Stochastic Turing patterns in the Brusselator model

A stochastic version of the Brusselator model is proposed and studied via the system size expansion. The mean-field equations are derived and shown to yield to organized Turing patterns within a specific parameters region. When determining the Turing condition for instability, we pay particular attention to the role of cross diffusive terms, often neglected in the heuristic derivation of reaction diffusion schemes. Stochastic fluctuations are shown to give rise to spatially ordered solutions, sharing the same quantitative characteristic of the mean-field based Turing scenario, in term of excited wavelengths. Interestingly, the region of parameter yielding to the stochastic self-organization is wider than that determined via the conventional Turing approach, suggesting that the condition for spatial order to appear can be less stringent than customarily believed.Comment: modified version submitted to Phys Rev. E. 5. 3 Figures (5 panels) adde

Drosophila histone locus bodies form by hierarchical recruitment of components

An assembly process involving sequential recruitment of components and hierarchical dependency drives formation of the nuclear structures known as histone locus bodies

How to build a paraspeckle

Noncoding RNAs have recently been identified as essential components of the enigmatic nuclear suborganelles called paraspeckles

Mechanical Attributes of Fractal Dragons

Fractals are ubiquitous natural emergences that have gained increased attention in engineering applications, thanks to recent technological advancements enabling the fabrication of structures spanning across many spatial scales. We show how the geometries of fractals can be exploited to determine their important mechanical properties, such as the first and second moments, which physically correspond to the center of mass and the moment of inertia, using a family of complex fractals known as the dragons

THE FORMATION AND FUNCTION OF THE HISTONE LOCUS BODY IN HISTONE mRNA BIOGENESIS

The genome exerts spatial and temporal control of gene expression through the compartmentalization of nuclear space into specialized substructures known as nuclear bodies (NBs). NBs are defined by light microscopy as the concentration of factors involved in specific biological reactions. In concentrating reaction factors and substrates in a distinct microenvironment, NBs are postulated to promote the efficiency of their associated reaction. However, a complete appreciation of how NBs form is needed to understand how NBs contribute to their in vivo reactions. To understand the relationship between formation and function of NBs I used the Drosophila melanogaster Histone Locus Body (HLB) as a model. The HLB assembles at replication-dependent (RD) histone genes and contains factors involved in histone mRNA biogenesis (i.e. transcription and processing). The RD histone mRNAs are of only known eukaryotic RNAs that do not end in a polyadenylated tail but rather end in a conserved stemloop. We defined critical sequences within the 300nt H3-H4 bidirectional promoter that are essential for HLB formation, histone expression, and recruitment of a zinc-finger DNA binding protein, CLAMP, that helps regulate the locus. I then used engineered histone locus transgenes and found that the cis sequences required for HLB formation are dependent on the presence of the endogenous histone gene locus. I demonstrated that the H2a-H2b promoter can nucleate HLB components but only in the absence of the endogenous histone genes. This work suggests a role of multivalent interactions in the formation of the HLB. This work provides insights into how the HLB forms and how this formation is related to the HLBs role in coordinating the steps in histone mRNA biosynthesis.Doctor of Philosoph

Analysis of time dynamics in wind records by means of multifractal detrended fluctuation analysis and Fisher-Shannon information plane

The time structure of more than 10 years of hourly wind data measured in one site in northern Italy from April 1996 to December 2007 is analysed. The data are recorded by the Sodar Rass system, which measures the speed and the direction of the wind at several heights above the ground level. To investigate the wind speed time series at seven heights above the ground level we used two different approaches: i) the Multifractal Detrended Fluctuation Analysis (MF-DFA), which permits the detection of multifractality in nonstationary series, and ii) the Fisher-Shannon (FS) information plane, which allows to discriminate dynamical features in complex time series. Our results point out to the existence of multifractal time fluctuations in wind speed and to a dependence of the results on the height of the wind sensor. Even in the FS information plane a height-dependent pattern is revealed, indicating a good agreement with the multifractality. The obtained results could contribute to a better understanding of the complex dynamics of wind phenomenon

In Vitro RNase and Nucleic Acid Binding Activities Implicate Coilin in U snRNA Processing

Coilin is known as the marker protein for Cajal bodies (CBs), subnuclear domains important for the biogenesis of small nuclear ribonucleoproteins (snRNPs) which function in pre-mRNA splicing. CBs associate non-randomly with U1 and U2 gene loci, which produce the small nuclear RNA (snRNA) component of the respective snRNP. Despite recognition as the CB marker protein, coilin is primarily nucleoplasmic, and the function of this fraction is not fully characterized. Here we show that coilin binds double stranded DNA and has RNase activity in vitro. U1 and U2 snRNAs undergo a processing event of the primary transcript prior to incorporation in the snRNP. We find that coilin displays RNase activity within the CU region of the U2 snRNA primary transcript in vitro, and that coilin knockdown results in accumulation of the 3′ pre-processed U1 and U2 snRNA. These findings present new characteristics of coilin in vitro, and suggest additional functions of the protein in vivo

Nuclear Bodies: Random Aggregates of Sticky Proteins or Crucibles of Macromolecular Assembly?

The principles of self-assembly and self-organization are major tenets of molecular and cellular biology. Governed by these principles, the eukaryotic nucleus is composed of numerous subdomains and compartments, collectively described as nuclear bodies. Emerging evidence reveals that associations within and between various nuclear bodies and genomic loci are dynamic and can change in response to cellular signals. This review will discuss recent progress in our understanding of how nuclear body components come together, what happens when they form, and what benefit these subcellular structures may provide to the tissues or organisms in which they are found