Predicting Cell Cycle Regulated Genes by Causal Interactions

The fundamental difference between classic and modern biology is that technological innovations allow to generate high-throughput data to get insights into molecular interactions on a genomic scale. These high-throughput data can be used to infer gene networks, e. g., the transcriptional regulatory or signaling network, representing a blue print of the current dynamical state of the cellular system. However, gene networks do not provide direct answers to biological questions, instead, they need to be analyzed to reveal functional information of molecular working mechanisms. In this paper we propose a new approach to analyze the transcriptional regulatory network of yeast to predict cell cycle regulated genes. The novelty of our approach is that, in contrast to all other approaches aiming to predict cell cycle regulated genes, we do not use time series data but base our analysis on the prior information of causal interactions among genes. The major purpose of the present paper is to predict cell cycle regulated genes in S. cerevisiae. Our analysis is based on the transcriptional regulatory network, representing causal interactions between genes, and a list of known periodic genes. No further data are used. Our approach utilizes the causal membership of genes and the hierarchical organization of the transcriptional regulatory network leading to two groups of periodic genes with a well defined direction of information flow. We predict genes as periodic if they appear on unique shortest paths connecting two periodic genes from different hierarchy levels. Our results demonstrate that a classical problem as the prediction of cell cycle regulated genes can be seen in a new light if the concept of a causal membership of a gene is applied consequently. This also shows that there is a wealth of information buried in the transcriptional regulatory network whose unraveling may require more elaborate concepts than it might seem at first.

Hyperacetylation in prostate cancer induces cell cycle aberrations, chromatin reorganization and altered gene expression profiles.

Histone acetylation is a fundamental mechanism in the regulation of local chromatin conformation and gene expression. Research has focused on the impact of altered epigenetic environments on the expression of specific genes and their pathways. However, changes in histone acetylation also have a global impact on the cell. In this study we used digital texture analysis to assess global chromatin patterns following treatment with trichostatin A (TSA) and have observed significant alterations in the condensation and distribution of higher-order chromatin, which were associated with altered gene expression profiles in both immortalised normal PNT1A prostate cell line and androgen-dependent prostate cancer cell line LNCaP. Furthermore, the extent of TSA-induced disruption was both cell cycle and cell line dependent. This was illustrated by the identification of sub-populations of prostate cancer cells expressing high levels of H3K9 acetylation in the G2/M phase of the cell cycle that were absent in normal cell populations. In addition, the analysis of enriched populations of G1 cells showed a global decondensation of chromatin exclusively in normal cells.

Lagrangian description of nonlinear dust-ion acoustic waves in dusty plasmas

An analytical model is presented for the description of nonlinear dust-ion-acoustic waves propagating in an unmagnetized, collisionless, three component plasma composed of electrons, ions and inertial dust grains. The formulation relies on a Lagrangian approach of the plasma fluid model. The modulational stability of the wave amplitude is investigated. Different types of localized envelope electrostatic excitations are shown to exist.

The vegetation and climate history of the last glacial cycle in a new pollen record from Lake Fimon (southern Alpine foreland, N-Italy)

