Digital RNA-seq transcriptome plus tissue anatomy analyses reveal the developmental mechanism of the calabash-shaped root in Tetrastigma hemsleyanum

2021 ◽  
Author(s):  
Taihe Xiang ◽  
Jiangshan Li ◽  
Shuying Bao ◽  
Zhengxian Xu ◽  
Leizhen Wang ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Chinese Herb ◽  
Acc Oxidase ◽  
Mapk Signaling ◽  
Cell Periphery ◽  
Vascular Bundles ◽  
Rna Seq ◽  
Short Root ◽  
Tetrastigma Hemsleyanum ◽  
Intrinsic Component

Abstract Tetrastigma hemsleyanum is a liana plant with promising medicinal and ornamental values. Its calabash-shaped roots (CRs) are served as a traditional Chinese herb. However, it takes a long growth period to form CRs. In the present study, three types of architectural roots, including fine roots (FRs), bar-shaped roots (BRs) and CRs, were employed as materials, and the characteristics of histo-anatomy and digital RNA-seq transcriptome profiles were analyzed. Among the three types of roots, the vascular bundles in FRs were intact, while some of the vascular bundles degenerated in BRs, and only few traces of vascular bundles existed in CRs. Meanwhile, no obvious cell inclusions were found in the cytoplasm of FRs, while a few inclusions were found in BRs, and abundant inclusions were detected in CRs, which might be the main source of medicinal components in roots. The transcriptome profiles and qRT-PCR validation indicated that seven up-regulated genes encoding xyloglucan glycosyltransferase, ACC oxidase, CYP711A1, SHORT-ROOT transcript factor, galacturonosyltransferas, WAT1 and WRKY, and two down-regulated genes encoded LRR receptor-like serine/threonine-protein kinase and CYP83B1, were probably involved in the formation and development of CRs. Besides, GO terms of intrinsic component of membrane, integral component of membrane, cell periphery, membrane part, plasma membrane, membrane, intrinsic component of plasma membrane, cellular chemical homeostasis, and plasma membrane part were probably related to the formation of CRs. KEGG pathways related to the development of CRs probably included MAPK signaling pathway-plant, plant hormone signal transduction, and circadian rhythm-plant. Our finding suggested a probable mode for the formation of CRs.

scholarly journals Glycosylation Modulates Plasma Membrane Trafficking of CD24 in Breast Cancer Cells

2021 ◽  
Vol 22 (15) ◽  
pp. 8165
Author(s):  
Amanda Chantziou ◽  
Kostas Theodorakis ◽  
Hara Polioudaki ◽  
Eelco de Bree ◽  
Marilena Kampa ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Plasma Membrane ◽  
Subcellular Localization ◽  
Cancer Cells ◽  
Membrane Trafficking ◽  
Breast Cancer Cells ◽  
Endocytic Pathway ◽  
Cell Periphery ◽  
Wild Type ◽  
Mcf 7

In breast cancer, expression of Cluster of Differentiation 24 (CD24), a small GPI-anchored glycoprotein at the cell periphery, is associated with metastasis and immune escape, while its absence is associated with tumor-initiating capacity. Since the mechanism of CD24 sorting is unknown, we investigated the role of glycosylation in the subcellular localization of CD24. Expression and localization of wild type N36- and/or N52-mutated CD24 were analyzed using immunofluorescence in luminal (MCF-7) and basal B (MDA-MB-231 and Hs578T) breast cancer cells lines, as well as HEK293T cells. Endogenous and exogenously expressed wild type and mutated CD24 were found localized at the plasma membrane and the cytoplasm, but not the nucleoplasm. The cell lines showed different kinetics for the sorting of CD24 through the secretory/endocytic pathway. N-glycosylation, especially at N52, and its processing in the Golgi were critical for the sorting and expression of CD24 at the plasma membrane of HEK293T and basal B type cells, but not of MCF-7 cells. In conclusion, our study highlights the contribution of N-glycosylation for the subcellular localization of CD24. Aberrant N-glycosylation at N52 of CD24 could account for the lack of CD24 expression at the cell surface of basal B breast cancer cells.

