* . *
  • About
  • Advertise
  • Privacy & Policy
  • Contact
Tuesday, June 3, 2025
Earth-News
  • Home
  • Business
  • Entertainment
    Entertainment-Focused Narrative and Culture Change Practice – New America

    Transforming Culture Through Engaging Entertainment Narratives

    Rising stars: Young classical musicians surging on social media – Yahoo

    Meet the Next Generation of Classical Music Sensations Making Waves on Social Media!

    Devin Harjes Dies: ‘Manifest’ & ‘Boardwalk Empire’ Actor Was 41 – WyomingNews.com

    Tragic Loss: Devin Harjes, Star of ‘Manifest’ and ‘Boardwalk Empire,’ Passes Away at 41

    Why Starz Entertainment Stock Soared Today – The Motley Fool

    Unpacking the Surge: What Fueled Starz Entertainment’s Stock Explosion Today!

    Unveiling the Enigmatic: First Looks at Destruction and Puck in ‘The Sandman

    Jackie Chan Reveals This Family Member ‘Never Watched’ The Whole Of Any Of His Movies – Yahoo

    Jackie Chan Reveals This Family Member ‘Never Watched’ The Whole Of Any Of His Movies – Yahoo

  • General
  • Health
  • News

    Cracking the Code: Why China’s Economic Challenges Aren’t Shaking Markets, Unlike America’s” – Bloomberg

    Trump’s Narrow Window to Spread the Truth About Harris

    Trump’s Narrow Window to Spread the Truth About Harris

    Israel-Gaza war live updates: Hamas leader Ismail Haniyeh assassinated in Iran, group says

    Israel-Gaza war live updates: Hamas leader Ismail Haniyeh assassinated in Iran, group says

    PAP Boss to Niger Delta Youths, Stay Away from the Protest

    PAP Boss to Niger Delta Youths, Stay Away from the Protest

    Court Restricts Protests In Lagos To Freedom, Peace Park

    Court Restricts Protests In Lagos To Freedom, Peace Park

    Fans React to Jazz Jennings’ Inspiring Weight Loss Journey

    Fans React to Jazz Jennings’ Inspiring Weight Loss Journey

    Trending Tags

    • Trump Inauguration
    • United Stated
    • White House
    • Market Stories
    • Election Results
  • Science
  • Sports
  • Technology
    Finland Set to Lead EU Quantum Technology Defense Project – IoT World Today

    Finland Set to Lead EU Quantum Technology Defense Project – IoT World Today

    AI for lawyers: Win back your time using technology – nationaljurist.com

    Reclaim Your Time: How AI is Transforming the Legal Profession

    Prosecutors accuse men of exporting U.S. military technology to China – Milwaukee Journal Sentinel

    Men Charged with Illegally Exporting U.S. Military Technology to China

    ROLAND’S NEW WIRELESS TRIGGER TECHNOLOGY, PORTER & DAVIES ON TOUR, NEW 64 AUDIO ASPIRE UNIVERSAL IEM MODELS, WAVES FREE PLUGIN PACK – Modern Drummer Magazine

    ROLAND’S NEW WIRELESS TRIGGER TECHNOLOGY, PORTER & DAVIES ON TOUR, NEW 64 AUDIO ASPIRE UNIVERSAL IEM MODELS, WAVES FREE PLUGIN PACK – Modern Drummer Magazine

    This giant microwave may change the future of war – MIT Technology Review

    Revolutionizing Warfare: The Impact of a Game-Changing Giant Microwave

    Bajeed Pattan Joins Forbes Technology Council as Innovation Leader – PRWeb

    Bajeed Pattan Takes the Helm as Innovation Leader at Forbes Technology Council!

    Trending Tags

    • Nintendo Switch
    • CES 2017
    • Playstation 4 Pro
    • Mark Zuckerberg
No Result
View All Result
  • Home
  • Business
  • Entertainment
    Entertainment-Focused Narrative and Culture Change Practice – New America

    Transforming Culture Through Engaging Entertainment Narratives

    Rising stars: Young classical musicians surging on social media – Yahoo

    Meet the Next Generation of Classical Music Sensations Making Waves on Social Media!

