Stress–response relationships related to ageing and death of orthodox seeds: a study comparing viability and RNA integrity in soya bean (Glycine max) cv. Williams 82

2020 ◽  
Vol 30 (2) ◽  
pp. 161-172
Author(s):  
Christina Walters ◽  
Margaret B. Fleming ◽  
Lisa M. Hill ◽  
Emma J. Dorr ◽  
Christopher M. Richards

AbstractCharacterizing non-lethal damage within dry seeds may allow us to detect early signs of ageing and accurately predict longevity. We compared RNA degradation and viability loss in seeds exposed to stressful conditions to quantify relationships between degradation rates and stress intensity or duration. We subjected recently harvested (‘fresh’) ‘Williams 82’ soya bean seeds to moisture, temperature and oxidative stresses, and measured time to 50% viability (P50) and rate of RNA degradation, the former using standard germination assays and the latter using RNA Integrity Number (RIN). RIN values from fresh seeds were also compared with those from accessions of the same cultivar harvested in the 1980s and 1990s and stored in the refrigerator (5°C), freezer (−18°C) or in vapour above liquid nitrogen (−176°C). Rates of viability loss (P50−1) and RNA degradation (RIN⋅d−1) were highly correlated in soya bean seeds that were exposed to a broad range of temperatures [holding relative humidity (RH) constant at about 30%]. However, the correlation weakened when fresh seeds were maintained at high RH (holding temperature constant at 35°C) or exposed to oxidizing agents. Both P50−1 and RIN⋅d−1 parameters exhibited breaks in Arrhenius behaviour near 50°C, suggesting that constrained molecular mobility regulates degradation kinetics of dry systems. We conclude that the kinetics of ageing reactions at RH near 30% can be simulated by temperatures up to 50°C and that RNA degradation can indicate ageing prior to and independent of seed death.

2018 ◽  
Vol 123 (7) ◽  
pp. 1133-1146 ◽  
Author(s):  
Margaret B Fleming ◽  
Lisa M Hill ◽  
Christina Walters

Abstract Background and Aims Determining seed longevity by identifying chemical changes that precede, and may be linked to, seed mortality, is an important but difficult task. The standard assessment, germination proportion, reveals seed longevity by showing that germination proportion declines, but cannot be used to predict when germination will be significantly compromised. Assessment of molecular integrity, such as RNA integrity, may be more informative about changes in seed health that precede viability loss, and has been shown to be useful in soybean. Methods A collection of seeds stored at 5 °C and 35–50 % relative humidity for 1–30 years was used to test how germination proportion and RNA integrity are affected by storage time. Similarly, a collection of seeds stored at temperatures from −12 to +32 °C for 59 years was used to manipulate ageing rate. RNA integrity was calculated using total RNA extracted from one to five seeds per sample, analysed on an Agilent Bioanalyzer. Results Decreased RNA integrity was usually observed before viability loss. Correlation of RNA integrity with storage time or storage temperature was negative and significant for most species tested. Exceptions were watermelon, for which germination proportion and storage time were poorly correlated, and tomato, which showed electropherogram anomalies that affected RNA integrity number calculation. Temperature dependencies of ageing reactions were not significantly different across species or mode of detection. The overall correlation between germination proportion and RNA integrity, across all experiments, was positive and significant. Conclusions Changes in RNA integrity when ageing is asymptomatic can be used to predict onset of viability decline. RNA integrity appears to be a metric of seed ageing that is broadly applicable across species. Time and molecular mobility of the substrate affect both the progress of seed ageing and loss of RNA integrity.


Catalysts ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 110 ◽  
Author(s):  
Isabel Garrido ◽  
Salvador Aznar-Cervantes ◽  
Marina Aliste ◽  
María J. Yáñez-Gascón ◽  
Nuria Vela ◽  
...  

We have evaluated the efficiency of silk fibroin (SF) coated with ZnO nanoparticles in the photocatalytic disappearance of one acaricide (etoxazole) and three fungicides (difenoconazole, myclobutanil and penconazole) in water exposed to sunlight irradiation. Electrospun SF/ZnO mats were successfully synthesized by electrospinning technique and characterized by XRD, FE-SEM, XPS, XDS, FTIR, and BET. The influence of catalyst loading on the degradation kinetics of the different pesticides was examined in order to gain knowledge of maximum degradation efficiency. A significant increment in degradation rates was observed with the addition of ZnO. SF mats with 25 mg of ZnO were finally selected since no significant differences (p < 0.05) were detected when the loading was enlarged from 25 to 50 mg for the majority of the compounds. In the experimental conditions, the half-lives ranged from 33 min to 93 min for etoxazole and myclobutanil, respectively. The comparison of SF materials coated with similar amount of TiO2 and ZnO showed that the later was slightly more efficient to remove pesticide residues. Hence, the use of electrospun SF/ZnO nanostructures would provide an environmentally friendly approach with photocatalytic activity to be applied in the reclamation of water polluted by pesticides.


