Design Equation: A Novel Approach to Heteropolymer Design

A novel approach to heteropolymer design is proposed. It is based on the criterion by Kurosky and Deutsch, with which the probability of a target conformation in a conformation space is maximized at low but finite temperature. The key feature of the proposed approach is the use of soft spins (fuzzy monomers) that leads to a design equation, which is an analog of the Boltzmann machine learning equation in the design problem. We implement an algorithm based on the design equation for the generalized HP model on the 3x3x3 cubic lattice and check its performance.Comment: 7 pages, 3 tables, 1 figures, uses jpsj.sty, jpsjbs1.sty, epsf.sty, Submitted to J. Phys. Soc. Jp

A hierarchical model for aging

We present a one dimensional model for diffusion on a hierarchical tree structure. It is shown that this model exhibits aging phenomena although no disorder is present. The origin of aging in this model is therefore the hierarchical structure of phase space.Comment: 10 pages LaTeX, 4 postscript-figures include

Comprehensive genomic screens identify a role for PLZF-RAR alpha as a positive regulator of cell proliferation via direct regulation of c-MYC

The t(11;17)(q23;q21) translocation is associated with a retinoic acid (RA)–insensitive form of acute promyelocytic leukemia (APL), involving the production of reciprocal fusion proteins, promyelocytic leukemia zinc finger–retinoic acid receptor α (PLZF-RARα) and RARα-PLZF. Using a combination of chromatin immunoprecipitation promotor arrays (ChIP-chip) and gene expression profiling, we identify novel, direct target genes of PLZF-RARα that tend to be repressed in APL compared with other myeloid leukemias, supporting the role of PLZF-RARα as an aberrant repressor in APL. In primary murine hematopoietic progenitors, PLZF-RARα promotes cell growth, and represses Dusp6 and Cdkn2d, while inducing c-Myc expression, consistent with its role in leukemogenesis. PLZF-RARα binds to a region of the c-MYC promoter overlapping a functional PLZF site and antagonizes PLZF-mediated repression, suggesting that PLZF-RARα may act as a dominant-negative version of PLZF by affecting the regulation of shared targets. RA induced the differentiation of PLZF-RARα–transformed murine hematopoietic cells and reduced the frequency of clonogenic progenitors, concomitant with c-Myc down-regulation. Surviving RA-treated cells retained the ability to be replated and this was associated with sustained c-Myc expression and repression of Dusp6, suggesting a role for these genes in maintaining a self-renewal pathway triggered by PLZF-RARα