scholarly journals Physical basis of lumen shape and stability in a simple epithelium

2019 ◽  
Author(s):  
Claudia G. Vasquez ◽  
Vipul T. Vachharajani ◽  
Carlos Garzon-Coral ◽  
Alexander R. Dunn
Keyword(s):  
Physical Mechanism ◽  
De Novo ◽  
Dominant Role ◽  
Three Dimensional ◽  
Intraluminal Pressure ◽  
Central Feature ◽  
Lumen Formation ◽  
Cortical Tension ◽  
Continuous Sheet ◽  
Geometrical Factors

AbstractA continuous sheet of epithelial cells surrounding a hollow opening, or lumen, defines the basic topology of numerous organs. De novo lumen formation is a central feature of embryonic development whose dysregulation leads to congenital and acquired diseases of the kidney and other organs. Hydrostatic pressure has been proposed to drive lumen expansion, a view that is supported by recent experiments in the mouse blastocyst. High luminal pressure should produce lumen surfaces that bow outwards toward the surrounding cells. However, lumens formed in other embryonic tissues adopt highly irregular shapes, with cell apical faces that are bowed inward, suggesting that pressure may not be the dominant contributor to lumen growth in all cases. We used three-dimensional live-cell imaging to study the physical mechanism of lumen formation in Madin Darby Canine Kidney (MDCK) cell spheroids, a canonical cell-culture model for lumenogenesis. Our experiments revealed that neither lumen pressure nor the actomyosin cytoskeleton were required to maintain lumen shape or stability. Instead, we find that, in our model system, lumen shape results from simple geometrical factors tied to the establishment of apico-basal polarity. A quantitative physical model that incorporates cell geometry, cortical tension, and intraluminal pressure can account for our observations as well as cases in which pressure indeed plays a dominant role. Our results thus support a unifying physical mechanism for the formation of luminal openings in a variety of physiological contexts.

scholarly journals Physical basis for the determination of lumen shape in a simple epithelium

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Claudia G. Vasquez ◽  
Vipul T. Vachharajani ◽  
Carlos Garzon-Coral ◽  
Alexander R. Dunn
Keyword(s):  
Developmental Process ◽  
Dominant Role ◽  
Intraluminal Pressure ◽  
Cell Geometry ◽  
Madin Darby Canine Kidney ◽  
Lumen Formation ◽  
Irregular Shapes ◽  
Culture Model ◽  
Darby Canine Kidney

AbstractThe formation of a hollow lumen in a formerly solid mass of cells is a key developmental process whose dysregulation leads to diseases of the kidney and other organs. Hydrostatic pressure has been proposed to drive lumen expansion, a view that is supported by experiments in the mouse blastocyst. However, lumens formed in other tissues adopt irregular shapes with cell apical faces that are bowed inward, suggesting that pressure may not be the dominant contributor to lumen shape in all cases. Here we use live-cell imaging to study the physical mechanism of lumen formation in Madin-Darby Canine Kidney cell spheroids, a canonical cell-culture model for lumenogenesis. We find that in this system, lumen shape reflects basic geometrical considerations tied to the establishment of apico-basal polarity. A physical model incorporating both cell geometry and intraluminal pressure can account for our observations as well as cases in which pressure plays a dominant role.

scholarly journals Molecular Mechanisms Controlling Vascular Lumen Formation in Three-Dimensional Extracellular Matrices

2012 ◽  
Vol 195 (1-2) ◽  
pp. 122-143 ◽  
Author(s):  
Anastasia Sacharidou ◽  
Amber N. Stratman ◽  
George E. Davis
Keyword(s):  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Extracellular Matrices ◽  
Lumen Formation ◽  
Vascular Lumen

scholarly journals Control of AMPA receptor activity by the extracellular loops of auxiliary proteins

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Irene Riva ◽  
Clarissa Eibl ◽  
Rudolf Volkmer ◽  
Anna L Carbone ◽  
Andrew JR Plested
Keyword(s):  
Ampa Receptor ◽  
Ampa Receptors ◽  
De Novo ◽  
Dominant Role ◽  
Mammalian Brain ◽  
Binding Assays ◽  
Receptor Kinetics ◽  
Receptor Complexes ◽  
Extracellular Loops ◽  
Kinetics Of

