Single Cell Structure Research Articles

Dedifferentiation- and aging-induced loss of mechanical contractility and polarity in vascular smooth muscle cells: Heterogeneous changes in macroscopic and microscopic behavior of cells in serial passage culture

Dedifferentiation and aging of vascular smooth muscle cells (VSMCs) are associated with serious vascular diseases, such as arteriosclerosis and aneurysm. However, how cell dedifferentiation and aging affect cellular mechanical behaviors at the single-cell and intracellular structure levels remains unclear. An in-depth understanding of these interactions is extremely important for understanding the mechanism underlying VSMC mechanical integrity and homeostatic regulation of vascular walls. Herein, we systematically investigated changes in VSMC morphology, structure, contractility, and motility during dedifferentiation and aging induced by serial passage culture using traction force microscopy with elastic micropillar substrates, laser nanodissection of cytoskeletons, confocal fluorescence microscopy, and atomic force microscopy. We found that VSMC dedifferentiation started in the middle stage of serial passage culture, accompanied by a transient cell spreading in the cell width and decrease in contractile protein expression. Dedifferentiated VSMCs showed a significant decrease in the contraction and stiffness of individual actin stress fibers; however, their overall cell traction forces were maintained. Simultaneously, a significant increase in cell motility and the number of actin fibers was observed in dedifferentiated VSMCs, which may be associated with the enhancement of cell migration and disruption of cell/tissue integrity during the early stage of vascular diseases. As cell senescence progressed in the later stage of serial passage culture, VSMCs displayed reduced cell spreading and migration with decrease in the overall cell traction forces and drastic reduction in mechanical polarity of cell structures and forces. These results suggested that cell senescence causes loss of mechanical contractility and polarity in VSMCs, which may be an important factor in vascular disease progression. The experimental systems established in this study can be powerful tools for understanding the mechanisms underlying cellular dedifferentiation and aging from a biomechanical perspective.

Dynamic response and failure characteristics of the fluid-filled concave multicell structure under combined blast and fragments loading

The deformation and damage characteristics of the fluid-filled concave multicell structure under the charge explosion with preset fragments are investigated to assess its performance against combined blast and fragments loading. The failure characteristics of the structure, the propagation process of loads, and the dynamic response characteristics of the structure are analyzed using experimental research and SPH-ALE numerical simulation. The results indicate that the deformation of the structure, caused by the explosion of a charge with preset fragments, is 400% greater than the deformation caused by the explosion alone. The propagation of the load is influenced by the panels of the structure and the irregular regions where fluid is filled. The deformation and failure of the fluid-filled concave multicell structure occur in two stages. The failure mode of this structure can be seen as a combination of the failure modes of individual single-cell structures, based on the method of fluid filling. The strength distribution of the structure plays a crucial role in determining the failure of the fluid-filled concave multicell structure.

Single-Cell Synchro-Subtractive-Additive Nanoscale Surgery with Femtosecond Lasers.

Herein, an in situ "synchro-subtractive-additive" technique of femtosecond laser single-cell surgery (FLSS) is presented to address the inadequacies of existing surgical methods for single-cell manipulation. This process is enabled by synchronized nanoscale three-dimensional (3D) subtractive and additive manufacturing with ultrahigh precision on various parts of the cells, in that the precise removal and modification of a single-cell structure are realized by nonthermal ablation, with synchronously ultrafast solidification of the specially designed hydrogel by two photopolymerizations. FLSS is a minimally invasive technique with a post-operative survival rate of 70% and stable proliferation. It opens avenues for bottom-up synthetic biology, offering new methods for artificially synthesizing organelle-like 3D structures and modifying the physiological activities of cells.

Properties and Characterization of Sunflower Seeds from Different Varieties of Edible and Oil Sunflower Seeds.

Sunflower seeds, oil, and protein powder are rich in nutritional value, but the quality of different varieties of sunflower seeds is quite different, and the comprehensive comparative analysis characteristics of edible and oil sunflower seeds are still unclear. The comprehensive analysis and comparison of the raw material indicators, physicochemical properties, and processing characteristics of four edible and four oil sunflower seed varieties were investigated. The results showed that the engineering properties, texture characteristics, single-cell structure, and oil, protein, and starch granule distribution were different between edible and oil sunflower seeds. The composition of fatty acids and amino acids was different among edible, oil sunflower seeds and different varieties. The oleic acid (18.72~79.30%) and linoleic acid (10.11~51.72%) were the main fatty acids in sunflower seed oil, and in amino acid composition, the highest content was glutamic acid (8.88~11.86 g/100 g), followed by aspartic acid (3.92~4.86 g/100 g) and arginine (4.03~4.80 g/100 g). Sunflower meal proteins were dominated by 11S globulin and 2S albumin, and the secondary structure was dominated by β-folding, with -SH and S-S varying greatly among different varieties. Sunflower meal proteins vary widely in terms of functional properties among different varieties, and specialized quality screening was necessary. This study provided a reference and theoretical support for understanding sunflower seeds to further promote the processing and utilization of sunflower seeds.

Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools.

We describe a new Python implementation of FlowSOM, a clustering method for cytometry data. This implementation is faster than the original version in R, better adapted to work with single-cell omics data including integration with current single-cell data structures and includes all the original visualizations, such as the star and pie plot. The FlowSOM Python implementation is freely available on GitHub: https://github.com/saeyslab/FlowSOM_Python.

Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion

Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss. Imaging experiments show that, at the single-cell level, TAD-like structures are present even without cohesin. To provide a structural basis for these findings, we first used polymer simulations to show that certain TADs with epigenetic switches across their boundaries survive after depletion of loops. More importantly, the three-dimensional structures show that many of the P-TADs have sharp physical boundaries. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and human colorectal carcinoma cell lines, which affirmed that epigenetic switches and physical boundaries (calculated using the predicted 3D structures using the data-driven HIPPS method that uses Hi-C as the input) explain the origin of the P-TADs. Single-cell structures display TAD-like features in the absence of cohesin that are remarkably similar to the findings in imaging experiments. Some P-TADs, with physical boundaries, are relevant to the retention of enhancer–promoter/promoter–promoter interactions. Overall, our study shows that preservation of a subset of TADs upon removing cohesin is a robust phenomenon that is valid across multiple cell lines.

Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion.

Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss. Imaging experiments show that, at the single-cell level, TAD-like structures are present even without cohesin. To provide a structural basis for these findings, we first used polymer simulations to show that certain TADs with epigenetic switches across their boundaries survive after depletion of loops. More importantly, the three-dimensional structures show that many of the P-TADs have sharp physical boundaries. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and human colorectal carcinoma cell lines, which affirmed that epigenetic switches and physical boundaries (calculated using the predicted 3D structures using the data-driven HIPPS method that uses Hi-C as the input) explain the origin of the P-TADs. Single-cell structures display TAD-like features in the absence of cohesin that are remarkably similar to the findings in imaging experiments. Some P-TADs, with physical boundaries, are relevant to the retention of enhancer-promoter/promoter-promoter interactions. Overall, our study shows that preservation of a subset of TADs upon removing cohesin is a robust phenomenon that is valid across multiple cell lines.

RNA structure profiling at single-cell resolution reveals new determinants of cell identity.

RNA structure is critical for multiple steps in gene regulation. However, how the structures of transcripts differ both within and between individual cells is unknown. Here we develop a SHAPE-inspired method called single-cell structure probing of RNA transcripts that enables simultaneous determination of transcript secondary structure and abundance at single-cell resolution. We apply single-cell structure probing of RNA transcripts to human embryonic stem cells and differentiating neurons. Remarkably, RNA structure is more homogeneous in human embryonic stem cells compared with neurons, with the greatest homogeneity found in coding regions. More extensive heterogeneity is found within 3' untranslated regions and is determined by specific RNA-binding proteins. Overall RNA structure profiles better discriminate cell type identity and differentiation stage than gene expression profiles alone. We further discover a cell-type variable region of 18S ribosomal RNA that is associated with cell cycle and translation control. Our method opens the door to the systematic characterization of RNA structure-function relationships at single-cell resolution.

Buffering energy-absorbing performance of multi-cell octagonal biomimetic structure with cylinder and sinusoidal guide line

In order to explore the bionic buffering energy-absorbing structure with better development and research performance, two bionic structural models (called EBETS or MBETS) with sinusoidal guide line and cylinder located at the end or center of the octagonal side are designed in this paper. In comparison between these two models and models without sinusoidal guide line (EBET, MBET), we use the finite element method and study the crashworthiness and its mechanism of influence under different amplitudes (A) and wavenumber (N): (1) The trend characteristics of change of crashworthiness indicators of EBETS and MBETS with the increase of N or A were discovered in this paper. On this basis, new buffering energy-absorbing structure with better performance ( A = 0.5, N = 20) were proposed. (2) Compared to common multi-cell and single-cell buffering energy-absorbing structures, we can safely confirm that the structure has better energy-absorption performance and have its superiority as well. (3) Based on the advantages of 3D printing technology, it is proposed to replace the single-cell structure with appropriate EBETS or MBETS, and the selection method is given in this paper.

