Journal articles: 'Degeneracy locus'

1

ZHAO, XU-AN, and HONGZHU GAO. "IRREDUCIBLE DECOMPOSITIONS OF DEGENERACY LOCI OF MATRICES." International Journal of Algebra and Computation 18, no. 02 (March 2008): 257–70. http://dx.doi.org/10.1142/s0218196708004433.

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In this paper, we study the irreducible decompositions of the degeneracy loci of matrices which are defined by rank conditions on upper left submatrices. By introducing the concepts of standard and essential rank functions, we give an explicit classification of these degeneracy loci. Based on standard rank functions, we design an algorithm to write a degeneracy locus as a union of its irreducible components. This gives an answer to a problem raised by Sturmfels.

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EBIHARA, Madoka. "Deformations of a Holomorphic Map and Its Degeneracy Locus." Tokyo Journal of Mathematics 35, no. 2 (December 2012): 253–77. http://dx.doi.org/10.3836/tjm/1358951317.

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SMALL, A. J. "OSCULATION AND SINGULARITY OF CHARGE 2 (COMPLEXIFIED) BPS MONOPOLES." International Journal of Mathematics 11, no. 07 (September 2000): 943–48. http://dx.doi.org/10.1142/s0129167x00000453.

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Hurtubise showed that the singular locus of the complexification of a BPS monopole intersects the degeneracy locus of the complex Higgs field in a null curve [Formula: see text] has a dual [Formula: see text]: by adapting a criterion of Hitchin it is shown that for a generic charge 2 monopole, [Formula: see text], the monopole's spectral curve.

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4

Tamvakis, Harry. "Giambelli and Degeneracy Locus Formulas for Classical G/P spaces." Moscow Mathematical Journal 16, no. 1 (2016): 125–77. http://dx.doi.org/10.17323/1609-4514-2016-16-1-125-177.

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Ran, Ziv. "A BOGOMOLOV UNOBSTRUCTEDNESS THEOREM FOR LOG-SYMPLECTIC MANIFOLDS IN GENERAL POSITION." Journal of the Institute of Mathematics of Jussieu 19, no. 5 (November 9, 2018): 1509–19. http://dx.doi.org/10.1017/s1474748018000464.

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We consider compact Kählerian manifolds $X$ of even dimension 4 or more, endowed with a log-symplectic holomorphic Poisson structure $\unicode[STIX]{x1D6F1}$ which is sufficiently general, in a precise linear sense, with respect to its (normal-crossing) degeneracy divisor $D(\unicode[STIX]{x1D6F1})$. We prove that $(X,\unicode[STIX]{x1D6F1})$ has unobstructed deformations, that the tangent space to its deformation space can be identified in terms of the mixed Hodge structure on $H^{2}$ of the open symplectic manifold $X\setminus D(\unicode[STIX]{x1D6F1})$, and in fact coincides with this $H^{2}$ provided the Hodge number $h_{X}^{2,0}=0$, and finally that the degeneracy locus $D(\unicode[STIX]{x1D6F1})$ deforms locally trivially under deformations of $(X,\unicode[STIX]{x1D6F1})$.

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Basok, M. "On some degeneracy loci in the moduli space of pointed odd spin curves." St. Petersburg Mathematical Journal 32, no. 5 (August 31, 2021): 819–45. http://dx.doi.org/10.1090/spmj/1672.

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Let C C be a smooth projective curve of genus g ≥ 3 g\geq 3 and let η \eta be an odd theta characteristic on it such that h 0 ( C , η ) = 1 h^0(C,\eta ) = 1 . Pick a point p p from the support of η \eta and consider the one-dimensional linear system | η + p | |\eta + p| . In general this linear system is base-point free and all its ramification points are simple. The locus in the moduli space of odd spin curves is studied where the linear system | η + p | |\eta + p| fails to have this general behavior. This locus is stratified with respect to multiplicities of degeneracies; these strata are called degeneracy schemes and their geometry is explored. Conormal spaces to these schemes are described in intrinsic terms and some consequences of this are presented.

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ITO, Toshikazu, Bruno SCÁRDUA, and Yoshikazu YAMAGISHI. "Degeneracy locus of critical points of the distance function on a holomorphic foliation." Journal of the Mathematical Society of Japan 66, no. 1 (January 2014): 123–37. http://dx.doi.org/10.2969/jmsj/06610123.

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8

Heier, Gordon. "Uniformly effective Shafarevich Conjecture on families of hyperbolic curves over a curve with prescribed degeneracy locus." Journal de Mathématiques Pures et Appliquées 83, no. 7 (July 2004): 845–67. http://dx.doi.org/10.1016/j.matpur.2004.02.001.

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9

Renshaw, A. A., and C. D. Mote. "Local Stability of Gyroscopic Systems Near Vanishing Eigenvalues." Journal of Applied Mechanics 63, no. 1 (March 1, 1996): 116–20. http://dx.doi.org/10.1115/1.2787185.

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Vanishing eigenvalues of a gyroscopic system are always repeated and, as a result of this degeneracy, their eigenfunctions represent a combination of constant displacements with zero velocity and the displacements derived from constant, nonzero velocity. In a second-order formulation of the equations of motion, the assumption of harmonic vibration is not sufficiently general to represent this motion as the displacements derived from constant, nonzero velocity are not included. In a first order formulation, however, the assumption of harmonic vibration is sufficient. Solvability criteria are required to determine the complete form of such eigenfunctions and in particular whether or not their velocities are identically zero. A conjecture for gyroscopic systems is proposed that predicts whether the eigenvalue locus is imaginary or complex in the neighborhood of a vanishing eigenvalue. If the velocities of all eigenfunctions with vanishing eigenvalues are identically zero, the eigenvalues are imaginary; if any eigenfunction exists whose eigenvalue is zero but whose velocity is nonzero, the corresponding eigenvalue locus is complex. The conjecture is shown to be true for many commonly studied gyroscopic systems; no counter examples have yet been found. The conjecture can be used to predict divergence instability in many cases without extensive computation.

