scholarly journals Foxd4l1.1 Negatively Regulates Chordin Transcription in Neuroectoderm of Xenopus Gastrula

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2779
Author(s):  
Vijay Kumar ◽  
Ravi Shankar Goutam ◽  
Zobia Umair ◽  
Soochul Park ◽  
Unjoo Lee ◽  
...  
Keyword(s):  
Bone Morphogenetic Proteins ◽  
Decisive Role ◽  
Feedback Mechanism ◽  
Bmp Signaling ◽  
Site Directed Mutagenesis ◽  
Marker Genes ◽  
Specific Marker ◽  
Germ Layer ◽  
Response Elements ◽  
Gene Assay

Inhibition of the bone morphogenetic proteins (BMPs) is the primary step toward neuroectoderm formation in vertebrates. In this process, the Spemann organizer of the dorsal mesoderm plays a decisive role by secreting several extracellular BMP inhibitors such as Chordin (Chrd). Chrd physically interacts with BMP proteins and inhibits BMP signaling, which triggers the expression of neural-specific transcription factors (TFs), including Foxd4l1.1. Thus, Chrd induces in a BMP-inhibited manner and promotes neuroectoderm formation. However, the regulatory feedback mechanism of Foxd4l1.1 on mesodermal genes expression during germ-layer specification has not been fully elucidated. In this study, we investigated the regulatory mechanism of Foxd4l1.1 on chrd (a mesodermal gene). We demonstrate that Foxd4l1.1 inhibits chrd expression during neuroectoderm formation in two ways: First, Foxd4l1.1 directly binds to FRE (Foxd4l1.1 response elements) within the chrd promoter region to inhibit transcription. Second, Foxd4l1.1 physically interacts with Smad2 and Smad3, and this interaction blocks Smad2 and Smad3 binding to activin response elements (AREs) within the chrd promoter. Site-directed mutagenesis of FRE within the chrd(-2250) promoter completely abolished repressor activity of the Foxd4l1.1. RT-PCR and reporter gene assay results indicate that Foxd4l1.1 strongly inhibits mesoderm- and ectoderm-specific marker genes to maintain neural fate. Altogether, these results suggest that Foxd4l1.1 negatively regulates chrd transcription by dual mechanism. Thus, our study demonstrates the existence of precise reciprocal regulation of chrd transcription during neuroectoderm and mesoderm germ-layer specification in Xenopus embryos.

scholarly journals scSorter: assigning cells to known cell types according to marker genes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hongyu Guo ◽  
Jun Li
Keyword(s):  
Real Data ◽  
Cell Types ◽  
Exact Expression ◽  
Marker Genes ◽  
Specific Marker ◽  
Sequencing Data ◽  
Reference Dataset ◽  
Over Expression ◽  
Higher Power ◽  
Cell Type Specific

AbstractOn single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact expression levels are unavailable, that is, without using a reference dataset. Based on an observation that the expected over-expression of marker genes is often absent in a nonnegligible proportion of cells, we develop a method called scSorter. scSorter allows marker genes to express at a low level and borrows information from the expression of non-marker genes. On both simulated and real data, scSorter shows much higher power compared to existing methods.

scholarly journals The Role of BMP Signaling in Osteoclast Regulation

2021 ◽  
Vol 9 (3) ◽  
pp. 24
Author(s):  
Brian Heubel ◽  
Anja Nohe
Keyword(s):  
Bone Formation ◽  
Bone Morphogenetic Proteins ◽  
Bone Diseases ◽  
Bmp Signaling ◽  
Bone Homeostasis ◽  
Direct Stimulation ◽  
Federal Drug Administration ◽  
Bmp Pathway ◽  
Stimulation Of

The osteogenic effects of Bone Morphogenetic Proteins (BMPs) were delineated in 1965 when Urist et al. showed that BMPs could induce ectopic bone formation. In subsequent decades, the effects of BMPs on bone formation and maintenance were established. BMPs induce proliferation in osteoprogenitor cells and increase mineralization activity in osteoblasts. The role of BMPs in bone homeostasis and repair led to the approval of BMP2 by the Federal Drug Administration (FDA) for anterior lumbar interbody fusion (ALIF) to increase the bone formation in the treated area. However, the use of BMP2 for treatment of degenerative bone diseases such as osteoporosis is still uncertain as patients treated with BMP2 results in the stimulation of not only osteoblast mineralization, but also osteoclast absorption, leading to early bone graft subsidence. The increase in absorption activity is the result of direct stimulation of osteoclasts by BMP2 working synergistically with the RANK signaling pathway. The dual effect of BMPs on bone resorption and mineralization highlights the essential role of BMP-signaling in bone homeostasis, making it a putative therapeutic target for diseases like osteoporosis. Before the BMP pathway can be utilized in the treatment of osteoporosis a better understanding of how BMP-signaling regulates osteoclasts must be established.