    Devin Harjes Dies: ‘Manifest’ & ‘Boardwalk Empire’ Actor Was 41 – WyomingNews.com

    Tragic Loss: Devin Harjes, Star of ‘Manifest’ and ‘Boardwalk Empire,’ Passes Away at 41

    Why Starz Entertainment Stock Soared Today – The Motley Fool

    Unpacking the Surge: What Fueled Starz Entertainment’s Stock Explosion Today!

    Unveiling the Enigmatic: First Looks at Destruction and Puck in ‘The Sandman

    Jackie Chan Reveals This Family Member ‘Never Watched’ The Whole Of Any Of His Movies – Yahoo

    Jackie Chan Reveals This Family Member ‘Never Watched’ The Whole Of Any Of His Movies – Yahoo

  • General
  • Health
  • News

    Cracking the Code: Why China’s Economic Challenges Aren’t Shaking Markets, Unlike America’s” – Bloomberg

    Trump’s Narrow Window to Spread the Truth About Harris

    Trump’s Narrow Window to Spread the Truth About Harris

    Israel-Gaza war live updates: Hamas leader Ismail Haniyeh assassinated in Iran, group says

    Israel-Gaza war live updates: Hamas leader Ismail Haniyeh assassinated in Iran, group says

    PAP Boss to Niger Delta Youths, Stay Away from the Protest

    PAP Boss to Niger Delta Youths, Stay Away from the Protest

    Court Restricts Protests In Lagos To Freedom, Peace Park

    Court Restricts Protests In Lagos To Freedom, Peace Park

    Fans React to Jazz Jennings’ Inspiring Weight Loss Journey

    Fans React to Jazz Jennings’ Inspiring Weight Loss Journey

    Trending Tags

    • Trump Inauguration
    • United Stated
    • White House
    • Market Stories
    • Election Results
  • Science
  • Sports
  • Technology
    Finland Set to Lead EU Quantum Technology Defense Project – IoT World Today

    Finland Set to Lead EU Quantum Technology Defense Project – IoT World Today

    AI for lawyers: Win back your time using technology – nationaljurist.com

    Reclaim Your Time: How AI is Transforming the Legal Profession

    Prosecutors accuse men of exporting U.S. military technology to China – Milwaukee Journal Sentinel

    Men Charged with Illegally Exporting U.S. Military Technology to China

    ROLAND’S NEW WIRELESS TRIGGER TECHNOLOGY, PORTER & DAVIES ON TOUR, NEW 64 AUDIO ASPIRE UNIVERSAL IEM MODELS, WAVES FREE PLUGIN PACK – Modern Drummer Magazine

    ROLAND’S NEW WIRELESS TRIGGER TECHNOLOGY, PORTER & DAVIES ON TOUR, NEW 64 AUDIO ASPIRE UNIVERSAL IEM MODELS, WAVES FREE PLUGIN PACK – Modern Drummer Magazine

    This giant microwave may change the future of war – MIT Technology Review

    Revolutionizing Warfare: The Impact of a Game-Changing Giant Microwave

    Bajeed Pattan Joins Forbes Technology Council as Innovation Leader – PRWeb

    Bajeed Pattan Takes the Helm as Innovation Leader at Forbes Technology Council!

    Trending Tags

    • Nintendo Switch
    • CES 2017
    • Playstation 4 Pro
    • Mark Zuckerberg
No Result
View All Result
Earth-News
No Result
View All Result
Home Science

Getting dynamic information from static snapshots

April 27, 2024
in Science
Getting dynamic information from static snapshots
Share on FacebookShare on Twitter

Getting dynamic information from static snapshots

Part of an interdisciplinary University of Chicago team behind a new method of using static data from single-cell RNA sequencing to study how cells and genes change over time. From left, Biophysics graduate student Hanna Hieromnimon, Pritzker School of Molecular Engineering graduate student Joey Federico, Computer Science graduate student Ryan Robinett, PME Asst. Prof. Samantha Riesenfeld, Chemistry graduate student and paper first author Cheng Frank Gao, Chemistry graduate student Joseph Sifakis and Biophysics graduate student Hope Anderson. Credit: Lorenzo Orecchia

Imagine predicting the exact finishing order of the Kentucky Derby from a still photograph taken 10 seconds into the race.

