scholarly journals Proteomic Insight Into the Molecular Principles of Grapevine Habituation

2011 ◽  
Vol 57 (4) ◽  
pp. 129-136
Author(s):  
Mária Čarná ◽  
Vladimír Repka ◽  
Ernest Šturdí
Keyword(s):  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Protein Microarray ◽  
Molecular Evidence ◽  
Two Dimensional Gel Electrophoresis ◽  
Expression Of Genes ◽  
Differential Expression Pattern ◽  
Protein Microarray Analysis ◽  
Related Proteins ◽  
Insight Into

Proteomic Insight Into the Molecular Principles of Grapevine Habituation Two-dimensional gel electrophoresis coupled to protein microarray analysis was used to examine, for the first time, the molecular mechanisms of grapevine (Vitis vinifera L., cv. Limberger) habituation. The examination of 2-D maps derived from control and habituated cell culture revealed the presence of 55 protein spots displaying a differential expression pattern. These facts have provide a molecular evidence suggesting that the habituated cells can be used as a model for study of cell differentiation and plant defense mechanisms. Cell death, extra-cellular alkalinization and expression of genes responsible for the formation of the defense-related proteins were analyzed in suspension cultures with hormonal autonomy (habituation). Results obtained using habituated grapevine cells compared with non-habituated cells were different and strongly depended on the concentration of elicitor applied.

Grapevine habituation: Understanding of factors that contribute to neoplastic transformation and somaclonal variation

2008 ◽  
Vol 56 (4) ◽  
pp. 399-408 ◽  
Author(s):  
V. Repka ◽  
I. Baumgartnerová
Keyword(s):  
Molecular Mechanisms ◽  
Protein Microarray ◽  
Neoplastic Transformation ◽  
Computational Prediction ◽  
Protein Family ◽  
Molecular Evidence ◽  
Family Interactions ◽  
Core Network ◽  
Two Dimensional Gel Electrophoresis ◽  
Differential Expression Pattern

Two-dimensional gel electrophoresis coupled to protein microarray analysis was used to examine for the first time the molecular mechanisms of grapevine habituation ( Vitis vinifera L., cv. Limberger) at both the proteome and the interactome level. The examination of 2-D maps derived from control and habituated cell cultures revealed the presence of 55 protein spots displaying a differential expression pattern. Using computational prediction methods, fundamental differences were found between eukaryotic interactomes. It was confirmed that all the predicted protein family interactomes (the full set of protein family interactions within a proteome) of six species are scale-free networks, and that they share a small core network comprising 16 protein families related to indispensable cellular functions predominantly involved in pathogenesis, apoptosis and plant tumorigenesis. There is molecular evidence suggesting that grapevine cells which have become habituated for one or more essential factors originated from heritable alterations in the pattern of gene expression and that they can, therefore, be used as a model for the study of cell differentiation and/or neoplastic transformation.

scholarly journals In Silico Investigation of the Anti-Tumor Mechanisms of Epigallocatechin-3-Gallate

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1445 ◽  
Author(s):  
Wang Wang ◽  
Xiuhong Xiong ◽  
Xue Li ◽  
Qinyang Zhang ◽  
Wentao Yang ◽  
...  
Keyword(s):  
Green Tea ◽  
Molecular Mechanisms ◽  
Protein Database ◽  
Tumor Target ◽  
Target Proteins ◽  
Pharmacological Mechanism ◽  
Putative Target ◽  
Docking Method ◽  
Related Proteins ◽  
Insight Into

The EGCG, an important component of polyphenol in green tea, is well known due to its numerous health benefits. We employed the reverse docking method for the identification of the putative targets of EGCG in the anti-tumor target protein database and these targets were further uploaded to public databases in order to understand the underlying pharmacological mechanisms and search for novel EGCG-associated targets. Similarly, the pharmacological linkage between tumor-related proteins and EGCG was manually constructed in order to provide greater insight into the molecular mechanisms through a systematic integration with applicable bioinformatics. The results indicated that the anti-tumor mechanisms of EGCG may involve 12 signaling transduction pathways and 33 vital target proteins. Moreover, we also discovered four novel putative target proteins of EGCG, including IKBKB, KRAS, WEE1 and NTRK1, which are significantly related to tumorigenesis. In conclusion, this work may provide a useful perspective that will improve our understanding of the pharmacological mechanism of EGCG and identify novel potential therapeutic targets.

