Vascular plants colonized land extensively by the early Silurian: Study

Peer-Reviewed Publication

CHINESE ACADEMY OF SCIENCES HEADQUARTERS

 

IMAGE: A COMPILATION OF (A) Δ199HG AND (B) Δ200HG FOR PALEOZOIC SEDIMENTS AT THE STAGE LEVEL view more 

CREDIT: IGCAS

The colonization and expansion of plants on land represent a defining landmark for the path of life on Earth. Terrestrial colonization has been attributed to a series of major innovations in plant body plans, anatomy, and biochemistry that transformed global biogeochemical cycles and climates.

It is crucial to identify the onset and track the expansion of those earliest land plants. However, the precise timing of land colonization by vascular plants remains controversial due to the sparseness of early land plant megafossils, poor stratigraphic controls on their distribution, and the uncertainties associated with molecular clock calculations.

Recently, scientists led by Prof. CHEN Daizhao from the Institute of Geology and Geophysics and Prof. FENG Xinbin from the Institute of Geochemistry of the Chinese Academy of Sciences (CAS) used mercury isotope to prove that vascular plants had already extensively colonized land by the early Silurian (~444 Ma).

This work was published in Science Advances on April 28.

Researchers from the Xishuangbanna Tropical Botanical Garden of CAS, the Nanjing Institute of Geology and Palaeontology of CAS, the Chinese Geological Survey, the Open University, UK, and the College of Charleston, USA, were also involved in the study.

Mercury (Hg) is the only heavy metal element that is liquid under natural conditions. It is also transported globally in gaseous elemental form (Hg0) via atmospheric circulation. The most important realization about modern forest Hg cycling in recent decades has been that Hg in vegetation is derived from atmospheric Hg0 assimilation via leaves rather than from precipitation Hg or geologic Hg transport.

Land vegetation preferentially transfers atmospheric Hg0, which displays distinct negative odd mass independent fractionation (odd-MIF, reported as Δ199Hg) and even-MIF (reported as Δ200Hg) signatures, into terrestrial ecosystems. As land plants expanded and affected weathering in terrestrial settings, Hg containing these unique negative Δ199Hg and Δ200Hg values would be transported to nearshore marine environments, which showed significant positive signatures primally. Therefore, the geologic record of these isotopic systems potentially provides a novel tracer to track the colonization and expansion of plants on land.

In this study, the researchers used Hg stable isotope data from marine sediments spanning the Cambrian to Permian from different depositional facies collected from South China to highlight two episodes of distinct negative excursions in both odd- and even-MIF values at the stage level in the Silurian and Carboniferous.

They established a numerical model to quantify secular variations in the contribution from terrestrial organisms for the Paleozoic. They found that the results pushed back in time the extensive spread of early vascular plants to ~444 Ma in the early Silurian, at least in low-latitude areas like South China—a time period that is significantly earlier than the first known macrofossil of a vascular plant.

The study linked the Paleozoic expansion of terrestrial organisms, notably vascular plants, to the co-evolution of a range of earth systems, particularly those of the atmosphere, oceans, weathering processes, and geochemical features.

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JOURNAL

Science Advances

DOI

10.1126/sciadv.ade9510 

ARTICLE TITLE

Mercury isotopes show vascular plants had colonized land extensively by the early Silurian

ARTICLE PUBLICATION DATE

28-Apr-2023

https://en.wikipedia.org/wiki/Silurian_(Doctor_Who)

Silurian (Doctor Who) - Wikipedia 

The Silurians are a race of reptilian humanoids in the long-running British science fiction television series Doctor Who. The species first appeared in ...

Shocking implications of electric fishes’ tailless sperm

Grant and Award Announcement

MICHIGAN STATE UNIVERSITY

 

IMAGE: THE SPERM OF THE MORMYRID WEALY ELECTRIC FISH IS THE ONLY KNOWN VERTEBRATE SPECIES THAT LACKS FLAGELLUM. PANEL A SHOWS A LIGHT MICROSCOPE IMAGE OF A SPERM SAMPLE: THE SPERM ARE COMPLETELY IMMOTILE. PANEL B SHOWS A SCANNING ELECTRON MICROSCOPE IMAGE OF A SINGLE SPERM CELL. view more 

CREDIT: JASON GALLANT, MICHIGAN STATE UNIVERSITY

Betting on tailless sperm that evolved from brave swimmers to hapless floaters seems like a crazy evolutionary gamble, but a group of fish seems to have done just that. Understanding that tradeoff holds promise to shed light on human disease and shake up biology lessons on traditional gender roles.

