Scientists identify genes behind tusklessness in African elephants

Shane Campbell-Staton, assistant professor of ecology and evolutionary biology. with an elephant at Gorongosa National Park in Mozambique. The elephant has been anesthetized for the collection of tissue samples for genomic and dietary analyses, and to be fitted with a GPS collar. 
Photo by Rob Pringle

In regions of Africa wracked by heavy poaching, people have observed an increased incidence of African elephants without their iconic white tusks, which are prized in the multibillion-dollar wildlife black market. But there has been no direct genetic evidence indicating how this was happening, or why this trait was occurring exclusively in female elephants.

Shane Campbell-Staton, assistant professor of ecology and evolutionary biology. with an elephant at Gorongosa National Park in Mozambique. The elephant has been anesthetized for the collection of tissue samples for genomic and dietary analyses, and to be fitted with a GPS collar.

A team led by Princeton University researchers has now implicated two genes associated with tooth development in mammals to be at the center of the tuskless elephant phenomenon, according to a study published in the journal Science. One of these genes is connected to the X chromosome and is lethal to males, while humans who have the same gene mutation exhibit similar teeth defects.

“Elephants are such an iconic species that is so important for the savanna ecosystem and now we have a better understanding of how human activity is impacting them,” said co-first author Shane Campbell-Staton, assistant professor of ecology and evolutionary biology at Princeton and associated faculty in Princeton’s High Meadows Environmental Institute (HMEI).

Researchers shed light on blind spot of shark attacks

Credit: Dr. Laura Ryan

Scientists have found more evidence to support the mistaken identity theory’ in juvenile white sharks during surface attacks on humans.

Research, which has been published in the Journal of the Royal Society Interface, suggests that sharks mistake humans for seal prey.

Shark attack on humans have long fascinated the general public but have remained a source of confusion for scientists. This is due to the fact that they often bite, but do not subsequently eat, their human targets.

To help unlock this mystery, a team from Macquarie University, in collaboration with the University of Bristol created a virtual white shark visual system. Videos of human and seal movements filmed from below the water’s surface were then processed in with this system to see visual motion and shape cues through the perspective of a white shark.

“Until now, the potential similarity between humans and seals has been assessed based on human vision. However, white sharks have much lower visual acuity than us, meaning they cannot see fine details, and lack color vision” explained Dr Laura Ryan, the lead author on the paper. “In these experiments, we were able to view the world through the eyes of a white shark.”

Dr Martin How of Bristol’s School of Biological Sciences said: “We used a computer simulation to compare the way that seals, swimmers and surfers move on the water's surface, when viewed from the perspective of white sharks below.

First overview of archaea in vertebrates

View of an archea colony in the scanning electron microscope. 
© MPI f. Developmental Biology

Uncovering how host relatedness influences the diversity of archaea in the vertebrate gut

Archaea are often mistaken as bacteria, given that both are small, single-cell organisms. However, archaea are as genetically different from bacteria as humans are from bacteria. While archaea are found in most environments, including the human gut microbiome, relatively little is known about them. An international team of researchers from Germany and Austria, led by Nicholas Youngblut at the Max Planck Institute for Developmental Biology in Tübingen, Germany, has compiled the first large scale assessment of archaeal diversity in the vertebrate gut. The study shows that the diversity of archaea in the vertebrate gut is greater than previously thought. Moreover, the study shows how the relatedness of animals and their diets affects archaeal diversity.

Archaea are the third domain of life, separate from the domains of bacteria and eukaryotes. While bacteria and archaea are both unicellular organisms that lack a nucleus, they are very different in key ways. For instance, archaea uniquely generate methane by consuming the waste products of bacterial fermentation. Unlike bacteria, no pathogenic species of archaea have been discovered, which is a major reason why more attention is paid to bacteria in the animal microbiome. As a result, little is known about the diversity of archaea in the vertebrate gut and what factors influence this diversity.

Like a biological fingerprint, specific groups of microbes colonize the guts of birds, mammals, amphibians, reptiles and fish. In a new paper, researchers revealed how archaea fit into this picture. "We were amazed by the specificity but also diversity of the archaeal species we found in the gut of vertebrates. Among them was the archaeon Methanothermobacter," explained Nicholas Youngblut of the Max Planck Institute for Developmental Biology, who is lead author of the study. "Methanothermobacter is known to occur only in hot environments of about 60 degrees Celsius, so its detection in a large number of different vertebrates was surprising. We saw the archaeal genus particularly common and widespread among birds, which may be due to their higher body temperature of about 40 degrees Celsius or warmer."

