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Embryonic stem cell (ESC) research is critical to the scientific community, as their application in regenerative medicine can be widely beneficial. ESCs eventually withdraw from their self-renewal program and subsequently differentiate into specific cell lineages; however, the mechanisms regulating these processes remain unclear. PKC inhibition using 3-[1-[3-(dimethylamino) propyl]-5-methoxy-1H-indol-3-yl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione (PKCi) is responsible for the derivation and maintenance of human, rat, and mouse ESCs, but the mechanism by which PKCi maintains stem cell self-renewal is poorly understood. By studying the PKCi stem cell (PKCi-mESC) transcriptome and epigenetic modification, we found the transcriptome of PKCi-mESC differed from 2i stem cells (2i-mESC), with 2010 up-regulated genes and 1784 down-regulated genes. Among them, genes related to core transcription factors, naïve-specific markers, and pluripotency are differentially expressed between the two stem cell lines. We analyzed epigenetic modification of PKCi-mESC and found the distribution of H3K27me3 signal was significantly reduced at transcription start sites (TSSs) throughout the genome and at differentially expressed genes (DEGs). Likewise, the H3K9me3 signal at TSSs throughout the genome was significantly reduced in PKCi-mESC, but the distribution on DEGs is reversed. Kdm4d and Kdm6a knockdown by RNA interference (RNAi) significantly altered the expression of genes related to self-renewal in PKCi-mESC. In conclusion, we revealed PKCi-mESC and 2i-mESC differentially express numerous genes, including stem cell-related genes. Furthermore, PKCi-mESC regulated gene expression through H3K27me3 and H3K9me3 modification, which maintained stem cell self-renewal capacity.

Additional file 3: Fig. S1. DNA transfection induced immunoreaction and its suppression with treatment with immune inhibitors in ST cells. Fig. S2. Assessment of the immunoreaction (DMSO) and treatment effect of immune inhibitors after DNA is transfected into cells. Fig. S3. Distribution of fragment sizes in the STARR-seq libraries. Fig. S4. Genome coverage of STARR-seq libraries in pig non-repetitive regions. Fig. S5. GC-content analysis for the STARR-seq libraries. Fig. S6. Reproducibility of STARR-seq. Fig. S7. Correlation analysis of enhancers strength in two biological replicates of ST cells. Fig. S8. Venn diagram showing the overlap of enhancers between our STARR-seq approach and other published studies. Fig. S9. GO analysis of genes in proximity to enhancers. Fig. S10. ATAC-seq and STARR-seq enhancers integrated analysis. Fig. S11. Snapshots of signals at three types of chromatin state for the STARR-seq enhancer regions. Fig. S12. The enhancer (Sscrofa11.1, 8:119,324,324-119,325,095) and PPP3CA gene interacted by a TAD region in pig muscle tissues. Fig. S13. The enhancer (Sscrofa11.1, 1:4,548,557-4,549,774) and QKI gene interacted by a TAD region in pig liver tissues.

The influences of hot air drying (AD), medium- and short-wave infrared drying (IR), instant controlled pressure drop drying (DIC), and vacuum freeze drying (FD) on cell wall polysaccharide modification were studied, and the relationship between the modifications and texture properties was analyzed. The results showed that the DIC treated apple chips exhibited the highest crispness (92) and excellent honeycomb-like structure among all the dried samples, whereas the FD dried apple chips had low crispness (10), the minimum hardness (17.4 N), and the highest volume ratio (0.76) and rehydration ratio (7.55). Remarkable decreases in the contents of total galacturonic acid and the amounts of water extractable pectin (WEP) were found in all the dried apple chips as compared with the fresh materials. The highest retention of WEP fraction (102.7 mg/g AIR) was observed in the FD dried apple chips, which may lead to a low structural rigidity and may be partially responsible for the lower hardness of the FD apple chips. In addition, the crispness of the apple chips obtained by DIC treatment, as well as AD and IR at 90°C, was higher than that of the samples obtained from the other drying processes, which might be due to the severe degradation of pectic polysaccharides, considering the results of the amounts of pectic fractions, the molar mass distribution, and concentrations of the WEP fractions. Overall, the data suggested that the modifications of pectic polysaccharides of apple chips, including the amount of the pectic fractions and their structural characteristics and the extent of degradation, significantly affect the texture of apple chips.

