Evolutionary conservation of maternal RNA localization in fishes and amphibians revealed by TOMO-Seq

Asymmetrical localization of biomolecules inside the egg, results in uneven cell division and establishment of many biological processes, cell types and the body plan. However, our knowledge about evolutionary conservation of localized mRNAs is still limited to a few candidates. Our goal was to compare localization profiles along the animal-vegetal axis of mature eggs from four models, Xenopus laevis, Danio rerio, Ambystoma mexicanum and Acipenser ruthenus using the spatial expression method called TOMO-Seq. We revealed that RNAs of many known important genes such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models. There was also a poor correlation between vegetally localized genes but a relatively good correlation between animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.

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The structure of the gills of the axolotl, Ambystoma mexicanum

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100128407 ◽

1987 ◽

Vol 45 ◽

pp. 824-825

Author(s):

Mohinder S. Jarial

Keyword(s):

Leydig Cells ◽

Secretory Granules ◽

Light And Electron Microscopy ◽

Cell Types ◽

Ambystoma Mexicanum ◽

Basal Cells ◽

Granular Cells ◽

Gill Filaments ◽

Mitotic Figures ◽

Apical Membranes

The axolotl is a strictly aquatic salamander in which the larval external gills are retained throughout life. The external gills of the adult axolotl have been studied by light and electron microscopy for ultrastructural evidence of ionic transport. The thin epidermis of the gill filaments and gill stems is composed of 3 cell types: granular cells, the basal cells and a sparce population of intervening Leydig cells. The gill epidermis is devoid of muscles, and no mitotic figures were observed in any of its cells.The granular cells cover the gill surface as a continuous layer (Fig. 1, G) and contain secretory granules of different forms, located apically (Figs.1, 2, SG). Some granules are found intimately associated with the apical membrane while others fuse with it and release their contents onto the external surface (Fig. 3). The apical membranes of the granular cells exhibit microvilli which are covered by a PAS+ fuzzy coat, termed “glycocalyx” (Fig. 2, MV).

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Extracellular-Vesicle-Based Coatings Enhance Bioactivity of Titanium Implants—SurfEV

Nanomaterials ◽

10.3390/nano11061445 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1445

Author(s):

Taisa Nogueira Pansani ◽

Thanh Huyen Phan ◽

Qingyu Lei ◽

Alexey Kondyurin ◽

Bill Kalionis ◽

...

Keyword(s):

Cell Proliferation ◽

Titanium Surface ◽

Wound Closure ◽

Cell Types ◽

Extracellular Vesicle ◽

Tissue Growth ◽

Titanium Implants ◽

The Body ◽

High Concentrations ◽

And Migration

Extracellular vesicles (EVs) are nanoparticles released by cells that contain a multitude of biomolecules, which act synergistically to signal multiple cell types. EVs are ideal candidates for promoting tissue growth and regeneration. The tissue regenerative potential of EVs raises the tantalizing possibility that immobilizing EVs on implant surfaces could potentially generate highly bioactive and cell-instructive surfaces that would enhance implant integration into the body. Such surfaces could address a critical limitation of current implants, which do not promote bone tissue formation or bond bone. Here, we developed bioactive titanium surface coatings (SurfEV) using two types of EVs: secreted by decidual mesenchymal stem cells (DEVs) and isolated from fermented papaya fluid (PEVs). For each EV type, we determined the size, morphology, and molecular composition. High concentrations of DEVs enhanced cell proliferation, wound closure, and migration distance of osteoblasts. In contrast, the cell proliferation and wound closure decreased with increasing concentration of PEVs. DEVs enhanced Ca/P deposition on the titanium surface, which suggests improvement in bone bonding ability of the implant (i.e., osteointegration). EVs also increased production of Ca and P by osteoblasts and promoted the deposition of mineral phase, which suggests EVs play key roles in cell mineralization. We also found that DEVs stimulated the secretion of secondary EVs observed by the presence of protruding structures on the cell membrane. We concluded that, by functionalizing implant surfaces with specialized EVs, we will be able to enhance implant osteointegration by improving hydroxyapatite formation directly at the surface and potentially circumvent aseptic loosening of implants.

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High-throughput screening of circRNAs reveals novel mechanisms of tuberous sclerosis complex-related renal angiomyolipoma

Human Genomics ◽

10.1186/s40246-021-00344-1 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Yang Zhao ◽

Hao Guo ◽

Wenda Wang ◽

Guoyang Zheng ◽

Zhan Wang ◽

...

