scholarly journals Transcriptome comparison between pluripotent and non-pluripotent calli derived from mature rice seeds

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sangrea Shim ◽  
Hee Kyoung Kim ◽  
Soon Hyung Bae ◽  
Hoonyoung Lee ◽  
Hyo Ju Lee ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Callus Formation ◽  
Molecular Processes ◽  
Rice Callus ◽  
Root Stem Cell ◽  
Cell Niche ◽  
Transcriptome Comparison ◽  
Cellular Competence

AbstractIn vitro plant regeneration involves a two-step practice of callus formation and de novo organogenesis. During callus formation, cellular competence for tissue regeneration is acquired, but it is elusive what molecular processes and genetic factors are involved in establishing cellular pluripotency. To explore the mechanisms underlying pluripotency acquisition during callus formation in monocot plants, we performed a transcriptomic analysis on the pluripotent and non-pluripotent rice calli using RNA-seq. We obtained a dataset of differentially expressed genes (DEGs), which accounts for molecular processes underpinning pluripotency acquisition and maintenance. Core regulators establishing root stem cell niche were implicated in pluripotency acquisition in rice callus, as observed in Arabidopsis. In addition, KEGG analysis showed that photosynthetic process and sugar and amino acid metabolism were substantially suppressed in pluripotent calli, whereas lipid and antioxidant metabolism were overrepresented in up-regulated DEGs. We also constructed a putative coexpression network related to cellular pluripotency in rice and proposed potential candidates conferring pluripotency in rice callus. Overall, our transcriptome-based analysis can be a powerful resource for the elucidation of the molecular mechanisms establishing cellular pluripotency in rice callus.

Targeting MDM2-dependent serine metabolism as a therapeutic strategy for liposarcoma

2020 ◽  
Vol 12 (547) ◽  
pp. eaay2163
Author(s):  
Madi Y. Cissé ◽  
Samuel Pyrdziak ◽  
Nelly Firmin ◽  
Laurie Gayte ◽  
Maud Heuillet ◽  
...  
Keyword(s):  
Therapeutic Strategy ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Negative Regulator ◽  
Nucleotide Synthesis ◽  
Metabolic Functions ◽  
Xenograft Models ◽  
Well Differentiated ◽  
Serine Metabolism

Well-differentiated and dedifferentiated liposarcomas (LPSs) are characterized by a systematic amplification of the MDM2 oncogene, which encodes a key negative regulator of the p53 pathway. The molecular mechanisms underlying MDM2 overexpression while sparing wild-type p53 in LPS remain poorly understood. Here, we show that the p53-independent metabolic functions of chromatin-bound MDM2 are exacerbated in LPS and mediate an addiction to serine metabolism that sustains nucleotide synthesis and tumor growth. Treatment of LPS cells with Nutlin-3A, a pharmacological inhibitor of the MDM2-p53 interaction, stabilized p53 but unexpectedly enhanced MDM2-mediated control of serine metabolism by increasing its recruitment to chromatin, likely explaining the poor clinical efficacy of this class of MDM2 inhibitors. In contrast, genetic or pharmacological inhibition of chromatin-bound MDM2 by SP141, a distinct MDM2 inhibitor triggering its degradation, or interfering with de novo serine synthesis, impaired LPS growth both in vitro and in clinically relevant patient-derived xenograft models. Our data indicate that targeting MDM2 functions in serine metabolism represents a potential therapeutic strategy for LPS.