Michigan State University associate professor of integrative biology Jason Gallant and colleagues are using nearly $1 million from the National Science Foundation to understand the implications from a small African fish which evolved to have sperm with no tails but an electric-powered mating call. 

“We want to know why electric fish get away with it when no other vertebrate can,” said Gallant, a member of MSU’s Ecology, Evolution, and Behavior Program. “A general notion in biology is that sperm are cheap, and eggs are expensive – but these fish may be telling us that sperm are more expensive than we might think. They could be saving energy by cutting back on sperm tails.” Gallant is part of MSU’s College of Natural Science.

The variety of fish called mormyroids are commonly called elephantfish because even though small, their elongated mouths look a bit like a trunk. They live in murky African waters so dense they rely on brief electric charges to find each other. The pulses of electrical output and the brainpower needed to pick analyze these pulses requires a lot of energy. Elephantfish may have prioritized spending their energy stores to finding females and then on relying on other ways to deliver sperm to egg.

And within that theory are so many questions.

Members of the MSU Electric Fish Lab will work to confirm the gene they believe turns off sperm tail development. One way they test that is to isolate the gene and insert it in another species of fish with traditionally wiggly sperm to see if those tails disappear. The researchers also have developed a way to measure respiration to determine how much energy the fish save by nixing sperm tails.

And the group believes the questions go beyond fish sperm. Flagella are abundant throughout our tree of life – including in the sperm of people. Flagella are related to another beating appendage called cilia, which are shorter hair-like structures that also move.

“It’s interesting that cilia make biological world go round: flagella are really just really long cilia and many of the same parts,” Gallant said.

And this is where both human health and gender norms enter the picture.

A human genetic disorder called primary ciliary dyskinesia (PCD) brings chronic respiratory infection, abnormally positioned organs, fluid on the brain and infertility, all stemming from the lack of normally functioning cilia and flagella. The gene Gallant’s team is focusing on appears to be one of several factors in PCD, yet he notes its intriguing the mormyroids seem well and normal except for the tailless sperm. A better understanding of the function of the gene in fish could provide another piece of the PCD puzzle to understand human health problems.

And since fish that procreate with sperm that don’t swim is perplexing, the researchers are exploring how Elephantfish are far from traditionalists. A part of the research project will engage undergraduates to explore one of biology’s less-known stories.

“What’s neat about this grant is that we’re working with biology that turns our assumptions on their head,” Gallant said. “As humans we have assumptions that males are programmed to be the fertilizer. Females are passive recipients of sperm. But these sperm can’t even swim – they also have small testes, so aren’t competitive with other males.

“My pet hypothesis is that a lot of people get their ideas of how men and women should behave from biology lessons. If we teach them how diverse nature is. Will that change the way they go about acting with each other?”

Michigan State University's Jason Gallant and his team surveying a stream for electric fishes in Gabon.

CREDIT

Lauren Koenig, Michigan State Univesity

REICH WAS RIGHT

Previously unknown intracellular electricity may power biology

Newly discovered electrical activity within cells could change the way researchers think about biological chemistry

Peer-Reviewed Publication

DUKE UNIVERSITY

The human body relies heavily on electrical charges. Lightning-like pulses of energy fly through the brain and nerves and most biological processes depend on electrical ions traveling across the membranes of each cell in our body.

These electrical signals are possible, in part, because of an imbalance in electrical charges that exists on either side of a cellular membrane. Until recently, researchers believed the membrane was an essential component to creating this imbalance. But that thought was turned on its head when researchers at Stanford University discovered that similar imbalanced electrical charges can exist between microdroplets of water and air.

Now, researchers at Duke University have discovered that these types of electric fields also exist within and around another type of cellular structure called biological condensates. Like oil droplets floating in water, these structures exist because of differences in density. They form compartments inside the cell without needing the physical boundary of a membrane.

Inspired by previous research demonstrating that microdroplets of water interacting with air or solid surfaces create tiny electrical imbalances, the researchers decided to see if the same was true for small biological condensates. They also wanted to see if these imbalances sparked reactive oxygen,  “redox,” reactions like these other systems.

Appearing on April 28 in the journal Chem, their foundational discovery could change the way researchers think about biological chemistry. It could also provide a clue as to how the first life on Earth harnessed the energy needed to arise.

“In a prebiotic environment without enzymes to catalyze reactions, where would the energy come from?” asked Yifan Dai, a Duke postdoctoral researcher working in the laboratory of Ashutosh Chilkoti, the Alan L. Kaganov Distinguished Professor of Biomedical Engineering and Lingchong You, the James L. Meriam Distinguished Professor of Biomedical Engineering.

