scholarly journals miRNAs play important roles in aroma weakening during the shelf life of ‘Nanguo’ pear after cold storage

2018 ◽  
Author(s):  
Fei Shi ◽  
Xin Zhou ◽  
Miao-miao Yao ◽  
Zhuo Tan ◽  
Qian Zhou ◽  
...  
Keyword(s):  
Shelf Life ◽  
Cold Storage ◽  
Room Temperature ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Environmental Stressors ◽  
Differentially Expressed ◽  
Transcript Profile ◽  
Rt Pcr

AbstractCold storage is commonly employed to delay senescence in ‘Nanguo’ pears after harvest. However, this technique also causes fruit aroma weakening. MicroRNAs play important roles in plant development and in eliciting responses to abiotic environmental stressors. In this study, the miRNA transcript profile of the fruit at the first day (C0, LT0) move in and out of cold storage and the optimum tasting period (COTP, LTOTP) during shelf life at room temperature were analyzed, respectively. More than 300 known miRNAs were identified in ‘Nanguo’ pears; 176 and 135 miRNAs were significantly differentially expressed on the C0 vs. LT0 and on the COTP vs. LTOTP, respectively. After prediction the target genes of these miRNAs, LOX2S, LOX1_5, HPL, and ADH1 were found differentially expressed, which were the key genes during aroma formation. The expression pattern of these target genes and the related miRNAs were identified by RT-PCR. Mdm-miR172a-h, mdm-miR159a/b/c, mdm-miR160a-e, mdm-miR395a-i, mdm/ppe-miR399a, mdm/ppe-miR535a/b, and mdm-miR7120a/b negatively regulated target gene expression. These results indicate that miRNAs play key roles in aroma weakening in refrigerated ‘Nanguo’ pear and provide valuable information for studying the molecular mechanisms of miRNAs in the aroma weakening of fruits due to cold storage.

scholarly journals Identification of miRNA and Their Regulatory Effects Induced by Total Flavonoids From Dracocephalum moldavica in the Treatment of Vascular Dementia

2021 ◽  
Vol 12 ◽  
Author(s):  
Mimin Liu ◽  
Guangzhi Shan ◽  
Hailun Jiang ◽  
Li Zeng ◽  
Kaiyue Zhao ◽  
...  
Keyword(s):  
Vascular Dementia ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Gene Profiling ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Total Flavonoids ◽  
Compound Target

Vascular dementia (VaD) is a general term used to describe difficulties in memory, reasoning, judgment, and planning caused by a reduced blood flow to the brain and consequent brain damage, in which microRNAs (miRNAs) are involved. Dracocephalum moldavica L. (D. moldavica) is traditionally used in the treatment of cardiovascular diseases as well as VaD, but the biomolecular mechanisms underlying its therapeutic effect are obscure. In the present study, the molecular mechanisms involved in the treatment of VaD by the total flavonoids from Dracocephalum moldavica L. (TFDM) were explored by the identification of miRNA profiling using bioinformatics analysis and experimental verification. A total of 2,562 differentially expressed miRNAs (DEMs) and 3,522 differentially expressed genes (DEGs) were obtained from the GSE120584 and GSE122063 datasets, in which the gene functional enrichment and protein-protein interaction network of 93 core targets, originated from the intersection of the top DEM target genes and DEGs, were established for VaD gene profiling. One hundred and eighty-five targets interacting with 42 flavonoids in the TFDM were included in a compound-target network, subsequently found that they overlapped with potential targets for VaD. These 43 targets could be considered in the treatment of VaD by TFDM, and included CaMKII, MAPK, MAPT, PI3K, and KDR, closely associated with the vascular protective effect of TFDM, as well as anti-oxidative, anti-inflammatory, and anti-apoptotic properties. The subsequent analysis of the compound-target gene-miRNA network indicated that eight miRNAs that mediated 43 targets had a close interaction with TFDM, suggesting that the neuroprotective effects were principally due to kaempferol, apigenin, luteolin, and quercetin, which were mostly associated with the miR-3184-3p/ESR1, miR-6762-3p/CDK1, miR-6777-3p/ESRRA, and other related axes. Furthermore, the in vitro oxygen-glucose deprivation (OGD) model demonstrated that the dysregulation of miR-3184-3p and miR-6875-5p found by qRT-PCR was consistent with the changes in the bioinformatics analysis. TFDM and its active compounds involving tilianin, luteolin, and apigenin showed significant effects on the upregulation of miR-3184-3p and downregulation of miR-6875-5p in OGD-injured cells, in line with the improved cell viability. In conclusion, our findings revealed the underlying miRNA-target gene network and potential targets of TFDM in the treatment of VaD.