Control of morphogenetic pathways in thin cell layers of tobacco by pH

1989 ◽  
Vol 67 (3) ◽  
pp. 650-654 ◽  
Author(s):  
A. Cousson ◽  
P. Toubart ◽  
K. Tran Thanh Van
Keyword(s):  
Butyric Acid ◽  
De Novo ◽  
Culture Media ◽  
Callus Formation ◽  
Medium Ph ◽  
Vegetative Buds ◽  
Cell Layers ◽  
Initial Medium ◽  
Vegetative Bud

Thin cell layer explants of tobacco were floated in vitro on the surface of liquid culture media. The initial exogenous concentrations of indolyl-3-butyric acid, and kinetin, the initial medium pH, and the explant density were varied. Various patterns of de novo and direct differentiation without any intermediate callus (flower, vegetative bud, root) as well as the absence of morphogenesis and callus formation without any subsequent organogenesis were separately controlled on 100% of the explants. On the same exogenous combination of glucose, indolyl-3-butyric acid, and kinetin, changes in initial medium pH changed the pattern of morphogenesis. For a given initial exogenous indolyl-3-butyric acid concentration, vegetative buds were obtained at either pH 6.1 or 7.8, whereas a mixture of flowers and vegetative buds was obtained at pH 6.8. Furthermore, changes in explant density changed the morphogenetic response. It is suggested that the effects of the initial medium pH and explant density on morphogenesis may be related partially to modifications of the physicochemical properties of the cell wall and (or) plasmalemma.

In vitro reconstitution of autophagic processes

2020 ◽  
Vol 48 (5) ◽  
pp. 2003-2014
Author(s):  
Jahangir Md. Alam ◽  
Nobuo N. Noda
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Membrane Structures ◽  
Autophagosome Formation ◽  
The Past ◽  
Atg Proteins ◽  
In Vitro Reconstitution ◽  
Complicated Process

Autophagy is a lysosomal degradation system that involves de novo autophagosome formation. A lot of factors are involved in autophagosome formation, including dozens of Atg proteins that form supramolecular complexes, membrane structures including vesicles and organelles, and even membraneless organelles. Because these diverse higher-order structural components cooperate to mediate de novo formation of autophagosomes, it is too complicated to be elaborated only by cell biological approaches. Recent trials to regenerate each step of this phenomenon in vitro have started to elaborate on the molecular mechanisms of such a complicated process by simplification. In this review article, we outline the in vitro reconstitution trials in autophagosome formation, mainly focusing on the reports in the past few years and discussing the molecular mechanisms of autophagosome formation by comparing in vitro and in vivo observations.

Psoralen photoactivation promotes morphological and functional changes in fibroblasts in vitro reminiscent of cellular senescence

1998 ◽  
Vol 111 (6) ◽  
pp. 759-767
Author(s):  
G. Herrmann ◽  
P. Brenneisen ◽  
M. Wlaschek ◽  
J. Wenk ◽  
K. Faisst ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Molecular Data ◽  
Cellular Aging ◽  
Premature Aging ◽  
Functional Changes ◽  
Uva Irradiation ◽  
High Level

Premature aging of the skin is a prominent side effect of psoralen photoactivation, a treatment used widely for various skin disorders. The molecular mechanisms underlying premature aging upon psoralen photoactivation are as yet unknown. Here we show that treatment of fibroblasts with 8-methoxypsoralen (8-MOP) and subsequent ultraviolet A (UVA) irradiation resulted in a permanent switch of mitotic to stably postmitotic fibroblasts which acquired a high level of de novo expression of SA-beta-galactosidase, a marker for fibroblast senescence in vitro and in vivo. A single exposure of fibroblasts to 8-MOP/UVA resulted in a 5.8-fold up-regulation of two matrix-degrading enzymes, interstitial collagenase (MMP-1) and stromelysin-1 (MMP-3), over a period of >120 days, while TIMP-1, the major inhibitor of MMP-1 and MMP-3, was only slightly induced. This imbalance between matrix-degrading metalloproteases and their inhibitor may lead to connective tissue damage, a hallmark of premature aging. Superoxide anion and hydrogen peroxide, but not singlet oxygen, were identified as important intermediates in the downstream signaling pathway leading to these complex fibroblast responses upon psoralen photoactivation. Collectively, the end phenotype induced upon psoralen photoactivation shares several criteria of senescent cells. In the absence of detailed molecular data on what constitutes normal aging, it is difficult to decide whether the changes reported here reflect mechanisms underlying normal cellular aging/senescence or rather produce a mimic of cellular aging/senescence by quite different pathways.