Elucidating the automobile proton exchange membrane fuel cell of innovative double-cell structure by full-morphology simulation

The structural design of PEM fuel cell is crucial to improving its power density, and the cell structure largely depends on the bipolar plate (BP). This study compares the conventional single-cell structure and double-cell structure through three-dimensional (3D) large-scale (cell area: 312 cm2) full-morphology simulation. As for the double-cell structure, the channels are arranged in a dislocation manner and there is one cooling flow field per two cells. For the structure of the BP, we also fully considered the realistic morphology of distribution area and the coolant flow. It is found that the heat dissipation effect of double-cell structure is worse but the performance is very close compared to single-cell structure. Moreover, its volumetric power density is significantly improved (∼ 20%) due to the reduction in height. It is also found that increasing the velocity of coolant in the double-cell structure increases the performance first and then decreases.

Low-frequency sound-absorbing metamaterial based on a series-parallel arrangement structure

Low-frequency noise has a long wavelength, decays very slowly, and is extremely penetrating. Traditional marine acoustic insulation materials have difficulty achieving effective control of this low-frequency noise. In this paper, a series-parallel arrangement structure of a low-frequency metamaterial is designed, which mainly comprises convoluted channels and Helmholtz cavities in series and a sandwich arrangement of multiple cells (as opposed to the traditional parallel arrangement). We use a numerical method to establish an acoustic-solid coupling model for the metamaterial, consider the influence of thermal and viscous losses on its sound absorption performance, and investigate the sound absorption characteristics and mechanisms of the single-cell and multicell structures. The metamaterial designed in this paper shows an average absorption coefficient of 0.97 in the range of 130–145 Hz. An experimental model was prepared by 3D printing, and the intended sound absorption effect was experimentally verified.

First Report of Leaf Spot Caused by Lasiodiplodia theobromae on Kadsura coccinea in China.

Kadsura coccinea (Lem.) A. C. Smith is an evergreen liana widely cultivated in China for its economic importance in traditional medicine. Many phytochemical studies on the stems and roots of K. coccinea have shown a variety of biological activities, such as anti-hepatitis, anti-HIV, and anti-tumor (Yang et al. 2020). In July 2021, symptoms of leaf spot were observed in a plantation of K. coccinea in Longan (23°03´N, 107°54´E), Guangxi province, China. The incidence of this disease was 36%, and severity varies from approximately 20 to 40% of leaf surface coverage. Symptoms began as small brown spots that expanded into irregular to nearly flower-shaped lesions. To isolate the pathogen, leaves with spots were collected, sterilized with 75% ethanol for 15 s followed by 2% sodium hypochlorite for 120 s, rinsed three times in sterilized distilled water, cut into 5 × 5 mm pieces, and placed onto potato dextrose agar (PDA) plates. The plates were kept in an incubator at 26°C in the dark for at least 2 days. A total of 27 fungal colonies of similar morphology out of 30 pieces of infected tissues were isolated. Four representative isolates (HBB1 to HBB4) were selected to study for further characterization. Fungal colonies were initially grayish-white and then turned greenish-gray on PDA. The black pycnidium and immature conidia appeared over PDA plates after 18 days. The immature conidia were colorless and transparent, elliptical, and had a single-cell structure. After 5 days, the immature conidia gradually become black and develop into mature conidia. The mature conidia were dark brown and two-celled with longitudinal striations, 20.41-29.93 × 12.42-17.19 μm (average 26.07×14.51 μm; n = 100). For DNA-based identification, the internal transcribed spacer (ITS) region, translation elongation factor 1 alpha (EF1-α), and β-tubulin (TUB) genes of the isolates were amplified and sequenced using the primers ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone and Kohn 1999), and Bt2a/Bt2b (Glass and Donaldson 1995), respectively. Sequences were submitted to GenBank (Accession nos. MW045412 to MW045415 for ITS, MW065559 to MW065562 for EF1-α, and MW065555 to MW065558 for TUB). A phylogenetic analysis was conducted using the Maximum Likelihood method on concatenated sequences of the three genes, which showed that the four Chinese isolates from K. coccinea were clustered with reference isolates of Lasiodiplodia theobromae including the ex-neotype CBS 164.96. Pathogenicity tests were performed on young, fully expanded leaves of 2-year seedlings. A 10 μL conidial suspension (1×106 conidia/mL) was inoculated on each wound on the left-half leaf and a 10 μL sterile water was inoculated on each wound on the right-half leaf (control). Each treatment was repeated three times. Inoculated leaves were wrapped in plastic bags for 5 days and plants were maintained in a growth chamber at 27°C, 85% relative humidity. Brown leaf spots appeared 5 to 6 days after inoculation, whereas the control leaves treated with sterile water showed no symptoms. All re-isolations from spots produced colonies with the same morphological characters as L. theobromae, completing Koch's postulates. To our knowledge, this is the first report of L. theobromae causing leaf spot on K. coccinea in China and worldwide. Severe leaf disease caused by L. theobromae threatens K. coccinea production. The disease threatens K. coccinea growth, and effective control measures should be identified to reduce losses.

