High order genome structure

Top PDF High order genome structure:

Sparse conserved under methylated CpGs are associated with high order chromatin structure

Sparse conserved under methylated CpGs are associated with high order chromatin structure

In this study, we used a total of 51 datasets (Additional file 3: Table S5) including 31 WGBS, 16 ChIP-seq, two ChIA-PET, and two RNA-seq obtained from Roadmap Epigenomics and ENCODE. CpG island (CGI) reference coordinates were downloaded from the UCSC genome annotation database. DHS clusters, peak clusters of 161 TFBS (wgEncodeRegTfb- sClusteredV3), wgEncodeBroadHmm tables were generated by the ENCODE Project Consortium and downloaded from the UCSC database. The wgEncodeBroadHmm datasets represent chromatin state segmentation for nine human cell types learned by computationally integrating ChIP-seq data for nine factors plus input using a HMM [38]. Promoter and Enhancer states presented in Fig. 2d represent the union of multiple states describing these same broader categories. Analyses including all predicted states for all nine cell types are presented in Additional file 1: Figure S3.
Show more

10 Read more

Chloroplast Genome Diversity in the Phototrophic Euglenoids, with Emphasis on Genome Structure, Synteny and Intron Evolution

Chloroplast Genome Diversity in the Phototrophic Euglenoids, with Emphasis on Genome Structure, Synteny and Intron Evolution

The three carefully selected taxa of phototrophic euglenoids in this study have been used to compare their chloroplast genomes with further chloroplast genomes of euglenoids to get an overview of chloroplast evolution in the highly diverse lineage within the Euglenozoa. Although the general gene composition was almost identical in all investigated cpGenomes, the chloroplast genomes show remarkable differences in size. The varying number of RNA repeats, IGS differences and as main factor intron and twintron content, have been identified as the three most pressing causes for size differences. The conducted intrageneric and intergeneric comparisons yielded large cluster rearrangements, which occurred between different clades and resulted in a high synteny of derived taxa due to merging clusters. Despite the approach to detect lineage encompassing trends and consistencies within the phototrophic euglenoids regarding the evolution of euglenoids and their chloroplasts, which could only be found in between species and only as an exception between genera, here molecular morphology trends have been detected in the chloroplast genomes of euglenoids for the first time. These metacharacters appear suitable to support phylogenomic and phylogenetic analyses and can be used to understand and possibly rule out questionable positions. Inter alia cluster arrangement, gene order and individual introns have been determined as significant metacharacters of the euglenoid chloroplast genome. Since plastid genomes from some euglenoid families are still not avaliable, an increasing sampling of euglenoid taxa across the tree would allow to explore and maybe confirm the described metacharacters in other taxa as well. Thereby it would be important to define more potential and appropriate molecular morphology features and to establish a standardized system for analyzing these genome-level features.
Show more

186 Read more

The Complete Mitochondrial Genome of Endemic Freshwater Sculpin Cottus dzungaricus (Scorpaeniformes: Cottidae) Revealed by High-Throughput NGS: Genome Structure and Its Phylogenetic Relationships

The Complete Mitochondrial Genome of Endemic Freshwater Sculpin Cottus dzungaricus (Scorpaeniformes: Cottidae) Revealed by High-Throughput NGS: Genome Structure and Its Phylogenetic Relationships

In order to explore the evolutionary status of C. dzungaricus within family Cottidae, the Neighbor- joining (NJ) phylogenetic tree was constructed by Mega6.0 using Kimura 2-parameter model (Tamura, Stecher, Peterson, Filipski, & Kumar, 2013) based on complete mitochondrial genomes of related species, and Mesocottus haitej KF170218, Icelus spatula KT004432, Gymnocanthus herzensteini KX148474 and G. intermedius KX148473 were selected as outgroups. All relative sequences were available from NCBI Genbank and aligned by multiple alignment program MAFFT v7.149 (Katoh & Toh, 2010; Yamada Tomii, & Katoh, 2016). To further explore the relationships between C. dzungaricus and C. sibiricus, the phylogenetic tree for the mtDNA control region was reconstructed by Maximum Likelihood (ML) method with 1,000 bootstrap replicates using PAUP4.0 (Swofford, 2002). Before tree building, MrModletest2.3 was used to determine the appropriate DNA substitution model and gamma rate heterogeneity using the Akaike Information Criterion (AIC) and the best-fit model HKY+I+G was selected (Nylander, 2004).
Show more

