A Comprehensive Assessment of Ultraviolet-Radiation-Induced Mutations in Flammulina filiformis Using Whole-Genome Resequencing.

Nucleotide substitutions have played an important role in molecular evolution, and understanding their dynamics would contribute to genetic studies. Related research with defined DNA sequences lasted for decades until whole-genome sequencing arose. UV radiation (UVR) can generate base changes and other genetic variations in a short period of time, so it would be more meaningful to explore mutations caused by UVR from a genomic perspective. The monokaryon enoki strain WT583 was selected as the experimental material in this study because it can spontaneously produce large amounts of oidia on PDA plates, and the monokaryons originating from oidia have the same genotype as their mother monokaryon. After exposure to UV radiation, 100 randomly selected mutants, with WT583 as the reference genome, were sent for genome sequencing. BWA, samtools, and GATK software were employed for SNP calling, and the R package CMplot was used to visualize the distribution of the SNPs on the contigs of the reference genome. Furthermore, a k-mer-based method was used to detect DNA fragment deletion. Moreover, the non-synonymous genes were functionally annotated. A total of 3707 single-base substitutions and 228 tandem mutations were analyzed. The immediate adjacent bases showed different effects on the mutation frequencies of adenine and cytosine. For adenine, the overall effects of the immediate 5'-side and 3'-side bases were T > A > C > G and A > T > G > C, respectively; for cytosine, the overall effects of the immediate 5'-side and 3'-side bases were T > C > A > G and C > T > A > G, respectively. Regarding tandem mutations, the mutation frequencies of double-transition, double-transversion, 3'-side transition, and 5'-side transition were 131, 8, 72, and 17, respectively. Transitions at the 3'-side with a high mutation frequency shared a common feature, where they held transversions at the 5'-side of A→T or T→A without covalent bond changes, suggesting that the sequence context of tandem motifs might be related to their mutation frequency. In total, 3707 mutation sites were non-randomly distributed on the contigs of the reference genome. In addition, pyrimidines at the 3'-side of adenine promoted its transversion frequency, and UVR generated DNA fragment deletions over 200 bp with a low frequency in the enoki genome. The functional annotation of the genes with non-synonymous mutation indicated that UVR could produce abundant mutations in a short period of time.

A pilot study of contrast-enhanced electrical impedance tomography for real-time imaging of cerebral perfusion.

Background: Real-time detection of cerebral blood perfusion can prevent adverse reactions, such as cerebral infarction and neuronal apoptosis. Our previous clinical trial have shown that the infusion of therapeutic fluid can significantly change the impedance distribution in the brain. However, whether this alteration implicates the cerebral blood perfusion remains unclear. To explore the feasibility of monitoring cerebral blood perfusion, the present pilot study established a novel cerebral contrast-enhanced electrical impedance tomography (C-EIT) technique. Materials and methods: Rabbits were randomly divided into two groups: the internal carotid artery non-occlusion (ICAN) and internal carotid artery occlusion (ICAO) groups. Both of groups were injected with glucose, an electrical impedance-enhanced contrast agent, through the right internal carotid artery under EIT monitoring. The C-EIT reconstruction images of the rabbits brain were analyzed according to the collected raw data. The paired and independent t-tests were used to analyze the remodeled impedance values of the left and right cerebral hemispheres within and between studied groups, respectively. Moreover, pathological examinations of brain were performed immediately after C-EIT monitoring. Results: According to the reconstructed images, the impedance value of the left cerebral hemisphere in the ICAN group did not change significantly, whereas the impedance value of the right cerebral hemisphere gradually increased, reaching a peak at approximately 10 s followed by gradually decreased. In the ICAO group, the impedance values of both cerebral hemispheres increased gradually and then began to decrease after reaching the peak value. According to the paired t-test, there was a significant difference (P < 0.001) in the remodeling impedance values between the left and right hemispheres in the ICAN group, and there was also a significant difference (P < 0.001) in the ICAO group. According to the independent t-test, there was a significant difference (P < 0.001) of the left hemispheres between the ICAN and ICAO groups. Conclusion: The cerebral C-EIT proposed in this pilot study can reflect cerebral blood perfusion. This method has potential in various applications in the brain in the future, including disease progression monitoring, collateral circulation judgment, tumor-specific detection, and brain function research.

Bioinformatics Analysis Combined With Experiments Predicts PUDP as a Potential Prognostic Biomarker for Hepatocellular Carcinoma Through Its Interaction With Tumor Microenvironment.