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Cheng, Lingyin, Xiaoqing Zhou, Yuling Zheng, Chengcheng Tang, Yu Liu, Shuwen Zheng, Yang Liu, et al. "Simple and Rapid Assembly of TALE Modules Based on the Degeneracy of the Codons and Trimer Repeats." Genes 12, no. 11 (November 5, 2021): 1761. http://dx.doi.org/10.3390/genes12111761.

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Transcription activator-like effectors (TALEs) have been effectively used for targeted genome editing, transcriptional regulation, epigenetic modification, and locus-specific DNA imaging. However, with the advent of the clustered regularly interspaced short palindromic repeat/Cas9 system, an easy-to-use tool with the same function as TALEs, TALEs have recently been abandoned because of their complexity, time consumption, and difficult handling in common labs. Here, we described a degenerated codon-based TALE assembly system for simple, rapid, and efficient TALE assembly. TALE trimers with nonrepetitive DNA sequences were amplified by PCR and sequentially assembled via Gibson assembly. Our method is cost-effective, requires only commonly used basic molecular biology reagents, and takes only 2 h from target sequence analysis to completion. This simple, rapid, and lab-friendly TALE assembly method will restore the value of TALEs in DNA targeting.

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11

Kruglikov, Boris. "Blow-ups and infinitesimal automorphisms of CR-manifolds." Mathematische Zeitschrift 296, no. 3-4 (March 7, 2020): 1701–24. http://dx.doi.org/10.1007/s00209-020-02488-7.

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Abstract For a real-analytic connected CR-hypersurface M of CR-dimension $$n\geqslant 1$$ n ⩾ 1 having a point of Levi-nondegeneracy the following alternative is demonstrated for its symmetry algebra $$\mathfrak {s}={\mathfrak {s}}(M)$$ s = s ( M ) : (i) either $$\dim {\mathfrak {s}}=n^2+4n+3$$ dim s = n 2 + 4 n + 3 and M is spherical everywhere; (ii) or $$\dim {\mathfrak {s}}\leqslant n^2+2n+2+\delta _{2,n}$$ dim s ⩽ n 2 + 2 n + 2 + δ 2 , n and in the case of equality M is spherical and has fixed signature of the Levi form in the complement to its Levi-degeneracy locus. A version of this result is proved for the Lie group of global automorphisms of M. Explicit examples of CR-hypersurfaces and their infinitesimal and global automorphisms realizing the bound in (ii) are constructed. We provide many other models with large symmetry using the technique of blow-up, in particular we realize all maximal parabolic subalgebras of the pseudo-unitary algebras as a symmetry.

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Pinskaya, Marina, Anitha Nair, David Clynes, Antonin Morillon, and Jane Mellor. "Nucleosome Remodeling and Transcriptional Repression Are Distinct Functions of Isw1 in Saccharomyces cerevisiae." Molecular and Cellular Biology 29, no. 9 (March 9, 2009): 2419–30. http://dx.doi.org/10.1128/mcb.01050-08.

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ABSTRACT The SANT domain is a nucleosome recognition module found in transcriptional regulatory proteins, including chromatin-modifying enzymes. It shows high functional degeneracy between species, varying in sequence and copy number. Here, we investigate functions in vivo associated with two SANT motifs, SANT and SLIDE, in the Saccharomyces cerevisiae Isw1 chromatin-remodeling ATPase. We show that differences in the primary structures of the SANT and SLIDE domains in yeast and Drosophila melanogaster reflect their different functions. In yeast, the SLIDE domain is required for histone interactions, while this is a function of the SANT domain in flies. In yeast, both motifs are required for optimal association with chromatin and for formation of the Isw1b complex (Isw1, Ioc2, and Ioc4). Moreover, nucleosome remodeling at the MET16 locus is defective in strains lacking the SANT or SLIDE domain. In contrast, the SANT domain is dispensable for the interaction between Isw1 and Ioc3 in the Isw1a complex. We show that, although defective in nucleosome remodeling, Isw1 lacking the SANT domain is able to repress transcription initiation at the MET16 promoter. Thus, chromatin remodeling and transcriptional repression are distinct activities of Isw1.

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Grigoriev, M., and P. Hsieh. "A histone octamer blocks branch migration of a Holliday junction." Molecular and Cellular Biology 17, no. 12 (December 1997): 7139–50. http://dx.doi.org/10.1128/mcb.17.12.7139.

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The Holliday junction is a key intermediate in genetic recombination. Here, we examine the effect of a nucleosome core on movement of the Holliday junction in vitro by spontaneous branch migration. Histone octamers consisting of H2A, H2B, H3, and H4 are reconstituted onto DNA duplexes containing an artificial nucleosome-positioning sequence consisting of a tandem array of an alternating AT-GC sequence motif. Characterization of the reconstituted branch migration substrates by micrococcal nuclease mapping and exonuclease III and hydroxyl radical footprinting reveal that 70% of the reconstituted octamers are positioned near the center of the substrate and the remaining 30% are located at the distal end, although in both cases some translational degeneracy is observed. Branch migration assays with the octamer-containing substrates reveal that the Holliday junction cannot migrate spontaneously through DNA organized into a nucleosomal core unless DNA-histone interactions are completely disrupted. Similar results are obtained with branch migration substrates containing an octamer positioned on a naturally occurring sequence derived from the yeast GLN3 locus. Digestion of Holliday junctions with T7 endonuclease I establishes that the junction is not trapped by the octamer but can branch migrate in regions free of histone octamers. Our findings suggest that migration of Holliday junctions during recombination and the recombinational repair of DNA damage requires proteins not only to accelerate the intrinsic rate of branch migration but also to facilitate the passage of the Holliday junction through a nucleosome.

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14

Torres, J. F., D. Henry, A. Komiya, and S. Maruyama. "Bifurcation analysis of steady natural convection in a tilted cubical cavity with adiabatic sidewalls." Journal of Fluid Mechanics 756 (September 4, 2014): 650–88. http://dx.doi.org/10.1017/jfm.2014.448.

