Editorial Material
Biochemical Research Methods
Leonard Drees, Jochen C. C. Rink
Summary: Planaria are flatworms that belong to the phylum Platyhelminthes. Species such as Schmidtea mediterranea have the ability to regenerate their bodies from small tissue fragments and are easily maintainable in laboratory settings, making them an excellent model system for studying whole-body regeneration.
Article
Biochemistry & Molecular Biology
Kexue Ma, Rui Li, Gege Song, Fangying Guo, Meng Wu, Qiong Lu, Xinwei Li, Guangwen Chen
Summary: This study investigates the role of HSP60 in tissue regeneration and homeostasis using freshwater planarians as a model system. HSP60 is found in all types of cells, but is particularly abundant in stem cells and head neural cells. Knockdown of HSP60 leads to head regression and loss of regenerating abilities, as well as disruption of mitochondrial structure and inhibition of intestinal tissue function.
Article
Computer Science, Software Engineering
Xingyi Du, Qingnan Zhou, Nathan Carr, Tao Ju
Summary: The novel representation of solid models, Boundary-Sampled Halfspaces (BSH), constructs solid shapes from a set of halfspaces using sparsely placed samples on the boundary of each halfspace. This method offers greater agility and expressiveness than Constructive Solid Geometry (CSG), while also simplifying the reverse engineering process through theoretical properties and practical algorithms for boundary extraction and conversion from other representations, as demonstrated in 2D and 3D examples.
ACM TRANSACTIONS ON GRAPHICS
(2021)
Article
Biochemistry & Molecular Biology
Shuo Liu, Meishan Chen, Xi Liu, Kang Zheng, Baohua Liu, Weiwei Wu, Qiuxiang Pang
Summary: The study reveals the crucial roles of DjApi5 and its interacting molecule DjAcinus in planarian homeostasis and regeneration, which may be correlated with their specific localization in neoblasts and anti-apoptotic functions.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Yael Dagan, Yarden Yesharim, Ashley R. Bonneau, Tamar Frankovits, Schraga Schwartz, Peter W. Reddien, Omri Wurtzel
Summary: m6A plays a critical role in the regulation of gene expression and chromatin modifications, contributing to the homeostasis and regeneration of planarian stem cells.
Article
Cell Biology
Pablo Coronel-Cordoba, M. Dolores Molina, Gemma Cardona, Susanna Fraguas, Eudald Pascual-Carreras, Emili Salo, Francesc Cebria, Teresa Adell
Summary: Fox genes, including the less characterized FoxK genes, play important roles in controlling various cellular processes. A recent study identified three foxK paralogs in the genome of Schmidtea mediterranea, showing that foxK1 inhibition affects regeneration of ectodermal tissues by influencing apoptosis. These results suggest that foxK1 is required for differentiation and maintenance of ectodermal tissues in planarians.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Genetics & Heredity
Jennifer K. Cloutier, Conor L. McMann, Isaac M. Oderberg, Peter W. Reddien
Summary: This study explores the decision-making process of head-tail regeneration polarity in planarians and reveals the crucial role of Activin signaling in determining the outcome. The findings provide important insights into understanding the mechanisms underlying regeneration.
Article
Engineering, Electrical & Electronic
Linlin Fan, Junyi Wang, Zhigang Xu, Xiao Yang
Summary: This study proposes a high-precision reverse engineering method based on a prior CAD model, which improves the accuracy and efficiency of reverse engineering by transmitting the geometric features and constraint information from the CAD model. Experimental results demonstrate the successful achievement of high-precision modeling in the reverse engineering process of an engine compartment.
Article
Multidisciplinary Sciences
M. Lucila Scimone, Jennifer K. Cloutier, Chloe L. Maybrun, Peter W. Reddien
Summary: The gene equinox is expressed in the planarian wound epidermis and is essential for the initiation of positional information regeneration and blastema formation.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Cui Ge, Cun Lin, Mengzhen Zhang, Jingchen Yuan, Xiyan Feng, Zhitai Hao, Shoutao Zhang, Qingnan Tian
Summary: Tubgcp3 is a crucial mitotic regulator in planarian flatworms, playing a significant role in maintaining epidermal lineage. Knockdown of Tubgcp3 results in reduced cell divisions and loss of mature epidermal cells.
Article
Developmental Biology
Stephanie H. Nowotarski, Erin L. Davies, Sofia M. C. Robb, Eric J. Ross, Nicolas Matentzoglu, Viraj Doddihal, Mol Mir, Melainia McClain, Alejandro Sanchez Alvarado
Summary: PLANA is a relational framework containing over 850 terms describing planarian anatomy, with imported terms from other anatomy ontologies to promote interoperability. In addition to serving as a data curation tool, PLANA includes resources for planarian embryogenesis and gene expression. It is an open-source tool built using FAIR principles, providing a platform for community-led growth and evolution of the resource.
