Bow-tie architecture of gene regulatory networks in species of varying complexity

The gene regulatory network (GRN) architecture plays a key role in explaining the biological differences between species. We aim to understand species differences in terms of some universally present dynamical properties of their gene regulatory systems. A network architectural feature associated with controlling system-level dynamical properties is the bow-tie, identified by a strongly connected subnetwork, the core layer, between two sets of nodes, the in and the out layers. Though a bow-tie architecture has been observed in many networks, its existence has not been extensively investigated in GRNs of species of widely varying biological complexity. We analyse publicly available GRNs of several well-studied species from prokaryotes to unicellular eukaryotes to multicellular organisms. In their GRNs, we find the existence of a bow-tie architecture with a distinct largest strongly connected core layer. We show that the bow-tie architecture is a characteristic feature of GRNs. We observe an increasing trend in the relative core size with species complexity. Using studied relationships of the core size with dynamical properties like robustness and fragility, flexibility, criticality, controllability and evolvability, we hypothesize how these regulatory system properties have emerged differently with biological complexity, based on the observed differences of the GRN bow-tie architectures

Poly(A)-Binding Protein Regulates the Efficiency of Translation Termination

Multiple factors influence translation termination efficiency, including nonsense codon identity and immediate context. To determine whether the relative position of a nonsense codon within an open reading frame (ORF) influences termination efficiency, we quantitate the production of prematurely terminated and/or readthrough polypeptides from 26 nonsense alleles of 3 genes expressed in yeast. The accumulation of premature termination products and the extent of readthrough for the respective premature termination codons (PTCs) manifest a marked dependence on PTC proximity to the mRNA 3\u27 end. Premature termination products increase in relative abundance, whereas readthrough efficiencies decrease progressively across different ORFs, and readthrough efficiencies for a PTC increase in response to 3\u27 UTR lengthening. These effects are eliminated and overall translation termination efficiency decreases considerably in cells harboring pab1 mutations. Our results support a critical role for poly(A)-binding protein in the regulation of translation termination and also suggest that inefficient termination is a trigger for nonsense-mediated mRNA decay (NMD)

Anomalous Neutrino Interaction, Muon g-2, and Atomic Parity Nonconservation

We propose a simple unified description of two recent precision measurements which suggest new physics beyond the Standard Model of particle interactions, i.e. the deviation of $\sin^2 \theta_W$ in deep inelastic neutrino-nucleon scattering and that of the anomalous magnetic moment of the muon. Our proposal is also consistent with a third precision measurement, i.e. that of parity nonconservation in atomic Cesium, which agrees with the Standard Model.Comment: 9 pages, including 1 figure, latest muon g-2 information adde

Evaluating Promotional Approaches for Citizen Science Biological Recording: Bumblebees as a Group Versus Harmonia axyridis as a Flagship for Ladybirds

Over the past decade, the number of biological records submitted by members of the public have increased dramatically. However, this may result in reduced record quality, depending on how species are promoted in the media. Here we examined the two main promotional approaches for citizen science recording schemes: flagship-species, using one charismatic species as an umbrella for the entire group (here, Harmonia axyridis (Pallas) for Coleoptera: Coccinellidae), and general-group, where the group is promoted as a whole and no particular prominence is given to any one species (here, bumblebees, genus Bombus (Hymenoptera: Apidae)). Of the two approaches, the general-group approach produced data that was not biased towards any one species, but far fewer records per year overall. In contrast, the flagship-species approach generated a much larger annual dataset, but heavily biased towards the flagship itself. Therefore, we recommend that the approach for species promotion is fitted to the result desired

Observational constraints on an interacting dark energy model

We use observations of cosmic microwave background anisotropies, supernova luminosities and the baryon acoustic oscillation signal in the galaxy distribution to constrain the cosmological parameters in a simple interacting dark energy model with a time-varying equation of state. Using a Monte Carlo Markov Chain technique we determine the posterior likelihoods. Constraints from the individual data sets are weak, but the combination of the three data sets confines the interaction constant $\Gamma$ to be less than 23% of the expansion rate of the Universe $H_0$; at 95% CL $-0.23 < \Gamma/H_0 < +0.15$. The CMB acoustic peaks can be well fitted even if the interaction rate is much larger, but this requires a larger or smaller (depending on the sign of interaction) matter density today than in the non-interacting model. Due to this degeneracy between the matter density and the interaction rate, the only observable effect on the CMB is a larger or smaller integrated Sachs-Wolfe (ISW) effect. While SN or BAO data alone do not set any direct constraints on the interaction, they exclude the models with very large matter density, and hence indirectly constrain the interaction rate when jointly analysed with the CMB data. To enable the analysis described in this paper, we present in a companion paper [arXiv:0907.4981] a new systematic analysis of the early radiation era solution to find the adiabatic initial conditions for the Boltzmann integration.Comment: 16 pages, 10 figures. V2: Improved typography (2-column format); References and a motivation of CPL parametrization added; Accepted by MNRA