Rearrangement Scenarios Research Articles

Physical aspects of epithelial cell-cell interactions: hidden system complexities.

The maintenance of homeostasis and the retention of ordered epithelial cell self-organization are essential for morphogenesis, wound healing, and the spread of cancer across the epithelium. However, cell-cell interactions in an overcrowded environment introduce a diversity of complications. Such interactions arise from an interplay between the cell compressive and shear stress components that accompany increased cell packing density. They can lead to various kinds of cell rearrangement such as: the epithelial-to-mesenchymal cell state transition; live cell extrusion; and cell jamming. All of these scenarios of cell rearrangement under mechanical stress relate to changes in the strengths of the cell-cell and cell-matrix adhesion contacts. The objective of this review study is twofold: first, to provide a comprehensive summary of the biological and physical factors influencing the effects of cell mechanical stress on cell-cell interactions, and the consequences of these interactions for the status of cell-cell and cell-matrix adhesion contacts; and secondly, to offer a bio-physical/mathematical analysis of the aforementioned biological aspects. By presenting these two approaches in conjunction, we seek to highlight the intricate nature of biological systems, which manifests in the form of complex bio-physical/mathematical equations. Furthermore, the juxtaposition of these apparently disparate approaches underscores the importance of conducting experiments to determine the multitude of parameters that contribute to the development of these intricate bio-physical/mathematical models.

Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera).

Insectmitochondrial genomes(mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinaeand Aleyrodinae are characterized by intense purifying selection pressure.

Tuning the Coefficient of Thermal Expansion of Transparent Lithium Aluminosilicate Glass-Ceramics by a Two-Stage Heat Treatment

Transparent glass-ceramics with a Li2O–Al2O3–SiO2 (LAS) system have been extensively utilized in optical systems in which thermal stability is of utmost importance. This study is aimed to develop thermal treatment routes that can effectively control the structure of transparent LAS glass-ceramics and tune its thermal expansion coefficient within a wide range for novel applications in photonics and integrated optics. The optimal conditions for the nucleation and crystallization of LAS glass were determined by means of differential scanning calorimetry and a polythermal analysis. XRD, Raman spectroscopy, and TEM microscopy were employed to examine the structural changes which occurred after heat treatments. It was found that the second stage of heat treatment promotes the formation of β-eucryptite-like solid solution nanocrystals, which enables effective control of the coefficient of thermal expansion of glass-ceramics in a wide temperature range of −120 to 500 °C. This work provides novel insights into structural rearrangement scenarios occurring in LAS glass, which are crucial for accurately predicting its crystallization behavior and ultimately achieving transparent glass-ceramics with desirable properties.