The sediments of Like Fimon N Italy contain the first continuous archive of the Late Pleistocene environmental and climate history of the southern Alpine foreland We present here the detailed palynological record of the interval between Termination II and the List Glacial Maximum The age-depth model is obtained by radiocarbon dating in the uppermost part of the record Downward we con elated major forest expansion and contraction events to isotopic events in the Greenland Ice core records via a stepping-stone approach involving intermediate correlation to isotopic events dated by TIMS U/Th in Alpine and Apennine stalagmites and to pollen records from mime cores of the Iberian margin Modelled ages obtained by Bayesian analysis of deposition are thoroughly consistent with actual ages with maximum offset of +/- 1700 years Sharp expansion of broad-leaved temperate forest and of sudden water table rise mark the onset of the Last Interglacial after a treeless steppe phase at the end of penultimate glaciation This event is actually a two-step process which matches the two step rise observed in the isotopic record of the nearby Antro del Corchia stalagmite respectively dated to 132 5 +/- 2 5 and 129 +/- 1 5 ka At the interglacial decline mixed oak forests were replaced by oceanic mixed forests the latter persisting further for 7 ka till the end of the Eemian succession Warm-temperate woody species are still abundant at the Eemian end corroborating a steep gradient between central Europe and the Alpine divide at the inception of the last glacial After a stadial phase marked by moderate forest decline a new expansion of warm broad leaved forests interrupted by minor events and followed by mixed oceanic forests can be identified with the north-alpine Saint Germain I The spread of beech during the oceanic phase is a valuable circumalpine marker The subsequent stadial-interstadial succession lacking the telocratic oceanic phase is also consistent with the evidence at the north alpine foreland The Middle Wurmian (full glacial) is marked by persistence of mixed forests dominated by conifers but with significant lime and other broad leaved species A major Arboreal Pollen decrease is observed at modelled age of 38 7 +/- 0 5 ka (larch expansion and last occurrence of lime) which his been related to Heinrich Event 4 The evidence of afforestation persisting south of the Alps throughout most of MIS 3 contrasts with a boreal and continental landscape known for the northern alpine foreland pointing to a sharp rainfall boundary at the Alpine divide and to southern air circulation This is in agreement with the Alpine paleoglaciological record and is supported by the pressure and rainfall patterns designed by mesoscale paleoclimate simulations Strenghtening the continental high pressure during the full glacial triggered cyclogenesis in the middle latitude eastern Europe and orographic rainfall in the eastern Alps and the Balkanic mountains thus allowing forests development at current sea level altitudes (C) 2010 Elsevier Ltd All rights reserved

RNA polymerase I-specific subunits promote polymerase clustering to enhance the rRNA gene transcription cycle.

RNA polymerase I (Pol I) produces large ribosomal RNAs (rRNAs). In this study, we show that the Rpa49 and Rpa34 Pol I subunits, which do not have counterparts in Pol II and Pol III complexes, are functionally conserved using heterospecific complementation of the human and Schizosaccharomyces pombe orthologues in Saccharomyces cerevisiae. Deletion of RPA49 leads to the disappearance of nucleolar structure, but nucleolar assembly can be restored by decreasing ribosomal gene copy number from 190 to 25. Statistical analysis of Miller spreads in the absence of Rpa49 demonstrates a fourfold decrease in Pol I loading rate per gene and decreased contact between adjacent Pol I complexes. Therefore, the Rpa34 and Rpa49 Pol I–specific subunits are essential for nucleolar assembly and for the high polymerase loading rate associated with frequent contact between adjacent enzymes. Together our data suggest that localized rRNA production results in spatially constrained rRNA production, which is instrumental for nucleolar assembly.

A Description of the Stationary Wave Pattern of a Marine Craft in Shallow and Intermediate Water Depths

A stationary phase model is used to study supercritical waves generated by high speed ferries. Some general relationships in terms of wave angle, propagation direction, dispersion relationship and depth wavelength relationship are explored and discussed. In particular, it is shown that the wave pattern generated by high speed craft at supercritical speeds depends mainly on the relationship of water depth and ship speed and that the wave patterns are similar in terms of location of crests and troughs for a given depth Froude number. In addition it is found that the far field wave pattern can be described adequately using a single moving point source. The theoretical model compares well with towing tank measurements and full scale data over a range of parameters and hull shapes. The paper also demonstrates that the far field wave pattern at supercritical speeds should be non-dimensionalised by water depth and not hull length unlike it is usually done for subcritical speeds.

The tumor suppressor gene DLEC1 is frequently silenced by DNA methylation in hepatocellular carcinoma and induces G1 arrest in cell cycle

Background/Aims: The chromosome locus 3p21.3 is a