Predicting locus-specific DNA methylation levels in cancer and paracancer tissues.

Aim: To predict base-resolution DNA methylation in cancerous and paracancerous tissues. Material & methods: We collected six cancer DNA methylation datasets from The Cancer Genome Atlas and five cancer datasets from Gene Expression Omnibus and established machine learning models using paired cancerous and paracancerous tissues. Tenfold cross-validation and independent validation were performed to demonstrate the effectiveness of the proposed method. Results: The developed cross-tissue prediction models can substantially increase the accuracy at more than 68% of CpG sites and contribute to enhancing the statistical power of differential methylation analyses. An XGBoost model leveraging multiple correlating CpGs may elevate the prediction accuracy. Conclusion: This study provides a powerful tool for DNA methylation analysis and has the potential to gain new insights into cancer research from epigenetics.

Interfacial Strengthening and Self-Monitoring in Carbon Fiber-Reinforced Composites via Carbon Nanotube-Based Damage Sensors.

Carbon fiber-reinforced polymers are important constituents of aerospace materials. However, due to the inert surface of CFs, their interfacial property is relatively weak, which severely hinders their practical applications. Here, we deposited multi-walled carbon nanotubes (MWCNTs) along with a coupling agent on the surface of carbon fiber to improve the interfacial properties of the carbon fiber/resin. Via a simple dip-coating method, the MWCNTs were uniformly distributed on the CF surface with the assistance of the pre-coated coupling agent. The interfacial shear strength between the fiber and the matrix was significant enhanceed when the CF was loaded with the coupling agent and the MWCNTs. In addition, the MWCNTs were used as sensors to in-situ monitor the interfacial state in order to elucidate the interfacial strengthening mechanism. It revealed that the collaborative contribution of the coupling agent and the MWCNTs in the interphase region is the key to the high interfacial strength.

Causal Associations of Anthropometric Measurements With Fracture Risk and Bone Mineral Density: A Mendelian Randomization Study.

Uncovering additional causal clinical traits and exposure variables is important when studying osteoporosis mechanisms and for the prevention of osteoporosis. Until recently, the causal relationship between anthropometric measurements and osteoporosis had not been fully revealed. In the present study, we utilized several state-of-the-art Mendelian randomization (MR) methods to investigate whether height, body mass index (BMI), waist-to-hip ratio (WHR), hip circumference (HC), and waist circumference (WC) are causally associated with two major characteristics of osteoporosis, bone mineral density (BMD) and fractures. Genomewide significant (p ≤ 5 × 10-8 ) single-nucleotide polymorphisms (SNPs) associated with the five anthropometric variables were obtained from previous large-scale genomewide association studies (GWAS) and were utilized as instrumental variables. Summary-level data of estimated bone mineral density (eBMD) and fractures were obtained from a large-scale UK Biobank GWAS. Of the MR methods utilized, the inverse-variance weighted method was the primary method used for analysis, and the weighted-median, MR-Egger, mode-based estimate, and MR pleiotropy residual sum and outlier methods were utilized for sensitivity analyses. The results of the present study indicated that each increase in height equal to a single standard deviation (SD) was associated with a 9.9% increase in risk of fracture (odds ratio [OR] = 1.099; 95% confidence interval [CI] 1.067-1.133; p = 8.793 × 10-10 ) and a 0.080 SD decrease of estimated bone mineral density (95% CI -0.106-(-0.054); p = 2.322 × 10-9 ). We also found that BMI was causally associated with eBMD (beta = 0.129, 95% CI 0.065-0.194; p = 8.113 × 10-5 ) but not associated with fracture. The WHR adjusted for BMI, HC adjusted for BMI, and WC adjusted for BMI were not found to be related to fracture occurrence or eBMD. In conclusion, the present study provided genetic evidence for certain causal relationships between anthropometric measurements and bone mineral density or fracture risk. © 2021 American Society for Bone and Mineral Research (ASBMR).

Tamoxifen activates Nrf2-dependent SQSTM1 transcription to promote endometrial hyperplasia.