9 Read more

Simulation of Fluid Structure Interactions by using High Order FEM and SPH

Simulation of Fluid Structure Interactions by using High Order FEM and SPH

FEM and SPH interact via pressure (nodal forces) respectively force that is exerted by the fluid particles on the FE mesh. This results in displacements of the FE nodes which are transferred to the particles; i.e. SPH provides the loads for the FEM, and the FEM transfers the resulting structural displacements and velocities to the SPH particles. The coupling implemented here is based on the work of Fourey [9]. The pressure at a FE node is determined by the mean value of the particle pressures in its influence domain. In Figure 4 this concept is visualized for a two-dimensional setting. Three fluid particles (blue) are de- tected in the influence area of the left FE-node (orange). The pressure values associated with these fluid particles are averaged and converted into an equivalent nodal load which is achieved by integrating the pressure distribution over the face of an immersed FE. In determining the nodal forces, it is important to accurately approximate the discrete pressure function (given only at the fluid particles). One idea is to interpolate the pressure function using a simple polynomial distribution along the boundary of immersed FEs. Figure 5 shows an example of the distribution of nodal forces for a constant pressure along an element boundary for linear, quadratic and higher-order finite elements. Here, already the non-constant distribution of the force values on the nodes is observed. This results from the computation of energet- ically equivalent nodal loads under consideration of the element ansatz functions. The equivalent nodal force F e is calculated based on the pressure values p ( ξ ) and the ansatz function N ( ξ ) along the surface Γ
Show more

11 Read more

HIGH ORDER NUMERICAL SIMULATION OF FLUID-STRUCTURE INTERACTION IN HUMAN PHONATION. Martin Larsson and Bernhard Müller

HIGH ORDER NUMERICAL SIMULATION OF FLUID-STRUCTURE INTERACTION IN HUMAN PHONATION. Martin Larsson and Bernhard Müller

Both fluid and structure used the same set of variables for nondimensionalization and the same time step was used for both fields so that the two solutions are always at the same time level. The structure grid consisted of 81 × 61 points for each vocal fold, i.e. for the upper and the lower vocal folds, and the fluid domain was 241 × 61 points. The time step was determined by the stability condition for the fluid, which was satisfied here by requiring CF L ≤ 1. Since the fluid domain changes with time, the CFL condition puts a stricter constraint on the time step when the glottis is nearly closed. The solution was marched in time with given initial and boundary conditions to dimensional time t = 12 ms (total number of time steps 277310).
Show more

17 Read more

Revival Structure of High-order Harmonic Generation Signals from Adiabatic and Switched- off Aligned Molecules

Revival Structure of High-order Harmonic Generation Signals from Adiabatic and Switched- off Aligned Molecules

Does region X and Y really do not have any revival structure or do revive but with small depth modulation? To overcome the question, it is worthwile to plot the dynamic signal from each region with a larger view, as shown in Fig. 2 (panel a) for region X, Fig. 2 (panel b) for region Y, and Fig. 2 (panel c) for region Z. From the figures, one can see that region X and Z show revival structure with the same revival period. Region Y, even though quite weak, also show the similar structure, as it will be discussed later. Because the experimental data has not been available, then the calculated signals are compared with one obtained by using non-adiabatic schema, obtained by using the same pulse parameters, except  on   off  40 fs . It is important to note that the calculated data in Fig. 2 (panel d) well agree with the experimental data [8].
Show more

6 Read more

Primary structure of the alcelaphine herpesvirus 1 genome.

Primary structure of the alcelaphine herpesvirus 1 genome.

