Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli.

Bacterial populations have a remarkable capacity to cope with extreme environmental fluctuations in their natural environments. In certain cases, adaptation to one stressful environment provides a fitness advantage when cells are exposed to a second stressor, a phenomenon that has been coined as cross-stress protection. A tantalizing question in bacterial physiology is how the cross-stress behavior emerges during evolutionary adaptation and what the genetic basis of acquired stress resistance is. To address these questions, we evolved Escherichia coli cells over 500 generations in five environments that include four abiotic stressors. Through growth profiling and competition assays, we identified several cases of positive and negative cross-stress behavior that span all strain-stress combinations. Resequencing the genomes of the evolved strains resulted in the identification of several mutations and gene amplifications, whose fitness effect was further assessed by mutation reversal and competition assays. Transcriptional profiling of all strains under a specific stress, NaCl-induced osmotic stress, and integration with resequencing data further elucidated the regulatory responses and genes that are involved in this phenomenon. Our results suggest that cross-stress dependencies are ubiquitous, highly interconnected, and can emerge within short timeframes. The high adaptive potential that we observed argues that bacterial populations occupy a genotypic space that enables a high phenotypic plasticity during adaptation in fluctuating environments.

A flood-based information flow analysis and network minimization method for gene regulatory networks.

BACKGROUND: Biological networks tend to have high interconnectivity, complex topologies and multiple types of interactions. This renders difficult the identification of sub-networks that are involved in condition- specific responses. In addition, we generally lack scalable methods that can reveal the information flow in gene regulatory and biochemical pathways. Doing so will help us to identify key participants and paths under specific environmental and cellular context. RESULTS: This paper introduces the theory of network flooding, which aims to address the problem of network minimization and regulatory information flow in gene regulatory networks. Given a regulatory biological network, a set of source (input) nodes and optionally a set of sink (output) nodes, our task is to find (a) the minimal sub-network that encodes the regulatory program involving all input and output nodes and (b) the information flow from the source to the sink nodes of the network. Here, we describe a novel, scalable, network traversal algorithm and we assess its potential to achieve significant network size reduction in both synthetic and E. coli networks. Scalability and sensitivity analysis show that the proposed method scales well with the size of the network, and is robust to noise and missing data. CONCLUSIONS: The method of network flooding proves to be a useful, practical approach towards information flow analysis in gene regulatory networks. Further extension of the proposed theory has the potential to lead in a unifying framework for the simultaneous network minimization and information flow analysis across various "omics" levels.

Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation.

BACKGROUND: During their lifetime, microbes are exposed to environmental variations, each with its distinct spatio-temporal dynamics. Microbial communities display a remarkable degree of phenotypic plasticity, and highly-fit individuals emerge quite rapidly during microbial adaptation to novel environments. However, there exists a high variability when it comes to adaptation potential, and while adaptation occurs rapidly in certain environmental transitions, in others organisms struggle to adapt. Here, we investigate the hypothesis that the rate of evolution can both increase or decrease, depending on the similarity and complexity of the intermediate and final environments. Elucidating such dependencies paves the way towards controlling the rate and direction of evolution, which is of interest to industrial and medical applications. RESULTS: Our results show that the rate of evolution can be accelerated by evolving cell populations in sequential combinations of environments that are increasingly more complex. To quantify environmental complexity, we evaluate various information-theoretic metrics, and we provide evidence that multivariate mutual information between environmental signals in a given environment correlates well with the rate of evolution in that environment, as measured in our simulations. We find that strong positive and negative correlations between the intermediate and final environments lead to the increase of evolutionary rates, when the environmental complexity increases. Horizontal Gene Transfer is shown to further augment this acceleration, under certain conditions. Interestingly, our simulations show that weak environmental correlations lead to deceleration of evolution, regardless of environmental complexity. Further analysis of network evolution provides a mechanistic explanation of this phenomenon, as exposing cells to intermediate environments can trap the population to local neighborhoods of sub-optimal fitness.

Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution.