Long-term application of Tamoxifen (TAM) is usually recommended for hormone receptor positive breast cancer patients. Unfortunately, TAM will inevitably increase the incidence of endometrial hyperplasia even endometrial cancer. Despite of substantial investigations, no effective approaches to prevent TAM-induced endometrial carcinogenesis have been acknowledged. In this study, we found that inhibition of Nrf2 could be valuable to prevent TAM-induced endometrial hyperplasia. Upon TAM treatment, the mRNA and protein expression of autophagy adaptor SQSTM1 was specifically increased in endometrial cells but not breast cancer cells. Knocking-down of SQSTM1 expression retarded TAM-promoted growth of endometrial cancer cells. TAM stimulated SQSTM1 transcription specifically in endometrial cells by enhancing phosphorylation and nuclear translocation of Nrf2. Indeed, the expression of Nrf2 and SQSTM1 were positively correlated in primary endometrial tissues. In rats with TAM-induced endometrial hyperplasia, both Nrf2 and SQSTM1 expression were increased. Nrf2 inhibitor brusatol effectively attenuated TAM-induced SQSTM1 upregulation and endometrial hyperplasia. The kinase of Nrf2, PRKCD, was activated by TAM. Once PRKCD was depleted, TAM failed to promote Nrf2 phosphorylation and SQSTM1 expression. In summary, TAM stimulated Nrf2-dependent SQSTM1 transcription to promote endometrial hyperplasia by activating PRKCD. Therefore, blocking PRKCD-Nrf2-SQSTM1 signaling could be useful to prevent TAM-induced endometrial hyperplasia.

Dynamic QTL analysis of linolenic acid content in different developmental stages of soybean seed.

Linolenic acid (LN) in soybean (Glycine max L. Merr.) seed mainly contributes to the undesirable odors and flavors commonly associated with poor oil quality. LN deposition at various stages of soybean seed development had not been reported by 2010. The objects of this study were (1) to identify and measure quantitative trait loci (QTL) underlying LN content and (2) to estimate the QTL effects expressed from earlier seed developmental stages to drying seed of soybean. One hundred and twenty-five F(5:8) and F(5:9) recombinant inbred lines derived from the cross of soybean cultivars 'Hefeng 25' and 'Dongnong L5' were used for the identification of QTL underlying LN content from the 37 day (D) to 86D stages after flowering, at Harbin in 2008 and 2009. QTL × Environment interactions (QE) effects were evaluated using a mixed genetic model (Zhu in J Zhejiang Univ (Natural Science) 33:327-335, 1999). Twelve unconditional QTL and 12 conditional QTL associated with LN content were identified at different developmental stages. Most of the QTL explained <10% of phenotypic variation of LN content. Unconditional QTL QLNF-1, QLNC2-1, QLND1b-1, QLNA2-1 and QLNH-1 influenced LN content across different development stages and environments. Conditional QTL QLNF-1, QLNC2-1 and QLNH-1 were identified in multiple developmental stages and environments. Conditional and unconditional QTL clustered in neighboring intervals on linkage groups A2, C2 and D1b. Ten QTL with conditional additive main effects (a) and/or conditional additive × environment interaction effects (ae) at specific developmental stage were identified on nine linkage groups. Of them, six QTL only possessed additive main effects and seven QTL had significant ae effects in different developmental stages. A total of 13 epistatic pairwise QTL were identified by conditional mapping in different developmental stages. Two pairs of QTL only showed aa effects and five pairs of QTL only showed aae effects at different developmental stages. QTL with aa effects, as well as their environmental interaction effects, appeared to vary at different developmental stages.

Pyramided QTL underlying tolerance to Phytophthora root rot in mega-environments from soybean cultivars 'Conrad' and 'Hefeng 25'.