Giant pandas’ distinctive black and white markings provide effective camouflage

Giant Panda Credit: Anssi Nokelainen

Researchers at the University of Bristol, Chinese Academy of Sciences and the University of Jyväskylä have used state-of-the art image analysis techniques to demonstrate, counterintuitively, that the unique colorings work to disguise the giant panda. The results have been published today in Scientific Reports.

While most mammals are drab browns and greys, there are a small number of well-known and intriguing exceptions such as zebras, skunks, and orcas. Perhaps the most famous of all however is the giant panda.

The international team analyzed rare photographs of the giant pandas, taken in their natural environment. They discovered that their black pelage patches blend in with dark shades and tree trunks, whereas their white patches match foliage and snow when present. Also, infrequent pale brown pelage tones match ground color, providing an intermediate color which bridges the gap between the very dark and very light visual elements in the natural habitat. The results are consistent whether viewed by human, felid or canine vision models; the last two represent panda predators.

Machine learning predicts antibiotic resistance spread

Genes aren’t only inherited through birth. Bacteria have the ability to pass genes to each other, or pick them up from their environment, through a process called horizonal gene transfer, which is a major culprit in the spread of antibiotic resistance.

Cornell researchers used machine learning to sort organisms by their functions and use this information to predict with near-perfect accuracy how genes are transferred between them, an approach that could potentially be used to stop the spread of antibiotic resistance.

The team’s paper, “Functions Predict Horizontal Gene Transfer and the Emergence of Antibiotic Resistance,” published Oct. 22 in Science Advances. The lead author is doctoral student Hao Zhou.

“Organisms basically can acquire resistance genes from other organisms. And so it would help if we knew which organisms bacteria were exchanging with, and not only that, but we could figure out what are the driving factors that implicate organisms in this transfer,” said Ilana Brito, assistant professor and the Mong Family Sesquicentennial Faculty Fellow in Biomedical Engineering in the College of Engineering, and the paper’s senior author. “If we can figure out who is exchanging genes with who, then maybe it would give insight into how this actually happens and possibly even control these processes.”

Many novel traits are shared through gene transfer. But scientists haven’t been able to determine why some bacteria engage in gene transfer while others do not.

A third of leukemia patients do not generate any antibody response to two doses of COVID-19 vaccination

A University of Birmingham-led study has shown that a third of patients with the most common type of leukemia fail to generate any measurable antibody response following two doses of COVID-19 vaccination.

Furthermore, the research showed that in the two thirds of patients who do develop antibodies, levels are much lower than compared to healthy people and also have a profoundly reduced ability to ‘neutralize’ the globally dominant Delta variant.

The largest study of its kind, the research identified a number of important new findings which researchers say will be crucial to shaping future management and public health policy for patients with this type of blood cancer, who are immunosuppressed and at an increased clinical risk from SARS-CoV-2 infection.

Key new findings are:

• Only 67% of the leukemia patients generated any measurable antibody response to double COVID-19 vaccination, compared to 100% of the age-matched healthy population.
• In those patients with leukemia who did have an antibody response, antibody levels were 3.7 times lower than that seen in the healthy control group.
• Antibody levels declined by 33% at four months after leukemia patients’ second vaccine.
• No difference in antibody responses were observed between those participants receiving the Oxford/AstraZeneca vaccine and those receiving the Pfizer/BioNTech vaccine.
• Antibody responses showed weak ability to neutralize the spike protein from the now globally dominant SARS-CoV-2 Delta variant compared to healthy controls.

500 patients with chronic lymphocytic leukemia - the most common leukemia in adults - were recruited to the study. 41% had received two doses of the Pfizer/BioNTech vaccine, whilst 59% had received two doses of the Oxford/AstraZeneca vaccine. The average age of participants was 67 and 53% of the cohort was male. Their antibody response to double COVID-19 vaccination was compared to that of 94 age-matched healthy ‘controls’. Blood samples were obtained from all study participants between two to three weeks following their second vaccination, and again up to 30 weeks later.

To selectively kill cancer cells, target a protein channel in the cell's lysosome

Cancer treatments necessarily target unchecked cell growth, and selectively kill cancer cells while sparing normal cells and avoiding general toxicity in the human body.

To develop new treatments for cancer, scientists are focused on finding the malfunctioning machinery within cancer cells that can be targeted using small molecule pharmaceuticals. Now, University of Michigan researchers have identified one of these targets: a zinc and calcium ion permeable channel within a cell’s lysosome, the organelle responsible for recycling cellular waste, nutrient sensing and cell metabolism.

The researchers discovered that this channel is upregulated—meaning both its protein expression and channel activity were substantially increased—in metastatic melanoma cells compared with healthy melanocytes. They found that targeting this channel protein with small pharmaceutical compounds triggers the rapid and selective death of cancer cells while completely sparing normal cells. Their research is published in the journal Cell Reports.

