Modularity Enhances the Rate of Evolution in a Rugged Fitness Landscape

Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. Approximately 25\% of the observed rate of fitness increase of the virus could be ascribed to a modular viral landscape.Comment: 45 pages; 7 figure

A halo bias function measured deeply into voids without stochasticity

We study the relationship between dark-matter haloes and matter in the MIP $N$-body simulation ensemble, which allows precision measurements of this relationship, even deeply into voids. What enables this is a lack of discreteness, stochasticity, and exclusion, achieved by averaging over hundreds of possible sets of initial small-scale modes, while holding fixed large-scale modes that give the cosmic web. We find (i) that dark-matter-halo formation is greatly suppressed in voids; there is an exponential downturn at low densities in the otherwise power-law matter-to-halo density bias function. Thus, the rarity of haloes in voids is akin to the rarity of the largest clusters, and their abundance is quite sensitive to cosmological parameters. The exponential downturn appears both in an excursion-set model, and in a model in which fluctuations evolve in voids as in an open universe with an effective $\Omega_m$ proportional to a large-scale density. We also find that (ii) haloes typically populate the average halo-density field in a super-Poisson way, i.e. with a variance exceeding the mean; and (iii) the rank-order-Gaussianized halo and dark-matter fields are impressively similar in Fourier space. We compare both their power spectra and cross-correlation, supporting the conclusion that one is roughly a strictly-increasing mapping of the other. The MIP ensemble especially reveals how halo abundance varies with `environmental' quantities beyond the local matter density; (iv) we find a visual suggestion that at fixed matter density, filaments are more populated by haloes than clusters.Comment: Changed to version accepted by MNRA

A CRY-BIC negative-feedback circuitry regulating blue light sensitivity of Arabidopsis.

Cryptochromes are blue light receptors that regulate various light responses in plants. Arabidopsis cryptochrome 1 (CRY1) and cryptochrome 2 (CRY2) mediate blue light inhibition of hypocotyl elongation and long-day (LD) promotion of floral initiation. It has been reported recently that two negative regulators of Arabidopsis cryptochromes, Blue light Inhibitors of Cryptochromes 1 and 2 (BIC1 and BIC2), inhibit cryptochrome function by blocking blue light-dependent cryptochrome dimerization. However, it remained unclear how cryptochromes regulate the BIC gene activity. Here we show that cryptochromes mediate light activation of transcription of the BIC genes, by suppressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), resulting in activation of the transcription activator ELONGATED HYPOCOTYL 5 (HY5) that is associated with chromatins of the BIC promoters. These results demonstrate a CRY-BIC negative-feedback circuitry that regulates the activity of each other. Surprisingly, phytochromes also mediate light activation of BIC transcription, suggesting a novel photoreceptor co-action mechanism to sustain blue light sensitivity of plants under the broad spectra of solar radiation in nature

Climate effects of seasonally varying Biomass Burning emitted Carbonaceous Aerosols (BBCA)

The climate impact of the seasonality of Biomass Burning emitted Carbonaceous Aerosols (BBCA) is studied using an aerosol-climate model coupled with a slab ocean model in a set of 60-year long simulations, driven by BBCA emission data with and without seasonal variation, respectively. The model run with seasonally varying emission of BBCA leads to an increase in the external mixture of carbonaceous aerosols as well as in the internal mixture of organic carbon and sulfate but a decrease in the internal mixture of black carbon and sulfate relative to those in the run with constant annual BBCA emissions, as a result of different strengths of source/sink processes. The differences in atmospheric direct radiative forcing (DRF) caused by BBCA seasonality are in phase with the differences in column concentrations of the external mixture of carbonaceous aerosols in space and time. In contrast, the differences in all-sky radiative forcing at the top of the atmosphere and at the earth's surface extend beyond the BBCA source regions due to climate feedback through cloud distribution and precipitation. The seasonality of biomass burning emissions uniquely affects the global distributions of convective clouds and precipitation, indicating that these emissions have an impact on atmospheric circulation. In addition, the climate response to the periodic climate forcing of BBCA is not limited to biomass burning seasons but dynamically extends into non-biomass burning seasons as well.United States. National Aeronautics and Space Administration (grant NNX07AI49G)National Science Foundation (U.S.) (grant ATM-0329759)MIT Joint Program on the Science and Policy of Global Chang

Disruption of the mouse MRF4 gene identifies multiple waves of myogenesis in the myotome