“This discovery provides a plausible explanation of where the reaction energy could have come from, just as the potential energy that is imparted on a point charge placed in an electric field,” Dai said.

When electric charges jump between one material and another, they can produce molecular fragments that can pair up and form hydroxyl radicals, which have the chemical formula OH. These can then pair again to form hydrogen peroxide (H2O2) in tiny but detectable amounts.

“But interfaces have seldom been studied in biological regimes other than the cellular membrane, which is one of the most essential part of biology,” said Dai. “So we were wondering what might be happening at the interface of biological condensates, that is, if it is an asymmetric system too.”

Cells can build biological condensates to either separate or trap together certain proteins and molecules, either hindering or promoting their activity. Researchers are just beginning to understand how condensates work and what they could be used for.

Because the Chilkoti laboratory specializes in creating synthetic versions of naturally occurring biological condensates, the researchers were easily able to create a test bed for their theory. After combining the right formula of building blocks to create minuscule condensates, with help from postdoctoral scholar Marco Messina in? Christopher J. Chang’s group at the University of California – Berkeley, they added a dye to the system that glows in the presence of reactive oxygen species.

Their hunch was right. When the environmental conditions were right, a solid glow started from the edges of the condensates, confirming that a previously unknown phenomenon was at work. Dai next talked with Richard Zare, the Marguerite Blake Wilbur Professor of Chemistry at Stanford, whose group established the electric behavior of water droplets. Zare was excited to hear about the new behavior in biological systems, and started to work with the group on the underlying mechanism.

“Inspired by previous work on water droplets, my graduate student, Christian Chamberlayne, and I thought that the same physical principles might apply and promote redox chemistry, such as the formation of hydrogen peroxide molecules,” Zare said. “These findings suggest why condensates are so important in the functioning of cells.”

“Most previous work on biomolecular condensates has focused on their innards,” Chilkoti said. “Yifan’s discovery that biomolecular condensates appear to be universally redox-active suggests that condensates did not simply evolve to carry out specific biological functions as is commonly understood, but that they are also endowed with a critical chemical function that is essential to cells.”

While the biological implications of this ongoing reaction within our cells is not known, Dai points to a prebiotic example of how powerful its effects might be. The powerhouses of our cells, called mitochondria, create energy for all of our life’s functions through the same basic chemical process. But before mitochondria or even the simplest of cells existed, something had to provide energy for the very first of life’s functions to begin working.

Researchers have proposed that the energy was provided by thermal vents in the oceans or hot springs. Others have suggested this same redox reaction that occurs in water microdroplets was created by the spray of ocean waves.

But why not condensates instead?

“Magic can happen when substances get tiny and the interfacial volume becomes enormous compared to its volume,” Dai said. “I think the implications are important to many different fields.”

This work was supported by the Air Force Office of Scientific Research (FA9550-20-1-0241, FA9550-21-1-0170) and the National Institutes of Health (MIRA R35GM127042; R01EB029466, R01 GM 79465, R01 GM 139245, R01 ES 28096).

CITATION: “Interface of Biomolecular Condensates Modulates Redox Reactions,” Yifan Dai, Christian F. Chamberlayne, Marco S. Messina, Christopher J. Chang, Richard N. Zare, Lingchong You, Ashutosh Chilkoti. Chem, April 28, 2023. DOI: 10.1016/j.chempr.2023.04.001

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JOURNAL

Chem

DOI

10.1016/j.chempr.2023.04.001 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Interface of Biomolecular Condensates Modulates Redox Reactions

ARTICLE PUBLICATION DATE

28-Apr-2023

'SHROOMS TALK!

Mushrooms and their post-rain, electrical conversations

Peer-Reviewed Publication

TOHOKU UNIVERSITY

 

IMAGE: MUSHROOMS IN THE FIELD WITH AN ELECTRODE ATTACHED TO THE TOP AND BOTTOM view more 

CREDIT: YU FUKASAWA

Certain fungi play a critical role in the ecological sustenance of forest trees. Ectomycorrhizal fungi are one such example. Commonly found on pine, oak, and birch trees, ectomycorrhizal fungi form a sheath around the outside of tree roots, and their mycelial body develops into vast underground networks that absorb vital nutrients from the soil and transfer it to the trees.

Scientists have been studying the possibility of electrical signal transfer between mushrooms and across trees via the mycelial networks. It is thought that fungi generate electrical signals in response to external stimuli and use these signals to communicate with each other, coordinating growth and other behavior. It has even been hypothesized that these signals can be used to help transfer nutrients to plants and trees.

