The Ets dominant repressor En/Erm enhances intestinal epithelial tumorigenesis in ApcMin mice

<p>Abstract</p> <p>Background</p> <p>Ets transcription factors have been widely implicated in the control of tumorigenesis, with most studies suggesting tumor-promoting roles. However, few studies have examined Ets tumorigenesis-modifying functions <it>in vivo </it>using model genetic systems.</p> <p>Methods</p> <p>Using mice expressing a previously characterized Ets dominant repressor transgene in the intestinal epithelium (Villin-En/Erm), we examined the consequences of blocking endogenous Ets-mediated transcriptional activation on tumorigenesis in the Apc^Minmodel of intestinal carcinoma.</p> <p>Results</p> <p>En/Erm expression in the intestine, at levels not associated with overt crypt-villus dysmorphogenesis, results in a marked increase in tumor number in Apc^Minanimals. Moreover, when examined histologically, tumors from En/Erm-expressing animals show a trend toward greater stromal invasiveness. Detailed analysis of crypt-villus homeostasis in these En/Erm transgenic animals suggests increased epithelial turnover as one possible mechanism for the enhanced tumorigenesis.</p> <p>Conclusion</p> <p>Our findings provide <it>in vivo </it>evidence for a tumor-restricting function of endogenous Ets factors in the intestinal epithelium.</p

Geometric phases for generalized squeezed coherent states

A simple technique is used to obtain a general formula for the Berry phase (and the corresponding Hannay angle) for an arbitrary Hamiltonian with an equally-spaced spectrum and appropriate ladder operators connecting the eigenstates. The formalism is first applied to a general deformation of the oscillator involving both squeezing and displacement. Earlier results are shown to emerge as special cases. The analysis is then extended to multiphoton squeezed coherent states and the corresponding anholonomies deduced.Comment: 15 page

Squeezing arbitrary cavity-field states through their interaction with a single driven atom

We propose an implementation of the parametric amplification of an arbitrary radiation-field state previously prepared in a high-Q cavity. This nonlinear process is accomplished through the dispersive interactions of a single three-level atom (fundamental |g>, intermediate |i>, and excited |e> levels) simultaneously with i) a classical driving field and ii) a previously prepared cavity mode whose state we wish to squeeze. We show that, in the adiabatic approximantion, the preparation of the initial atomic state in the intermediate level |i> becomes crucial for obtaing the degenerated parametric amplification process.Comment: Final published versio

Retrodictively Optimal Localisations in Phase Space

In a previous paper it was shown that the distribution of measured values for a retrodictively optimal simultaneous measurement of position and momentum is always given by the initial state Husimi function. This result is now generalised to retrodictively optimal simultaneous measurements of an arbitrary pair of rotated quadratures x_theta1 and x_theta2. It is shown, that given any such measurement, it is possible to find another such measurement, informationally equivalent to the first, for which the axes defined by the two quadratures are perpendicular. It is further shown that the distribution of measured values for such a meaurement belongs to the class of generalised Husimi functions most recently discussed by Wuensche and Buzek. The class consists of the subset of Wodkiewicz's operational probability distributions for which the filter reference state is a squeezed vaccuum state.Comment: 11 pages, 2 figures. AMS Latex. Replaced with published versio

Generalized Husimi Functions: Analyticity and Information Content

The analytic properties of a class of generalized Husimi functions are discussed, with particular reference to the problem of state reconstruction. The class consists of the subset of Wodkiewicz's operational probability distributions for which the filter reference state is a squeezed vacuum state. The fact that the function is analytic means that perfectly precise knowledge of its values over any small region of phase space provides enough information to reconstruct the density matrix. If, however, one only has imprecise knowledge of its values, then the amplification of statistical errors which occurs when one attempts to carry out the continuation seriously limits the amount of information which can be extracted. To take account of this fact a distinction is made between explicate, or experimentally accessible information, and information which is only present in implicate, experimentally inaccessible form. It is shown that an explicate description of various aspects of the system can be found localised on various 2 real dimensional surfaces in complexified phase space. In particular, the continuation of the function to the purely imaginary part of complexified phase space provides an explicate description of the Wigner function.Comment: 16 pages, 2 figures, AMS-latex. Replaced with published versio

