Unique Inversion Research Articles

The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses

We determined the complete nucleotide sequence of the chloroplast genome of Selaginella uncinata, a lycophyte belonging to the basal lineage of the vascular plants. The circular double-stranded DNA is 144,170 bp, with an inverted repeat of 25,578 bp separated by a large single copy region (LSC) of 77,706 bp and a small single copy region (SSC) of 40,886 bp. We assigned 81 protein-coding genes including four pseudogenes, four rRNA genes and only 12 tRNA genes. Four genes, rps15, rps16, rpl32 and ycf10, found in most chloroplast genomes in land plants were not present in S. uncinata. While gene order and arrangement of the chloroplast genome of another lycophyte, Hupertzia lucidula, are almost the same as those of bryophytes, those of S. uncinata differ considerably from the typical structure of bryophytes with respect to the presence of a unique 20 kb inversion within the LSC, transposition of two segments from the LSC to the SSC and many gene losses. Thus, the organization of the S. uncinata chloroplast genome provides a new insight into the evolution of lycophytes, which were separated from euphyllophytes approximately 400 million years ago.

Isolation and characterization of the mating type locus of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana

SUMMARY Idiomorphs mat1-1 and mat1-2 from Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana, were isolated. Degenerate oligos were used to amplify the HMG box of the mat1-2 idiomorph from M. fijiensis, showing homology with the HMG box of Mycosphaerella graminicola. Using a DNA walking strategy, anchored on the DNA lyase gene towards the HMG box, a 9-kb-long region of mat1-2 was obtained. A 5-kb fragment from the mat1-1 region was obtained by long-range PCR using primers on the flanking regions, which have close to 100% identity between both idiomorphs. High-identity (77-89%), inverted regions within both idiomorphs were found, which suggest unique inversion events, which have not been found before, and that could have been significant in the evolution of this species. The predicted genes showed the conserved introns in both idiomorphs as well as an additional intron within the alpha box. The implications for the evolution of species in the Mycosphaerella complex on banana are discussed.

A three-level problem-centric strategy for selecting NMR precursor labeling and analytes

We have developed a sequential set of computational screens that may prove useful for evaluating analyte sets for their ability to accurately report on metabolic fluxes. The methodology is problem-centric in that the screens are used in the context of a particular metabolic engineering problem. That is, flux bounds and alternative flux routings are first identified for a particular problem, and then the information is used to inform the design of nuclear magnetic resonance (NMR) experiments. After obtaining the flux bounds via MILP, analytes are first screened for whether the predicted NMR spectra associated with various analytes can differentiate between different extreme point (or linear combinations of extreme point) flux solutions. The second screen entails determining whether the analytes provide unique flux values or multiple flux solutions. Finally, the economics associated with using different analytes is considered in order to further refine the analyte selection process in terms of an overall utility index, where the index summarizes the cost–benefit attributes by quantifying benefit (contrast power) per cost (e.g., NMR instrument time required). We also demonstrate the use of an alternative strategy, the Analytical Hierarchy Process, for ranking analytes based on the individual experimentalist's-generated weights assigned for the relative value of flux scenario contrast, unique inversion of NMR data to fluxes, etc.

Chromosome segregation in an infertile man carrying a unique pericentric inversion, inv(21)(p12q22.3), analysed using fluorescence in situ hybridization on sperm nuclei: significance for clinical genetics. A case report

We report the case of a 40-year-old patient referred to our centre after 3 years of infertility. Karyotyping with the aid of fluorescence in situ hybridization (FISH) analysis showed a unique pericentric inversion of chromosome 21:46,XY,inv(21)(p12q22.3). This type of intrachromosomal structural rearrangement can lead to chromosome imbalance in offspring by producing unbalanced gametes if an odd number of crossover events occur within the inverted segment. Therefore, partial trisomy/monosomy with clinical consequences can be observed in the progeny of carriers. Semen samples from the inversion carrier were analysed by FISH using a combination of probes [a subtelomeric 21q probe and a locus-specific Down's syndrome critical region (DSCR) probe] to evaluate the proportion of recombinant chromosomes. Sperm-FISH analysis of 3400 spermatozoa revealed a 67.4% rate of balanced chromosomes (normal or inverted). The frequencies of recombinant chromosomes with duplication of the long arm and deletion of the short arm, and vice versa, were 11.2 and 21.4%, respectively. The risk for the couple of conceiving a child with an unbalanced chromosome 21 is estimated to be around 32%. This case study shows the utility of sperm-FISH analysis in the genetic counselling of a pericentric inversion in a male carrier to assess the frequency of recombinant chromosomes and therefore evaluate the probability of having a normal conception.

