scholarly journals Analysis of Stored mRNA Degradation in Acceleratedly Aged Seeds of Wheat and Canola in Comparison to Arabidopsis

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1707
Author(s):  
Liang Zhao ◽  
Hong Wang ◽  
Yong-Bi Fu
Keyword(s):  
Aging Time ◽  
Fragment Size ◽  
Mrna Degradation ◽  
Recent Analysis ◽  
Seed Aging ◽  
Degradation Rates ◽  
Stable Conditions ◽  
Stored Mrna ◽  
Aging Conditions ◽  
Aged Seeds

Seed aging has become a topic of renewed interest but its mechanism remains poorly understood. Our recent analysis of stored mRNA degradation in aged Arabidopsis seeds found that the stored mRNA degradation rates (estimated as the frequency of breakdown per nucleotide per day or β value) were constant over aging time under stable conditions. However, little is known about the generality of this finding to other plant species. We expanded the analysis to aged seeds of wheat (Triticum aestivum) and canola (Brassica napus). It was found that wheat and canola seeds required much longer periods than Arabidopsis seeds to lose seed germination ability completely under the same aging conditions. As what had been observed for Arabidopsis, stored mRNA degradation (∆Ct value in qPCR) in wheat and canola seeds correlated linearly and tightly with seed aging time or mRNA fragment size, while the quality of total RNA showed little change during seed aging. The generated β values reflecting the rate of stored mRNA degradation in wheat or canola seeds were similar for different stored mRNAs assayed and constant over seed aging time. The overall β values for aged seeds of wheat and canola showed non-significant differences from that of Arabidopsis when aged under the same conditions. These results are significant, allowing for better understanding of controlled seed aging for different species at the molecular level and for exploring the potential of stored mRNAs as seed aging biomarkers.

scholarly journals Neural Model for the Prediction of Volume Losses in the Aging Process of Rums

2020 ◽  
Vol 29 (54) ◽  
pp. e10514
Author(s):  
Beatriz García-Castellanos ◽  
Osney Pérez-Ones ◽  
Lourdes Zumalacárregui-de-Cárdenas ◽  
Idania Blanco-Carvajal ◽  
Luis Eduardo López-de-la-Maza
Keyword(s):  
Aging Time ◽  
Aging Process ◽  
Neural Model ◽  
Correlation Factor ◽  
Coefficient Of Determination ◽  
Training Algorithms ◽  
The Neural Network ◽  
Aging Conditions ◽  
The Mean ◽  
Input Variables

The rum aging process shows volume losses, called wastage. The numerical operation variables: product, boardwalk, horizontal and vertical positions, date, volume, alcoholic degree, temperature, humidity and aging time, recorded in databases, contain valuable information to study the process. MATLAB 2017 software was used to estimate volume losses. In the modeling of the rum aging process, the multilayer perceptron neuronal network with one and two hidden layers was used, varying the number of neurons in these between 4 and 10. The Levenberg-Marquadt (LM) and Bayesian training algorithms were compared (Bay) The increase in 6 consecutive iterations of the validation error and 1,000 as the maximum number of training cycles were the criteria used to stop the training. The input variables to the network were: numerical month, volume, temperature, humidity, initial alcoholic degree and aging time, while the output variable was wastage. 546 pairs of input/output data were processed. The statistical Friedman and Wilcoxon tests were performed to select the best neural architecture according to the mean square error (MSE) criteria. The selected topology has a 6-4-4-1 structure, with an MSE of 2.1∙10-3 and a correlation factor (R) with experimental data of 0.9898. The neural network obtained was used to simulate thirteen initial aging conditions that were not used for training and validation, detecting a coefficient of determination (R2) of 0.9961.

scholarly journals Identification of Maize Kernel Vigor under Different Accelerated Aging Times Using Hyperspectral Imaging

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3078 ◽  
Author(s):  
Lei Feng ◽  
Susu Zhu ◽  
Chu Zhang ◽  
Yidan Bao ◽  
Xuping Feng ◽  
...  
Keyword(s):  
Aging Time ◽  
Hyperspectral Imaging ◽  
Accelerated Aging ◽  
Principal Component ◽  
Seed Vigor ◽  
Support Vector ◽  
Classification Models ◽  
Maize Kernel ◽  
Seed Aging ◽  
Maize Kernels

