Breaking ammonia: A new catalyst to generate hydrogen from ammonia at low temperatures

Peer-Reviewed Publication

TOKYO INSTITUTE OF TECHNOLOGY

 

IMAGE: - view more 

CREDIT: TOKYO TECH

The current global climate emergency and our rapidly receding energy resources have people looking out for cleaner alternatives like hydrogen fuel. When burnt in the presence of oxygen, hydrogen gas generates huge amounts of energy but none of the harmful greenhouse gases, unlike fossil fuels. Unfortunately, most of the hydrogen fuel produced today comes from natural gas or fossil fuels, which ultimately increases its carbon footprint.

Ammonia (NH3), a carbon-neutral hydrogen compound has recently garnered a lot of attention owing to its high energy density and high hydrogen storage capacity. It can be decomposed to release nitrogen and hydrogen gases. Ammonia can be easily liquified, stored, and transported, and converted into hydrogen fuel when required. However, the production of hydrogen from ammonia is a slow reaction with very high energy demands. To speed up production, metal catalysts are often used, which help reduce the overall energy consumption during hydrogen production as well.

Recent studies have found that Nickel (Ni) is a promising catalyst for splitting ammonia. Ammonia gets adsorbed on the surface of Ni catalysts, following which the bonds between nitrogen and hydrogen in ammonia are broken and they are released as individual gases. However, obtaining a good conversion of ammonia using a Ni catalyst often involves very high operating temperatures.

In a recent study published in ACS Catalysis, a team of researchers from Tokyo Tech led by Associate Professor Masaaki Kitano described a solution to overcome the issues faced by Ni-based catalysts. They developed a state-of-the-art calcium imide (CaNH)-supported Ni-catalyst that can achieve good ammonia conversion at lower operating temperatures. Dr. Kitano explains, “Our aim was to develop a highly active catalyst that would be energy efficient. Our addition of the metal imide to the catalyst system not only improved its catalytic activity but also helped us unravel the elusive working mechanism of such systems.”

The team discovered that the presence of CaNH resulted in the formation of NH2- vacancies (VNH) on the surface of the catalyst. These active species resulted in the improved catalytic performance of the Ni/CaNH at reaction temperatures that were 100°C lower than those necessary for the functioning of Ni-based catalysts. The researchers also developed computational models and conducted isotope-labeling to understand what is happening on the catalyst surface. The calculations proposed a Mars−van Krevelen mechanism that involved adsorption of ammonia onto the CaNH surface, its activation at the NH2- vacancy sites, formation of nitrogen and hydrogen gas, and finally regeneration of vacancy sites promoted by Ni nanoparticles.

The highly active and durable Ni/CaNH catalyst can be successfully deployed for the generation of hydrogen gas from ammonia. Also, the insight into the mechanism of catalysis provided by this study can be utilized to develop a new generation of catalysts. “As the whole world is working together to build a sustainable future, our research is aimed at resolving the hiccups faced on our way to a cleaner hydrogen fuel economy,” concludes Dr. Kitano.

This is a ray of hope for the world’s low carbon-emission mission!

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JOURNAL

ACS Catalysis

DOI

10.1021/acscatal.1c01934 

METHOD OF RESEARCH

Experimental study

ARTICLE TITLE

Ammonia Decomposition over CaNH-Supported Ni Catalysts via an NH2−-Vacancy-Mediated Mars−van Krevelen Mechanism

ARTICLE PUBLICATION DATE

18-Aug-2021

Research reveals location and intensity of global threats to biodiversity

Peer-Reviewed Publication

INTERNATIONAL INSTITUTE FOR APPLIED SYSTEMS ANALYSIS

 

IMAGE: PROBABILITY OF IMPACT FOR MAMMALS view more 

CREDIT: HARFOOT ET AL., (2021) USING THE IUCN RED LIST TO MAP THREATS TO TERRESTRIAL VERTEBRATES AT GLOBAL SCALE, NATURE ECOLOGY AND EVOLUTION. HTTPS://DOI.ORG/10.1038/S41559-021- 01542-9

Using a novel modelling approach, new research published today in Nature Ecology and Evolution reveals the location and intensity of key threats to biodiversity on land and identifies priority areas across the world to help inform conservation decision making at national and local levels.