scholarly journals Transcriptome Analysis of Pre-Storage 1-MCP and High CO2-Treated ‘Madoka’ Peach Fruit Explains the Reduction in Chilling Injury and Improvement of Storage Period by Delaying Ripening

2021 ◽  
Vol 22 (9) ◽  
pp. 4437
Author(s):  
Han Ryul Choi ◽  
Min Jae Jeong ◽  
Min Woo Baek ◽  
Jong Hang Choi ◽  
Hee Cheol Lee ◽  
...  
Keyword(s):  
Cold Storage ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Chilling Injury ◽  
Chemical Properties ◽  
Storage Period ◽  
Differentially Expressed ◽  
Peach Fruit ◽  
High Co2 ◽  
Physico Chemical

Cold storage of peach fruit at low temperatures may induce chilling injury (CI). Pre-storage 1-MCP and high CO2 treatments were reported among the methods to ameliorate CI and reduce softening of peach fruit. However, molecular data indicating the changes associated with pre-storage 1-MCP and high CO2 treatments during cold storage of peach fruit are insufficient. In this study, a comparative analysis of the difference in gene expression and physico-chemical properties of fruit at commercial harvest vs. stored fruit for 12 days at 0 °C (cold-stored (CS), pre-storage 1-MCP+CS, and pre-storage high CO2+CS) were used to evaluate the variation among treatments. Several genes were differentially expressed in 1-MCP+CS- and CO2+CS-treated fruits as compared to CS. Moreover, the physico-chemical and sensory data indicated that 1-MCP+CS and CO2+CS suppressed CI and delayed ripening than the CS, which could lead to a longer storage period. We also identified the list of genes that were expressed commonly and exclusively in the fruit treated by 1-MCP+CS and CO2+CS and compared them to the fruit quality parameters. An attempt was also made to identify and categorize genes related to softening, physiological changes, and other ripening-related changes. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR). These results add information on the molecular mechanisms of the pre-storage treatments during cold storage of peach fruit. Understanding the genetic response of susceptible cultivars such as ‘Madoka’ to CI-reducing pre-storage treatments would help breeders release CI-resistant cultivars and could help postharvest technologists to develop more CI-reducing technologies.

Drugs used to treat bipolar disorder act via microRNAs to regulate expression of genes involved in neurite outgrowth

2020 ◽  
Vol 34 (3) ◽  
pp. 370-379 ◽  
Author(s):  
Srisaiyini Kidnapillai ◽  
Ben Wade ◽  
Chiara C Bortolasci ◽  
Bruna Panizzutti ◽  
Briana Spolding ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Neurite Outgrowth ◽  
Neural Plasticity ◽  
Drug Combination ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Drug Effects ◽  
Differentially Expressed ◽  
Transcriptional Level ◽  
Expression Of Genes