A comparative proteomic analysis for adventitious root formation in lotus root (Nelumbo nucifera Gaertn)

2017 ◽  
Vol 72 (5-6) ◽  
pp. 181-196
Author(s):  
Cheng Libao ◽  
Jiang Runzhi ◽  
Yang Mengli ◽  
Li Liangjun ◽  
Li Shuyan
Keyword(s):  
Molecular Mechanisms ◽  
Root Formation ◽  
Molecular Level ◽  
Adventitious Root Formation ◽  
Lotus Root ◽  
Liquid Chromatography Tandem Mass ◽  
Three Stages ◽  
Isobaric Tags ◽  
Related Proteins ◽  
Insight Into

AbstractAdventitious roots (ARs) directly affect lotus seedling growth and product quality because principal root is not well developed. However, the details of AR formation at the molecular level have not been determined in lotus. Therefore, three stages were chosen to identify the change of proteins abundant during rhizome formation, using isobaric tags for relative and absolute quantization coupled with liquid chromatography–tandem mass spectrometry to gain insight into the molecular mechanisms involved in AR formation. We totally obtained 323,375 spectra during AR formation. After filtering to eliminate low-scoring spectra, 66,943 spectra, including 53,106 unique spectra, were identified. These unique spectra matched 28,905 peptides, including 24,992 unique peptides, which were assembled into 6686 proteins. In the C0/C1 and C1/C2 stages, 66 and 32 proteins showed enhanced abundance, and 173 and 73 proteins showed decreased abundance, respectively. Seventeen important AR formation-related proteins from the three stages were identified, and the expressions of nine genes from the above-identified proteins were assessed by qRT-PCR. This article provides a comprehensive understanding of the changes in metabolism during AR formation, and is helpful to accelerate the progress of breeding in fulture in lotus root.

scholarly journals Transcriptome analysis of the human tibial nerve identifies sexually dimorphic expression of genes involved in pain, inflammation and neuro-immunity

2018 ◽  
Author(s):  
Pradipta Ray ◽  
Jawad Khan ◽  
Andi Wangzhou ◽  
Diana Tavares-Ferreira ◽  
Armen N. Akopian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Pain ◽  
Sex Differences ◽  
Molecular Mechanisms ◽  
Tibial Nerve ◽  
Sexually Dimorphic ◽  
Pain Mechanisms ◽  
Expression Of Genes ◽  
Sexually Dimorphic Expression ◽  
Insight Into

AbstractSex differences in gene expression are important contributors to normal physiology and mechanisms of disease. This is increasingly apparent in understanding and potentially treating chronic pain where molecular mechanisms driving sex differences in neuronal plasticity are giving new insight into why certain chronic pain disorders preferentially affect women versus men. Large transcriptomic resources are increasingly available and can be used to mine for sex differences and molecular insight using donor cohorts. We analyzed more than 250 human tibial nerve (hTN) transcriptomes from the GTex Consortium project to gain insight into sex-dependent gene expression in the peripheral nervous system (PNS). We discover 149 genes with sex differential expression. Many of the genes upregulated in men are associated with inflammation, and appear to be primarily expressed by glia or immune cells. In women, we find the differentially upregulated transcription factor SP4 that drives a regulatory program, and may impact sex differences in PNS physiology. Many of these 149 DE genes have some previous association with chronic pain but few of them have been explored thoroughly. Additionally, using clinical data in the GTex database, we identify a subset of differentially expressed (DE) genes in diseases associated with chronic pain, arthritis and type II diabetes. Our work identifies sexually dimorphic gene expression in the human PNS with implications for discovery of sex-specific pain mechanisms.

