Rotations of nuclei with reflection asymmetry correlations

We propose a collective Hamiltonian which incorporates interactions capable to generate rotations in nuclei with simultaneous presence of octupole and quadrupole deformations. It is demonstrated that the model formalism could be applied to reproduce the staggering effects observed in nuclear octupole bands. On this basis we propose that the interactions involved would provide a relevant handle in the study of collective phenomena in nuclei and other quantum mechanical systems with reflection asymmetry correlations.Comment: LaTeX, 9 pages plus 3 figures given in separate .ps files. To appear in the proceedings of the International Conference on Nuclear Structure and Related Topics (Dubna, Russia, 6-10/6/2000), ed. R. Jolos, V. Voronov, et a

Parametrizations of triaxial deformation and E2 transitions of the wobbling band

By the very definition the triaxial deformation parameter $\gamma$ is related to the expectation values of the K=0 and K=2 components of the intrinsic quadrupole tensor operator. On the other hand, using the same symbol "$\gamma$", various different parametrizations of triaxial deformation have been employed, which are suitable for various types of the mean-field potentials. It is pointed out that the values of various "$\gamma$" are quite different for the same actual triaxial deformation, especially for the large deformation; for example, the difference can be almost a factor two for the case of the triaxial superdeformed bands recently observed in the Hf and Lu nuclei. In our previous work, we have studied the wobbling band in Lu nuclei by using the microscopic framework of the cranked Nilsson mean-field and the random phase approximation, where the most serious problem is that the calculated B(E2) value is about factor two smaller. It is shown that the origin of this underestimation can be mainly attributed to the small triaxial deformation; if is used the same triaxial deformation as in the analysis of the particle-rotor model, the calculated B(E2) increases and gives correct magnitude compared with the experimental data.Comment: 10 pages, 9 figure

Point symmetries in the Hartree-Fock approach: Densities, shapes and currents

Three mutually perpendicular symmetry axes of the second order, inversion,and time reversal can be used to construct a double point group denoted byD2h(TD). Properties of this group are analyzed in relation to the symmetry andsymmetry-breaking effects within the mean-field (Hartree-Fock) theories, bothin even and odd fermion systems. We enumerate space symmetries of localone-body densities, and symmetries of electromagnetic moments, that appear whensome or all of the D2h(TD) elements represent self-consistent mean-fieldsymmetries

Breaking and restoring symmetries within the nuclear energy density functional method

We review the notion of symmetry breaking and restoration within the frame of nuclear energy density functional methods. We focus on key differences between wave-function- and energy-functional-based methods. In particular, we point to difficulties to formulate the restoration of symmetries within the energy functional framework. The problems tackled recently in connection with particle-number restoration serve as a baseline to the present discussion. Reaching out to angular-momentum restoration, we identify an exact mathematical property of the energy density $E^{LM}(\vec{R})$ that could be used to constrain energy density functional kernels. Consequently, we suggest possible routes towards a better formulation of symmetry restorations within energy density functional methods.Comment: 16 pages, 3 figures, contribution to the "Focus issue on Open Problems in Nuclear Structure", Journal of Physics

Parametrization of the octupole degrees of freedom

A simple parametrization for the octupole collective variables is proposed and the symmetries of the wave functions are discussed in terms of the solutions corresponding to the vibrational limit. [PACS: 21.60Ev, 21.60.Fw, 21.10.Re]Comment: 14 page

Characterization of virus-like particles associated with the human faecal and caecal microbiota

This work represents an investigation into the presence, abundance and diversity of virus-like particles (VLPs) associated with human faecal and caecal samples. Various methodologies for the recovery of VLPs from faeces were tested and optimized, including successful down-stream processing of such samples for the purpose of an in-depth electron microscopic analysis, pulsed-field gel electrophoresis and efficient DNA recovery. The applicability of the developed VLP characterization method beyond the use of faecal samples was then verified using samples obtained from human caecal fluid

TALEN-mediated editing of the mouse Y chromosome

The functional study of Y chromosome genes has been hindered by a lack of mouse models with specific Y chromosome mutations. We used transcription activator-like effector nuclease (TALEN)-mediated gene editing in mouse embryonic stem cells (mESCs) to produce mice with targeted gene disruptions and insertions in two Y-linked genes—Sry and Uty. TALEN-mediated gene editing is a useful tool for dissecting the biology of the Y chromosome.National Institutes of Health (U.S.) (US NIH grant R01-HG000257)National Institutes of Health (U.S.) (US NIH grant R01-CA084198)National Institutes of Health (U.S.) (US NIH grant R37-HD045022)Croucher Foundation (Scholarship)Howard Hughes Medical Institute (Investigator

