Daily Archives: October 24, 2024

Groundbreaking 3D Brain Atlas Helps Scientists Track Developmental Disorders in Stunning Detail

Researchers developed a 3D atlas of the developing mouse brain, offering insights into brain growth and disorders. The atlas, available online, was created using advanced imaging techniques across seven developmental stages.
New high-resolution maps of the mouse brain provide researchers with valuable insights into brain development and offer a powerful tool for studying neurodevelopmental disorders.
Researchers at Penn State College of Medicine, in collaboration with five other institutes, have developed a 3D atlas of developing mouse brains using advanced imaging and microscopy techniques. This innovative atlas offers a comprehensive, 360-degree view of the entire mammalian brain during embryonic and early postnatal stages. It serves as a valuable reference and anatomical framework, aiding researchers in studying brain development and neurodevelopmental disorders.
They recently published their work in Nature Communications.
“Maps are a fundamental infrastructure to build knowledge upon but we don’t have a high-resolution 3D atlas of the developing brain,” said Yongsoo Kim, associate professor of neural and behavioral sciences at Penn State College of Medicine and senior author on the paper. “We are generating high-resolution maps that we can use to understand how the brain grows under normal circumstances and what happens when a brain disorder emerges.”
The Importance of Brain Atlases
Geographical atlases are a collection of maps that provide a comprehensive view of the Earth’s geography including boundaries between regions and countries, features like mountains and rivers, and thoroughfares like roads and highways. Importantly, they provide a common understanding that allows users to pinpoint specific locations and understand the spatial relationship between regions.
Similarly, brain atlases are foundational for understanding the architecture of the brain. They help researchers visualize how the brain is organized spatially and understand brain structure, function, and how different regions and neurons are connected. Previously, scientists have been limited to 2D histology-based snapshots, which makes it challenging to interpret anatomical regions in three dimensions and any changes that may occur, Kim said.
Researchers developed a 3D atlas of the developing mouse brain, with such images as this. Credit: Provided by the Kim Lab / Penn State
In recent years, there has been tremendous progress in whole brain imaging techniques that let researchers look at the whole brain at high resolution and produce large-scale 3D datasets. To analyze this data, Kim explained, scientists have developed 3D reference atlases of the adult mouse brain, which is a model for the mammalian brain. The atlases provide a universal anatomical framework that allows researchers to overlay diverse datasets and conduct comparative analyses. However, there’s no equivalent for the developing mouse brain, which undergoes rapid changes in shape and volume during the embryonic and post-natal stages.
“Without this 3D map of the developing brain, we cannot integrate data from emerging 3D studies into a standard spatial framework or analyze the data in a consistent manner,” Kim said. In other words, the lack of a 3D map hinders the advancement of neuroscience research.
The research team created a multimodal 3D common coordinate framework of the mouse brain across seven developmental timepoints — four points of time during the embryonic period and three periods during the immediate postnatal phase. Using MRI, they captured images of the brain’s overall form and structure. They then employed light sheet fluorescence microscopy, an imaging technique that enables visualization of the whole brain at a single-cell resolution. These high-resolution images were then matched to the shape of the MRI templates of the brain to create the 3D map. The team pooled samples from both male and female mice.
Creation of the 3D Brain Atlas
To demonstrate how the atlas can be used to analyze different datasets and track how individual cell types emerge in the developing brain, the team focused on GABAergic neurons, which are nerve cells that play a key communication role in the brain. This cell type has been implicated in schizophrenia, autism and other neurological disorders.
While scientists have studied GABAergic neurons in the outermost region of the brain called the cortex, not much is known about how these cells arise in the whole brain during development, according to the researchers. Understanding how these clusters of cells develop under normal conditions may be key to assessing what happens when something goes awry.
To facilitate collaboration and further advancement in neuroscience research, the team created an interactive web-based version that is publicly available and free. The aim is to significantly lower technical barriers for researchers around the world to access this resource.
“This provides a roadmap that can integrate a lot of different data — genomic, neuroimaging, microscopy, and more — into the same data infrastructure. It will drive the next evolution of brain research driven by machine learning and artificial intelligence,” Kim said.
Reference: “Developmental mouse brain common coordinate framework” by Fae N. Kronman, Josephine K. Liwang, Rebecca Betty, Daniel J. Vanselow, Yuan-Ting Wu, Nicholas J. Tustison, Ashwin Bhandiwad, Steffy B. Manjila, Jennifer A. Minteer, Donghui Shin, Choong Heon Lee, Rohan Patil, Jeffrey T. Duda, Jian Xue, Yingxi Lin, Keith C. Cheng, Luis Puelles, James C. Gee, Jiangyang Zhang, Lydia Ng and Yongsoo Kim, 21 October 2024, Nature Communications.DOI: 10.1038/s41467-024-53254-w
Other Penn State College of Medicine authors on the paper include: Fae Kronman, joint degree student in the MD/PhD Medical Scientist Training Program; Josephine Liwang, doctoral student; Rebecca Betty, research technologist; Daniel Vanselow, research project manager; Steffy Manjila, postdoctoral scholar; Jennifer Minteer, research technologist; Donghui Shin, research technologist; Rohan Patil, student; and Keith Cheng, distinguished professor, department of pathology.
Nicholas Tustison at the University of Virginia School of Medicine; Ashwin Bhandiwad and Lydia Ng at the Allen Institute for Brain Science; Choong Heon Lee and Jiangyang Zhang at the NYU Grossman School of Medicine; Jeffrey Duda and James Gee at the University of Pennsylvania; Jian Xue and Yingxi Lin at the University of Texas Southwestern Medical Center; Luis Puelles at the Universidad de Murcia; and Yuan-Ting Wu, who was previously research scientist at Penn State and currently project scientist at Cedars-Sinai Medical Center, also contributed to the paper.
The National Institutes of Health’s grants RF1MH12460501 from the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, R01NS108407, R01MH116176 and R01EB031722 supported this work.

