scholarly journals Omics approaches in Allium research: Progress and way ahead

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9824
Author(s):  
Kiran Khandagale ◽  
Ram Krishna ◽  
Praveen Roylawar ◽  
Avinash B. Ade ◽  
Ashwini Benke ◽  
...  
Keyword(s):  
Male Sterility ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Micro Rna ◽  
Present Review ◽  
Research Progress ◽  
Sequence Information ◽  
Metabolite Level ◽  
Omics Technologies ◽  
Micro Rnas

Background The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops. Method In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. Results Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars. Conclusion All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

scholarly journals The role of micro-RNA in the regulation of signal pathways in gliomas

2017 ◽  
Vol 63 (6) ◽  
pp. 481-498
Author(s):  
O.I. Kit ◽  
D.I. Vodolazhsky ◽  
E.E. Rostorguev ◽  
D.H. Porksheyan ◽  
S.B. Panina
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Treatment Strategies ◽  
Micro Rna ◽  
Present Review ◽  
Signal Pathways ◽  
Aberrant Expression ◽  
Micro Rnas ◽  
Non Coding Rnas

Gliomas are invasive brain tumors with high rates of recurrence and mortality. Glioblastoma multiforme (GBM) is the most deadly form of glioma with nearly 100% rate of recurrence and unfavorable prognosis in patients. Micro-RNAs (miR) are the class of wide-spread short non-coding RNAs that inhibit translation via binding to the mRNA of target genes. The aim of the present review is to analyze recent studies and experimental results concerning aberrant expression profiles of miR, which target components of the signaling pathways Hedgehog, Notch, Wnt, EGFR, TGFb, HIF1a in glioma/glioblastoma. Particularly, the interactions of miR with targets of 2-hydroxyglutarate (the product of mutant isocytrate dehydrogenase, R132H IDH1, which is specific for the glioma pathogenesis) have been considered in the present review. Detecting specific miRNAs in tissue and serum may serve as a diagnostic and prognostic tool for glioma, as well as for predicting treatment response of an individual patient, and potentially serving as a mechanism for creating personalized treatment strategies

NOB1: A Potential Biomarker or Target in Cancer

2019 ◽  
Vol 20 (10) ◽  
pp. 1081-1089
Author(s):  
Weiwei Ke ◽  
Zaiming Lu ◽  
Xiangxuan Zhao
Keyword(s):  
Cancer Treatment ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Binding Protein ◽  
Tumor Development ◽  
Anticancer Therapy ◽  
Research Progress ◽  
Normal Tissues ◽  
Potential Biomarker

Human NIN1/RPN12 binding protein 1 homolog (NOB1), an RNA binding protein, is expressed ubiquitously in normal tissues such as the lung, liver, and spleen. Its core physiological function is to regulate protease activities and participate in maintaining RNA metabolism and stability. NOB1 is overexpressed in a variety of cancers, including pancreatic cancer, non-small cell lung cancer, ovarian cancer, prostate carcinoma, osteosarcoma, papillary thyroid carcinoma, colorectal cancer, and glioma. Although existing data indicate that NOB1 overexpression is associated with cancer growth, invasion, and poor prognosis, the molecular mechanisms behind these effects and its exact roles remain unclear. Several studies have confirmed that NOB1 is clinically relevant in different cancers, and further research at the molecular level will help evaluate the role of NOB1 in tumors. NOB1 has become an attractive target in anticancer therapy because it is overexpressed in many cancers and mediates different stages of tumor development. Elucidating the role of NOB1 in different signaling pathways as a potential cancer treatment will provide new ideas for existing cancer treatment methods. This review summarizes the research progress made into NOB1 in cancer in the past decade; this information provides valuable clues and theoretical guidance for future anticancer therapy by targeting NOB1.