BACKGROUND: Horizontal gene transfer (HGT) is a process that facilitates the transfer of genetic material between organisms that are not directly related, and thus can affect both the rate of evolution and emergence of traits. Recent phylogenetic studies reveal HGT events are likely ubiquitous in the Tree of Life. However, our knowledge of HGT's role in evolution and biological organization is very limited, mainly due to the lack of ancestral evolutionary signatures and the difficulty to observe complex evolutionary dynamics in a laboratory setting. Here, we utilize a multi-scale microbial evolution model to comprehensively study the effect of HGT on the evolution of complex traits and organization of gene regulatory networks. RESULTS: Large-scale simulations reveal a distinct signature of the Distribution of Fitness Effect (DFE) for HGT events: during evolution, while mutation fitness effects become more negative and neutral, HGT events result in a balanced effect distribution. In either case, lethal events are significantly decreased during evolution (33.0% to 3.2%), a clear indication of mutational robustness. Interestingly, evolution was accelerated when populations were exposed to correlated environments of increasing complexity, especially in the presence of HGT, a phenomenon that warrants further investigation. High HGT rates were found to be disruptive, while the average transferred fragment size was linked to functional module size in the underlying biological network. Network analysis reveals that HGT results in larger regulatory networks, but with the same sparsity level as those evolved in its absence. Observed phenotypic variability and co-existing solutions were traced to individual gain/loss of function events, while subsequent re-wiring after fragment integration was necessary for complex traits to emerge.

Electronic structure and spectroscopy of oxyallyl: a theoretical study.

Electronic structure of the oxyallyl diradical and the anion is investigated using high-level ab initio methods. Converged theoretical estimates of the energy differences between low-lying electronic states of oxyallyl (OXA) as well as detachment energies of the anion are reported. Our best estimates of the adiabatic energy differences between the anion (2)A(2) and the neutral (3)B(2) and (3)B(1) states are 1.94 and 2.73 eV, respectively. The (1)A(1) state lies above (3)B(2) vertically, but geometric relaxation brings it below the triplet. The two-dimensional scan of the singlet (1)A(1) potential energy surface (PES) reveals that there is no minimum corresponding to a singlet diradical structure. Thus, singlet OXA undergoes prompt barrierless ring closure. However, a flat shape of the PES results in the resonance trapping in the Franck-Condon region, giving rise to the experimentally observable features in the photoelectron spectrum. By performing reduced-dimensionality wave packet calculations, we estimated that the wave packet lingers in the Franck-Condon region for about 170 fs, which corresponds to the spectral line broadening of about 200 cm(-1). We also present calculations of the photodetachment spectrum and compare it with experimental data. Our calculations lend strong support to the assignment of the photoelectron spectrum of the OXA anion reported in Ichino et al. (Angew. Chem., Int. Ed. Engl. 2009, 48, 8509).

Ab initio calculation of the photoelectron spectra of the hydroxycarbene diradicals.

Photoelectron spectra of the cis and trans isomers of HCOH were computed using vibrational wave functions calculated by diagonalizing the Watson Hamiltonian, including up to four mode couplings. The full-dimensional CCSD(T)/cc-pVTZ potential energy surfaces were employed in the calculation. Photoionization induces significant changes in equilibrium structures, which results in long progressions in the nu(5), nu(4), and nu(3) modes. The two isomers show progressions in different modes, which leads to qualitatively distinguishable spectra. The spectra were also calculated in the double harmonic parallel-mode (i.e, neglecting Duschinsky rotation) approximation. Calculating displacements along the normal coordinates of the cation state was found to give a better approximation to the vibrational configuration interaction spectrum; this is due to the effects of Duschinsky rotations on the vibrational wave functions.

Conical for stepwise, glancing for concerted: the role of the excited-state topology in the three-body dissociation of sym-triazine.

The highly debated three-body dissociation of sym-triazine to three HCN products has been investigated by translational spectroscopy and high-level ab initio calculations. Dissociation was induced by charge exchange between the sym-triazine radical cation and cesium. Calculated state energies and electronic couplings suggest that sym-triazine is produced in the 3s Rydberg and pi* <-- n manifolds. Analysis of the topology of these manifolds along with momentum correlation in the dissociation products suggest that the 3s Rydberg manifold characterized by a conical intersection of two potential energy surfaces leads to stepwise dissociation, while the pi* <-- n manifold consisting of a four-fold glancing intersection leads to a symmetric concerted reaction.

TEG-seq: an ion torrent-adapted NGS workflow for in cellulo mapping of CRISPR specificity.

GUIDE-seq was developed to detect CRISPR/Cas9 off-target. However, as originally reported, it was associated with a high level of nonspecific amplification. In an attempt to improve it, we developed target-enriched GUIDE-seq (TEG-seq). The sensitivity level reached 0.1-10 reads-per-million  depending on the NGS platform used, which was equivalent to 0.0002-1% measured by Targeted Amplicon-seq. Application of TEG-seq was demonstrated for the evaluation of various Cas9/gRNA configurations, which suggests delivery of Cas9/gRNA ribonucleoprotein results in significantly fewer off-targets than Cas9/gRNA plasmid. TEG-seq was also applied to 22 gRNAs with relatively high in silico ranking score that targeted the biological relevant SNPs. The result indicated the initial selection of gRNAs with high score is important, although it cannot exclude the possibility of off-target.