Groundbreaking 3D Brain Atlas Helps Scientists Track Developmental Disorders in Stunning Detail

Researchers developed a 3D atlas of the developing mouse brain, offering insights into brain growth and disorders. The atlas, available online, was created using advanced imaging techniques across seven developmental stages.
New high-resolution maps of the mouse brain provide researchers with valuable insights into brain development and offer a powerful tool for studying neurodevelopmental disorders.
Researchers at Penn State College of Medicine, in collaboration with five other institutes, have developed a 3D atlas of developing mouse brains using advanced imaging and microscopy techniques. This innovative atlas offers a comprehensive, 360-degree view of the entire mammalian brain during embryonic and early postnatal stages. It serves as a valuable reference and anatomical framework, aiding researchers in studying brain development and neurodevelopmental disorders.
They recently published their work in Nature Communications.
“Maps are a fundamental infrastructure to build knowledge upon but we don’t have a high-resolution 3D atlas of the developing brain,” said Yongsoo Kim, associate professor of neural and behavioral sciences at Penn State College of Medicine and senior author on the paper. “We are generating high-resolution maps that we can use to understand how the brain grows under normal circumstances and what happens when a brain disorder emerges.”
The Importance of Brain Atlases
Geographical atlases are a collection of maps that provide a comprehensive view of the Earth’s geography including boundaries between regions and countries, features like mountains and rivers, and thoroughfares like roads and highways. Importantly, they provide a common understanding that allows users to pinpoint specific locations and understand the spatial relationship between regions.
Similarly, brain atlases are foundational for understanding the architecture of the brain. They help researchers visualize how the brain is organized spatially and understand brain structure, function, and how different regions and neurons are connected. Previously, scientists have been limited to 2D histology-based snapshots, which makes it challenging to interpret anatomical regions in three dimensions and any changes that may occur, Kim said.
Researchers developed a 3D atlas of the developing mouse brain, with such images as this. Credit: Provided by the Kim Lab / Penn State
In recent years, there has been tremendous progress in whole brain imaging techniques that let researchers look at the whole brain at high resolution and produce large-scale 3D datasets. To analyze this data, Kim explained, scientists have developed 3D reference atlases of the adult mouse brain, which is a model for the mammalian brain. The atlases provide a universal anatomical framework that allows researchers to overlay diverse datasets and conduct comparative analyses. However, there’s no equivalent for the developing mouse brain, which undergoes rapid changes in shape and volume during the embryonic and post-natal stages.
“Without this 3D map of the developing brain, we cannot integrate data from emerging 3D studies into a standard spatial framework or analyze the data in a consistent manner,” Kim said. In other words, the lack of a 3D map hinders the advancement of neuroscience research.
The research team created a multimodal 3D common coordinate framework of the mouse brain across seven developmental timepoints — four points of time during the embryonic period and three periods during the immediate postnatal phase. Using MRI, they captured images of the brain’s overall form and structure. They then employed light sheet fluorescence microscopy, an imaging technique that enables visualization of the whole brain at a single-cell resolution. These high-resolution images were then matched to the shape of the MRI templates of the brain to create the 3D map. The team pooled samples from both male and female mice.
