MODELING IMMUNE NETWORK THROUGH CELLULAR AUTOMATA: A UNIFIED MECHANISM OF IMMUNOLOGICAL MEMORY

The populations of the various types of immunocompetent cells in the immune system are described as cellular automata and the population dynamics of these cells are formulated in terms of dynamical maps in discrete time. Both intra-clonal interactions (i.e., interactions among the cell types belonging to the same clone) and inter-clonal interactions (i.e., interactions among the cell types belonging to different clones) are included in the models proposed here. While the intra-clonal interactions are shown to play a crucial role in the primary response of some clones and in the formation of the immunological memory, the inter-clonal interactions are responsible for retaining the memory through a dynamical process driven by the mutual stimulation of the clones. We present the results for two different types of connectivity, namely, a “necklace” network and a network in “shape space”.

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Study of the Molecular Architecture of Keratin Filaments by Electron Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100053310 ◽

1982 ◽

Vol 40 ◽

pp. 118-119

Author(s):

U. Aebi ◽

P. Rew ◽

T.-T. Sun

Keyword(s):

Electron Microscopy ◽

Structural Organization ◽

Cell Types ◽

Structural Features ◽

Molecular Architecture ◽

The Past ◽

Keratin Filaments ◽

Different Types ◽

10 Nm Filaments ◽

Different Cell Types

Various types of intermediate-sized (10-nm) filaments have been found and described in many different cell types during the past few years. Despite the differences in the chemical composition among the different types of filaments, they all yield common structural features: they are usually up to several microns long and have a diameter of 7 to 10 nm; there is evidence that they are made of several 2 to 3.5 nm wide protofilaments which are helically wound around each other; the secondary structure of the polypeptides constituting the filaments is rich in ∞-helix. However a detailed description of their structural organization is lacking to date.

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Simulating Self-Regeneration and Self-Replication Processes Using Movable Cellular Automata with a Mutual Equilibrium Neighborhood

Complex Systems ◽

10.25088/complexsystems.29.4.741 ◽

2020 ◽

Vol 29 (4) ◽

pp. 741-757

Author(s):

Kateryna Hazdiuk ◽

◽

Volodymyr Zhikharevich ◽

Serhiy Ostapov ◽

◽

...

Keyword(s):

Cellular Automata ◽

Cellular Automaton ◽

Three Dimensional ◽

Computer Models ◽

The Self ◽

Model Construction ◽

Natural Phenomena ◽

Different Types ◽

Movable Cellular Automata ◽

Self Replication

This paper deals with the issue of model construction of the self-regeneration and self-replication processes using movable cellular automata (MCAs). The rules of cellular automaton (CA) interactions are found according to the concept of equilibrium neighborhood. The method is implemented by establishing these rules between different types of cellular automata (CAs). Several models for two- and three-dimensional cases are described, which depict both stable and unstable structures. As a result, computer models imitating such natural phenomena as self-replication and self-regeneration are obtained and graphically presented.

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Transcriptional and morphological profiling of parvalbumin interneuron subpopulations in the mouse hippocampus

Nature Communications ◽

10.1038/s41467-020-20328-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Lin Que ◽

David Lukacsovich ◽

Wenshu Luo ◽

Csaba Földy

Keyword(s):

Large Scale ◽

Cell Types ◽

Rna Seq ◽

Neuronal Identity ◽

Parvalbumin Interneurons ◽

Different Types ◽

Parvalbumin Interneuron ◽

Cam Profile ◽

Developmental Domains

AbstractThe diversity reflected by >100 different neural cell types fundamentally contributes to brain function and a central idea is that neuronal identity can be inferred from genetic information. Recent large-scale transcriptomic assays seem to confirm this hypothesis, but a lack of morphological information has limited the identification of several known cell types. In this study, we used single-cell RNA-seq in morphologically identified parvalbumin interneurons (PV-INs), and studied their transcriptomic states in the morphological, physiological, and developmental domains. Overall, we find high transcriptomic similarity among PV-INs, with few genes showing divergent expression between morphologically different types. Furthermore, PV-INs show a uniform synaptic cell adhesion molecule (CAM) profile, suggesting that CAM expression in mature PV cells does not reflect wiring specificity after development. Together, our results suggest that while PV-INs differ in anatomy and in vivo activity, their continuous transcriptomic and homogenous biophysical landscapes are not predictive of these distinct identities.