scholarly journals Characterization of JsWOX1 and JsWOX4 during Callus and Root Induction in the Shrub Species Jasminum sambac

Plants ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 79 ◽  
Author(s):  
Ying Lu ◽  
Zhuoyi Liu ◽  
Meiling Lyu ◽  
Yuan Yuan ◽  
Binghua Wu
Keyword(s):  
Stem Cells ◽  
De Novo ◽  
Callus Formation ◽  
Homeobox Gene ◽  
Woody Species ◽  
Root Induction ◽  
Wox Genes ◽  
Callus Proliferation ◽  
Jasminum Sambac

Plant regeneration in vitro and the underlying molecular regulatory network are of great interest to developmental biology, and have potential applications in agriculture and biotechnology. Cell growth and re-differentiation during de novo organogenesis require the activation and reprogramming of stem cells within the stem cell niche of the tissues. The WUSCHEL-related homeobox (WOX) factors play important roles in the maintenance and regulation of plant stem cells and are involved in many developmental processes. However, in woody species such as the Jasminum sambac, little is known about the involvement of WOX genes in de novo organogenesis. Here we show that two WOXs, JsWOX4 and JsWOX1, are implicated in callus proliferation and root regeneration, respectively. The expression of both, together with another member JsWOX13, are upregulated during later stage of callus formation. The JsWOX4 is associated with callus proliferation, or cell division during the redifferentiation. The overexpression of this gene results in up-regulation of JsWOX13 and another homeobox gene. The JsWOX1 plays a role in root primordium initiation, as its overexpression leads to more rooty calli and more roots per callus. JsWOX1 also possibly acts upstream of JsWOX4 and JsWOX13 transcriptionally. Our results provide further evidence regarding the functions of WOX genes in organogenesis in a woody plant.

Novel CUL3 Variant Causing Familial Hyperkalemic Hypertension Impairs Regulation and Function of Ubiquitin Ligase Activity

Hypertension ◽  
2021 ◽  
Author(s):  
Harish E. Chatrathi ◽  
Jason C. Collins ◽  
Lynne A. Wolfe ◽  
Thomas C. Markello ◽  
David R. Adams ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Dermal Fibroblasts ◽  
In Vitro Assays ◽  
High Systolic Blood Pressure ◽  
Ubiquitin E3 Ligase ◽  
Pathogenic Variants ◽  
Signaling Axis ◽  
Familial Hyperkalemic Hypertension

Familial hyperkalemic hypertension is caused by pathogenic variants in genes of the CUL3 (cullin-3)-KLHL3 (kelch-like-family-member-3)-WNK (with no-lysine [K] kinase) pathway, manifesting clinically as hyperkalemia, metabolic acidosis, and high systolic blood pressure. The ubiquitin E3 ligase CUL3-KLHL3 targets WNK kinases for degradation to limit activation of the thiazide-sensitive NCC (Na-Cl cotransporter). All known variants in CUL3 lead to exon 9 skipping (CUL3Δ9) and typically result in severe familial hyperkalemic hypertension and growth disturbances in patients. Whether other variants in CUL3 cause familial hyperkalemic hypertension is unknown. Here, we identify a novel de novo heterozygous CUL3 variant (CUL3Δ474–477) in a pediatric familial hyperkalemic hypertension patient with multiple congenital anomalies and reveal molecular mechanisms by which CUL3Δ474–477 leads to dysregulation of the CUL3-KLHL3-WNK signaling axis. Using patient-derived urinary extracellular vesicles and dermal fibroblasts, in vitro assays, and cultured kidney cells, we demonstrate that CUL3Δ474–477 causes reduced total CUL3 levels due to increased autoubiquitination. The CUL3Δ474–477 that escapes autodegradation shows enhanced modification with NEDD8 (neural precursor cell expressed developmentally down-regulated protein 8) and increased formation of CUL3-KLHL3 complexes that are impaired in ubiquitinating WNK4. Proteomic analysis of CUL3 complexes revealed that, in addition to increased KLHL3 binding, the CUL3Δ474–477 variant also exhibits increased interactions with other BTB (Bric-a-brac, Tramtrack, and Broad complex) substrate adaptors, providing a rationale for the patient’s diverse phenotypes. We conclude that the pathophysiological effects of CUL3Δ474–477 are caused by reduced CUL3 levels and formation of catalytically impaired CUL3 ligase complexes.