Creation of the 3D Brain Atlas
To demonstrate how the atlas can be used to analyze different datasets and track how individual cell types emerge in the developing brain, the team focused on GABAergic neurons, which are nerve cells that play a key communication role in the brain. This cell type has been implicated in schizophrenia, autism and other neurological disorders.
While scientists have studied GABAergic neurons in the outermost region of the brain called the cortex, not much is known about how these cells arise in the whole brain during development, according to the researchers. Understanding how these clusters of cells develop under normal conditions may be key to assessing what happens when something goes awry.
To facilitate collaboration and further advancement in neuroscience research, the team created an interactive web-based version that is publicly available and free. The aim is to significantly lower technical barriers for researchers around the world to access this resource.
“This provides a roadmap that can integrate a lot of different data — genomic, neuroimaging, microscopy, and more — into the same data infrastructure. It will drive the next evolution of brain research driven by machine learning and artificial intelligence,” Kim said.
Reference: “Developmental mouse brain common coordinate framework” by Fae N. Kronman, Josephine K. Liwang, Rebecca Betty, Daniel J. Vanselow, Yuan-Ting Wu, Nicholas J. Tustison, Ashwin Bhandiwad, Steffy B. Manjila, Jennifer A. Minteer, Donghui Shin, Choong Heon Lee, Rohan Patil, Jeffrey T. Duda, Jian Xue, Yingxi Lin, Keith C. Cheng, Luis Puelles, James C. Gee, Jiangyang Zhang, Lydia Ng and Yongsoo Kim, 21 October 2024, Nature Communications.DOI: 10.1038/s41467-024-53254-w
Other Penn State College of Medicine authors on the paper include: Fae Kronman, joint degree student in the MD/PhD Medical Scientist Training Program; Josephine Liwang, doctoral student; Rebecca Betty, research technologist; Daniel Vanselow, research project manager; Steffy Manjila, postdoctoral scholar; Jennifer Minteer, research technologist; Donghui Shin, research technologist; Rohan Patil, student; and Keith Cheng, distinguished professor, department of pathology.
Nicholas Tustison at the University of Virginia School of Medicine; Ashwin Bhandiwad and Lydia Ng at the Allen Institute for Brain Science; Choong Heon Lee and Jiangyang Zhang at the NYU Grossman School of Medicine; Jeffrey Duda and James Gee at the University of Pennsylvania; Jian Xue and Yingxi Lin at the University of Texas Southwestern Medical Center; Luis Puelles at the Universidad de Murcia; and Yuan-Ting Wu, who was previously research scientist at Penn State and currently project scientist at Cedars-Sinai Medical Center, also contributed to the paper.
The National Institutes of Health’s grants RF1MH12460501 from the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, R01NS108407, R01MH116176 and R01EB031722 supported this work.

Maharashtra Reduces Passing Marks For Math And Science In Class 10

The certificates of these students will declare them ‘pass’. New Delhi: The Maharashtra State Council for Educational Research and Training (SCERT), has decided to reduce the passing mark for Math and Science subjects in Class 10. The board will lower the marks from 35 to 20 for the students. The decision has been announced in…

Maharashtra Reduces Passing Marks For Math And Science In Class 10

The certificates of these students will declare them ‘pass’. New Delhi: The Maharashtra State Council for Educational Research and Training (SCERT), has decided to reduce the passing mark for Math and Science subjects in Class 10. The board will lower the marks from 35 to 20 for the students. The decision has been announced in…

Becoming Christlike through political science

Moana Numanga, an assistant professor in the Faculty of Business & Government, teaches a class in Ethics and the Legal Environment.