Background: The drugs commonly used to treat bipolar disorder have limited efficacy and drug discovery is hampered by the paucity of knowledge of the pathophysiology of this disease. This study aims to explore the role of microRNAs in bipolar disorder and understand the molecular mechanisms of action of commonly used bipolar disorder drugs. Methods: The transcriptional effects of bipolar disorder drug combination (lithium, valproate, lamotrigine and quetiapine) in cultured human neuronal cells were studied using next generation sequencing. Differential expression of genes ( n=20) and microRNAs ( n=6) was assessed and the differentially expressed microRNAs were confirmed with TaqMan MicroRNA Assays. The expression of the differentially expressed microRNAs were inhibited to determine bipolar disorder drug effects on their target genes ( n=8). Independent samples t-test was used for normally distributed data and Kruskal-Wallis/Mann-Whitney U test was used for data not distributed normally. Significance levels were set at p<0.05. Results: We found that bipolar disorder drugs tended to increase the expression of miR-128 and miR-378 ( p<0.05). Putative target genes of these microRNAs targeted pathways including those identified as “neuron projection development” and “axonogenesis”. Many of the target genes are inhibitors of neurite outgrowth and neurogenesis and were downregulated following bipolar disorder drug combination treatment (all p<0.05). The bipolar disorder drug combination tended to decrease the expression of the target genes ( NOVA1, GRIN3A, and VIM), however this effect could be reversed by the application of microRNA inhibitors. Conclusions: We conclude that at a transcriptional level, bipolar disorder drugs affect several genes in concert that would increase neurite outgrowth and neurogenesis and hence neural plasticity, and that this effect is mediated (at least in part) by modulation of the expression of these two key microRNAs.

scholarly journals EFFECT OF MATURITY STAGES ON QUALITY AND SHELF LIFE OF “SOLO” PAPAYA FRUITS DURING STORAGE

2019 ◽  
pp. 57-68
Keyword(s):  
Ambient Temperature ◽  
Shelf Life ◽  
Cold Storage ◽  
Room Temperature ◽  
Colour Change ◽  
Soluble Solids ◽  
Maturity Stages ◽  
Solids Content ◽  
Sensorial Evaluation ◽  
Stage 1

“Solo” papaya fruits were harvested in October, 2016 & 2017 seasons from a commercial orchard located in Ismailia Governorate, Egypt. Papaya fruits were harvested at three maturity stages: 25% yellow (stage 1), 50% yellow (stage 2) and 100% yellow (stage 3) and evaluated during storage at ambient temperature (20°C ± 2) for 4 days + at 80- 85% RH or during cold storage at 6°C + 90- 95% RH for 20 days. Papaya fruits softened very rapidly at room temperature after harvest and had 4 days shelf life. However, the fruit can be stored for 20 days at 6°C with little changes in firmness and the fruit apparently progressed in normal ripening upon removal to ambient temperature (20°C) for 3 days. All colour values (a*, L* and C*) were linearly increased during cold storage. Conversely, as a result of colour change from green to orange-red, h° values decreased. Soluble solids content was not affected during ripening at 20°C and remained steady. Fruit harvested at stage 2 and stored at 6°C for 20 days following 3 days at 20°C had superior score for sensorial evaluation.

scholarly journals Multi-Omics Characterization of Circular RNA-Encoded Novel Proteins Associated With Bladder Outlet Obstruction

2022 ◽  
Vol 9 ◽  
Author(s):  
Baoyi Zhu ◽  
Zhanfang Kang ◽  
Sihua Zhu ◽  
Yuying Zhang ◽  
Xiangmao Lai ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Proteomics ◽  
Bladder Outlet Obstruction ◽  
Molecular Mechanisms ◽  
Outlet Obstruction ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Protein Profiles ◽  
Rt Pcr ◽  
Novel Proteins