Still, current scientific evidence remains sparse. Moreover, many studies have been limited to the laboratory, failing to recreate what happens in the wild.

Now, a group of researchers has recently headed to the forest floor to examine small, tan-colored ectomycorrhizal mushrooms known as Laccaria bicolor. Attaching electrodes to six mushrooms in a cluster, the researchers discovered that the electrical signals increased after rainfall.

"In the beginning, the mushrooms exhibited less electrical potential, and we boiled this down to the lack of precipitation," says Yu Fukasawa from Tohoku University, who lead the project along with Takayuki Takehi and Daisuke Akai from the National Institute of Technology, Nagaoka College, and Masayuki Ushio from the Hakubi Center, Kyoto University (presently at the Hong Kong University of Science and Technology). "However, the electrical potential began to fluctuate after raining, sometimes going over 100 mV."

The researcher correlated this fluctuation with precipitation and temperature, and causality analysis revealed that the post-rain electric potential showed signal transport among mushrooms. This transport was particularly strong between spatially close mushrooms and demonstrated directionality.

"Our results confirm the need for further studies on fungal electrical potentials under a true ecological context," adds Fukasawa.

Details of their research were reported in the journal Fungal Ecology on March 14, 2023.

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JOURNAL

Fungal Ecology

DOI

10.1016/j.funeco.2023.101229 

Texas A&M research redefines mammalian tree of life

The research uses the genomes of 241 species and can be used to support animal and human health outcomes.

Peer-Reviewed Publication

TEXAS A&M UNIVERSITY

 

IMAGE: FOLEY’S EFFORTS IN THE RESEARCH PRODUCED THE WORLD'S LARGEST MAMMALIAN PHYLOGENETIC TREE TO DATE. THE “MAMMALIAN TREE OF LIFE” MAPS OUT THE EVOLUTION OF MAMMALS OVER MORE THAN 100 MILLION YEARS AND IS CRUCIAL TO THE GOALS OF THE ZOONOMIA PROJECT. view more 

CREDIT: TEXAS A&M UNIVERSITY

Research led by a team of scientists from the Texas A&M School of Veterinary Medicine and Biomedical Sciences puts to bed the heated scientific debate regarding the history of mammal diversification as it relates to the extinction of the non-avian dinosaurs. Their work provides a definitive answer to the evolutionary timeline of mammals throughout the last 100 million years.

The study, published in Science, is part of a series of articles released by the Zoonomia Project, a consortium of scientists from around the globe that is using the largest mammalian genomic dataset in history to determine the evolutionary history of the human genome in the context of mammalian evolutionary history. Their ultimate goal is to better identify the genetic basis for traits and diseases in people and other species.

The Texas A&M University research — led by Dr. William J. Murphy, a professor in the Department of Veterinary Integrative Biosciences, and Dr. Nicole Foley, an associate research scientist in Murphy’s lab — is rooted in phylogeny, a branch of biology that deals with the evolutionary relationships and diversification of living and extinct organisms.

“The central argument is about whether placental mammals (mammals that develop within placentas) diverged before or after the Cretaceous-Paleogene (or K-Pg) extinction event that wiped out the non-avian dinosaurs,” Foley shared. “By performing new types of analyses only possible because of Zoonomia’s massive scope, we answer the question of where and when mammals diversified and evolved in relation to the K-Pg mass extinction.”

The research — which was conducted with collaborators at the University of California, Davis; University of California, Riverside; and the American Museum of Natural History — concludes that mammals began diversifying before the K-Pg extinction as the result of continental drifting, which caused the Earth's land masses to drift apart and come back together over millions of years. Another pulse of diversification occurred immediately following the K-Pg extinction of the dinosaurs, when mammals had more room, resources and stability.

This accelerated rate of diversification led to the rich diversity of mammal lineages — such as carnivores, primates and hoofed animals — that share the Earth today.

Murphy and Foley’s research was funded by the National Science Foundation and is one part of the Zoonomia Project led by Elinor Karlsson and Kerstin Lindblad-Toh, of the Broad Institute, which also compares mammal genomes to understand the basis of remarkable phenotypes — the expression of certain genes such as brown vs. blue eyes — and the origins of disease.

Foley pointed out that the diversity among placental mammals is exhibited both in their physical traits and in their extraordinary abilities.

“Mammals today represent enormous evolutionary diversity — from the whizzing flight of the tiny bumblebee bat to the languid glide of the enormous Blue Whale as it swims through Earth’s vast oceans. Multiple species have evolved to echolocate, some produce venom, while others have evolved cancer resistance and viral tolerance,” she said.

