scholarly journals Game of Tissues: How the Epidermis Thrones C. elegans Shape

2020 ◽  
Vol 8 (1) ◽  
pp. 7 ◽  
Author(s):  
Cátia A. Carvalho ◽  
Limor Broday
Keyword(s):  
Cell Structure ◽  
Epithelial Morphogenesis ◽  
Special Importance ◽  
Biological Processes ◽  
Feedback Mechanisms ◽  
C Elegans ◽  
Tissue Interactions ◽  
Continuous Sheet ◽  
Morphogenic Process ◽  
Organismal Development

The versatility of epithelial cell structure is universally exploited by organisms in multiple contexts. Epithelial cells can establish diverse polarized axes within their tridimensional structure which enables them to flexibly communicate with their neighbors in a 360° range. Hence, these cells are central to multicellularity, and participate in diverse biological processes such as organismal development, growth or immune response and their misfunction ultimately impacts disease. During the development of an organism, the first task epidermal cells must complete is the formation of a continuous sheet, which initiates its own morphogenic process. In this review, we will focus on the C. elegans embryonic epithelial morphogenesis. We will describe how its formation, maturation, and spatial arrangements set the final shape of the nematode C. elegans. Special importance will be given to the tissue-tissue interactions, regulatory tissue-tissue feedback mechanisms and the players orchestrating the process.

Deficiency of innate immunity against P. aeruginosa enhances behavioral avoidance via the HECW-1/NPR-1 module in C. elegans

2021 ◽  
Author(s):  
Hua Bai ◽  
Wei Zou ◽  
Wenhui Zhou ◽  
Keqin Zhang ◽  
Xiaowei Huang
Keyword(s):  
Innate Immunity ◽  
Pathogenic Bacteria ◽  
Immune Gene ◽  
Biological Processes ◽  
Defensive Strategy ◽  
C Elegans ◽  
Defensive Strategies ◽  
Behavioral Avoidance ◽  
Neuropeptide Y Receptor ◽  
G Protein Coupled

To antagonize infection of pathogenic bacteria in soil and confer increased survival, Caenorhabditis elegans employs innate immunity and behavioral avoidance synchronously as the two main defensive strategies. Although both biological processes and their individual signaling pathways have been partially elucidated, knowledge of their interrelationship remains limited. The current study reveals that deficiency of innate immunity triggered by mutation of the classic immune gene pmk-1 promotes avoidance behavior in C. elegans ; and vice versa. Restoration of pmk-1 expression using the tissue-specific promoters suggested that the functional loss of both intestinal and neuronal pmk-1 is necessary for the enhanced avoidance. Additionally, PMK-1 co-localized with the E3 ubiquitin ligase HECW-1 in OLL neurons and regulated the expressional level of the latter, which consequently affected the production of NPR-1, a G-protein-coupled receptor homologous to the mammalian neuropeptide Y receptor, in RMG neurons in a non-cell-autonomous manner. Collectively, our study illustrates, once the innate immunity is impaired when C. elegans antagonizes bacterial infection, the other defensive strategy of behavioral avoidance can be enhanced accordingly via the HECW-1/NPR-1 module, suggesting that GPCRs in neural circuits may receive the inputs from immune system and integrate those two systems for better adapting to the real-time status.

scholarly journals Effects of NAD+ in Caenorhabditis elegans Models of Neuronal Damage

Biomolecules ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 993
Author(s):  
Yuri Lee ◽  
Hyeseon Jeong ◽  
Kyung Hwan Park ◽  
Kyung Won Kim
Keyword(s):  
Caenorhabditis Elegans ◽  
Therapeutic Strategy ◽  
Axon Regeneration ◽  
Neuronal Damage ◽  
Biological Processes ◽  
Nematode Caenorhabditis Elegans ◽  
C Elegans ◽  
Neuronal Functions ◽  
Molecular Components

Nicotinamide adenine dinucleotide (NAD+) is an essential cofactor that mediates numerous biological processes in all living cells. Multiple NAD+ biosynthetic enzymes and NAD+-consuming enzymes are involved in neuroprotection and axon regeneration. The nematode Caenorhabditis elegans has served as a model to study the neuronal role of NAD+ because many molecular components regulating NAD+ are highly conserved. This review focuses on recent findings using C. elegans models of neuronal damage pertaining to the neuronal functions of NAD+ and its precursors, including a neuroprotective role against excitotoxicity and axon degeneration as well as an inhibitory role in axon regeneration. The regulation of NAD+ levels could be a promising therapeutic strategy to counter many neurodegenerative diseases, as well as neurotoxin-induced and traumatic neuronal damage.