A team of leading researchers have produced global maps for the six main threats affecting terrestrial amphibians, birds and mammals: agriculture, hunting and trapping, logging, pollution, invasive species, and climate change. Results show that agriculture and logging are pervasive in the tropics and that hunting and trapping is the most geographically widespread threat to mammals and birds. There are sizeable continental areas in which there is more than a 50% chance that any particular amphibian, mammal or bird species is threatened by logging, hunting and trapping, agriculture, invasive species or climate change.

The world is facing a global nature crisis, yet information about the location and intensity of the threats responsible for biodiversity loss remains limited. Information on the spatial intensity of threats and how they affect species on the ground is critically important to improving and targeting conservation responses. This study presents both a first attempt to map this information and a research track to improve our understanding of how threats to biodiversity vary across the world.

Using the IUCN Red List to map threats to terrestrial vertebrates on a global scale identifies the most prevalent threat for each taxa. It finds that agriculture is the greatest threat to amphibians, being the most prevalent threat to these species across 44% of global lands. For birds and mammals, hunting and trapping is most prevalent, ranking as the highest threat across 50% of land for birds and 73% of land for mammals. Agriculture is the most prevalent threat for amphibians, mammals, and birds combined.

The research also identifies locations where threats are particularly prevalent. In Southeast Asia, particularly the islands of Sumatra and Borneo, as well as Madagascar, there is a high risk of impact from all six threats to amphibians, birds, and mammals. For amphibians, Europe stood out as a region of high threat impact due to a combination of agriculture, invasive species and pollution. Polar regions, the east coast of Australia and South Africa are mostly likely to be impacted by climate change, affecting birds in particular.

Dr. Mike Harfoot, one of the two lead authors of the paper, UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), says: “We are facing a global nature crisis, and the next ten years is a crucial window for taking decisive action to tackle biodiversity loss. Our results reveal the location and intensity of human-caused threats to nature. This information can support decision-makers at a range of levels in identifying where action to reduce these threats could yield the best results for people and planet. With further work, we will improve this information in terms of accuracy and the breadth of nature considered.”

To help guide conservation action, the authors also combined threat impact data with spatial information on biodiversity importance to create conservation risk maps that identify high priority areas for threat mitigation. These maps are one tool that can support and inform decision-making on national and other levels as appropriate. The areas identified include the Himalayas, Southeast Asia, the east coast of Australia, the dry forest of Madagascar, the Albertine Rift and East Arc Mountains in eastern Africa, the Guinean forests of West Africa, the Atlantic Forest, the Amazon basin and the Northern Andes into Panama and Costa Rica in South and Central America.

Dr. Jonas Geldmann, Assistant Professor, Center for Macroecology, Evolution and Climate, University of Copenhagen, and co-lead author of this paper says: “These maps also reveal that priority areas for one threat rarely overlap with that of other threats, meaning that to effectively respond to the current human impact on biodiversity we need a global response.”

Dr. Piero Visconti, a study co-author who leads the Biodiversity, Ecology, and Conservation Research Group at IIASA, says: "Despite ubiquitous sensors and advanced technology, we still know so little

about  the exact location and intensity of some of the most important threats to species such as hunting and trapping and the presence of invasive species. On-the-ground surveys are irreplaceable to have an accurate local picture of the distribution and impacts of these threats, but they are challenging and resource-intensive, therefore difficult to do at the scale at which some conservation decisions are made. This analysis is an important first step that can help efficiently direct local assessments of specific threats to terrestrial biodiversity, and start identifying the most appropriate local solutions."

In 2022, the Conference of the Parties to the UN Convention on Biological Diversity will meet in Kunming, China, and is expected to adopt a post-2020 global biodiversity framework, a new global plan for nature. The research released today helps to demonstrate the various types and geographic breadth of the threats to terrestrial species, and so the scale of the challenge for transformation that the framework must deliver if we are to conserve life on Earth.