“Being able to look at shared differences and similarities across the mammalian species at a genetic level can help us figure out the parts of the genome that are critical to regulate the expression of genes,” she continued. “Tweaking this genomic machinery in different species has led to the diversity of traits that we see across today’s living mammals.”

Murphy shared that Foley’s resolved phylogeny of mammals is crucial to the goals of the Zoonomia Project, which aims to harness the power of comparative genomics as a tool for human medicine and biodiversity conservation.

“The Zoonomia Project is really impactful because it's the first analysis to align 241 diverse mammalian genomes at one time and use that information to better understand the human genome,” he explained. “The major impetus for putting together this big data set was to be able to compare all of these genomes to the human genome and then determine which parts of the human genome have changed over the course of mammalian evolutionary history.”

Determining which parts of genes can be manipulated and which parts cannot be changed without causing harm to the gene’s function is important for human medicine. A recent study in Science Translational Medicine led by one of Murphy and Foley’s colleagues, Texas A&M geneticist Dr. Scott Dindot, used the comparative genomics approach to develop a molecular therapy for Angelman syndrome, a devastating, rare neurogenetic disorder that is triggered by the loss of function of the maternal UBE3A gene in the brain.

Dindot’s team took advantage of the same measures of evolutionary constraint identified by the Zoonomia Project and applied them to identify a crucial but previously unknown genetic target that can be used to rescue the expression of UBE3A in human neurons.

Murphy said expanding the ability to compare mammalian genomes by using the largest dataset in history will help develop more cures and treatments for other species' ailments rooted in genetics, including cats and dogs.

“For example, cats have physiological adaptations rooted in unique mutations that allow them to consume an exclusively high-fat, high-protein diet that is extremely unhealthy for humans,” Murphy explained. “One of the beautiful aspects of Zoonomia’s 241-species alignment is that we can pick any species (not just human) as the reference and determine which parts of that species’ genome are free to change and which ones cannot tolerate change. In the case of cats, for example, we may be able to help identify genetic adaptations in those species that could lead to therapeutic targets for cardiovascular disease in people.”

Murphy and Foley’s phylogeny also played an instrumental role in many of the subsequent papers that are part of the project.

“It’s trickle-down genomics,” Foley explained. “One of the most gratifying things for me in working as part of the wider project was seeing how many different research projects were enhanced by including our phylogeny in their analyses. This includes studies on conservation genomics of endangered species to those that looked at the evolution of different complex human traits.”

Foley said it was both meaningful and rewarding to definitively answer the heavily debated question about the timing of mammal origins and to produce an expanded phylogeny that lays the foundation for the next several generations of researchers.

“Going forward, this massive genome alignment and its historical record of mammalian genome evolution will be the basis of everything that everyone's going to do when they're asking comparative questions in mammals,” she said. “That is pretty cool.”

By Rachel Knight, Texas A&M University School of Veterinary Medicine & Biomedical Sciences

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JOURNAL

Science

DOI

10.1126/science.abl8189 

ARTICLE TITLE

A genomic timescale for placental mammal evolution

ARTICLE PUBLICATION DATE

28-Apr-2023

New study reveals DNA analysis can help predict which animals face highest risk of extinction

Genomes from 240 mammal species could change how conservation efforts are applied

Peer-Reviewed Publication

SAN DIEGO ZOO WILDLIFE ALLIANCE

DOWNLOAD VIDEO & PHOTOS AT: [https://sandiegozoo.box.com/s/xt7ea9blsdq9k10u3tkiw2o1fo77n79e]

SAN DIEGO (April 28, 2023) – A team of scientists led by San Diego Zoo Wildlife Alliance and University of California, Santa Cruz has discovered that animals’ genomic information can help predict which mammal species are more likely to face extinction.

Species with smaller historical populations carry higher burdens of damaging mutations and have elevated extinction risk, they found, which suggests that long-term demographic statistics are relevant to today’s conservation status and resiliency.

The findings, which could change how conservation actions and resources are strategically applied to help save endangered wildlife, are part of a series of papers from the Zoonomia Consortium that will be published this spring in a special issue of the renowned journal Science.

The planet is experiencing a rapid biodiversity loss, with tens of thousands of species at risk of dying out, and identifying the ones in most urgent need is a long and costly process. But there’s little information known about thousands of species, which makes it difficult to allocate limited conservation resources to target those closest to the brink.

To help circumvent these limitations, the scientists examined 240 mammal species, from tiny tree shrews to towering giraffes, killer whales and even humans. They found that the DNA encoded within a single genome – reflecting the species’ history over millions of years – can provide a rapid, cost-effective conservation risk assessment, even when we know little about the animals’ physiological, behavioral and life history characteristics, or even how many individuals remain.