Keyword(s):

Lipid Metabolism ◽

Tuberous Sclerosis ◽

Tuberous Sclerosis Complex ◽

Regulatory Network ◽

High Throughput Screening ◽

Kidney Tissue ◽

Cell Types ◽

The Body ◽

Differentially Expressed ◽

Renal Angiomyolipoma

Abstract Objective Tuberous sclerosis complex (TSC) is a rare autosomal dominant disease characterized by lesions throughout the body. Our previous study showed the abnormal up-regulation of miRNAs plays an important part in the pathogenesis of TSC-related renal angiomyolipoma (TSC-RAML). circRNAs were known as important regulators of miRNA, but little is known about the circRNAs in TSC-RAMLs. Methods Microarray chips and RNA sequencing were used to identify the circRNAs and mRNAs that were differently expressed between the TSC-RAML and normal kidney tissue. A competitive endogenous RNA (ceRNA) regulatory network was constructed to reveal the regulation of miRNAs and mRNAs by the circRNAs. The biological functions of circRNA and mRNA were analyzed by pathway analysis. Microenvironmental cell types were estimated with the MCP-counter package. Results We identified 491 differentially expressed circRNAs (DECs) and 212 differentially expressed genes (DEGs), and 6 DECs were further confirmed by q-PCR. A ceRNA regulatory network which included 6 DECs, 5 miRNAs, and 63 mRNAs was established. Lipid biosynthetic process was significantly up-regulated in TSC-RAML, and the humoral immune response and the leukocyte chemotaxis pathway were found to be down-regulated. Fibroblasts are enriched in TSC-RAML, and the up-regulation of circRNA_000799 and circRNA_025332 may be significantly correlated to the infiltration of the fibroblasts. Conclusion circRNAs may regulate the lipid metabolism of TSC-RAML by regulation of the miRNAs. Fibroblasts are enriched in TSC-RAMLs, and the population of fibroblast may be related to the alteration of circRNAs of TSC-RAML. Lipid metabolism in fibroblasts is a potential treatment target for TSC-RAML.

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Glucocorticoid Receptor β (GRβ): Beyond Its Dominant-Negative Function

International Journal of Molecular Sciences ◽

10.3390/ijms22073649 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3649

Author(s):

Patricia Ramos-Ramírez ◽

Omar Tliba

Keyword(s):

Current Knowledge ◽

Inflammatory Diseases ◽

Cell Communication ◽

Cell Types ◽

The Body ◽

Dominant Negative ◽

Negative Effects ◽

Independent Manner ◽

Distinct Cell ◽

Induced Apoptosis

Glucocorticoids (GCs) act via the GC receptor (GR), a receptor ubiquitously expressed in the body where it drives a broad spectrum of responses within distinct cell types and tissues, which vary in strength and specificity. The variability of GR-mediated cell responses is further extended by the existence of GR isoforms, such as GRα and GRβ, generated through alternative splicing mechanisms. While GRα is the classic receptor responsible for GC actions, GRβ has been implicated in the impairment of GRα-mediated activities. Interestingly, in contrast to the popular belief that GRβ actions are restricted to its dominant-negative effects on GRα-mediated responses, GRβ has been shown to have intrinsic activities and “directly” regulates a plethora of genes related to inflammatory process, cell communication, migration, and malignancy, each in a GRα-independent manner. Furthermore, GRβ has been associated with increased cell migration, growth, and reduced sensitivity to GC-induced apoptosis. We will summarize the current knowledge of GRβ-mediated responses, with a focus on the GRα-independent/intrinsic effects of GRβ and the associated non-canonical signaling pathways. Where appropriate, potential links to airway inflammatory diseases will be highlighted.

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Insights into how environment shapes post-mortem RNA transcription in mouse brain

Scientific Reports ◽

10.1038/s41598-021-92268-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Raphael Severino Bonadio ◽

Larissa Barbosa Nunes ◽

Patricia Natália S. Moretti ◽

Juliana Forte Mazzeu ◽

Stefano Cagnin ◽

...

Keyword(s):

Lipid Metabolism ◽

Mouse Brain ◽

Molecular Mechanisms ◽

Cell Communication ◽

Rna Degradation ◽

The Body ◽

Biological Processes ◽

Post Mortem ◽

Gene Expression Alterations ◽

Upregulated Genes

AbstractMost biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.