Alcelaphine herpesvirus 1 (AHV-1) causes wildebeest-associated malignant catarrhal fever, a lymphopro- liferative syndrome in ungulate species other than the natural host. Based on biological properties and limited structural data, it has been classified as a member of the genus Rhadinovirus of the subfamily Gammaherpes- virinae. Here, we report on cloning and structural analysis of the complete genome of AHV-1 C500. The low GC content DNA (L-DNA) region of the genome consists of 130,608 bp with low (46.17%) GC content and marked suppression of CpG dinucleotide frequency. Like in herpesvirus saimiri, the prototype of the rhadinoviruses, the L-DNA is flanked by approximately 20 to 25 GC-rich (71.83%) high GC content DNA (H-DNA) repeats of 1,113 to 1,118 nucleotides. The analysis of the L-DNA sequence revealed 70 open reading frames (ORFs), 61 of which showed homology to other herpesviruses. The conserved ORFs are arranged in four blocks collinear to other Rhadinovirus genomes. These gene blocks are flanked by nonconserved regions containing ORFs without similarities to known herpesvirus genes. Notably, a spliced reading frame with a coding capacity for a 199-amino-acid protein is located in a position homologous to the transforming genes of herpesvirus saimiri at the left end of the L-DNA. A gene with homology to the semaphorin family is located adjacent to this. Despite common biological and epidemiological properties, AHV-1 differs significantly from herpesvirus saimiri with regard to cell homologous genes, probably using a different set of effector proteins to achieve a similar T-lymphocyte-transforming phenotype.
Show more

9 Read more

GENETIC STRUCTURE OF THE cysC REGION OF THE SALMONELLA GENOME

GENETIC STRUCTURE OF THE cysC REGION OF THE SALMONELLA GENOME

implicit in the working hypothesis: that the silent section is able to synapse with a long section located beyond the right end of locus cysJ (to produce ditto deletions) and wi[r]

13 Read more

High-Diversity Genes in the Arabidopsis Genome

High-Diversity Genes in the Arabidopsis Genome

fication and isolation of loci responsible for speciation with directional selection have also been identified by (Greenberg et al. 2003; Barbash et al. 2004), species scanning dense sets of genome-wide molecular markers differences (Doebley et al. 1997; Gompel and Carroll for reduced levels of variation (Harr et al. 2002; Pay- 2003), and adaptive intraspecific variation (Johanson seur et al. 2002; Schlotterer 2002; Vigouroux et al. et al. 2000; Kroymann et al. 2003). Several approaches 2002; Wootton et al. 2002; Storz et al. 2004). The latter based on patterns of molecular evolution have been pro- approach, referred to as hitchhiking mapping, is based posed to scan genomes for genes associated with adapta- on the premise that a beneficial mutation that rapidly tion (Nielsen 2001; Swanson et al. 2001a,b; Schlotterer spreads in a population will also reduce nucleotide varia- 2002; Bamshad and Wooding 2003; Barrier et al. tion at linked neutral loci. Hitchhiking mapping has 2003). These methods provide opportunities to analyze successfully identified several genomic regions con- evolutionary diversification at both molecular genetic taining putative adaptive trait loci that were thought to and phenotypic levels. contribute to the worldwide colonization of Drosophila Approaches for mapping adaptive trait loci are based melanogaster out of Africa ⵑ10,000 years ago (Harr et al. on detecting regions of the genome in which intraspe- 2002). Although genome scanning for putative adaptive cific sequence variation and/or interspecific divergence trait loci on the basis of levels of molecular diversity deviate either from predictions of a neutral-equilibrium has focused largely on identifying genes associated with model (Nielsen 2001) or from the norm of a genome- directional selection, this approach could also be em- wide distribution (Otto 2000; Luikart et al. 2003). Evolu- ployed in identifying genes and/or genomic regions that tionary expressed sequence tag (EST) (Swanson et al. harbor balanced polymorphisms. This could complement 2001a,b; Barrier et al. 2003) and comparative genomic other genome-scanning approaches, such as screens for approaches (Clark et al. 2003), for example, use inter- elevated F ST estimates in marker loci between two popula-
Show more