At synapses throughout the mammalian brain, AMPA receptors form complexes with auxiliary proteins, including TARPs. However, how TARPs modulate AMPA receptor gating remains poorly understood. We built structural models of TARP-AMPA receptor complexes for TARPs γ2 and γ8, combining recent structural studies and de novo structure predictions. These models, combined with peptide binding assays, provide evidence for multiple interactions between GluA2 and variable extracellular loops of TARPs. Substitutions and deletions of these loops had surprisingly rich effects on the kinetics of glutamate-activated currents, without any effect on assembly. Critically, by altering the two interacting loops of γ2 and γ8, we could entirely remove all allosteric modulation of GluA2, without affecting formation of AMPA receptor-TARP complexes. Likewise, substitutions in the linker domains of GluA2 completely removed any effect of γ2 on receptor kinetics, indicating a dominant role for this previously overlooked site proximal to the AMPA receptor channel gate.

scholarly journals A three-dimensional culture model of innervated human skeletal muscle enables studies of the adult neuromuscular junction and disease modeling

2018 ◽  
Author(s):  
Mohsen Afshar Bakooshli ◽  
Ethan S Lippmann ◽  
Ben Mulcahy ◽  
Nisha R Iyer ◽  
Christine T Nguyen ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Neuromuscular Junction ◽  
Motor Neuron ◽  
Motor Neurons ◽  
Human Skeletal Muscle ◽  
Disease Modeling ◽  
De Novo ◽  
Muscle Fibers ◽  
Three Dimensional ◽  
Adult Human

SummaryTwo-dimensional (2D) human skeletal muscle fiber cultures are ill equipped to support the contractile properties of maturing muscle fibers. This limits their application to the study of adult human neuromuscular junction (NMJ) development, a process requiring maturation of muscle fibers in the presence of motor neuron endplates. Here we describe a three-dimensional (3D) co-culture method whereby human muscle progenitors mixed with human pluripotent stem cell-derived motor neurons self-organize to form functional NMJ connections within two weeks. Functional connectivity between motor neuron endplates and muscle fibers is confirmed with calcium transient imaging and electrophysiological recordings. Notably, we only observed epsilon acetylcholine receptor subunit protein upregulation and activity in 3D co-culture. This demonstrates that the 3D co-culture system supports a developmental shift from the embryonic to adult form of the receptor that does not occur in 2D co-culture. Further, 3D co-culture treatments with myasthenia gravis patient sera shows the ease of studying human disease with the system. This work delivers a simple, reproducible, and adaptable method to model and evaluate adult human NMJ de novo development and disease in culture.

scholarly journals A Novel Missense Variant in the Gene PPP2R5D Causes a Rare Neurodevelopmental Disorder with Increased Phenotype

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Lulu Yan ◽  
Ru Shen ◽  
Zongfu Cao ◽  
Chunxiao Han ◽  
Yuxin Zhang ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Disorder ◽  
Neurodevelopmental Disorder ◽  
Three Dimensional ◽  
Missense Variant ◽  
Pathogenic Variant ◽  
Dimensional Structure ◽  
Chinese Family ◽  
Speech Impairment ◽  
Pathogenic Variants

PPP2R5D-related neurodevelopmental disorder, which is mainly caused by de novo missense variants in the PPP2R5D gene, is a rare autosomal dominant genetic disorder with about 100 patients and a total of thirteen pathogenic variants known to exist globally so far. Here, we present a 24-month-old Chinese boy with developmental delay and other common clinical characteristics of PPP2R5D-related neurodevelopmental disorder including hypotonia, macrocephaly, intellectual disability, speech impairment, and behavioral abnormality. Trio-whole exome sequencing (WES) and Sanger sequencing were performed to identify the causal gene variant. The pathogenicity of the variant was evaluated using bioinformatics tools. We identified a novel pathogenic variant in the PPP2R5D gene (c.620G>T, p.Trp207Leu). The variant is located in the variant hotspot region of this gene and is predicted to cause PPP2R5D protein dysfunction due to an increase in local hydrophobicity and unstable three-dimensional structure. We report a novel pathogenic variant of PPP2R5D associated with PPP2R5D-related neurodevelopmental disorder from a Chinese family. Our findings expanded the phenotypic and mutational spectrum of PPP2R5D-related neurodevelopmental disorder.

scholarly journals How to investigate perceptual projection: a commentary on Pereira Jr., “The projective theory of consciousness: from neuroscience to philosophical psychology”