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Contacts:

Researcher contact

Piero Visconti
Research Group Leader
Biodiversity, Ecology, and Conservation Research Group
IIASA Biodiversity and natural Resources Program
visconti@iiasa.ac.at

About IIASA:

The International Institute for Applied Systems Analysis (IIASA) is an international scientific institute that conducts research into the critical issues of global environmental, economic, technological, and social change that we face in the twenty-first century. Our findings provide valuable options to policymakers to shape the future of our changing world. IIASA is independent and funded by prestigious research funding agencies in Africa, the Americas, Asia, and Europe. www.iiasa.ac.at

About UNEP-WCMC:

The UN Environment Programme World Conservation Monitoring Centre is a world leader in biodiversity knowledge. It works with scientists and policymakers worldwide to place biodiversity at the heart of environment and development decision-making to enable enlightened choices for people and the planet. https://www.unep-wcmc.org/

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JOURNAL

Nature Ecology & Evolution

DOI

10.1038/s41559-021-01542-9 

ARTICLE TITLE

Using the IUCN Red List to map threats to terrestrial vertebrates on a global scale

ARTICLE PUBLICATION DATE

29-Aug-2021

Tracking genetically modified animals

New CSI-like methods for detecting artificial transgenes

Peer-Reviewed Publication

MCGILL UNIVERSITY

 

IMAGE: GLOFISH TETRNECTIA GENETICALLY MODIFIED FISH. view more 

CREDIT: CHARLES XU

McGill University researchers have discovered a new way to track genetically modified animals using the artificial transgenes they leave behind in the environment. The discovery provides a powerful new tool to locate and manage genetically modified animals that have escaped or been released into the wild.

The magic of eDNA

In a study published in PLOS ONE, the researchers show for the first time that artificial transgenes from a variety of genetically modified animals like fruit flies, mice, and tetra fish can be detected and sequenced from the DNA left behind in soil, water, and in the form of feces, urine, or saliva. These findings could be used, for example, to detect the transgenes of genetically modified mosquitoes from pools of standing water in areas where they were recently released.

Compared to traditional animal monitoring methods, environmental DNA (eDNA) has proven to be more accurate and efficient, requiring less time and lower costs.

“Until now no one had applied these environmental DNA methods to genetically modified animals, even though they are already in the wild,” says Charles Xu, a PhD student in Department of Biology at McGill University. “Detection of animal transgenes from eDNA can be very useful because it can tell you whether genetically modified animals are there without the need to find them.”

An explosion of genetically modified animals

Advances in genome-editing technologies like CRISPR have dramatically simplified the process of creating genetically modified organisms, leading to an explosion in the number and types of genetically modified animals being produced around the world. With them come concerns about the ecological, evolutionary, and bioethical implications of these new creatures. Some genetically modified animals, like glowing aquarium fish, can be purchased by the public, while others, like mosquitos, have been released into the wild. The creatures carry artificial transgenes, or genes that have either been altered by scientists or introduced from another species by artificial means.

“Because genetically modified animals are often indistinguishable from their natural counterparts based on appearance alone, environmental DNA or eDNA methods could be especially useful for early detection and monitoring purposes,” he adds. “That is especially true in cases where these animals may escape from the lab or the farm, move to places they don’t belong, or crossbreed with natural animals.”

In the future, labs, companies, and governments involved in producing and managing genetically modified animals will be able to use eDNA methods to detect and track them in real-life contexts.

CAPTION

Researchers have discovered a new way to track genetically modified animals using the artificial transgenes they leave behind in the environment.

CREDIT

About this study

“Transgenes of genetically modified animals detected non-invasively via environmental DNA” by Charles C.Y. Xu, Claire Ramsay, Mitra Cowan, Mehmoush Dehghani, Paul Lasko, and Rowan D.H. Barrett was published in PLOS ONE. The research was supported by Natural Science and Engineering Research Council, Discovery Grant Canada, Canada Research Chair, Vanier Canada Graduate Scholarship, Quebec Fonds de recherche du Quebec – Nature et technologies.

DOI: https://doi.org/10.1371/journal.pone.0249439

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JOURNAL

PLoS ONE

DOI

10.1371/journal.pone.0249439 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Transgenes of genetically modified animals detected non-invasively via environmental DNA

ARTICLE PUBLICATION DATE

26-Aug-2021

Companion dogs may be a key to solving dementia

The data support that cognitive dysfunction in dogs models several key aspects of human dementia

Peer-Reviewed Publication

EÖTVÖS LORÁND UNIVERSITY (ELTE), FACULTY OF SCIENCE

 

IMAGE: NEW RESEARCH MEASURED AN ALZHEIMER’S DISEASE-ASSOCIATED PEPTIDE (AΒ42) IN COMPANION DOG BRAINS AND FOUND THAT HIGHER ABUNDANCE IS ASSOCIATED WITH INCREASED COGNITIVE DECLINE. (EÖTVÖS LORÁND UNIVERSITY) view more 

CREDIT: PHOTO: KUBINYI

New research measured an Alzheimer’s disease-associated peptide (Aβ42) in companion dog brains and found that higher abundance is associated with increased cognitive decline. The data support that cognitive dysfunction in dogs models several key aspects of human dementia, underscoring the suitability and usefulness of companion dogs as an animal model for aging studies.