Crashworthiness analysis and multi-objective optimization of spatial lattice structure under dynamic compression

A spatial lattice structure is proposed to improve the structural crashworthiness and energy absorption. First, a single-cell structure is proposed via a bionic honeycomb, and then the single-cell structure is arrayed to form a spatial lattice structure. The finite element model of the spatial lattice structure for crashworthiness analysis is established. The theoretical model of the plateau stress of the lattice structure under compressive conditions is derived, and its accuracy is verified by the corresponding finite element analysis. After that, the effect of geometrical parameters of single-cell structure on crashworthiness is analyzed. Then, geometrical parameters of single-cell structure and number of single-cell in the X, Y, and Z directions are used as design variables, the mass, and overall size are used as constraints, and specific energy absorption and collision peak force are used as optimization objectives. The multi-objective crashworthiness optimization of spatial lattice structure is carried out, and the optimal lattice structure design is determined via the gray relational analysis coupling entropy weight method. The validity of the finite element model and optimal design is verified by the drop weight impact test. The crashworthiness optimization of spatial lattice structures has important guiding significance for the design of energy-absorbing structures.

Synaptic memory and CaMKII: a review.

CaMKII and long-term potentiation (LTP) were discovered within a decade of each other and have been inextricably intertwined ever since. However, like many marriages, it has had its up and downs. Based on the unique biochemical properties of CaMKII, it was proposed as a memory molecule before any direct physiological linkage was made to LTP. This review will assess the state of this marriage 40 years on. How well does the physiological evidence support the role of CaMKII in synaptic memory and what are the remaining outstanding issues?

Multi-objective crashworthiness optimization of energy-absorbing box with gradient lattice structure

To improve the lightweight and crashworthiness of energy-absorbing box, an energy-absorbing box with spatial lattice structure and multi-objective optimization method are proposed. First, a novel single-cell structure is proposed, which is replicated and arranged to form the spatial lattice structure. Then, the mechanical properties of the material are tested by quasi-static and high-speed tensile tests. The finite element model of the spatial lattice structure is established, and the numerical results are verified by the drop weight impact test. Finally, four different types of approximate models are used to fit different responses, and the combination of approximate models with higher accuracy is obtained. And the multi-objective optimization of our model is carried out. The optimal design of our model is obtained based on the grey relational analysis coupling entropy weight method. Compared with the energy-absorbing box with initial lattice, the specific energy absorption of the optimal design of our model is increased from 6.23kJ/kg to 8.91kJ/kg, an increase of 43.0%, and the mass is reduced from 1.1kg to 0.798kg, a reduction of 27.4%. The results show that the optimal design of our model has the advantages of lightweight and energy absorption.

Impact resistance of single-cell and multi-cell sandwich aluminum plates filled with aluminum foam

The aim of this paper is to investigate the impact resistance and energy dissipation capacity of a new type of multi-cell sandwich aluminum alloy plate filled with aluminum foam, in comparison to the single-cell structure. To achieve this goal, 30 sandwich aluminum alloy plates were tested using a drop hammer test machine, varying impact velocity, wall thickness, and the number of internal diaphragms. The results were analyzed and finite element analysis was conducted to explore the energy dissipation mechanisms and the effect of aluminum foam on multi-cell plates. The findings revealed three failure modes and three stages of the impact force time history curve. Multi-cell plate exhibited showed much better specific energy absorption compared with the single-cell plate. Taking an example displacement of 22.5 mm, which differentiates the specific energy absorption the most between the two types of structures, the multi-cell plate exhibited an average increase of 332% in specific energy absorption compared to the single-cell plate. The numerical simulations were consistent with experimental results and highlighted the contribution of different components to energy dissipation in both structures.