“These results show that genetic information, even if only from a single individual for a given species, offers immediate, actionable guidance for scientists designing conservation strategies as well as those with boots in the field,” said Aryn P. Wilder, Ph.D., a conservation scientist at San Diego Zoo Wildlife Alliance and one of the paper’s two lead authors.

“The limited resources available for the conservation of wildlife species requires triage,” said Megan Supple, a research scientist with the UCSC Paleogenomics Lab and co-lead of the project. “Our genomic assessment provides a relatively inexpensive method to rapidly identify species at risk of becoming endangered in the future, even when little else is known about that species.  This genomic triage enables managers to target limited resources toward species most in need.”

The genomic research was used to train models that quickly distinguish between threatened and non-threatened species, based on demography, diversity, and mutations that impact fitness. This will help assess extinction risk and identify which of the thousands of threatened species stand to benefit the most from conservation support, especially as the number of sequenced genomes grows and the models continue to improve.

Three species – the Upper Galilee Mountains blind mole rat, lesser chevrotain and orca – are highlighted as just three examples of the thousands of species lacking information on whether they’re threatened. The scientists applied their models to these “data-deficient” species to demonstrate how a genomic risk assessment could work.

What makes the research groundbreaking is the overall number of species included in the study, which is the largest of its kind. By examining 240 species, scientists were able to estimate the genomic characteristics that best predict extinction risk and build genomic risk assessment models that can be used when other information is lacking.

That led the paper’s authors to call for genomic information to be included in conservation status assessments of species, to bridge the gap between geneticists and conservation managers and provide a framework for deploying money and resources to species at highest risk.

“Many potentially endangered species are classified as ‘data deficient,’ meaning that we simply have too little information to determine whether immediate conservation action is required,” said Beth Shapiro, Ph.D., Professor of Ecology and Evolutionary Biology at UC Santa Cruz and an HHMI Investigator. “Our results show that a genome from a single individual can be sufficient to identify the most threatened of these ‘data deficient’ species, enabling us to focus our limited resources where they can be most impactful.”

“Our rapidly changing world threatens animal and plant species worldwide – but the use of genomics in conservation is a massive, underappreciated opportunity to protect them,” said Oliver Ryder, Ph.D., the Kleberg Endowed Director of Conservation Genetics at San Diego Zoo Wildlife Alliance and co-senior author of the paper.

“We are in an unprecedented era of discovery – a whole new way of seeing the world. We’ve long thought this potential existed, but it’s profound to see it crystallize into a catalyst that will help conservationists make crucial decisions that may save the world as we know it.”

The genomics manuscript is part of the work of the Zoonomia Consortium, the largest comparative mammalian genomics resource in the world, involving more than 150 people worldwide. The Science series papers also demonstrate how comparative genomics can shed light on how certain species achieve extraordinary feats, and help scientists better understand the parts of our genome that are functional and how they might influence health and disease. They also identified part of the genetic basis for rare mammal traits, such as the ability to sniff faint scents from miles away.

The San Diego Zoo Wildlife Alliance’s “Frozen Zoo” provided many of the genetic samples, including those of threatened and endangered species, for the DNA analyses performed at more than 50 institutions worldwide as part of the Zoonomia Consortium. The Frozen Zoo, or Wildlife Biodiversity Bank, is the largest repository of genetic material of its kind, containing viable cell cultures and reproductive material from approximately 10,000 animals representing over 1,100 species and subspecies.

The Zoonomia effort is led by Elinor Karlsson, Ph.D., director of the vertebrate genomics group at the Broad Institute of MIT and Harvard and a professor of bioinformatics and integrative biology at the UMass Chan Medical School, and Kerstin Lindblad-Toh, Ph.D., scientific director of vertebrate genomics at the Broad and a professor of comparative genomics at Uppsala University in Sweden.