2021 ◽  
Author(s):  
Amanda J. Haack ◽  
Fang Yun Lim ◽  
Dakota S. Kennedy ◽  
John H. Day ◽  
Karen N. Adams ◽  
...  

ABSTRACTGene expression analysis (e.g., targeted small gene panels, transcriptomics) from whole blood can elucidate mechanisms of immune function and aid in the discovery of biomarkers. Conventional in-clinic venipuncture offers only a small snapshot of our broad immune landscape as immune responses may occur outside of the time and location parameters available for conventional venipuncture. A self-operated method that enables flexible sampling of liquid whole blood coupled with an immediate stabilization of cellular RNA is instrumental in facilitating capture and preservation of acute or transient immune fluxes. To this end, we developed homeRNA: a kit that allows for self-collection of peripheral blood (∼0.5 mL) and immediate stabilization of cellular RNA, using the Tasso-SST™ blood collection device paired with a specially designed stabilizer tube containing RNAlater™. To assess the usability and feasibility of homeRNA for self-collection and stabilization of whole blood RNA, we conducted a pilot study (n = 41 participants) where we sent homeRNA to participants aged 21-69, located across 10 US states (94% successful blood collections, n = 51). Among participants who successfully collected blood, 91% reported no or minimal pain/discomfort using the kit (n = 35), and 77% reported easy or somewhat easy stabilization protocol. Total RNA yield from the stabilized samples ranged between 0.24 µg and 5.99 µg (mean = 1.65 µg), while RNA Integrity Number (RIN) values were above 7.0 (mean = 7.9), indicating limited RNA degradation. Results from this study demonstrate the self-collection and RNA stabilization of whole blood with homeRNA by participants themselves, in their own home.


2012 ◽  
Vol 518-523 ◽  
pp. 272-276
Author(s):  
Yang Liu ◽  
Kun Ming Dong ◽  
Li Miao ◽  
Xiao Jian Zhou ◽  
Cui Li Jin ◽  
...  

The 4-t-octylphenol (4-t-OP) biodegradation by alginate immobilized cells of Acinetobacter sp. was compared with its respective free cells in different media. The effects of different bead densities, pH values and practical applications of artificial seawater and wastewater on the biodegradation rate of 4-t-OP were investigated. Degradation kinetics of 4-t-OP by free and immobilized cells was well fitted with first order kinetic. The immobilized Acinetobacter sp. cells could enhance the efficiency of 4-t-OP degradation. The degradation rate and 4-t-OP half-life were 97.6% and 0.7 d, respectively. Increasing level of bead amount could also improve the degradation effects, when 400 beads per 100 mL were added, the degradation rate and 4-t-OP half-life were 96.5 % and 0.2 d respectively. The immobilized Acinetobacter sp. cells could degrade 4-t-OP both in artificial seawater and wastewater. The degradation rates were 87.7% and 84.3%, respectively, indicating its potential application of removing and biodegrading 4-t-OP under practical environment.


2018 ◽  
Author(s):  
Fabien Cholet ◽  
Umer Z. Ijaz ◽  
Cindy J. Smith

AbstractBackgroundReliability and reproducibility of transcriptomics-based studies are highly dependent on the integrity of RNA. Microfluidics-based techniques based on ribosomal RNA such as the RNA Integrity Number (RIN) are currently the only approaches to evaluate RNA integrity. However, it is not known if ribosomal RNA reflects the integrity of the meaningful part of the sample, the mRNA. Here we test this assumption and present a new integrity index, the Ratio amplicon, Ramp, to monitor mRNA integrity based on the differential amplification of long to short RT-Q-PCR amplicons of the glutamine synthetase A (glnA) transcript.ResultsWe successfully designed and tested two Rampindexes targetingglnAtranscripts. We showed in a suite of experimental degradations of RNA extracted from sediment that while the RIN in general did reflect the degradation status of the RNA well the Rampmapped mRNA degradation better as reflected by changes in Reverse Transcriptase Quantitative PCR (RT-Q-PCR) results. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of the16S rRNA, amoAandglnAtranscript which was successful even form the highly-degraded samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed between successively degraded 16S rRNA transcripts profiles.ConclusionAs demonstrated, transcripts can be quantified and sequenced even from highly degraded samples. Therefore, we strongly recommend that a quality check of RNA is conducted to ensure validity of results. For this both the RIN and Rampare useful, with the Rampbetter evaluating mRNA integrity in this study.