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Identifying cell types from single-cell data based on similarities and dissimilarities between cells

BMC Bioinformatics ◽

10.1186/s12859-020-03873-z ◽

2021 ◽

Vol 22 (S3) ◽

Author(s):

Yuanyuan Li ◽

Ping Luo ◽

Yi Lu ◽

Fang-Xiang Wu

Keyword(s):

Gene Expression ◽

Single Cell ◽

Spectral Clustering ◽

Incidence Matrix ◽

Expression Patterns ◽

Cell Types ◽

Clustering Method ◽

Different Types ◽

Cell Data ◽

Spectral Clustering Method

Abstract Background With the development of the technology of single-cell sequence, revealing homogeneity and heterogeneity between cells has become a new area of computational systems biology research. However, the clustering of cell types becomes more complex with the mutual penetration between different types of cells and the instability of gene expression. One way of overcoming this problem is to group similar, related single cells together by the means of various clustering analysis methods. Although some methods such as spectral clustering can do well in the identification of cell types, they only consider the similarities between cells and ignore the influence of dissimilarities on clustering results. This methodology may limit the performance of most of the conventional clustering algorithms for the identification of clusters, it needs to develop special methods for high-dimensional sparse categorical data. Results Inspired by the phenomenon that same type cells have similar gene expression patterns, but different types of cells evoke dissimilar gene expression patterns, we improve the existing spectral clustering method for clustering single-cell data that is based on both similarities and dissimilarities between cells. The method first measures the similarity/dissimilarity among cells, then constructs the incidence matrix by fusing similarity matrix with dissimilarity matrix, and, finally, uses the eigenvalues of the incidence matrix to perform dimensionality reduction and employs the K-means algorithm in the low dimensional space to achieve clustering. The proposed improved spectral clustering method is compared with the conventional spectral clustering method in recognizing cell types on several real single-cell RNA-seq datasets. Conclusions In summary, we show that adding intercellular dissimilarity can effectively improve accuracy and achieve robustness and that improved spectral clustering method outperforms the traditional spectral clustering method in grouping cells.

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The paracaspase MALT1 in psoriasis

Biological Chemistry ◽

10.1515/hsz-2021-0250 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Stephan Hailfinger ◽

Klaus Schulze-Osthoff

Keyword(s):

T Cells ◽

Dendritic Cells ◽

Transcription Factors ◽

Skin Disease ◽

Cell Types ◽

Cytokine Receptors ◽

Molecular Scaffold ◽

Therapeutic Implications ◽

Stimulation Of

Abstract Psoriasis is a frequent autoimmune-related skin disease, which involves various cell types such as T cells, keratinocytes and dendritic cells. Genetic variations, such as mutations of CARD14, can promote the development of the disease. CARD14 mutations as well as the stimulation of immune and cytokine receptors activate the paracaspase MALT1, a potent activator of the transcription factors NF-κB and AP-1. The disease-promoting role of MALT1 for psoriasis is mediated by both its protease activity as well as its molecular scaffold function. Here, we review the importance of MALT1-mediated signaling and its therapeutic implications in psoriasis.

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Effects of Gut Metabolites and Microbiota in Healthy and Marginal Livers Submitted to Surgery

International Journal of Molecular Sciences ◽

10.3390/ijms22010044 ◽

2020 ◽

Vol 22 (1) ◽

pp. 44

Author(s):

Marc Micó-Carnero ◽

Carlos Rojano-Alfonso ◽

Ana Isabel Álvarez-Mercado ◽

Jordi Gracia-Sancho ◽

Araní Casillas-Ramírez ◽

...

Keyword(s):

Immune Responses ◽

Ischemia Reperfusion Injury ◽

Ischemia Reperfusion ◽

Cell Types ◽

Microbial Populations ◽

Operative Outcomes ◽

Bidirectional Relationship ◽

Preclinical And Clinical Studies ◽

Different Cell Types ◽

Stimulation Of

Microbiota is defined as the collection of microorganisms within the gastrointestinal ecosystem. These microbes are strongly implicated in the stimulation of immune responses. An unbalanced microbiota, termed dysbiosis, is related to the development of several liver diseases. The bidirectional relationship between the gut, its microbiota and the liver is referred to as the gut–liver axis. The translocation of bacterial products from the intestine to the liver induces inflammation in different cell types such as Kupffer cells, and a fibrotic response in hepatic stellate cells, resulting in deleterious effects on hepatocytes. Moreover, ischemia-reperfusion injury, a consequence of liver surgery, alters the microbiota profile, affecting inflammation, the immune response and even liver regeneration. Microbiota also seems to play an important role in post-operative outcomes (i.e., liver transplantation or liver resection). Nonetheless, studies to determine changes in the gut microbial populations produced during and after surgery, and affecting liver function and regeneration are scarce. In the present review we analyze and discuss the preclinical and clinical studies reported in the literature focused on the evaluation of alterations in microbiota and its products as well as their effects on post-operative outcomes in hepatic surgery.