Periodontal Pathogens and Neuropsychiatric Health

2020 ◽  
Vol 20 (15) ◽  
pp. 1353-1397 ◽  
Author(s):  
Abhishek Wadhawan ◽  
Mark A. Reynolds ◽  
Hina Makkar ◽  
Alison J. Scott ◽  
Eileen Potocki ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Metabolic Diseases ◽  
Low Grade ◽  
Periodontal Pathogens ◽  
Synergistic Interactions ◽  
Brain Vasculature ◽  
Micro Rnas ◽  
Clinical Conditions ◽  
Low Grade Inflammation ◽  
Neuropsychiatric Illness

Increasing evidence incriminates low-grade inflammation in cardiovascular, metabolic diseases, and neuropsychiatric clinical conditions, all important causes of morbidity and mortality. One of the upstream and modifiable precipitants and perpetrators of inflammation is chronic periodontitis, a polymicrobial infection with Porphyromonas gingivalis (P. gingivalis) playing a central role in the disease pathogenesis. We review the association between P. gingivalis and cardiovascular, metabolic, and neuropsychiatric illness, and the molecular mechanisms potentially implicated in immune upregulation as well as downregulation induced by the pathogen. In addition to inflammation, translocation of the pathogens to the coronary and peripheral arteries, including brain vasculature, and gut and liver vasculature has important pathophysiological consequences. Distant effects via translocation rely on virulence factors of P. gingivalis such as gingipains, on its synergistic interactions with other pathogens, and on its capability to manipulate the immune system via several mechanisms, including its capacity to induce production of immune-downregulating micro-RNAs. Possible targets for intervention and drug development to manage distal consequences of infection with P. gingivalis are also reviewed.

Natural Products for Regulating Macrophages M2 Polarization

2020 ◽  
Vol 15 (7) ◽  
pp. 559-569 ◽  
Author(s):  
Zhen Chang ◽  
Youhan Wang ◽  
Chang Liu ◽  
Wanli Smith ◽  
Lingbo Kong
Keyword(s):  
Molecular Mechanisms ◽  
Inflammatory Diseases ◽  
Therapeutic Strategies ◽  
Research Progress ◽  
Cellular Mechanisms ◽  
Pharmacological Activities ◽  
Current Review ◽  
M2 Polarization ◽  
Macrophages Polarization ◽  
Herbal Plants

Macrophages M2 polarization have been taken as an anti-inflammatory progression during inflammation. Natural plant-derived products, with potential therapeutic and preventive activities against inflammatory diseases, have received increasing attention in recent years because of their whole regulative effects and specific pharmacological activities. However, the molecular mechanisms about how different kinds of natural compounds regulate macrophages polarization still unclear. Therefore, in the current review, we summarized the detailed research progress on the active compounds derived from herbal plants with regulating effects on macrophages, especially M2 polarization. These natural occurring compounds including flavonoids, terpenoids, glycosides, lignans, coumarins, alkaloids, polyphenols and quinones. In addition, we extensively discussed the cellular mechanisms underlying the M2 polarization for each compound, which could provide potential therapeutic strategies aiming macrophages M2 polarization.

scholarly journals MiRNA-200C expression in Fanconi anemia pathway functionally deficient lung cancers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenrui Duan ◽  
Shirley Tang ◽  
Li Gao ◽  
Kathleen Dotts ◽  
Andrew Fink ◽  
...  
Keyword(s):  
Fanconi Anemia ◽  
Epithelial Mesenchymal Transition ◽  
Micro Rna ◽  
Negative Regulator ◽  
Migration And Invasion ◽  
Pcr Analysis ◽  
Tissue Samples ◽  
Lung Cancers ◽  
Mesenchymal Transition ◽  
Micro Rnas

AbstractThe Fanconi Anemia (FA) pathway is essential for human cells to maintain genomic integrity following DNA damage. This pathway is involved in repairing damaged DNA through homologous recombination. Cancers with a defective FA pathway are expected to be more sensitive to cross-link based therapy or PARP inhibitors. To evaluate downstream effectors of the FA pathway, we studied the expression of 734 different micro RNAs (miRNA) using NanoString nCounter miRNA array in two FA defective lung cancer cells and matched control cells, along with two lung tumors and matched non-tumor tissue samples that were deficient in the FA pathway. Selected miRNA expression was validated with real-time PCR analysis. Among 734 different miRNAs, a cluster of microRNAs were found to be up-regulated including an important cancer related micro RNA, miR-200C. MiRNA-200C has been reported as a negative regulator of epithelial-mesenchymal transition (EMT) and inhibits cell migration and invasion by promoting the upregulation of E-cadherin through targeting ZEB1 and ZEB2 transcription factors. miRNA-200C was increased in the FA defective lung cancers as compared to controls. AmpliSeq analysis showed significant reduction in ZEB1 and ZEB2 mRNA expression. Our findings indicate the miRNA-200C potentially play a very important role in FA pathway downstream regulation.

scholarly journals Epigenetic memory effects in forest trees: a victory of “Michurinian biology”?