Article
Biochemistry & Molecular Biology
Yajun Guo, Yujia Sun, Mengwen Ma, Yongding Huang, Shoutao Zhang, Qingnan Tian
Summary: Regulators of adult neurogenesis are crucial for neuronal repair. Freshwater planarians, with their pluripotent adult stem cells, serve as ideal model systems for studying neuronal regeneration. In this study, Djfoxk1 and its downstream gene Djsnon were identified as important regulators of planarian central nervous system (CNS) regeneration. Knockdown of Djfoxk1 or Djsnon resulted in impaired regeneration of the cephalic ganglia and failure of eye regeneration. Our findings highlight the role of Djfoxk1-Djsnon signaling in planarian CNS regeneration.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Elena Tsarkova, Kristina Filippova, Vera Afanasyeva, Olga Ermakova, Anastasia Kolotova, Artem Blagodatski, Artem Ermakov
Summary: Ionizing radiation and radiation-related oxidative stress significantly reduce the regeneration capacity of living organisms. Planarian flatworms, known for their abundant stem cells, serve as a valuable model for studying regeneration and testing novel antioxidants and radioprotective substances. Our study demonstrates that Tameron, an antiviral and antioxidant drug, effectively protects planarians from oxidative stress and enhances their regenerative capacity by modulating gene expression related to neoblasts and oxidative stress response.
Article
Environmental Sciences
Changjian Xie, Xiaowei Li, Lisha Hei, Yiqing Chen, Yuling Dong, Shujing Zhang, Shan Ma, Jianing Xu, Qiuxiang Pang, Iseult Lynch, Zhiling Guo, Peng Zhang
Summary: In this study, the toxic effects of cerium oxide nanoparticles (n-CeO2) on stem cells, tissue regeneration, and neuro-regeneration were investigated using freshwater planarian Dugesia japonica as a model. The study found that n-CeO2 not only disrupted the homeostasis of normal planarians, but also inhibited the regeneration processes of regenerated planarians. Ce3+ exhibited higher toxicity than n-CeO2.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Review
Zoology
Jia-Jia Chen, Kai Lei
Summary: Planarians, the most primitive bilateral triploblastic animals, possess robust whole-body regeneration capacity, making them ideal model organisms for regenerative research. Recent studies have elucidated the cellular mechanisms underlying regeneration, particularly the role of stem cells in tissue homeostasis and regeneration.
ZOOLOGICAL RESEARCH
(2023)
Article
Evolutionary Biology
Wesley P. Clawson, Michael Levin
Summary: The rich variety of biological forms and behaviours on Earth is the result of evolutionary history, with accidental and selective influences. However, our understanding of the origin of anatomical novelty, the relationship between genome and form, and strategies for large-scale structure and function control is still limited. The analysis of new and unique living forms is crucial to uncover deep design principles of life. The concept of goal-seeking and problem-solving behavior in various environments is proposed as a powerful invariant across possible beings. The creation and analysis of novel living forms will be an essential testbed for the emerging field of diverse intelligence, with implications in regenerative medicine, robotics, and ethics.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Review
Behavioral Sciences
Michael Levin
Summary: Each of us undergoes a remarkable journey from basic matter to complex mind, starting as a quiescent oocyte and gradually transforming into an adult with metacognitive processes. We are not a singular self, but rather a collective intelligence comprising countless cells working together to generate a coherent cognitive being. The ability to turn physiological competencies into large-scale behavioral intelligences extends beyond the brain's electrical dynamics and has deep connections to embryogenesis, regeneration, and cancer suppression. Understanding the bioelectric dynamics underlying the construction of complex bodies and brains is crucial for comprehending the evolution and design of diverse intelligences across Earth's phylogenetic history.
Review
Biochemistry & Molecular Biology
Michael Levin
Summary: The layer of developmental physiology, operating between genotype and phenotype, plays a critical role in evolution. Cellular capabilities derived from ancestral unicellular organisms contribute to the evolutionary process in multicellular organisms. The multiscale competency architecture of biological structures, encompassing cells, tissues, and organs, allows for regulative plasticity and adaptation across metabolic, transcriptional, physiological, and anatomical problem spaces.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Robotics
Douglas Blackiston, Sam Kriegman, Josh Bongard, Michael Levin
Summary: Advancements in science and engineering expose the limitations of classical approaches, necessitating the re-evaluation of conceptual categories and resolution of conflicting boundaries to facilitate experimental approaches. This essay addresses critiques regarding the intersection of developmental biology, computer science, and robotics, and explores how recent advances have transformed our understanding across fields. By embracing the convergence of disciplines, the essay argues that insights can be gained on issues of multiscale control and the relationship between form and function, leading to practical applications in regenerative medicine and synthetic living machines.