Human Platelet-Derived Factors Regulate Mesenchymal Stem Cell Gene Expression.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4255-4255
Author(s):  
Christina Malischnik ◽  
Katharina Schallmoser ◽  
Eva Rohde ◽  
Andreas Reinisch ◽  
Christian Guelly ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Growth Factors ◽  
Human Platelet ◽  
Ex Vivo ◽  
Expression Profiles ◽  
Cell Structure ◽  
Considerable Proportion ◽  
Biological Processes ◽  
Regulated Gene Expression

Abstract The use of animal-derived products during human stem cell processing bears the evident risk of xenogeneic prion, virus, or zoonose contamination. Human platelet lysate (HPL) has recently been recognized as a rich source of cytokines and growth factors with the potential to replace fetal bovine serum (FBS) during ex vivo stem cell manipulation. In this study we compared the gene expression profile of human multipotent mesenchymal stromal/stem cells (MSC) during ex vivo expansion for clinical applications under the aegis of either FBS or HPL. The Applied Biosystems 1700 Expression Array System was used for full genome expression profiling of MSC after a 12–14 day expansion period in a previously optimized low density expansion system. Data have been obtained from biological as well as technical replicates. A starting amount of 40μg total RNA was directly labeled and DIG-labeled cDNA was hybridized to Human Genome Survey Microarray V2.0. Attribution of regulated genes to biological processes and pathways was done using the PANTHER® db analysis software. We identified more than 300 genes that are differentially regulated upon culture of MSC in HPL compared to FBS. Biological processes specifically activated in HPL culture include mesoderm development, cell cycle control, hematopoiesis and angiogenesis which interestingly correspond to a considerable proportion of the regenerative function of MSC. In contrast, processes related to cell adhesion and adhesion-mediated signaling, cell structure, cell motility and cell communication are significantly upregulated in MSC after FBS in comparison to HPL culture. Replacing FBS with HPL not only avoids bovine prion, viral and zoonose contamination of MSC for clinical use. The tightly regulated gene expression profiles under the aegis of human growth factors and cytokines provided by HPL may even help to develop new stem cell therapy strategies.

scholarly journals Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors, LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development

2020 ◽  
Author(s):  
Yukihiro Kubota ◽  
Yuto Ohnishi ◽  
Tasuku Hamasaki ◽  
Gen Yasui ◽  
Natsumi Ota ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Embryonic Development ◽  
Histone Deacetylases ◽  
Class I ◽  
Biological Processes ◽  
Nucleosome Remodeling ◽  
C Elegans ◽  
Histone Deacetylase 1 ◽  
Genome Wide ◽  
Sin3 Complex

AbstractHistone deacetylases (HDACs) are divided into four classes. Class-I HDAC, HDAC-1 forms three types of complexes, namely the Nucleosome Remodeling Deacetylase complex, the Sin3 complex, and the CoREST complex, with specific corepressor component Mi2/CHD-3, Sin3, and RCOR1 in human, respectively. The functions of these HDAC-1 complexes are regulated by their corepressors, however, their exact mechanistic roles in several biological processes remain unexplored, such as in embryonic development. Here, we report that each of the corepressors, LET-418, SIN-3, and SPR-1, the homologous of Mi2, Sin3, and RCOR1, respectively, were expressed throughout Caenorhabditis elegans embryonic development and served essential roles in the process. Moreover, genetic analysis suggested that three pathways (i.e., LET-418– SIN-3–SPR-1, SIN-3–SPR-1, and LET-418) participated in embryonic development. Our terminal-phenotype observations of single mutants of each corepressor implied that LET-418, SIN-3, and SPR-1 played similar roles in promoting advancement to the middle and late embryonic stages. Genome-wide comparative-transcriptome analysis indicated that 47.5% and 42.3% of genes were commonly increased and decreased in sin-3 and spr-1 mutants, respectively. These results suggest that among the three pathways studied, the SIN-3–SPR-1 pathway mainly serves to regulate embryonic development. Comparative-Gene Ontology analysis indicated that these three pathways played overlapping and distinct roles in regulating C. elegans embryonic development.

