson, Michael A McMurray
G3 Genes|Genomes|Genetics 2021; jkab252
https://doi.org/10.1093/g3journal/jkab252

Discovery of thiabendazole target explains vascular disrupting action.

Even after hundreds of millions of years of evolution, some yeast genes persist mostly intact in humans and other vertebrates. Despite the huge differences between yeast and humans, these genes perform the same molecular function in both organisms but have been adapted over time into new contexts. Learning about these evolutionarily enduring genes can provide important insight into complex systems in large organisms.

About a decade ago, researchers led by molecular biologist Edward Marcotte and John Wallingford of the University of Texas at Austin discovered that a medication used to treat fungal infections and ringworm could also stop new blood vessel formation in vertebrates. The drug, called thiabendazole (TBZ), would even cause recently formed blood vessels to break apart and dissolve. Although TBZ had been in clinical use for decades, nobody knew exactly how the drug worked at the molecular level.

Now, in a new paper in GENETICS, Marcotte and colleagues have identified the molecular target of TBZ’s blood vessel-disrupting action. It’s called beta-tubulin 8, or TUBB8, a structural protein that helps provide the cell’s skeletal system. The discovery explains why TBZ kills fungi but not vertebrates.

Studying human genes in yeast

The story began with the realization that certain interacting networks of genes needed for survival in single-celled organisms like yeast had survived billions of years of evolution and remained active in vertebrates, including humans. 

“They’re inherited intact as a system,” Marcotte explains. As new organisms emerged through evolutionary processes, they developed different body plans and ecological niches. During these changes, many gene networks continued working together, but were recruited to different systems in different organisms. 

“In yeast, they get wired up to do one thing, and ultimately in the vertebrate lineage they get wired up to do something else,” Marcotte says. “That’s the kind of process we’re talking about.”

Studying these networks revealed that a set of genes that keep the yeast cell wall intact also help blood vessels grow properly in vertebrates. This led to the discovery that TBZ could stop blood vessel formation.

“That discovery got us really intrigued about the extent that human and yeast genes were still doing the same thing,” says Marcotte. “Questions like that made us wonder how much yeast and human genes were still equivalent.”

To study the questions, the researchers created strains of yeast in which they substituted the original yeast gene with its human counterpart. In cases where the human gene adequately sufficed for the lost yeast gene, the “humanized” strain of yeast became a valuable research tool. They successfully created several hundred of these strains.

“What’s great about yeast is that we can study human genes in a simplified context,” says Riddhiman Garge, the paper’s co-first author, who is now a postdoctoral fellow at the University of Washington and performed the work collaboratively with researcher Hye Ji Cha.

Tracing the tubulin family tree

TBZ, they knew, killed yeast by disrupting a structural protein called beta-tubulin. While yeast have one beta-tubulin gene, humans have accumulated nine versions of the gene, and two of them can substitute for the yeast gene. 

“We used molecular modeling to build models of the yeast beta-tubulin and the various beta-tubulins in humans,” Marcotte says. Using these computer models, they simulated interactions between TBZ and each tubulin.

“Out of the nine beta-tubulins, only one looked like it would actually be responsive to the drug,” says Marcotte. 

Over the course of evolution, the one beta-tubulin ancestral gene had been copied and changed until humans had 9 beta-tubulins. Eight of them contain naturally occurring mutations that confer resistance to TBZ. The one that doesn’t, TUBB8, is expressed in blood vessels.

“Thiabendazole doesn’t kill humans, like it does fungus and nematodes, because most human cells have resistant forms of tubulin,” Marcotte says. “It’s known to have a very good safety profile over the decades of use. This result explains why that’s the case, but also explains why it turns out to be active in just a particular tissue in human.”

Potentially, TBZ could be used to treat diseases in which abnormal blood vessel growth is a problem, such as hemangiomas, which are bright red rubbery lumps on the skin made up of excess blood vessels that grow in a cluster. Cancers also tend to spur new blood vessel formation to feed the energy needs of a fast-growing tumor.

Libraries of yeast strains containing human genes can also be used to identify other genetic interactions, or screen for other drugs that have tissue-specific functions in humans.

“I truly believe this is just scratching the surface,” says Garge. “I would love to see more of the community leverage such systems-wide comparisons to gain insights into human health.”

CITATION

Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast

Riddhiman K Garge,  Hye Ji Cha,  Chanjae Lee,  Jimmy D Gollihar,  Aashiq H Kachroo, John B Wallingford,  Edward M Marcotte

GENETICS 2021, iyab101, https://doi.org/10.1093/genetics/iyab101