Phytophthora root rot (PRR) of soybean (Glycine max (L.) Merr.) is the second most important cause of yield loss by disease in North America, surpassed only by soybean cyst nematode (Wrather et al. in Can J Plant Pathol 23:115-121, 2001). Tolerance can provide economically useful disease control, conditioning partial resistance of soybean to PRR. The aims of this study were to identify new quantitative trait loci (QTL) underlying tolerance to PRR, and to evaluate the effects of pyramided or stacked loci on the level of tolerance. A North American cultivar 'Conrad' (tolerant to PRR) was crossed with a northeastern China cultivar 'Hefeng 25' (tolerant to PRR). Through single-seed descent, 140 F2:5 and F2:6 recombinant inbred lines were advanced. A total of 164 simple sequence repeat (SSR) markers were used to construct a genetic linkage map. The percentage of seedling death was measured over 2 years (2007 and 2008) in the field at four naturally infested locations in Canada and China following additional soil infestation and in the greenhouse following inoculation with Phytophthora sojae isolate. A total of eight QTL underlying tolerance to PRR were identified, located in five linkage groups (F, D1b+w, A2, B1, and C2). The phenotypic variation contributed by the loci ranged from 4.24 to 27.98%. QPRR-1 (anchored in the interval of SSR markers Satt325 and Satt343 of LG F), QPRR-2 (anchored in the interval of Satt005 and Satt600 of LG D1b+w), and QPRR-3 (anchored in the interval of Satt579 and Sat_089 of LG D1b+w) derived their beneficial allele from 'Conrad'. They were located at chromosomal locations known to underlie PRR tolerance in diverse germplasm. Five QTL that derived beneficial alleles from 'Hefeng 25' were identified. The QTL (QPRR-1 to QPRR-7) that were detected across at least three environments were selected for loci stacking and to analyze the relationship between number of tolerance loci and disease loss percentage. The accumulation of tolerance loci was positively correlated with decreases in disease loss percentage. The pyramid of loci underlying tolerance to PRR provided germplasm useful for crop improvement by marker-assisted selection and may provide durable cultivar tolerance against the PRR disease.

[Cloning, expression and the characterization of beta-amylase from a Bacillus megaterium WS06].

A beta-amylase gene (amyG) was cloned from a Bacillus megaterium WS06 and expressed in the Escherichia coli. Nucleotide sequence anlysis showed the amyG gene is composed of 1638 bp (545 amino acid residues with a Mr of 60.194 kD). The AmyG shows 94.5% sequence homologies with beta-amylase from Bacillus megaterium DSM319 and presents a normal beta-amylase primary structure, constituted by three parts: the N-terminal signal sequence, the catalytic domain and the C-terminal starch binding domains. The deduced amino acid sequence revealed that several highly conserved regions of the glycosylhydrolase family 14. The amyG gene was overexpressed using the pET21a vector and Escherichia coli BL21(DE3). The recombinant enzyme was purified 7.4 fold to electrophoretic homogeneity and had a Mr of 57 kD (by SDS-PAGE). The enzyme was optimally active at pH 7.0 and 60 degrees C and showed stability at the temperature below 60 degrees C. This enzyme efficiently hydrolyzed starch to yield maltose from non-reducing chain ends by exo-cleavage mode.

[Clinicopathologic and prognostic study of pediatric immature teratoma].