Background Carrot carotenoids are typically located in chromoplasts, forming a crystalline substructure. Cell walls and chromoplasts therefore constitute two major physical barriers to the release of carotenoids from the food matrix during digestion. The release of carotenoids from these physical barriers is supposed to be substantially affected by mechanical factors during food processing and oral mastication. Given the implications of this, the effects of four different processing procedures, and various mastication levels, on the carotenoid bioaccessibility of carrot chips were evaluated. Results Restructuring and drying methods substantially affected the carotenoid bioaccessibility of carrot chips. The highest carotenoid bioaccessibility was obtained for the air-dried combined with instant pressure-drop-dried (AD-DIC) restructured chips. Although the fresh carrots possessed the highest carotenoid content, their bioaccessibility was lower than that of the carrot chips. The evolution of the particle sizes of the samples was responsible for the changes in carotenoid bioaccessibility due to oral masitication. The particle size of the fresh carrots decreased with increasing oral masitication, which favored carotenoid bioaccessibilty. However, the restructured chips that combined freeze drying with instant pressure-drop drying (R-FD-DIC) demonstrated the opposite trend, probably caused by the severe aggregation of the sample during digestion, which compromised the effect of mastication on the release of carotenoid. Conclusion Data regarding the effects of the drying process and oral mastication digestion behavior on the samples suggested that AD-DIC-dried restructured carrot chips are effective in enhancing carotenoid bioaccessibility, which explains the key factors involved in the release of carotenoids from carrot chips prepared by different processes. © 2020 Society of Chemical Industry.

An abundance of shiitake mushrooms is consumed in dried form around the world. In the present study, changes in water state, water distribution and microstructure of shiitake mushrooms during hot-air drying (HAD) and far-infrared radiation drying (FIRD) processes were investigated using low-field nuclear magnetic resonance and scanning electron microscopy. Quality attributes of the dried products were compared in terms of drying property, appearance, rehydration behavior, texture and storage stability. RESULTS Compared with HAD, the rate of water diffusion and evaporation of the shiitake mushrooms dried by FIRD was higher, thus resulting in a shorter drying time (630?min), a lower water content (0.07?g?g?1 wet basis) and a higher glass transition temperature (7.88?°C) for dried products. Moreover, a homogenous and porous microstructure with less shrinkage and case hardening was demonstrated by the FIRD samples, indicating a superior texture, including a larger pileus diameter (3.4?cm), a higher rehydration ratio (7.31), a lower hardness (37.93?N) and a higher crispness (1.41?mm) for FIRD shiitake mushrooms. CONCLUSION High-quality shiitake mushrooms with a desirable texture could be produced by FIRD by enhancing the diffusion of internal water and alleviating the case hardening during a relatively short drying process. ? 2018 Society of Chemical Industry

Combined freeze-drying and instant controlled pressure drop process (FD-DIC) for restructured carrot-potato chips was developed and its processing conditions were optimized using response surface methodology (RSM) with the purpose of improving the quality of products and reducing energy consumption. Three critical variables including the amount of carrot, the moisture content of the partially dried product before DIC treatment, and equilibrium temperature of DIC for the restructured chips were considered. Response parameters such as the final moisture content, color value (L, a, and b), and texture properties of restructured carrot-potato chips were investigated. The results showed that the graphical optimal ranges of FD-DIC drying process were as follows: the amount of carrot was 46–54% w/w, the moisture content of the partially dried product before DIC treatment was 0.20–0.35 g/g, and the equilibrium temperature of DIC was 85–95°C. Furthermore, the numerical optimization suggested that conditions were 47.43% w/w, 0.29 g/g, and 90.57°C, respectively. It could be concluded that the combined drying method of FD-DIC provided the restructured carrot-potato chips with higher quality, as compared to the freeze-dried chips. Considering the relatively high production cost of FD, this novel FD-DIC could be an alternative method for obtaining desirable restructured fruit and vegetable chips.