About San Diego Zoo Wildlife Alliance

San Diego Zoo Wildlife Alliance is a nonprofit international conservation leader, committed to inspiring a passion for nature and working toward a world where all life thrives. The Alliance empowers people from around the globe to support their mission to conserve wildlife through innovation and partnerships. San Diego Zoo Wildlife Alliance supports cutting-edge conservation and brings the stories of their work back to the San Diego Zoo and San Diego Zoo Safari Park—giving millions of guests, in person and virtually, the opportunity to experience conservation in action. The work of San Diego Zoo Wildlife Alliance extends from San Diego to eco-regional conservation “hubs” across the globe, where their expertise and assets—including the renowned Wildlife Biodiversity Bank—are able to effectively align with hundreds of regional partners to improve outcomes for wildlife in more coordinated efforts. By leveraging these skills in wildlife care and conservation science, and through collaboration with hundreds of partners, San Diego Zoo Wildlife Alliance has reintroduced more than 44 endangered species to native habitats. Each year, San Diego Zoo Wildlife Alliance’s work reaches over 1 billion people in 150 countries via news media, social media, their websites, educational resources and the San Diego Zoo Wildlife Explorers television programming, which is in children’s hospitals in 13 countries. Success is made possible by the support of members, donors and guests to the San Diego Zoo and San Diego Zoo Safari Park, who are Wildlife Allies committed to ensuring all life thrives.

About the UC Santa Cruz Genomics Institute
The UC Santa Cruz Genomics Institute is one of the premier public institutions for storing, cataloging, assembling, validating, and analyzing huge volumes of genomic data. Its mission is to use genomics to positively impact health, nature, and society. It creates advanced technologies and open-source genomics platforms to unravel evolutionary patterns, molecular processes, and the underpinnings of disease. Its platforms, technologies, and scientists unite global communities to create and deploy data-driven, life-saving treatments and innovative conservation efforts. The Genomics Institute is dedicated to openly and responsibly sharing what it learns and creates in order to contribute to creating a healthier world.

 

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JOURNAL

Science

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

The contribution of historical processes to contemporary extinction risk in placental mammals

ARTICLE PUBLICATION DATE

28-Apr-2023

One-hour endoscopic procedure could eliminate need for insulin for type 2 diabetes

Electrical pulses that stimulate changes in the small intestine may improve glucose control

Reports and Proceedings

DIGESTIVE DISEASE WEEK

BETHESDA, Md. (April 28, 2023) — A procedure that uses controlled electrical pulses to induce changes to the lining of the first part of the small intestine could allow patients with Type 2 diabetes to stop taking insulin and still maintain glycemic control, according to a preliminary first-in-human study that will be presented at Digestive Disease Week® (DDW) 2023.

“The potential for controlling diabetes with a single endoscopic treatment is spectacular,” said Celine Busch, the study’s lead researcher and PhD candidate in gastroenterology at Amsterdam University Medical Center. “One of the biggest advantages of this treatment is that a single outpatient endoscopic procedure provides glycemic control, a potential improvement over drug treatment, which depends on patients taking their medication day in, day out.”

More than 37 million Americans have diabetes, and more than 90% of them have Type 2 diabetes. Type 2 diabetes most often develops in people over age 45, but more and more children, teens and young adults are also developing it. Glucose lowering medication can be expensive, and the injection of insulin has several side effects, including the risk of low blood sugar and weight gain.

In this early-stage study, 14 patients underwent an endoscopic procedure in which alternating electrical pulses were delivered to the duodenum, a portion of the lining of the small intestine just below the stomach. After the hour-long procedure, patients were discharged on the same day and then put on a calorie-controlled liquid diet for two weeks. Patients then began taking semaglutide, a diabetes medicine, titrating up to 1 mg a week.

Semaglutide on its own sometimes allows patients with Type 2 diabetes to quit taking insulin, but only in about 20% of cases, Busch said. In this study, 12 of 14 patients, or 86%, maintained good glycemic control without insulin for a year, suggesting the improvement is related to the procedure and not just to the semaglutide. Authors are beginning work on a double-blind randomized controlled trial to test these results.

“While drug therapy is ‘disease-controlling,’ it only reduces high blood sugar as long as the patient continues taking the medication,” said Jacques Bergman, M.D., PhD, principal investigator on the study and professor of gastrointestinal endoscopy at Amsterdam University Medical Center. “This one procedure is ‘disease-modifying’ in that it reverses the body’s resistance to its own insulin, the root cause of the Type-2 diabetes.”

Previous researchers explored the impact of ablation, using heat to modify the lining of the small intestine, after observing that patients who underwent gastric bypass experienced improved insulin control immediately after the surgery, even before any weight loss could occur, indicating that bypassing this portion of the small intestine plays a role in the glycemic control in Type 2 diabetes.

Researchers hypothesized that chronic exposure to a high-sugar, high caloric diet results in a yet unknown change to this portion of the small intestine, making the body resistant to its own insulin, Busch said. Researchers believe rejuvenating the tissue in this part of the intestine improves the body’s ability to respond to its own insulin, particularly in patients with Type 2 diabetes whose bodies still produce some insulin.

