Hi-C data is important for studying chromatin three-dimensional structure. However, the resolution of most existing Hi-C data is generally coarse due to sequencing cost. Therefore, it will be helpful ...if we can predict high-resolution Hi-C data from low-coverage sequencing data. Here we developed a novel and simple computational method based on deep learning named super-resolution Hi-C (SRHiC) to enhance the resolution of Hi-C data. We verified SRHiC on Hi-C data in human cell line. We also evaluated the generalization power of SRHiC by enhancing Hi-C data resolution in other human and mouse cell types. Results showed that SRHiC outperforms the state-of-the-art methods in accuracy of prediction.
Eucalyptus urophydis E. grandis green wood with different lengths were dewatered using CO2 that was cyclically alternated between the supercritical fluid and gas phases. The results indicate that ...shorter specimens can be dewatered to below the fiber saturation point (FSP). There was no significant difference in the dewatering rate between the specimens of 20 and 50 mm in length. The dewatering was faster when the moisture content (MC) was over the FSP, leading to a greater gradient and a non-uniform distribution of moisture. The MC distributions in all specimens had no clear differences between in tangential and radial directions. Supercritical CO2 dewatering generated a different moisture gradient than conventional kiln drying. Most water was dewatered from the end-grain section of the wood along the fiber direction, but a small amount of water was also removed in the transverse directions. There was no deformation in the specimens when the MC was above the FSP.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
It is critical to understand the mechanisms of human cancers in order to develop the effective anti-cancer therapeutic strategies. Recent studies indicated that primase polymerase (PRIMPOL) is ...strongly associated with the development of human cancers. Nevertheless, a systematic pan-cancer analysis of PRIMPOL remains to be further clarified.
Comprehensive multi-omics bioinformatics algorithms, such as TIMER2.0, GEPIA2.0 and cBioPortal, were utilized to evaluate the biological roles of PRIMPOL in pan-cancer, including the expression profiles, genomic alterations, prognostic values and immune regulation.
PRIMPOL was upregulated in glioblastoma multiforme and kidney renal clear cell carcinoma. The brain lower grade glioma patients with enhanced PRIMPOL expression displayed poor prognostic values. We also demonstrated the PRIMPOL's immunomodulating effects on pan-cancer as well as its genomic changes and methylation levels. The aberrant expression of PRIMPOL was linked to various cancer-associated pathways, including DNA damage response, DNA repair, and angiogenesis, according to single-cell sequencing and function enrichment.
This pan-cancer analysis offers a thorough review of the functional roles of PRIMPOL in human cancers, suggesting PRIMPOL as a potentially important biomarker for the progression and immunotherapy of various cancers.
Iguratimod is a novel synthetic, small-molecule immunosuppressive agent used to treat rheumatoid arthritis. Through ongoing exploration of its role and mechanisms of action, iguratimod has been ...observed to have antifibrotic effects in the lung and skin; however, its effect on renal fibrosis remains unknown. This study aimed to investigate whether iguratimod could affect renal fibrosis progression. Three different concentrations of iguratimod (30 mg/kg/day, 10 mg/kg/day, and 3 mg/kg/day) were used to intervene in unilateral ureteral obstruction (UUO) model mice. Iguratimod at 10 mg/kg/day was observed to be effective in slowing UUO-mediated renal fibrosis. In addition, stimulating bone marrow-derived macrophages with IL-4 and/or iguratimod, or with TGF-β and iguratimod or SRC inhibitors
, suggested that iguratimod mitigates the progression of renal fibrosis in UUO mice, at least in part, by inhibiting the IL-4/STAT6 signaling pathway to attenuate renal M2 macrophage infiltration, as well as by impeding SRC activation to reduce macrophage-myofibroblast transition. These findings reveal the potential of iguratimod as a treatment for renal disease.
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To investigate the effect of moderate thermal modification (TM) on wood properties, American alder (
) wood was treated at 140 °C for 4 h, 8 h and 13 h, the physical and mechanical properties, ...dimensional stability and color changes of wood were compared and studied. The results showed that the absolute dry density of moderate-TM wood decreased significantly with time except for the 4 h treatment. Moderate TM can significantly reduce the residual stress of wood up to 90.3%. There were no significant differences in MOR and MOE between most moderate TM wood and the control group; moderate TM decreased the moisture absorption and water up-taking of wood significantly; compared to the control group, the swelling of TM wood for 13 h decreased by 24.2% and 16.0% in the tangential and radial direction, respectively, showing a significant improvement in dimensional stability. There were almost no color changes even when wood endured 140 °C and 13 h TM. The moderate TM at 140 °C for 13 h can efficiently improve wood dimensional stability and retains the natural color of wood while causing almost no damage to the wood's mechanical strength.
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Although fish oil has been considered to have an anti-inflammatory effect and has been proven to play a beneficial role in the incidence of numerous diseases, the association between fish oil ...supplementation and the risk of systemic lupus erythematosus (SLE) is still unknown. This study aimed at evaluating the correlation between fish oil use and incident SLE in a large population-based prospective cohort. 390,277 participants without SLE at baseline from the UK Biobank were enrolled. Fish oil use was ascertained through a touchscreen questionnaire at baseline. The incidence of SLE was identified by the International Classification of Diseases version 10 code in medical records or self-report. Cox proportional hazard models were employed to estimate the association between fish oil use and SLE risk. Fish oil users accounted for 31.47% of participants. During a median follow-up duration of 11.57 years, 141 participants without fish oil use (4.56/100 000 person-years) and 68 participants with fish oil use (4.78/100 000 person-years) developed SLE. In four models with adjustments for different amounts of confounders, there was no significant difference in the risk of SLE between fish oil users and fish oil non-users (all p-values > 0.05). In subgroup analyses, we found that fish oil supplementation was associated with a lower risk of SLE among females with ultraviolet radiation greater than or equal to 3 h/day (hazard ratio: 0.63, 95% confidence interval: 0.40-0.98), which turned insignificant after further adjustment for female-related factors and sun protection measures. No significant association between fish oil use and overall incident SLE was observed, except in females exposed to prolonged ultraviolet radiation. Subgroup analysis suggested that females exposed to prolonged ultraviolet radiation might benefit from fish oil supplementation in terms of preventing SLE, but it needs to be confirmed in further studies.