Bladder outlet obstruction (BOO) is a common urologic disease associated with poorly understood molecular mechanisms. This study aimed to investigate the possible involvements of circRNAs (circular RNAs) and circRNA-encoded proteins in BOO development. The rat BOO model was established by the partial bladder outlet obstruction surgery. Differential expression of circRNA and protein profiles were characterized by deep RNA sequencing and iTRAQ quantitative proteomics respectively. Novel proteins encoded by circRNAs were predicted through ORF (open reading frame) selection using the GETORF software and verified by the mass spectrometry in proteomics, combined with the validation of their expressional alterations by quantitative RT-PCR. Totally 3,051 circRNAs were differentially expressed in bladder tissues of rat BOO model with widespread genomic distributions, including 1,414 up-regulated, and 1,637 down-regulated circRNAs. Our following quantitative proteomics revealed significant changes of 85 proteins in rat BOO model, which were enriched in multiple biological processes and signaling pathways such as the PPAR and Wnt pathways. Among them, 21 differentially expressed proteins were predicted to be encoded by circRNAs and showed consistent circRNA and protein levels in rat BOO model. The expression levels of five protein-encoding circRNAs were further validated by quantitative RT-PCR and mass spectrometry. The circRNA and protein profiles were substantially altered in rat BOO model, with great expressional changes of circRNA-encoded novel proteins.

scholarly journals Pre-harvest application of salicylic acid influence physicochemical and quality characteristics of ‘Chimarrita’ peaches during cold storage

2019 ◽  
pp. 46
Author(s):  
Jakellinye Miranda ◽  
Suélen Braga de Andrade, Andressa Vighi Schiavon ◽  
Pedro Luis Panisson Kaltbach Lemos ◽  
Cláudia Simone Madruga Lima ◽  
Marcelo Barbosa Malgarim
Keyword(s):  
Salicylic Acid ◽  
Shelf Life ◽  
Cold Storage ◽  
Room Temperature ◽  
Soluble Solids ◽  
Acid Solutions ◽  
Post Harvest ◽  
Hue Angle ◽  
Cold Chamber

Peach is a climacteric highly-perishable fruit whose post-harvest preservation relies largely on cold storage. The combination of the last with other technologies allows to extend the shelf life of this product. One alternative is the utilization of salicylic acid, a natural compound involved in many physiological phenomena such as resistance against diseases and ripening. Considering these facts, the objective of the present work was to evaluate the effect of pre-harvest application of salicylic acid solutions on the quality of ‘Chimarrita’ peaches during post-harvest cold storage. The experiment was conducted at the Federal University of Pelotas/RS, in the campus of Capão do Leão/RS - Brazil. The application of salicylic acid solutions was performed by direct pulverization on the fruits, 30 days prior to harvest. The concentrations were: 0,0 (control); 1,0; 1,5; and 2,0 mM. After harvest, the fruits were stored in a cold chamber at 1,0 ± 0,5°C and 85-90% RH, for 30 days. The analyses were performed at the following cold storage periods (plus 2 days at room temperature of 20°C to all treatments, in order to simulate commercialization conditions): 10 (+2) days; 20 (+2) days; e 30 (+2) days. The variables evaluated were: mass loss (%); flesh firmness (N); DA index; color (L, a*, b* and hue angle); wooliness incidence (%); rot incidence (%); total soluble solids (°Brix); pH; titrable acidity (% of organic acids); and ratio. The salicylic acid doses and/or the cold storage periods had significant effects on all the evaluated parameters. For most of the parameters analyzed, the intermediate dosis of 1mM (and also 1,5mM) of salicilic acid showed the most promising results. Therefore, the application of salicylic acid solutions 30 days prior to harvest is a technique which can be combined to cold storage in order to shift the quality and the shelf-life of ‘Chimarrita’ peaches.

scholarly journals Phytochemical Profile of Opuntia ficus-indica (L.) Mill Fruits (cv. ‘Orito’) Stored at Different Conditions

Foods ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 160
Author(s):  
Francisca Hernández ◽  
Lucía Andreu-Coll ◽  
Andreia Bento-Silva ◽  
Ana Teresa Serra ◽  
Pedro Mena ◽  
...  
Keyword(s):  
Shelf Life ◽  
Cold Storage ◽  
Product Life Cycle ◽  
High Performance ◽  
Room Temperature ◽  
Phenylalanine Ammonia Lyase ◽  
High Performance Liquid Chromatographic ◽  
Array Detector ◽  
Phytochemical Profile ◽  
Liquid Chromatographic