scholarly journals Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White Pigs

2020 ◽  
Author(s):  
Dawei Zhang ◽  
Wenjing Wu ◽  
Xin Huang ◽  
Ke Xu ◽  
Cheng Zheng ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Fat Deposition ◽  
Mapk Signaling Pathway ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Domestic Pig ◽  
Large White ◽  
Pig Breeds

Abstract Background: Chinese domestic pig breeds are reputed for pork quality, but their low ratio of lean-to-fat carcass weight decreases production efficiency. A better understanding of the genetic regulation network of SC fat tissue is necessary for the rational selection of Chinese domestic pig breeds. In the present study, SC adipocytes were isolated from Jiaxing Black pigs (a Chinese indigenous pig breed with redundant SC fat deposition) and Large White pigs (a lean-type pig breed with relatively low SC fat deposition) and the expression profiles of mRNAs and lncRNAs were compared by RNA-seq analysis to identify biomarkers correlated with the differences of SC fat deposition between the two breeds.Results: A total of 3,371 differentially expressed genes (DEGs) and 1,182 differentially expressed lncRNAs (DELs) were identified in SC adipocytes between Jiaxing Black (JX) and Large White (LW) pigs, which included 797 upregulated mRNAs, 2,574 downregulated mRNAs, 461 upregulated lncRNAs and 721 downregulated lncRNAs. Gene Ontology and KEGG pathway analyses revealed that the DEGs and DELs were mainly involved in the immune response, cell fate determination, PI3K-Akt signaling pathway and MAPK signaling pathway, which are known to be related to adipogenesis and lipid metabolism. The expression levels of DEGs and DELs according to the RNA-seq data were verified by quantitative PCR, which showed 81.8% consistency. The differences in MAPK pathway activity between JX and LW pigs was confirmed by western blot analysis, with <100-fold elevated p38 phosphorylation in JX pigs.Conclusions: This study offers a detailed characterization of mRNAs and lncRNAs in fat- and lean-type pig breeds. The activity of the MAPK signaling pathway was found to be associated with subcutaneous adipogenesis. These results greatly enhance our understanding of the molecular mechanisms regulating SC fat deposition in pigs.

scholarly journals Highly specific antibody to Rous sarcoma virus src gene product recognizes a novel population of pp60v-src and pp60c-src molecules.

1985 ◽  
Vol 100 (2) ◽  
pp. 409-417 ◽  
Author(s):  
M D Resh ◽  
R L Erikson
Keyword(s):  
Plasma Membrane ◽  
Specific Antibody ◽  
Rous Sarcoma Virus ◽  
Distinct Pattern ◽  
Cell Periphery ◽  
Equal Distribution ◽  
Rous Sarcoma ◽  
Src Gene ◽  
Sarcoma Virus ◽  
Infected Cells

Antiserum to the Rous sarcoma virus (RSV)-transforming protein, pp60v-src, was produced in rabbits immunized with p60 expressed in Escherichia coli. alpha p60 serum immunoprecipitated quantitatively more pp60v-src than did tumor-bearing rabbit (TBR) sera. When RSV-transformed cell lysates were preadsorbed with TBR serum, the remaining lysate contained additional pp60v-src, which was recognized only by reimmunoprecipitation with alpha p60 serum and not by TBR serum. In subcellular fractions of RSV-infected chicken embryo fibroblasts (RSV-CEFs) and field vole cells probed with TBR serum, the majority of the pp60v-src was associated with the plasma membrane-enriched P100 fraction. However, alpha p60 serum revealed equal distribution of pp60v-src and its kinase activity between the P1 (nuclear) and P100 fractions. The same results were obtained for pp60c-src in uninfected CEFs. On discontinuous sucrose gradients nearly 50% of the P1-pp60v-src sedimented with nuclei, in fractions where no plasma membrane was detected. Indirect immunofluorescence microscopy of RSV-CEFs with alpha p60 serum revealed a distinct pattern of perinuclear fluorescence, in addition to staining at the cell periphery. Thus the use of a highly specific antibody reveals that enzymatically active pp60v-src and pp60c-src molecules are present in other intracellular structures, probably juxtareticular nuclear membranes, in addition to the plasma membrane in normal, uninfected, and wild-type RSV-infected cells.