The nuclear energy density functional formalism

The present document focuses on the theoretical foundations of the nuclear energy density functional (EDF) method. As such, it does not aim at reviewing the status of the field, at covering all possible ramifications of the approach or at presenting recent achievements and applications. The objective is to provide a modern account of the nuclear EDF formalism that is at variance with traditional presentations that rely, at one point or another, on a {\it Hamiltonian-based} picture. The latter is not general enough to encompass what the nuclear EDF method represents as of today. Specifically, the traditional Hamiltonian-based picture does not allow one to grasp the difficulties associated with the fact that currently available parametrizations of the energy kernel $E[g',g]$ at play in the method do not derive from a genuine Hamilton operator, would the latter be effective. The method is formulated from the outset through the most general multi-reference, i.e. beyond mean-field, implementation such that the single-reference, i.e. "mean-field", derives as a particular case. As such, a key point of the presentation provided here is to demonstrate that the multi-reference EDF method can indeed be formulated in a {\it mathematically} meaningful fashion even if $E[g',g]$ does {\it not} derive from a genuine Hamilton operator. In particular, the restoration of symmetries can be entirely formulated without making {\it any} reference to a projected state, i.e. within a genuine EDF framework. However, and as is illustrated in the present document, a mathematically meaningful formulation does not guarantee that the formalism is sound from a {\it physical} standpoint. The price at which the latter can be enforced as well in the future is eventually alluded to.Comment: 64 pages, 8 figures, submitted to Euroschool Lecture Notes in Physics Vol.IV, Christoph Scheidenberger and Marek Pfutzner editor

Chromatin Immunoprecipitation to Analyze DNA Binding Sites of HMGA2

BACKGROUND: HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors. The protein harbours three basically charged DNA binding domains and an acidic protein binding C-terminal domain. DNA binding induces changes of DNA conformation and hence results in global overall change of gene expression patterns. Recently, using a PCR-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure two consensus sequences for HMGA2 binding have been identified. METHODOLOGY/PRINCIPAL FINDINGS: In this investigation chromatin immunoprecipitation (ChIP) experiments and bioinformatic methods were used to analyze if these binding sequences can be verified on chromatin of living cells as well. CONCLUSION: After quantification of HMGA2 protein in different cell lines the colon cancer derived cell line HCT116 was chosen for further ChIP experiments because of its 3.4-fold higher HMGA2 protein level. 49 DNA fragments were obtained by ChIP. These fragments containing HMGA2 binding sites have been analyzed for their AT-content, location in the human genome and similarities to sequences generated by a SELEX study. The sequences show a significantly higher AT-content than the average of the human genome. The artificially generated SELEX sequences and short BLAST alignments (11 and 12 bp) of the ChIP fragments from living cells show similarities in their organization. The flanking regions are AT-rich, whereas a lower conservation is present in the center of the sequences

Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival

<p>Abstract</p> <p>Background</p> <p>Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three complementary events: lifetime, overall and progression-free glioblastoma survival.</p> <p>Methods</p> <p>A novel analytical strategy was developed to identify general associations between the biomarkers and glioblastoma, and associations that depend on cohort groups, such as race, gender, and therapy. Gene network inference, cross-validation and functional analyses further supported the identified biomarkers.</p> <p>Results</p> <p>A total of 61, 47 and 60 gene expression profiles were significantly associated with lifetime, overall, and progression-free survival, respectively. The vast majority of these genes have been previously reported to be associated with glioblastoma (35, 24, and 35 genes, respectively) or with other cancers (10, 19, and 15 genes, respectively) and the rest (16, 4, and 10 genes, respectively) are novel associations. <it>Pik3r1</it>, <it>E2f3, Akr1c3</it>, <it>Csf1</it>, <it>Jag2</it>, <it>Plcg1</it>, <it>Rpl37a</it>, <it>Sod2</it>, <it>Topors</it>, <it>Hras</it>, <it>Mdm2, Camk2g</it>, <it>Fstl1</it>, <it>Il13ra1</it>, <it>Mtap </it>and <it>Tp53 </it>were associated with multiple survival events.</p> <p>Most genes (from 90 to 96%) were associated with survival in a general or cohort-independent manner and thus the same trend is observed across all clinical levels studied. The most extreme associations between profiles and survival were observed for <it>Syne1</it>, <it>Pdcd4</it>, <it>Ighg1</it>, <it>Tgfa</it>, <it>Pla2g7</it>, and <it>Paics</it>. Several genes were found to have a cohort-dependent association with survival and these associations are the basis for individualized prognostic and gene-based therapies. <it>C2</it>, <it>Egfr</it>, <it>Prkcb</it>, <it>Igf2bp3</it>, and <it>Gdf10 </it>had gender-dependent associations; <it>Sox10</it>, <it>Rps20</it>, <it>Rab31</it>, and <it>Vav3 </it>had race-dependent associations; <it>Chi3l1</it>, <it>Prkcb</it>, <it>Polr2d</it>, and <it>Apool </it>had therapy-dependent associations. Biological processes associated glioblastoma survival included morphogenesis, cell cycle, aging, response to stimuli, and programmed cell death.</p> <p>Conclusions</p> <p>Known biomarkers of glioblastoma survival were confirmed, and new general and clinical-dependent gene profiles were uncovered. The comparison of biomarkers across glioblastoma phases and functional analyses offered insights into the role of genes. These findings support the development of more accurate and personalized prognostic tools and gene-based therapies that improve the survival and quality of life of individuals afflicted by glioblastoma multiforme.</p