This research analyzed the phytochemical profile of prickly pear fruits from ‘Orito’ cultivar stored under cold conditions (2 °C, 85–90% RH) and shelf-life conditions at room temperature (stored at 20 °C for three days after cold storage) for 28 days, mimicking the product life cycle. A total of 18 compounds were identified and quantitated through HPLC-DAD-MS/MS (High-Performance Liquid Chromatographic -Diode Array Detector- Mass Spectrometry) analyses. Phenolic acids such as eucomic acid and betalains such as indicaxanthin were the predominant chemical families, and piscidic acid was the most abundant compound. During cold storage, the content of eucomic acid isomer/derivative and syringaresinol increased, and citric acid decreased, which could be caused by the cold activation of the phenylalanine ammonia-lyase (PAL) and polyphenol oxidase (PPO) enzymes. However, no significant differences were found in the content of these compounds during shelf-life storage. These results showed that ‘Orito’ fruit marketability would be possible up to 28 days after harvesting, retaining its profile, which is rich in bioactive compounds.

scholarly journals Identification of key genes and associated pathways in neuroendocrine tumors through bioinformatics analysis and predictions of small drug molecules

2020 ◽  
Author(s):  
Praveenkumar Devarbhavi ◽  
Basavaraj Vastrad ◽  
Anandkumar Tengli ◽  
Chanabasayya Vastrad ◽  
Iranna Kotturshetti
Keyword(s):  
Drug Target ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Regulatory Elements ◽  
Future Research ◽  
High Morbidity ◽  
Hub Genes ◽  
Go Enrichment ◽  
Significant Difference

AbstractNeuroendocrine tumor (NET) is one of malignant cancer and is identified with high morbidity and mortality rates around the world. With indigent clinical outcomes, potential biomarkers for diagnosis, prognosis and drug target are crucial to explore. The aim of this study is to examine the gene expression module of NET and to identify potential diagnostic and prognostic biomarkers as well as to find out new drug target. The differentially expressed genes (DEGs) identified from GSE65286 dataset was used for pathway enrichment analyses and gene ontology (GO) enrichment analyses and protein - protein interaction (PPI) analysis and module analysis. Moreover, miRNAs and transcription factors (TFs) that regulated the up and down regulated genes were predicted. Furthermore, validation of hub genes was performed. Finally, molecular docking studies were performed. DEGs were identified, including 453 down regulated and 459 up regulated genes. Pathway and GO enrichment analysis revealed that DEGs were enriched in sucrose degradation, creatine biosynthesis, anion transport and modulation of chemical synaptic transmission. Important hub genes and target genes were identified through PPI network, modules, target gene - miRNA network and target gene - TF network. Finally, survival analyses, receiver operating characteristic (ROC) curve and RT-PCR validated the significant difference of ATP1A1, LGALS3, LDHA, SYK, VDR, OBSL1, KRT40, WWOX, NINL and PPP2R2B between metastatic NET and normal controls. In conclusion, the DEGs and hub genes with their regulatory elements identified in this study will help us understand the molecular mechanisms underlying NET and provide candidate targets for future research.

Elevation of MicroRNA-126 Levels in Intracranial Aneurysm and Bioinformatic Analysis of Potential Molecular Mechanisms

2021 ◽  
Vol 11 (4) ◽  
pp. 573-579
Author(s):  
Pan Huang ◽  
Min Xu ◽  
Xiao-Ying He
Keyword(s):  
Intracranial Aneurysm ◽  
Peripheral Blood ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Kegg Pathway ◽  
Bioinformatic Analysis ◽  
Control Group ◽  
Potential Target ◽  
Fas Signaling

