The Average Mutual Information Profile as a Genomic Signature

Background: Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also provide the means for identifying and discriminating organisms using genomic data. Species specific genomic signatures are useful in a variety of contexts such as evolutionary analysis, assembly and classification of genomic sequences from large uncultivated microbial communities and a rapid identification system in health hazard situations. Results: We have analyzed genomic sequences of eukaryotic and prokaryotic chromosomes as well as various subtypes of viruses using an information theoretic framework. We confirm the existence of a species specific average mutual information (AMI) profile. We use these profiles to define a very simple, computationally efficient, alignment free, distance measure that reflects the evolutionary relationships between genomic sequences. We use this distance measure to classify chromosomes according to species of origin, to separate and cluster subtypes of the HIV-1 virus, and classify DNA fragments to species of origin. Conclusion: AMI profiles of DNA sequences prove to be species specific and easy to compute. The structure of AMI profiles are conserved, even in short subsequences of a species\u27 genome, rendering a pervasive signature. This signature can be used to classify relatively short DNA fragments to species of origin

GMC Collisions as Triggers of Star Formation. V. Observational Signatures

We present calculations of molecular, atomic and ionic line emission from simulations of giant molecular cloud (GMC) collisions. We post-process snapshots of the magneto-hydrodynamical simulations presented in an earlier paper in this series by Wu et al. (2017) of colliding and non-colliding GMCs. Using photodissociation region (PDR) chemistry and radiative transfer we calculate the level populations and emission properties of $^{12}$CO $J=1-0$, [CI] $^3{\rm P}_1\rightarrow{^3{\rm P}}_0$ at $609\,\mu$m, [CII] $158\,\mu$m and [OI] $^3{\rm P}_1\rightarrow{^3{\rm P}}_0$ transition at $63\,\mu$m. From integrated intensity emission maps and position-velocity diagrams, we find that fine-structure lines, particularly the [CII] $158\,\mu$m, can be used as a diagnostic tracer for cloud-cloud collision activity. These results hold even in more evolved systems in which the collision signature in molecular lines has been diminished.Comment: 10 pages, 7 figures, accepted for publication in ApJ, comments welcom

An Information-Theoretic Approach to Optimize JWST Observations and Retrievals of Transiting Exoplanet Atmospheres

We provide an example of an analysis to explore the optimization of observations of transiting hot jupiters with JWST to characterize their atmospheres, based on a simple three-parameter forward model. We construct expansive forward model sets for eleven hot jupiters, ten of which are relatively well-characterized, exploring a range of parameters such as equilibrium temperature and metallicity, as well as considering host stars over a wide range in brightness. We compute posterior distributions of our model parameters for each planet with all of the available JWST spectroscopic modes and several programs of combined observations and compute their effectiveness using the metric of estimated mutual information per degree of freedom. From these simulations, clear trends emerge that provide guidelines for designing a JWST observing program. We demonstrate that these guidelines apply over a wide range of planet parameters and target brightnesses for our simple forward model.Comment: Accepted to ApJ, 25 pages, 14 figures, 8 table

Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes

Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription factor and its target(s). These include, among others, transcription factor activation by phosphorylation and acetylation, formation of active complexes with one or more co-factors, and mRNA/protein degradation and stabilization processes. This paper presents a first step towards the systematic, genome-wide computational inference of genes that modulate the interactions of specific transcription factors at the post-transcriptional level. The method uses a statistical test based on changes in the mutual information between a transcription factor and each of its candidate targets, conditional on the expression of a third gene. The approach was first validated on a synthetic network model, and then tested in the context of a mammalian cellular system. By analyzing 254 microarray expression profiles of normal and tumor related human B lymphocytes, we investigated the post transcriptional modulators of the MYC proto-oncogene, an important transcription factor involved in tumorigenesis. Our method discovered a set of 100 putative modulator genes, responsible for modulating 205 regulatory relationships between MYC and its targets. The set is significantly enriched in molecules with function consistent with their activities as modulators of cellular interactions, recapitulates established MYC regulation pathways, and provides a notable repertoire of novel regulators of MYC function. The approach has broad applicability and can be used to discover modulators of any other transcription factor, provided that adequate expression profile data are available.Comment: 15 pages, 3 figures, 2 tables; minor changes following referees' comments; accepted to RECOMB0