Seed aging during storage is irreversible, and a rapid, accurate detection method for seed vigor detection during seed aging is of great importance for seed companies and farmers. In this study, an artificial accelerated aging treatment was used to simulate the maize kernel aging process, and hyperspectral imaging at the spectral range of 874–1734 nm was applied as a rapid and accurate technique to identify seed vigor under different accelerated aging time regimes. Hyperspectral images of two varieties of maize processed with eight different aging duration times (0, 12, 24, 36, 48, 72, 96 and 120 h) were acquired. Principal component analysis (PCA) was used to conduct a qualitative analysis on maize kernels under different accelerated aging time conditions. Second-order derivatization was applied to select characteristic wavelengths. Classification models (support vector machine−SVM) based on full spectra and optimal wavelengths were built. The results showed that misclassification in unprocessed maize kernels was rare, while some misclassification occurred in maize kernels after the short aging times of 12 and 24 h. On the whole, classification accuracies of maize kernels after relatively short aging times (0, 12 and 24 h) were higher, ranging from 61% to 100%. Maize kernels with longer aging time (36, 48, 72, 96, 120 h) had lower classification accuracies. According to the results of confusion matrixes of SVM models, the eight categories of each maize variety could be divided into three groups: Group 1 (0 h), Group 2 (12 and 24 h) and Group 3 (36, 48, 72, 96, 120 h). Maize kernels from different categories within one group were more likely to be misclassified with each other, and maize kernels within different groups had fewer misclassified samples. Germination test was conducted to verify the classification models, the results showed that the significant differences of maize kernel vigor revealed by standard germination tests generally matched with the classification accuracies of the SVM models. Hyperspectral imaging analysis for two varieties of maize kernels showed similar results, indicating the possibility of using hyperspectral imaging technique combined with chemometric methods to evaluate seed vigor and seed aging degree.

scholarly journals Global analysis of gene expression dynamics identifies factors required for accelerated mRNA degradation

2018 ◽  
Author(s):  
Darach Miller ◽  
Nathan Brandt ◽  
David Gresham
Keyword(s):  
Single Molecule ◽  
Translational Control ◽  
Environmental Changes ◽  
Global Analysis ◽  
Mrna Degradation ◽  
Branched Dna ◽  
Degradation Rates ◽  
Gene Expression Dynamics ◽  
Mrna Destabilization ◽  
Barcode Sequencing

AbstractCellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeastSaccharomyces cerevisiaeduring a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming. To explore the molecular basis of destabilization we implemented a SortSeq approach to screen using the pooled deletion collection library fortransfactors that mediate rapidGAP1mRNA repression. We combined low-input multiplexed Barcode sequencing with branched-DNA single-molecule mRNA FISH and Fluorescence-activated cell sorting (BFF) to identify that the Lsm1-7p/Pat1p complex and general mRNA decay machinery are important forGAP1mRNA clearance. We also find that the decapping modulatorSCD6,translation factor eIF4G2, and the 5’ UTR ofGAP1are important for this repression, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.

scholarly journals Ribosomal RNA degradation induced by the bacterial RNA polymerase inhibitor rifampicin

2021 ◽  
Author(s):  
Lina Hamouche ◽  
Leonora Poljak ◽  
Agamemnon J. Carpousis
Keyword(s):  
16S Rrna ◽  
Rna Polymerase ◽  
Growth Conditions ◽  
Rna Degradation ◽  
Mrna Degradation ◽  
Rnase E ◽  
Rifampicin Treatment ◽  
Bacterial Rna ◽  
Degradation Rates ◽  
Rrna Degradation