OBJECTIVE: To study the clinicopathologic features and biologic behavior of pediatric immature teratoma. METHODS: The clinical data, pathologic features, immunohistochemical findings (for cyclin D1, P27 and Ki-67) and follow-up information of 39 cases of pediatric immature teratoma were analyzed. RESULTS: Amongst the 39 cases studied, 12 arose in the sacrococcygeal region, 12 in testis, 5 in retroperitoneum, 4 in ovary, 4 in abdomen and 2 in mediastinum. Histologically, 16 cases were of grade 1, 8 cases of grade 2 and 15 cases of grade 3. Seven of the cases contained foci of yolk sac tumor. Immature neuroepithelial features used in histologic grading included the presence of primitive neural tubules, immature rosettes, undifferentiated neuroblastoma cells and primitive neuroectodermal structures. Immunohistochemical study showed that cyclin D1 was positive in 3 cases of grade 1 tumors, 4 cases of grade 2 tumors and 9 cases of grade 3 tumors. The positivity rates for p27 were 8, 3 and 6 cases respectively, while those for Ki-67 were 3, 4 and 13 cases respectively. Follow-up data were available in 30 cases. Three of them, including 2 cases with histologic grade 3 (with or without yolk sac tumor component), recurred after operation. CONCLUSIONS: The expression of cyclin D1 and Ki-67 is a useful adjunct in histologic grading. On the other hand, p27 overexpression shows little correlation with tumor grade. The prognosis of immature teratoma in children is different from that in adults. Sacrococcygeal immature teratoma occurring in patients younger than 1 year old and with low histologic grade do not require postoperative chemotherapy if the tumor is completely excised. Similarly, for testicular immature teratoma occurring in patients below 1 year of age, regardless of tumor grading, need no adjunctive therapy. On the other hand, ovarian immature teratoma with high histologic grade requires postoperative chemotherapy, regardless of age of the patients. The presence of microscopic foci of yolk sac tumor is a useful predictor of recurrence in pediatric immature teratoma.

Separation and determination of phthalates by micellar electrokinetic chromatography.

A method has been developed for the separation and determination of dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), di-(2-ethylhexyl) phthalate (DEHP) and di-n-octyl phthalate (DnOP) by micellar electrokinetic chromatography (MEKC). The baseline separation of phthalates was achieved by using a buffer of 100 mM sodium cholate, 50 mM borate and 15% methanol (pH 8.5). The optimized MEKC method was used to quantify the concentrations of phthalates in 11 soil samples from different regions of China. The contents of DEP, DBP and DEHP in soils were ranged 0-0.42, 0-1.43, and 0.24-2.35 mg/kg, respectively, and no DMP and DnOP was detected. The limits of detection for DMP, DEP, DBP, DEHP, and DnOP were found to be 0.050, 0.051, 0.052, 0.054, and 0.063 mg/kg, respectively. The results obtained by the MEKC method were compared with those obtained by gas chromatography with flame ionization detector (GC-FID), and a good agreement was achieved.

Separation and determination of phospholipids in plant seeds by nonaqueous capillary electrophoresis.

A method has been developed for the separation and determination of phospholipids by nonaqueous capillary electrophoresis in a separation medium of acetonitrile-2-proponol (3:2, v/v), 0.3% acetic acid and 60 mM ammonium acetate. To optimize the separation conditions, the composition of separation medium including alcohols, acetic acid, n-hexane and ammonium acetate was studied. The solvation interaction and ion-dipole interaction were also investigated. The contents of phospholipids in soybean, sunflower, peanut, apricot kernel, filbert and walnut were determined by the recommended method. The results obtained by the nonaqueous capillary electrophoreses were in good agreement with those determined by micellar electrokinetic chromatography.

[Cloning and expression of the alpha-amylase gene from a Bacillus sp. WS06, and characterization of the enzyme].

A Bacillus sp. WS06, which produces an extracellular alpha-amylase, was isolated from the cecum in a piglet. An amyF gene from this Bacillus strain was cloned and its nucleotide sequence was determined. An open reading frame composed of 1581 bases, which encodes 526 amino acid residues was found. The amyF gene shows high sequence homologies with other microbial amylase genes, such as Bacillus megaterium and Bacillus polymyxa (93% and 53% identity). The deduced amino acid sequence revealed that four highly conserved regions of the alpha-amylase family. The amyF gene was overepressed using the pET21a vector and Escherichia coli BL21 (DE3). The recombinant enzyme was purified 22.2 fold to electrophoretic homogeneity and had a molecular mass of 57kD (by SDS-PAGE). The enzyme was optimally active at pH 7 and 55 approximately 60 degrees C and showed stability at the temperature below 55 degrees C. This enzyme efficiently hydrolyzed various types of starch to yield a series of malto-oligosaccharides by endo-cleavage mode.

Responses of antioxidative enzymes to accumulation of copper in a copper hyperaccumulator of Commoelina communis.

