Prognostic implication and immunotherapy response prediction of a novel ubiquitination-related gene signature in liver cancer.

HCC, also known as hepatocellular carcinoma, is a frequently occurring form of cancer with an unfavorable prognosis. This research constructed a prognostic signature related to ubiquitination and investigated its correlation with the response to immunotherapy in HCC. The Molecular Signatures Database provided a compilation of genes associated with ubiquitination. A gene signature related to ubiquitination was obtained through Cox regression using the Least Absolute Shrinkage and Selection Operator method. The genetic factors CPY26B1, MCM10, SPINK4, and TRIM54 notably impacted the outcomes of HCC. The patients were divided into two groups: one group had a high risk of poor survival while the other had a low risk but a greater chance of controlling HCC progression. Both univariate and multivariate analyses using Cox regression found the risk score to be an independent predictor of HCC prognosis. Gene set enrichment analysis (GSEA) indicated enrichment in cell cycle and cancer-related microRNAs in high-risk groups. The tumor microenvironment (TME), response to immunotherapy, and effectiveness of chemotherapy medications positively correlated with the risk score. In the high-risk group, erlotinib showed higher IC50 values compared to the low-risk group which exhibited higher IC50 values for VX-11e, AKT inhibitor VIII, AT-7519, BMS345541, Bortezomib, CP466722, FMK, and JNK-9L. The results of RT-qPCR revealed that the expression of four UEGs was higher in tumor tissue as compared to normal tissue. Based on the genes that were expressed differently and associated with ubiquitination-related tumor categorization, we have developed a pattern of four genes and a strong nomogram that can predict the prognosis of HCC, which could be useful in identifying and managing HCC.

Dominance complementation of parental heading date alleles of Hd1, Ghd7, DTH8, and PRR37 confers transgressive late maturation in hybrid rice.

Rice (Oryza sativa L.) is a short-day plant whose heading date is largely determined by photoperiod sensitivity (PS). Many parental lines used in hybrid rice breeding have weak PS, but their F1 progenies have strong PS and exhibit an undesirable transgressive late-maturing phenotype. However, the genetic basis for this phenomenon is unclear. Therefore, effective methods are needed for selecting parents to create F1 hybrid varieties with the desired PS. In this study, we used bulked segregant analysis with F1 Ningyou 1179 (strong PS) and its F2 population, and through analyzing both parental haplotypes and PS data for 918 hybrid rice varieties, to identify the genetic basis of transgressive late maturation which is dependent on dominance complementation effects of Hd1, Ghd7, DTH8, and PRR37 from both parents rather than from a single parental genotype. We designed a molecular marker-assisted selection system to identify the genotypes of Hd1, Ghd7, DTH8, and PRR37 in parental lines to predict PS in F1 plants prior to crossing. Furthermore, we used CRISPR/Cas9 technique to knock out Hd1 in Ning A (sterile line) and Ning B (maintainer line) and obtained an hd1-NY material with weak PS while retaining the elite agronomic traits of NY. Our findings clarified the genetic basis of transgressive late maturation in hybrid rice and developed effective methods for parental selection and gene editing to facilitate the breeding of hybrid varieties with the desired PS for improving their adaptability.

A novel electron transfer flavoprotein dehydrogenase (ETFDH) gene mutation identified in a newborn with glutaric acidemia type II: a case report of a Chinese family.

BACKGROUND: Glutaric acidemia type II (GA II) or multiple acyl-CoA dehydrogenase deficiency (MADD, OMIM 231680) is an inherited autosomal recessive disease affecting fatty acid, amino acid and choline metabolism, due to mutations in one of three genes namely, electron transfer flavoprotein alpha-subunit, ETFA, electron transfer flavoprotein ß-subunit, ETFB and electron transfer flavoprotein dehydrogenase, ETFDH. Currently, few studies have reported genetic profiling of neonatal-onset GA II. This study aimed to identify the genetic mutations in a Chinese family with GA II. CASE PRESENTATION: We reported a case of GA II with purulent meningitis and septicemia and identified a novel ETFDH gene mutation in a female infant. The patient developed an episode of hypoglycemia and hypotonicity on the postnatal first day. Laboratory investigations revealed elevations of multiple acylcarnitines indicating glutaric acidemia type II in newborn screening analysis. Urinary organic acids were evaluated for the confirmation and revealed a high glutaric acid excretion. Genetic analysis revealed two mutations in the ETFDH gene (c.623_626 del / c. 1399G > C), which were considered to be the etiology for the disease. The novel mutation c.623_626 del was identified in the proband infant and her father, her mother was carriers of the mutation c.1399G > C. CONCLUSIONS: A novel variant (c.623_626 del) and a previously reported missense (c.1399G > C) in the ETFDH gene have been identified in the family. The two variants of ETFDH gene identified probably underlie the pathogenesis of Glutaric acidemia type II in this family, and also enlarge ETFDH genotype-phenotype correlations spectrum.