New algorithms for structure informed genome rearrangement

We define two new computational problems in the domain of perfect genome rearrangements, and propose three algorithms to solve them. The rearrangement scenarios modeled by the problems consider Reversal and Block Interchange operations, and a PQ-tree is utilized to guide the allowed operations and to compute their weights. In the first problem, ConstrainedTreeToStringDivergence\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathsf {Constrained \\ TreeToString \\ Divergence}$$\\end{document} (CTTSD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ extsf{CTTSD}{}$$\\end{document}), we define the basic structure-informed rearrangement measure. Here, we assume that the gene order members of the gene cluster from which the PQ-tree is constructed are permutations. The PQ-tree representing the gene cluster is ordered such that the series of gene IDs spelled by its leaves is equivalent to that of the reference gene order. Then, a structure-informed genome rearrangement distance is computed between the ordered PQ-tree and the target gene order. The second problem, TreeToStringDivergence\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mathsf {TreeToString \\ Divergence}$$\\end{document} (TTSD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ extsf{TTSD}{}$$\\end{document}), generalizes CTTSD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ extsf{CTTSD}{}$$\\end{document}, where the gene order members are not necessarily permutations and the structure informed rearrangement measure is extended to also consider up to dS\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$d_S$$\\end{document} and dT\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$d_T$$\\end{document} gene insertion and deletion operations, respectively, when modelling the PQ-tree informed divergence process from the reference gene order to the target gene order. The first algorithm solves CTTSD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ extsf{CTTSD}{}$$\\end{document} in O(nγ2·(mp·1.381γ+mq))\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$O(n \\gamma ^2 \\cdot (m_p \\cdot 1.381^\\gamma + m_q))$$\\end{document} time and O(n2)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$O(n^2)$$\\end{document} space, where γ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\gamma $$\\end{document} is the maximum number of children of a node, n is the length of the string and the number of leaves in the tree, and mp\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$m_p$$\\end{document} and mq\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$m_q$$\\end{document} are the number of P-nodes and Q-nodes in the tree, respectively. If one of the penalties of CTTSD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ extsf{CTTSD}$$\\end{document} is 0, then the algorithm runs in O(nmγ2)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$O(n m \\gamma ^2)$$\\end{document} time and O(n2)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$O(n^2)$$\\end{document} space. The second algorithm solves TTSD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ extsf{TTSD}{}$$\\end{document} in O(n2γ2dT2dS2m2(mp·5γγ+mq))\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$O(n^2 \\gamma ^2 {d_T}^2 {d_S}^2\\,m^2 (m_p \\cdot 5^\\gamma \\gamma + m_q))$$\\end{document} time and O(dTdSm(mn+5γ))\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$O(d_T d_S m (m n + 5^\\gamma ))$$\\end{document} space, where γ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\gamma $$\\end{document} is the maximum number of children of a node, n is the length of the string, m is the number of leaves in the tree, mp\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$m_p$$\\end{document} and mq\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$m_q$$\\end{document} are the number of P-nodes and Q-nodes in the tree, respectively, and allowing up to dT\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$d_T$$\\end{document} deletions from the tree and up to dS\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$d_S$$\\end{document} deletions from the string. The third algorithm is intended to reduce the space complexity of the second algorithm. It solves a variant of the problem (where one of the penalties of TTSD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ extsf{TTSD}$$\\end{document} is 0) in O(nγ2dT2dS2m2(mp·4γγ2n(dT+dS+m+n)+mq))\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$O(n \\gamma ^2 {d_T}^2 {d_S}^2\\,m^2 (m_p \\cdot 4^{\\gamma }\\gamma ^2n(d_T+d_S+m+n) + m_q))$$\\end{document} time and O(γ2nm2dTdS(dT+dS+m+n))\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$O(\\gamma ^2 n m^2 d_T d_S (d_T+d_S+m+n))$$\\end{document} space. The algorithm is implemented as a software tool, denoted MEM-Rearrange, and applied to the comparative and evolutionary analysis of 59 chromosomal gene clusters extracted from a dataset of 1487 prokaryotic genomes.

Solving Rearrangement Puzzles Using Path Defragmentation in Factored State Spaces

Rearrangement puzzles are variations of rearrangement problems in which the elements of a problem are potentially logically linked together. To efficiently solve such puzzles, we develop a motion planning approach based on a new state space that is logically <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">factored</i> , integrating the capabilities of the robot through factors of simultaneously manipulatable joints of an object. Based on this factored state space, we propose less-actions RRT (LA-RRT), a planner which optimizes for a low number of actions to solve a puzzle. At the core of our approach lies a new path defragmentation method, which rearranges and optimizes consecutive edges to minimize action cost. We solve six rearrangement scenarios with a Fetch robot, involving planar table puzzles and an escape room scenario. LA-RRT significantly outperforms the next best asymptotically-optimal planner by 4.01 to 6.58 times improvement in final action cost.

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken.

Black-bone chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis (Fm) locus on the 20th chromosome results in increased endothelin-3 (EDN3) gene expression and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the Silkie breed to resolve high-confidence haplotypes at the Fm locus spanning both Dup1 and Dup2 regions and establish that the Fm_2 scenario is correct of the three possible scenarios of the complex chromosomal rearrangement. The relationship between Chinese and Korean BBC breeds with Kadaknath native to India is underexplored. Our data from whole-genome re-sequencing establish that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify two Fm locus proximal regions (∼70 Kb and ∼300Kb) with signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the bactericidal/permeability-increasing-protein-like gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in the bactericidal/permeability-increasing-protein-like gene hitchhiked with the Fm locus in Kadaknath due to close physical linkage. Identifying this Fm locus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.