That challenge pales in comparison to what researchers face when using single-cell RNA-sequencing (scRNA-seq) to study how embryos develop, cells differentiate, cancers form, and the immune system reacts.

In a paper published today in Proceedings of the National Academy of Sciences, researchers from the UChicago Pritzker School of Molecular Engineering and the Chemistry Department have created TopicVelo, a powerful new method of using the static snapshots from scRNA-seq to study how cells and genes change over time.

The team took an interdisciplinary, collaborative approach, incorporating concepts from classical machine learning, computational biology, and chemistry.

“In terms of unsupervised machine learning, we use a very simple, well-established idea. And in terms of the transcriptional model we use, it’s also a very simple, old idea. But when you put them together, they do something more powerful than you might expect,” said PME Assistant Professor of Molecular Engineering and Medicine Samantha Riesenfeld, who wrote the paper with Chemistry Department Prof. Suriyanarayanan Vaikuntanathan and their joint student, UChicago Chemistry Ph.D. candidate Cheng Frank Gao.

The trouble with pseudotime

Researchers use scRNA-seq to get measurements that are powerful and detailed, but by nature are static.

“We developed TopicVelo to infer cell-state transitions from scRNA-seq data,” Riesenfeld said. “It’s hard to do that from this kind of data because scRNA-seq is destructive. When you measure the cell this way, you destroy the cell.”

This leaves researchers a snapshot of the moment the cell was measured/destroyed. While scRNA-seq gives the best available transcriptome-wide snapshot, the information many researchers need, however, is how the cells transition over time. They need to know how a cell becomes cancerous or how a particular gene program behaves during an immune response.

To help figure out dynamic processes from a static snapshot, researchers traditionally use what’s called “pseudotime.” It’s impossible to watch an individual cell or gene’s expression change and grow in a still image, but that image also captured other cells and genes of the same type that might be a little further on in the same process. If the scientists connect the dots correctly, they can gain powerful insights into how the process looks over time.

Connecting those dots is difficult guesswork, based on the assumption that similar-looking cells are just at different points along the same path. Biology is much more complicated, with false starts, stops, bursts, and multiple chemical forces tugging on each gene.

Instead of traditional pseudotime approaches, which look at the expression similarity among the transcriptional profiles of cells, RNA velocity approaches look at the dynamics of transcription, splicing and degradation of the mRNA within those cells.

It’s a promising but early technology.

“The persistent gap between the promise and reality of RNA velocity has largely restricted its application,” the authors wrote in the paper.

To bridge this gap, TopicVelo puts aside deterministic models, embracing—and gleaning insights from—a far more difficult stochastic model that reflects biology’s inescapable randomness.

“Cells, when you think about them, are intrinsically random,” said Gao, the first author on the paper. “You can have twins or genetically identical cells that will grow up to be very different. TopicVelo introduces the use of a stochastic model. We’re able to better capture the underlying biophysics in the transcription processes that are important for mRNA transcription.”

Machine learning shows the way

The team also realized that another assumption limits standard RNA velocity. “Most methods assume that all cells are basically expressing the same big gene program, but you can imagine that cells have to do different kinds of processes simultaneously, to varying degrees,” Riesenfeld said. Disentangling these processes is a challenge.

Probabilistic topic modeling—a machine learning tool traditionally used to identify themes from written documents—provided the UChicago team with a strategy. TopicVelo groups scRNA-seq data not by the types of cell or gene, but by the processes those cells and genes are involved in. The processes are inferred from the data, rather than imposed by external knowledge.

“If you look at a science magazine, it will be organized along topics like ‘physics,’ ‘chemistry’ and ‘astrophysics,’ these kinds of things,” Gao said. “We applied this organizing principle to single-cell RNA-sequencing data. So now, we can organize our data by topics, like ‘ribosomal synthesis,’ ‘differentiation,’ ‘immune response,’ and ‘cell cycle’. And we can fit stochastic transcriptional models specific to each process.”

After TopicVelo disentangles this kludge of processes and organizes them by topic, it applies topic weights back onto the cells, to account for what percentage of each cell’s transcriptional profile is involved in which activity.

According to Riesenfeld, “This approach helps us look at the dynamics of different processes and understand their importance in different cells. And that’s especially useful when there are branch points, or when a cell is pulled in different directions.”