MRF4 (herculin/Myf-6) is one of the four member MyoD family of transcription factors identified by their ability to enforce skeletal muscle differentiation upon a wide variety of nonmuscle cell types. In this study the mouse germline MRF4 gene was disrupted by targeted recombination. Animals homozygous for the MRF4bh1 allele, a deletion of the functionally essential bHLH domain, displayed defective axial myogenesis and rib pattern formation, and they died at birth. Differences in somitogenesis between homozygous MRF4bh1 embryos and their wild-type littermates provided evidence for three distinct myogenic regulatory programs (My1-My3) in the somite, which correlate temporally and spatially with three waves of cellular recruitment to the expanding myotome. The first program (My1), marked initially by Myf-5 expression and followed by myogenin, began on schedule in the MRF4bh1/bh1 embryos at day 8 post coitum (E8). A second program (My2) was highly deficient in homozygous mutant MRF4 embryos, and normal expansion of the myotome failed. Moreover, expression of downstream muscle-specific genes, including FGF-6, which is a candidate regulator of inductive interactions, did not occur normally. The onset of MyoD expression around E10.5 in wild-type embryos marks a third myotomal program (My3), the execution of which was somewhat delayed in MRF4 mutant embryos but ultimately led to extensive myogenesis in the trunk. By E15 it appeared to have largely compensated for the defective My2 program in MRF4 mutants. Homozygous MRF4bh1 animals also showed improper rib pattern formation perhaps due to the absence of signals from cells expressing the My2 program. Finally, a later and relatively mild phenotype was detected in intercostal muscles of newborn animals

Characterization of copy numbers of 16S rDNA and 16S rRNA of Candidatus Liberibacter asiaticus and the implication in detection in planta using quantitative PCR

<p>Abstract</p> <p>Background</p> <p>Citrus Huanglongbing (HLB) is one of the most devastating diseases on citrus and is associated with <it>Candidatus </it>Liberibacter spp.. The pathogens are phloem limited and have not been cultured <it>in vitro</it>. The current management strategy of HLB is to remove infected citrus trees and reduce psyllid populations with insecticides to prevent the spreading. This strategy requires sensitive and reliable diagnostic methods for early detection.</p> <p>Results</p> <p>We investigated the copy numbers of the 16S rDNA and 16S rRNA of the HLB pathogen and the implication of improving the diagnosis of HLB for early detection using Quantitative PCR. We compared the detection of HLB with different Quantitative PCR based methods with primers/probe targeting either 16S rDNA, beta-operon DNA, 16S rRNA, or beta-operon RNA. The 16S rDNA copy number of <it>Ca</it>. Liberibacter asiaticus was estimated to be three times of that of the beta-operon region, thus allowing detection of lower titer of <it>Ca</it>. L. asiaticus. Quantitative reverse transcriptional PCR (QRT-PCR) indicated that the 16S rRNA averaged 7.83 times more than that of 16S rDNA for the same samples. Dilution analysis also indicates that QRT-PCR targeting 16S rRNA is 10 time more sensitive than QPCR targeting 16S rDNA. Thus QRT-PCR was able to increase the sensitivity of detection by targeting 16S rRNA.</p> <p>Conclusion</p> <p>Our result indicates that <it>Candidatus </it>Liberibacter asiaticus contains three copies of 16S rDNA. The copy number of 16S rRNA of <it>Ca</it>. L. asiaticus <it>in planta </it>averaged about 7.8 times of 16S rDNA for the same set of samples tested in this study. Detection sensitivity of HLB could be improved through the following approaches: using 16S rDNA based primers/probe in the QPCR assays; and using QRT-PCR assays targeting 16S rRNA.</p

Design of a Formation of Solar Pumped Lasers for Asteroid Deflection

This paper presents the design of a multi-spacecraft system for the deflection of asteroids. Each spacecraft is equipped with a fibre laser and a solar concentrator. The laser induces the sublimation of a portion of the surface of the asteroid. The jet of gas and debris thrusts the asteroid off its natural course. The main idea is to have a swarm of spacecraft flying in the proximity of the asteroid with all the spacecraft beaming to the same location to achieve the required deflection thrust. The paper presents the design of the formation orbits and the multi-objective optimization of the swarm in order to minimize the total mass in space and maximize the deflection of the asteroid. The paper demonstrates how significant deflections can be obtained with relatively small sized, easy-to-control spacecraft.Comment: Advances in Space Research, 201

Entropy Optimization of Scale-Free Networks Robustness to Random Failures

Many networks are characterized by highly heterogeneous distributions of links, which are called scale-free networks and the degree distributions follow $p(k)\sim ck^{-\alpha}$. We study the robustness of scale-free networks to random failures from the character of their heterogeneity. Entropy of the degree distribution can be an average measure of a network's heterogeneity. Optimization of scale-free network robustness to random failures with average connectivity constant is equivalent to maximize the entropy of the degree distribution. By examining the relationship of entropy of the degree distribution, scaling exponent and the minimal connectivity, we get the optimal design of scale-free network to random failures. We conclude that entropy of the degree distribution is an effective measure of network's resilience to random failures.Comment: 9 pages, 5 figures, accepted by Physica