Review
Neurosciences
Georgia Rapti
Summary: The classification of neural circuits has been a challenging task, and traditional methods are limited in molecular, morphological, and electrophysiological aspects. Transcriptomics provides a new approach for classifying neurons and glial cells. However, it faces technical challenges and unveils spatiotemporal heterogeneity. Multifaceted classification schemes from different perspectives have advantages in studying the nervous system.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Linda Su-Feher, Anna N. Rubin, Shanni N. Silberberg, Rinaldo Catta-Preta, Kenneth J. Lim, Athena R. Ypsilanti, Iva Zdilar, Christopher S. McGinnis, Gabriel L. McKinsey, Thomas E. Rubino, Michael J. Hawrylycz, Carol Thompson, Zev J. Gartner, Luis Puelles, Hongkui Zeng, John L. R. Rubenstein, Alex S. Nord
Summary: Enhancers play a crucial role in driving cell fate specification in the developing brain. In this study, the researchers used enhancer labeling and single-cell RNA sequencing to map and distinguish different neuronal lineages in the mouse embryonic brain. The results showed that combining enhancer activity profiling with scRNA-seq improved the resolution of regional and developmental populations and identified specific neuronal populations derived from different brain regions. This study highlights the importance of enhancers and the power of scRNA-seq in understanding the complex paths of neuronal specification in mouse brain development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Rohan Subramanian, Debashis Sahoo
Summary: We present a bioinformatic approach using Boolean implication to discover retinal cell type-specific genes and genes involved in retinal cell fate. Our method improves the prediction accuracy of marker genes and identifies new high confidence cone and rod-specific genes. This approach has potential applications in regenerative medicine and other areas of gene expression analyses in human diseases.
BMC BIOINFORMATICS
(2022)
Article
Ophthalmology
Simon Dulz, C. Schwering, Jan Wildner, Christoph Spartalis, Frank Schuettauf, Udo Bartsch, Eva Wibbeler, Miriam Nickel, Martin Stephan Spitzer, Yevgeniya Atiskova, Angela Schulz
Summary: This study aimed to evaluate the progression of CLN2-associated retinal degeneration in patients receiving intraventricular enzyme replacement therapy (ERT). The results showed a negative correlation between central retinal thickness (CRT) and age at examination, as well as significant correlations between preferential looking test (PLT) results, Weill Cornell Batten Scale (WCBS) scores, and CRT values. The Hamburg Motor-Language (M-L) score also correlated with ocular measurements. Therefore, retina-directed therapies should be initiated before or as early as possible during the phase of rapid retinal degeneration, and PLT and WCBS are valuable outcome measures for monitoring disease progression.
BRITISH JOURNAL OF OPHTHALMOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jules Duruz, Cyrielle Kaltenrieder, Peter Ladurner, Remy Bruggmann, Pedro Martinez, Simon G. Sprecher
Summary: By utilizing whole-body single-cell transcriptomics on the acoel Isodiametra pulchra, researchers identified ten major cell type categories contributing to main biological functions, as well as a large number of clade-specific marker genes, indicating the emergence of clade-specific common molecular machineries functioning in distinct cell types. These results offer novel insights into the evolution of bilaterian cell types.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Jelena Pozojevic, Malte Spielmann
Summary: Neurodegenerative disorders are characterized by progressive damage to specific populations of nervous system cells that are essential for various functions. Single-cell omics technologies have emerged as a powerful tool to study the heterogeneity of complex tissues like the post-mortem human brain. This review discusses the use of single-cell RNA sequencing in understanding neurodegenerative diseases and the potential applications in diagnostics and therapy. However, there are still limitations and further technological advancements are needed to fully manipulate the affected pathways.
MOLECULAR DIAGNOSIS & THERAPY
(2023)
Article
Cell Biology
Kevin Perez, Serban Ciotlos, Julia McGirr, Chandani Limbad, Ryosuke Doi, Joshua P. Nederveen, Mats Nilsson, Daniel A. Winer, William Evans, Mark Tarnopolsky, Judith Campisi, Simon Melov
Summary: The study reveals that muscle aging is associated with various factors such as inflammation, muscle stem cell depletion, mitochondrial dysfunction, and loss of motor neurons. Transcriptome profiling identifies changes in gene expression related to age and frailty, including key genes like MYH8, PDK4, and IGFN1. Additionally, a subpopulation expressing CDKN1A in aged samples suggests cellular senescence driven by p21(cip1). These findings provide valuable insights into age-related muscle loss and can guide the development of therapeutic strategies.