16 Read more

High order approximation of degree nine and order eighteen

High order approximation of degree nine and order eighteen

Setting X m (0) = 1, then the problem is characterized by the 2m free parameters. The number of equations is compared with the number of parameters to get the order of ap- proximation of 2m; this is justified in [10]. This is the Hermite-type interpolation to rep- resent a curve. In this paper, the issue is to find the polynomial of best uniform approxi- mation. The classical case of approximating using a polynomial of degree m that has best uniform approximation was studied by Chebyshev and Borel [9]. They showed that such a polynomial exists and is unique, and its error equioscillates m + 2 times; but so far there has been no method to find the approximating polynomial. The polynomial of best ap- proximation of degree nine is found in this paper; it has nineteen equioscillations rather than eleven equioscillations theoretically guaranteed by the theorems of Chebyshev and Borel but cannot be found. The cases of n = 2, 3, 4 are considered in [12–14]; i.e., the nonic piecewise approximation for planar curves α 1 = α 2 = 9 is studied. The approximation or-
Show more

10 Read more

Chromosomes in a genome-wise order: evidence for metaphase architecture

Chromosomes in a genome-wise order: evidence for metaphase architecture

In the last decade nuclear architecture was recognized as an independent, emerging mechanism orchestrating gene expression (reviewed in [39]. The observation that homologous chromosomes - depending on their parental origin - have a defined position in the interphase nuclei as well as in the metaphase strengthens this concept and adds the parental origin information as an additional “ epigenetic layer ” . Architectural changes are priming events that happen before subsequent changes in gene expression and might therefore serve as future diagnos- tic and therapy markers e.g. in malignancys. which are well known as being associated with genetic instability and may very much be initiated by any loss of large scale chromatin order [54].
Show more

11 Read more

A rebuttal to the comments on the genome order index and the Z-curve

A rebuttal to the comments on the genome order index and the Z-curve

and so we effectively have only 1 degree of freedom left (which is essentially GC-content). Since both S and H are invertible functions of the remaining degree of freedom, it immediately follows that S can be calculated from H and H from S. Whether you want to call this equivalent or not is a matter of semantics. The point is that when all three constrains are acting, there is only one degree of freedom left. Instead of calculating S or H, I think it would be much more straight-forward to just talk about GC-content directly. Indeed, it is remarkable that CG-content ranges from as low as 0.22 to as high as 0.77 and the relevant bio- logical question, in my opinion, is not whether to use S or H or whatever other derived statistic, but rather trying to explain why GC-content varies so much in bacterial gen- omes. Indeed there has been quite some interesting devel- opments in this area recently. See for example the discussion in: Rocha EP, Feil EJ. Mutational patterns can- not explain genome composition: are there any neutral sites in the genomes of bacteria? PLoS Genet. 2010 Sep 9;6(9). The discussion about Renyi entropies is useless in my opinion. Yes, both S and H are both members of a family of functions (Renyi entropies) but I fail to see how this is relevant for any biological question.
Show more

9 Read more

Pharasiot Greek : word order and clause structure

Pharasiot Greek : word order and clause structure

In chapter 4, a detailed analysis of the interpretive and structural properties of the morpheme ki, a particle borrowed into Pharasiot Greek from Turkish, is provided. Ki may be employed in five configurations that seem different from one another at first sight; however, closer inspection reveals that these ki-environments are all declara- tive main clauses, in which ki fulfills a single general function. Specifically, ki can be qualified as a discourse marker geared toward influencing the epistemic vigilance mechanism of the hearer. Following Speas and Tenny (2003), according to whom the pragmatic roles “speaker” and “hearer” and the relation between the two are en- coded in a Speech Act Phrase (SAP), a predicative structure above ForceP, ki is iden- tified as the overt exponent of SA 0 . It is further proposed that ki is endowed with a [+sentience] feature indexing the speaker as the “sentient mind”. I conclude that the apparently unrelated configurations featuring the particle ki can be derived from one and the same underlying structure, namely [ SAP ki [ ForceP ]]. The surface differences between the ki environments are argued to stem from, among other things, whether Spec,SAP is filled by an internally or externally merging category that checks the [+sentience] feature on ki. This chapter also provides evidence for the existence of two recursive topic positions, one above SAP and one between SAP and ForceP. The difference between topic expressions hosted in these two positions and bona fide clitic left-dislocated topics is argued to be the fact that both of these additional topic posi- tions can only host hanging topics, which are first-merged in the left periphery rather than moved there.
Show more