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AbstractNatural convection in an inclined cubical cavity heated from two opposite walls maintained at different temperatures and with adiabatic sidewalls is investigated numerically. The cavity is inclined by an angle $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\theta $ around a lower horizontal edge and the isothermal wall set at the higher temperature is the lower wall in the horizontal situation ($\theta = 0^\circ $). A continuation method developed from a three-dimensional spectral finite-element code is applied to determine the bifurcation diagrams for steady flow solutions. The numerical technique is used to study the influence of ${\theta }$ on the stability of the flow for moderate Rayleigh numbers in the range $\mathit{Ra} \leq 150\, 000$, focusing on the Prandtl number $\mathit{Pr} = 5.9$. The results show that the inclination breaks the degeneracy of the stable solutions obtained at the first bifurcation point in the horizontal cubic cavity: (i) the transverse stable rolls, whose rotation vector is in the same direction as the inclination vector ${\boldsymbol{\Theta}}$, start from $\mathit{Ra} \to 0$ forming a leading branch and becoming more predominant with increasing $\theta $; (ii) a disconnected branch consisting of transverse rolls, whose rotation vector is opposite to ${\boldsymbol{\Theta}}$, develops from a saddle-node bifurcation, is stabilized at a pitchfork bifurcation, but globally disappears at a critical inclination angle; (iii) the semi-transverse stable rolls, whose rotation axis is perpendicular to ${\boldsymbol{\Theta}}$ at $\theta \to 0^\circ $, develop from another saddle-node bifurcation, but the branch also disappears at a critical angle. We also found the stability thresholds for the stable diagonal-roll and four-roll solutions, which increase with $\theta $ until they disappear at other critical angles. Finally, the families of stable solutions are presented in the $\mathit{Ra}-\theta $ parameter space by determining the locus of the primary, secondary, saddle-node, and Hopf bifurcation points as a function of $\mathit{Ra}$ and $\theta $.

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15

Merker, Joël. "On Propagation of Sphericity of Real Analytic Hypersurfaces across Levi Degenerate Loci." Journal of Complex Analysis 2017 (March 28, 2017): 1–8. http://dx.doi.org/10.1155/2017/1314874.

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A connected real analytic hypersurface M⊂Cn+1 whose Levi form is nondegenerate in at least one point—hence at every point of some Zariski-dense open subset—is locally biholomorphic to the model Heisenberg quadric pseudosphere of signature (k,n-k) in one point if and only if, at every other Levi nondegenerate point, it is also locally biholomorphic to some Heisenberg pseudosphere, possibly having a different signature (l,n-l). Up to signature, pseudosphericity then jumps across the Levi degenerate locus and in particular across the nonminimal locus, if there exists any.

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16

Marini, Alfio. "On a family of (1,7)-polarised abelian surfaces." MATHEMATICA SCANDINAVICA 95, no. 2 (December 1, 2004): 181. http://dx.doi.org/10.7146/math.scand.a-14456.

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We study the geometry of the moduli space of $(1,7)$-polarised abelian surfaces with canonical level structure in detail. In particular we describe the locus where the syzygies of the embedded Heisenberg-invariant abelian surface degenerate, and relate this to the other known descriptions of the moduli space in question.

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17

LUDWIG, Lars R., Tina C. SUMMERFIELD, Janice M. LORD, and Garima SINGH. "Characterization of the mating-type locus (MAT) reveals a heterothallic mating system inKnightiella splachnirima." Lichenologist 49, no. 4 (July 2017): 373–85. http://dx.doi.org/10.1017/s0024282917000214.

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AbstractIn the present study, we characterized the mating-type locus ofKnightiella splachnirima(Icmadophilaceae) using degenerate and inverse PCR techniques. We screened for the presence of both mating-type locus idiomorphs in DNA extracts of minuscule samples of haploid thalline tissue. We found that only one of the two idiomorphs was present in each sample, and the mating-type ratio (MAT1-1:MAT1-2) was very balanced, being 8:10 and 13:14 at local and global scales, respectively. This indicates that the species is probably self-incompatible and requires the presence of compatible mating partners for sexual reproduction (heterothallic mating system). Furthermore, we provide a mating-type screening protocol withK. splachnirimaspecific mating-type locus primers, which could serve as an essential tool for the conservation management of this rare Australasian endemic.

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18

HWANG, JUN-MUK. "VARIETIES WITH DEGENERATE GAUSS MAPPINGS IN COMPLEX HYPERBOLIC SPACE FORMS." International Journal of Mathematics 13, no. 02 (March 2002): 209–16. http://dx.doi.org/10.1142/s0129167x02001186.

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In analogy with the Gauss mapping for a subvariety in the complex projective space, the Gauss mapping for a subvariety in a complex hyperbolic space form can be defined as a map from the smooth locus of the subvariety to the quotient of a suitable domain in the Grassmannian. For complex hyperbolic space forms of finite volume, it is proved that the Gauss mapping is degenerate if and only if the subvariety is totally geodesic.

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19

Newby, L. M., L. White, S. M. DiBartolomeis, B. J. Walker, H. B. Dowse, J. M. Ringo, N. Khuda, and F. R. Jackson. "Mutational analysis of the Drosophila miniature-dusky (m-dy) locus: effects on cell size and circadian rhythms." Genetics 128, no. 3 (July 1, 1991): 571–82. http://dx.doi.org/10.1093/genetics/128.3.571.

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Abstract A mutational analysis has been performed to explore the function of the Drosophila melanogaster miniature-dusky (m-dy) locus. Mutations at this locus affect wing development, fertility and behavior. The genetic characterization of 13 different mutations suggests that m and dy variants are alleles of a single complex gene. All of these mutations alter wing size, apparently by reducing the volume of individual epidermal cells of the developing wing. In m mutants, epidermal cell boundaries persist in the mature wing, whereas they normally degenerate 1-2 hr after eclosion in wild-type or dy flies. This has permitted the direct visualization of cell size differences among several m mutants. Mutations at the m-dy locus also affect behavioral processes. Three out of nine dy alleles (dyn1, dyn3 and dyn4) lengthen the circadian period of the activity and eclosion rhythms by approximately 1.5 hr. In contrast, m mutants have normal circadian periods, but an abnormally large percentage of individuals express aperiodic bouts of activity. These behavior genetic studies also indicate that an existing "rhythm" mutation known as Andante is an allele of the m-dy locus. The differential effects of certain m-dy mutations on wing and behavioral phenotypes suggest that separable domains of function exist within this locus.