Non-Specific Endothelial Cell Interactions With the Substrate Result in Cell Activation and Angiogenesis In Vitro

2010 ◽  
Author(s):  
Hongkwan Cho ◽  
Abdul Sheikh ◽  
Daria A. Narmoneva
Keyword(s):  
Tissue Engineering ◽  
Endothelial Cells ◽  
Cell Activation ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Specific Binding ◽  
Cell Interactions ◽  
Αvβ3 Integrin ◽  
Engineering Applications

Vascularization is critical for success of tissue engineering applications. Previous studies by us and others have shown that self-assembling peptide nanoscaffold RAD16-II promotes de novo capillary formation (angiogenesis) in vitro and neovascularization in vivo, and is a promising material for tissue engineering applications [1, 2]. However, the molecular mechanisms for cell interactions with this material are not known. Angiogenesis is mediated via interactions between integrins, which are expressed on the surface of activated endothelial cells (ECs), and extracellular matrix proteins. Among several integrins, αvβ3 is the most abundant and influential receptor regulating angiogenesis [3]. The αvβ3 integrin binds to its ligands via Arg-Gly-Asp (RGD) biding motif. However, there are no RGD motifs on RAD 16-II peptide. Instead, it contains three RAD motifs. Studies have shown that non-specific binding of αvβ3 with RAD can be retained through R and D sides [4]. The objective of this study, therefore, is to elucidate the underlying molecular mechanisms of RAD16-II nanoscaffold interactions with microvascular endothelial cells. We hypothesize that non-specific interactions between RAD16-II peptide nanoscaffold and αvβ3 integrin result in phosphorylations of β3 cytoplasmic domain, which then activate downstream angiogenic signaling pathways and promote angiogenesis.

scholarly journals Endothelial Sphingolipid De Novo Synthesis Controls Blood Pressure by Regulating Signal Transduction and NO via Ceramide

Hypertension ◽  
2020 ◽  
Vol 75 (5) ◽  
pp. 1279-1288 ◽  
Author(s):  
Anna Cantalupo ◽  
Linda Sasset ◽  
Antonella Gargiulo ◽  
Luisa Rubinelli ◽  
Ilaria Del Gaudio ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Signal Transduction ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Control Flow ◽  
Serine Palmitoyltransferase ◽  
Blood Pressure Homeostasis

Ceramides are sphingolipids that modulate a variety of cellular processes via 2 major mechanisms: functioning as second messengers and regulating membrane biophysical properties, particularly lipid rafts, important signaling platforms. Altered sphingolipid levels have been implicated in many cardiovascular diseases, including hypertension, atherosclerosis, and diabetes mellitus–related conditions; however, molecular mechanisms by which ceramides impact endothelial functions remain poorly understood. In this regard, we generated mice defective of endothelial sphingolipid de novo biosynthesis by deleting the Sptlc2 (long chain subunit 2 of serine palmitoyltransferase)—the first enzyme of the pathway. Our study demonstrated that endothelial sphingolipid de novo production is necessary to regulate (1) signal transduction in response to NO agonists and, mainly via ceramides, (2) resting eNOS (endothelial NO synthase) phosphorylation, and (3) blood pressure homeostasis. Specifically, our findings suggest a prevailing role of C16:0-Cer in preserving vasodilation induced by tyrosine kinase and GPCRs (G-protein coupled receptors), except for Gq-coupled receptors, while C24:0- and C24:1-Cer control flow-induced vasodilation. Replenishing C16:0-Cer in vitro and in vivo reinstates endothelial cell signaling and vascular tone regulation. This study reveals an important role of locally produced ceramides, particularly C16:0-, C24:0-, and C24:1-Cer in vascular and blood pressure homeostasis, and establishes the endothelium as a key source of plasma ceramides. Clinically, specific plasma ceramides ratios are independent predictors of major cardiovascular events. Our data also suggest that plasma ceramides might be indicative of the diseased state of the endothelium.