2017 ◽  
Vol 63 (4) ◽  
pp. 173-179 ◽  
Author(s):  
Dušan Gömöry ◽  
Matúš Hrivnák ◽  
Diana Krajmerová ◽  
Roman Longauer
Keyword(s):  
Molecular Mechanisms ◽  
Cytosine Methylation ◽  
Epigenetic Inheritance ◽  
Memory Effects ◽  
Forest Trees ◽  
Small Interfering Rnas ◽  
Adaptation To Climate Change ◽  
Growth Environment ◽  
Micro Rnas ◽  
Covalent Modifications

AbstractThe study reviews trait inheritance, which is in contradiction with the rules of Mendelian genetics, and which was object of controversies among biologists (sometimes with grave political consequences) in the USSR and Sovietcontrolled countries in the 1930s-1960s. “Carryover” or “memory” effects of the climate, to which maternal trees are exposed during seed development, on phenological behavior and other adaptively relevant traits of their offspring in conifers are mentioned; similar effects are associated with the germination and early growth environment. Molecular mechanisms underlying these effects include covalent modifications of DNA or DNA-associated proteins (cytosine methylation, various types of histone modifications), micro-RNAs and small interfering RNAs. Tools for the identification of these modifications are reviewed with a focus on cytosine methylation, along with an overview of the hitherto knowledge on the occurrence of DNA modifications in forest trees. The practical implications of epigenetic inheritance in forest trees are discussed with the focus on the adaptation to climate change and legislation on forest reproductive materials.

scholarly journals When nutrition interacts with osteoblast function: molecular mechanisms of polyphenols

2009 ◽  
Vol 22 (1) ◽  
pp. 68-81 ◽  
Author(s):  
Anna Trzeciakiewicz ◽  
Véronique Habauzit ◽  
Marie-Noëlle Horcajada
Keyword(s):  
Bone Health ◽  
Molecular Mechanisms ◽  
Vegetable Intake ◽  
Cell Metabolism ◽  
Bone Cell ◽  
Mitogen Activated Protein Kinase ◽  
Present Review ◽  
Activator Protein 1 ◽  
Cellular Signalling ◽  
Osteoblast Function

Recent research has provided insights into dietary components that may optimise bone health and stimulate bone formation. Fruit and vegetable intake, as well as grains and other plant-derived food, have been linked to decreased risk of major chronic diseases including osteoporosis. This effect has been partially attributed to the polyphenols found in these foods. Thus, it has been suggested that these compounds may provide desirable bone health benefits through an action on bone cell metabolism. The present review will focus on how some polyphenols can modulate osteoblast function and reports which cellular signalling pathways are potentially implicated. However, to date, despite numerous investigations, few studies have provided clear evidence that phenolic compounds can act on osteoblasts. Polyphenols cited in the present review seem to be able to modulate the expression of transcription factors such as runt-related transcription factor-2 (Runx2) and Osterix, NF-κB and activator protein-1 (AP-1). It appears that polyphenols may act on cellular signalling such as mitogen-activated protein kinase (MAPK), bone morphogenetic protein (BMP), oestrogen receptor and osteoprotegerin/receptor activator of NF-κB ligand (OPG/RANKL) and thus may affect osteoblast functions. However, it is also important to take in account the possible interaction of these compounds on osteoclast metabolism to better understand the positive correlation reported between the consumption of fruit and vegetables and bone mass.