“Many traditional cancer therapies target a well-known cell death pathway called apoptosis to trigger cancer cell death. However, many aggressive cancer cells harbor numerous mutations of genes that help them escape these treatments. We saw an urgent need to develop new therapeutic strategies that target nonapoptotic cell death pathways to eradicate cancer cells,” said Wanlu Du, an assistant research scientist in the U-M Department of Molecular, Cellular, and Developmental Biology.

In metastatic cancers, lysosomes turn hypertrophic, which means they actively contribute to tumor progression by increasing their ability to provide nutrients to the rapidly dividing cells and secreting enzymes to digest extracellular matrix—the material that provides the physical scaffolding for cells to help cancer cell invasion. But designing cancer therapies that target lysosomes may also harm normal cells and tissues by compromising lysosomes’ ability to provide nutrients for healthy cells.

Researchers identify new pathways to target breast cancer

A pathway helping the breast cancer protein BRCA1 repair damaged DNA has been identified by University of Queensland researchers in a study that will inform future targeted therapies.

Professor Robert Parton, Professor Alpha Yap and Dr Kerrie-Ann McMahon from UQ’s Institute for Molecular Bioscience (IMB) identified an association between two proteins that are lost in cancer cells – the well-known BReast CAncer gene 1 (BRCA1) and a new player - cavin3.

“In healthy cells, BRCA1 repairs DNA damage and suppresses tumor formation, but cells with mutations in their BRCA1 genes struggle to keep up with DNA repairs, which is when cancer can take over,” Dr McMahon said.

“We discovered that cavin3 helps BRCA1 function when cells are stressed and that when it’s absent, levels of BRCA1 decrease.

Untangling the heart’s genome: now in 3D

Research led by Australian Regenerative Medicine Institute and Monash Biomedicine Discovery Institute (BDI) researchers at Monash University has combined cutting-edge genomics and 3D “gaming” modelling to understand how all genes are expressed in different parts of the heart, unveiling complex patterns and novel markers. To help visualize this new research, the team, led by Monash group leaders Associate Professor Mirana Ramialison and Professor Jose Polo in collaboration with Dr Fernando Rossello, has developed a powerful tool called 3D-cardiomics.

This work has been recently published in the Journal of Molecular and Cellular Cardiology.

“One of the outstanding challenges in genomics research is understanding the physical context,” noted Associate Professor Ramialison, who has recently moved her research group to the Murdoch Children Research Institute to continue her work in heart development and genomics. “We can detect when gene expression is up or down-regulated in any number of tissues on a global level, but what is more complicated is understanding the spatial relationships in three dimensions. This is key to uncovering developmental and physiological processes of the heart, during both homeostasis and disease.”

The research team micro dissected and sequenced transcriptome-wide 18 anatomical sections of the adult mouse heart with this aim in mind. The study results unveiled known and novel genes that display complex spatial expression across the heart sub-compartments.

Birds learn to avoid plants that host dangerous insects

Cinnabar larvae feeding on ragwort
Credit: Callum McLellan

Young birds that eat insects with conspicuous warning coloration to advertise their toxicity to would-be predators quickly learn to avoid other prey that carry the same markings. Developing on this understanding, a University of Bristol team have shown for the very first time that birds don’t just learn the colors of dangerous prey, they can also learn the appearance of the plants such insects live on.

To do this, the scientists exposed artificial cinnabar caterpillars, characterized by bright yellow and black stripes, and non-signaling fake caterpillar targets to wild avian predation by presenting them on ragwort and a non-toxic plant - bramble, which is not a natural host of the cinnabar. Both target types survived better on ragwort compared to bramble when experienced predators were abundant in the population.

They were also interested in whether birds use the bright yellow flowers of ragwort as a cue for

An adult cinnabar moth on a ragwort stem
Credit: Callum McLellan

avoidance. They tested this by removing spikes of flowers from the ragwort and pinning them onto bramble, then recording target survival on either plant. In this second experiment, only the non-signaling targets survived better on plants with ragwort flowers, compared to the same plant type without the flowers. The survival of the cinnabar-like target was equal across all plant treatments

Lead author Callum McLellan, a graduate student at the School of Biological Sciences, said “Cinnabar caterpillars have this really recognizable, stripy yellow and black appearance. They also only live and feed on ragwort, which itself has distinctive yellow flowers. We have shown that birds learn that the ragwort flowers are a cue for danger, so can avoid going anywhere near toxic prey. It’s more efficient to avoid the whole plant than make decisions about individual caterpillars.”

