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“Revolutionizing Protein Science with AI: Introducing InstaNovo and InstaNovo+”

Researchers have developed new AI models that can vastly improve accuracy and discovery within protein science. Potentially, the models will assist the medical sciences in overcoming present challenges within, e.g. personalised medicine, drug discovery, and diagnostics.

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In a breakthrough that promises to revolutionize protein science, researchers have developed two novel AI models, InstaNovo and InstaNovo+, which can vastly improve accuracy and discovery within this critical field. These models are designed to assist medical practitioners, commercial entities, and researchers in finding exactly the necessary information in vast amounts of data.

Proteomics, the study of proteins on a large scale, is an essential sub-field where vast amounts of protein data are gathered in databases against which a sample can be compared. While these tools are very useful and effective, there are limits to what they can do. Traditional methods rely on pre-existing databases, which often don’t include everything relevant to specific needs.

InstaNovo and InstaNovo+ change this paradigm by proposing novel AI models that exceed state-of-the-art performance and are significantly more precise than currently available tools. These models can identify proteins that have never been documented before, expanding the landscape of proteomic discovery.

To assess the usefulness of their models, the researchers have trained and tested them on several specific tasks within major areas of interest. One investigation was performed on wound fluid from venous leg ulcer patients. The models could map ten times as many sequences as a database search, among them E. coli and Pseudomonas aeruginosa – the latter being a multidrug-resistant bacterium.

Another use case was conducted on small pieces of protein, called peptides, displayed on the surface of cells. These help the immune system recognize infections and diseases such as cancer. The InstaNovo models identified thousands of new peptides that were not found using traditional methods. In personalised cancer treatments empowering the immune system – immunotherapy for short – these peptides are all potential attack points.

The paper provides six additional cases that demonstrate how these models improve therapeutic sequencing, discover novel peptides, detect unreported organisms, and significantly enhance proteomics searches. The implications of their results extend far beyond the medical sciences, says Timothy Patrick Jenkins:

“Looking at it from a purely technical, scientific perspective, it is also true that with these tools, we can improve our understanding of the biological world as a whole, not only in terms of healthcare but also in industry and academia. Within every field using proteomics – be it plant science, veterinary science, industrial biotech, environmental monitoring, or archaeology – we can gain insights into protein landscapes that have been inaccessible until now.”

The InstaNovo models are available to researchers through the InstaDeep website, providing a powerful tool for accelerating biological discovery.

Animals

A “Roadmap” to Understanding the Fruit Fly Brain: Breakthrough Study Reveals Comprehensive Insights into Entire Nervous System

Researchers have gained comprehensive insights into the entire nervous system of the fruit fly (Drosophila melanogaster). The study describes in detail the neurons that span the entire nervous system of the adult fruit fly. The researchers also compared the complete set of neural connections (the connectome) in a female and a male specimen — and identified differences.

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The fruit fly (Drosophila melanogaster) has long been a model organism for scientists studying genetics, development, and behavior. However, despite its importance, the intricacies of the fruit fly’s nervous system have remained somewhat of a mystery – until now. Researchers at Leipzig University and other institutions have made a groundbreaking discovery, publishing a study in Nature that provides comprehensive insights into the entire nervous system of the adult fruit fly.

For the first time, scientists have mapped out the neural connections (the connectome) in a female and a male specimen, revealing differences between the two sexes. This breakthrough is a significant step forward in understanding the complex interactions within the fruit fly’s brain and nervous system.

The study, led by Dr. Katharina Eichler from Leipzig University, involved analyzing three connectomes: one female brain data set and two nerve cord data sets (one male, one female). The researchers used light microscopy to identify all neurons in the neck of the fruit fly that could be visualized using this technique.

This allowed them to analyze the circuits formed by these cells in their entirety. When comparing male and female neurons, the scientists identified sex-specific differences for the first time. They found previously unknown cells that exist only in one sex and are absent in the other.

One notable example is a descending neuron known as aSP22, which communicates with neurons present only in females. This finding provides an explanation for the behavioral differences observed when this neuron is active: female flies extend their abdomen to lay eggs, while males curl theirs forward to mate.

The study’s findings are significant not only because they provide a comprehensive overview of the fruit fly connectome but also because they offer a “roadmap” for future research. By understanding the intricate connections within the nervous system, scientists can design more intelligent experiments to investigate the function of individual neurons or entire circuits – saving time and resources.

As Eichler notes, now that the technical challenges in analyzing the fruit fly’s nervous system have been overcome, her research group is working on two new data sets covering the entire central nervous system of both a female and a male specimen. This continued research will undoubtedly shed more light on the complexities of the fruit fly brain and its implications for our understanding of nervous systems in general.