scholarly journals Bone Morphogenetic Proteins and Diabetic Retinopathy

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 593
Author(s):  
Khaled Elmasry ◽  
Samar Habib ◽  
Mohamed Moustafa ◽  
Mohamed Al-Shabrawey
Keyword(s):  
Diabetic Retinopathy ◽  
Bone Morphogenetic Proteins ◽  
Potential Role ◽  
Microvascular Dysfunction ◽  
Cardiovascular Complications ◽  
Bmp Signaling ◽  
Age Related Macular Degeneration ◽  
Age Related ◽  
Retinal Inflammation ◽  
Underlying Mechanisms

Bone morphogenetic proteins (BMPs) play an important role in bone formation and repair. Recent studies underscored their essential role in the normal development of several organs and vascular homeostasis in health and diseases. Elevated levels of BMPs have been linked to the development of cardiovascular complications of diabetes mellitus. However, their particular role in the pathogenesis of microvascular dysfunction associated with diabetic retinopathy (DR) is still under-investigated. Accumulated evidence from our and others’ studies suggests the involvement of BMP signaling in retinal inflammation, hyperpermeability and pathological neovascularization in DR and age-related macular degeneration (AMD). Therefore, targeting BMP signaling in diabetes is proposed as a potential therapeutic strategy to halt the development of microvascular dysfunction in retinal diseases, particularly in DR. The goal of this review article is to discuss the biological functions of BMPs, their underlying mechanisms and their potential role in the pathogenesis of DR in particular.

scholarly journals Identification of cell-type-specific marker genes from co-expression patterns in tissue samples

2021 ◽  
Author(s):  
Yixuan Qiu ◽  
Jiebiao Wang ◽  
Jing Lei ◽  
Kathryn Roeder
Keyword(s):  
Single Cell ◽  
Expression Patterns ◽  
R Package ◽  
Supplementary Information ◽  
Marker Genes ◽  
Specific Marker ◽  
Cell Type ◽  
Correlation Pattern ◽  
Tissue Samples ◽  
Bulk Data

Abstract Motivation Marker genes, defined as genes that are expressed primarily in a single cell type, can be identified from the single cell transcriptome; however, such data are not always available for the many uses of marker genes, such as deconvolution of bulk tissue. Marker genes for a cell type, however, are highly correlated in bulk data, because their expression levels depend primarily on the proportion of that cell type in the samples. Therefore, when many tissue samples are analyzed, it is possible to identify these marker genes from the correlation pattern. Results To capitalize on this pattern, we develop a new algorithm to detect marker genes by combining published information about likely marker genes with bulk transcriptome data in the form of a semi-supervised algorithm. The algorithm then exploits the correlation structure of the bulk data to refine the published marker genes by adding or removing genes from the list. Availability and implementation We implement this method as an R package markerpen, hosted on CRAN (https://CRAN.R-project.org/package=markerpen). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Dual Inhibition of Activin/Nodal/TGF-βand BMP Signaling Pathways by SB431542 and Dorsomorphin Induces Neuronal Differentiation of Human Adipose Derived Stem Cells

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Vedavathi Madhu ◽  
Abhijit S. Dighe ◽  
Quanjun Cui ◽  
D. Nicole Deal
Keyword(s):  
Stem Cells ◽  
Nervous System ◽  
Neuronal Differentiation ◽  
Adult Stem Cells ◽  
Embryonic Stem ◽  
Bmp Signaling ◽  
Specific Marker ◽  
Adipose Derived Stem Cells ◽  
Neuronal Marker ◽  
Dual Inhibition

Damage to the nervous system can cause devastating diseases or musculoskeletal dysfunctions and transplantation of progenitor stem cells can be an excellent treatment option in this regard. Preclinical studies demonstrate that untreated stem cells, unlike stem cells activated to differentiate into neuronal lineage, do not survive in the neuronal tissues. Conventional methods of inducing neuronal differentiation of stem cells are complex and expensive. We therefore sought to determine if a simple, one-step, and cost effective method, previously reported to induce neuronal differentiation of embryonic stem cells and induced-pluripotent stem cells, can be applied to adult stem cells. Indeed, dual inhibition of activin/nodal/TGF-βand BMP pathways using SB431542 and dorsomorphin, respectively, induced neuronal differentiation of human adipose derived stem cells (hADSCs) as evidenced by formation of neurite extensions, protein expression of neuron-specific gamma enolase, and mRNA expression of neuron-specific transcription factors Sox1 and Pax6 and matured neuronal marker NF200. This process correlated with enhanced phosphorylation of p38, Erk1/2, PI3K, and Akt1/3. Additionally,in vitrosubcutaneous implants of SB431542 and dorsomorphin treated hADSCs displayed significantly higher expression of active-axonal-growth-specific marker GAP43. Our data offers novel insights into cell-based therapies for the nervous system repair.

