A systematic evaluation of isolation techniques and freeze-thaw effects on plasma extracellular vesicle heterogeneity and subpopulation profiling
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE283848 | GEO | 2025/07/02
REPOSITORIES: GEO
Similar Datasets
Project description:DNA computing harnesses the immense potential of DNA molecules to enable sophisticated and transformative computational processes but is hindered by low computing speed. Here, we propose freeze-thaw cycling as a simple yet powerful method for high-speed DNA computing without complex procedures. Through iterative cycles, we achieve a substantial 20-fold speed enhancement in basic strand displacement reactions. This acceleration arises from the utilization of eutectic ice phase as a medium, temporarily increasing the effective local concentration of molecules during each cycle. In addition, the acceleration effect follows the Hofmeister series, where kosmotropic anions such as sulfate (SO42-) reduce eutectic phase volume, leading to a more notable enhancement in strand displacement reaction rates. Leveraging this phenomenon, freeze-thaw cycling demonstrates its generalizability for high-speed DNA computing across various circuit sizes, achieving up to a remarkable 120-fold enhancement in reaction rates. We envision its potential to revolutionize molecular computing and expand computational applications in diverse fields.
| S-EPMC10456841 | biostudies-literature
Project description:We studied the effect of freeze-thaw on isoflavone composition in germinated soybeans, particularly the conversion of aglycones, the isoflavone monomers with high biological activity. Germinated soybeans were frozen at -20 °C, -80 °C, and -196 °C respectively, and then the frozen samples (-20 °C) were thawed at 4 °C, 10 °C, and 25 °C respectively. Results showed total isoflavone increased after germination. Aglycones content increased most at -20 °C, which increased about 24 times. The effect of thaw temperature and time indicated there were approximately 89 % glucosides forms converted to aglycones during freeze-thaw. Isoflavone conjugate-hydrolyzing β-glucosidase (ICHG) activity increased by 65.78 % (25 °C) and 59.14 % (48 h) with freeze-thaw. The cells of germinated soybeans were broken, promoting ICHG contact with glucosides and malonyl-glucosides. These results indicated that freeze-thaw greatly changed the content and profile of isoflavones, resulting in a sharp increase in the content of aglycones.
| S-EPMC9743152 | biostudies-literature
Project description:In biopharmaceutical production processes, freeze-thaw operations are used to ensure product integrity during long hold times, but they also introduce additional stresses such as freeze concentration gradients that might lead to a loss of protein activity. Process characterization of freeze-thaw operations at different scales should be conducted with attention to freezing time and boundary effects to ensure the product stability throughout the process and process development. Currently, process characterization often relies on one or very few temperature probes that detect freezing times based on raw temperature, which is largely influenced by freezing-point depression in case of concentrated solutions. A method to detect freezing based on the second derivative of temperature measurements from Fiber-Bragg-Grating sensors is presented to overcome this issue. The applicability of the method is demonstrated by process characterization of a novel small-scale freeze-thaw device with minimized boundary effects using freezing times of purified water and concentrated formulations. Freezing times varied from 35 to 81 min for temperatures between -60 and -20°C and impacted freeze concentration profiles. Furthermore, freezing time estimations based on the Plank equation revealed model limitations due to start-up temperature gradients, that can be corrected by an empirically extended Plank model. As a hypothesis, we conclude that freezing temperature, from a freeze concentration view, is less important in containers with small characteristic freezing distances such as freeze bags. Using a 2D-resolved temperature profile, a shift of the last point to freeze position from top to bottom of a container was observed when freezing above -30°C.
| S-EPMC8062970 | biostudies-literature
Project description:The emergence of an RNA catalyst capable of self-replication is considered a key transition in the origin of life. However, how such replicase ribozymes emerged from the pools of short RNA oligomers arising from prebiotic chemistry and non-enzymatic replication is unclear. Here we show that RNA polymerase ribozymes can assemble from simple catalytic networks of RNA oligomers no longer than 30 nucleotides. The entropically disfavoured assembly reaction is driven by iterative freeze-thaw cycles, even in the absence of external activation chemistry. The steep temperature and concentration gradients of such cycles result in an RNA chaperone effect that enhances the otherwise only partially realized catalytic potential of the RNA oligomer pool by an order of magnitude. Our work outlines how cyclic physicochemical processes could have driven an expansion of RNA compositional and phenotypic complexity from simple oligomer pools.
| S-EPMC4495579 | biostudies-literature
Project description:BackgroundCirculating inflammation markers are being increasingly measured in prospective cohorts to investigate cancer etiology. However, it is unclear how the measurements are affected by the freeze-thaw cycles of the specimens prior to marker analysis.MethodsWe compared concentrations of 45 inflammation markers between paired serum vials of 55 participants in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial that have undergone one (T1), two (T2), and three (T3) freeze-thaw cycles at the time of assay. We computed the difference of analyte concentrations across paired vials (T1 vs. T2, T2 vs. T3) and tested whether the difference deviated from zero using the Wilcoxon signed-rank test. We also calculated Spearman rank correlation and weighted kappa statistics for T1 vs. T2 and T2 vs. T3 comparisons to assess agreement in rank ordering of subjects.ResultsMeasurements between paired T1 and T2 samples were largely similar, with the difference not statistically deviating from zero for 36 of the 45 markers. In contrast, tests of the difference between paired T2 and T3 samples were statistically significant for 36 markers. However, the rank ordering of participants by marker concentration remained largely consistent across T2 and T3 samples, with Spearman correlation coefficients >0.8 for 42 markers and weighted kappas >0.7 for 37 markers.ConclusionWe recommend that studies measuring inflammation markers use previously unthawed specimens to the extent possible, or match on the number of prior freeze-thaw cycles in nested case-control studies.
