Sep 8, 2026 04:54 PM
AI model decodes the language cells use to communicate
https://www.eurekalert.org/news-releases/1142799
INTRO: As an embryo develops from a small cluster of stem cells, those once “blank slate” cells begin to take on more specialized roles like brain, liver, or muscle cells, and organize themselves into three-dimensional structures such as tissues and organs.
The fate of each cell — what type of specialized cell it will become — depends on which genes are turned on or off in the cell. These patterns of gene activity shape the cell’s structure and function, enabling it to take on a specific role in the body.
But this decision isn’t up to individual cells. They constantly send and receive chemical signals to and from neighboring cells, which help them understand where they are, what stage of development they are in, and what they should become. These messages spread through multi-step sequences called signaling pathways, which translate external signals into specific changes in gene activity in the cell.
For researchers, being able to retrace the sequence of instructions a cell has received would offer a powerful way to understand how tissues develop and how these processes go awry in disease. But this has been difficult to achieve because scientists have long assumed that the effects of signaling pathways vary widely across cell types, meaning they would need to map each pathway separately in each cell type — an arduous and painstaking process.
Now, in a new study led by Whitehead Institute Member Pulin Li and graduate student Nicholas Hutchins, researchers have discovered that each signaling pathway leaves behind a unique “fingerprint” — a distinctive pattern of gene activity that reflects the particular signals the cell has encountered.
Importantly, these fingerprints are consistent across different cell types for the same signaling pathway, which means that instead of mapping each cell type separately, scientists can reconstruct signaling histories across many cell types using these pathway-specific fingerprints.
This discovery was made possible through a machine learning model called IRIS. This model can detect fingerprints of different signaling pathways and pinpoint which signals a cell received at different stages of development inside an embryo, even for cell types it hasn’t encountered before... (MORE - no ads)
Worm’s radical transformation shows metamorphosis can change the functions of cells
https://www.eurekalert.org/news-releases/1142673
INTRO: A squishy worm that starts its life as something of a floating head in the Pacific Ocean is changing what scientists know about metamorphosis at the cellular level.
Unlike humans, about 80% of animal species undergo metamorphosis, a stepped development from egg to larva to adult, but how it works at a cellular level is not well understood. Some theories and prior research suggested that the original cells in the larva die and are replaced with newly generated adult cells. Other work pointed to cells growing into their same function-for example, larval skin cells would become adult skin cells.
Instead, a Stanford-led study has found strong evidence in an acorn worm called Schizocardium californicum that most larval cells were reprogrammed, with even neurons taking on a new role in the adult organism.
“Reprogramming is a bit of an exotic fruit in developmental biology,” said Christopher Lowe, senior author on the study and biology professor in the Stanford School of Humanities and Sciences. “Generally, we used to think that as cells develop, they become increasingly restricted in their function. But when we start looking at more animals that go through metamorphosis, they may reveal that reprogramming is a much more common feature of development.”
Cellular reprogramming is thought to happen after an injury, or in some species that regenerate organs or whole limbs-but not as a feature of normal development. This study, published in Nature Communications, is the first known research to suggest extensive cellular reprogramming during normal development in an animal with a bilateral body plan, where one side of the body matches the other, as in humans.
Previous research has found some of this developmental type of reprogramming in sponges and jellyfish, two organisms that are far from humans on the evolutionary tree. In contrast, these acorn worms are part of the hemichordata phylum, considered an evolutionary link to vertebrate animals, including all mammals.
For this study, the team, led by first author Paul Bump, a former doctoral student in Lowe’s lab at Stanford’s Hopkins Marine Station, conducted genetic analyses on more than 87,000 cells from these acorn worms... (MORE - no ads)
https://www.eurekalert.org/news-releases/1142799
INTRO: As an embryo develops from a small cluster of stem cells, those once “blank slate” cells begin to take on more specialized roles like brain, liver, or muscle cells, and organize themselves into three-dimensional structures such as tissues and organs.
The fate of each cell — what type of specialized cell it will become — depends on which genes are turned on or off in the cell. These patterns of gene activity shape the cell’s structure and function, enabling it to take on a specific role in the body.
But this decision isn’t up to individual cells. They constantly send and receive chemical signals to and from neighboring cells, which help them understand where they are, what stage of development they are in, and what they should become. These messages spread through multi-step sequences called signaling pathways, which translate external signals into specific changes in gene activity in the cell.
For researchers, being able to retrace the sequence of instructions a cell has received would offer a powerful way to understand how tissues develop and how these processes go awry in disease. But this has been difficult to achieve because scientists have long assumed that the effects of signaling pathways vary widely across cell types, meaning they would need to map each pathway separately in each cell type — an arduous and painstaking process.
Now, in a new study led by Whitehead Institute Member Pulin Li and graduate student Nicholas Hutchins, researchers have discovered that each signaling pathway leaves behind a unique “fingerprint” — a distinctive pattern of gene activity that reflects the particular signals the cell has encountered.
Importantly, these fingerprints are consistent across different cell types for the same signaling pathway, which means that instead of mapping each cell type separately, scientists can reconstruct signaling histories across many cell types using these pathway-specific fingerprints.
This discovery was made possible through a machine learning model called IRIS. This model can detect fingerprints of different signaling pathways and pinpoint which signals a cell received at different stages of development inside an embryo, even for cell types it hasn’t encountered before... (MORE - no ads)
Worm’s radical transformation shows metamorphosis can change the functions of cells
https://www.eurekalert.org/news-releases/1142673
INTRO: A squishy worm that starts its life as something of a floating head in the Pacific Ocean is changing what scientists know about metamorphosis at the cellular level.
Unlike humans, about 80% of animal species undergo metamorphosis, a stepped development from egg to larva to adult, but how it works at a cellular level is not well understood. Some theories and prior research suggested that the original cells in the larva die and are replaced with newly generated adult cells. Other work pointed to cells growing into their same function-for example, larval skin cells would become adult skin cells.
Instead, a Stanford-led study has found strong evidence in an acorn worm called Schizocardium californicum that most larval cells were reprogrammed, with even neurons taking on a new role in the adult organism.
“Reprogramming is a bit of an exotic fruit in developmental biology,” said Christopher Lowe, senior author on the study and biology professor in the Stanford School of Humanities and Sciences. “Generally, we used to think that as cells develop, they become increasingly restricted in their function. But when we start looking at more animals that go through metamorphosis, they may reveal that reprogramming is a much more common feature of development.”
Cellular reprogramming is thought to happen after an injury, or in some species that regenerate organs or whole limbs-but not as a feature of normal development. This study, published in Nature Communications, is the first known research to suggest extensive cellular reprogramming during normal development in an animal with a bilateral body plan, where one side of the body matches the other, as in humans.
Previous research has found some of this developmental type of reprogramming in sponges and jellyfish, two organisms that are far from humans on the evolutionary tree. In contrast, these acorn worms are part of the hemichordata phylum, considered an evolutionary link to vertebrate animals, including all mammals.
For this study, the team, led by first author Paul Bump, a former doctoral student in Lowe’s lab at Stanford’s Hopkins Marine Station, conducted genetic analyses on more than 87,000 cells from these acorn worms... (MORE - no ads)