scholarly journals Study of expression analysis of SIRT4 and the coordinate regulation of bovine adipocyte differentiation by SIRT4 and its transcription factors

2018 ◽  
Vol 38 (6) ◽  
Author(s):  
Jieyun Hong ◽  
Shijun Li ◽  
Xiaoyu Wang ◽  
Chugang Mei ◽  
Linsen Zan
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Adipocyte Differentiation ◽  
Binding Protein ◽  
Core Promoter ◽  
Critical Role ◽  
Luciferase Reporter ◽  
Marker Genes ◽  
Gene Assay ◽  
Bovine Adipocytes

Sirtuins, NAD+-dependent deacylases and ADP-ribosyltransferases, are critical regulators of metabolism involved in many biological processes, and are involved in mediating adaptive responses to the cellular environment. SIRT4 is a mitochondrial sirtuin and has been shown to play a critical role in maintaining insulin secretion and glucose homeostasis. As a regulator of lipid homeostasis, SIRT4 can repress fatty acid oxidation and promote lipid anabolism in nutrient-replete conditions. Using real-time quantitative PCR (qPCR) to explore the molecular mechanisms of transcriptional regulation of bovine SIRT4 during adipocyte differentiation, we found that bovine SIRT4 is expressed at high levels in bovine subcutaneous adipose tissue. SIRT4 knockdown led to decreased expression of adipogenic differentiation marker genes during adipocyte differentiation. The core promoter of bovine SIRT4 was identified in the −402/−60 bp region of the cloned 2-kb fragment containing the 5′-regulatory region. Binding sites were identified in this region for E2F transcription factor-1 (E2F1), CCAAT/enhancer-binding protein β (CEBPβ), homeobox A5 (HOXA5), interferon regulatory factor 4 (IRF4), paired box 4 (PAX4), and cAMP responsive element-binding protein 1 (CREB1) by using Electrophoretic mobility shift assay (EMSA) and luciferase reporter gene assay. We also found that E2F1, CEBPβ, and HOXA5 transcriptionally activate SIRT4 expression, whereas, IRF4, PAX4, and CREB1 transcriptionally repress SIRT4 expression. We further verified that SIRT4 knockdown could affect the ability of these transcription factors (TFs) to regulate the differentiation of bovine adipocytes. In conclusion, our results shed light on the mechanisms underlying the transcriptional regulation of SIRT4 expression in bovine adipocytes.

scholarly journals JIND: Joint Integration and Discrimination for Automated Single-Cell Annotation

2020 ◽  
Author(s):  
Mohit Goyal ◽  
Guillermo Serrano ◽  
Ilan Shomorony ◽  
Mikel Hernaez ◽  
Idoia Ochoa
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Marker Genes ◽  
Specific Marker ◽  
Rna Seq ◽  
Batch Effects ◽  
Cell Type ◽  
Latent Space ◽  
Cell Type Specific ◽  
Low Dimensional

AbstractSingle-cell RNA-seq is a powerful tool in the study of the cellular composition of different tissues and organisms. A key step in the analysis pipeline is the annotation of cell-types based on the expression of specific marker genes. Since manual annotation is labor-intensive and does not scale to large datasets, several methods for automated cell-type annotation have been proposed based on supervised learning. However, these methods generally require feature extraction and batch alignment prior to classification, and their performance may become unreliable in the presence of cell-types with very similar transcriptomic profiles, such as differentiating cells. We propose JIND, a framework for automated cell-type identification based on neural networks that directly learns a low-dimensional representation (latent code) in which cell-types can be reliably determined. To account for batch effects, JIND performs a novel asymmetric alignment in which the transcriptomic profile of unseen cells is mapped onto the previously learned latent space, hence avoiding the need of retraining the model whenever a new dataset becomes available. JIND also learns cell-type-specific confidence thresholds to identify and reject cells that cannot be reliably classified. We show on datasets with and without batch effects that JIND classifies cells more accurately than previously proposed methods while rejecting only a small proportion of cells. Moreover, JIND batch alignment is parallelizable, being more than five or six times faster than Seurat integration. Availability: https://github.com/mohit1997/JIND.

scholarly journals Evaluation of BMP-mediated patterning in a 3D mathematical model of the zebrafish blastula embryo