Bone-derived biochar and magnetic biochar for effective removal of fluoride in groundwater: Effects of synthesis method and coexisting chromium.

The presence of fluoride in groundwater in excess of 1.5 mg L-1 is a major environmental health concern, and biochar is a promising low-cost adsorbent for the treatment of such water. In the present study, pristine and magnetic biochars were synthesized by peanut hull and bovine bone for the adsorption of fluoride. The biochars were systematically characterized by SEM-EDS, BET, XRD, VSM, FT-IR, and XPS. The experiment results showed that the magnetic biochar prepared by soaking biomass in FeCl3 solution and then pyrolyzing ("prepyrolysis") had a higher adsorption capacity than that prepared by mixing pristine biochar with Fe2+ /Fe3+ solution and then treating with NaOH ("postpyrolysis"). The bone-derived biochar and magnetic biochar exhibited high adsorption capacity of fluoride (>5 mg g-1 ) due to the presence of hydroxyapatite (HAP) and γ-Fe2 O3 . The 0.1 M NaOH solution could be optimal desorption agent, and the adsorption-desorption experiments indicated the bone biochars maintained the reasonable adsorption capacity after several cycles. Moreover, the coexisting Cr(VI) and fluoride could be removed simultaneously by bone-derived biochars. It is suggested that bovine bone-derived pristine and magnetic biochars can be used as preferential adsorbents for fluoride removal from contaminated groundwater. PRACTITIONER POINTS: Bone-derived pristine and magnetic biochars exhibit high adsorption capacity for fluoride in weakly alkaline solution. The presence of hydroxyapatite and γ-Fe2 O3 in bone-derived biochars plays an important role for fluoride adsorption. Magnetic biochars prepared by soaking biomass in FeCl3 solution and then pyrolyzing ("prepyrolysis") perform better. The coexisting Cr(VI) and fluoride can be simultaneously removed in groundwater by bone biochars.

Adsorption and reductive degradation of Cr(VI) and TCE by a simply synthesized zero valent iron magnetic biochar.

To address inorganic and organic contaminants in the environment, economic new adsorbents are required. Here we test magnetic biochar for efficient capture of the typical pollutants Cr(VI) and trichloroethylene (TCE) from solution. We used a simple synthesis using 2M FeCl3 solution and peanut hull biomass to prepare magnetic ZVI biochar at alternate pyrolysis temperatures between 650 and 800 °C. The physicochemical character of the biochars were assessed using X-ray diffraction (XRD) and the Brunauer-Emmett-Teller (BET) method for surface area. The magnetic ZVI biochars were highly effective in the removal of Cr(VI) and TCE. The most effective magnetic biochar produced at 800 °C was further examined using scanning electron microscopy (SEM), revealing a high and even loading of ZVI. After sorption the same magnetic biochar was examined by X-ray photoelectron spectroscopy (XPS) to ascertain the underlying mechanisms. The dependence of Cr(VI) capture on solution pH was also examined. Our interpretation suggests that when pH < pHzpc (2.5) electrostatic attraction and redox reactions dominated the adsorption of Cr(VI). When pH > pHzpc the removal process was controlled mainly by redox reaction and substitution of chromate anions for hydroxyl (OH) groups. Capture of TCE in contrast involved hydrophobic partitioning, pore-filling and reductive degradation. Overall our results suggest that simple synthesis of magnetic ZVI biochar could offer an economic and effective option to address water contamination issues.

[Involvement of coronin-1 in foam cell formation of macrophages induced by mycolic acid and its mechanism].

OBJECTIVE: To study the correlation of coronin-1 and mycolic acid (MA)-induced foam cell formation of macrophages and explore its possible mechanism. METHODS: According to the difference of coronin-1 expression level, the experiment included three types of cells: RAW264.7-Cor.Plus, RAW264.7 and RAW264.7-Cor.Minus. After the cells were treated with the polystyrene microspheres coated with 100 µg/mL MA for 24 hours, total proteins were extracted and the level of coronin-1 in each group was detected by Western blotting. With the microspheres coated with 0, 25, 50, 75 and 100 µg/mL MA as phagocytic particles, the cells were swallowed for 24, 48, 72 hours, 5 and 8 days before and after the treatment with 2 µmol/L cytochalasin D (ctyD), and the levels of total cholesterol (TC) and free cholesterol (FC) were tested by TC enzyme kit and FC enzyme kit, respectively; then the cholesterol ester (CE) and the CE/TC ratio were used to quantitatively evaluate the level of foam cell formation. The ctyD-treated cells (RAW264.7-ctyD, RAW264.7-ctyD-MA) and their control groups were stained with FITC-phalloidin, and then the percentage of F-actin rearrangement was calculated. RESULTS: After MA induction, the coronin-1 level of the three experimental groups were significantly higher than that of the corresponding control groups, and there was also obvious difference between the three experimental groups (RAW264.7-Cor.Plus>RAW264.7>RAW264.7-Cor.Minus). The level of foam cell formation of macrophages in each group with different coronin-1 level was positively correlated with the MA coating concentration and its phagocytic time. The highest coronin-1 expression group (RAW264.7-Cor.Plus) had the highest foam cell formation level, and the lowest coronin-1 expression group (RAW264.7-Cor.Minus) had the lowest foam cell formation level. The inhibition of F-actin by ctyD significantly decreased the foam cell formation induced by MA, but the inhibition of F-actin had no significant impact on the positive correlation between coronin-1 and the foam cell formation induced by MA. After phalloidin staining, the F-actin rearrangement rate of MA-treated cells was significantly higher than that of non-MA control cells. CONCLUSION: MA could induce the expression of coronin-1 of macrophage, and the coronin-1 level was positively correlated with the foam cell formation induced by MA. F-actin was involved in the process of lipid accumulation in MA-treated macrophages, but the F-actin was not the key or the only way in coronin-1 regulating the foam cell formation induced by MA.

