Phylogenetic reconstruction from transpositions

Background Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangement of these entities through computational means. As a result, genome rearrangement data has attracted increasing attentions from both biologists and computer scientists as a new type of data for phylogenetic analysis. The main events of genome rearrangements include inversions, transpositions and transversions. To date, GRAPPA and MGR are the most accurate methods for rearrangement phylogeny, both assuming inversion as the only event. However, due to the complexity of computing transposition distance, it is very difficult to analyze datasets when transpositions are dominant. Results We extend GRAPPA to handle transpositions. The new method is named GRAPPA-TP, with two major extensions: a heuristic method to estimate transposition distance, and a new transposition median solver for three genomes. Although GRAPPA-TP uses a greedy approach to compute the transposition distance, it is very accurate when genomes are relatively close. The new GRAPPA-TP is available from http://phylo.cse.sc.edu/ Conclusion Our extensive testing using simulated datasets shows that GRAPPA-TP is very accurate in terms of ancestor genome inference and phylogenetic reconstruction. Simulation results also suggest that model match is critical in genome rearrangement analysis: it is not accurate to simulate transpositions with other events including inversions

Phylogeny Analysis from Gene-Order Data with Massive Duplications

Background: Gene order changes, under rearrangements, insertions, deletions and duplications, have been used as a new type of data source for phylogenetic reconstruction. Because these changes are rare compared to sequence mutations, they allow the inference of phylogeny further back in evolutionary time. There exist many computational methods for the reconstruction of gene-order phylogenies, including widely used maximum parsimonious methods and maximum likelihood methods. However, both methods face challenges in handling large genomes with many duplicated genes, especially in the presence of whole genome duplication. Methods: In this paper, we present three simple yet powerful methods based on maximum-likelihood (ML) approaches that encode multiplicities of both gene adjacency and gene content information for phylogenetic reconstruction. Results: Extensive experiments on simulated data sets show that our new method achieves the most accurate phylogenies compared to existing approaches. We also evaluate our method on real whole-genome data from eleven mammals. The package is publicly accessible at http://www.geneorder.org. Conclusions: Our new encoding schemes successfully incorporate the multiplicity information of gene adjacencies and gene content into an ML framework, and show promising results in reconstruct phylogenies for whole-genome data in the presence of massive duplications

Plasma transferred arc surface alloying of Cr-Ni-Mo powders on compacted graphite iron

A Cr-Ni-Mo overlayer was deposited on the surface of compacted graphite iron (CGI) by the plasma transferred arc (PTA) alloying technique. The microstructure of Cr-Ni-Mo overlayer was characterized by optical microscopy (OM), scanning electron microscopy (SEM) equipped with energy dispersive spectroscopy (EDS), and X-ray diffractometer (XRD). Results show that the cross-section consists of four regions: alloying zone (AZ), molten zone (MZ), heat affected zone (HAZ), and the substrate (SUB). The microstructure of AZ mainly consists of cellular γ-(Fe, Ni) solid solution, residual austenite and a network of eutectic Cr7C3 carbide while the MZ area has a typical feature of white cast iron (M3C-type cementite). The martensite/ledeburite double shells are observed in the HAZ. With decreasing the concentration of Cr-Ni-Mo alloys, the fracture mode changes from ductile in the AZ to brittle in the MZ. The maximum hardness of the AZ (450 HV0.2) is lower than that of the MZ (800 HV0.2). The eutectic M3C and M7C3 carbides increase the microhardness, while the austenite decreases that of the AZ

Graphene Nucleation on Transition Metal Surface: Structure Transformation and Role of the Metal Step Edge

The nucleation of graphene on a transition metal (TM) surface, either on a terrace or near a step edge, is systematically explored using density functional theory (DFT) calculations and applying the two-dimensional (2D) crystal nucleation theory. Careful optimization of the supported carbon clusters, CN (with size N ranging from 1 to 24), on the Ni(111) surface indicates a ground state structure transformation from a one-dimensional (1D) C chain to a two-dimensional (2D) sp2 C network at N ~ 10-12. Furthermore, the crucial parameters controlling graphene growth on the metal surface, nucleation barrier, nucleus size, and the nucleation rate on a terrace or near a step edge, are calculated. In agreement with numerous experimental observations, our analysis shows that graphene nucleation near a metal step edge is superior to that on a terrace. Based on our analysis, we propose the use of seeded graphene to synthesize high-quality graphene in large area.Comment: 19 pages, 6 figures, accepted in Journal of the American Chemical Societ