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Mesenchymal Stem Cells and Cancer Stem Cells: An Overview of Tumor-Mesenchymal Stem Cell Interaction for therapeutic interventions

Current Drug Targets ◽

10.2174/1389450122666210824142247 ◽

2021 ◽

Vol 22 ◽

Author(s):

Soheila Montazersaheb ◽

Ezzatollah Fathi ◽

Ayoub Mamandi ◽

Raheleh Farahzadi ◽

Hamid Reza Heidari

Keyword(s):

Stem Cells ◽

Mesenchymal Stem Cells ◽

Tumor Microenvironment ◽

Cancer Stem Cells ◽

Tumor Cells ◽

Cell Types ◽

Cell Interaction ◽

Therapeutic Interventions ◽

Tumorigenic Potential ◽

Different Types

: Tumors are made up of different types of cancer cells that contribute to tumor heterogeneity. Among these cells, cancer stem cells (CSCs) have a significant role in the onset of cancer and development. Like other stem cells, CSCs are characterized by the capacity for differentiation and self-renewal. A specific population of CSCs is constituted by mesenchymal stem cells (MSCs) that differentiate into mesoderm-specific cells. The pro-or anti-tumorigenic potential of MSCs on the proliferation and development of tumor cells has been reported as contradictory results. Also, tumor progression is specified by the corresponding tumor cells like the tumor microenvironment. The tumor microenvironment consists of a network of reciprocal cell types such as endothelial cells, immune cells, MSCs, and fibroblasts as well as growth factors, chemokines, and cytokines. In this review, recent findings related to the tumor microenvironment and associated cell populations, homing of MSCs to tumor sites, and interaction of MSCs with tumor cells will be discussed.

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Properties of Unitary IPSCs in Hippocampal Pyramidal Cells Originating From Different Types of Interneurons in Young Rats

Journal of Neurophysiology ◽

10.1152/jn.1997.77.4.1939 ◽

1997 ◽

Vol 77 (4) ◽

pp. 1939-1949 ◽

Cited By ~ 37

Author(s):

Mohamed Ouardouz ◽

Jean-Claude Lacaille

Keyword(s):

Reversal Potential ◽

Pyramidal Cells ◽

Mean Amplitude ◽

Paired Pulse ◽

Young Rats ◽

Different Types ◽

The Mean ◽

Paired Pulse Depression ◽

Types Of Interneurons ◽

Stimulation Of

Ouardouz, Mohamed and Jean-Claude Lacaille. Properties of unitary IPSCs in hippocampal pyramidal cells originating from different types of interneurons in young rats. J. Neurophysiol. 77: 1939–1949, 1997. Whole cell recordings were used in hippocampal slices of young rats to examine unitary inhibitory postsynaptic currents (uIPSCs) evoked in CA1 pyramidal cells at room temperature. Loose cell-attached stimulation was applied to activate single interneurons of different subtypes located in stratum oriens (OR), near stratum pyramidale (PYR), and at the border of stratum radiatum and lacunosum-moleculare (LM). uIPSCs evoked by stimulation of PYR and OR interneurons had similar onset latency, rise time, peak amplitude, and decay. In contrast, uIPSCs elicited by activation of LM interneurons were significantly smaller in amplitude and had a slower time course. The mean reversal potential of uIPSCs was −53.1 ± 2.1 (SE) mV during recordings with intracellular solution containing potassium gluconate. With the use of recording solution containing the potassium channel blocker cesium, the reversal potential of uIPSCs was not significantly different (−58.5 ± 2.6 mV), suggesting that these synaptic currents were not mediated by potassium conductances. Bath application of the γ-aminobutyric acid-A (GABAA) receptor antagonist bicuculline (25 μM) reversibly blocked uIPSCs evoked by stimulation of all interneuron subtypes. In bicuculline, the mean peak amplitude of uIPSCs recorded with potassium gluconate was reduced to 3.5 ± 4.4% of control ( n = 7). Similarly, with cesium methanesulfonate, the mean amplitude in bicuculline was 2.9 ± 3.1% of control ( n = 13). Application of the GABAB receptor antagonist CGP 55845A (5 μM) resulted in a significant and reversible increase in the mean amplitude of uIPSCs recorded with cesium-containing intracellular solution. Thus uIPSCs from all cell types appeared under tonic presynaptic inhibition by GABAB receptors. Paired stimulation of individual interneurons at 100- to 200-ms intervals did not result in paired pulse depression of uIPSCs. For individual responses, a significant negative correlation was observed between the amplitude of the first and second uIPSCs. A significant paired pulse facilitation (154.0 ± 8.0%) was observed when the first uIPSC was smaller than the mean of all first uIPSCs. A small, but not significant, paired pulse depression (90.8 ± 4.0%) was found when the first uIPSC was larger than the mean of all first uIPSCs. Our results indicate that these different subtypes of hippocampal interneurons generate Cl−-mediated GABAA uIPSCs. uIPSCs originating from different types of interneurons may have heterogeneous properties and may be subject to tonic presynaptic inhibition via heterosynaptic GABAB receptors. These results suggest a specialization of function for inhibitory interneurons and point to complex presynaptic modulation of interneuron function.

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