Tunable microfluidic chip for single-cell deformation study

Microfluidic phenotyping methods have been of vital importance for cellular characterization, especially for evaluating single cells. In order to study the deformability of a single cell, we devised and tested a tunable microfluidic chip-based method. A pneumatic polymer polydimethylsiloxane (PDMS) membrane was designed and fabricated abutting a single-cell trapping structure, so the cell could be squeezed controllably in a lateral direction. Cell contour changes under increasing pressure were recorded, enabling the deformation degree of different types of single cell to be analyzed and compared using computer vision. This provides a new perspective for studying mechanical properties of cells at the single cell level.

A new design for the RF electron gun of the Iranian Light Source Facility (ILSF)

A new π mode RF electron gun is proposed for the Iranian Light Source Facility. This RF gun will be fabricated using a newly developed method based on clamping the parts together instead of vacuum brazing. In this method, RF contact and vacuum seal are mutually provided by a special copper gasket. The first section of this article describes the new π mode RF gun and its expected performance in detail. The report of our recent R&D tests on the new fabrication method is discussed in the next section. We performed the RF and vacuum measurements on a single-cell structure, and the copper gasket provided suitable RF contact, and a vacuum pressure of 2.5×10−7 mbar was also reached after 1 h of pumping with a turbo-molecular pump without baking. In the last section, we investigated using a high-current and low-emittance DC triode electron gun to be mounted on the RF gun as an alternative cathode assembly. The simulation results of this proposed scheme were compatible with our previous studies. The research and development of the new π mode RF electron gun and the proposed cathode assembly will begin soon.

Computational predictions of 3D chromatin many-body interactions reveal roles of chromatin hubs in gene expression.

Chromatin 3D organization plays important roles in the regulation of gene expression. Hi-C measurements provide a projection of 3D chromatin organization onto a 2D heatmap, which depicts the population-averaged pairwise contact frequencies between all genomic elements. These 2D heatmaps highlight structural units of chromatin organization such as TADs. As distal cis-regulatory elements such as enhancers interact with promoters to increase the transcriptional output of target genes in a tissue-specific manner, quantifying cell-type specific chromatin spatial organization is therefore critical. However, TADs have been found to be largely invariant across cell types, suggesting that features of 2D Hi-C heatmaps are insufficient to gain understanding of tissue-specific gene expression. Another challenge is when multiple genomic elements are involved: It is not possible to obtain higher-order many-body interactions from Hi-C data. In order to address these problems, we apply CHROMATIX, a computational method which reconstructs ensembles of single-cell chromatin conformations by deconvolving Hi-C data. We reconstructed large ensembles (2×104) of independent 3D single-cell chromatin conformations which reproduce imaging, Dip-C, and 3D FISH single cell measurements. The reconstructed ensembles of single-cell chromatin structures further enable us to uncover statistically significant 3D hubs of higher-order many-body interactions. We uncovered chromatin hubs of many-bodies across hundreds of loci in B-lymphocyte cells. We illustrate the functional roles of these 3D hubs of many-body interactions in regulating gene expression. Using the example of eQTL associated genes, we show that higher-order 3D hubs provide the physical basis of differential gene expression, with detailed examples of hubs of 1-gene-to-many-eQTLs and many-genes-to-1-eQTL. Overall, our results show 3D chromatin many-body hubs are important for regulating gene expression, and they can be discovered through CHROMATIX computational modeling single-cell 3D chromatin conformations using population Hi-C data.

Performance of hollow and aluminum foam-filled multi-cell thin-walled aluminum alloy tubes (6063-T5) under axial impact

This study investigates a new form of multi-cell thin-walled structures under axial impact. Eighteen multi-cell thin-walled aluminum alloy tubes were tested under drop hammer impacts. Nine of the specimens were hollow tubes and the other nine specimens were aluminum foam-filled multi-cell thin-walled aluminum alloy tubes. This paper presents the entire duration of the impact including the time history curves of forces and vertical displacement. The influence of impact velocity, wall thickness and aluminum foam on the impact resistance of multi-cell thin-walled aluminum alloy tubes were discussed. Then, the energy dissipation performance of multi-cell thin-walled structures tested in this study and single-cell thin-walled structures tested in prior research is compared. The results show that the foam infill improves the energy dissipation capacity of the multi-cell thin-walled aluminum alloy tubes, but the specific energy absorption (the energy absorbed per unit mass) decreases. Although the specific energy absorption is reduced, using foam infill is still an effective method to improve energy dissipation capacity without increasing the size of the member. Compared with the single-cell thin-walled aluminum alloy tubes, the specific energy absorption of the multi-cell thin-walled aluminum alloy tubes is higher by 7.35%–55.51%, which means that multi-cell thin-walled columns are a better energy absorption component compared with single-cell columns.