AbstractRifampicin, a broad-spectrum antibiotic, inhibits bacterial RNA polymerase. Here we show that rifampicin treatment of Escherichia coli results in a 50% decrease in cell size due to a terminal cell division. This decrease is a consequence of inhibition of transcription as evidenced by an isogenic rifampicin-resistant strain. There is also a 50% decrease in total RNA due mostly to a 90% decrease in 23S and 16S rRNA levels. Control experiments showed this decrease is not an artifact of our RNA purification protocol and therefore due to degradation in vivo. Since chromosome replication continues after rifampicin treatment, ribonucleotides from rRNA degradation could be recycled for DNA synthesis. Rifampicin-induced rRNA degradation occurs under different growth conditions and in different strain backgrounds. However, rRNA degradation is never complete thus permitting the re-initiation of growth after removal of rifampicin. The orderly shutdown of growth under conditions where the induction of stress genes is blocked by rifampicin is noteworthy. Inhibition of protein synthesis by chloramphenicol resulted in a partial decrease in 23S and 16S rRNA levels whereas kasugamycin treatment had no effect. Analysis of temperature-sensitive mutant strains implicate RNase E, PNPase and RNase R in rifampicin-induced rRNA degradation. We cannot distinguish between a direct role for RNase E in rRNA degradation versus an indirect role involving a slowdown of mRNA degradation. Since mRNA and rRNA appear to be degraded by the same ribonucleases, competition by rRNA is likely to result in slower mRNA degradation rates in the presence of rifampicin than under normal growth conditions.

scholarly journals Metabolism of aged seeds. Changes in rye embryo polyribosomes during seed aging

2014 ◽  
Vol 61 (3-4) ◽  
pp. 369-379
Author(s):  
Kazimierz Zalewski
Keyword(s):  
Dehydrogenase Activity ◽  
Ribosomal Proteins ◽  
Control Sample ◽  
Electrophoretic Analysis ◽  
Winter Rye ◽  
Control Embryo ◽  
Ribonucleic Acids ◽  
Seed Aging ◽  
Almost All ◽  
Aged Seeds

Germination, total dehydrogenase activity, ribosomal proteins and ribonucleic acids of embryos obtained from winter rye harvested in different years and of distinctly differing viability were studied. Diminishing viability was accompanied by declines in the amount of ribosome-bound mRNA and a drop in the intensity of its synthesis during germination. Electrophoretic analysis of control embryo (fully viable) ribosome proteins revealed 55 different bands: 10 acidic and 45 basic. The embryos of aged seeds had 43 different bands of which 8 were acidic, 35 basic and almost all of which had an altered electrophoretic mobility as compared with the control sample. As aging progressed, the percentages of lysine, histidine and arginine increased while those of tyrosine, methionine, proline and serine decreased.

ISSUES WITH APPROACHES FOR SIMULATING AGING OF NUCLEAR POWER PLANT CABLE MATERIALS

2021 ◽  
Author(s):  
Kenneth T. Gillen ◽  
Mathew C. Celina
Keyword(s):  
Power Law ◽  
Nuclear Power ◽  
Power Plants ◽  
Time Dependent ◽  
International Electrotechnical Commission ◽  
Ambient Conditions ◽  
Energy Agency ◽  
Degradation Rates ◽  
Simplified Method ◽  
Aging Conditions

ABSTRACT Over the past 20 y, the International Electrotechnical Commission and the International Atomic Energy Agency have published several Technical Documents describing recommended methods for carrying out accelerated radiation plus temperature aging of cable materials in nuclear power plants. These methods include the power law method, the time-dependent model, the dose to equivalent damage approach, and the simplified method approach. Because of the expected and observed changes in chemistry that occur as aging conditions transition radiation–temperature space, we highlight issues with the time-dependent and simplified method approaches by showing that they do not simulate the chemistry occurring under ambient conditions. The DED approach and a recent modification, the Matched Accelerated Conditions approach, can handle the changes in chemistry for many important cable materials and therefore offer more confident accelerated simulations. Problems with the power law method are then briefly described. Also discussed are the significant issues that occur when trying to simulate the aging of semicrystalline cable materials that show inverse-temperature effects. For these materials, degradation rates under radiation can increase as the aging temperature drops below ∼60 °C, in temperature regions where typical ambient aging conditions occur. A possible approach for dealing with such materials is suggested.

scholarly journals The Effect of Hydro-Priming on Germination Characteristics, Seedling Growth and Antioxidant Activity of Accelerated Aging Wheat Seeds

