Magnetization reversal and magnetic interactions in anisotropic Nd-Dy-Fe-Co-B/MgO/α-Fe disks and multilayers.

We report on a field induced domain evolutionary procedure in the anisotropic Nd-Dy-Fe-Co-B/MgO/Fe multilayers by using first-order-reversal-curves and magnetic force microscopy. Different reversal behaviors and domain sizes are found in well coupled and decoupled multilayers by changing the thickness of the spacer layer. The competition between dipolar magnetostatic energy and Zeeman energy is evaluated by in-field observation throughout nucleation and annihilation processes. In addition, lithography-patterned arrays of soft Fe disks onto a continuous Nd-Dy-Fe-Co-B hard-magnetic layer are designed. By decreasing the applied field, it is found that magnetization orientations of the Fe disk and Nd-Dy-Fe-Co-B layer are aligned parallel. In the decoupled disk, although the out-of-plane magnetization orientations are observed, the orientation of the domains in the Fe disk is random. Furthermore, it is found that a stronger anisotropy of the Nd-Dy-Fe-Co-B layer decreases the interaction length. Our results provide a new understanding of anisotropic nanocomposite magnets with long-ranged magnetic interactions.

Gene expression profiling of somatic and pluripotent cells reveals novel pathways involved in reprogramming.

We investigated gene expression in embryonic stem (ES) cells, induced pluripotent stem (iPS) cells, and fibroblasts. Microarray expression data sets obtained from the Gene Expression Omnibus were analyzed using the Partek software. Human genes from ES cells, iPS cells, and fibroblasts were ranked from low to high according to their expression levels. The gene expression mode in iPS cells was much more like the mode in ES cells, and the expression levels of fibroblast genes fluctuated more dramatically than those of iPS and ES cells. The number of genes with significantly different expression was lower in the iPS and ES cells. Several genes with the expression levels that were significantly different between ES and iPS cells were found, including LEFTY2, DLK1, and NLRP2. Four genes belonged to the low expression category in fibroblasts with the high expression category occurring in ES cells, i.e., HESRG, PROM1, NTS, and LRRN1. Analyzing the expression of these genes is helpful to elucidate the mechanisms of cell fate regulation and efficiently obtain iPS cells.

Genome-scale meta-analysis of DNA methylation during progression of lung adenocarcinoma.

Identification of epigenetic alterations in tumors has become a common method for identifying genes critical to cancer development and progression. Thus, we identified DNA methylation alterations on the genome scale during lung adenocarcinoma (LADC) progression to understand the carcinogenic process and identify clinically relevant biomarkers. We found that epigenetic alterations in LADC mainly occur during the early stage of LADC progression, and there are no significant methylation differences between early-stage and late-stage LADCs. This suggests that DNA methylation alterations characterize a turning point of early events in LADC progression. By comparing DNA methylation between early-stage LADCs and normal lung tissues, we further identified 940 genes with significant alterations in DNA methylation. Sixty-seven genes were found to exhibit strong correlation between methylation alterations and expression changes, based on associated gene expression data. According to gene ontology analysis, these genes are involved in lung development, respiratory system development, cell cycle, histidine metabolism, the Wnt signaling pathway, and the p53 signaling pathway. We also found that genes on chromosome 18 most frequently showed promoter hypermethylation. Moreover, we found that LADC-associated DNA hypomethylation occurred preferentially at neither histone H3 lysine 4 nor histone H3 lysine 27 mark domains in human embryonic stem cells (NMDs) and that hypomethylation of NMDs was associated with a poor prognostic signature in LADC. Our findings have important implications for LADC progression because of the identification of novel epigenetic biomarkers potentially involved in early-stage LADC and for establishing the importance of NMD DNA hypomethylation for predicting prognosis in LADC.

The determinations of nucleosome positioning.

OBJECTIVE: Nucleosomes are the basic packaging units of chromatin, determinants of nucleosome organization playing a major role in genome packaging. Although a wide variety of nucleosome organization factors have been considered separately across the whole or partial human genomic regions, it is unclarified that what the major determinants and their roles in scale are when being put all together. And it is also unknown that what the similarities and differences of determinants between different genomic features such as genes of different expression levels or genomic regions with different functions. MATERIALS AND METHODS: We detected commonalities and characteristics of nucleosome positioning determinants in different genes and regions with 1591486 nucleosomes identified by ourselves in human CD4+ cell. RESULTS: It was found that a distinct linear combination of about 20 nucleosome-positioning factors explained nucleosome occupancy for each genomic feature. In those linear combinations, 6 DNA sequence attributes (Roll stiffness and Twist stiffness, CT and AG, CG and shift stiffness) and a histone modification (H4R3me2) are shared. And other factors are varied. Roll stiffness and Twist stiffness are the most important features. They are dominant, alone explaining 96.61-98.45% of the positioning weight in each genomic feature. The characteristic factors in each combination are larger in number, but weaker in power. Numerous histone modifications play a subtle role for nucleosome positioning. CONCLUSIONS: The present study provides a more accurate positioning nucleosome-map with higher resolution and a dramatically simplified means to predict and understand intrinsic nucleosome occupancy in different genomic features in human CD4+ cell. Roll stiffness and Twist stiffness are the two most important determinants in all genomic features. They may dominate because they both determine the degree of DNA bending and correlates with many other DNA structural characteristics. Histone modifications play a role of subtle allocation for nucleosome occupancy.

Comparison of CA 125 after three courses of chemotherapy and results of second-look surgery.

OBJECTIVE: To compare CA 125 levels after three courses of cisplatin-based chemotherapy and the results of second-look surgery. METHODS AND MATERIALS: From January 1990 to December 1996, the medical records of 72 patients diagnosed with epithelial ovarian cancer were reviewed. After initial staging surgery, all patients received cisplatin-based chemotherapy. Prior to each course of chemotherapy, patients underwent physical exams and serum CA 125 was obtained. After 6 courses of chemotherapy, if CA 125 levels were normal (< or = 35 IU/ml) and there was no clinical evidence of disease, the patient was offered second-look surgery. The sensitivity, specificity, and negative predicative value of CA 125 levels after 3 courses of chemotherapy and results of second-look surgery were calculated. Survival curves were constructed using Kaplan-Meier actuarial methods. RESULTS: Seventy-two patients were enrolled in the study. After completing 3 courses of chemotherapy, 43 out of 72 patients were reported to have normal CA 125 levels and were offered second-look surgery. Forty-six out of 72 patients underwent second-look surgery, 28 patients (60%) were reported to have positive second-look surgery. Of the patients with normal CA 125 levels after 3 courses of chemotherapy, 23 patients (57.5%) had a positive second-look surgery. The sensitivity and specificity of CA 125 values after 3 courses of chemotherapy were 17.9% and 94.7%, respectively and the negative predicative value was 43.9%. Patients with normal CA 125 values after 3 courses of chemotherapy had a significantly improved survival compared to those who failed to normalized their CA 125 levels after three courses of chemotherapy. CONCLUSION: Normalization of CA 125 after 3 courses of chemotherapy is a poor predicator of findings at second-look surgery.