Cholesterol synthesis and import contribute to protective cholesterol increments in acute myeloid leukemia cells

Blood ◽  
2004 ◽  
Vol 104 (6) ◽  
pp. 1816-1824 ◽  
Author(s):  
Deborah E. Banker ◽  
Sasha J. Mayer ◽  
Henry Y. Li ◽  
Cheryl L. Willman ◽  
Frederick R. Appelbaum ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Cholesterol Synthesis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Ldl Receptor ◽  
Density Lipoprotein ◽  
Cholesterol Levels ◽  
Acute Myeloid

Abstract Cholesterol levels are abnormally increased in many acute myeloid leukemia (AML) samples exposed in vitro to chemotherapy. Blocking these acute cholesterol responses selectively sensitizes AML cells to therapeutics. Thus, defining the molecular mechanisms by which AML cells accomplish these protective cholesterol increments might elucidate novel therapeutic targets. We now report that the levels of mRNAs encoding the cholesterol synthesis-regulating enzyme, 3-hydroxy-3-methylglutaryl coenzyme A reductase, and the cholesterol-importing low-density lipoprotein (LDL) receptor were both increased by daunorubicin (DNR) or cytarabine (ARA-C) treatments in almost three fourths of cultured AML samples. However, less than one third of AML samples significantly increased LDL accumulation during drug treatments, suggesting that de novo synthesis is the primary mechanism by which most AML cells increase cholesterol levels during drug exposures. LDL increments were not correlated with cholesterol increments in ARA-C–treated AML samples. However, LDL and cholesterol increments did correlate in DNR-treated AML samples where they were measured, suggesting that a subset of AMLs may rely on increased LDL accumulation during treatment with particular drugs. Our data suggest that cholesterol synthesis inhibitors may improve the efficacy of standard antileukemia regimens, but that for maximum benefit, therapy may need to be tailored for individual patients with leukemia.

scholarly journals Gene bb0318 Is Critical for the Oxidative Stress Response and Infectivity of Borrelia burgdorferi

2016 ◽  
Vol 84 (11) ◽  
pp. 3141-3151 ◽  
Author(s):  
Adrienne C. Showman ◽  
George Aranjuez ◽  
Philip P. Adams ◽  
Mollie W. Jewett
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Borrelia Burgdorferi ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Oxidative Stress Response ◽  
Growth Defect ◽  
Content Type

A greater understanding of the molecular mechanisms that Borrelia burgdorferi uses to survive during mammalian infection is critical for the development of novel diagnostic and therapeutic tools to improve the clinical management of Lyme disease. By use of an in vivo expression technology (IVET)-based approach to identify B. burgdorferi genes expressed in vivo , we discovered the bb0318 gene, which is thought to encode the ATPase component of a putative riboflavin ABC transport system. Riboflavin is a critical metabolite enabling all organisms to maintain redox homeostasis. B. burgdorferi appears to lack the metabolic capacity for de novo synthesis of riboflavin and so likely relies on scavenging riboflavin from the host environment. In this study, we sought to investigate the role of bb0318 in B. burgdorferi pathogenesis. No in vitro growth defect was observed for the Δ bb0318 clone. However, the mutant spirochetes displayed reduced levels of survival when exposed to exogenous hydrogen peroxide or murine macrophages. Spirochetes lacking bb0318 were found to have a 100-fold-higher 50% infectious dose than spirochetes containing bb0318 . In addition, at a high inoculum dose, bb0318 was found to be important for effective spirochete dissemination to deep tissues for as long as 3 weeks postinoculation and to be critical for B. burgdorferi infection of mouse hearts. Together, these data implicate bb0318 in the oxidative stress response of B. burgdorferi and indicate the contribution of bb0318 to B. burgdorferi mammalian infectivity.

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