Co-author Prof Nick Scott-Samuel of the School of Psychological Science, said “Our findings suggest that insect herbivores that specialize on easily recognizable host plants gain enhanced protection from predation, independent of their warning signal alone.”

Ragwort Credit: Callum McLellan

Prof Innes Cuthill, who conceived the study, added “Interestingly, any camouflaged caterpillars living on the same plant also benefit from birds’ learnt wariness of ragwort, despite being perfectly good to eat.

“Our results provide the opening to a brand-new discussion on how toxicity initially evolved in insect prey, and the conditions under which warning coloration is, or is not, favored.”

Paper:
‘Birds learn to avoid aposematic prey by using the appearance of host plants’ in Current Biology by Callum F. McLellan, Nicholas E. Scott-Samueland Innes C. Cuthill

Source/Credit: University of Bristol

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Crayfish and carp among invasive species pushing lakes towards ecosystem collapse

Asian silver carp

Human activity and climate change are causing invasive non-native species to spread rapidly across the globe. Researchers have found that certain invasive species can push lake ecosystems beyond a critical ‘tipping point’, causing a sudden shift from healthy to degraded conditions that is difficult to reverse.

Invasive fish such as Asian silver carp Hypophthalmichthys molitrix, and crustaceans such as American signal crayfish Pacifastacus leniusculus, were found to significantly reduce the abundance of other important organisms in lakes and degrade water quality. The findings, published today in the journal Global Change Biology, also provide guidance on the best ways to manage waterbodies.

Shallow lakes naturally exist in one of two alternative stable states: either healthy - with clear water with an abundance of vegetation, or degraded - with cloudy water dominated by algae. When a lake is in the latter state, algae use up all the nutrients in the water and block sunlight, preventing the growth of aquatic vegetation that would aid ecosystem recovery.

Deteriorated, algae-dominated freshwater ecosystems also threaten the health and water security of human populations. Blooms of cyanobacteria, known as ‘blue-green algae’ can produce toxins that contaminate food webs and poison water supplies.

The smarter the bird, the more mental stimulation it needs in captivity, a study has found

African grey parrot Photo by Magda Ehlers from Pexels

Researchers have discovered that intelligent birds have unique welfare needs in captivity.

These findings may apply to other brainy captive creatures including great apes, elephants and whales, said the head of the research group, Dr. Georgia Mason, Director of the University of Guelph’s Campbell Centre for the Study of Animal Welfare.

“This study provides the first empirical evidence that intelligent animals can struggle in captivity,” said Dr Mason, a professor in the Department of Integrative Biology. "Our findings could help pet owners identify which species may be more challenging to cater for as pets, because of their welfare requirements” added one of the lead authors, Dr Emma Mellor from the University of Bristol.

The study, also conducted by other researchers at University of Bristol and Utrecht University in the Netherlands, revealed for the first time that this issue can in particular hinder large-brained parrots’ in confinement.

Published recently in Proceedings of the Royal Society B, the study highlights cognitive stimulation and foods that require more complicated physical handling as ways to improve care of birds.

The researchers examined two main data sources. One was an early 1990s survey on captive breeding success involving more than 30,000 birds in the United States. The team also ran an online survey involving almost 1,400 pet parrots in 50 species for stereotypic behavior: repetitive abnormal activity such as biting at cage bars, chewing or even pulling out feathers, and swaying, bouncing or route pacing in cages.

Cracking the code of cellular defense

Purdue University will serve as the main site of the new Emergent Mechanisms in Biology of Robustness, Integration and Organization (EMBRIO) Institute. The institute, which will use AI to expand biology and engineering, has received $12.5 million from the National Science Foundation over five years as part of the agency’s Biology Integration Institutes program.
(EMBRIO illustration by Second Bay Studios. Courtesy of Purdue University.)

Imagine the day when any tissue or organ can be repaired or the replacements personalized to the patient.

That’s one of the goals of work being done by David Umulis of Purdue University and a team of scientists using artificial intelligence in biology to see how cells defend themselves from chemical or mechanical attack and/or repair their damage with the help of biochemical and mechanical inputs and reactions.

If this is successful, Umulis says, scientists could have a new way to address human health and longevity.

“If you can touch a network and modify three or four locations at once, the capability to treat diseases or damage will improve as you are signaling all these different biological pathways simultaneously,” he says.

Unlocking new potentials

Umulis uses AI in several of his biomedical engineering projects, including quantifying images and simulating developing cells. He finds that it provides results better, earlier and faster, and can be inexpensive compared with many hours simulating cell features.