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Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells

BMC Genomics ◽

10.1186/s12864-021-07712-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wiruntita Chankeaw ◽

Sandra Lignier ◽

Christophe Richard ◽

Theodoros Ntallaris ◽

Mariam Raliou ◽

...

Keyword(s):

Gene Expression ◽

Protein Localization ◽

Expression Profiles ◽

Cell Types ◽

Molecular Signature ◽

Receptor Protein ◽

Specific Gene ◽

Specific Cell ◽

Biological Processes ◽

Endometrial Cells

Abstract Background A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole endometrium which is a complex tissue. Consequently, the knowledge of cell-specific gene expression, when analysis performed with whole endometrium, is still weak and obviously limits the relevance of the results of gene expression studies. Thus, the aim of this study was to characterize specific transcriptome of the three main cell-types of the bovine endometrium at day-15 of the estrus cycle. Results In the RNA-Seq analysis, the number of expressed genes detected over 10 transcripts per million was 6622, 7814 and 8242 for LE, GE and ST respectively. ST expressed exclusively 1236 genes while only 551 transcripts were specific to the GE and 330 specific to LE. For ST, over-represented biological processes included many regulation processes and response to stimulus, cell communication and cell adhesion, extracellular matrix organization as well as developmental process. For GE, cilium organization, cilium movement, protein localization to cilium and microtubule-based process were the only four main biological processes enriched. For LE, over-represented biological processes were enzyme linked receptor protein signaling pathway, cell-substrate adhesion and circulatory system process. Conclusion The data show that each endometrial cell-type has a distinct molecular signature and provide a significantly improved overview on the biological process supported by specific cell-types. The most interesting result is that stromal cells express more genes than the two epithelial types and are associated with a greater number of pathways and ontology terms.

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Energetics of mesoscale cell turbulence in two-dimensional monolayers

Communications Physics ◽

10.1038/s42005-021-00530-6 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Shao-Zhen Lin ◽

Wu-Yang Zhang ◽

Dapeng Bi ◽

Bo Li ◽

Xi-Qiao Feng

Keyword(s):

Kinetic Energy ◽

Tumor Metastasis ◽

Cell Types ◽

Boltzmann Distribution ◽

Scaling Exponent ◽

Biological Processes ◽

Two Dimensional ◽

Cell Monolayers ◽

Wide Range ◽

Epithelial Cell Monolayers

AbstractInvestigation of energy mechanisms at the collective cell scale is a challenge for understanding various biological processes, such as embryonic development and tumor metastasis. Here we investigate the energetics of self-sustained mesoscale turbulence in confluent two-dimensional (2D) cell monolayers. We find that the kinetic energy and enstrophy of collective cell flows in both epithelial and non-epithelial cell monolayers collapse to a family of probability density functions, which follow the q-Gaussian distribution rather than the Maxwell–Boltzmann distribution. The enstrophy scales linearly with the kinetic energy as the monolayer matures. The energy spectra exhibit a power-decaying law at large wavenumbers, with a scaling exponent markedly different from that in the classical 2D Kolmogorov–Kraichnan turbulence. These energetic features are demonstrated to be common for all cell types on various substrates with a wide range of stiffness. This study provides unique clues to understand active natures of cell population and tissues.

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Quantitative Studies of Fibronectin Adsorption on Submicron Scaffolds

ASME 2012 Summer Bioengineering Conference, Parts A and B ◽

10.1115/sbc2012-80633 ◽

2012 ◽

Author(s):

Shawn Regis ◽

Manisha Jassal ◽

Sina Youssefian ◽

Nima Rahbar ◽

Sankha Bhowmick

Keyword(s):

Surface Functionalization ◽

Cultured Cells ◽

Cell Attachment ◽

Md Simulations ◽

Cell Types ◽

Biological Processes ◽

Integrin Receptors ◽

Tissue Engineering Scaffolds ◽

Quantitative Studies

Fibronectin plays a crucial role in adhesion of several cell types, mainly due to the fact that it is recognized by at least ten different integrin receptors. Since most cell types can bind to fibronectin, it becomes involved in many various biological processes. The interaction of cells with ECM proteins such as fibronectin provides the signals affecting morphology, motility, gene expression, and survival of cells [1]. Fibronectin exists in both soluble and insoluble forms; soluble fibronectin is secreted by cells and exits in cell media or body fluids, whereas insoluble fibronectin exists in tissues or the extracellular matrix of cultured cells [2]. The ability to control adsorption of fibronectin on tissue engineering scaffolds would therefore play a huge role in controlling cell attachment and survival in vivo. This can be achieved through surface functionalization of the scaffolds. The goal of these studies is to use molecular dynamics (MD) simulations to mechanistically understand how fibronectin adsorption is enhanced by surface functionalization of submicron scaffolds.