Dementia is an umbrella term for loss of memory and ability to learn, deterioration in thinking, behaviour, and the ability to carry out daily tasks. The chance of getting dementia rises as one gets older: In general, 5-8% of people over 60 are thought to have some degree of dementia. The most common cause of dementia is Alzheimer’s Disease, for which unfortunately no cure exists yet. One main limitation in Alzheimer’s research is the lack of useful animal models that develop dementia spontaneously, without genetic engineering, and also adequately reflect the genetic and environmental complexity of humans. Companion dogs recently emerged as exciting new models for human aging because they share the human environment, they are exposed to similar risk factors, they age roughly ten times faster than humans, and a subset of dogs spontaneously develop canine dementia in old age. “When an old dog shows decreased ability to learn, increased anxiety, loss of normal sleep patterns, and aimless wandering, he may be struggling with Canine Cognitive Dysfunction,” said Silvan Urfer, a veterinarian and researcher at the University of Washington, who is the first author of the study published in GeroScience. “It can be reliably diagnosed using a validated questionnaire that assesses the dog’s cognitive function. Scores of 50 points and above are indicative of a diagnosis of cognitive dysfunction.”

Molecular features of Alzheimer’s disease in humans include the deposition of a peptide in the brain, called amyloid beta 42 (Aβ42). The canine Aβ42 peptide is identical to the human form. “We were interested in whether Aβ42 levels in companion dog brains are linked to cognitive function and age. In collaboration with Martin Darvas, our laboratory developed a new assay to measure Aβ42 in primate and canine brains and cerebrospinal fluid (CSF), but we did not yet have access to enough samples” said Matt Kaeberlein, one of the founders of the Dog Aging Project. This is where Urfer and Kaeberlein turned to Eniko Kubinyi, who has established the Canine Brain and Tissue Bank together with Kalman Czeibert, veterinarian, and Sara Sandor, geneticist, at the Department of Ethology, ELTE in Budapest. “We developed a unique pet dog body donation protocol for owners who, in agreement with their veterinarians, voluntarily offer their dog’s body for research after medically reasoned euthanasia.” said Kubinyi. The Hungarian researchers collect the brain and cerebrospinal fluid of the deceased subjects, together with thorough documentation of the dogs’ previous cognitive performance. This system allowed the team to correlate the post-mortem histological and molecular data with the behavioural measurements. They found significant positive correlations between Aβ42 and age in all three investigated brain regions (prefrontal cortex, temporal cortex, hippocampus/entorhinal cortex) while Aβ42 in the cerebrospinal fluid negatively correlated with age. Brain Aβ42 abundance in all three brain regions was also correlated with the Canine Cognitive Dysfunction Scale score. The relationship between cognitive impairment and Aβ42 abundance may mirror a similar trajectory in the aging dog, as in humans. It is well established that Aβ42 and other Alzheimer’s disease-related pathologies emerge in the brain years or even decades before clinical symptoms manifest. 

CAPTION

Dogs can help study human dementia

CREDIT

Photo: Kubinyi / Eötvös Loránd University

Both the Dog Aging Project and the Senior Family Dog Project aim to leverage privately owned companion dogs as models for aging and age-related disease in humans. Companion dogs living with their owners capture the genetic and environmental diversity that is impossible to recapitulate in laboratory animals.  To investigate aging in dogs, an important aspect is the availability of biospecimens from various organs for research, which should also include clinical and demographic information for these animals. Both the existing Canine Brain and Tissue Bank (CBTB) at ELTE and the Dog Aging Project Biobank at Cornell University address this emerging need by allowing citizen scientist owners to donate their dog’s body at the time of its natural end of life. These resources will be useful to conduct larger-scale studies in the future as more specimens become available.