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20

Odehnal, Boris. "A Rarity in Geometry." KoG, no. 25 (2021): 25–39. http://dx.doi.org/10.31896/k.25.3.

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We study the locus C of all points in the plane whose pedal points on the six sides of a complete quadrangle lie on a conic. In the Euclidean plane, it turns out that C is an algebraic curve of degree 7 and genus 5 and not of degree 12 as it could be expected. Septic curves occur rather seldom in geometry which motivates a detailed study of this particular curve. We look at its singularities, focal points, and those points on C whose pedal conics degenerate. Then, we show that the septic curve occurs as the locus curve for a more general question. Further, we describe those cases where C degenerates or is of degree less than 7 depending on the shape of the initial quadrilateral

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21

WANG, S., X. LIU, X. XU, Y. ZHAO, D. YANG, X. HAN, M. TIAN, C. DING, D. PENG, and S. YU. "Escherichia coli type III secretion system 2 (ETT2) is widely distributed in avian pathogenic Escherichia coli isolates from Eastern China." Epidemiology and Infection 144, no. 13 (April 22, 2016): 2824–30. http://dx.doi.org/10.1017/s0950268816000820.

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SUMMARYPathogens utilize type III secretion systems to deliver effector proteins, which facilitate bacterial infections. The Escherichia coli type III secretion system 2 (ETT2) which plays a crucial role in bacterial virulence, is present in the majority of E. coli strains, although ETT2 has undergone widespread mutational attrition. We investigated the distribution and characteristics of ETT2 in avian pathogenic E. coli (APEC) isolates and identified five different ETT2 isoforms, including intact ETT2, in 57·6% (141/245) of the isolates. The ETT2 locus was present in the predominant APEC serotypes O78, O2 and O1. All of the ETT2 loci in the serotype O78 isolates were degenerate, whereas an intact ETT2 locus was mostly present in O1 and O2 serotype strains, which belong to phylogenetic groups B2 and D, respectively. Interestingly, a putative second type III secretion-associated locus (eip locus) was present only in the isolates with an intact ETT2. Moreover, ETT2 was more widely distributed in APEC isolates and exhibited more isoforms compared to ETT2 in human extraintestinal pathogenic E. coli, suggesting that APEC might be a potential risk to human health. However, there was no distinct correlation between ETT2 and other virulence factors in APEC.

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22

Vyshnyepolskiy, Vladimir, E. Zavarihina, and D. Peh. "Geometric Locations of Points Equally Distance from Two Given Geometric Figures. Part 4: Geometric Locations of Points Equally Remote from Two Spheres." Geometry & Graphics 9, no. 3 (December 9, 2021): 12–29. http://dx.doi.org/10.12737/2308-4898-2021-9-3-12-29.

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The article deals with the geometric locations of points equidistant from two spheres. In all variants of the mutual position of the spheres, the geometric places of the points are two surfaces. When the centers of the spheres coincide with the locus of points equidistant from the spheres, there will be spheres equal to the half-sum and half-difference of the diameters of the original spheres. In three variants of the relative position of the initial spheres, one of the two surfaces of the geometric places of the points is a two-sheet hyperboloid of revolution. It is obtained when: 1) the spheres intersect, 2) the spheres touch, 3) the outer surfaces of the spheres are removed from each other. In the case of equal spheres, a two-sheeted hyperboloid of revolution degenerates into a two-sheeted plane, more precisely, it is a second-order degenerate surface with a second infinitely distant branch. The spheres intersect - the second locus of the points will be the ellipsoid of revolution. Spheres touch - the second locus of points - an ellipsoid of revolution, degenerated into a straight line, more precisely into a zero-quadric of the second order - a cylindrical surface with zero radius. The outer surfaces of the spheres are distant from each other - the second locus of points will be a two-sheet hyperboloid of revolution. The small sphere is located inside the large one - two coaxial confocal ellipsoids of revolution. In all variants of the mutual position of spheres of the same diameters, the common geometrical place of equidistant points is a plane (degenerate surface of the second order) passing through the middle of the segment perpendicular to it, connecting the centers of the original spheres. The second locus of points equidistant from two spheres of the same diameter can be either an ellipsoid of revolution (if the original spheres intersect), or a straight (cylindrical surface with zero radius) connecting the centers of the original spheres when the original spheres touch each other, or a two-sheet hyperboloid of revolution (if continue to increase the distance between the centers of the original spheres).

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23

Nelson, M. I., and H. S. Sidhu. "Bifurcation phenomena for an oxidation reaction in a continuously stirred tank reactor. II Diabatic operation." ANZIAM Journal 45, no. 3 (January 2004): 303–26. http://dx.doi.org/10.1017/s1446181100013389.

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AbstractWe extend an investigation into the bifurcation phenomena exhibited by an oxidation reaction in an adiabatic reactor to the case of a diabatic reactor. The primary bifurcation parameter is the fuel fraction; the inflow pressure and inflow temperature are the secondary bifurcation parameters. The inclusion of heat loss in the model does not change the static steady-state bifurcation diagram; the organising centre is a pitchfork singularity for both the adiabatic and diabatic reactors. However, unlike the adiabatic reactor, Hopf bifurcations may occur in the diabatic reactor. We construct the degenerate Hopf bifurcation curve by determining the double-Hopf locus. When the steady-state and degenerate Hopf bifurcation diagrams are combined it is found that there are 23 generic steady-state diagrams over the parameter region of interest. The implications of these structures from the perspective of flammability in the CSTR are discussed.