But he wants to innovate and push further. The new Emergent Mechanisms in Biology of Robustness, Integration & Organization (EMBRIO) Institute will use AI to expand biology and engineering through exploring how cell signals are integrated to fight off invaders or activated to repair wounds, which are both essential to survive.

Over a third of COVID-19 patients diagnosed with at least one long-COVID symptom

37% of people had at least one long-COVID symptom diagnosed in the 3-6 month period after COVID-19 infection. The most common symptoms were breathing problems, abdominal symptoms, fatigue, pain and anxiety/depression.

This new study from the University of Oxford and the National Institute for Health Research (NIHR) Oxford Health Biomedical Research Centre (BRC) investigated long-COVID in over 270,000 people recovering from COVID-19 infection, using data from the US-based TriNetX electronic health record network.

The study reports on how commonly nine core long-COVID symptoms were diagnosed, and how this rate compared to people recovering from influenza. The nine core long-COVID symptoms, occurring 90-180 days after COVID-19 was diagnosed, comprise:

Male giraffes are more socially connected than females

 

A team of researchers has constructed the social network of more than 1,000 Masai giraffes in Tanzania and found that, while female giraffes have closer “friends” than males, male giraffes have more “acquaintances.” Understanding the complex multilevel society could have important conservation implications for these endangered giraffes. 
Image Credit: Derek Lee

Although female giraffes have closer “friends” than male giraffes, male giraffes have more “acquaintances” than females, according to a new study by an international team that includes a Penn State biologist. The study demonstrates that giraffes form a complex multilevel society that is driven by differences in the social connections among individuals, which could have conservation implications for the endangered giraffes.

“The degree to which an animal is connected to others in its social network influences reproductive success and population ecology, spread of information, and even how diseases move through a population,” said Derek Lee, associate research professor at Penn State and an author of the paper. “Information about sociality therefore can provide important guidance for conservation.”

The research team examined social connectedness and social movements of endangered Masai giraffes in the Tarangire Ecosystem of northern Tanzania using data collected over 5 years. The work, led by Juan Lavista Ferres of the Microsoft AI for Good Research Lab, involved constructing the social network of more than 1,000 free-ranging giraffes. The team presents their results in a paper appearing Sept. 27 in the journal Animal Behaviour.

Vampire bats may coordinate with ‘friends’ over a bite to eat

 

Photo: Sherri and Brock Fenton

Vampire bats that form bonds in captivity and continue those “friendships” in the wild also hunt together, meeting up over a meal after independent departures from the roost, according to a new study.

Researchers attached tiny “backpack” computers to 50 vampire bats – some that had previously been in captivity together and others that had lived only in the wild – to track their movement during their nightly foraging outings. By day, the bats shared a hollow tree in Panama, and at night they obtained their meals by drinking blood from wounds they made on cows in nearby pastures.

Tracking data showed that vampire bats set out to forage separately rather than as a group – and those that had established social relationships would reunite during the hunt for what the researchers speculated was some sort of coordination over food.

The findings suggest “making friends” in the roost could create more interdependence among socially bonded vampire bats – meaning they could benefit from each other’s success at obtaining blood meals and join forces when competing with other groups of bats for food resources.

“Everything we’ve been studying with vampire bats has looked at what they’re doing inside of a roost. What nobody has really known up until now is whether these social relationships serve any function outside the roost,” said study co-author Gerald Carter, assistant professor of evolution, ecology and organismal biology at The Ohio State University.

“Understanding their interactions with a completely different group of bats out on the pasture can help us understand what’s going on inside the colony. If every time they leave the roost they’re getting into battles, that can increase the amount of cooperation within the colony.”

Co-author Simon Ripperger, a former postdoctoral researcher in Carter’s lab, later supplemented the tracking data by capturing video and audio of foraging vampire bats. He observed bats clustered together on one cow and others atop separate cows, some drinking from different wounds and some fighting over food access. He also made what are likely the first audio recordings of a specific type of vampire bat vocalization associated with foraging.

Targeting tickborne diseases

"Benedict Khoo" Source: University of Minnesota

For Benedict Khoo, making a breakthrough discovery in health-related research doesn’t mean much if it can’t be put to use bettering people’s lives.

For Benedict Khoo, making a breakthrough discovery in health-related research doesn’t mean much if it can’t be put to use bettering people’s lives.

He knows from experience. When he worked in a research lab in Ohio, he felt “divorced from having a tangible impact,” due largely to regulatory hurdles in the field.

But that all changed when he turned to public health. There, he says, however his work turns out, he learns something that could help people make their own health decisions or influence policies. 

“That’s what drove me—to have that impact on the world and feel like I’m doing something,” says Khoo, a doctoral student in the School of Public Health (SPH). 