The correlation between Aβ42 in dog brains and the cognitive scores supports the suitability of the companion dog as a model for Alzheimer’s disease. Besides, it illustrates the utility of veterinary biobanking to make biospecimens available to researchers for analysis. In the future, dogs could be used to study interventions aimed at preventing or treating Alzheimer-like pathology. Such research can also contribute to increasing the healthy lifespan of our pets.

  

CAPTION

Dogs can help study human dementia

CREDIT

Photo: Kubinyi / Eötvös Loránd University

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JOURNAL

GeroScience

DOI

/10.1007/s11357-021-00422-1 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animal tissue samples

ARTICLE TITLE

Canine Cognitive Dysfunction (CCD) scores correlate with amyloid beta 42 levels in dog brain tissue

ARTICLE PUBLICATION DATE

19-Aug-2021

 

High cod catches could have been sustained in Eastern Canada for decades, simple stock assessment method shows

Peer-Reviewed Publication

UNIVERSITY OF BRITISH COLUMBIA

A simple fish stock assessment model applied to over 500 years of catch data demonstrated that if Canadian authorities had allowed for the rebuilding of northern Atlantic cod stock off Newfoundland and Labrador in the 1980s, annual catches of about 200,000 tonnes could have been sustained.

A new study by researchers from the Sea Around Us initiative at the University of British Columbia, the GEOMAR Helmholtz Centre for Ocean Research and Dalhousie University modelled the cod population trajectory for the entire period from 1508 to 2019. 

“Our assessment suggests that the biomass—the weight of the population in the water— of northern cod is currently around 2 per cent of what it was earlier,” said Rebecca Schijns, lead author of the study and a researcher with the Sea Around Us at UBC’s Institute for the Oceans and Fisheries.

“The interesting thing is that we got to these results by applying a computer-intensive but very simple stock assessment methods—known as CMSY—to catch data for five centuries. Different from previous assessments that required large amounts of information, this method basically requires only a time series of annual catches,” Schijns said. “The other information that is required is available from the scientific literature, and from people with knowledge of the fishery.”

Working with such a long time series allowed the researchers to reliably estimate maximum sustainable yield–or the highest catch that a fish stock can support in the long-term, given that environmental conditions remain more or less constant– for northern cod at 380,000 tonnes per year.  

But such high catches are now only a dream.  

Fisheries used lines and later traps for 400 years and were sustainable, generating catches of 100,000 to 200,000 tonnes per year. However, in the mid-1950s the introduction of bottom trawlers reduced northern cod biomass to levels that could not sustain high catches.

Although Canada declared a fishery exclusion zone in 1977, fishing did not actually halt to allow the stock to rebuild. This led to a final collapse of the northern Atlantic cod fishery, which remained open to small-scale fishers even during a moratorium imposed in 1992.

And in recent years, every time northern cod populations appear to increase, the fishing quota is raised.

“As a student, I was on board a German trawler fishing off Newfoundland and Labrador in 1973 and I have vivid memories of this cod rush,” said Dr. Daniel Pauly, co-author of the study and the Sea Around Us principal investigator.

“If artisanal fishers in the outports had been listened to when they warned about running out of cod to catch, things would be different now,” said Dr. Pauly. “The scientists then monitoring the cod stock ignored small-scale fishers and relied only on the data from trawlers which, however, did not reflect the cod stock’s decline because the trawlers could follow the cod further out than the small-scale fishers.”

Paying attention to what local and/or Indigenous fishers have to say—and integrating centuries-old catch data into stock assessments— can help manage marine populations more effectively for the long term. This approach is also helpful to understand the total impact of fisheries on marine ecosystems, Dr. Pauly noted.

“The CMSY method proved to be useful to assess the data-rich cod stock, but it also works with stocks for which we have only a catch data. This method is able to provide more reliable estimates of stock status by incorporating past data-limited periods,” Dr. Pauly said.

The CMSY method offers researchers, fisheries managers and policymakers the possibility of taking a comprehensive look into the status of the world’s most important fish stocks.