The study is to investigation of microRNA-126 levels in patients with intracranial aneurysm and bioinformatic analysis of the molecular mechanisms involved. A total of 166 patients with ICA who were hospitalized or examined in our hospital from September 2015 to December 2017 were used as the experimental group (ICA group). This group included 120 patients with unruptured intracranial aneurysm (UICA; UICA group) and 46 patients with ruptured intracranial aneurysm (RICA); RICA group). The UICA group was further subdivided into 42 surgical groups (S group) and 78 nonsurgical groups (NS group). Sixty-three normal people without intracranial aneurysms were selected as the control group. RT-PCR was used to quantitatively detect the relative expression of microRNA- 126 in peripheral blood mononuclear cells at the time of admission and immediately after surgery. The UCSC database was used to analyze the gene locus and homology of microRNA-126. The TargetScan database and CoMeTa database were used to predict the potential target genes of microRNA-126. The DAVID database was used to enrich the function of potential target genes of microRNA-126 (GO enrichment) and KEGG pathway enrichment for analysis. The expression level of microRNA-126 in peripheral blood was significantly higher in the ICA group than in the control group (P <0.01), significantly higher in the RICA group than in the UICA group (P <0.05). Expression was also higher in the NS group than in the S group but the difference was nonsignificant (P >0.05). A total of 15 potential target genes including ITGA6, CRK, PCDH7, and ADAM9 were identified through the target gene prediction software and GO analysis and KEGG pathway analysis showed that the function of the microRNA-126 target gene was mainly focused on protein binding and the FAS signaling pathway. In Conclusion the microRNA-126 is up-regulated in ICA patients and affects ICA by regulating multiple target genes in the FAS signaling pathway.

scholarly journals Control of postharvest gray mold of ‘BRS Nubia’ table grape under cold storage

2020 ◽  
Vol 41 (6supl2) ◽  
pp. 3457-3465
Author(s):  
Ronan Carlos Colombo ◽  
◽  
Deived Uilian de Carvalho ◽  
Maria Aparecida da Cruz ◽  
Ciro Hideki Sumida ◽  
...  
Keyword(s):  
Shelf Life ◽  
Cold Storage ◽  
Room Temperature ◽  
Gray Mold ◽  
Soluble Solids ◽  
Experimental Unit ◽  
Table Grapes ◽  
Randomized Design ◽  
Commercial Vineyard ◽  
Solids Content

The demand for high-quality nutritional products has increased fruit consumption, as grapes, for this reason postharvest techniques are required to prevent losses, to preserve quality, to extend shelf life, and to attend to consumer needs. In this way, the objective of this study was to evaluate strategies to control gray mold caused by Botrytis cinerea in ‘BRS Nubia’ grapes during cold storage and shelf life periods. Grape bunches were harvested from a commercial vineyard in Marialva, Parana, Brazil. Grapes were subjected to the following treatments: cold storage at 2 ºC (control), cold storage at 2 ºC with SO2-generating pads, cold storage at 2 ºC and inoculated with B. cinerea suspension, and cold storage at 2 ºC with SO2-generating pads and inoculated with B. cinerea suspension. The experiment was conducted in a complete randomized design with five replications per treatment using four bunches per experimental unit. A factorial arrangement (absence/presence of SO2 pads × absence/presence of Botrytis inoculation) was applied. At the end of 30 days of cold storage and 7 days of shelf life (22 ºC), gray mold incidence, shattered berries, and physicochemical parameters were evaluated. The gray mold incidence on ‘BRS Nubia’ grapes decreased when SO2-generating pads were used during cold storage. Berry weight loss was greater in the treatments without SO2-generating pads after 30 days of cold storage followed by 7 days of shelf life. Berry firmness, soluble solids content (SS), total acidity (TA), SS/TA ratio, and anthocyanins concentration were not negatively affected by SO2-generating pad treatments. However, a slight increase in the shattered berries percentage was recorded for the SO2-generating pad treatments. No significant quality loss of ‘BRS Nubia’ grape was evident after 30 days of cold storage followed by 7 days of exposure at room temperature. In this context, SO2-generating pads can be used to control the gray mold incidence on ‘BRS Nubia’ table grapes during cold storage.

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