He found his niche with Jonathan Oliver, an assistant professor of environmental health sciences in SPH, who is now his adviser. Together they study the prevalence of Lyme disease and other tickborne diseases of humans, in a study area comprising Minnesota and adjacent northern Iowa and western Wisconsin. 

Flipping the “genetic paradox of invasions”

A close-up look at a green crab. Image credit: Ted Grosholz

The green crab, Carcinus maenas, is considered a globally distributed invasive species, an organism introduced by humans that eventually becomes overpopulated, with increased potential to negatively alter its new environment. Traditionally, it’s been assumed that successful populations contain high genetic diversity, or a variety of characteristics allowing them to adapt and thrive. On the contrary, the green crab - like many successful invasive populations - has low genetic diversity, while still spreading rapidly in a new part of the world.

A new study led by Carolyn Tepolt, an associate scientist of biology at Woods Hole Oceanographic Institution, is investigating the adaptive mechanisms of the green crab along the west coast of North America, where it has shown extensive dispersal in the last decade despite minimal genetic diversity. The study was published recently in Molecular Ecology and is a collaboration between WHOI, the University of California at Davis, Portland State University, and the Smithsonian Environmental Research Center.

“Invasive species like these are generally unwelcome. Green crabs can compete with native species, rip up eelgrass ‘nurseries’, and eat small shellfish before they have a chance to be harvested. Green crabs can be an ecological menace and an economic burden,” Tepolt said. “In this study, we found that one of the world's most serious marine invasive species has evolved specific genetic variation that likely helps it adapt to new environments really quickly, even when it's lost a lot of genetic diversity overall.”

Genetic diversity refers to small individual-to-individual differences in DNA, and often translates into a range of different inherited traits within a species. A population with high genetic diversity is more likely to include individuals with a wide range of different traits. In order for a population to adjust to changing environments, this variation can be crucial - or so scientists have often thought. Invasive species often challenge this assumption, successfully spreading in new regions despite low genetic diversity caused by descending from a small number of initial colonists.

This study focuses on a northwest Pacific population of green crab that has spread within the last 35 years from a single source. High-profile marine invasive species, such as green crabs, often live across thousands of kilometers of ocean, spanning countless environmental differences, both small and large. Using six U.S. west coast locations spanning over 900 miles from central California to British Columbia, Tepolt and her team examined the species’ genetic structure at thousands of places across its genome. While this population has lost a large amount of overall genetic diversity relative to its European source, a piece of DNA associated with cold tolerance in a prior study appears to be under strong selection from north to south across its invasive West Coast range.

This may represent a type of genetic feature - a balanced polymorphism - that evolved to promote rapid adaptation in variable environments despite high gene flow, and which now contributes to successful invasion and spread in a novel environment. Researchers do occasionally find incredibly successful populations that have passed through severe bottlenecks, dramatically decreasing their genetic diversity relative to their source. This study is amplifying the need to consider that diversity at specific parts of the genome (rather than genome-wide diversity) may play a critical role in resilience in new or changing environments.

“This is exciting for two main reasons. First, the study tests a partial resolution to ‘the genetic paradox of invasions’, demonstrating that variation at key parts of the genome permits rapid adaptation even in a population with low overall genetic diversity. Second, it suggests that high gene flow in a widespread species’ native range may generate evolutionary mechanisms, like this one, which provide that species with the substrate for rapid adaptive change as it spreads across new environments,” Tepolt explained.

Identifying invasive species spread can also be a job for non-scientists. As the climate changes and as humans get better and better at moving stuff around the globe, there’s more potential for species to come along for the ride and expand into new environments. Tepolt says it’s important to keep an eye out for cues, changes in the environment and possible new species in places they haven’t been before. She recommends seizing the opportunity to tell officials and researchers if there is something unusual at the coastline. There may be signs at beaches and boat ramps asking people to keep a lookout for particular species and giving contact information. If there are suddenly green crabs in an area for the first time, for example, on the West Coast in the Salish Sea and in Alaska, they likely should not be there and should be reported.

Source/Credit: Woods Hole Oceanographic Institution

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How land birds cross the open ocean

 

Terrestrial birds are capable of flying for hundreds of kilometers over the open sea. Nourani et al. show that the autumn migration trajectories of some of these birds correspond with uplift over the sea surface. Suitable uplift means less drag, making sea-crossing less energetically demanding. Moreover, strong uplift can allow the birds to soar.
© Elham Nourani / Max Planck Institute of Animal Behavior

Migrating birds choose routes with the best wind and uplift conditions, helping them to fly nonstop for hundreds of kilometers over the sea

Researchers at the Max Planck Institute of Animal Behavior and University of Konstanz in Germany have identified how large land birds fly nonstop for hundreds of kilometers over the open ocean—without taking a break for food or rest. Using GPS tracking technology, the team monitored the global migration of five species of large land birds that complete long sea crossings. They found that all birds exploited wind and uplift to reduce energy costs during flight—even adjusting their migratory routes to benefit from the best atmospheric conditions. This is the most wide-ranging study of sea-crossing behavior yet and reveals the important role of the atmosphere in facilitating migration over the open sea for many terrestrial birds.