2018 ◽  
Vol 41 (spe) ◽  
pp. 233-242
Author(s):  
Max Velmans
Keyword(s):  
Sense Of Self ◽  
Conscious Experience ◽  
Three Dimensional ◽  
Human Information Processing ◽  
Central Feature ◽  
Bipolar Structure ◽  
Target Article ◽  
Third Person ◽  
The Third Person

Abstract: This commentary focuses on the scientific status of perceptual projection-a central feature of Pereira’s projective theory of consciousness. In his target article, he draws on my own earlier work to develop an explanatory framework for integrating first-person viewable conscious experience with the third-person viewable neural correlates and antecedent causes that form conscious experience into a bipolar structure that contains both a sense of self (created by interoceptive projective processes) and a sense of the world (created by exteroceptive projective processes). I stress that perceptual projection is a psychological effect (not an explanation for that effect) and list many of the ways it has been studied within experimental psychology, for example in studies of depth perception in vision and audition and experiences of depth arising from cues arranged on two-dimensional surfaces in stereoscopic pictures, 3D cinemas, holograms, and virtual realities. I then juxtapose Pereira’s explanatory model with two other models that have similar aims and background assumptions but different orientations, Trehub’s Retinoid model, which focuses largely on the neural functioning of the visual system, and Rudrauf et al’s Projective Consciousness Model, which draws largely on projective geometries to specify the requirements of organisms that need to navigate a three-dimensional world, and how these might be implemented in human information processing. Together, these models illustrate both converging and diverging approaches to understanding the role of projective processes in human consciousness.

scholarly journals FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution

2020 ◽  
Author(s):  
Jiangyan Feng ◽  
Diwakar Shukla
Keyword(s):  
Ligand Binding ◽  
Structure Prediction ◽  
De Novo ◽  
Three Dimensional ◽  
Sequence Information ◽  
Structural Constraints ◽  
Complex Signals ◽  
Residue Contacts ◽  
Small Clusters ◽  
Functional Mechanisms

AbstractProteins are dynamic molecules which perform diverse molecular functions by adopting different three-dimensional structures. Recent progress in residue-residue contacts prediction opens up new avenues for the de novo protein structure prediction from sequence information. However, it is still difficult to predict more than one conformation from residue-residue contacts alone. This is due to the inability to deconvolve the complex signals of residue-residue contacts, i.e. spatial contacts relevant for protein folding, conformational diversity, and ligand binding. Here, we introduce a machine learning based method, called FingerprintContacts, for extending the capabilities of residue-residue contacts. This algorithm leverages the features of residue-residue contacts, that is, (1) a single conformation outperforms the others in the structural prediction using all the top ranking residue-residue contacts as structural constraints, and (2) conformation specific contacts rank lower and constitute a small fraction of residue-residue contacts. We demonstrate the capabilities of FingerprintContacts on eight ligand binding proteins with varying conformational motions. Furthermore, FingerprintContacts identifies small clusters of residue-residue contacts which are preferentially located in the dynamically fluctuating regions. With the rapid growth in protein sequence information, we expect FingerprintContacts to be a powerful first step in structural understanding of protein functional mechanisms.

scholarly journals De Novo Molecule Design Through Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites

2020 ◽  
Author(s):  
Mingyuan Xu ◽  
Ting Ran ◽  
Hongming Chen
Keyword(s):  
Protein Binding ◽  
De Novo ◽  
Structural Information ◽  
Chemical Space ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Generative Model ◽  
Coarse Grained ◽  
Molecule Design ◽  
3D Information

<p><i>De novo</i> molecule design through molecular generative model is gaining increasing attention in recent years. Here a novel generative model was proposed by integrating the 3D structural information of the protein binding pocket into the conditional RNN (cRNN) model to control the generation of drug-like molecules. In this model, the composition of protein binding pocket is effectively characterized through a coarse-grain strategy and the three-dimensional information of the pocket can be represented by the sorted eigenvalues of the coulomb matrix (EGCM) of the coarse-grained atoms composing the binding pocket. In current work, we used our EGCM method and a previously reported binding pocket descriptor DeeplyTough to train cRNN models and compared their performance. It has been shown that the molecules generated with the control of protein environment information have a clear tendency on generating compounds with higher similarity to the original X-ray bound ligand than normal RNN model and also achieving better performance in terms of docking scores. Our results demonstrate the potential application of EGCM controlled generative model for the targeted molecule generation and guided exploration on the drug-like chemical space. </p><p> </p>

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