2015 ◽  
Vol 47 (4) ◽  
pp. 41-48 ◽  
Author(s):  
E. Ghasemi ◽  
M. Goodarzian Ghahfarokhi ◽  
B. Darvishi ◽  
Z. Heidari Kazafi
Keyword(s):  
Electrical Conductivity ◽  
Peroxidase Activity ◽  
Dry Weight ◽  
Germination Percentage ◽  
Percentage Germination ◽  
Seed Aging ◽  
Seedling Length ◽  
Normal Seedling ◽  
Mean Time ◽  
Aged Seeds

Abstract Seed aging is an important problem in developing countries which seeds stored in inappropriate condition. Delayed germination, reduced normal seedling percentage and changed antioxidant enzymes activity are some indications of aged seeds. Priming is a technique applied before planting and can improve seed characteristics especially under abiotic stress conditions. The main objective of the study was to evaluate aging effect on seed quality and to study the interaction between seed aging and seed priming. A factorial experiment based on completely randomized design with three replicates was conducted. The experimental treatments included cultivar, priming and aging. Results showed that seed aging reduced germination percentage, germination index, seedling length, normal seedling percentage, seedling dry weight, catalase and ascorbate peroxidase activity and increased the germination mean time and electrical conductivity of seeds. The highest germination percentage, germination index, seedling length, normal seedling percentage, seedling dry weight, catalase and ascorbate peroxidase activity and the minimum germination mean time and electrical conductivity of seeds were attained from hydro-priming treatment under non aged condition. Hydro-priming improved aged seeds quality and increased enzymes activity. Therefore, priming is a technique can be applied to improve aged seeds germination and seedling characteristics.

scholarly journals Development of SSR markers related to seed storability traits in maize subjected to artificial seed aging conditions

2019 ◽  
Author(s):  
Xiaoyang Guo ◽  
Chengxu Gong ◽  
Shan Liu ◽  
Chenchen Feng ◽  
Xiao Han ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Germination Rate ◽  
Aging Treatment ◽  
Inbred Lines ◽  
Seed Aging ◽  
Maize Germplasm ◽  
Chi Squared ◽  
Aging Conditions ◽  
Combined Selection ◽  
Seed Storability

AbstractSeed storability is an important and complex agronomic trait in maize because annual seed production considerably exceeds consumption. The viability of seeds decreases over time, even when stored at low temperature, until seeds finally lose viability. In our previous study, two inbred lines with significantly different storability, Dong156 with high storage tolerance and Dong237 with low storage tolerance, were selected over six years using a natural seed aging test. In the present study, an F2:3 population and a RIL (recombinant inbred line) population were constructed from these two inbred lines and used to map QTL (quantitative trait loci) with SSR (simple sequence repeat) markers. A phenotypic index of traits related to seed storability that includes germination rate, germination potential, a germination index, a vigor index, seedling weight, and seedling length was generated using the results of an artificial aging treatment. Two consistent regions, cQTL-7 on chromosome 7 and cQTL-10 on chromosome 10, were identified by comparing QTL analysis results from these two populations. After genotyping SSR markers in these two regions, cQTL-7 was remapped to between umc1671 and phi328175 in a 7.97-Mb region, and cQTL-10 was remapped to between umc1648 and phi050 in a 39.15-Mb region. Four SSR markers linked to cQTL-7 and cQTL-10, including umc1671, phi328175, umc1648, and phi050, were identified using a Chi-squared test. The combined selection efficiency of these four markers was 83.94% in 85 RIL lines with high storability, and marker umc1648 exhibited the highest efficiency value of 88.89%. These results indicated that the four SSR markers developed in this study could be used for selection of maize germplasm with high seed storability.

scholarly journals The metabolism of aged seeds The formation of polyribosomes in the embryos of germinating rye grains of different viability

2014 ◽  
Vol 54 (4) ◽  
pp. 417-427
Author(s):  
Kazimierz Zalewski
Keyword(s):  
Seed Germination ◽  
Rna Synthesis ◽  
Seed Aging ◽  
Quantitative Changes ◽  
Aged Seeds

Changes during seed germination in the cytoplasmic ribosomal fraction, the formation of polysomes and RNA synthesis in rye grain embryos of different age, were studied. Quantitative changes in embryo ribosomes accompanied seed aging. As the viability of the grain decreased, monosomes constituted an increasing proportion of the total ribosome content. The observed fall in RNA synthesis is considered a symptom of the deteriorative processes involved in seed aging.

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