scholarly journals Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

2016 ◽  
Author(s):  
Aaron C. Daugherty ◽  
Robin Yeo ◽  
Jason D. Buenrostro ◽  
William J. Greenleaf ◽  
Anshul Kundaje ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Developmental Stages ◽  
Model Organism ◽  
High Sensitivity ◽  
Chromatin Accessibility ◽  
Chromatin Dynamics ◽  
C Elegans ◽  
Crucial Component ◽  
Organismal Development

AbstractChromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogeneous and simple systems, such as isolated cell populations or early-development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism C. elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development. We find that over 5,000 distal non-coding regions exhibit dynamic changes in chromatin accessibility between developmental stages, and could thereby represent putative enhancers. When tested in vivo, several of these putative enhancers indeed drive novel cell-type-and temporal-specific patterns of expression. Finally, by integrating transcription factor binding motifs in a machine learning framework, we identify EOR-1 as a unique transcription factor that may regulate chromatin dynamics during development. Our study provides a unique resource for C. elegans, a system in which the prevalence and importance of enhancers remains poorly characterized, and demonstrates the power of using whole organism chromatin accessibility to identify novel regulatory regions in complex systems.

scholarly journals MTQuant: “Seeing” Beyond the Diffraction Limit in Fluorescence Images to Quantify Neuronal Microtubule Organization

2016 ◽  
Author(s):  
Roshni Cooper ◽  
Shaul Yogev ◽  
Kang Shen ◽  
Mark Horowitz
Keyword(s):  
Average Length ◽  
Cell Structure ◽  
Ground Truth ◽  
Supplementary Information ◽  
Data Sets ◽  
Microtubule Organization ◽  
Ground Truth Data ◽  
C Elegans ◽  
Supplementary Material

AbstractMotivation:Microtubules (MTs) are polarized polymers that are critical for cell structure and axonal transport. They form a bundle in neurons, but beyond that, their organization is relatively unstudied.Results:We present MTQuant, a method for quantifying MT organization using light microscopy, which distills three parameters from MT images: the spacing of MT minus-ends, their average length, and the average number of MTs in a cross-section of the bundle. This method allows for robust and rapid in vivo analysis of MTs, rendering it more practical and more widely applicable than commonly-used electron microscopy reconstructions. MTQuant was successfully validated with three ground truth data sets and applied to over 3000 images of MTs in a C. elegans motor neuron.Availability:MATLAB code is available at http://roscoope.github.io/MTQuantContact:[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Conserved Patterns in Developmental Processes and Phases, Rather than Genes, Unite the Highly Divergent Bilateria

Life ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 182
Author(s):  
Luca Ferretti ◽  
Andrea Krämer-Eis ◽  
Philipp H. Schiffer
Keyword(s):  
Expression Profiles ◽  
Biological Processes ◽  
Model Species ◽  
Enrichment Method ◽  
Developmental Processes ◽  
Developmental Patterns ◽  
C Elegans ◽  
Go Enrichment ◽  
Conserved Genes ◽  
Phylotypic Stage

Bilateria are the predominant clade of animals on Earth. Despite having evolved a wide variety of body plans and developmental modes, they are characterized by common morphological traits. By default, researchers have tried to link clade-specific genes to these traits, thus distinguishing bilaterians from non-bilaterians, by their gene content. Here we argue that it is rather biological processes that unite Bilateria and set them apart from their non-bilaterian sisters, with a less complex body morphology. To test this hypothesis, we compared proteomes of bilaterian and non-bilaterian species in an elaborate computational pipeline, aiming to search for a set of bilaterian-specific genes. Despite the limited confidence in their bilaterian specificity, we nevertheless detected Bilateria-specific functional and developmental patterns in the sub-set of genes conserved in distantly related Bilateria. Using a novel multi-species GO-enrichment method, we determined the functional repertoire of genes that are widely conserved among Bilateria. Analyzing expression profiles in three very distantly related model species—D. melanogaster, D. rerio and C. elegans—we find characteristic peaks at comparable stages of development and a delayed onset of expression in embryos. In particular, the expression of the conserved genes appears to peak at the phylotypic stage of different bilaterian phyla. In summary, our study illustrate how development connects distantly related Bilateria after millions of years of divergence, pointing to processes potentially separating them from non-bilaterians. We argue that evolutionary biologists should return from a purely gene-centric view of evolution and place more focus on analyzing and defining conserved developmental processes and periods.

