02281nas a2200169   4500008004100000245008800041210006900129490000800198520173400206100001701940700002301957700002101980700002002001700001802021700002002039856005202059       2021                        eng d00aScaling of joint mass and metabolism fluctuations in in silico cell-laden spheroids0 aScaling of joint mass and metabolism fluctuations in in silico c0 v1183 a<p>Variations and fluctuations are characteristic features of biological systems and are also manifested in cell cultures. Here, we describe a computational pipeline for identifying the range of three-dimensional (3D) cell-aggregate sizes in which nonisometric scaling emerges in the presence of joint mass and metabolic rate fluctuations. The 3D cell-laden spheroids with size and single-cell metabolic rates described by probability density functions were randomly generated in silico. The distributions of the resulting metabolic rates of the spheroids were computed by modeling oxygen diffusion and reaction. Then, a method for estimating scaling exponents of correlated variables through statistically significant data collapse of joint probability distributions was developed. The method was used to identify a physiologically relevant range of spheroid sizes, where both nonisometric scaling and a minimum oxygen concentration (0.04 mol⋅m−3) is maintained. The in silico pipeline described enables the prediction of the number of experiments needed for an acceptable collapse and, thus, a consistent estimate of scaling parameters. Using the pipeline, we also show that scaling exponents may be significantly different in the presence of joint mass and metabolic-rate variations typically found in cells. Our study highlights the importance of incorporating fluctuations and variability in size and metabolic rates when estimating scaling exponents. It also suggests the need for taking into account their covariations for better understanding and interpreting experimental observations both in vitro and in vivo and brings insights for the design of more predictive and physiologically relevant in vitro models.</p>
1 aBotte, Ermes1 aBiagini, Francesco1 aMagliaro, Chiara1 aRinaldo, Andrea1 aMaritan, Amos1 aAhluwalia, Arti  uhttps://www.pnas.org/content/118/38/e202521111802497nas a2200169   4500008004100000245013000041210006900171520179800240653011902038100001902157700002102176700002402197700001802221700002002239700002202259856004602281       2021                        eng d00aTools and approaches for analysing the role of mitochondria in health, development and disease using human cerebral organoids0 aTools and approaches for analysing the role of mitochondria in h3 a<p>Mitochondria are cellular organelles involved in generating energy to power various processes in the cell. Although the pivotal role of mitochondria in neurogenesis was demonstrated (first in animal models), very little is known about their role in human embryonic neurodevelopment and its pathology. In this respect human-induced pluripotent stem cells (hiPSC)-derived cerebral organoids provide a tractable, alternative model system of the early neural development and disease that is responsive to pharmacological and genetic manipulations, not possible to apply in humans. Although the involvement of mitochondria in the pathogenesis and progression of neurodegenerative diseases and brain dysfunction has been demonstrated, the precise role they play in cell life and death remains unknown, compromising the development of new mitochondria-targeted approaches to treat human diseases. The cerebral organoid model of neurogenesis and disease in vitro provides an unprecedented opportunity to answer some of the most fundamental questions about mitochondrial function in early human neurodevelopment and neural pathology. Largely an unexplored territory due to the lack of tools and approaches, this review focuses on recent technological advancements in fluorescent and molecular tools, imaging systems, and computational approaches for quantitative and qualitative analyses of mitochondrial structure and function in three-dimensional cellular assemblies-cerebral organoids. Future developments in this direction will further facilitate our understanding of the important role or mitochondrial dynamics and energy requirements during early embryonic development. This in turn will provide a further understanding of how dysfunctional mitochondria contribute to disease processes.</p>
10acerebral organoids; computational models; mitochondria imaging; mitochondrial dyes; reporter fluorescent proteins.1 aLiput, Michał1 aMagliaro, Chiara1 aKuczyńska, Zuzanna1 aZayat, Valery1 aAhluwalia, Arti1 aBuzanska, Leonora  uhttps://pubmed.ncbi.nlm.nih.gov/33725382/