The results of combining the stochastic model with the topic model are striking. For example, TopicVelo was able to reconstruct trajectories that previously required special experimental techniques to recover. These improvements greatly broaden potential applications.

Gao compared the paper’s findings to the paper itself—the product of many areas of study and expertise.

“At PME, if you have a chemistry project, chances are there’s a physics or engineering student working on it,” he said. “It’s never just chemistry.”

More information:
Cheng Frank Gao et al, Dissection and integration of bursty transcriptional dynamics for complex systems, Proceedings of the National Academy of Sciences (2024). DOI: 10.1073/pnas.2306901121

Citation:
Getting dynamic information from static snapshots (2024, April 27)
retrieved 27 April 2024
from https://phys.org/news/2024-04-dynamic-static-snapshots.html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no
part may be reproduced without the written permission. The content is provided for information purposes only.

>>> Read full article>>>
Copyright for syndicated content belongs to the linked Source : Phys.org – https://phys.org/news/2024-04-dynamic-static-snapshots.html

Tags: dynamicGettingscience
Previous Post

Ancient Maya blessed their ballcourts: Researchers find evidence of ceremonial offerings in Mexico

Next Post

‘Everyone sits out’: Yangon parks offer heat wave relief

Finland Set to Lead EU Quantum Technology Defense Project – IoT World Today

Finland Set to Lead EU Quantum Technology Defense Project – IoT World Today

June 3, 2025
Road accident in northern Nigeria kills 22 athletes returning from a sports festival – ABC News

Tragic Road Accident Claims Lives of 22 Athletes Returning from Sports Festival in Northern Nigeria

June 3, 2025
AI carves out a niche in ecology and conservation research – Nature

AI carves out a niche in ecology and conservation research – Nature

June 3, 2025
Opinion | JD Vance Defies the Market’s Gravity – WSJ

JD Vance: Challenging Market Norms and Defying Expectations

June 3, 2025
RFK Jr. Says Healthy Pregnant Women Don’t Need Covid Boosters. What the Science Says. – KFF Health News

RFK Jr. Challenges Covid Booster Necessity for Healthy Pregnant Women: What the Research Reveals

June 3, 2025
Updates to Lifestyle’s Spring Quarter bucket list – The UCSD Guardian

Exciting New Additions to Your Spring Quarter Bucket List!

June 3, 2025
It’s Waymo’s World. We’re All Just Riding in It. – WSJ

Welcome to Waymo’s World: The Future of Autonomous Driving Awaits!

June 3, 2025
Fed’s Logan: The US economy remains resilient – FXStreet

Fed’s Logan: The US economy remains resilient – FXStreet

June 3, 2025
Entertainment-Focused Narrative and Culture Change Practice – New America

Transforming Culture Through Engaging Entertainment Narratives

June 3, 2025
NC lawmakers target pharmacy “middlemen” in proposed reforms – North Carolina Health News

NC Lawmakers Take Aim at Pharmacy Middlemen with Bold Reform Proposals

June 3, 2025

Categories

Archives

June 2025
MTWTFSS
 1
2345678
9101112131415
16171819202122
23242526272829
30 
« May    
Earth-News.info

The Earth News is an independent English-language daily published Website from all around the World News

Browse by Category

  • Business (20,132)
  • Ecology (661)
  • Economy (675)
  • Entertainment (21,581)
  • General (15,257)
  • Health (9,718)
  • Lifestyle (678)
  • News (22,149)
  • People (677)
  • Politics (684)
  • Science (15,896)
  • Sports (21,181)
  • Technology (15,663)
  • World (663)

Recent News

Finland Set to Lead EU Quantum Technology Defense Project – IoT World Today

Finland Set to Lead EU Quantum Technology Defense Project – IoT World Today

June 3, 2025
Road accident in northern Nigeria kills 22 athletes returning from a sports festival – ABC News

Tragic Road Accident Claims Lives of 22 Athletes Returning from Sports Festival in Northern Nigeria

June 3, 2025
  • About
  • Advertise
  • Privacy & Policy
  • Contact

© 2023 earth-news.info

No Result
View All Result

© 2023 earth-news.info

No Result
View All Result

© 2023 earth-news.info

Go to mobile version