Flying over the open sea can be dangerous for land birds. Unlike seabirds, land birds are not able to rest or feed on water, and so sea crossings must be conducted as nonstop flights. For centuries, bird-watchers assumed that large land birds only managed short sea crossings of less than 100 kilometers and completely avoided flying over the open ocean.

However, recent advances in GPS tracking technology have overturned that assumption. Data obtained by attaching small tracking devices on wild birds has shown that many land birds fly for hundreds or even thousands of kilometers over the open seas and oceans as a regular part of their migration.

But scientists are still unraveling how land birds are able to accomplish this. Flapping is an energetically costly activity, and trying to sustain nonstop flapping flight for hundreds of kilometers would not be possible for large, heavy land birds. Some studies have suggested that birds sustain such journeys using tailwind, a horizontal wind blowing in the bird’s direction of flight, which helps them save energy. Most recently, a study revealed that a single species—the osprey—used rising air thermals known as “uplift” to soar over the open sea.

Now, the new study has examined sea-crossing behavior of 65 birds across five species to gain the most wide-ranging insight yet into how land birds survive long flights over the open sea. The researchers analyzed 112 sea-crossing tracks, collected over nine years, with global atmospheric information to pinpoint the criteria that the birds use for selecting their migration routes over the open sea. A large international collaboration of scientists shared their tracking data to make this study possible.

The findings not only confirm the role of tailwind in facilitating sea-crossing behavior, but also reveal the widespread use of uplift for saving energy during these nonstop flights. Suitable uplift means less drag, making sea crossing less energetically demanding.

“Until recently, uplift was assumed to be weak or absent over the sea surface. We show that is not the case,” says first author Elham Nourani, a DAAD PRIME postdoctoral fellow at the Department of Biology at the University of Konstanz, who did the work when she was at the Max Planck Institute of Animal Behavior.

Terrestrial birds are capable of flying for hundreds of kilometers over the open sea. Nourani et al. show that the autumn migration trajectories of

some of these birds correspond with uplift over the sea surface. Suitable uplift means less drag, making sea-crossing less energetically demanding. Moreover, strong uplift can allow the birds to soar.

“Instead, we find that migratory birds adjust their flight routes to benefit from the best wind and uplift conditions when they fly over the sea. This helps them sustain flight for hundreds of kilometers,” says Nourani.

The oriental honey buzzard, for example, flies 700 kilometers over the East China Sea during its annual migration from Japan to southeast Asia. The roughly 18-hour nonstop sea crossing is conducted in autumn when the air movement conditions are optimal. “By making use of uplift, these birds can soar up to one kilometer above the sea surface,” says Nourani.

The study also raises the question of how migration will be affected by a changing climate. “Our findings show that many land birds are dependent on atmospheric support to complete their migrations over the open sea, indicating their vulnerability to any changes to the Earth’s atmospheric circulation patterns,” says Nourani. “Collaborative studies like this are important to unravel general patterns about how migratory birds depend on the weather patterns. This enables future studies to make robust predictions about how these birds will be impacted by climate change.”

Source/Credit: Max-Planck-Gesellschaft

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Newly developed software unveils relationships between RNA modifications and cancers

Researchers from CSI Singapore have developed a software called ModTect that identifies relationships between RNA modifications and the development of diseases as well as survival outcomes

 In a research breakthrough, a team of researchers from the Cancer Science Institute of Singapore (CSI Singapore) at the National University of Singapore has developed a software that can help reveal the relationships between RNA modifications and the development of diseases and disorders.

Led by Professor Daniel Tenen and Dr Henry Yang, the scientists devised ModTect – a new computational software that can identify RNA modifications using pre-existing sequencing data from clinical cohort studies. With ModTect, the team carried out their own novel pan-cancer study covering 33 different cancer types. They found associations between these RNA modifications and the different survival outcomes of cancer patients.

“This work is one of few studies demonstrating the association of mRNA modification with cancer development. We show that the epitranscriptome was dysregulated in patients across multiple cancer types and was additionally associated with cancer progression and survival outcomes,” explained Dr Henry Yang, Research Associate Professor from CSI Singapore.