Microbial evolution in vivo and in silico: methods and applications.

Microbial evolution has been extensively studied in the past fifty years, which has lead to seminal discoveries that have shaped our understanding of evolutionary forces and dynamics. It is only recently however, that transformative technologies and computational advances have enabled a larger in-scale and in-depth investigation of the genetic basis and mechanistic underpinnings of evolutionary adaptation. In this review we focus on the strengths and limitations of in vivo and in silico techniques for studying microbial evolution in the laboratory, and we discuss how these complementary approaches can be integrated in a unifying framework for elucidating microbial evolution.

The Role of excited-state topology in three-body dissociation of sym-triazine.

Molecular fragmentation into three products poses an analytical challenge to theory and experiment alike. We used translational spectroscopy and high-level ab initio calculations to explore the highly debated three-body dissociation of sym-triazine to three hydrogen cyanide molecules. Dissociation was induced by charge exchange between the sym-triazine radical cation and cesium. Calculated state energies and electronic couplings suggest that reduction initially produces a population of sym-triazine partitioned between the 3s Rydberg and pi* <-- n electronically excited manifolds. Analysis of the topology of these manifolds, along with momentum correlation in the dissociation products, suggests that a conical intersection of two potential energy surfaces in the 3s Rydberg manifold leads to stepwise dissociation, whereas a four-fold glancing intersection in the pi* <-- n manifold leads to a symmetric concerted reaction.

Use of helium nanodroplets for assembly, transport, and surface deposition of large molecular and atomic clusters.

The utility of continuous beam of helium droplets for assembly, transport, and surface deposition of metal and molecular clusters is studied. Clusters of propyne having from about 10 to 10(4) molecules were obtained via sequential pickup of molecules by He droplets with average sizes in the range of 10(4)-10(7) atoms. The maximum attainable flux of the propyne molecules carried by He droplets was found to be in the range of (5-15)x10(15) molecules sr(-1) s(-1), being larger in larger droplets. The size of the clusters and the flux of the transported species are ultimately limited by the evaporative extinction of the entire helium droplet upon capture of particles. It is shown that the attenuation of the He droplet beam in the process of the cluster growth can be used in order to obtain the average size and the binding energy of the clusters. Furthermore, we used He droplets for assembling and surface deposition of gold and silver clusters having about 500 atoms. Typical deposition rate of metal atoms of about 3 x 10(15) atoms sr(-1) s(-1) is comparable to or larger than obtained with other beam deposition techniques. We propose that doping of He droplets by Au and Ag atoms in two separate pickup chambers leads to formation of the bimetal clusters having core-shell structure.

Conical and glancing Jahn-Teller intersections in the cyclic trinitrogen cation.

The ground and electronically excited states of cyclic N(3) (+) are characterized at the equilibrium D(3h) geometry and along the Jahn-Teller distortions. Lowest excited states are derived from single excitations from the doubly degenerate highest occupied molecular orbitals (HOMOs) to the doubly degenerate lowest unoccupied molecular orbitals (LUMOs), which give rise to two exactly and two nearly degenerate states. The interaction of two degenerate states with two other states eliminates linear terms and results in a glancing rather than conical Jahn-Teller intersection. HOMO-2-->LUMOs excitations give rise to two regular Jahn-Teller states. Optimized structures, vertical and adiabatic excitation energies, frequencies, and ionization potential (IP) are presented. IP is estimated to be 10.595 eV, in agreement with recent experiments.

The photoelectron spectrum of elusive cyclic-N3 and characterization of the potential energy surface and vibrational states of the ion.

A potential energy surface is constructed for the ground X (1)A(1) electronic state of cyclic-N(3) (+) based on three-dimensional spline interpolation of ab initio points. The vibrational states of this molecular ion are calculated in the range up to 14 500 cm(-1) using hyperspherical coordinates and the coupled-channel (sector-adiabatic) approach. All the vibrational states are analyzed and assigned. The Franck-Condon overlaps of these states with the vibrational states of the neutral are calculated to predict the photoelectron spectrum of cyclic-N(3). Peak intensities are governed by the nodal structure of the vibrational wave functions and reflect the large geometric phase effect predicted for cyclic-N(3). Experimental validation may shed light on the existence of this elusive molecule and confirm the magnitude of the geometric phase effect.