scholarly journals Function of Dynein and Dynactin in Herpes Simplex Virus Capsid Transport

2002 ◽  
Vol 13 (8) ◽  
pp. 2795-2809 ◽  
Author(s):  
Katinka Döhner ◽  
André Wolfstein ◽  
Ute Prank ◽  
Christophe Echeverri ◽  
Denis Dujardin ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Cytoplasmic Dynein ◽  
Transport Processes ◽  
Viral Envelope ◽  
Cell Periphery ◽  
Virus Binding ◽  
Viral Protein Synthesis ◽  
Simplex Virus

After fusion of the viral envelope with the plasma membrane, herpes simplex virus type 1 (HSV1) capsids are transported along microtubules (MTs) from the cell periphery to the nucleus. The motor ATPase cytoplasmic dynein and its multisubunit cofactor dynactin mediate most transport processes directed toward the minus-ends of MTs. Immunofluorescence microscopy experiments demonstrated that HSV1 capsids colocalized with cytoplasmic dynein and dynactin. We blocked the function of dynein by overexpressing the dynactin subunit dynamitin, which leads to the disruption of the dynactin complex. We then infected such cells with HSV1 and measured the efficiency of particle binding, virus entry, capsid transport to the nucleus, and the expression of immediate-early viral genes. High concentrations of dynamitin and dynamitin-GFP reduced the number of viral capsids transported to the nucleus. Moreover, viral protein synthesis was inhibited, whereas virus binding to the plasma membrane, its internalization, and the organization of the MT network were not affected. We concluded that incoming HSV1 capsids are propelled along MTs by dynein and that dynein and dynactin are required for efficient viral capsid transport to the nucleus.

scholarly journals MEMBRANE-COATING GRANULES OF KERATINIZING EPITHELIA

1965 ◽  
Vol 24 (2) ◽  
pp. 297-307 ◽  
Author(s):  
A. Gedeon Matoltsy ◽  
Paul F. Parakkal
Keyword(s):  
Electron Microscopy ◽  
Plasma Membrane ◽  
Epithelial Cells ◽  
Cell Envelope ◽  
Cell Periphery ◽  
Cell Surfaces ◽  
Intercellular Spaces ◽  
Cytoplasmic Granules ◽  
Coated Cell ◽  
Membrane Coating

The purpose of this study has been to obtain information on the development of the envelop of horny cells that resists the action of keratinolytic agents. Toward this end the epidermis, oral mucosa, and tongue epithelium of various vertebrates, as well as the isolated envelopes of horny cells, were examined by electron microscopy. It was found that small cytoplasmic granules (1,000 to 5,000 A) that develop within differentiating epithelial cells move toward the cell periphery, and after fusion with the plasma membrane, empty their contents into the intercellular spaces. The content of the granules spreads over the cell surfaces, and subsequently a thickened and coated cell envelope is formed that resists the action of keratinolytic agent. The membrane-coating granule is regarded as a specific differentiation product of the keratinizing epithelium. It contains numerous inner membranes and is assumed to engage in synthetic activities such as, perhaps, the formation of polysaccharides.