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In plants, fatty acids (FAs) and FA-derived complex lipids are major carbon and energy reserves in seeds. They are essential components of cellular membranes and cellular signal or hormone molecules. ...Although TRANSPARENT TESTAI (TT2) is well studied for its function in regulating proanthocyanidin biosynthesis in the seed coat, little attention has been given to its role in affecting seed FA accumulation and tolerance to environmental stresses. We demonstrate that the tt2 mutation remarkably increased the seed FA content, decreased seed weight, and altered the FA composition. The increase in FA content in the tt2 seeds was due to the relative decrease of seed coat proportion as well as the more efficient FA synthesis in the tt2 embryo. Microarray analysis revealed that tt2 mutation up-regulated a group of genes critical to FA biosynthesis and embryonic development. The mutation also altered the gene expressions that respond to stress. The microarray analysis discovered that the increase in FA accumulation of the ttl seeds were accompanied by the significant up-regulation of FUSCA3, a transcriptional factor for embryonic development and FATTY ACID ELONGASE1, which catalyzes the elongation of FA chains. Moreover, lower seed protein accumulation during seed maturation also contributed to the increased seed FA accumulation in ttl mutants. This study advances the understanding of the TT2 gene in seed FA accumulation and abiotic stresses during seed germination and seedling establishment.
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BFBNIB, NMLJ, NUK, PNG, SAZU, UL, UM, UPUK
Tocopherols are lipophilic molecules, ubiquitously synthesized in all photosynthetic organisms. Being a group of vitamin E compounds, they play an essential role in human nutrition and health. ...Despite their structural and functional attributes as important antioxidants in plants, it would be misleading to ignore the potential roles of tocopherols beyond their antioxidant properties in planta. Detailed characterization of mutants and transgenic plants, including Arabidopsis (vte1, vte2, vte4, and so on), maize (sxd1) mutants, and transgenic potato and tobacco lines altered in tocopherol biosynthesis and contents, has led to surprising outcomes regarding the additional functions of these molecules. Thus, the aim of this review is to highlight the past and present research findings on tocopherols’ structural, biosynthesis, and functional properties in plants. Special emphasis is given to their suggested functions in planta, such as cell signaling, hormonal interactions, and coordinated response of tocopherols to other antioxidants under abiotic stresses. Moreover, some important questions about possible new functions of tocopherols will be discussed as future prospects to stimulate further research.
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The nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3) inflammasome is a vital component of many inflammatory responses. Here, we intended to investigate the involvement of ...NLRP3 in lipopolysaccharide (LPS)-induced sepsis-associated acute kidney injury (S-AKI) and explore its mechanisms. For the first time, we validated elevated NLRP3 expression in the renal tissues of S-AKI patients by immunohistochemistry analysis. Through LPS injection in both wild-type and Nlrp3−/− mice, a S-AKI model was developed. It was found that LPS-induced kidney injury, including an abnormal morphology in a histological examination, abnormal renal function in a laboratory examination, and an increase in the expression of AKI biomarkers, was dramatically reversed in Nlrp3-deficient mice. Nlrp3 deletion alleviated renal inflammation, as evidenced by the suppression of the expression of pro-inflammatory cytokines and chemokines. A combinative analysis of RNA sequencing and the FerrDb V2 database showed that Nlrp3 knockout regulated multiple metabolism pathways and ferroptosis in LPS-induced S-AKI. Further qPCR coupled with Prussian blue staining demonstrated that Nlrp3 knockout inhibited murine renal ferroptosis, indicating a novel mechanism involving S-AKI pathogenesis by NLRP3. Altogether, the aforementioned findings suggest that Nlrp3 deficiency alleviates LPS-induced S-AKI by reducing renal inflammation and ferroptosis. Our data highlight that NLRP3 is a potential therapeutic target for S-AKI.
Efficient molecular markers for the selection of rapeseed genetic materials with high seed oil content and ideal fatty acid (FA) composition are preferred by rapeseed breeders. Recently, we reported ...the molecular mechanism of TRANSPARENT TESTA 2 (TT2) in inhibiting seed FA biosynthesis in Arabidopsis. However, evidence showing the association of rapeseed TT2 homologs and seed FA production are still insufficient. In this study, we collected 83 rapeseed (Brassica napus L.) landraces from different geographical backgrounds to conduct association mapping of BnaC.TT2.a in relation to seed coat color and FA biosynthesis. Population background was corrected by 84 pairs of SSR markers that were uniformly distributed among the linkage groups of the Tapidor-Ningyou-7 DH population. A single copy of BnaC.TT2.a for single nucleotide polymorphism (SNP) assay was cloned by a pair of previously reported specific primers. From the analysis of BnaC.TT2.a allelic variations using GLM+Q model, four SNPs on intron 1 of BnaC.TT2.a that were associated with seed FA were discovered. Moreover, an InDel at position 738 on exon 3 of BnaC.TT2.a indicated a change of protein function that was significantly associated with seed coat color, linoleic acid (C18:2), and total FA content. These findings revealed the role of BnaC.TT2.a in regulating the seed color formation and seed FA biosynthesis in rapeseed, thereby suggesting effective molecular markers for rapeseed breeding.
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