Unusual segregation products in sperm from a pericentric inversion 17 heterozygote

Chromosome segregation and interchromosomal effect were studied in spermatozoa from a carrier of a pericentric chromosome 17 inversion, 46,XY,inv(17)(p13.1q25.3). Sperm chromosome segregation, lymphocytes of the inversion carrier, and cells from his offspring were analysed by multicolour fluorescence in situ hybridization. The frequency of balanced sperm was 73%. An unusual segregation of recombinants was observed, viz. deletion of the p arm (14.6%) or duplication of the p arm with the presence of one q arm (8.4%), instead of the expected recombinants, viz. duplication of one arm with deletion of the other and vice versa. These unusual recombinants were explained by the position of the 17q breakpoint, which was between the q arm telomere-associated repeats and the unique q subtelomere region. The offspring of the donor were found to have a 17p deletion including the Miller-Dieker critical region, similar to the most frequent recombinant sperm class. The disomy frequency was significantly increased for chromosome 17 compared with other autosomes, suggesting that pairing and recombination of the inversion may predispose to non-disjunction. There was no significant difference between the frequencies of aneuploidy for chromosomes 13, 21, X and Y in the chromosome inversion heterozygote compared with controls. Thus, this unique pericentric inversion of chromosome 17 produces unusual recombinant products; no evidence was apparent of an interchromosomal effect in any of the tested chromosomes.

BIFURCATIONS OF STABLE SETS IN NONINVERTIBLE PLANAR MAPS

Many applications give rise to systems that can be described by maps that do not have a unique inverse. We consider here the case of a planar noninvertible map. Such a map folds the phase plane, so that there are regions with different numbers of preimages. The locus, where the number of preimages changes, is made up of so-called critical curves, that are defined as the images of the locus where the Jacobian is singular. A typical critical curve corresponds to a fold under the map, so that the number of preimages changes by two.We consider the question of how the stable set of a hyperbolic saddle of a planar noninvertible map changes when a parameter is varied. The stable set is the generalization of the stable manifold for the case of an invertible map. Owing to the changing number of preimages, the stable set of a noninvertible map may consist of finitely or even infinitely many disjoint branches. It is now possible to compute stable sets with the Search Circle algorithm that we developed recently.We take a bifurcation theory point of view and consider the two basic codimension-one interactions of the stable set with a critical curve, which we call the outer-fold and the inner-fold bifurcations. By taking into account how the stable set is organized globally, these two bifurcations allow one to classify the different possible changes to the structure of a basin of attraction that are reported in the literature. The fundamental difference between the stable set and the unstable manifold is discussed. The results are motivated and illustrated with a single example of a two-parameter family of planar noninvertible maps.

Intriguing Double‐Inversion Stereochemistry in the Denitrogenation of 2,3‐Diazabicyclo[2.2.1]heptene‐type Azoalkanes: A Model Mechanistic Study in Physical Organic Chemistry

AbstractFor Abstract see ChemInform Abstract in Full Text.

Sculpting the vacuum in a photonic band gap micro-chip

We describe the engineering of the electromagnetic vacuum in a 2D–3D photonic bandgap (PBG) hetero-structure. This facilitates the development of novel active devices and the observation of novel quantum electrodynamic phenomena. We consider a specific architecture suitable as an all-optical micro-transistor capable of novel ultra-fast response with low switching power requirements. This relies on a unique collective atomic switching and population inversion achieved by coherent resonant pumping in a suitably engineered vacuum. Specific waveguide architectures within the 3D PBG micro-chip provide local density-of-states (LDOS) peaks near their cutoff frequency. These provide “building blocks” for electromagnetic vacuum engineering without recourse to conventional high Q-factor micro-cavities. For the all-optical micro-transistor, a fork shape LDOS within the micro-chip is desirable, using trimodal waveguide architecture. We delineate the functional robustness of these architectures to disorder caused by manufacturing errors within the PBG micro-chip.

Intriguing double‐inversion stereochemistry in the denitrogenation of 2,3‐diazabicyclo[2.2.1]heptene‐type azoalkanes: a model mechanistic study in physical organic chemistry

AbstractIn this review is given a detailed account of the mechanistic elucidation of the unique stereochemical double inversion observed in the nitrogen extrusion of bicyclic azoalkanes. It is shown that the judicious choice of experimental tools and theoretical approaches provides insight into and understanding of this perplexing stereoselectivity. This long‐standing mechanistic query serves as an example par excellence of harnessing the structural variation of the DBH‐type substrate (internal effects) and the change of medium properties (external effects) to diagnose a complex reaction mechanism. The particular case reviewed here is specific, but the focus in resolving its mechanistic complexities is general and, thus, may be applied to the elucidation of other intricate reaction mechanisms, primarily stereoselective and product‐selective organic transformations. Copyright © 2004 John Wiley & Sons, Ltd.