“Ancient catch data exist for several stocks, such as bluefin tuna in the Mediterranean, which started being commercialized around the 8th century, Atlantic herring in the Baltic Sea, whose fishery started in the 13th century, and Atlantic salmon in the Celtic Sea, whose fishery started in the 14th century," said Dr. Jeffrey Hutchings, co-author of the study and a researcher at Dalhousie University. “There is a real opportunity to use these data to design policies that prevent collapses similar to that of the cod stock.”

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JOURNAL

ICES Journal of Marine Science

DOI

10.1093/icesjms/fsab153 

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Five centuries of cod catches in Eastern Canada

Bowfin genome reveals old dogfish can teach researchers new tricks

International team of researchers sequence genome of the enigmatic bowfin fish

Peer-Reviewed Publication

HARVARD UNIVERSITY, DEPARTMENT OF ORGANISMIC AND EVOLUTIONARY BIOLOGY

 

IMAGE: FRESHLY DEPOSITED BOWFIN EGGS ATTACHED TO NEST MATERIAL. MALE BOWFIN BUILD NESTS IN WHICH FEMALES LAY EGGS. AFTER THE MALE FERTILIZES THE EGGS, IT WILL REMAIN WITH THE NEST TO GUARD THE YOUNG view more 

CREDIT: M. BRENT HAWKINS

The fish species Amia calva goes by many names including bowfin, freshwater dogfish, grinnel, and mud pike. No matter what you call it, this species is an evolutionary enigma because it embodies a unique combination of ancestral and advanced fish features.

In a paper published August 30 in Nature Genetics an international and collaborative team of researchers, headed by Ingo Braasch and Andrew Thompson of Michigan State University, have begun to unravel the enigma by sequencing the genome of the bowfin fish. Their collaborative analysis yielded unexpected insights into diverse aspects of the biology of this mysterious, ancient lineage.

The bowfin is a bony fish endemic to eastern North America and is the sole surviving member of a once large lineage of many species that are now known only from fossils. Scientists have long been fascinated with the bowfin because it bears a combination of ancestral features, such as lung-like air breathing and a robust fin skeleton, and derived features like simplified scales and a reduced tail. The bowfin also occupies a key position in the fish family tree, where it sits between the teleosts, a large and diverse group that arose recently, and more ancient branches that include sturgeons, paddlefish, and bichirs.

Due to this special position in the fish family tree, the bowfin can help scientists understand how aspects of modern fishes evolved from their ancient antecedents. By examining the bowfin genome, scientists can investigate the genetic basis of the unique set of old and new features of the bowfin. They can also use this genomic information as a framework to better understand the origin of the teleosts, which have duplicated and extensively modified their genomes since separating from the bowfin lineage and emerging as the dominant lineage in most aquatic habitats.

As a doctoral candidate in the Department of Organismic and Evolutionary Biology at Harvard University, study co-author M. Brent Hawkins (PhD ’20) examined the evolution and development of the bowfin pectoral fin. Hawkins’ doctoral thesis, conducted with Professor Matthew P. Harris, Harvard Medical School and Boston Children’s Hospital, and Professor James Hanken, Department of Organismic and Evolutionary Biology at Harvard university, contributed some of the study’s most surprising findings.

Hawkins focused on the pectoral fin of the bowfin because of its ancestral configuration of the skeleton. The bowfin retains the metapterygium, which is a portion of the fin skeleton that is homologous to the limb bones of tetrapods. Model organisms such as the widely used zebrafish and medaka have lost the metapterygium, which makes comparisons between the fin and the limb difficult. By studying the bowfin fin, scientists can use knowledge of bowfin development as a steppingstone to bridge teleost fin development to tetrapod limb development and help explain the evolution of the fin-to-limb transition.

CAPTION

Schematics show the arrangement of bones in fins and limbs. Elements that are derived from the ancestral metapterygium are shown in magenta. The tetrapod limb and a portion of the bowfin fin arose from the metapterygium, while teleosts have lost the metapterygial components

CREDIT

M. Brent Hawkins

With co-authors Emily Funk and Amy McCune, both at Cornell University, Hawkins collected young bowfin embryos from nests in the wild in upstate New York. Hawkins raised the embryos, collecting pectoral fin samples as they developed. He extracted mRNA from the samples and performed Transcriptome Sequencing with the help of the Harvard University Bauer Core to determine which genes are turned on in the developing fin by parsing the transcriptome data using the genomic reference sequence. Once identified, he used in situ hybridization to visualize where these genes are activated during fin outgrowth. Initially, Hawkins expected the bowfin gene data to look very similar to other fins and limbs. “As a field, we have characterized many of the genes involved in appendage patterning. We have a good idea of what the essential fin and limb genes are and where they should be turned on,” said Hawkins. However, when he analyzed the fin data he was shocked by the results.