2019 ◽  
Author(s):  
Linlin Li ◽  
Xu Wang ◽  
Mary C. Mullins ◽  
David M. Umulis
Keyword(s):  
Bone Morphogenetic Proteins ◽  
Zebrafish Embryo ◽  
Three Dimensional ◽  
Bmp Signaling ◽  
Multiple Time ◽  
Blastula Stage ◽  
Starting Point ◽  
Gene And Protein Expression ◽  
Multiple Time Points ◽  
Source Sink

AbstractBone Morphogenetic Proteins (BMPs) play an important role in dorsal-ventral (DV) patterning of the early zebrafish embryo. BMP signaling is regulated by a network of extracellular and intracellular factors that impact the range and signaling of BMP ligands. Recent advances in understanding the mechanism of pattern formation support a source-sink mechanism, however it is not clear how the source-sink mechanism shapes patterns in 3D, nor how sensitive the pattern is to biophysical rates and boundary conditions along both the anteroposterior (AP) and DV axes of the embryo. We propose a new three-dimensional growing Partial Differential Equation (PDE)-based model to simulate the BMP patterning process during the blastula stage. This model provides a starting point to elucidate how different mechanisms and components work together in 3D to create and maintain the BMP gradient in the embryo. We also show how the 3D model fits the BMP signaling gradient data at multiple time points along both axes. Furthermore, sensitivity analysis of the model suggests that the spatiotemporal patterns of Chordin and BMP ligand gene expression are dominant drivers of shape in 3D and more work is needed to quantify the spatiotemporal profiles of gene and protein expression to further refine the models.

scholarly journals Revealing immune responses in the Mycobacterium avium subsp. paratuberculosis-infected THP-1 cells using single cell RNA-sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254194
Author(s):  
Hong-Tae Park ◽  
Woo Bin Park ◽  
Suji Kim ◽  
Jong-Sung Lim ◽  
Gyoungju Nah ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Single Cell ◽  
Mycobacterium Avium ◽  
Expression Patterns ◽  
Cell Types ◽  
Marker Genes ◽  
Specific Marker ◽  
Cell Type ◽  
Cytokines And Chemokines

Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic and debilitating disease in ruminants. MAP is also considered to be a possible cause of Crohn’s disease in humans. However, few studies have focused on the interactions between MAP and human macrophages to elucidate the pathogenesis of Crohn’s disease. We sought to determine the initial responses of human THP-1 cells against MAP infection using single-cell RNA-seq analysis. Clustering analysis showed that THP-1 cells were divided into seven different clusters in response to phorbol-12-myristate-13-acetate (PMA) treatment. The characteristics of each cluster were investigated by identifying cluster-specific marker genes. From the results, we found that classically differentiated cells express CD14, CD36, and TLR2, and that this cell type showed the most active responses against MAP infection. The responses included the expression of proinflammatory cytokines and chemokines such as CCL4, CCL3, IL1B, IL8, and CCL20. In addition, the Mreg cell type, a novel cell type differentiated from THP-1 cells, was discovered. Thus, it is suggested that different cell types arise even when the same cell line is treated under the same conditions. Overall, analyzing gene expression patterns via scRNA-seq classification allows a more detailed observation of the response to infection by each cell type.

scholarly journals Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea, with MetaPhlAn 3.0

2020 ◽  
Author(s):  
Orestis Nousias ◽  
Federica Montesanto
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Reference Database ◽  
Marker Genes ◽  
Specific Marker ◽  
Bacterial Genomes ◽  
Associated Bacteria ◽  
Pan Genome ◽  
Nucleotide Database ◽  
Porphyra Purpurea

AbstractMicrobial communities play a fundamental role in the association with marine algae, in fact they are recognized to be actively involved in growth and morphogenesis.Porphyra purpurea is a red algae commonly found in the intertidal zone with an high economical value, indeed several species belonging to the genus Porphyra are intensely cultivated in the Eastern Asian countries. Moreover, P. purpurea is widely used as model species in different fields, mainly due to its peculiar life cycle. Despite of that, little is known about the microbial community associated to this species. Here we report the microbial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and USA) through the analysis of eight metagenomic datasets obtained from the publicly available metagenomic nucleotide database (https://www.ebi.ac.uk/ena/). The metagenomic datasets were quality controlled with FastQC version 0.11.8, pre-processed with Trimmomatic version 0.39 and analysed with Methaplan 3.0, with a reference database containing clade specific marker genes from ~ 99.500 bacterial genomes, following the pan-genome approach, in order to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared the results to the 16S rRNA metagenomic analysis pipeline of MGnify database to evaluate the effectiveness of the two methods. Out of the 43 bacterial species identified with MetaPhlAn 3.0 only 5 were common with the MGnify results and from the 21 genera, only 9 were common. This approach highlighted the different taxonomical resolution of a 16S rRNA OTU-based method in contrast to the pan-genome approach deployed by MetaPhlAn 3.0.

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