Spectral analysis of Gene co-expression network of Zebrafish

We analyze the gene expression data of Zebrafish under the combined framework of complex networks and random matrix theory. The nearest neighbor spacing distribution of the corresponding matrix spectra follows random matrix predictions of Gaussian orthogonal statistics. Based on the eigenvector analysis we can divide the spectra into two parts, first part for which the eigenvector localization properties match with the random matrix theory predictions, and the second part for which they show deviation from the theory and hence are useful to understand the system dependent properties. Spectra with the localized eigenvectors can be characterized into three groups based on the eigenvalues. We explore the position of localized nodes from these different categories. Using an overlap measure, we find that the top contributing nodes in the different groups carry distinguished structural features. Furthermore, the top contributing nodes of the different localized eigenvectors corresponding to the lower eigenvalue regime form different densely connected structure well separated from each other. Preliminary biological interpretation of the genes, associated with the top contributing nodes in the localized eigenvectors, suggests that the genes corresponding to same vector share common features.Comment: 6 pages, four figures (accepted in EPL

Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands

Microbial genes that are “novel” (no detectable homologs in other species) have become of increasing interest as environmental sampling suggests that there are many more such novel genes in yet-to-be-cultured microorganisms. By analyzing known microbial genomic islands and prophages, we developed criteria for systematic identification of putative genomic islands (clusters of genes of probable horizontal origin in a prokaryotic genome) in 63 prokaryotic genomes, and then characterized the distribution of novel genes and other features. All but a few of the genomes examined contained significantly higher proportions of novel genes in their predicted genomic islands compared with the rest of their genome (Paired t test = 4.43E-14 to 1.27E-18, depending on method). Moreover, the reverse observation (i.e., higher proportions of novel genes outside of islands) never reached statistical significance in any organism examined. We show that this higher proportion of novel genes in predicted genomic islands is not due to less accurate gene prediction in genomic island regions, but likely reflects a genuine increase in novel genes in these regions for both bacteria and archaea. This represents the first comprehensive analysis of novel genes in prokaryotic genomic islands and provides clues regarding the origin of novel genes. Our collective results imply that there are different gene pools associated with recently horizontally transmitted genomic regions versus regions that are primarily vertically inherited. Moreover, there are more novel genes within the gene pool associated with genomic islands. Since genomic islands are frequently associated with a particular microbial adaptation, such as antibiotic resistance, pathogen virulence, or metal resistance, this suggests that microbes may have access to a larger “arsenal” of novel genes for adaptation than previously thought

Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation

Using the Pseudomonas aeruginosa Genome Project as a test case, we have developed a database and submission system to facilitate a community-based approach to continually updated genome annotation (http://www.pseudomonas.com). Researchers submit proposed annotation updates through one of three web-based form options which are then subjected to review, and if accepted, entered into both the database and log file of updates with author acknowledgement. In addition, a coordinator continually reviews literature for suitable updates, as we have found such reviews to be the most efficient. Both the annotations database and updates-log database have Boolean search capability with the ability to sort results and download all data or search results as tab-delimited files. To complement this peer-reviewed genome annotation, we also provide a linked GBrowse view which displays alternate annotations. Additional tools and analyses are also integrated, including PseudoCyc, and knockout mutant information. We propose that this database system, with its focus on facilitating flexible queries of the data and providing access to both peer-reviewed annotations as well as alternate annotation information, may be a suitable model for other genome projects wishing to use a continually updated, community-based annotation approach. The source code is freely available under GNU General Public Licence

Re-integerization of fractional charges in the correlated quarter-filled band

Previous work has demonstrated the existence of soliton defect states with charges +/- e/2 in the limits of zero and of infinite on-site Coulomb interactions in the one-dimensional (1D) quarter-filled band. For large but finite on-site Coulomb interaction, the low temperature 2k_F bond distortion that occurs within the 4k_F bond-distorted phase is accompanied by charge-ordering on the sites. We show that a ``re-integerization'' of the defect charge occurs in this bond-charge density wave (BCDW) state due to a ``binding'' of the fractional charges. We indicate briefly possible implications of this result for mechanisms of organic superconductivity.Comment: 4 eps figure

Nuclear Envelope Composition Determines The Ability Of Neutrophil-Type Cells To Passage Through Micron-Scale Constrictions

Neutrophils are characterized by their distinct nuclear shape, which is thought to facilitate the transit of these cells through pore spaces less than one-fifth of their diameter. We used human promyelocytic leukemia (HL-60) cells as a model system to investigate the effect of nuclear shape in whole cell deformability. We probed neutrophil-differentiated HL-60 cells lacking expression of lamin B receptor, which fail to develop lobulated nuclei during granulopoiesis and present an in vitro model for Pelger-Huët anomaly; despite the circular morphology of their nuclei, the cells passed through micron-scale constrictions on similar timescales as scrambled controls. We then investigated the unique nuclear envelope composition of neutrophil-differentiated HL-60 cells, which may also impact their deformability; although lamin A is typically down-regulated during granulopoiesis, we genetically modified HL-60 cells to generate a subpopulation of cells with well defined levels of ectopic lamin A. The lamin A-overexpressing neutrophil-type cells showed similar functional characteristics as the mock controls, but they had an impaired ability to pass through micron-scale constrictions. Our results suggest that levels of lamin A have a marked effect on the ability of neutrophils to passage through micron-scale constrictions, whereas the unusual multilobed shape of the neutrophil nucleus is less essential

