scholarly journals Regenerating proteins and their expression, regulation, and signaling

2012 ◽  
Vol 3 (1) ◽  
pp. 57-70 ◽  
Author(s):  
Abhirath Parikh ◽  
Anne-Fleur Stephan ◽  
Emmanuel S. Tzanakakis
Keyword(s):  
Signaling Pathways ◽  
Gastrointestinal Cancer ◽  
Expression Patterns ◽  
Cell Types ◽  
Biological Processes ◽  
Islet Regeneration ◽  
Regulation Of Expression ◽  
Proliferation And Differentiation ◽  
Protein Group ◽  
Different Cell Types

AbstractThe regenerating (Reg) protein family comprises C-type lectin-like proteins discovered independently during pancreatitis and pancreatic islet regeneration. However, an increasing number of studies provide evidence of participation of Reg proteins in the proliferation and differentiation of diverse cell types. Moreover, Reg family members are associated with various pathologies, including diabetes and forms of gastrointestinal cancer. These findings have led to the emergence of key roles for Reg proteins as anti-inflammatory, antiapoptotic, and mitogenic agents in multiple physiologic and disease contexts. Yet, there are significant gaps in our knowledge regarding the regulation of expression of different Reg genes. In addition, the pathways relaying Reg-triggered signals, their targets, and potential cross-talk with other cascades are still largely unknown. In this review, the expression patterns of different Reg members in the pancreas and extrapancreatic tissues are described. Moreover, factors known to modulate Reg levels in different cell types are discussed. Several signaling pathways, which have been implicated in conferring the effects of Reg ligands to date, are also delineated. Further efforts are necessary for elucidating the biological processes underlying the action of Reg proteins and their involvement in various maladies. Better understanding of the function of Reg genes and proteins will be beneficial in the design and development of therapies utilizing or targeting this protein group.

Growth and differentiation factors in tracheobronchial epithelium

1991 ◽  
Vol 260 (6) ◽  
pp. L361-L373 ◽  
Author(s):  
A. M. Jetten
Keyword(s):  
Normal Structure ◽  
Cell Types ◽  
Regulatory Factors ◽  
Biochemical Processes ◽  
Polypeptide Growth Factors ◽  
Tracheobronchial Epithelium ◽  
Cell Proliferation And Differentiation ◽  
Proliferation And Differentiation ◽  
Population Interactions ◽  
Different Cell Types

The normal tracheobronchial epithelium is continuously renewing itself: cells are lost and replaced by the proliferation and differentiation of stem cells. The proliferation and differentiation of these cells have to be tightly controlled in order to maintain the normal structure of the epithelium. A variety of biological and biochemical processes are involved in controlling the proliferation and differentiation of the tracheobronchial epithelium. Since the trachea and bronchus are comprised of a heterogeneous cell population, interactions between the different cell types are of crucial importance not only in controlling the normal maintenance of this tissue but also in the regulation of repair processes following injury and morphogenesis during lung development. A variety of factors, including several polypeptide growth factors and cytokines, have been identified that regulate positively or negatively the growth and differentiation of tracheobronchial epithelial cells by autocrine or paracrine mechanisms. Retinoids are another group of regulatory factors that appear to play a crucial role in controlling cell proliferation and differentiation in the tracheobronchial epithelium. Recently, many advances have been made in understanding the action of these agents in these cells. Alterations in the balance between growth and differentiation regulatory factors appear to play an important role in several pathophysiological changes such as hyperplasia, fibrosis, and neoplasia.

scholarly journals Chemical and Light Inducible Epigenome Editing

2020 ◽  
Vol 21 (3) ◽  
pp. 998
Author(s):  
Weiye Zhao ◽  
Yufan Wang ◽  
Fu-Sen Liang
Keyword(s):  
Small Molecules ◽  
Expression Patterns ◽  
Cell Types ◽  
Epigenome Editing ◽  
Specific Targeting ◽  
Conditional Control ◽  
Cellular Behaviors ◽  
Different Cell Types ◽  
Kinetics Of ◽  
Epigenetic Research

The epigenome defines the unique gene expression patterns and resulting cellular behaviors in different cell types. Epigenome dysregulation has been directly linked to various human diseases. Epigenome editing enabling genome locus-specific targeting of epigenome modifiers to directly alter specific local epigenome modifications offers a revolutionary tool for mechanistic studies in epigenome regulation as well as the development of novel epigenome therapies. Inducible and reversible epigenome editing provides unique temporal control critical for understanding the dynamics and kinetics of epigenome regulation. This review summarizes the progress in the development of spatiotemporal-specific tools using small molecules or light as inducers to achieve the conditional control of epigenome editing and their applications in epigenetic research.