Use of Average Mutual Information and Derived Measures to Find Coding Regions

One of the important steps in the annotation of genomes is the identification of regions in the genome which code for proteins. One of the tools used by most annotation approaches is the use of signals extracted from genomic regions that can be used to identify whether the region is a protein coding region. Motivated by the fact that these regions are information bearing structures we propose signals based on measures motivated by the average mutual information for use in this task. We show that these signals can be used to identify coding and noncoding sequences with high accuracy. We also show that these signals are robust across species, phyla, and kingdom and can, therefore, be used in species agnostic genome annotation algorithms for identifying protein coding regions. These in turn could be used for gene identification

Information theoretical study of cross-talk mediated signal transduction in MAPK pathways

Biochemical networks related to similar functional pathways are often correlated due to cross-talk among the homologous proteins in the different networks. Using a stochastic framework, we address the functional significance of the cross-talk between two pathways. Our theoretical analysis on generic MAPK pathways reveals cross-talk is responsible for developing coordinated fluctuations between the pathways. The extent of correlation evaluated in terms of the information theoretic measure provides directionality to net information propagation. Stochastic time series and scattered plot suggest that the cross-talk generates synchronization within a cell as well as in a cellular population. Depending on the number of input and output, we identify signal integration and signal bifurcation motif that arise due to inter-pathway connectivity in the composite network. Analysis using partial information decomposition quantifies the net synergy in the information propagation through these branched pathways.Comment: Revised version, 17 pages, 5 figure

Photochemical hazes in sub-Neptunian atmospheres with focus on GJ 1214 b

We study the properties of photochemical hazes in super-Earths/mini-Neptunes atmospheres with particular focus on GJ1214b. We evaluate photochemical haze properties at different metallicities between solar and 10000$\times$solar. Within the four orders of magnitude change in metallicity, we find that the haze precursor mass fluxes change only by a factor of $\sim$3. This small diversity occurs with a non-monotonic manner among the different metallicity cases, reflecting the interaction of the main atmospheric gases with the radiation field. Comparison with relative haze yields at different metallicities from laboratory experiments reveals a qualitative similarity with our theoretical calculations and highlights the contributions of different gas precursors. Our haze simulations demonstrate that higher metallicity results into smaller average particle sizes. Metallicities at and above 100$\times$solar with haze formation yields of $\sim$10$\%$ provide enough haze opacity to satisfy transit observation at visible wavelengths and obscure sufficiently the H$_2$O molecular absorption features between 1.1 $\mu$m and 1.7 $\mu$m. However, only the highest metallicity case considered (10000$\times$solar) brings the simulated spectra into closer agreement with transit depths at 3.6 $\mu$m and 4.5 $\mu$m indicating a high contribution of CO/CO$_2$ in GJ1214b's atmosphere. We also evaluate the impact of aggregate growth in our simulations, in contrast to spherical growth, and find that the two growth modes provide similar transit signatures (for D$_f$=2), but with different particle size distributions. Finally, we conclude that the simulated haze particles should have major implications for the atmospheric thermal structure and for the properties of condensation clouds

A universal formula for the relativistic correction to the mutual friction coupling time-scale in neutron stars

Vortex-mediated mutual friction governs the coupling between the superfluid and normal components in neutron star interiors. By, for example, comparing precise timing observations of pulsar glitches with theoretical predictions it is possible to constrain the physics in the interior of the star, but to do so an accurate model of the mutual friction coupling in general relativity is needed. We derive such a model directly from Carter's multifluid formalism, and study the vortex structure and coupling time-scale between the components in a relativistic star. We calculate how general relativity modifies the shape and the density of the quantized vortices and show that, in the quasi-Schwarzschild coordinates, they can be approximated as straight lines for realistic neutron star configurations. Finally, we present a simple universal formula (given as a function of the stellar compactness alone) for the relativistic correction to the glitch rise-time, which is valid under the assumption that the superfluid reservoir is in a thin shell in the crust or in the outer core. This universal relation can be easily employed to correct, a posteriori, any Newtonian estimate for the coupling time-scale, without any additional computational expense.Comment: 20 pages, 7 figure