Article
Behavioral Sciences
Anna Ciaunica, Evgeniya V. Shmeleva, Michael Levin
Summary: Significant efforts have been made to understand how mental and cognitive processes are supported by neural mechanisms in the brain. This paper suggests a promising approach to understand human cognition by considering how neurons work together with other types of cells, such as immune cells, for self-organization and adaptive behavior. The focus is on immune cellular processing as a complement to neuronal processing, challenging the idea that neurons are the exclusive cells responsible for learning and cognition. Ultimately, the paper argues that cognition should not be limited to the neural system in the brain, but should be seen as a multiscale web of dynamic information processing distributed across various cellular and network systems throughout the body.
FRONTIERS IN INTEGRATIVE NEUROSCIENCE
(2023)
Article
Mathematical & Computational Biology
Santosh Manicka, Kathleen Johnson, Michael Levin, David Murrugarra
Summary: The extent of nonlinearity in the regulation of biological systems affects their susceptibility to therapy and control. Analysis of 137 published Boolean network models revealed that biological regulation tends to be less nonlinear than expected on average, but cancer and disease networks can exhibit higher levels of nonlinearity and variability. This variation is attributed to differences in the distribution of information among different orders of regulatory nonlinearity.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Engineering, Multidisciplinary
Joshua Bongard, Michael Levin
Summary: The applicability of computational models to the biological world is being debated, with the suggestion to adopt an observer-dependent view rather than strict boundaries between categories. Living systems are polycomputing, simultaneously performing multiple functions in the same place, which challenges prediction and control. Understanding and harnessing polycomputing can have significant impacts on fields like regenerative medicine, robotics, and computer engineering.
Article
Engineering, Electrical & Electronic
Chris Fields, Filippo Fabrocini, Karl Friston, James F. Glazebrook, Hananel Hazan, Michael Levin, Antonino Marciano
Summary: Living systems are confronted with environmental complexity and limited access to free-energy resources. To survive under these circumstances, a control system is necessary to activate and deploy perception and action resources in a context specific way. This article introduces the free-energy principle (FEP), active inference, and discusses how control problems arise in active inference systems. The authors illustrate that when systems execute active inference according to the FEP, their control flow systems can be represented as tensor networks (TNs), which can be implemented within the framework of quantum topological neural networks.
IEEE TRANSACTIONS ON MOLECULAR BIOLOGICAL AND MULTI-SCALE COMMUNICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Chris Fields, Filippo Fabrocini, Karl Friston, James F. Glazebrook, Hananel Hazan, Michael Levin, Antonino Marciano
Summary: Living systems face environmental complexity and limited access to free-energy resources, necessitating a control system that can activate perception and action resources in a context-specific way. This article introduces the free-energy principle and active inference as a solution to the control problem in active inference systems. It also reviews the classical and quantum formulations of the free-energy principle.
IEEE TRANSACTIONS ON MOLECULAR BIOLOGICAL AND MULTI-SCALE COMMUNICATIONS
(2023)
Article
Computer Science, Artificial Intelligence
Juanita Mathews, Alan (Jaelyn) Chang, Liam Devlin, Michael Levin
Summary: Many aspects of health and disease are modeled using protein pathways, which exhibit interesting capabilities such as trainability and context-sensitive information processing. Understanding the functionality and tractability of pathways beyond the mechanistic details of proteins and drugs is crucial for addressing health and disease. Exploiting tools and concepts from cognitive sciences may provide a new roadmap for overcoming the limitations of current pharmacological strategies and inferring future therapeutic interventions.
Editorial Material
Biochemistry & Molecular Biology
Mustafa B. A. Djamgoz, Michael Levin
Article
Biochemistry & Molecular Biology
Allison Witucki, David W. Rudge, Brandy Pleasants, Peng Dai, Wendy S. Beane
Summary: This article tells the story of how an instructor transformed a Course-based Undergraduate Research Experience into a synchronous online course using the Backwards Design Method. It provides recommendations for implementing an online CURE, including scaffolding the design, promoting collaboration, and allowing students to iterate. The Backwards Design framework facilitates a scaffolded instructional approach and encourages iteration through feedback and revision.
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
(2023)
Article
Biology
Chris Fields, Michael Levin
Summary: Using the Free Energy Principle, we demonstrate that bidirectional information exchange between a system and its environment can generate complexity, resulting in the emergence of hierarchical computational architectures in systems operating away from thermal equilibrium. In this context, the environment enhances its ability to predict system behavior by increasing the morphological complexity of the system, leading to larger-scale, more macroscopic behaviors. Therefore, we propose that life is thermodynamically favorable, and when creating artificial living systems, human engineers act as generic environments.
Article
Chemistry, Analytical
Joel Dungan, Juanita Mathews, Michael Levin, Valencia Koomson
Summary: In this study, an oligomer stamping technique for selective bonding of normally closed valves is optimized for PDMS devices on glass substrates. The process is quantitatively characterized using contact angle and blister bursting testing measurements, and recommendations are made for plasma treatment conditions, microstamping technique, and valve construction. The glass-PDMS devices demonstrate electrical isolation and sealing capability under a pulsed actuation scheme.
Correction
Evolutionary Biology
Wesley P. Clawson, Michael Levin
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)