Hepatocellular carcinoma (HCC) is one of the deadliest tumors in the world and is notorious for poor prognosis. There is mounting evidence that pseudouridine performs key functions in the initiation and progression of several cancers. A previous study demonstrated that Pseudouridine 5'-phosphatase (PUDP) may be a novel prognostic biomarker in colorectal cancer. However, in the past, we have paid little attention to PUDP and we are still not clear about its function and role in cancer. In this study, a pan-cancer analysis of PUDP expression and prognosis was performed firstly using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) data and we found that PUDP may be a potential oncogene for HCC. Then the most potential upstream microRNA contributing to PUDP was identified as let-7c-5p through expression analysis, correlation analysis, and survival analysis. Subsequently, the result of single cell RNA sequencing (scRNA-seq) demonstrated that PUDP was significantly highly expressed on malignant cells. In addition, there are significantly positive correlations between PUDP and tumor immune cell infiltration, biomarkers of immune cells, and immune checkpoint expression, especially with tumor-promoting immune cells such as T cell regulatory (Treg), Myeloid-derived suppressor cell (MDSC), cancer-associated fibroblast (CAF). Moreover, we found the methylation level of three loci was positively correlated with PUDP expression and four loci were negatively correlated. 15 pairs of HCC and normal adjacent tissues from HCC patients who were treated at our center were used to verify the results of the bioinformatics analysis and the results of experiments are similar to the bioinformatics analysis. Our study demonstrated that HCC patients with high PUDP expression are less likely to benefit from immunotherapy, and in addition, we explored the relationship between PUDP and anticancer drugs. Finally, we explored the clinical relevance of PUDP, identified PUDP as an independent risk factor for HCC patients and constructed a prognostic model, used International Cancer Genome Consortium (ICGC) data to do external validation. Collectively, our study demonstrated that high expression of PUDP suggested a poor prognosis and low response to immunotherapy, providing new insight into the treatment and prognosis of HCC.

Libertellenone H, a Natural Pimarane Diterpenoid, Inhibits Thioredoxin System and Induces ROS-Mediated Apoptosis in Human Pancreatic Cancer Cells.

Libertellenone H (LH), a marine-derived pimarane diterpenoid isolated from arctic fungus Eutypella sp. D-1, has shown effective cytotoxicity on a range of cancer cells. The present study is to explore the anticancer effect of LH on human pancreatic cancer cells and to investigate the intracellular molecular target and underlying mechanism. As shown, LH exhibited anticancer activity in human pancreatic cancer cells by promoting cell apoptosis. Mechanistic studies suggested that LH-induced reactive oxygen species (ROS) accumulation was responsible for apoptosis as antioxidant N-acetylcysteine (NAC) and antioxidant enzyme superoxide dismutase (SOD) antagonized the inhibitory effect of LH. Zymologic testing demonstrated that LH inhibited Trx system but had little effect on the glutathione reductase and glutaredoxin. Mass spectrometry (MS) analysis revealed that the mechanism of action was based on the direct conjugation of LH to the Cys32/Cys35 residue of Trx1 and Sec498 of TrxR, leading to a decrease in the cellular level of glutathione (GSH) and activation of downstream ASK1/JNK signaling pathway. Taken together, our findings revealed LH was a marine derived inhibitor of Trx system and an anticancer candidate.

Hyperproduction of exopolysaccharides by submerged mycelial culture of Ganoderma lucidum using a solid seed grown in fine-powder of wheat bran and in vitro evaluation of the antioxidant activity of the exopolysaccharides produced.

To facilitate Ganoderma lucidum submerged culture and obtain high productivity, a fine powder of wheat bran was used to grow the fungus for solid-state fermentation and as solid seed for its submerged cultures. The results indicated that the optimal inoculum size was low, being 0.75 g in 250 mL-sized flasks containing 80 mL medium. The maximal exopolysaccharide concentration and biomass produced was 0.74 and 14.71 g/L, respectively, which is considerably higher than that obtained with the commonly used mycelial pellet liquid seed (0.47 and 8.56 g/L, respectively). The EPS and biomass productivity of the solid seed cultures decreased only slightly, even after a 6-month storage period. EPS produced showed higher antioxidant activity compared with that produced in the liquid seed cultures. The developed solid seed can serve as a ready-to-use inoculum for long-term use in G. lucidum submerged culture for the hyperproduction of highly bioactive EPS and biomass.

Construction of multifunctional porous silica nanocarriers for pH/enzyme-responsive drug release.

pH/enzyme-responsive nanocarriers based on porous silica (pSiO2) nanospheres (NSs) were developed for controlled release of drug. The pSiO2 NSs present uniform spheres and have an average diameter of 100nm. The pSiO2 NSs with high specific surface area (835m2·g-1) and the pore volume (1.24cm3·g-1) are suitable for drug loading and the loading capacity reaches to 29% for amoxicillin (AMX) model drug. In this system, protocatechuic acid (PCA) and L-glutamic acid (Glu) as linkers were grafting onto the surface of pSiO2 NSs to conjugate the capping lids. Acid-decomposable ZnO quantum dots (QDs) were introduced to block the partial pores of pSiO2 via amido bonds, which could act as gates and fluorescence probes. To minimize the premature release, hyaluronic acid (HA) was further coating on the outer surface of pSiO2, which would be degraded by over-expressed hyaluronidase (Hyal-1) in the tumor microenvironment. The controlled release of the drug from the ZnO/HA-gated delivery system was realized by the acidic dissolution of ZnO QDs and enzymatic hydrolysis of HA. The obtained ZnO/HA-gated pSiO2 delivery system would achieve minimized premature release and responsive release under a physiological environment.