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Biodiversity

Unveiling Hidden Gems: Two New Crocodile Species Discovered in Mexico

Biologists have discovered two previously unknown species of crocodiles, one living on the island of Cozumel and the other on the atoll of Banco Chinchorro, both off the Yucat n Peninsula. The findings challenge long-held assumptions about the American crocodile (Crocodylus acutus) and highlight the urgent need for conservation efforts, the researchers say.

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The American crocodile, a species once thought to be widespread across the Caribbean, Central America, and Mexico’s Pacific coast, has been hiding secrets. Researchers from McGill University, in collaboration with Mexican scientists, have made a groundbreaking discovery that challenges long-held assumptions about this iconic creature. Two previously unknown species of crocodiles have been found on the island of Cozumel and the atoll of Banco Chinchorro, both located off the Yucatán Peninsula.

“Biodiversity is disappearing faster than we can discover what we’re losing,” said Biology Professor Hans Larsson, the principal investigator. “Most species of crocodiles are already endangered, and rapid shoreline development threatens nearly every population. Our research aimed to uncover the true diversity of crocodiles on these isolated islands.”

Larsson and his team analyzed the genetic sequences of crocodile populations from Cozumel and Banco Chinchorro. By comparing these sequences to those of crocodiles across the Caribbean, Central America, and Mexico’s Pacific coast, they found striking levels of genetic differentiation, leading them to conclude that these populations were not simply variants of Crocodylus acutus.

“These results were totally unexpected,” former Larsson graduate student and lead author José Avila-Cervantes said. “We assumed Crocodylus acutus was a single species ranging from Baja California to Venezuela and across the Caribbean. Our study is the first to extensively explore genomic and anatomical variation in these animals.”

This discovery has significant conservation implications, as the newly identified species live in small, isolated populations, each numbering fewer than 1,000 breeding individuals. While both populations appear stable, their limited numbers and habitat restrictions make them vulnerable.

“The rapid loss of biodiversity can only be slowed if we know what species are most at risk,” said Larsson. “Now that we recognize these crocodiles as distinct species, it’s crucial to protect their habitats. Limiting land development and implementing careful conservation strategies on Cozumel and Banco Chinchorro will be key to ensuring their survival.”

The research was conducted with the help of local colleagues, including Pierre Charruau at El Colegio de la Frontera Sur in Mexico. The team captured and released crocodiles, collecting blood and scale samples for analysis. Genetic sequencing was carried out at McGill by José Avila-Cervantes during his graduate studies, with additional research on skull morphology by fellow McGill graduate student Hoai-Nam Bui.

This research was funded by the Canadian Foundation for Innovation, the Digital Research Alliance of Canada), the Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, and the Natural Sciences and Engineering Research Council of Canada.

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Biochemistry

Unraveling Nature’s Secret: How Velvet Worm Slime Could Revolutionize Sustainable Materials Design

A new discovery about the slime ejected by velvet worms could revolutionize sustainable material design. The findings outline how a naturally occurring protein structure, conserved across species from Australia, Singapore and Barbados over nearly 400 million years of evolution, enables the slime’s transformation from liquid to fiber and back again. It’s a discovery that could inspire next-generation recyclable bioplastics.

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The discovery of the remarkable properties of velvet worm slime has sent shockwaves through the scientific community, offering new hope for sustainable material design. Researchers from McGill University have made a groundbreaking find that could lead to the development of next-generation recyclable bioplastics.

Velvet worms, small caterpillar-like creatures found in humid forests of the southern hemisphere, possess an extraordinary ability – their slime can transform from liquid to fibre and back again. This remarkable property has puzzled scientists for centuries, but a team led by Matthew Harrington, a chemistry professor and Canada Research Chair in green chemistry, has finally decoded the molecular structure behind this phenomenon.

Using protein sequencing and AI-driven structure prediction (AlphaFold), the researchers identified previously unknown proteins in the slime that function similarly to cell receptors in the immune system. These receptor proteins appear to link large structural proteins during fibre formation, enabling the slime’s remarkable reversibility.

The implications of this discovery are profound. Traditional plastics and synthetic fibres require energy-intensive processes to manufacture and recycle, often involving heat or chemical treatments. In contrast, the velvet worm uses simple mechanical forces – pulling and stretching – to generate strong, durable fibres from biorenewable precursors, which can later be dissolved and reused without harmful byproducts.

While a plastic bottle that dissolves in water may seem like an impractical solution, Harrington believes that adjusting the chemistry of this binding mechanism could overcome this limitation. The team’s next challenge will be to experimentally verify the binding interactions and explore whether the principle can be adapted for engineered materials.

The study was co-authored by researchers from McGill University and Nanyang Technological University (NTU) in Singapore, highlighting the importance of international collaboration in addressing pressing global challenges.

As Harrington aptly puts it, “Nature has already figured out a way to make materials that are both strong and recyclable. By decoding the molecular structure of velvet worm slime, we’re now one step closer to replicating that efficiency for the materials we use every day.”

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