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24

Grieve, Nathan. "Index conditions and cup-product maps on Abelian varieties." International Journal of Mathematics 25, no. 04 (April 2014): 1450036. http://dx.doi.org/10.1142/s0129167x14500360.

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We study questions surrounding cup-product maps which arise from pairs of non-degenerate line bundles on an abelian variety. Important to our work is Mumford's index theorem which we use to prove that non-degenerate line bundles exhibit positivity analogous to that of ample line bundles. As an application we determine the asymptotic behavior of families of cup-product maps and prove that vector bundles associated to these families are asymptotically globally generated. To illustrate our results we provide several examples. For instance, we construct families of cup-product problems which result in a zero map on a one-dimensional locus. We also prove that the hypothesis of our results can be satisfied, in all possible instances, by a particular class of simple abelian varieties. Finally, we discuss the extent to which Mumford's theta groups are applicable in our more general setting.

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Gross, Joshua B., James Weagley, Bethany A. Stahl, Li Ma, Luis Espinasa, and Suzanne E. McGaugh. "A local duplication of the Melanocortin receptor 1 locus in Astyanax." Genome 61, no. 4 (April 2018): 254–65. http://dx.doi.org/10.1139/gen-2017-0049.

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In this study, we report evidence of a novel duplication of Melanocortin receptor 1 (Mc1r) in the cavefish genome. This locus was discovered following the observation of excessive allelic diversity in a ∼820 bp fragment of Mc1r amplified via degenerate PCR from a natural population of Astyanax aeneus fish from Guerrero, Mexico. The cavefish genome reveals the presence of two closely related Mc1r open reading frames separated by a 1.46 kb intergenic region. One open reading frame corresponds to the previously reported Mc1r receptor, and the other open reading frame (duplicate copy) is 975 bp in length, encoding a receptor of 325 amino acids. Sequence similarity analyses position both copies in the syntenic region of the single Mc1r locus in 16 representative craniate genomes spanning bony fish (including Astyanax) to mammals, suggesting we discovered tandem duplicates of this important gene. The two Mc1r copies share ∼89% sequence similarity and, within Astyanax, are more similar to one another compared to other melanocortin family members. Future studies will inform the precise functional significance of the duplicated Mc1r locus and if this novel copy number variant may have adaptive significance for the Astyanax lineage.

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Hezemans, Frank H., Noham Wolpe, Claire O’Callaghan, Rong Ye, Catarina Rua, P. Simon Jones, Alexander G. Murley, et al. "Noradrenergic deficits contribute to apathy in Parkinson’s disease through the precision of expected outcomes." PLOS Computational Biology 18, no. 5 (May 9, 2022): e1010079. http://dx.doi.org/10.1371/journal.pcbi.1010079.

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Apathy is a debilitating feature of many neuropsychiatric diseases, that is typically described as a reduction of goal-directed behaviour. Despite its prevalence and prognostic importance, the mechanisms underlying apathy remain controversial. Degeneration of the locus coeruleus-noradrenaline system is known to contribute to motivational deficits, including apathy. In healthy people, noradrenaline has been implicated in signalling the uncertainty of expectations about the environment. We proposed that noradrenergic deficits contribute to apathy by modulating the relative weighting of prior beliefs about action outcomes. We tested this hypothesis in the clinical context of Parkinson’s disease, given its associations with apathy and noradrenergic dysfunction. Participants with mild-to-moderate Parkinson’s disease (N = 17) completed a randomised double-blind, placebo-controlled, crossover study with 40 mg of the noradrenaline reuptake inhibitor atomoxetine. Prior weighting was inferred from psychophysical analysis of performance in an effort-based visuomotor task, and was confirmed as negatively correlated with apathy. Locus coeruleus integrity was assessed in vivo using magnetisation transfer imaging at ultra-high field 7T. The effect of atomoxetine depended on locus coeruleus integrity: participants with a more degenerate locus coeruleus showed a greater increase in prior weighting on atomoxetine versus placebo. The results indicate a contribution of the noradrenergic system to apathy and potential benefit from noradrenergic treatment of people with Parkinson’s disease, subject to stratification according to locus coeruleus integrity. More broadly, these results reconcile emerging predictive processing accounts of the role of noradrenaline in goal-directed behaviour with the clinical symptom of apathy and its potential pharmacological treatment.

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Provencher, Cathy, GisÃ¯Â¿Â½le LaPointe, StÃ¯Â¿Â½phane Sirois, Marie-Rose Van Calsteren, and Denis Roy. "Consensus-Degenerate Hybrid Oligonucleotide Primers for Amplification of Priming Glycosyltransferase Genes of the Exopolysaccharide Locus in Strains of the Lactobacillus casei Group." Applied and Environmental Microbiology 69, no. 6 (June 2003): 3299–307. http://dx.doi.org/10.1128/aem.69.6.3299-3307.2003.

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ABSTRACT A primer design strategy named CODEHOP (consensus-degenerate hybrid oligonucleotide primer) for amplification of distantly related sequences was used to detect the priming glycosyltransferase (GT) gene in strains of the Lactobacillus casei group. Each hybrid primer consisted of a short 3′ degenerate core based on four highly conserved amino acids and a longer 5′ consensus clamp region based on six sequences of the priming GT gene products from exopolysaccharide (EPS)-producing bacteria. The hybrid primers were used to detect the priming GT gene of 44 commercial isolates and reference strains of Lactobacillus rhamnosus, L. casei, Lactobacillus zeae, and Streptococcus thermophilus. The priming GT gene was detected in the genome of both non-EPS-producing (EPS−) and EPS-producing (EPS+) strains of L. rhamnosus. The sequences of the cloned PCR products were similar to those of the priming GT gene of various gram-negative and gram-positive EPS+ bacteria. Specific primers designed from the L. rhamnosus RW-9595M GT gene were used to sequence the end of the priming GT gene in selected EPS+ strains of L. rhamnosus. Phylogenetic analysis revealed that Lactobacillus spp. form a distinctive group apart from other lactic acid bacteria for which GT genes have been characterized to date. Moreover, the sequences show a divergence existing among strains of L. rhamnosus with respect to the terminal region of the priming GT gene. Thus, the PCR approach with consensus-degenerate hybrid primers designed with CODEHOP is a practical approach for the detection of similar genes containing conserved motifs in different bacterial genomes.