scholarly journals Inference of the drivers of collective movement in two cell types: Dictyostelium and melanoma

2016 ◽  
Vol 13 (123) ◽  
pp. 20160695 ◽  
Author(s):  
Elaine A. Ferguson ◽  
Jason Matthiopoulos ◽  
Robert H. Insall ◽  
Dirk Husmeier
Keyword(s):  
Model Comparison ◽  
Cell Movement ◽  
Information Criterion ◽  
Cell Types ◽  
Human Melanoma ◽  
Diffusion Reaction ◽  
Biological Processes ◽  
Melanoma Model ◽  
Underlying Mechanisms ◽  
Different Cell Types

Collective cell movement is a key component of many important biological processes, including wound healing, the immune response and the spread of cancers. To understand and influence these movements, we need to be able to identify and quantify the contribution of their different underlying mechanisms. Here, we define a set of six candidate models—formulated as advection–diffusion–reaction partial differential equations—that incorporate a range of cell movement drivers. We fitted these models to movement assay data from two different cell types: Dictyostelium discoideum and human melanoma. Model comparison using widely applicable information criterion suggested that movement in both of our study systems was driven primarily by a self-generated gradient in the concentration of a depletable chemical in the cells' environment. For melanoma, there was also evidence that overcrowding influenced movement. These applications of model inference to determine the most likely drivers of cell movement indicate that such statistical techniques have potential to support targeted experimental work in increasing our understanding of collective cell movement in a range of systems.

scholarly journals Global Analysis of Cell Type-Specific Gene Expression

2003 ◽  
Vol 4 (2) ◽  
pp. 208-215 ◽  
Author(s):  
David W. Galbraith
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Global Analysis ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
Cell Types ◽  
Reasonable Assumption ◽  
Specific Gene ◽  
Different Cell Types

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

scholarly journals The Influence of Structural Gradients in Large Pore Organosilica Materials on the Capabilities for Hosting Cellular Communities

2020 ◽  
Author(s):  
Hannah Bronner ◽  
Anna-Katharina Holzer ◽  
Alexander Finke ◽  
Marius Kunkel ◽  
Andreas Marx ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Special Property ◽  
Cell Types ◽  
Living Cells ◽  
Biological Processes ◽  
Native State ◽  
Chemical Gradient ◽  
Polymeric Foam ◽  
Different Cell Types ◽  
Organosilica Materials

<div><div><div><div><p>Cells exist in the so-called extracellular matrix (ECM) in their native state, and numerous future applications require reliable and potent ECM-mimics. A perspective, which goes beyond ECM emulation, is the design of a host-material with features, which are not accessible in the biological portfolio. Such a feature would, for instance be, the creation of a structural or chemical gradient, and to explore how this special property influences the biological processes. First, we wanted to test if macroporous organosilica materials with appropriate surface modification can act as a host for the implementation of human cells like HeLa or LUHMES. It was possible to use a commercially available polymeric foam as a scaffold and coat it with a layer of a thiophenol-containing organosilica layer, followed by biofunctionalization with biotin using click chemistry and the subsequent coupling of streptavidin - fibronectin to it. More importantly, deformation of the scaffold allowed the generation of a permanent structural gradient. In this work, we show that the structural gradient has a tremendous influence on the capability of the described material for the accommodation of living cells. The introduction of a bi-directional gradient enabled the establishment of a cellular community comprising different cell types in spatially distinct regions of the material. An interesting perspective is to study communication between cell types or to create cellular communities, which can never exist in a natural enviornment.</p></div></div></div></div>

scholarly journals A genetic, genomic, and computational resource for exploring neural circuit function

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Fred P Davis ◽  
Aljoscha Nern ◽  
Serge Picard ◽  
Michael B Reiser ◽  
Gerald M Rubin ◽  
...  
Keyword(s):  
Neural Circuits ◽  
Neural Circuit ◽  
Individual Cell ◽  
Probabilistic Method ◽  
Expression Patterns ◽  
Cell Types ◽  
Receptor Expression ◽  
Generating Functional ◽  
Circuit Function ◽  
Different Cell Types

The anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the Drosophila visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of apparent co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.

scholarly journals Genetic reagents for making split-GAL4 lines in Drosophila

2017 ◽  
Author(s):  
Heather Dionne ◽  
Karen L. Hibbard ◽  
Amanda Cavallaro ◽  
Jui-Chun Kao ◽  
Gerald M. Rubin
Keyword(s):  
Nervous System ◽  
Genomic Dna ◽  
Expression Patterns ◽  
Cell Types ◽  
Biological Processes ◽  
Single Segment ◽  
Distinct Cell ◽  
Experimental Tool ◽  
Transgenic Lines

AbstractThe ability to reproducibly target expression of transgenes to small, defined subsets of cells is a key experimental tool for understanding many biological processes. The Drosophila nervous system contains thousands of distinct cell types and it has generally not been possible to limit expression to one or a few cell types when using a single segment of genomic DNA as an enhancer to drive expression. Intersectional methods, in which expression of the transgene only occurs where two different enhancers overlap in their expression patterns, can be used to achieve the desired specificity. This report describes a set of over 2,800 transgenic lines for use with the split-GAL4 intersectional method.

scholarly journals A genetic, genomic, and computational resource for exploring neural circuit function

2018 ◽  
Author(s):  
Fred P. Davis ◽  
Aljoscha Nern ◽  
Serge Picard ◽  
Michael B. Reiser ◽  
Gerald M. Rubin ◽  
...  
Keyword(s):  
Neural Circuit ◽  
Affinity Purification ◽  
Probabilistic Method ◽  
Expression Patterns ◽  
Cell Types ◽  
Receptor Expression ◽  
List Type ◽  
Visual Neurons ◽  
Circuit Function ◽  
Different Cell Types

AbstractThe anatomy of many neural circuits is being characterized with increasing resolution, but their molecular properties remain mostly unknown. Here, we characterize gene expression patterns in distinct neural cell types of the Drosophila visual system using genetic lines to access individual cell types, the TAPIN-seq method to measure their transcriptomes, and a probabilistic method to interpret these measurements. We used these tools to build a resource of high-resolution transcriptomes for 100 driver lines covering 67 cell types, available at http://www.opticlobe.com. Combining these transcriptomes with recently reported connectomes helps characterize how information is transmitted and processed across a range of scales, from individual synapses to circuit pathways. We describe examples that include identifying neurotransmitters, including cases of co-release, generating functional hypotheses based on receptor expression, as well as identifying strong commonalities between different cell types.HighlightsTranscriptomes reveal transmitters and receptors expressed in Drosophila visual neuronsTandem affinity purification of intact nuclei (TAPIN) enables neuronal genomicsTAPIN-seq and genetic drivers establish transcriptomes of 67 Drosophila cell typesProbabilistic modeling simplifies interpretation of large transcriptome catalogs

scholarly journals Allograft Inflammatory Factor-1 in Metazoans: Focus on Invertebrates

Biology ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 355
Author(s):  
Jacopo Vizioli ◽  
Tiziano Verri ◽  
Patrizia Pagliara
Keyword(s):  
Calcium Binding ◽  
Current Knowledge ◽  
Inflammatory Diseases ◽  
Adaptor Protein ◽  
Cell Types ◽  
Inflammatory Factor ◽  
Biological Processes ◽  
Activated Macrophages ◽  
Different Cell Types ◽  
Physical Challenges

Allograft inflammatory factor-1 (AIF-1) is a calcium-binding scaffold/adaptor protein often associated with inflammatory diseases. Originally cloned from active macrophages in humans and rats, this gene has also been identified in other vertebrates and in several invertebrate species. Among metazoans, AIF-1 protein sequences remain relatively highly conserved. Generally, the highest expression levels of AIF-1 are observed in immunocytes, suggesting that it plays a key role in immunity. In mammals, the expression of AIF-1 has been reported in different cell types such as activated macrophages, microglial cells, and dendritic cells. Its main immunomodulatory role during the inflammatory response has been highlighted. Among invertebrates, AIF-1 is involved in innate immunity, being in many cases upregulated in response to biotic and physical challenges. AIF-1 transcripts result ubiquitously expressed in all examined tissues from invertebrates, suggesting its participation in a variety of biological processes, but its role remains largely unknown. This review aims to present current knowledge on the role and modulation of AIF-1 and to highlight its function along the evolutionary scale.

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