scholarly journals Antioxidant Capacity of “Mexican Arnica”Heterotheca inuloidesCass Natural Products and Some Derivatives: Their Anti-Inflammatory Evaluation and Effect onC. elegansLife Span

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
José Luis Rodríguez-Chávez ◽  
Elvia Coballase-Urrutia ◽  
Antonio Nieto-Camacho ◽  
Guillermo Delgado-Lamas
Keyword(s):  
Life Span ◽  
Antioxidant Capacity ◽  
Harmful Effect ◽  
Inflammatory Activity ◽  
Biological Processes ◽  
Ros Scavenging ◽  
C Elegans ◽  
Scavenging Capacity ◽  
Anti Inflammatory ◽  
Stable Free Radicals

It has been suggested that the accumulation of biomolecular damage caused by reactive oxygen species (ROS) contributes to aging. The antioxidant activity is related to the ability of certain compounds to protect against the potentially harmful effect of processes or reactions involving ROS. This ability is associated with the termination of free radical propagation in biological systems. FromHeterotheca inuloidesvarious compounds which have shown to possess antioxidant capacity and scavenging ROS. The aim of this study was to determine the antioxidant capacity of additional natural components isolated fromH. inuloidesand some semisynthetic derivatives, their anti-inflammatory activity and the effect onCaenorhabditis elegansnematode life span. Compounds showed ability to inhibit various biological processes such as lipid peroxidation, scavenge nonbiological important oxidants such as1O2,OH∙, H2O2, and HOCl and scavenge non biological stable free radicals (DPPH). Some cadinane type compounds showed possess antioxidant, ROS scavenging capacity, anti-inflammatory activity, and effect on theC. eleganslife span. Flavonoid type compounds increased the life of the nematode and quercetin was identified as the compound with the greatest activity. The modification of chemical structure led to a change in the antioxidant capacity, the anti-inflammatory activity, and the survival of the worm.

scholarly journals C. elegans colony formation as a condensation phenomenon

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yuping Chen ◽  
James E. Ferrell
Keyword(s):  
Phase Separation ◽  
Colony Formation ◽  
Ostwald Ripening ◽  
Equation Model ◽  
Biological Processes ◽  
Ordinary Differential Equation Model ◽  
Differential Equation Model ◽  
Collective Behaviors ◽  
C Elegans ◽  
Living Organisms

AbstractPhase separation at the molecular scale affects many biological processes. The theoretical requirements for phase separation are fairly minimal, and there is growing evidence that analogous phenomena occur at other scales in biology. Here we examine colony formation in the nematode C. elegans as a possible example of phase separation by a population of organisms. The population density of worms determines whether a colony will form in a thresholded fashion, and a simple two-compartment ordinary differential equation model correctly predicts the threshold. Furthermore, small, round colonies sometimes fuse to form larger, round colonies, and a phenomenon akin to Ostwald ripening – a coarsening process seen in many systems that undergo phase separation – also occurs. These findings support the emerging view that the principles of microscopic phase separation can also apply to collective behaviors of living organisms.

scholarly journals Aging and Neurodegeneration: New Approaches to Neurodegeneration and Aging

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 738-738
Author(s):  
Nancy Bonini
Keyword(s):  
Molecular Genetic ◽  
Model Organisms ◽  
Biological Processes ◽  
C Elegans ◽  
New Approaches

Abstract Model organisms like C. elegans and Drosophila are powerful systems to help dissect molecular genetic aspects of complex biological processes. Here we will present a number of biological questions and approaches that have been used to study questions of neural integrity and healthful aging using these systems.

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