"In the past decade, the ability to sequence the Human Genome has transformed the study of normal processes and diseases such as cancer. We anticipate that studies like this one, eventually leading to complete sequencing of RNA and detecting modifications directly in RNA, will also have a major impact on the characterization of disease and lead to novel therapeutic approaches," commented Prof Tenen, Senior Principal Investigator from CSI Singapore.

What are RNA modifications?

While most people are familiar with DNA, RNA plays just as much of a vital role in the human body’s cellular functions. Unlike DNA, which has the double-helix structure that most people are familiar with, RNA is a family of single-stranded molecules that perform various essential biological roles.

For example, messenger RNA (mRNA) conveys genetic information that directs the production of different proteins. Imagine DNA as an expansive library filled with books that carry instructions on how to make different proteins. Each letter in the sequences of words that make up the books’ contents are called nucleotides, which are small molecules that are used to store genetic information. To make sure these instructions are followed, mRNA makes copies of the books and carries them from a cell’s nucleus, where DNA is stored, to the ribosomes. These ribosomes are the “factories” where proteins are synthesized. Without RNA, the valuable genetic instructions stored in our cells would never be used.

Additional types of RNA perform other important functions. Some help catalyze biochemical reactions, just like enzymes, while others regulate gene expression.

Small chemical modifications to RNA can sometimes occur and alter the function and stability of the molecules. The study of these modifications and their effects is called ‘epitranscriptomics’. Research in the past has suggested a link between the development of diseases like Alzheimer’s disease and cancer with certain RNA modifications. However, despite multiple attempts to study these associations in deeper detail, the study of epitranscriptomes has proven to be difficult until this breakthrough by scientists from CSI Singapore.

In large patient cohorts, collecting and processing patient samples is challenging. Detecting RNA modifications often involves technically complex processes, such as treating the samples with chemicals that are difficult to access. These techniques often also require the use of large quantities of sample that are hard to obtain for rarer conditions. Because of this, scientists have been limited in their capacity to establish relationships between specific RNA modifications and various human diseases.

Software makes epitranscriptomics easier

The software that the CSI Singapore team created uses RNA sequences available from other large clinical cohort studies. To detect modifications in these RNA sequences, ModTect looks for mismatch signals and deletion signals. Mismatch signals arise when the experimental enzymes scientists use to turn RNA back into DNA incorporates random nucleotides during sequencing. Deletion signals, on the other hand, are when the enzymes sometimes skip a portion of the sequence. Together, these signals are referred to as misincorporation signals.

Unlike other models, ModTect does not require a database of misincorporation signal profiles corresponding to different types of RNA modifications to identify or classify them. ModTect can even identify new signal profiles that drastically differ from what has been previously recorded.

By applying the software to around 11,000 cancer patient RNA-sequencing datasets, the CSI Singapore team was able to embark on a novel study that investigated the associations between RNA modifications and clinical outcomes in patients. ModTect was able to utilize these large datasets and process them with robust statistical filtering. It unveiled that some types of epitranscriptome were associated with cancer progression and survival outcomes in patients. This finding highlighted the potential use of RNA modifications as biomarkers – molecules that can be used to test for diseases.

Unravelling the mystery of sequence differences that escape detection

As explored before, the transmission of genetic information from DNA in a cell’s nucleus to RNA molecules that carry it to a cell’s ribosomes is a critical process. However, this transmission process is not perfect and leads to differences in RNA-DNA sequences. The sites of these mismatches have been widely documented. However, it is unclear whether these observations are caused by modifications in mRNA and why these sites have escaped detection by Sanger sequencing (one of the most popular methods of DNA sequencing).

The group at CSI Singapore uncovered a potential explanation as to why these RNA modification signals have eluded detection over the years. They explained how some epitranscriptomes impede the use of standard reverse transcriptase (RT), the enzyme that is used to convert RNA into DNA. This enzyme is used by scientists in genome sequencing and its use is one of the most critical steps for experimental success. Hence, RNAs that had these impeding modifications were under-represented in Sanger sequencing techniques.

To combat this, the team used newly developed RT enzymes that have been known for their ability to bypass the effects of these modification sites. This allowed them to observe epitranscriptomes that were originally undetectable with Sanger sequencing.

The discipline of epitranscriptomics is still an emerging and rapidly developing field with around 170 RNA modifications being detected so far. By harnessing ModTect, Prof Tenen and his team were able to provide novel insights into the relationships between human diseases – like cancer – and such RNA modifications. The software will be publicly available on Github for other scientists to use.

The team is hopeful that their contribution will help further research that establishes any potential causal or mechanistic relationships between RNA modifications and tumor formation.

Source/Credit: National University of Singapore

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