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Li, Wenli, Jianhua Ju, Hiroyuki Osada, and Ben Shen. "Utilization of the Methoxymalonyl-Acyl Carrier Protein Biosynthesis Locus for Cloning of the Tautomycin Biosynthetic Gene Cluster from Streptomyces spiroverticillatus." Journal of Bacteriology 188, no. 11 (June 1, 2006): 4148–52. http://dx.doi.org/10.1128/jb.00172-06.

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ABSTRACT Tautomycin (TTM), a potent protein phosphatase inhibitor, consists of a polyketide chain containing a spiroketal moiety and an acyl chain bearing a dialkylmaleic anhydride structure. PCR using degenerate primers was used to clone genes from Streptomyces spiroverticillatus for formation of the methoxymalonyl-acyl carrier protein. This locus was found to contain five genes (ttmC, ttmA, ttmD, ttmB, and ttmE), one of which was used as a probe to clone the 110-kb TTM biosynthetic gene cluster. The involvement of the ttmA gene in TTM biosynthesis was confirmed by gene inactivation and mutation complementation experiments.

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MacConaill, Laura E., Derek Butler, Mary O'Connell-Motherway, Gerald F. Fitzgerald, and Douwe van Sinderen. "Identification of Two-Component Regulatory Systems in Bifidobacterium infantis by Functional Complementation and Degenerate PCR Approaches." Applied and Environmental Microbiology 69, no. 7 (July 2003): 4219–26. http://dx.doi.org/10.1128/aem.69.7.4219-4226.2003.

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ABSTRACT Two-component signal transduction systems (2CSs) are widely used by bacteria to sense and adapt to changing environmental conditions. With two separate approaches, three different 2CSs were identified on the chromosome of the probiotic bacterium Bifidobacterium infantis UCC 35624. One locus was identified by means of functional complementation of an Escherichia coli mutant. Another two were identified by PCR with degenerate primers corresponding to conserved regions of one protein component of the 2CS. The complete coding regions for each gene cluster were obtained, which showed that each 2CS-encoding locus specified a histidine protein kinase and an assumed cognate response regulator. Transcriptional analysis of the 2CSs by Northern blotting and primer extension identified a number of putative promoter sequences for this organism while revealing that the expression of each 2CS was growth phase dependent. Analysis of the genetic elements involved revealed significant homology with several distinct regulatory families from other high-G+C-content bacteria. The conservation of the genetic organization of these three 2CSs in other bacteria, including a number of recently published Bifidobacterium genomes, was investigated.

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Jellison, Brandon J., Harold R. Kess, Douglas E. Adams, and David C. Nelson. "Nondestructive Evaluation of Parts With Degenerate Modes Using Pseudorepeated Roots." Journal of Dynamic Systems, Measurement, and Control 126, no. 3 (September 1, 2004): 498–508. http://dx.doi.org/10.1115/1.1789536.

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The modes of vibration of manufactured parts can be good indicators of the overall quality of the manufacturing process. That is, deviations in the modal frequencies or modal vectors of mechanical parts can help to identify outlier or systemic problems in the raw materials or fabrication procedure. A novel method for characterizing nonuniformities in homogeneous symmetric parts using pseudorepeated modal frequencies is discussed in this paper. It is demonstrated that the spacing between pseudorepeated roots in dominantly symmetric manufactured parts is a direct indicator of nonuniformities (i.e., inclusions, voids) in the stiffness or mass distributions. Smaller differences between split-peaks indicate less nonuniformity, and hence, higher quality parts. A simple fourth-order lumped parameter model is used to elaborate on this technique analytically, a representative finite element model is used to further this development, root locus techniques are used to study the sensitivity to nonuniformities, and acceleration response data from impact vibration tests on deep drawn hemispherical shells are used to verify the approach experimentally.

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Daryono, Budi Setiadi. "Application of Molecular Biology for Identification of Virus Resistance Gene in Melon." Indonesian Journal of Biotechnology 20, no. 1 (November 8, 2016): 19. http://dx.doi.org/10.22146/ijbiotech.15265.

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Source of resistance to an Indonesia isolate of Cucumber mosaic virus (CMV-B2) in melon cultivarYamatouri has been reported. Moreover, Creb-2, a locus that confers resistance to CMV-B2 in Yamatouri hasbeen determined as a single dominant gene. To elucidate the resistance mechanism conferred by Creb-2 inmore detail, it is necessary to clone the Creb-2 gene and determine its molecular structure. One approach isby amplification and cloning of melon resistance gene analogs (MRGAs) based on degenerated PCR primersdesigned from conserved amino acids in the NBS-LRR motifs (P-loop, Kinase-2, and the GLPL) and Toll/Interleukin-1 receptor-like region (TIR). This study was aimed to identify and characterize the resistance geneanalogs from Cucumis melo L. cv. Yamatouri by employing polymerase chain reactions (PCR) as a molecularbiology tools with degenerate primers based on conserved motifs of cloned R genes. The application of molecularbiology such as DNA isolation, degenerate primers and PCR condition, cloning, sequencing, linkage analysisand mapping of resistance gene analogs to Creb-2 gene in melon will be widely discussed in this paper

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Rydholm, C., P. S. Dyer, and F. Lutzoni. "DNA Sequence Characterization and Molecular Evolution of MAT1 and MAT2 Mating-Type Loci of the Self-Compatible Ascomycete Mold Neosartorya fischeri." Eukaryotic Cell 6, no. 5 (March 23, 2007): 868–74. http://dx.doi.org/10.1128/ec.00319-06.