While the bowfin pectoral fins did express many of the expected appendage growth genes, some of the most critical of these genes were in fact entirely absent. One such gene called fibroblast growth factor 8 (Fgf8) is turned on at the far tip of developing fins and limbs and is required for the outgrowth of these appendages. When Fgf8 is lost appendage outgrowth is impaired, and if extra Fgf8 is applied to an embryo, it can cause a new limb to form. “Every other fin and limb we know of expresses Fgf8 during development,” Hawkins said. “Discovering that bowfin fins don’t express Fgf8 is like finding a car that runs without a gas pedal. That the bowfin has accomplished this rewiring indicates unexpected flexibility in the fin development program. With the genome in hand, we can now unlock how this flexibility evolved.”

While some genes like Fgf8 were mysteriously absent from the bowfin fin, other genes were unexpectedly activated in the fins. The HoxD14 gene is expressed in the fins of fishes from the deeper branches of the fish family tree, such as paddlefish, but this gene was lost in more recent branches including the teleosts. When the authors found this gene in the bowfin genome data, they thought it must not be expressed because the DNA sequence did not encode a functional protein. Surprisingly, Hawkins and colleagues found that bowfin fins made HoxD14 gene transcripts at high levels, even though it did not code for a protein. “The fact that the HoxD14 gene can no longer make a protein, but it still transcribed into mRNA at such high levels suggests that there might be another function that we do not yet understand. We might be seeing a new level of Hox gene regulation at play in the bowfin,” said Hawkins.

CAPTION

A recently hatched bowfin larva facing to the left as seen through a microscope.

CREDIT

M. Brent Hawkins

Taken together the Fgf8 and HoxD14 results indicate that genetic programs, even those that guide the formation of important structures such as fins and limbs, are not as invariable as previously thought. “By studying more species, we learn which rules are hard and fast and which ones evolution can tinker with. Our study shows the importance of sampling a broader swath of natural diversity. We might just find important exceptions to established rules,” said Hawkins.

Hawkins also suggests that the results of the bowfin study serve as a warning against treating members of deeper branches of the tree of life as stand-ins for actual ancestors. “Some people might describe species like the bowfin as a ‘living fossil’ that reliably represents the ancestral condition of a lineage. In reality, these deeper branches have been evolving past that ancestor for just as long as the more recent branches, doing their own thing and changing in their own ways. In evolution, old dogs do learn new tricks.”

Hawkins is currently a postdoctoral researcher in the lab of Matthew P. Harris at Harvard Medical School and Boston Children’s Hospital.

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JOURNAL

Nature Genetics

DOI

DOI: 10.1038/s41588-021-00914-y 

ARTICLE TITLE

The bowfin genome illuminates the developmental evolution of ray-finned fishes

ARTICLE PUBLICATION DATE

30-Aug-2021

Learning from a ‘living fossil’

A Spartan-led team has probed the genetics of bowfin fish like never before to reveal insights about human health and evolutionary history

Peer-Reviewed Publication

MICHIGAN STATE UNIVERSITY

As we live and breathe, ancient-looking fish known as bowfin are guarding genetic secrets that that can help unravel humanity’s evolutionary history and better understand its health.

Michigan State researchers Ingo Braasch and Andrew Thompson are now decoding some of those secrets. Leading a project that included more than two dozen researchers spanning three continents, the Spartans have assembled the most complete picture of the bowfin genome to date.

“For the first time, we have what’s called a chromosome-level genome assembly for the bowfin,” said Braasch, an assistant professor of integrative biology in the College of Natural Science. “If you think of the genome like a book, what we had in the past was like having all the pages ripped out in pieces. Now, we’ve put them back in the book.”

“And in order,” added Thompson, a postdoctoral researcher in Braasch’s lab and the first author of the new research report, published Aug. 30 in the journal Nature Genetics.

This is really important information for a few reasons, the duo said, and it starts with the bowfin being what Charles Darwin referred to as a “living fossil.” The bowfin, or dogfish, looks like an ancient fish.