Hyperpolygons generated by the invertible Minkowski sum of polygons

The paper gives a new formulation of the Minkowski sum of polygons. In the conventional Minkowski sum, the inverse operation is not well defined unless the polygons are restricted to be convex. In the proposed formulation, on the other hand, the set of polygons is extended to the set of “hyperpolygons”, in which the Minkowski sum forms a commutative group. Consequently, every polygon has its unique inverse, and the sum and the inverse operations can be taken freely. A relation between hyperpolygons and physical reality is also discussed.

Blind restoration of nonlinearly mixed signals using multilayer polynomial neural network

It is shown how nonlinearly mixed signals can be retrieved uniquely by using a novel approach based on signal restoration methodology rather than the conventional technique of mere signal separation. A new mathematical model of the nonlinear mixing system has been developed culminating in the formulation of a stable unique inverse solution, which has an identical structure to the multilayer neural network. In addition, it is shown how the optimum framework for the nonlinear demixing system can be obtained directly from the derived mixing model. It is further shown how the proposed schemes using the multilayer polynomial neural network (PNN) can be utilised to acquire the desired solution. Moreover, the corresponding learning algorithm based on the generalised stochastic gradient descent method combined with a modified genetic algorithm (GA) has been developed to yield a novel and more effective approach in updating the parameters of the PNN. Both synthetic and real-time simulations have been conducted to verify the efficacy of each proposed scheme.

A Cramer rule for solution of the general restricted matrix equation

A Cramer rule for finding the unique W-weighted Drazin inverse solution of a class of restricted matrix equations WAWX WB W=D, R(X)⊂R[(AW) k 1 ], N(X)⊃N[( WB) k ̃ 2 ] is presented, and the results in [Linear Algebra Appl. 116 (1989) 27, Appl. Math. Comput. 125 (2002) 303] can be deduced from this paper. Where A∈ C m× n , W∈ C n× m , Ind( AW)= k 1, B∈ C p× q , W∈C q×p , Ind( WB)= k ̃ 2 , and D∈ C n× p .

Flexibility of the endogenous progesterone lactonisation pathway in Aspergillus tamarii KITA: transformation of a series of cortical steroid analogues

A range of cortical steroids have been transformed by the fungus Aspergillus tamarii, which has the ability to convert progesterone to testololactone in high yield through a four step enzymatic pathway. 16α,17α-Epoxyprogesterone underwent a rare epoxide opening resulting in a unique inversion of stereochemistry to give 16β-hydroxy-17α-oxa- d-homo-androst-4-en-3,17-dione. The metabolism of deoxycorticosterone resulted in relatively efficient transformation to testololactone with no other products isolated. Transformation of 17α-hydroxyprogesterone yielded 17α-oxa- d-homo-androst-1,4-dien-3,17-dione, a lactone not previously isolated from A. tamarii. Cortexolone was transformed to the 20( R)-alcohol with no further transformation observed. Evidence is also presented for the presence of a highly flexible but stereospecific keto-reductase. All metabolites were isolated by column chromatography and were identified by 1 H , 13 C NMR, DEPT analysis and other spectroscopic data.

Bottom Topography as a Control Variable in an Ocean Model

The possibility of using topography in a state estimation context as a control parameter is explored in a linear barotropic shallow water model. Along with its adjoint, the model is used to systematically assess the influence of the depth field on the modeled circulation in a steady state. Sensitivity of the flow field to the topography is greater in a partially blocked zonal channel than in a subtropical gyre. Hypothetical surface elevations are used to represent the types of data actually available. In neither case can all the details of the topography be recovered, showing that the relationship between topography and elevation does not have a unique inverse, and that many details of the topography are irrelevant to the particular physics under consideration.

Invertibility of current density from near-field electromagnetic data

The problem of determining a current density confined to a volume from measurements of the magnetic and electric fields it produces exterior to that volume is known to have nonunique solutions. Despite the nonuniqueness of the inversion we show that one may nevertheless uniquely determine certain moments of the vector spherical harmonic expansion of the current. It is demonstrated that the determination of these moments allows for the unique inversion of a current density confined to a spherical shell. Although unique the inversion may be ill conditioned and require a regularization of the inversion as demonstrated in an example numerical inversion.