MEK inhibitors impair insulin-stimulated glucose uptake in 3T3-L1 adipocytes

2004 ◽  
Vol 287 (4) ◽  
pp. E758-E766 ◽  
Author(s):  
Anne W. Harmon ◽  
David S. Paul ◽  
Yashomati M. Patel
Keyword(s):  
Plasma Membrane ◽  
Glucose Uptake ◽  
Glucose Transporter ◽  
Mapk Pathway ◽  
Mek Inhibitor ◽  
Pi3k Pathway ◽  
Mapk Signaling ◽  
Mitogen Activated Protein Kinase ◽  
Mek Inhibitors ◽  
Transport Assay

In 3T3-L1 adipocytes, insulin activates three major signaling cascades, the phosphoinositide 3-kinase (PI3K) pathway, the Cbl pathway, and the mitogen-activated protein kinase (MAPK) pathway. Although PI3K and Cbl mediate insulin-stimulated glucose uptake by promoting the translocation of the insulin-responsive glucose transporter (GLUT4) to the plasma membrane, the MAPK pathway does not have an established role in insulin-stimulated glucose uptake. We demonstrate in this report that PI3K inhibitors also inhibit the MAPK pathway. To investigate the role of the MAPK pathway separately from that of the PI3K pathway in insulin-stimulated glucose uptake, we used two specific inhibitors of MAPK kinase (MEK) activity, PD-98059 and U-0126, which reduced insulin-stimulated glucose uptake by ∼33 and 50%, respectively. Neither MEK inhibitor affected the activation of Akt or PKCζ/λ, downstream signaling molecules in the PI3K pathway. Inhibition of MEK with U-0126 did not prevent GLUT4 from translocating to the plasma membrane, nor did it inhibit the subsequent docking and fusion of GLUT4- myc with the plasma membrane. MEK inhibitors affected glucose transport mediated by GLUT4 but not GLUT1. Importantly, the presence of MEK inhibitors only at the time of the transport assay markedly impaired both insulin-stimulated glucose uptake and MAPK signaling. Conversely, removal of MEK inhibitors before the transport assay restored glucose uptake and MAPK signaling. Collectively, our studies suggest a possible role for MEK in the activation of GLUT4.

The Functional Role of TLR9 in Human Platelets

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 366-366
Author(s):  
Jonathan Noah Thon ◽  
Christian G. Peters ◽  
Rukhsana Aslam ◽  
Jesse Rowley ◽  
Andrew S. Weyrich ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Type Iv Collagen ◽  
Surface Expression ◽  
Dense Granule ◽  
Immunogold Electron Microscopy ◽  
Cell Periphery ◽  
Severe Thrombocytopenia ◽  
Viral Dna ◽  
Type Iv ◽  
Type C

Abstract Abstract 366 Human and murine platelets (PLTs) variably express toll-like receptors (TLRs), which link the innate and adaptive immune responses during infectious inflammation and atherosclerotic vascular disease. This is perhaps best exemplified by the observation that severe thrombocytopenia is associated with sepsis. While recent phenotypic and functional studies have addressed the roles of TLRs 2 and 4 in human/murine PLTs, which are primarily extracellular receptors, very little is known about the cellular localization, expression, and physiological significance of intracellular TLR9. Here we show that TLR9 localizes to unique granular compartments along the cell periphery (underlying the plasma membrane) in human PLTs. While thought to reside exclusively in the endosomes of monocytes, macrophages, and plasmacytoid dendritic cells, TLR9 expression is significantly enhanced in PLTs following incubation with thombin, ADP, PMA, CRP and type IV collagen, suggesting activation-mediated granule release. Surprisingly, TLR9 surface expression did not coincide with CD62P and CD61 expression levels upon PLT activation (which were not increased following type IV collagen incubation), and TLR9 was shown not to co-localize with known alpha-granule (fibrinogen, CD62P, PDGF-B, VEGF, CD42a, CD42b), dense granule (serotonin), endosomal (M6P, syntaxin-13), or lysosomal (LAMP-1) proteins. Immunogold electron microscopy revealed that TLR9 was expressed instead in a novel intracellular electron-dense granule (T-granule) that is mostly distributed along the plasma membrane. Incubation of resting PLTs with synthetic unmethylated Type C CpG dinucleotides (characteristic of bacterial/viral DNA) resulted in increased TLR9 surface expression, followed by increased Type C CpG sequestration and CD62P surface expression over 20 minutes. Interestingly, when TLR9 surface expression was specifically upregulated by pre-incubating PLTs with type IV collagen, subsequent incubation with Type C CpG resulted in considerably increased Type C CpG sequestration, CD62P surface expression, and PLT aggregation within 30 seconds of addition. These results imply that PLTs must be primed to express TLR9 on their surface prior to signal transduction through TLR9, and provide a mechanism for PLT regulation of the immune response to infection in human whole blood by sequestering bacterial/viral DNA and marking themselves for clearance. Taken together, this paper; (1) tracks TLR9 to a new intracellular compartment in PLTs, (2) describes a novel mechanism of TLR9 signaling, and (3) reveals a unique role for human PLTs as mediators of innate immunity at sites of vascular damage. Disclosures: No relevant conflicts of interest to declare.