Micro-RNA Regulation of Vascular Smooth Muscle Cells and Its Significance in Cardiovascular Diseases

2021 ◽  
Author(s):  
Duong Ngoc Diem Nguyen ◽  
William M Chilian ◽  
Shamsul Mohd Zain ◽  
Muhammad Fauzi Daud ◽  
Yuh Fen Pung
Keyword(s):  
Smooth Muscle ◽  
Vascular Smooth Muscle ◽  
Smooth Muscle Cells ◽  
Vascular Smooth Muscle Cells ◽  
Intracellular Signaling ◽  
Neointimal Hyperplasia ◽  
Muscle Cells ◽  
Micro Rna ◽  
Phenotypic Switching ◽  
Micro Rnas

Cardiovascular disease (CVD) is among the leading causes of death worldwide. Micro-RNAs (miRNAs), regulatory molecules that repress protein expression, have attracted considerable attention in CVD research. The vasculature plays a big role in CVD development and progression and dysregulation of vascular cells underlies the root of many vascular diseases. This review provides a brief introduction of the biogenesis of miRNAs and exosomes, followed by overview of the regulatory mechanisms of miRNAs in vascular smooth muscle cells (VSMCs) intracellular signaling during phenotypic switching, senescence, calcification and neointimal hyperplasia. Evidence of extracellular signaling of VSMCs and other cells via exosomal and circulating miRNAs was also presented. Lastly, current drawbacks and limitations of miRNA studies in CVD research and potential ways to overcome these disadvantages were discussed in detail. In-depth understanding of VSMC regulation via miRNAs will add substantial knowledge and advance research in diagnosis, disease progression and/or miRNA-derived therapeutic approaches in CVD research.

Abstract 347: Identification and Characterization of a miRNA Cohort Initiated Transitional Program That Controls Cell Cycle Arrest of the Perinatal Heart

2015 ◽  
Vol 117 (suppl_1) ◽  
Author(s):  
Patrick G Burgon ◽  
Jonathan J Weldrick
Keyword(s):  
Cell Cycle ◽  
Empirical Bayes ◽  
Molecular Mechanisms ◽  
Fetal Heart ◽  
Micro Rna ◽  
Bayes Estimation ◽  
Oligonucleotide Array ◽  
Array Analysis ◽  
Adult Heart ◽  
Perinatal Heart

During fetal and early perinatal development the myocardium undergoes a period of hyperplastic growth, which results in an exponential increase in the number of cardiomyocytes (CM) that will constitute the adult heart. Soon after birth, CMs proceed through a final round of cell division in the absence cytokinesis that results in binucleation of >95% of adult CMs. Fetal heart genes are re-activated with the onset of pathological hypertrophic or dilated cardiomyopathies, yet there is no evidence of CM re-entry into the cell cycle. Despite the importance of this phenomenon, little is known about the molecular basis for the transition from hyperplastic to hypertrophic-based myocardial growth. Hypothesis: A perinatal heart gene program is necessary for the normal transition from a fetal heart gene program to an adult heart gene program. To identify the molecular mechanisms and pathways involved in CM differentiation during the perinatal transition, RNA was isolated from E18, and 1, 3, 5, 7, 10 and 35d old mouse hearts. CM gene expression and micro-RNA profiles (n=3 arrays/time point) were determined by oligonucleotide array analysis. The raw array data was normalized by Robust Multi-array analysis. Empirical Bayes estimation of gene-specific variances was performed between each of the time points in order to identify genes that are transiently and significantly changed at days 3 and 5 as compare to E18 and 10d post-birth. The analysis identified 2,799 genes (E18 v 5d) and 3,347 genes (5d v 10d) that were then clustered to determine significant pathway enrichment (p<0.05) with Ingenuity Pathway Analysis. Our analysis confirmed previous observations of a down regulation of glucose oxidative metabolism (p=0.02) with an up-regulation of fatty acid metabolism (p=0.0001) between E18 and 5d post-birth. Also, 63 cell cycle genes are collectively down regulated (p=4.3x10-4) between 5d and 10d post-birth. We identified 131 genes that are transiently up regulated at 5d compared to E18 and 10d and this transition was proceeded by a specific cohort of miRNAs. The data generated from this study provide new insight into the molecular mechanisms by which CMs regulate and permanently exit from the cell cycle.

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