scholarly journals Deciphering the Role of Autophagy in Treatment of Resistance Mechanisms in Glioblastoma

2021 ◽  
Vol 22 (3) ◽  
pp. 1318
Author(s):  
Imran Khan ◽  
Mohammad Hassan Baig ◽  
Sadaf Mahfooz ◽  
Moniba Rahim ◽  
Busra Karacam ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Treatment Strategies ◽  
Resistance Mechanisms ◽  
Therapeutic Interventions ◽  
Cellular Mechanisms ◽  
Cellular Energy ◽  
Survival And Growth ◽  
Insight Into

Autophagy is a process essential for cellular energy consumption, survival, and defense mechanisms. The role of autophagy in several types of human cancers has been explicitly explained; however, the underlying molecular mechanism of autophagy in glioblastoma remains ambiguous. Autophagy is thought to be a “double-edged sword”, and its effect on tumorigenesis varies with cell type. On the other hand, autophagy may play a significant role in the resistance mechanisms against various therapies. Therefore, it is of the utmost importance to gain insight into the molecular mechanisms deriving the autophagy-mediated therapeutic resistance and designing improved treatment strategies for glioblastoma. In this review, we discuss autophagy mechanisms, specifically its pro-survival and growth-suppressing mechanisms in glioblastomas. In addition, we try to shed some light on the autophagy-mediated activation of the cellular mechanisms supporting radioresistance and chemoresistance in glioblastoma. This review also highlights autophagy’s involvement in glioma stem cell behavior, underlining its role as a potential molecular target for therapeutic interventions.

scholarly journals Comparative proteomic analysis of the sweetpotato provides insights into response mechanisms to Fusarium oxysporum f. sp. batatas

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
ShiQiang Lin ◽  
ZhiJian Yang ◽  
BiFang Huang ◽  
ChuYun Bi ◽  
XiaoFang Huang ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Proteomic Analysis ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Defense Responses ◽  
Biological Processes ◽  
Go Annotation ◽  
Parallel Reaction Monitoring ◽  
Annotation Information ◽  
Insight Into

AbstractThe Fusarium wilt disease caused by Fusarium oxysporum f. sp. batatas (Fob) is one of the devastating diseases of sweetpotato. However, the molecular mechanisms of sweetpotato response to Fob is poorly understood. In the present study, comparative quantitative proteomic analysis was conducted to investigate the defense mechanisms involved. Two sweetpotato cultivars with differential Fob infection responses were inoculated with Fob spore suspensions and quantitatively analyzed by Tandem Mass Tags (TMT). 2267 proteins were identified and 1897 of them were quantified. There were 817 proteins with quantitative ratios of 1.2-fold change between Fob-inoculated and mock-treated samples. Further, nine differentially expressed proteins were validated by Parallel Reaction Monitoring (PRM). According to Gene Ontology (GO) annotation information, the proteins functioned in molecular metabolism, cellular component formation, and biological processes. Interestingly, the results showed that sweetpotato resistant response to Fob infection included many proteins associated with signaling transduction, plant resistance, chitinase and subtilisin-like protease. The functions and possible roles of those proteins were discussed. The results provides first insight into molecular mechanisms involved in sweetpotato defense responses to Fob.

scholarly journals Clinical Candidates Targeting the ATR–CHK1–WEE1 Axis in Cancer

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 795
Author(s):  
Lukas Gorecki ◽  
Martin Andrs ◽  
Jan Korabecny
Keyword(s):  
Cell Cycle ◽  
Cancer Cells ◽  
Molecular Mechanisms ◽  
Patient Survival ◽  
Current Status ◽  
Future Perspectives ◽  
Phase Ii Trials ◽  
Anticancer Treatment ◽  
Positive Outlook ◽  
Insight Into