| S-EPMC6411278 | biostudies-literature
Project description:This study aims to characterize and understand the effects of freezing on collagen structures and functionality. Specifically, thermodynamic destabilization of collagen at molecular- and fibril-levels by combination of low temperatures and freezing were experimentally characterized using modulated differential scanning calorimetry. In order to delineate the effects of sub-zero temperature and water-ice phase change, we hypothesized that the extent of destabilization can be determined based on post-thaw heat induced thermal denaturation of collagen. It is found that thermal denaturation temperature of collagen in hydrogel decreases by 1.4-1.6°C after freeze/thaw while no such decrease is observed in the case of molecular solution. The destabilization is predominantly due to ice formation. Exposure to low temperatures in the absence of ice has only minimal effect. Calorimetry measurements combined with morphological examination of collagen matrices by scanning electron microscopy suggest that freezing results in destabilization of collagen fibrils due to expansion of intrafibrillar space by ice formation. This fibril-level damage can be alleviated by use of cryoprotectant DMSO at concentrations as low as 0.5 M. A theoretical model explaining the change in collagen post-thaw thermal stability by freezing-induced fibril expansion is also proposed.
| S-EPMC4713088 | biostudies-literature
Project description:Climate change can have substantial impacts on nitrogen runoff, which is a major cause of eutrophication, harmful algal blooms, and hypoxia in freshwaters and coastal regions. We examined responses of nitrate loading to climate change in the Upper Mississippi River Basin (UMRB) with an enhanced Soil and Water Assessment Tool with physically based Freeze-Thaw cycle representation (SWAT-FT), as compared with the original SWAT model that employs an empirical equation. Driven by future climate projections from five General Circulation Models (GCMs) from 1960 to 2099 under the Representative Concentrations Pathways (RCP) 8.5 scenario, we analyzed changes in riverine nitrate loadings, as well as terrestrial surface and subsurface contributions of the UMRB in the 21st century relative to the baseline period of 1960-1999. By the end of the 21st century, the original SWAT model predicted about a 50% increase in riverine nitrate loadings which is nearly twice as much as that estimated by SWAT-FT (ca. 25%). Such a large difference in projected nitrate changes can potentially mislead mitigation strategies that aim to reduce nitrogen runoff from the UMRB. Further analysis shows that the difference between the original SWAT model and SWAT-FT led to substantial discrepancies in the spatial distribution of surface and subsurface nitrate loadings in the UMRB. In general, SWAT-FT predicted more nitrate leaching for northwestern parts of the UMRB which are more sensitive to freeze-thaw cycle, mainly because SWAT-FT simulated less frequent frozen soils. This study highlights the importance of using physically based freeze-thaw cycle representation in water quality modeling. Design of future nitrogen runoff reduction strategies should include careful assessment of effects that land management has on the freeze-thaw cycles to provide reliable projection of water quality under climate change.
| S-EPMC7722621 | biostudies-literature
Project description:Biochar may improve soil hydrology by altering soil porosity, density, hydraulic conductivity, and water-holding capacity. These properties are associated with the grain size distributions of both soil and biochar, and therefore may change as biochar weathers. Here we report how freeze-thaw (F-T) cycling impacts the grain size of pine, mesquite, miscanthus, and sewage waste biochars under two drainage conditions: undrained (all biochars) and a gravity-drained experiment (mesquite biochar only). In the undrained experiment plant biochars showed a decrease in median grain size and a change in grain-size distribution consistent with the flaking off of thin layers from the biochar surface. Biochar grain size distribution changed from unimodal to bimodal, with lower peaks and wider distributions. For plant biochars the median grain size decreased by up to 45.8% and the grain aspect ratio increased by up to 22.4% after 20 F-T cycles. F-T cycling did not change the grain size or aspect ratio of sewage waste biochar. We also observed changes in the skeletal density of biochars (maximum increase of 1.3%), envelope density (maximum decrease of 12.2%), and intraporosity (porosity inside particles, maximum increase of 3.2%). In the drained experiment, mesquite biochar exhibited a decrease of median grain size (up to 4.2%) and no change of aspect ratio after 10 F-T cycles. We also document a positive relationship between grain size decrease and initial water content, suggesting that, biochar properties that increase water content, like high intraporosity and pore connectivity large intrapores, and hydrophilicity, combined with undrained conditions and frequent F-T cycles may increase biochar breakdown. The observed changes in biochar particle size and shape can be expected to alter hydrologic properties, and thus may impact both plant growth and the hydrologic cycle.
| S-EPMC5766239 | biostudies-literature
Project description:The data submitted is for the proteomics data published in the paper: A systematic evaluation of isolation techniques and freeze-thaw effects on plasma extracellular vesicle heterogeneity and subpopulation profiling
2025-06-30 | PXD058661 | Pride
Project description:The aroma attributes of sulfurous, mushroom and earthy are the most important characteristics of the aroma of Tuber melanosporum. However, these three aroma attributes are absent in the T. melanosporum fermentation system. To improve the quality of the aroma, repeated freeze-thaw treatment (RFTT) was adopted to affect the interplay of volatile organic compounds (VOCs). Using RFTT, not only was the score on the hedonic scale of the aroma increased from the "liked slightly" to the "liked moderately" grade, but the aroma attributes of sulfurous, mushroom and earthy could also be smelled in the T. melanosporum fermentation system for the first time. A total of 29 VOCs were identified, and 9 compounds were identified as the key discriminative volatiles affected by RFTT. Amino acid analysis revealed that methionine, valine, serine, phenylalanine, isoleucine and threonine were the key substrates associated with the biosynthesis of the 9 key discriminative VOCs. This study noted that amino acid metabolism played an important role in the regulation of the aroma of the T. melanosporum fermentation system.
| S-EPMC4660818 | biostudies-literature