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ABSTRACT Degenerate PCR and chromosome-walking approaches were used to identify mating-type (MAT) genes and flanking regions from the homothallic (sexually self-fertile) euascomycete fungus Neosartorya fischeri, a close relative of the opportunistic human pathogen Aspergillus fumigatus. Both putative alpha- and high-mobility-group-domain MAT genes were found within the same genome, providing a functional explanation for self-fertility. However, unlike those in many homothallic euascomycetes (Pezizomycotina), the genes were not found adjacent to each other and were termed MAT1 and MAT2 to recognize the presence of distinct loci. Complete copies of putative APN1 (DNA lyase) and SLA2 (cytoskeleton assembly control) genes were found bordering the MAT1 locus. Partial copies of APN1 and SLA2 were also found bordering the MAT2 locus, but these copies bore the genetic hallmarks of pseudogenes. Genome comparisons revealed synteny over at least 23,300 bp between the N. fischeri MAT1 region and the A. fumigatus MAT locus region, but no such long-range conservation in the N. fischeri MAT2 region was evident. The sequence upstream of MAT2 contained numerous candidate transposase genes. These results demonstrate a novel means involving the segmental translocation of a chromosomal region by which the ability to undergo self-fertilization may be acquired. The results are also discussed in relation to their significance in indicating that heterothallism may be ancestral within the Aspergillus section Fumigati.

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Zhao, Chunhua, Jianhua Ju, Steven D. Christenson, Wyatt C. Smith, Danfeng Song, Xiufen Zhou, Ben Shen, and Zixin Deng. "Utilization of the Methoxymalonyl-Acyl Carrier Protein Biosynthesis Locus for Cloning the Oxazolomycin Biosynthetic Gene Cluster from Streptomyces albus JA3453." Journal of Bacteriology 188, no. 11 (June 1, 2006): 4142–47. http://dx.doi.org/10.1128/jb.00173-06.

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ABSTRACT Oxazolomycin (OZM), a hybrid peptide-polyketide antibiotic, exhibits potent antitumor and antiviral activities. Using degenerate primers to clone genes encoding methoxymalonyl-acyl carrier protein (ACP) biosynthesis as probes, a 135-kb DNA region from Streptomyces albus JA3453 was cloned and found to cover the entire OZM biosynthetic gene cluster. The involvement of the cloned genes in OZM biosynthesis was confirmed by deletion of a 12-kb DNA fragment containing six genes for methoxymalonyl-ACP biosynthesis from the specific region of the chromosome, as well as deletion of the ozmC gene within this region, to generate OZM-nonproducing mutants.

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Wheeler, J. Craig. "Type IA Supernovae." Symposium - International Astronomical Union 151 (1992): 225–34. http://dx.doi.org/10.1017/s0074180900122223.

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Spectral calculations show that a model based on the thermonuclear explosion of a degenerate carbon/oxygen white dwarf provides excellent agreement with observations of Type Ia supernovae. Identification of suitable evolutionary progenitors remains a severe problem. General problems with estimation of supernova rates are outlined and the origin of Type Ia supernovae from double degenerate systems are discussed in the context of new rates of explosion per H band luminosity, the lack of observed candidates, and the likely presence of H in the vicinity of some SN Ia events. Re-examination of the problems of triggering Type Ia by accretion of hydrogen from a companion shows that there may be an avenue involving cataclysmic variables, especially if extreme hibernation occurs. Novae may channel accreting white dwarfs to a unique locus in accretion rate/mass space. Systems that undergo secular evolution to higher mass transfer rates could lead to just the conditions necessary for a Type Ia explosion. Tests involving fluorescence or absorption in a surrounding circumstellar medium and the detection of hydrogen stripped from a companion, which should appear at low velocity inside the white dwarf ejecta, are suggested. Possible observational confirmation of the former is described.

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Li, Baokun, Yi Cao, Qiuju Zhang, and Zhen Huang. "Position-singularity analysis of a special class of the Stewart parallel mechanisms with two dissimilar semi-symmetrical hexagons." Robotica 31, no. 1 (April 20, 2012): 123–36. http://dx.doi.org/10.1017/s0263574712000148.

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SUMMARYIn this paper, for a special class of the Stewart parallel mechanism, whose moving platform and base one are two dissimilar semi-symmetrical hexagons, the position-singularity of the mechanism for a constant-orientation is analyzed systematically. The force Jacobian matrix [J]T is constructed based on the principle of static equilibrium and the screw theory. After expanding the determinant of the simplified matrix [D], whose rank is the same as the rank of the matrix [J]T, a cubic symbolic expression that represents the 3D position-singularity locus of the mechanism for a constant-orientation is derived and graphically represented. Further research shows that the 3D position-singularity surface is extremely complicated, and the geometric characteristics of the position-singularity locus lying in a general oblique plane are very difficult to be identified. However, the position-singularity locus lying in the series of characteristic planes, where the moving platform coincides, are all quadratic curves compromised of infinite many sets of hyperbolas, four pairs of intersecting lines and a parabola. For some special orientations, the quadratic curve can degenerate into two lines or even one line, all of which are parallel to the ridgeline. Two theorems are presented and proved for the first time when the geometric characteristics of the position-singularity curves in the characteristic plane are analyzed. Moreover, the kinematic property of the position-singularity curves is obtained using the Grassmann line geometry and the screw theory. The theoretical results are demonstrated with several numeric examples.

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Horvath, Philippe, Dennis A. Romero, Anne-Claire Coûté-Monvoisin, Melissa Richards, Hélène Deveau, Sylvain Moineau, Patrick Boyaval, Christophe Fremaux, and Rodolphe Barrangou. "Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus." Journal of Bacteriology 190, no. 4 (December 7, 2007): 1401–12. http://dx.doi.org/10.1128/jb.01415-07.