Selective killing of cancer cells while sparing healthy ones is the principle of the perfect cancer treatment and the primary aim of many oncologists, molecular biologists, and medicinal chemists. To achieve this goal, it is crucial to understand the molecular mechanisms that distinguish cancer cells from healthy ones. Accordingly, several clinical candidates that use particular mutations in cell-cycle progressions have been developed to kill cancer cells. As the majority of cancer cells have defects in G1 control, targeting the subsequent intra‑S or G2/M checkpoints has also been extensively pursued. This review focuses on clinical candidates that target the kinases involved in intra‑S and G2/M checkpoints, namely, ATR, CHK1, and WEE1 inhibitors. It provides insight into their current status and future perspectives for anticancer treatment. Overall, even though CHK1 inhibitors are still far from clinical establishment, promising accomplishments with ATR and WEE1 inhibitors in phase II trials present a positive outlook for patient survival.

scholarly journals Progress in understanding the role of lncRNA in programmed cell death

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Na Jiang ◽  
Xiaoyu Zhang ◽  
Xuejun Gu ◽  
Xiaozhuang Li ◽  
Lei Shang
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Molecular Mechanisms ◽  
Membrane Receptors ◽  
Gene Expressions ◽  
Apoptosis Pathway ◽  
Stem Cell Pluripotency ◽  
Extrinsic Apoptosis ◽  
Related Proteins ◽  
Cycle Regulation

AbstractLong non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but not translated into proteins. LncRNAs regulate gene expressions at multiple levels, such as chromatin, transcription, and post-transcription. Further, lncRNAs participate in various biological processes such as cell differentiation, cell cycle regulation, and maintenance of stem cell pluripotency. We have previously reported that lncRNAs are closely related to programmed cell death (PCD), which includes apoptosis, autophagy, necroptosis, and ferroptosis. Overexpression of lncRNA can suppress the extrinsic apoptosis pathway by downregulating of membrane receptors and protect tumor cells by inhibiting the expression of necroptosis-related proteins. Some lncRNAs can also act as competitive endogenous RNA to prevent oxidation, thereby inhibiting ferroptosis, while some are known to activate autophagy. The relationship between lncRNA and PCD has promising implications in clinical research, and reports have highlighted this relationship in various cancers such as non-small cell lung cancer and gastric cancer. This review systematically summarizes the advances in the understanding of the molecular mechanisms through which lncRNAs impact PCD.

scholarly journals Molecular Pathways Involved in the Development of Congenital Erythrocytosis

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1150
Author(s):  
Jana Tomc ◽  
Nataša Debeljak
Keyword(s):  
Signal Transduction ◽  
Iron Homeostasis ◽  
Molecular Mechanisms ◽  
Oxygen Affinity ◽  
Molecular Pathways ◽  
Disease Development ◽  
Post Translational Modifications ◽  
Hemoglobin Oxygen Affinity ◽  
Insight Into ◽  
Idiopathic Erythrocytosis

Patients with idiopathic erythrocytosis are directed to targeted genetic testing including nine genes involved in oxygen sensing pathway in kidneys, erythropoietin signal transduction in pre-erythrocytes and hemoglobin-oxygen affinity regulation in mature erythrocytes. However, in more than 60% of cases the genetic cause remains undiagnosed, suggesting that other genes and mechanisms must be involved in the disease development. This review aims to explore additional molecular mechanisms in recognized erythrocytosis pathways and propose new pathways associated with this rare hematological disorder. For this purpose, a comprehensive review of the literature was performed and different in silico tools were used. We identified genes involved in several mechanisms and molecular pathways, including mRNA transcriptional regulation, post-translational modifications, membrane transport, regulation of signal transduction, glucose metabolism and iron homeostasis, which have the potential to influence the main erythrocytosis-associated pathways. We provide valuable theoretical information for deeper insight into possible mechanisms of disease development. This information can be also helpful to improve the current diagnostic solutions for patients with idiopathic erythrocytosis.

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