Photo by Camille Jovenes

Heather Walker’s majors in intercultural peacebuilding and political science have helped her to develop a hopeful view of politics and learn how to create communities more closely aligned with Christ’s teachings, she said. Similar to Walker, who is a senior from California, two current BYU–Hawaii students and two alumnae who studied political science share how they feel politics has the potential to be used for the common good.Mari Kojima, a BYUH alumna from Japan who studied intercultural peacebuilding, emphasized how Christ’s teachings of unconditional love can be found in politics. “I feel that political science has given me a training to be open to and explore other people’s perspectives,” she shared. “Our beliefs mean the world to us, so we should be respectful to what others think and feel because if we deny [their perspectives], we might end up hurting them as if their worlds are illegitimate.”Rachel Akana, a BYUH alumna from the Island of Hawai’i who studied political science and social work, observed similarly to Kojima that studying political science, “does a good job of unifying people through understanding. That grows our empathy for people, our compassion, our patience.” Both Akana and Kojima emphasized how studying political science can humanize other perspectives and lifestyles and allow diverse communities to become more loving and unified. Akana said politics and history are intertwined, and an understanding of these two disciplines can strengthen communities through lives devoted to public service. “Political science does a really good job of recognizing those who came before us, where we are now, how we can move forward and what we can do to help one another,” she explained.Camilla Marie Fajardo, a BYUH senior and political science major, commented, “Jesus Christ teaches us about the importance of following the laws of the land. Political science has not only helped me to understand the law of the land better but also helped me understand how communities work. It has helped me understand why wars happen and what we can do to build peace.” She also said majoring in political science helped her understand how legislation can be used to serve others and spread God’s love.Just as Fajardo noted the value in being a good citizen, Vilai Ilolahia, a current political science senior from Tonga, said he felt the realm of politics cannot be inherently evil because, “Jesus Christ was a politician [who advocated] for Gentiles and those who weren’t of a Jewish faith. His point was to focus on Him to get to the Father.” Moreover, Ilolahia also said political science “taught [him] how to suss out … leaders who are for the people and those who are in it for personal gain,” highlighting how individuals can use the spiritual gift of discernment when deciding who to elect to public office.

Political science students learn in a classroom on BYUH’s campus.

Photo by Camille Jovenes

Walker said political science has helped her be a better disciple of Jesus Christ, “because so much of political science is focused on meeting people’s needs with the resources available to you,” which she said is what God does for His children. “Aside from the church, it is the most influential way to build up the kingdom of God. Government is established to help people and raise their quality of life, which I would say is exactly what Christ asks us to do when we make covenants with Him.”Being at BYUH has helped Fajardo develop a more hopeful view of politics, she said. “Our teachers don’t just talk about [what bad things are happening in the world], but they bring to us ways in which we can change it … to make the world a better place.” She also said being at a school with students from dozens of different nationalities and cultures has helped her to learn how communities can, “come together more instead of separating … We live in this world together. We have to figure out how to work together. It’s never going to be a world of just one country or just one culture, so we have to figure out how to work together.” She said BYUH is a university that excels at building cross-cultural dialogue and cooperation.Akana said living in Laie was formative in helping her learn how she can help her native Hawaiian community. She shared, “Rubbing shoulders with community mentors here has empowered me to hone in on my cultural heritage.” She specified the ways in which they lead Pacific Island-based cultural education reminds her that all peoples of the Pacific are connected. “They are maintaining focus in ancestral knowledge and writing the holistic playbook to how our [Asian American and Pacific Islander] communities can thrive within our cultures. I am very grateful for the work they are doing inside and outside of the church.”However, she said she does not care for what the term “political science” sometimes represents. “Our systems are nothing without our communities and our culture. It takes a village. Accrediting it all to a system of power discounts our communities,” she noted. Despite the complicated nature of politics, she said she was grateful for the opportunity to study at BYUH because she said, “[it] helped me carve a space to seek my ancestral knowledge and grow into that understanding in my work, education, family, community and more.”