scholarly journals SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples

2014 ◽  
Vol 42 (15) ◽  
pp. e121-e121 ◽  
Author(s):  
Hari Krishna Yalamanchili ◽  
Zhaoyuan Li ◽  
Panwen Wang ◽  
Maria P. Wong ◽  
Jianfeng Yao ◽  
...  
Keyword(s):  
Sample Size ◽  
Gene Networks ◽  
Simulated Data ◽  
Exon Array ◽  
R Package ◽  
Mapk Signaling ◽  
Rna Seq ◽  
Gene Expressions ◽  
Exon Level ◽  
Splicing Isoforms

Abstract Conventionally, overall gene expressions from microarrays are used to infer gene networks, but it is challenging to account splicing isoforms. High-throughput RNA Sequencing has made splice variant profiling practical. However, its true merit in quantifying splicing isoforms and isoform-specific exon expressions is not well explored in inferring gene networks. This study demonstrates SpliceNet, a method to infer isoform-specific co-expression networks from exon-level RNA-Seq data, using large dimensional trace. It goes beyond differentially expressed genes and infers splicing isoform network changes between normal and diseased samples. It eases the sample size bottleneck; evaluations on simulated data and lung cancer-specific ERBB2 and MAPK signaling pathways, with varying number of samples, evince the merit in handling high exon to sample size ratio datasets. Inferred network rewiring of well established Bcl-x and EGFR centered networks from lung adenocarcinoma expression data is in good agreement with literature. Gene level evaluations demonstrate a substantial performance of SpliceNet over canonical correlation analysis, a method that is currently applied to exon level RNA-Seq data. SpliceNet can also be applied to exon array data. SpliceNet is distributed as an R package available at http://www.jjwanglab.org/SpliceNet.

scholarly journals A CYTOCHEMICAL LOCALIZATION OF REDUCTIVE SITES IN A GRAM-POSITIVE BACTERIUM

1964 ◽  
Vol 20 (3) ◽  
pp. 361-375 ◽  
Author(s):  
Woutera van Iterson ◽  
W. Leene
Keyword(s):  
Plasma Membrane ◽  
Cell Periphery ◽  
Gram Positive ◽  
Cytochemical Localization ◽  
Potassium Tellurite ◽  
Thin Sections ◽  
Gram Positive Bacteria ◽  
Cytoplasmic Membranes ◽  
Reducing Activity ◽  
The One

In bacteria the exact location of a respiratory enzyme system comparable to that of the mitochondria of other cells has remained uncertain. On the one hand, the existence of particulate "bacterial mitochondria" has been advocated (Mudd); on the other hand, important enzymes of the respiratory chain were recovered in the cytoplasmic membranes associated with some granular material (Weibull). In order to gain insight into this question, sites of reducing activity were localized in thin sections of bacteria using the reduction of potassium tellurite as an indicator. When this salt was added to the culture medium of Bacillus subtilis, it turned out that in this Gram-positive organism the reduced product is strictly bound at two sites, and that the plasma membrane does not materially gain in electron opacity through deposition of the reduced product. The reduction product is found on or in the membranes of particular organelles, which may possibly be regarded as the mitochondrial equivalents in Gram-positive bacteria, and which are sometimes seen connected to the plasma membrane. The second location is in thin rod-like elements at the cell periphery, possibly the sites from which the flagella emerge.

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