This doesn’t mean that the bowfin hasn’t evolved since ancient times, but it has evolved more slowly than most fishes. This means that the bowfin has more in common with the last ancestor shared by fish and humans, hundreds of millions of years ago, than, say, today’s zebrafish.

Zebrafish — which are modern, so-called teleost fishes — are a notable example because they’re widely used by scientists as a model to test and develop theories about human health. Having more genetic information about the bowfin helps make the zebrafish a better model.

“A lot of research on human health and disease is done on model organisms, like mice and zebrafish,” Thompson said. “But once you identify important genes and the elements that regulate those genes in zebrafish, it can be hard to find their equivalents in humans. It’s easier to go from zebrafish to bowfin to human.”

For example, one particularly interesting gene is one that’s used in developing the bowfin’s gas bladder, an organ the fish uses to breathe and store air. Scientists believe that the last common ancestor shared by fish and humans had air-filled organs like these that were evolutionary predecessors to human lungs.

In their new study, the Spartan researchers could see that a certain genetic process in the bowfin’s gas bladder development bore striking similarities to what’s known about human lung development. A similar process is also present in the modern teleost fishes, but it’s been obscured by eons of evolution.

“When you looked for the human genetic elements of this organ development in zebrafish, you couldn’t find it because teleost fishes have higher rates of evolution,” Thompson said. “It’s there in modern fishes, but it’s hidden from view until you see it in bowfin and gar.”

The gar is another air-breathing fish with “living fossil” status that’s studied by Braasch and his team. With both the gar and bowfin genomes, the team was able to show where these genetic elements linked to gas bladder and lung formation were hiding out in the modern teleost fishes. The ancient fish enable researchers to build a better bridge between the established modern fish model organisms and human biology.

“You don’t want to base that bridge on one species,” said Braasch, who added this finding also strengthens the implications for evolutionary history. “This is another piece of the puzzle that suggests the common ancestor of fish and humans had an air-filled organ and used it for breathing at the water surface, quite similar to what you see in bowfin and gar.”

Although these findings have insights that are pertinent to all of humanity, Spartans might feel a special affinity for the bowfin. For starters, male fish turn their fins and throats a bright shade of green during spawning season. Also, famed biologist William Ballard of Dartmouth College studied bowfin development from eggs to larval fish at Michigan State’s W.K. Kellogg Biological Station during the 1980s. This was what he called his “Odyssey of Strange Fish,” and Braasch’s team now uses his work to guide their genomic analyses of bowfin development.

Bowfins are native to Michigan. They could be in the Red Cedar River on MSU’s campus now, according to Thompson, but they also can be quite elusive and, sometimes, very aggressive. This made collaborations essential for securing specimens. With colleagues at Nicholls State University in Louisiana, the team caught bowfins for genome sequencing. Amy McCune, a collaborator and professor at Cornell University, knew where to find bowfin eggs in upstate New York and had a graduate student gifted at securing these unique samples for investigating bowfin development.

The Spartans also had connections at other universities and institutions with experts in bowfin biology, chromosome evolution and more. All told, the team included researchers from six states as well as France, Japan and Switzerland. Back in East Lansing, graduate students Mauricio Losilla and Olivia Fitch, research technologist Brett Racicot, and Kevin Childs, director of the MSU Genomics Core facility, also contributed to the study, which comes with an interesting twist at the end.

Almost all vertebrate creatures that grow paired limbs or fins share a common gene.

“Humans use it, mice use it. All fishes that have been studied so far use it,” Braasch said. “The naïve expectation would be that bowfin do, too.”

But that’s not what the team found. The bowfin, the “living fossil,” has evolved a different way of growing its paired fins.

“For whatever reason, it changed its genetic programming. Even ‘living fossils’ keep evolving. They’re not frozen in time,” Braasch said. “It’s sort of a cautionary tale that we shouldn’t take these things for granted. You have to look trait by trait, gene by gene and across many different species to paint the complete picture.”

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JOURNAL

Nature Genetics

DOI

10.1038/s41588-021-00914-y 

ARTICLE TITLE

The bowfin genome illuminates the developmental evolution of ray-finned fishes

ARTICLE PUBLICATION DATE

30-Aug-2021