Molecular Profiles of Pyramidal Neurons in the Superior Temporal Cortex in Schizophrenia

Disrupted synchronized oscillatory firing of pyramidal neuronal networks in the cerebral cortex in the gamma frequency band (i.e., 30–100 Hz) mediates many of the cognitive deficits and symptoms of schizophrenia. In fact, the density of dendritic spines and the average somal area of pyramidal neurons in layer 3 of the cerebral cortex, which mediate both long-range (associational) and local (intrinsic) corticocortical connections, are decreased in subjects with this illness. To explore the molecular pathophysiology of pyramidal neuronal dysfunction, we extracted ribonucleic acid (RNA) from laser-captured pyramidal neurons from layer 3 of Brodmann’s area 42 of the superior temporal gyrus (STG) from postmortem brains from schizophrenia and normal control subjects. We then profiled the messenger RNA (mRNA) expression of these neurons, using microarray technology. We identified 1331 mRNAs that were differentially expressed in schizophrenia, including genes that belong to the transforming growth factor beta (TGF-β) and the bone morphogenetic proteins (BMPs) signaling pathways. Disturbances of these signaling mechanisms may in part contribute to the altered expression of other genes found to be differentially expressed in this study, such as those that regulate extracellular matrix (ECM), apoptosis, and cytoskeletal and synaptic plasticity. In addition, we identified 10 microRNAs (miRNAs) that were differentially expressed in schizophrenia; enrichment analysis of their predicted gene targets revealed signaling pathways and gene networks that were found by microarray to be dysregulated, raising an interesting possibility that dysfunction of pyramidal neurons in schizophrenia may in part be mediated by a concerted dysregulation of gene network functions as a result of the altered expression of a relatively small number of miRNAs. Taken together, findings of this study provide a neurobiological framework within which specific hypotheses about the molecular mechanisms of pyramidal cell dysfunction in schizophrenia can be formulated

Bond and charge density waves in the isotropic interacting two-dimensional quarter-filled band and the insulating state proximate to organic superconductivity

We report two surprising results regarding the nature of the spatial broken symmetries in the two-dimensional (2D), quarter-filled band with strong electron-electron interactions. First, in direct contradiction to the predictions of one-electron theory, we find a coexisting ``bond-order and charge density wave'' (BCDW) insulating ground state in the 2D rectangular lattice for all anisotropies, including the isotropic limit. Second, we find that the BCDW further coexists with a spin-density wave (SDW) in the range of large anisotropy. Further, in contrast to the interacting half-filled band, in the interacting quarter-filled band there are two transitions: first, a similar singlet-to-AFM/SDW transition for large anisotropy and second, an AFM/SDW-to-singlet transition at smaller anisotropy. We discuss how these theoretical results apply to the insulating states that are proximate to the superconducting states of 2:1 cationic charge-transfer solids (CTS). An important consequence of this work is the suggestion that organic superconductivity is related to the proximate Coulomb-induced BCDW, with the SDW that coexists for large anisotropies being also a consequence of the BCDW, rather than the driver of superconductivity.Comment: 29 pages, 18 eps figures. Revised with new appendices; to appear in Phys. Rev. B 62, Nov 15, 200

Theoretical Aspects of Charge Ordering in Molecular Conductors

Theoretical studies on charge ordering phenomena in quarter-filled molecular (organic) conductors are reviewed. Extended Hubbard models including not only the on-site but also the inter-site Coulomb repulsion are constructed in a straightforward way from the crystal structures, which serve for individual study on each material as well as for their systematic understandings. In general the inter-site Coulomb interaction stabilizes Wigner crystal-type charge ordered states, where the charge localizes in an arranged manner avoiding each other, and can drive the system insulating. The variety in the lattice structures, represented by anisotropic networks in not only the electron hopping but also in the inter-site Coulomb repulsion, brings about diverse problems in low-dimensional strongly correlated systems. Competitions and/or co-existences between the charge ordered state and other states are discussed, such as metal, superconductor, and the dimer-type Mott insulating state which is another typical insulating state in molecular conductors. Interplay with magnetism, e.g., antiferromagnetic state and spin gapped state for example due to the spin-Peierls transition, is considered as well. Distinct situations are pointed out: influences of the coupling to the lattice degree of freedom and effects of geometrical frustration which exists in many molecular crystals. Some related topics, such as charge order in transition metal oxides and its role in new molecular conductors, are briefly remarked.Comment: 21 pages, 19 figures, to be published in J. Phys. Soc. Jpn. special issue on "Organic Conductors"; figs. 4 and 11 replaced with smaller sized fil