Binder Jetting Additive Manufacturing: Powder Packing in Shell Printing

Shell printing is an advantageous binder jetting technique that prints only a thin shell of the intended object to enclose the loose powder in the core. In this study, powder packing in the shell and core was investigated for the first time. By examining the density and microstructure of the printed samples, powder packing was found to be different between the shell and core. In addition, the powder particle size and layer thickness were found to affect the powder packing in the shell and core differently. At a 200 µm layer thickness, for the 10 µm and 20 µm powders, the core was less dense than the shell and had a layered microstructure. At a 200 µm layer thickness, for the 70 µm powder, the core was denser and had a homogeneous microstructure. For the 20 µm powder, by reducing the layer thickness from 200 µm to 70 µm, the core became denser than the shell, and the microstructure of the core became homogeneous. The different results could be attributed to the different scenarios of particle rearrangement between the shell and core for powders of different particle sizes and at different layer thicknesses. Considering that the core was denser and more homogeneous than the shell when the proper layer thickness and powder particle size were selected, shell printing could be a promising method to tailor density and reduce anisotropy.

Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus.

BackgroundThe order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna.MethodsTo confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the “primer-walking” method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship.ResultsThe three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.

Predicting the Evolution of Syntenies—An Algorithmic Review

Syntenies are genomic segments of consecutive genes identified by a certain conservation in gene content and order. The notion of conservation may vary from one definition to another, the more constrained requiring identical gene contents and gene orders, while more relaxed definitions just require a certain similarity in gene content, and not necessarily in the same order. Regardless of the way they are identified, the goal is to characterize homologous genomic regions, i.e., regions deriving from a common ancestral region, reflecting a certain gene co-evolution that can enlighten important functional properties. In addition of being able to identify them, it is also necessary to infer the evolutionary history that has led from the ancestral segment to the extant ones. In this field, most algorithmic studies address the problem of inferring rearrangement scenarios explaining the disruption in gene order between segments with the same gene content, some of them extending the evolutionary model to gene insertion and deletion. However, syntenies also evolve through other events modifying their content in genes, such as duplications, losses or horizontal gene transfers, i.e., the movement of genes from one species to another. Although the reconciliation approach between a gene tree and a species tree addresses the problem of inferring such events for single-gene families, little effort has been dedicated to the generalization to segmental events and to syntenies. This paper reviews some of the main algorithmic methods for inferring ancestral syntenies and focus on those integrating both gene orders and gene trees.

Convection in viscoplastic fluids in rectangular cavities at lateral heating

The paper is devoted to the study of convective motions of viscoplastic fluids in closed two-dimensional rectangular domains with different aspect ratios under lateral heating. The problem was solved numerically using the ANSYS Fluent software. The Herschel-Bulkley model was chosen for describing the rheological behavior of the fluid. Under certain rheological parameters, this model was transformed into a Newtonian fluid model, whose behavior was also simulated as a limiting case. Based on the calculated results, the dependences of the maximum value of the stream function in the cavity on the Rayleigh number are plotted. It was found that at small Rayleigh numbers the intensity of motion is close to zero. At a certain value of the Rayleigh number there is a sharp increase in the intensity of motion, and a further increase in the Rayleigh number causes an almost linear growth of the maximum value of the stream function. For each of the considered ratios of cavity sides, the threshold values of the Rayleigh number, at which a sharp increase in the intensity of motion of liquid is observed, were determined. The obtained values of Rayleigh numbers turned out to be close to the threshold values of the Rayleigh number for the Bingham fluid found in the works of other authors earlier. The fields of the stream function and the square root of the second invariant of the viscous stress tensor were obtained for different values of the Rayleigh number and different aspect ratios. The scenarios of rearrangement of quasisolid motion zones with increasing Rayleigh number were compared with the available results for the Bingham fluid.