512 Read more

Word order and information structure in Makhuwa-Enahara

Word order and information structure in Makhuwa-Enahara

If the verbal word is actually a phonologically joined sequence of morphemes, its position in the derivation is fixed, and moving the verb would require movement of the whole chunk, a phrasal remnant; unlike moving one head when the verb has head-moved to AgrS or T, as in French, for example. When the position of the verb is less flexible, the sentence is naturally divided into a domain preceding it and a domain following it. A second hint for why the elements are ordered around the verb is found in diachronic processes. Givón (1976) proposes that the subject and object markers on the verb historically started out as pronouns, used for reference to topics. These then became cliticised to the verb, were reanalysed as anaphoric/pronominal subject and object markers, and then grammaticalised to grammatical agreement markers. In the stage where the prefixes were always used pronominally, the whole argument structure of the verb was expressed on that verb by means of the prefixes; other elements in the sentence were in a sense optional. Even synchronically in a language such as Makhuwa, where the object markers are grammaticalised and function as purely grammatical agreement markers, the verb is still the necessary and central part of the sentence, and other phrases find their positions around it.
Show more

309 Read more

Structure discovery in mixed order hyper networks

Structure discovery in mixed order hyper networks

are 10 non-zero weights—those connecting adjacent pairs. The algorithm finds no use- ful weights at other orders, so the weight picking probability distribution very quickly becomes close to zero everywhere except at order 2, where it is close to 1. The algo- rithm then quickly includes all the second order weights and the regularisation removes all except the required 10. 40 attempts at learning the function with an MLP and with a MOHN were made. On all trials, the MOHN found the exact weights needed and the error went to zero in an average of 8 iterations of the algorithm. The MLP converged more slowly and failed to reach zero after 200 iterations, at which point most of the attempts had reached an error plateau. The MLP also showed far greater variance across its mod- els, with some becoming trapped at higher error levels than others. Figure 5 shows the results. The set of lines to the bottom left of the plot are the error traces from the MOHNs and those that spread out towards the upper right hand side are from the MLPs. A set of local optimum at an error of around 0.001 is clearly visible in the MLP data, as are a few that settle below that point.
Show more

23 Read more

Order Behavior In High Frequency Markest

Order Behavior In High Frequency Markest

How frequent are flash crashes? To what extent was the May 2010 flash crash an isolated event? Bhattacharya and Spiegel (1998) find that approximately every day from 1974-1988, four stocks on the NYSE have a market failure that results in a trading suspension. Gao and Mizrach (2013) find that market quality breakdowns are common in equity markets. In their sample, 1993- 2011, there are approximately 44 breakdowns each day in the TAQ database, with the post Reg NMS period having fewer breakdowns than the pre Reg NMS period. Golub, Keane, and Poon (2012) find that Reg NMS and intermarket sweep orders (ISOs) contribute to mini-flash crashes. From these studies it is clear that mini-flash crashes are common in financial markets, and that the May 2010 flash crash was not an isolated event. Our study compliments the existing work by identifying crashes in a nanosecond framework. In fast and automated markets, computers respond to market conditions at incredible speeds. Studies at lower latencies may miss potential crashes. In addition, our methodology does not rely on the automated quote feed to determine crashes, since we use order level data to calculate crashes that would be revealed to traders in real-time. Our paper also studies the depth implications of flash crashes. As O’Hara (2014) has pointed out, studies regarding high speed markets should look at other measures of liquidity beyond spread and top of book depth. We find that flash crashes are frequent events. In our sample period of three months, over 40% of the securities experienced at least one crash.
Show more

181 Read more

COURT STRUCTURE, JUDGES TITLES AND ORDER OF SENIORITY

COURT STRUCTURE, JUDGES TITLES AND ORDER OF SENIORITY

1.4 Cases which involve interpretation of the Constitution, or where the Court may be invited to depart from one of its previous decisions, or where the Court considers the principle of law involved to be one of major public importance, are normally determined by a full bench comprising all seven Justices if they are available to sit. Other cases which come to the High Court for final determination involve appeals against the decisions of the Supreme Courts of the states and territories, of the Federal Court of Australia and of the Family Court of Australia. These cases are usually determined by a bench of five justices. In addition, there are certain matters which can be heard and determined by a single Justice.
Show more

