Telomerase reverse transcriptase promoter mutation and its clinical implication in thyroid cancer

Considering the long-term survival in most patients with thyroid cancer, it is very important to distinguish patients who need aggressive treatment from those who do not. Clinicopathological prognostic factors have been used to predict their prognoses, but they could not completely predict the final outcome of each patient. Recently, molecular marker-based risk stratification of thyroid cancer has been proposed to better estimate the risk. BRAF mutation has drawn much attention based on its high prevalence. However, its association with recurrence/mortality is not clear, and it is debatable. Telomerase reverse transcriptase (TERT) promoter mutation has been identified in over 50 human cancers including thyroid cancer after its first discovery in melanoma. It increases telomerase activity, which allows cancer cells to immortalize. It was found in approximately 10% of papillary thyroid carcinoma, 17% of follicular thyroid carcinoma, and 40% of poorly differentiated or anaplastic thyroid carcinoma. It is highly prevalent in old age, large tumors, aggressive histology, advanced stages, and distant metastasis. It is associated with increased recurrence and mortality. Concomitant TERT and BRAF mutations diminished the survival rate. Inclusion of TERT promoter mutation analysis with conventional clinicopathological evaluation could lead to better prognostication and management for individual patients

Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites

We have developed a new bioinformatics approach called ECMFinder (Evolutionary Conserved Motif Finder). This program searches for a given DNA motif within the entire genome of one species and uses the gene association information of a potential transcription factor-binding site (TFBS) to screen the homologous regions of a second and third species. If multiple species have this potential TFBS in homologous positions, this program recognizes the identified TFBS as an evolutionary conserved motif (ECM). This program outputs a list of ECMs, which can be uploaded as a Custom Track in the UCSC genome browser and can be visualized along with other available data. The feasibility of this approach was tested by searching the genomes of three mammals (human, mouse and cow) with the DNA-binding motifs of YY1 and CTCF. This program successfully identified many clustered YY1- and CTCF-binding sites that are conserved among these species but were previously undetected. In particular, this program identified CTCF-binding sites that are located close to the Dlk1, Magel2 and Cdkn1c imprinted genes. Individual ChIP experiments confirmed the in vivo binding of the YY1 and CTCF proteins to most of these newly discovered binding sites, demonstrating the feasibility and usefulness of ECMFinder

Competing states for the fractional quantum Hall effect in the 1/3-filled second Landau level

In this work, we investigate the nature of the fractional quantum Hall state in the 1/3-filled second Landau level (SLL) at filling factor $\nu=7/3$ (and 8/3 in the presence of the particle-hole symmetry) via exact diagonalization in both torus and spherical geometries. Specifically, we compute the overlap between the exact 7/3 ground state and various competing states including (i) the Laughlin state, (ii) the fermionic Haffnian state, (iii) the antisymmetrized product state of two composite fermion seas at 1/6 filling, and (iv) the particle-hole (PH) conjugate of the $Z_4$ parafermion state. All these trial states are constructed according to a guiding principle called the bilayer mapping approach, where a trial state is obtained as the antisymmetrized projection of a bilayer quantum Hall state with interlayer distance $d$ as a variational parameter. Under the proper understanding of the ground-state degeneracy in the torus geometry, the $Z_4$ parafermion state can be obtained as the antisymmetrized projection of the Halperin (330) state. Similarly, it is proved in this work that the fermionic Haffnian state can be obtained as the antisymmetrized projection of the Halperin (551) state. It is shown that, while extremely accurate at sufficiently large positive Haldane pseudopotential variation $\delta V_1^{(1)}$, the Laughlin state loses its overlap with the exact 7/3 ground state significantly at $\delta V_1^{(1)} \simeq 0$. At slightly negative $\delta V_1^{(1)}$, it is shown that the PH-conjugated $Z_4$ parafermion state has a substantial overlap with the exact 7/3 ground state, which is the highest among the above four trial states.Comment: 22 pages, 5 figure

Realization of giant magnetoelectricity in helimagnets

We show that low field magnetoelectric (ME) properties of helimagnets Ba0.5Sr1.5Zn2(Fe1-xAlx)12O22 can be efficiently tailored by Al-substitution level. As x increases, the critical magnetic field for switching electric polarization is systematically reduced from ~1 T down to ~1 mT, and the ME susceptibility is greatly enhanced to reach a giant value of 2.0 x 10^4 ps/m at an optimum x = 0.08. We find that control of nontrivial orbital moment in the octahedral Fe sites through the Al-substitution is crucial for fine tuning of magnetic anisotropy and obtaining the conspicuously improved ME characteristics

Allele-specific deposition of macroH2A1 in imprinting control regions

In the current study, we analyzed the deposition patterns of macroH2A1 at a number of different genomic loci located in X chromosome and autosomes. MacroH2A1 is preferentially deposited at methylated CpG-rich regions located close to promoters. The macroH2A1 deposition patterns at the methylated CpG islands of several imprinted domains, including the imprinting control regions (ICRs) of Xist, Peg3, H19/Igf2, Gtl2/Dlk1 and Gnas domains, show consistent allele-specificity towards inactive, methylated alleles. The macroH2A1 deposition levels at the ICRs and other differentially methylated regions of these domains are also either higher or comparable to those observed at the inactive X chromosome of female mammals. Overall, our results indicate that besides DNA methylation macroH2A1 is another epigenetic component in the chromatin of ICRs displaying differential association with two parental alleles. © The Author 2006. Published by Oxford University Press. All rights reserved

Electric polarization enhancement in multiferroic CoCr2O4 crystals with Cr-site mixing

Single crystals of multiferroic cobalt chromite Co (Cr2-x Cox) O4 have been grown via several methods to have different Co3+ doping levels (x=0.0, 0.14, and 0.18). Under magnetic fields, all the crystals display electric polarization reversal below their spiral spin ordering temperatures. We find that both saturated electric polarization and magnetization under magnetic fields increase significantly with the increase in x. This result can be qualitatively explained by a broken balance between at least two electric polarization contributions existing in CoCr2 O4 and is expected to be useful in tailoring electric polarization in similar kinds of multiferroics. © 2009 American Institute of Physics.open222

Electric field control of nonvolatile four-state magnetization at room temperature

We find the realization of large converse magnetoelectric (ME) effects at room temperature in a multiferroic hexaferrite Ba$_{0.52}$Sr$_{2.48}$Co$_{2}$Fe$_{24}$O$_{41}$ single crystal, in which rapid change of electric polarization in low magnetic fields (about 5 mT) is coined to a large ME susceptibility of 3200 ps/m. The modulation of magnetization then reaches up to 0.62 $\mu$$_{B}$/f.u. in an electric field of 1.14 MV/m. We find further that four ME states induced by different ME poling exhibit unique, nonvolatile magnetization versus electric field curves, which can be approximately described by an effective free energy with a distinct set of ME coefficients