Hangar Utility Simulation as a Traffic Flow Density Scenario in Giwangan Market Yogyakarta

Giwangan Market as a fruit and vegetable wholesale market needs to be evaluated, organized and improved in the services. Currently, its development has undergone many changes. The hangar, which is the main block for loading and unloading fruits and vegetables, has shifted its function in several places. With the addition of semi-permanent buildings on the sides of hangars, the loading and unloading area are reduced and the entry and exit routes for vehicles are not functioning properly. 86% of vehicles with a tonnage of 2000 - 5000 kg that entered the Giwangan market were in the market for an average of 89.9 minutes. It is because the vehicle is not only loading and unloading but also selling in the market. So that other vehicles cannot load and unload. This study aims to measure the system performance which is estimated from the average actual travel time and the loading and unloading time of vehicles in the system. The alternative of rearranging hangar used is based on the development plan of the Giwangan Market Management Office. The simulation model has been verified and validated. The first rearrangement scenario is that all traders are moved to a new location (slaughterhouse). Second, the flow in and out of the hangar is one-way. Thus, the average vehicle in the system becomes 54.44 minutes and the hangar utility is 16.13% as an indicator that the hangar performance can be improved by increasing the number of vehicles capable of loading and unloading.

Comparative mitogenomic analysis of the superfamily Tellinoidea (Mollusca: Bivalvia): Insights into the evolution of the gene rearrangements

The superfamily Tellinoidea is widespread and contains approximately 180 living species, which is one of the most diverse and representative groups among the bivalves. In order to extend our knowledge on evolution of tellinoidean species, we newly determined five tellinoidean mitochondrial genomes (mitogenomes). The newly determined mitogenome vary in size from 16,333 to 16,986 bp. The results show that the genome size and genome organization are conserved in tellinoideans. However, gene arrangement and the location of the major non-coding region (NCR) show diversity. The atp8 gene presents in all the five new mitogenomes. Two trnK and trnP genes were detected in Gari togata mitogenome. Phylogenetic analysis supports the monophyly of Tellinoidea, however, it's family Psammobiidae is polyphyletic. CREx analysis suggests that the gene order of Nuttallia olivacea is assumed as the most primitive condition of Tellinoidea. We map the gene order onto the phylogeny and infers the possible gene rearrangement scenarios among tellinoidean mitogenomes. The mitochondrial gene rearrangement is a useful information that help reassessing the phylogeny of Tellinoidea. Phylogenetic relationship and gene arrangement analyses suggest that a careful review for the current taxonomy of the family Psammobiidae is required.

Adsorbate-Induced Segregation of Cobalt from PtCo Nanoparticles: Modeling Au Doping and Core AuCo Alloying for the Improvement of Fuel Cell Cathode Catalysts.

Platinum, when used as a cathode material for the oxygen reduction reaction, suffers from high overpotential and possible dissolution, in addition to the scarcity of the metal and resulting cost. Although the introduction of cobalt has been reported to improve reaction kinetics and decrease the precious metal loading, surface segregation or complete leakage of Co atoms causes degradation of the membrane electrode assembly, and either of these scenarios of structural rearrangement eventually decreases catalytic power. Ternary PtCo alloys with noble metals could possibly maintain activity with a higher dissolution potential. First-principles-based theoretical methods are utilized to identify the critical factors affecting segregation in Pt–Co binary and Pt–Co–Au ternary nanoparticles in the presence of oxidizing species. With a decreasing share of Pt, surface segregation of Co atoms was already found to become thermodynamically viable in the PtCo systems at low oxygen concentrations, which is assigned to high charge transfer between species. While the introduction of gold as a dopant caused structural changes that favor segregation of Co, creation of CoAu alloy core is calculated to significantly suppress Co leakage through modification of the electronic properties. The theoretical framework of geometrically different ternary systems provides a new route for the rational design of oxygen reduction catalysts.

Femtosecond Fluorescence Spectra of NADH in Solution: Ultrafast Solvation Dynamics.