Atoh8, a bHLH transcription factor, is required for the development of retina and skeletal muscle in zebrafish.

BACKGROUND: Math6/atoh8, a bHLH transcription factor, is thought to be indispensable for early embryonic development and likely has important roles in vertebrate tissue-specific differentiation. However, the function of Atoh8 during early development is not clear because homozygous knockout causes embryonic lethality in mice. We have examined the effects of the atoh8 gene on the differentiation of retina and skeletal muscle during early development in zebrafish. RESULTS: We isolated a Math6 homologue in zebrafish, designated as zebrafish atoh8. Whole -mount in situ hybridization analysis showed that zebrafish atoh8 is dynamically expressed mainly in developing retina and skeletal muscle. Atoh8-MO knock-down resulted in reduced eye size with disorganization of retinal lamination. The reduction of atoh8 function also affected the arrangement of paraxial cells and differentiated muscle fibers during somite morphogenesis. CONCLUSION: Our results show that Atoh8 is an important regulator for the development of both the retina and skeletal muscles necessary for neural retinal cell and myogenic differentiation during zebrafish embryogenesis.

Identification and developmental expression of Dec2 in zebrafish.

The involvement of Dec2, a member of the basic helix-loop-helix (bHLH) family, in cellular differentiation, hypoxia response, and circadian regulation has been investigated. Here we report the previously unknown spatiotemporal expression of Dec2 in zebrafish embryogenesis. Dec2 is dynamically expressed in zebrafish pineal gland, tract of the postoptic commissure, brain, notochord, heart, common cardinal vein (CCV), axial vein, pronephric duct, swim bladder, and early somites during embryogenesis, which implies that Dec2 is involved in zebrafish central nervous system development, cardiogenesis, and internal organs and somites formation. The embryonic expression patterns of zebrafish Dec2 and its homolog Dec1 partially overlap, but are distinct from each other. The Dec2 expression level was lower than that of Dec1 during zebrafish embryogenesis. Although Dec1 also contributed to zebrafish somites formation, cardiogenesis, and internal organs and central nervous system development, the two Dec genes were not likely to be simply redundant during zebrafish embryogenesis. Our results imply that Dec2, like its homolog Dec1, is involved in zebrafish cardiogenesis, central nervous system development, and internal organs and somites formation with distinct developmental roles.

U6 promoter-driven siRNA injection has nonspecific effects in zebrafish.

RNA interference (RNAi) is a posttranscriptional gene silencing mechanism triggered by double-stranded RNA (dsRNA), which causes degradation of homologous mRNAs. RNAi has been observed in a wide range of eukaryotes, including fungi, plants and animals. In vertebrates, long dsRNA activates the interferon response and yields nonspecific degradation of mRNA. In contrast, small interference RNA (siRNA) duplexes with a length of 21-23 nucleotides trigger specific gene silencing and thus are widely used in gene function studies. The use of siRNA for gene silencing in zebrafish has rarely been reported. In this report, we studied mammalian U6 promoter-driven siRNA-mediated RNA interference in zebrafish. The well characterized genes Myf5, Dlg3 and Nacre were selected as targets. Two to four target siRNAs were synthesized with incorporation of the U6 promoter. Constructs were introduced into early zebrafish embryos through microinjection, followed by in situ hybridization and embryonic development was monitored to determine whether U6 promoter-driven siRNAs could efficiently suppress specific gene expression. We showed that these siRNAs could partially suppress endogenous gene expression and that the siRNA efficiency varied at different targeted positions. However, the U6 promoter-driven siRNAs may also have induced nonspecific gene suppression (off-target effects). It appears that, despite the findings of previous reports, the current methodology of siRNA interference is not practical for studying gene function during early zebrafish development.