The study was fully funded by Endogenex, a Minnesota-based company that owns the technology used for the endoscopic procedure. Dr. Bergman serves on the advisory board of Endogenex.

DDW Presentation Details

Dr. Busch will present data from the study, “Re-cellularization via electroporation therapy (ReCET) combined with GLP1ra to replace insulin therapy in patients with Type 2 diabetes: Six-month results of the EMINENT study,” abstract 1272, on Tuesday, May 9, at 4:22 p.m. CDT.  For more information about featured studies, as well as a schedule of availability for featured researchers, please visit www.ddw.org/press.

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Digestive Disease Week® (DDW) is the largest international gathering of physicians, researchers and academics in the fields of gastroenterology, hepatology, endoscopy and gastrointestinal surgery. Jointly sponsored by the American Association for the Study of Liver Diseases (AASLD), the American Gastroenterological Association (AGA) Institute, the American Society for Gastrointestinal Endoscopy (ASGE) and the Society for Surgery of the Alimentary Tract (SSAT), DDW takes place May 6 – 9 in Chicago and virtually. The meeting showcases more than 3,500 abstracts and hundreds of lectures on the latest advances in GI research, medicine and technology. More information can be found at www.ddw.org.

Gut microbiome fluctuates throughout the day and across seasons

Study sheds light on the ever-changing balance of bacteria that make up half the human body

Reports and Proceedings

DIGESTIVE DISEASE WEEK

BETHESDA, Md. (April 28, 2023) — The balance of microbes in the human gut varies substantially from morning to night and even more by season — with profound fluctuations completely transforming the microbiome from summer to winter, according to a study to be presented at Digestive Disease Week® (DDW) 2023.

The microbiome — bacteria that live in and on the body — accounts for about half of the cells that make a human, and fluctuations in the makeup of the microbiome could have wide-ranging implications for health and medicine. 

“The seasonal variations we see in conditions like allergies or the flu occur in context of completely different microbiomes,” said Carolina Dantas Machado, PhD, the study’s lead author and a researcher in the laboratory of Amir Zarrinpar, MD, PhD, at University of California, San Diego. “We may need to put our understanding of how seasons affect health and disease in context of a microbiome that is much more variable and dynamic than we have previously thought.”

For this study, researchers reviewed data for about 20,000 stool samples collected by the American Gut Project, the world’s largest citizen science microbiome project, from countries around the world between 2013 and 2019. Analyzing the collection time, date and location, researchers found nearly 60% of the phyla — related groups of bacteria — have a distinct 24-hour cycle. Seasonal fluctuations were even more pronounced, with certain types of bacteria following one of two distinct patterns over the course of a year.

Two examples illustrate some of the numerous daily and seasonal trends identified: The number of organisms known as Actinobacteriota fluctuated during the day, with lower levels in samples taken in the morning and much higher levels found toward the end of the day. Over a year, Proteobacteria consistently dip to low levels in the winter and steadily rise until peaking in the summer.

Dr. Zarrinpar and his colleagues think that diet and sleep are likely big factors in daily fluctuations.

“You can imagine that the gut environment is radically different in terms of nutrient and water availability and pH when the person is sleeping compared to right after they eat breakfast,” Dr. Zarrinpar said. Seasonal variation is harder to explain, but researchers are exploring data by latitude and climate, which could indicate whether light and temperature play a role. Pollen and humidity are among other possible influences.

The findings are important not only for other researchers studying the microbiome but also those whose research could be affected by variation in the microbiome, such as medication studies where the microbiome may have a role in metabolizing medicines. Researchers need to be aware that the

timing of stool sample collection could influence research results in unexpected ways, especially for smaller studies.

DDW Presentation Details

Dr. Dantas Machado will present results of the study, “The human gut microbiome displays diurnal and seasonal rhythmic patterns,” abstract 395, on Sunday, May 7, at 11:20 a.m. CDT.  For more information about featured studies, as well as a schedule of availability for featured researchers, please visit www.ddw.org/press.

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Digestive Disease Week® (DDW) is the largest international gathering of physicians, researchers and academics in the fields of gastroenterology, hepatology, endoscopy and gastrointestinal surgery. Jointly sponsored by the American Association for the Study of Liver Diseases (AASLD), the American Gastroenterological Association (AGA) Institute, the American Society for Gastrointestinal Endoscopy (ASGE) and the Society for Surgery of the Alimentary Tract (SSAT), DDW takes place May 6 – 9 in Chicago and virtually. The meeting showcases more than 3,500 abstracts and hundreds of lectures on the latest advances in GI research, medicine and technology. More information can be found at www.ddw.org.

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METHOD OF RESEARCH

Observational study