61 Read more

The Complete Genome Sequence of J Virus Reveals a Unique Genome Structure in the Family Paramyxoviridae

The Complete Genome Sequence of J Virus Reveals a Unique Genome Structure in the Family Paramyxoviridae

At least three novel paramyxoviruses have been isolated from rodents since the early 1960s. Nariva virus (NaV) was isolated on four occasions form the pooled organs of a forest rodent species trapped in Eastern Trinidad during 1962 and 1963 (55). It was classified as a paramyxovirus based on virion morphology and nucleocapsid structure (59) but has yet to be characterized molecularly and remains unclassified below the family level. Mossman virus (MoV) was isolated on two occa- sions during the early 1970s from the pooled organs of native rats trapped in Queensland, Australia (4). Recent character- ization of the full-length MoV genome revealed it to be a novel member of the subfamily Paramyxovirinae and most closely related to TPMV (37). J virus (J-V) was isolated on four occasions by kidney autoculture from moribund mice (Mus musculus) trapped in 1972 in northern Queensland, Australia (23, 35). It was reported that all four mice from which the virus was isolated had extensive hemorrhagic lung lesions (23). Syn- cytium formation was observed in kidney autoculture mono- layers, and electron microscopy revealed virion morphology and nucleocapsid structure typical of the paramyxoviruses. The name J virus was assigned in reference to M. H. Jun, the virologist responsible for much of the initial virus character- ization. A serological study investigating the presence of anti- bodies against J-V in Australian mammals was carried out during the 1970s (23). Serum neutralizing antibodies were de- tected in 27/96 wild mice, 17/106 wild rats, 13/107 pigs, 1/157 cattle, and 2/91 humans. A smaller-scale serological survey carried out on North American mammals failed to detect an- tibodies against J-V in laboratory mice, humans, or hamsters. A number of J-V animal infection experiments were also car- ried out during the mid-1970s (22, 23). Intranasal and subcu- taneous inoculation of J-V into weanling laboratory mice and rats was not associated with clinical signs of disease. Autopsies up to 3 weeks postinoculation revealed various degrees of hemorrhagic interstitial pneumonia, and virus was isolated from blood, lungs, and pooled liver, kidney, and spleen sam- ples. Intranasal J-V inoculation of four pigs did not cause any clinical signs of disease or pathology. No virus was isolated from any of the four pigs, although two did develop significant serum neutralizing antibody levels.
Show more

11 Read more

A notion of functional completeness for first order
structure

A notion of functional completeness for first order structure

Using -congruences and implications, Weaver (1993) introduced the concepts of pre- variety and quasivariety of first-order structures as generalizations of the corresponding concepts for algebras. The notion of functional completeness on algebras has been de- fined and characterized by Burris and Sankappanavar (1981), Kaarli and Pixley (2001), Pixley (1996), and Quackenbush (1981). We study the notion of functional completeness with respect to -congruences. We extend some results on functionally complete alge- bras to first-order structures A = (A;F A ;R A ) and find conditions for these structures to
Show more

9 Read more

COURT STRUCTURE, JUDGES TITLES AND ORDER OF SENIORITY

COURT STRUCTURE, JUDGES TITLES AND ORDER OF SENIORITY

1.4 Cases which involve interpretation of the Constitution, or where the Court may be invited to depart from one of its previous decisions, or where the Court considers the principle of law involved to be one of major public importance, are normally determined by a full bench comprising all seven Justices if they are available to sit. Other cases which come to the High Court for final determination involve appeals against the decisions of the Supreme Courts of the states and territories, of the Federal Court of Australia and of the Family Court of Australia. These cases are usually determined by a bench of five justices. In addition, there are certain matters which can be heard and determined by a single Justice.
Show more

60 Read more

Show all 10000 documents...