Review
Developmental Biology
Elin Vinsland, Sten Linnarsson
Summary: Understanding human brain development is challenging due to its complexity and dynamics. Single-cell RNA-sequencing studies have revealed previously concealed cellular heterogeneity. This review summarizes published studies on mouse and human brain development, identifies gaps in the field, proposes future directions, and necessary techniques to create an integrated atlas of human brain development in space and time.
Article
Biology
Sachin Sharma, Russell Littman, John D. Tompkins, Douglas Arneson, Jaime Contreras, Al-Hassan Dajani, Kaitlyn Ang, Amit Tsanhani, Xin Sun, Patrick Y. Jay, Herbert Herzog, Xia Yang, Olujimi A. Ajijola
Summary: The study reveals the diversity and distinction of sympathetic neurons innervating the heart in the stellate ganglion. Three subtypes of these neurons primarily innervate the heart, with high and low neuropeptide-Y expression cells exhibiting distinct morphological, neurochemical, and electrophysiological characteristics. Modulating NPY signaling differentially controls cardiac responses by these subpopulations.
Article
Biology
Trygve E. Bakken, Cindy T. J. van Velthoven, Vilas Menon, Rebecca D. Hodge, Zizhen Yao, Thuc Nghi Nguyen, Lucas T. Graybuck, Gregory D. Horwitz, Darren Bertagnolli, Jeff Goldy, Anna Marie Yanny, Emma Garren, Sheana Parry, Tamara Casper, Soraya Shehata, Eliza R. Barkan, Aaron Szafer, Boaz P. Levi, Nick Dee, Kimberly A. Smith, Susan M. Sunkin, Amy Bernard, John Phillips, Michael J. Hawrylycz, Christof Koch, Gabe J. Murphy, Ed Lein, Hongkui Zeng, Bosiljka Tasic
Summary: Abundant evidence supports the presence of at least three distinct types of thalamocortical (TC) neurons in the primate dorsal lateral geniculate nucleus (dLGN). These neurons have different morphologies, connectivity patterns, and convey different aspects of visual information to the cortex. Through RNA-sequencing, four distinct types of TC neurons were identified in the primate dLGN. Despite some transcriptional differences, the dominant feature is high transcriptomic similarity among TC neurons.
Article
Neurosciences
Zachary Gaertner, Maite Azcorra, Daniel A. Dombeck, Rajeshwar Awatramani
Summary: With advancements in technology, neuroscientists have identified numerous molecular subtypes in the brain, offering unique insights into various diseases such as depression and chronic pain.
NEUROBIOLOGY OF DISEASE
(2022)
Review
Agriculture, Dairy & Animal Science
Roman Wenne
Summary: In recent decades, the importance of considering genetic changes in aquatic populations for effective management and protection of aquatic ecosystems has been recognized. Single nucleotide polymorphism (SNP) is a high-resolution molecular marker suitable for studying the genetic diversity of populations. This review highlights the benefits of using SNPs to identify natural populations of aquatic animals and detect threats to them from released farm animals, fishery, and climate changes.
Article
Biochemistry & Molecular Biology
Xingyan Liu, Qunlun Shen, Shihua Zhang
Summary: Cross-species comparative analysis of scRNA-seq data is important for understanding the cellular diversity and evolutionary mechanisms. However, assigning cell identities for nonmodel species is challenging due to limited genome annotation and known biomarkers. In this study, we propose a heterogeneous graph neural network model, CAME, which improves cell-type characterization across distant species by using non-one-to-one homologous gene mapping.
Article
Ophthalmology
Romain Touze, Marc M. Abitbol, Dominique Bremond-Gignac, Matthieu P. Robert
Summary: Retinal vascular abnormalities were found in 37.1% of children with NF1, with most cases exhibiting simple vascular tortuosity and a smaller percentage showing a corkscrew pattern. The study also observed the evolution of RVAs from simple vascular tortuosity to a more complex corkscrew pattern in some cases.