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Analyses of the pericyte transcriptome in ischemic skeletal muscles

Stem Cell Research & Therapy ◽

10.1186/s13287-021-02247-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yuan-chi Teng ◽

Alfredo Leonardo Porfírio-Sousa ◽

Giulia Magri Ribeiro ◽

Marcela Corso Arend ◽

Lindolfo da Silva Meirelles ◽

...

Keyword(s):

Endothelial Cells ◽

Vascular Endothelial Cells ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Limb Ischemia ◽

Inflammatory Cells ◽

Cell Types ◽

Arterial Disease ◽

The Body ◽

Time Points

Abstract Background Peripheral arterial disease (PAD) affects millions of people and compromises quality of life. Critical limb ischemia (CLI), which is the most advanced stage of PAD, can cause nonhealing ulcers and strong chronic pain, and it shortens the patients’ life expectancy. Cell-based angiogenic therapies are becoming a real therapeutic approach to treat CLI. Pericytes are cells that surround vascular endothelial cells to reinforce vessel integrity and regulate local blood pressure and metabolism. In the past decade, researchers also found that pericytes may function as stem or progenitor cells in the body, showing the potential to differentiate into several cell types. We investigated the gene expression profiles of pericytes during the early stages of limb ischemia, as well as the alterations in pericyte subpopulations to better understand the behavior of pericytes under ischemic conditions. Methods In this study, we used a hindlimb ischemia model to mimic CLI in C57/BL6 mice and explore the role of pericytes in regeneration. To this end, muscle pericytes were isolated at different time points after the induction of ischemia. The phenotypes and transcriptomic profiles of the pericytes isolated at these discrete time points were assessed using flow cytometry and RNA sequencing. Results Ischemia triggered proliferation and migration and upregulated the expression of myogenesis-related transcripts in pericytes. Furthermore, the transcriptomic analysis also revealed that pericytes induce or upregulate the expression of a number of cytokines with effects on endothelial cells, leukocyte chemoattraction, or the activation of inflammatory cells. Conclusions Our findings provide a database that will improve our understanding of skeletal muscle pericyte biology under ischemic conditions, which may be useful for the development of novel pericyte-based cell and gene therapies.

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Clock gene-independent daily regulation of haemoglobin oxidation in red blood cells

10.1101/2021.10.11.463714 ◽

2021 ◽

Author(s):

Andrew D. Beale ◽

Priya Crosby ◽

Utham K. Valekunja ◽

Rachel S. Edgar ◽

Johanna E. Chesham ◽

...

Keyword(s):

Circadian Rhythms ◽

Red Blood Cells ◽

Blood Cells ◽

Human Subjects ◽

Developmental Regulation ◽

Physiological Role ◽

Cell Types ◽

The Body

AbstractCellular circadian rhythms confer daily temporal organisation upon behaviour and physiology that is fundamental to human health and disease. Rhythms are present in red blood cells (RBCs), the most abundant cell type in the body. Being naturally anucleate, RBC circadian rhythms share key elements of post-translational, but not transcriptional, regulation with other cell types. The physiological function and developmental regulation of RBC circadian rhythms is poorly understood, however, partly due to the small number of appropriate techniques available. Here, we extend the RBC circadian toolkit with a novel biochemical assay for haemoglobin oxidation status, termed “Bloody Blotting”. Our approach relies on a redox-sensitive covalent haem-haemoglobin linkage that forms during cell lysis. Formation of this linkage exhibits daily rhythms in vitro, which are unaffected by mutations that affect the timing of circadian rhythms in nucleated cells. In vivo, haemoglobin oxidation rhythms demonstrate daily variation in the oxygen-carrying and nitrite reductase capacity of the blood, and are seen in human subjects under controlled laboratory conditions as well as in freely-behaving humans. These results extend our molecular understanding of RBC circadian rhythms and suggest they serve an important physiological role in gas transport.

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