Discovery of 3-Formyl-Tyrosine Metabolites from Pseudoalteromonas tunicata through Heterologous Expression

Genome mining and identification of natural product gene clusters typically relies on the presence of canonical nonribosomal polypeptide synthetase (NRPS) or polyketide synthase (PKS) domains. Recently, other condensation enzymes, such as the ATP-grasp ligases, have been recognized as important players in natural product biosynthesis. In this study, sequence based searching for homologues of DdaF, the ATP-grasp amide ligase from dapdiamide biosynthesis, led to the identification of a previously unannotated biosynthetic gene cluster in Pseudoalteromonas tunicata. Heterologous expression of the cluster in Escherichia coli allowed for the production and structure determination of two new 3-formyl tyrosine metabolites.Molecular and Cellular Biolog

Squeezed States for General Systems

We propose a ladder-operator method for obtaining the squeezed states of general symmetry systems. It is a generalization of the annihilation-operator technique for obtaining the coherent states of symmetry systems. We connect this method with the minimum-uncertainty method for obtaining the squeezed and coherent states of general potential systems, and comment on the distinctions between these two methods and the displacement-operator method.Comment: 8 pages, LAUR-93-1721, LaTe

Thermalized Displaced and Squeezed Number States in Coordinate Representation

Within the framework of thermofield dynamics, the wavefunctions of the thermalized displaced number and squeezed number states are given in the coordinate representation. Furthermore, the time evolution of these wavefunctions is considered by introducing a thermal coordinate representation, and we also calculate the corresponding probability densities, average values and variances of position coordinate, which are consistent with results in the literature.Comment: 12 pages, no figures, Revtex. v3: substantially revise

Two Mode Quantum Systems: Invariant Classification of Squeezing Transformations and Squeezed States

A general analysis of squeezing transformations for two mode systems is given based on the four dimensional real symplectic group Sp(4,\Re)\/. Within the framework of the unitary metaplectic representation of this group, a distinction between compact photon number conserving and noncompact photon number nonconserving squeezing transformations is made. We exploit the Sp(4,\Re)-SO(3,2)\/ local isomorphism and the U(2)\/ invariant squeezing criterion to divide the set of all squeezing transformations into a two parameter family of distinct equivalence classes with representative elements chosen for each class. Familiar two mode squeezing transformations in the literature are recognized in our framework and seen to form a set of measure zero. Examples of squeezed coherent and thermal states are worked out. The need to extend the heterodyne detection scheme to encompass all of U(2)\/ is emphasized, and known experimental situations where all U(2)\/ elements can be reproduced are briefly described.Comment: Revtex 37 pages, Latex figures include

An integrated ChIP-seq analysis platform with customizable workflows

<p>Abstract</p> <p>Background</p> <p>Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq), enables unbiased and genome-wide mapping of protein-DNA interactions and epigenetic marks. The first step in ChIP-seq data analysis involves the identification of peaks (i.e., genomic locations with high density of mapped sequence reads). The next step consists of interpreting the biological meaning of the peaks through their association with known genes, pathways, regulatory elements, and integration with other experiments. Although several programs have been published for the analysis of ChIP-seq data, they often focus on the peak detection step and are usually not well suited for thorough, integrative analysis of the detected peaks.</p> <p>Results</p> <p>To address the peak interpretation challenge, we have developed ChIPseeqer, an integrative, comprehensive, fast and user-friendly computational framework for in-depth analysis of ChIP-seq datasets. The novelty of our approach is the capability to combine several computational tools in order to create easily customized workflows that can be adapted to the user's needs and objectives. In this paper, we describe the main components of the ChIPseeqer framework, and also demonstrate the utility and diversity of the analyses offered, by analyzing a published ChIP-seq dataset.</p> <p>Conclusions</p> <p>ChIPseeqer facilitates ChIP-seq data analysis by offering a flexible and powerful set of computational tools that can be used in combination with one another. The framework is freely available as a user-friendly GUI application, but all programs are also executable from the command line, thus providing flexibility and automatability for advanced users.</p