RETINA-THE JOURNAL OF RETINAL AND VITREOUS DISEASES
(2021)
Article
Neurosciences
Anchel Gonzalez-Barriga, Louison Lallemant, Diana M. Dinca, Sandra O. Braz, Helene Polveche, Paul Magneron, Cedric Pionneau, Aline Huguet-Lachon, Jean-Baptiste Claude, Cerina Chhuon, Ida Chiara Guerrera, Cyril F. Bourgeois, Didier Auboeuf, Genevieve Gourdon, Mario Gomes-Pereira
Summary: Myotonic dystrophy type 1 is a neuromuscular disorder caused by non-coding CTG repeat expansion in the DMPK gene, generating toxic CUG RNA that interferes with RNA processing in multiple tissues. The impact of expanded CUG RNA on glial cells is more significant than on neuronal cells, suggesting impaired cell differentiation. This study provides insights into the molecular events of RNA toxicity in the CNS with a focus on non-neuronal mechanisms and proteomic changes in DM1 brain disease.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Biochemical Research Methods
Charles J. Labuzzetta, Margaret L. Antonio, Patricia M. Watson, Robert C. Wilson, Lauren A. Laboissonniere, Jeffrey M. Trimarchi, Baris Genc, P. Hande Ozdinler, Dennis K. Watson, Paul E. Anderson
Review
Neurosciences
Jean-Francois Poulin, Bosiljka Tasic, Jens Hjerling-Leffler, Jeffrey M. Trimarchi, Rajeshwar Awatramani
NATURE NEUROSCIENCE
(2016)
Article
Multidisciplinary Sciences
Jillian J. Goetz, Lauren A. Laboissonniere, Andrea K. Wester, Madison R. Lynch, Jeffrey M. Trimarchi
Article
Multidisciplinary Sciences
Wei Zhu, Oliver W. Gramlich, Lauren Laboissonniere, Ankur Jain, Val C. Sheffield, Jeffrey M. Trimarchi, Budd A. Tucker, Markus H. Kuehn
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Developmental Biology
Madelyn Mullally, Caitlin Albrecht, Mary Horton, Lauren A. Laboissonniere, Jillian J. Goetz, Rebecca Chowdhury, Alicia Manning, Andrea K. Wester, Quinton Bose, Jeffrey M. Trimarchi
Article
Neurosciences
Lauren A. Laboissonniere, Gregory M. Martin, Jillian J. Goetz, Ran Bi, Brock Pope, Kallie Weinand, Laura Ellson, Diane Fru, Miranda Lee, Andrea K. Wester, Peng Liu, Jeffrey M. Trimarchi
JOURNAL OF COMPARATIVE NEUROLOGY
(2017)
Article
Multidisciplinary Sciences
Lauren A. Laboissonniere, Takuma Sonoda, Seul Ki Lee, Jeffrey M. Trimarchi, Tiffany M. Schmidt
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2017)
Article
Cell Biology
Mark M. Emerson, Natalia Surzenko, Jillian J. Goetz, Jeffrey Trimarchi, Constance L. Cepko
DEVELOPMENTAL CELL
(2013)
Article
Anatomy & Morphology
Karolina Mizeracka, Jeffrey M. Trimarchi, Michael B. Stadler, Constance L. Cepko
DEVELOPMENTAL DYNAMICS
(2013)
Article
Developmental Biology
Lauren A. Laboissonniere, Courtney L. Smith, Jacquelyn Mesenbrink, Rebecca Chowdhury, Abbie Burney, Margaret Lang, Matthew Sierra, Amy Stark, Gabriel Maldonado-Casalduc, Madison Muller, Jeffrey M. Trimarchi
GENE EXPRESSION PATTERNS
(2018)
Article
Multidisciplinary Sciences
Kylie S. Chew, Tiffany M. Schmidt, Alan C. Rupp, Paulo Kofuji, Jeffrey M. Trimarchi
Article
Multidisciplinary Sciences
Jillian J. Goetz, Gregory M. Martin, Rebecca Chowdhury, Jeffrey M. Trimarchi
Article
Multidisciplinary Sciences
Rebecca Chowdhury, Lauren A. Laboissonniere, Andrea K. Wester, Madison Muller, Jeffrey M. Trimarchi
Editorial Material
Genetics & Heredity
Caitlin Farris, Jeffrey M. Trimarchi
Article
Genetics & Heredity
Jillian J. Goetz, Jeffrey M. Trimarchi