Discovery of a copper hyperaccumulator is very important for phytoremediation of copper-contaminated soil. In the present study a link was established between the copper accumulation in hyperaccumulator and that in nonaccumulator species of Commelina communis and its responses of antioxidative enzymes, including superoxide dismutase, guaiacol peroxidase, and ascorbate peroxidase. It was verified that copper exerted little physiological damage to copper hyperaccumulator species of Commelina communis at copper accumulation of >1,000 microg/g in dry leaf tissue. However, in nonaccumulator species of Commelina communis superoxide dismutase, guaiacol peroxidase, and ascorbate peroxidase were activated, and malondialdehyde content was increased, which were symptoms of physiological damage by copper intoxication. Therefore, antioxidative enzymes can be used as an indicator of copper toxicity before the visible symptoms can be observed.

[A strategy for targeting gene therapy against cancer mediated by epidermal growth factor receptor].

OBJECTIVE: To establish a protocol for the targeting gene therapy against cancer with rich epidermal growth factor receptor (EGFR). METHODS: A recombinant pcDNA3.1-PE III mut was constructed and combined with a non-viral vector, a fusion protein histone H1, epidermal growth factor C-loop previously expressed by us, to be a protein-DNA complex in vitro. Using the complex to treat BT-325 and Hela cancer cells with EGFR and JK cells without EGFR. The killing rates of the cells was calculated after 48 h of incubation at 37 degrees C. RESULTS: To BT-325 and Hela cells, the killing rates were 46.03% and 48.12% respectively. To JK cells, the complex had no killing function. CONCLUSION: The protocol for targeting gene therapy against cancer with EGFR has been established successfully.

[Production of a novel heparinase from Sphingobacterium sp].

The novel heparinase-producing bacterial strain Sphingobacterium sp. was isolated and screened from soil. The optimum medium composition is (g/L): Soytone 20, NaCl 1, K2HPO4 2.5, MgSO4 0.5, Heparin 2, Sucrose 15, pH 7.5. The optimum temperature for growth and enzyme production was 32 degrees C. When cultured at a rotating shaker at 30 degrees C for 36 hours, 200 r/min, 50 mL medium in 500 mL flask, the production of heparinase reached 4000 U/L.

[Cloning and expression of a thermostable beta-glycosidase gene from Thermus nonproteolyticus HG102].

The gene coding for beta-glycosidase (EC3.2.1.21) from Thermus nonproteolyticus HG102 has been cloned and expressed in E. coli. The gene open reading frame was 1311 bp and it codes for 436 amino acids. The deduced amino acid sequence of the enzyme showed identity with members of glycosyl hydrolase family I. The enzyme had high content of hydrophobic amino acid (Ala 12.8%, Leu 10.9%), Arg(9.6%), Glu(9.4%) and Pro(8.0%), but low content Cys(0.45%) and Met (0.9%). From the alignment of enzyme amino acid sequence with other glycosyl hydrolase family I members, Glu164 and Glu338 were predicated as the proton donor and nucleophile group. The DNASTAR program was used to predict the secondary structure. According to the Chou-Fasman model, the enzyme has 41.4% of alpha-helics, 16.2%, beta-strands, 14.4%, beta-turns. 14 of the 35 Pro were located at the second sites of beta-turns. Hydrophobic interaction, ion bond, alpha-helics and Pro had important contribution to Tn-gly thermostability.

[Expression and purification of gene transfer vehicle mediated by epidermal growth factor receptor].

OBJECTIVE: To create a gene transfer vehicle for targeting gene therapy of cancer with epidermal growth factor receptor overexpressing. METHODS: Encoding sequences of the first domain of histone gene (H1) and EGF C-loop (EGFc) were obtained by PCR amplification. These two DNA fragments were ligated by EcoR I site, and cloned and sequenced. E. coli expression vector of the fusion gene was then constructed. The fusion protein H1EGFc was purified by specific band isolation from SDS-PAGE. RESULTS: The molecular weight of purified protein was consistent with the designed request. Its purity reached 94.02%. CONCLUSION: A fusion protein H1EGFc was expressed and purified.