A Generalization of Odd and Even Functions

Algebra of functional composition In this note we will only consider functions that map zero onto zero and which are continuous on an interval of the form (-6, 6), where 6 may depend on the function. We are assured that the composition of any two such functions is defined, and that the composite function also has these properties. For convenience we call such functions continuously fixed at zero. The functions M1 and Mo act as identity and zero functions, respectively, since for each f, M1 o f = f = f o M1, and Mo o f = Mo = f o Mo. Although functional composition is not commutative, it is associative, and we usually just write f o g o h rather than (f o g) o h, or f o (g o h). There is a right distributive law: (f + g) o h = f o h + g o h. Functional composition is not in general left distributive, but we do have a special case: Mx o (g + h) = Mx o g + Mx o h. We will also need to use the fact that if f is strictly monotonic on an open interval containing zero, then, restricted to that interval, f has a unique functional inverse, which we write f-1. The functional inverse satisfies the equation f o f-1 = M1 = f-1 o f. If f and g are invertible, then so is f o g and (f o g)-l = g-1 o f-1. (The basic properties of composition of functions and of functional inverses is covered in most calculus texts. For example see Larson [1] and Stewart [2].)

Chironomus suwai, a New Species of the plumosus Group (Diptera, Chironomidae) from Japan

Cytological examination of the larvae of the species previously referred to as Chironomus plumosus in Japan, reveals that it is actually a new member of the plumosus group. This species is described as C. suwai on the basis of the karyotype, since this is the most reliable method for recognizing the species. It belongs to the thummi cytocomplex, and is polymorphic in chromosome arms A, B and E. A B-chromosome was present in one of the two populations (Tsukuba) studied. The banding pattern of the polytene chromosomes indicates that C. suwai is most closely related to C. borokensis, from which it differs by the smaller centromeric bands, and the presence of three unique inversion polymorphisms. The difference in centromeric size is an important indicator that these are separate species, since such differences are common between species of Chironomus. Some notes are included on the larvae, particularly in relation to their use in lake typology, and the later life history stages.

Strong identities and fortification in transposition hypergroups

An element e in a hypergroup H is a strong identity if x ∈ ex = xe ⊂ x ⋃ e. The elements of H separate into two classes, the set A = {x ∈ H | ex = xe = x ⋃ e}, including e, of attractive elements and the set C = {x ∈ H – e | ex = xe = x} of canonical elements. If H is a transposition hypergroup then A is shown to be a closed subhypergroup of essentially indistinguishable elements. The structure of H is then determined, for A can be contracted into e leaving the “resulting” C ⋃ e, which is a polygroup under the relativized hyperoperation. Therefore, H can be reconstructed from A and C ⋃ e, as H is isomorphic to the expansion of the polygroup C ⋃ e by the transposition hypergroup A through e. The study of transposition hypergroups containing a strong identity separates into the study of polygroups and the study of transposition hypergroups of all attractive elements. A fortified transposition hypergroup H is defined and shown to contain a unique strong identity. Moreover, each nonidentity element is shown to have unique nonidentity left and right inverses that are identical. For H consisting of all attractive elements, the subhypergroups K that are symmetric, K = K –1, are studied. The double cosets of K, the sets K \\ (x/K) = (K \\ x)/K if x ∉ K, otherwise K, partition H. The resulting quotient space H : K of double cosets is proven to be a fortified transposition hypergroup in which K is the strong identity and every member is attractive.

Chromosomal polymorphism in Drosophila willistoni populations from Uruguay

Chromosomal polymorphism in natural populations of Drosophila willistoni from Uruguay and southern Brazil was investigated in order to understand the genetic characteristics and evolutionary potential of these almost geographically marginal populations. The level of chromosomal polymorphism in samples from Uruguay was higher than in those from the southernmost Brazilian state of Rio Grande do Sul. The increase in the polymorphism of these populations, in which the species almost reaches its southern limit, contradicts the low level of paracentric inversion polymorphism expected under the central-marginal chromosomal polymorphism cline previously reported. The high frequency of some inversions and the presence of unique inversions in samples from Uruguay indicate the uniqueness of these populations.

A Matlab toolkit for three-dimensional electrical impedance tomography: acontribution to the Electrical Impedance and Diffuse Optical ReconstructionSoftware project

The objective of the Electrical Impedance and Diffuse Optical ReconstructionSoftware project is to develop freely available software that can be usedto reconstruct electrical or optical material properties from boundarymeasurements. Nonlinear and ill posed problems such as electrical impedanceand optical tomography are typically approached using a finite elementmodel for the forward calculations and a regularized nonlinear solver forobtaining a unique and stable inverse solution. Most of the commerciallyavailable finite element programs are unsuitable for solving these problemsbecause of their conventional inefficient way of calculating the Jacobian, andtheir lack of accurate electrode modelling. A complete package for thetwo-dimensional EIT problem was officially released by Vauhkonen et al atthe second half of 2000. However most industrial and medical electricalimaging problems are fundamentally three-dimensional. To assist thedevelopment we have developed and released a free toolkit of Matlabroutines which can be employed to solve the forward and inverse EITproblems in three dimensions based on the complete electrode model alongwith some basic visualization utilities, in the hope that it will stimulatefurther development. We also include a derivation of the formula for theJacobian (or sensitivity) matrix based on the complete electrode model.