The ultrafast solvation dynamics of reduced nicotinamide adenine dinucleotide (NADH) free in solution has been investigated, using both a femtosecond upconversion spectrophotofluorometer and a picosecond time-correlated single-photon counting (TCSPC) apparatus. The familiar time constant of solvent relaxation originating in "bulk water" was found to be ∼1.4 ps, revealing ultrafast solvent reorientation upon excitation. We also found a slower spectral relaxation process with an apparent time of 27 ps, suggesting there could either be dissociable "biological water" hydration sites on the surface of NADH or internal dielectric rearrangements of the flexible solvated molecule on that timescale. In contrast, the femtosecond fluorescence anisotropy measurement revealed that rotational diffusion happened on two different timescales (3.6 ps (local) and 141 ps (tumbling)); thus, any dielectric rearrangement scenario for the 27 ps relaxation must occur without significant chromophore oscillator rotation. The coexistence of quasi-static self quenching (QSSQ) with the slower relaxation is also discussed.

Electronic properties of graphene with point defects (Review Article)

This review is an attempt to consistently examine the electronic spectrum of graphene containing defects (such as adsorbed atoms, substitutional atoms, vacancies) that can be adequately described using the Lifshitz model. Therefore, the known Hamiltonian of this model is chosen for the case of two-dimensional relativistic electrons, and the criteria for the appearance of an impurity resonance near the Dirac point are provided. The theory of concentration band structure transformation in graphene is outlined, from which it follows that a transport gap opens in the vicinity of the impurity resonance energy when a specific value of the impurity concentration is reached. Along the way, the question of whether or not it is possible (or impossible) for Dirac quasiparticles to become localized in such a spatially disordered system is analyzed. Based on this, it is feasible to explain and describe the recently observed in impure graphene phenomenon of metal-insulator transition, which turns out to be a direct consequence of the system’s Fermi energy falling into the domain of the transport gap. The concept of local spectrum rearrangement, which can also unfold as the defect concentration increases, is introduced and justified for graphene. We formulate the physical reasons why the minimum of graphene’s low-temperature conductivity dependence on the Fermi energy of electrons does correspond to the impurity resonance energy, and not the Dirac point, as it has been claimed in a number of theoretical and experimental studies. Furthermore, the mentioned minimum value proves to be not universal, but is dependent, instead, on the concentration of defects. The analytical considerations of the impurity effects are accompanied by numerical simulations of the examined system, and a complete correspondence between these two approaches is established as a result. In particular, the general scenarios of spectrum rearrangement, electron state localization, as well as of effects having a local nature, are confirmed.

Large-scale mammalian genome rearrangements coincide with chromatin interactions.

MotivationGenome rearrangements drastically change gene order along great stretches of a chromosome. There has been initial evidence that these apparently non-local events in the 1D sense may have breakpoints that are close in the 3D sense. We harness the power of the Double Cut and Join model of genome rearrangement, along with Hi-C chromosome conformation capture data to test this hypothesis between human and mouse.ResultsWe devise novel statistical tests that show that indeed, rearrangement scenarios that transform the human into the mouse gene order are enriched for pairs of breakpoints that have frequent chromosome interactions. This is observed for both intra-chromosomal breakpoint pairs, as well as for inter-chromosomal pairs. For intra-chromosomal rearrangements, the enrichment exists from close (<20 Mb) to very distant (100 Mb) pairs. Further, the pattern exists across multiple cell lines in Hi-C data produced by different laboratories and at different stages of the cell cycle. We show that similarities in the contact frequencies between these many experiments contribute to the enrichment. We conclude that either (i) rearrangements usually involve breakpoints that are spatially close or (ii) there is selection against rearrangements that act on spatially distant breakpoints.Availability and implementationOur pipeline is freely available at https://bitbucket.org/thekswenson/locality.Supplementary information Supplementary data are available at Bioinformatics online.

Sorting Signed Permutations by Inverse Tandem Duplication Random Losses.

Gene order evolution of unichromosomal genomes, for example mitochondrial genomes, has been modelled mostly by four major types of genome rearrangements: inversions, transpositions, inverse transpositions, and tandem duplication random losses. Generalizing models that include all those rearrangements while admitting computational tractability are rare. In this paper, we study such a rearrangement model, namely the inverse tandem duplication random loss (iTDRL) model, where an iTDRL duplicates and inverts a continuous segment of a gene order followed by the random loss of one of the redundant copies of each gene. The iTDRL rearrangement has currently been proposed by several authors suggesting it to be a possible mechanisms of mitochondrial gene order evolution. We initiate the algorithmic study of this new model of genome rearrangement by proving that a shortest rearrangement scenario that transforms one given gene order into another given gene order can be obtained in quasilinear time. Furthermore, we show that the length of such a scenario, i.e., the minimum number of iTDRLs in the transformation, can be computed in linear time.

GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences

BackgroundGenome rearrangements describe changes in the genetic linkage relationship of large chromosomal regions, involving reversals, transpositions, block interchanges, deletions, insertions, fissions, fusions and translocations etc. Many algorithms for calculating rearrangement scenarios between two genomes have been proposed. Very often, the calculated rearrangement scenario is not unique for the same pair of permutations. Hence, how to decide which calculated rearrangement scenario is more biologically meaningful becomes an essential task. Up to now, several mechanisms for genome rearrangements have been studied. One important theory is that genome rearrangement may be mediated by repeats, especially for reversal events. Many reversal regions are found to be flanked by a pair of inverted repeats. As a result, whether there are repeats at the breakpoints of the calculated rearrangement events can shed a light on deciding whether the calculated rearrangement events is biologically meaningful. To our knowledge, there is no tool which can automatically identify rearrangement events and check whether there exist repeats at the breakpoints of each calculated rearrangement event.ResultsIn this paper, we describe a new tool named GRSR which allows us to compare multiple unichromosomal genomes to identify “independent” (obvious) rearrangement events such as reversals, (inverted) block interchanges and (inverted) transpositions and automatically searches for repeats at the breakpoints of each rearrangement event. We apply our tool on the complete genomes of 28 Mycobacterium tuberculosis strains and 24 Shewanella strains respectively. In both Mycobacterium tuberculosis and Shewanella strains, our tool finds many reversal regions flanked by a pair of inverted repeats. In particular, the GRSR tool also finds an inverted transposition and an inverted block interchange in Shewanella, where the repeats at the ends of rearrangement regions remain unchanged after the rearrangement event. To our knowledge, this is the first time such a phenomenon for inverted transposition and inverted block interchange is reported in Shewanella.ConclusionsFrom the calculated results, there are many examples supporting the theory that the existence of repeats at the breakpoints of a rearrangement event can make the sequences at the breakpoints remain unchanged before and after the rearrangement events, suggesting that the conservation of ends could possibly be a popular phenomenon in many types of genome rearrangement events.

Finding local genome rearrangements

BackgroundThe double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been devoted to the understanding of minimum length scenarios transforming one genome into another. In this paper we search instead for rearrangement scenarios that minimize the number of rearrangements whose breakpoints are unlikely due to some biological criteria. One such criterion has recently become accessible due to the advent of the Hi-C experiment, facilitating the study of 3D spacial distance between breakpoint regions.ResultsWe establish a link between the minimum number of unlikely rearrangements required by a scenario and the problem of finding a maximum edge-disjoint cycle packing on a certain transformed version of the adjacency graph. This link leads to a 3/2-approximation as well as an exact integer linear programming formulation for our problem, which we prove to be NP-complete. We also present experimental results on fruit flies, showing that Hi-C data is informative when used as a criterion for rearrangements.ConclusionsA new variant of the weighted DCJ distance problem is addressed that ignores scenario length in its objective function. A solution to this problem provides a lower bound on the number of unlikely moves necessary when transforming one gene order into another. This lower bound aids in the study of rearrangement scenarios with respect to chromatin structure, and could eventually be used in the design of a fixed parameter algorithm with a more general objective function.

Nonstationary Dynamics of Vortex-Like Domain Walls in Magnetic Films with In-Plane Anisotropy

The dynamic rearrangement of the structure of vortex domain walls (DWs) in films with uniaxial in-plane anisotropy has been examined based on two-dimensional micromagnetic model simulation. The optimum computational region has been chosen; grids with up to 270 × 75 cells 3 nm in size have been used. The scenarios of dynamic rearrangement of the DW structure in strong fields (up to 450 Oe) and in films with thicknesses exceeding 100 nm have been revealed for the first time. The emergence of multivortex instantaneous distributions of magnetization upon an increase in the film thickness and the external field intensity have been established. The dependence of the critical field on the film thickness has been refined.