Becoming Christlike through political science

Moana Numanga, an assistant professor in the Faculty of Business & Government, teaches a class in Ethics and the Legal Environment.

Photo by Camille Jovenes

Heather Walker’s majors in intercultural peacebuilding and political science have helped her to develop a hopeful view of politics and learn how to create communities more closely aligned with Christ’s teachings, she said. Similar to Walker, who is a senior from California, two current BYU–Hawaii students and two alumnae who studied political science share how they feel politics has the potential to be used for the common good.Mari Kojima, a BYUH alumna from Japan who studied intercultural peacebuilding, emphasized how Christ’s teachings of unconditional love can be found in politics. “I feel that political science has given me a training to be open to and explore other people’s perspectives,” she shared. “Our beliefs mean the world to us, so we should be respectful to what others think and feel because if we deny [their perspectives], we might end up hurting them as if their worlds are illegitimate.”Rachel Akana, a BYUH alumna from the Island of Hawai’i who studied political science and social work, observed similarly to Kojima that studying political science, “does a good job of unifying people through understanding. That grows our empathy for people, our compassion, our patience.” Both Akana and Kojima emphasized how studying political science can humanize other perspectives and lifestyles and allow diverse communities to become more loving and unified. Akana said politics and history are intertwined, and an understanding of these two disciplines can strengthen communities through lives devoted to public service. “Political science does a really good job of recognizing those who came before us, where we are now, how we can move forward and what we can do to help one another,” she explained.Camilla Marie Fajardo, a BYUH senior and political science major, commented, “Jesus Christ teaches us about the importance of following the laws of the land. Political science has not only helped me to understand the law of the land better but also helped me understand how communities work. It has helped me understand why wars happen and what we can do to build peace.” She also said majoring in political science helped her understand how legislation can be used to serve others and spread God’s love.Just as Fajardo noted the value in being a good citizen, Vilai Ilolahia, a current political science senior from Tonga, said he felt the realm of politics cannot be inherently evil because, “Jesus Christ was a politician [who advocated] for Gentiles and those who weren’t of a Jewish faith. His point was to focus on Him to get to the Father.” Moreover, Ilolahia also said political science “taught [him] how to suss out … leaders who are for the people and those who are in it for personal gain,” highlighting how individuals can use the spiritual gift of discernment when deciding who to elect to public office.

Political science students learn in a classroom on BYUH’s campus.

Photo by Camille Jovenes

Walker said political science has helped her be a better disciple of Jesus Christ, “because so much of political science is focused on meeting people’s needs with the resources available to you,” which she said is what God does for His children. “Aside from the church, it is the most influential way to build up the kingdom of God. Government is established to help people and raise their quality of life, which I would say is exactly what Christ asks us to do when we make covenants with Him.”Being at BYUH has helped Fajardo develop a more hopeful view of politics, she said. “Our teachers don’t just talk about [what bad things are happening in the world], but they bring to us ways in which we can change it … to make the world a better place.” She also said being at a school with students from dozens of different nationalities and cultures has helped her to learn how communities can, “come together more instead of separating … We live in this world together. We have to figure out how to work together. It’s never going to be a world of just one country or just one culture, so we have to figure out how to work together.” She said BYUH is a university that excels at building cross-cultural dialogue and cooperation.Akana said living in Laie was formative in helping her learn how she can help her native Hawaiian community. She shared, “Rubbing shoulders with community mentors here has empowered me to hone in on my cultural heritage.” She specified the ways in which they lead Pacific Island-based cultural education reminds her that all peoples of the Pacific are connected. “They are maintaining focus in ancestral knowledge and writing the holistic playbook to how our [Asian American and Pacific Islander] communities can thrive within our cultures. I am very grateful for the work they are doing inside and outside of the church.”However, she said she does not care for what the term “political science” sometimes represents. “Our systems are nothing without our communities and our culture. It takes a village. Accrediting it all to a system of power discounts our communities,” she noted. Despite the complicated nature of politics, she said she was grateful for the opportunity to study at BYUH because she said, “[it] helped me carve a space to seek my ancestral knowledge and grow into that understanding in my work, education, family, community and more.”