Point defects in epitaxial silicene on Ag(111) surface

Silicene, a counterpart of graphene, has achieved rapid development due to its exotic electronic properties and excellent compatibility with the mature silicon-based semiconductor technology. Its low room-temperature mobility of about 100 cm2V-1s-1, however, inhibits device applications such as in field-effect transistors. Generally, defects and grain boundaries would act as scattering centers and thus reduce the carrier mobility. In this paper, the morphologies of various point defects in epitaxial silicene on Ag(111) surfaces have been systematically investigated using first-principles calculations combined with experimental scanning tunneling microscope (STM) observations. The STM signatures for various defects in epitaxial silicene on Ag(111) surface are identified. In particular, the formation energies of point defects in Ag(111)-supported silicene sheets show an interesting dependence on the superstructures, which, in turn, may have implications for controlling the defect density during the synthesis of silicene. Through estimating the concentrations of various point defects in different silicene superstructures, the mystery of the defective appearance of v13*v13 silicene in experiments is revealed, and 4*4 silicene sheet is thought to be the most suitable structure for future device applications.Comment: 29 pages, 14 figure

Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat

Background Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction. Results We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR using divergent chloroplast genomes from land plants and green algae recovers the phylogeny congruent with prior studies, while analysis that do not consider IR structure fail to obtain the accepted topology. Our extensive simulation study also confirms that GRAPPA has better accuracy then the existing methods. Conclusions Tests on a biological and simulated dataset show GRAPPA-IR can accurately recover the genome phylogeny as well as ancestral gene orders. Close analysis of the ancestral genome structure suggests that genome rearrangement in chloroplasts is probably limited by inverted repeats with a conserved core region. In addition, the boundaries of inverted repeats are hot spots for gene duplications or deletions. The new GRAPPA-IR is available from http://phylo.cse.sc.ed

The genetic determinants of language network dysconnectivity in drug-naïve early stage schizophrenia

Schizophrenia is a neurocognitive illness of synaptic and brain network-level dysconnectivity that often reaches a persistent chronic stage in many patients. Subtle language deficits are a core feature even in the early stages of schizophrenia. However, the primacy of language network dysconnectivity and language-related genetic variants in the observed phenotype in early stages of illness remains unclear. This study used two independent schizophrenia dataset consisting of 138 and 53 drug-naïve first-episode schizophrenia (FES) patients, and 112 and 56 healthy controls, respectively. A brain-wide voxel-level functional connectivity analysis was conducted to investigate functional dysconnectivity and its relationship with illness duration. We also explored the association between critical language-related genetic (such as FOXP2) mutations and the altered functional connectivity in patients. We found elevated functional connectivity involving Broca’s area, thalamus and temporal cortex that were replicated in two FES datasets. In particular, Broca’s area - anterior cingulate cortex dysconnectivity was more pronounced for patients with shorter illness duration, while thalamic dysconnectivity was predominant in those with longer illness duration. Polygenic risk scores obtained from FOXP2-related genes were strongly associated with functional dysconnectivity identified in patients with shorter illness duration. Our results highlight the criticality of language network dysconnectivity, involving the Broca’s area in early stages of schizophrenia, and the role of language-related genes in this aberration, providing both imaging and genetic evidence for the association between schizophrenia and the determinants of language

Shared and Distinct Neural Bases of Large- and Small-Scale Spatial Ability: A Coordinate-Based Activation Likelihood Estimation Meta-Analysis

Background: Spatial ability is vital for human survival and development. However, the relationship between large-scale and small-scale spatial ability remains poorly understood. To address this issue from a novel perspective, we performed an activation likelihood estimation (ALE) meta-analysis of neuroimaging studies to determine the shared and distinct neural bases of these two forms of spatial ability.Methods: We searched Web of Science, PubMed, PsycINFO, and Google Scholar for studies regarding “spatial ability” published within the last 20 years (January 1988 through June 2018). A final total of 103 studies (Table 1) involving 2,085 participants (male = 1,116) and 2,586 foci were incorporated into the meta-analysis.Results: Large-scale spatial ability was associated with activation in the limbic lobe, posterior lobe, occipital lobe, parietal lobe, right anterior lobe, frontal lobe, and right sub-lobar area. Small-scale spatial ability was associated with activation in the parietal lobe, occipital lobe, frontal lobe, right posterior lobe, and left sub-lobar area. Furthermore, conjunction analysis revealed overlapping regions in the sub-gyrus, right superior frontal gyrus, right superior parietal lobule, right middle occipital gyrus, right superior occipital gyrus, left inferior occipital gyrus, and precuneus. The contrast analysis demonstrated that the parahippocampal gyrus, left lingual gyrus, culmen, right middle temporal gyrus, left declive, left superior occipital gyrus, and right lentiform nucleus were more strongly activated during large-scale spatial tasks. In contrast, the precuneus, right inferior frontal gyrus, right precentral gyrus, left inferior parietal lobule, left supramarginal gyrus, left superior parietal lobule, right inferior occipital gyrus, and left middle frontal gyrus were more strongly activated during small-scale spatial tasks. Our results further indicated that there is no absolute difference in the cognitive strategies associated with the two forms of spatial ability (egocentric/allocentric).Conclusion: The results of the present study verify and expand upon the theoretical model of spatial ability proposed by Hegarty et al. Our analysis revealed a shared neural basis between large- and small-scale spatial abilities, as well as specific yet independent neural bases underlying each. Based on these findings, we proposed a more comprehensive version of the behavioral model