2020 ◽  
Author(s):  
Angel Mojarro ◽  
Lin Jin ◽  
Jack W. Szostak ◽  
James W. Head ◽  
Maria T. Zuber

AbstractAdvances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is in part due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earth’s prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation >4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe2+, Mg2+, and Mn2+), spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis and evaluate whether early Mars could have been permissive towards the accumulation of long-lived RNA polymers. Our results indicate that a Mg2+-rich basalt sourcing metals to a slightly acidic (pH 5.4) aqueous environment mediates the slowest rates of metal-catalyzed RNA hydrolysis, though geologic evidence and modeling of basalt weathering suggest that aquifers on Mars would be near neutral (pH ∼7). Moreover, oxidizing conditions on Mars have major consequences regarding the availability oxygen-sensitive prebiotic metals (i.e., Fe2+ and Mn2+) very early in its history due to increased RNA degradation rates and precipitation. Overall, 1) low pH better preserves RNA than basic conditions at high concentrations; 2) acidic to neutral pH environments with Fe2+ or Mn2+ will hydrolyze more RNA; and 3) alkaline environments with Mg2+ dramatically hydrolyze more RNA.


Author(s):  
Zafirah Mahyun ◽  
Noor Fazliani Shoparwe ◽  
Ahmad Zuhairi Abdullah ◽  
Abdul Latif Ahmad ◽  
Mardawani Mohamad ◽  
...  

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1597
Author(s):  
Iman Jafari ◽  
Mohamadreza Shakiba ◽  
Fatemeh Khosravi ◽  
Seeram Ramakrishna ◽  
Ehsan Abasi ◽  
...  

The incorporation of nanofillers such as graphene into polymers has shown significant improvements in mechanical characteristics, thermal stability, and conductivity of resulting polymeric nanocomposites. To this aim, the influence of incorporation of graphene nanosheets into ultra-high molecular weight polyethylene (UHMWPE) on the thermal behavior and degradation kinetics of UHMWPE/graphene nanocomposites was investigated. Scanning electron microscopy (SEM) analysis revealed that graphene nanosheets were uniformly spread throughout the UHMWPE’s molecular chains. X-Ray Diffraction (XRD) data posited that the morphology of dispersed graphene sheets in UHMWPE was exfoliated. Non-isothermal differential scanning calorimetry (DSC) studies identified a more pronounced increase in melting temperatures and latent heat of fusions in nanocomposites compared to UHMWPE at lower concentrations of graphene. Thermogravimetric analysis (TGA) and derivative thermogravimetric (DTG) revealed that UHMWPE’s thermal stability has been improved via incorporating graphene nanosheets. Further, degradation kinetics of neat polymer and nanocomposites have been modeled using equations such as Friedman, Ozawa–Flynn–Wall (OFW), Kissinger, and Augis and Bennett’s. The "Model-Fitting Method” showed that the auto-catalytic nth-order mechanism provided a highly consistent and appropriate fit to describe the degradation mechanism of UHMWPE and its graphene nanocomposites. In addition, the calculated activation energy (Ea) of thermal degradation was enhanced by an increase in graphene concentration up to 2.1 wt.%, followed by a decrease in higher graphene content.


2021 ◽  
pp. 100757
Author(s):  
Akshay Sonawane ◽  
O.P. Chauhan ◽  
Shubhankar D. Semwal ◽  
A.D. Semwal

Materials ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 2872
Author(s):  
Seyed Mohamad Reza Paran ◽  
Ghasem Naderi ◽  
Elnaz Movahedifar ◽  
Maryam Jouyandeh ◽  
Krzysztof Formela ◽  
...  

The effect of several concentrations of carboxylated nitrile butadiene rubber (XNBR) functionalized halloysite nanotubes (XHNTs) on the vulcanization and degradation kinetics of XNBR/epoxy compounds were evaluated using experimental and theoretical methods. The isothermal vulcanization kinetics were studied at various temperatures by rheometry and differential scanning calorimetry (DSC). The results obtained indicated that the nth order model could not accurately predict the curing performance. However, the autocatalytic approach can be used to estimate the vulcanization reaction mechanism of XNBR/epoxy/XHNTs nanocomposites. The kinetic parameters related to the degradation of XNBR/epoxy/XHNTs nanocomposites were also assessed using thermogravimetric analysis (TGA). TGA measurements suggested that the grafted nanotubes strongly enhanced the thermal stability of the nanocomposite.


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