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ABSTRACT Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel Streptococcus thermophilus locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several S. thermophilus strains. We show that both CRISPR repeats and cas genes are locus specific and functionally coupled. A total of 124 strains were studied, and 109 unique spacer arrangements were observed across the three CRISPR loci. Overall, 3,626 spacers were analyzed, including 2,829 for CRISPR1 (782 unique), 173 for CRISPR2 (16 unique), and 624 for CRISPR3 (154 unique). Sequence analysis of the spacers revealed homology and identity to phage sequences (77%), plasmid sequences (16%), and S. thermophilus chromosomal sequences (7%). Polymorphisms were observed for the CRISPR repeats, CRISPR spacers, cas genes, CRISPR motif, locus architecture, and specific sequence content. Interestingly, CRISPR loci evolved both via polarized addition of novel spacers after exposure to foreign genetic elements and via internal deletion of spacers. We hypothesize that the level of diversity is correlated with relative CRISPR activity and propose that the activity is highest for CRISPR1, followed by CRISPR3, while CRISPR2 may be degenerate. Globally, the dynamic nature of CRISPR loci might prove valuable for typing and comparative analyses of strains and microbial populations. Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes.

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Baranovskii, Serhij, Andrij Bomba, and Oksana Pryshchepa. "Modeling the Influence of Small-Scale Diffusion Perturbations on the Development of Infectious Diseases under Immunotherapy." Modeling, Control and Information Technologies, no. 4 (October 22, 2020): 15–18. http://dx.doi.org/10.31713/mcit.2020.12.

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The article proposes a modification of the mathematical model of the immunotherapy influence on the immune response dynamics taking into account small-scale diffusion perturbations. The solution of the corresponding singularly perturbed model problem with time-delay is reduced to a sequence of solutions without time-delay, for that representations of the required functions in the form of asymptotic series as disturbances of solutions of the corresponding degenerate problems are constructed. We present the results of numerical modeling that illustrate the influence of diffusion redistribution of active factors on the infectious disease dynamics in the conditions of immunotherapy. The decrease in the level of the maximum concentration of antigens in the locus of infection as a result of their diffusion redistribution is illustrated.

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WOLF, CHRISTIAN. "Variation of topological pressure and dimension: from polynomials to complex Hénon maps." Ergodic Theory and Dynamical Systems 34, no. 3 (March 14, 2013): 1018–36. http://dx.doi.org/10.1017/etds.2012.166.

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AbstractWe study the topological pressure and dimension theory of complex Hénon maps which are small perturbations of one-dimensional polynomials. In particular, we derive regularity results for the generalized pressure function in a neighborhood of the degenerate map (i.e. the polynomial). This unifies results concerning the regularity of the pressure function for polynomials by Ruelle and for complex Hénon maps by Verjovsky and Wu. We then apply this regularity to show that the Hausdorff dimension of the Julia set is a continuous non-differentiable function in a neighborhood of the polynomial. Furthermore, we establish uniqueness of the measure of maximal dimension and show that the Hausdorff dimension of the Julia set of a complex Hénon map is discontinuous at the boundary of the hyperbolicity locus.

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Jackson, Colin J., Takashi Mochizuki, and Richard C. Barton. "PCR fingerprinting of Trichophyton mentagrophytes var. interdigitale using polymorphic subrepeat loci in the rDNA nontranscribed spacer." Journal of Medical Microbiology 55, no. 10 (October 1, 2006): 1349–55. http://dx.doi.org/10.1099/jmm.0.46691-0.

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The sequence of the nontranscribed spacer (NTS) region of the rDNA of Trichophyton mentagrophytes var. interdigitale strain 2111 was determined, and three individual subrepeat loci identified. The first repeat region contained eight tandem copies of a degenerate 33–43 bp sequence, whilst the second had two complete and two partial 300 bp repeats. The third locus contained six tandemly repetitive elements of between 67 and 89 bp, which showed sequence identity to the TrS2 repeats of Trichophyton rubrum. PCR amplification of the individual repetitive regions from 42 random isolates of T. mentagrophytes var. interdigitale identified fragment length polymorphisms at each locus. Sequence analysis of the PCR products revealed that the size variations resulted from differences in the copy number of each of the three sets of subrepeat elements, TmiS0, TmiS1 and TmiS2. In addition, some indels were present in the flanking regions of the TmiS1 repeats. Combining PCR fingerprints from each of the three polymorphic loci produced a total of 19 individual strain profiles. The method was rapid, reproducible and discriminatory, and the fragment patterns simple to interpret. PCR fingerprint analysis of variable tandem repeat loci in the T. mentagrophytes var. interdigitale NTS represents a valuable molecular typing method for future epidemiological investigations in this species.

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Arbarello, Enrico, Giulio Codogni, and Giuseppe Pareschi. "Characterizing Jacobians via the KP equation and via flexes and degenerate trisecants to the Kummer variety: An algebro-geometric approach." Journal für die reine und angewandte Mathematik (Crelles Journal) 2021, no. 777 (May 8, 2021): 251–71. http://dx.doi.org/10.1515/crelle-2021-0020.

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Abstract We give completely algebro-geometric proofs of a theorem by T. Shiota, and of a theorem by I. Krichever, characterizing Jacobians of algebraic curves among all irreducible principally polarized abelian varieties. Shiota’s characterization is given in terms of the KP equation. Krichever’s characterization is given in terms of trisecant lines to the Kummer variety. Here we treat the case of flexes and degenerate trisecants. The basic tool we use is a theorem we prove asserting that the base locus of the linear system associated to an effective line bundle on an abelian variety is reduced. This result allows us to remove all the extra assumptions that were introduced in the theorems by the first author, C. De Concini, G.Marini, and O. Debarre, in order to achieve algebro-geometric proofs of the results above.

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Hiszczynska-Sawicka, Ela, Dongmei Li, and Karen F. Armstrong. "Universal Mitochondrial Multi-Locus Sequence Analysis (mtMLSA) to Characterise Populations of Unanticipated Plant Pest Biosecurity Detections." Biology 11, no. 5 (April 24, 2022): 654. http://dx.doi.org/10.3390/biology11050654.

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Biosecurity responses to post-border exotic pest detections are more effective with knowledge of where the species may have originated from or if recurrent detections are connected. Population genetic markers for this are typically species-specific and not available in advance for any but the highest risk species, leaving other less anticipated species difficult to assess at the time. Here, new degenerate PCR primer sets are designed for within the Lepidoptera and Diptera for the 3′ COI, ND3, ND6, and 3′ plus 5′ 16S gene regions. These are shown to be universal at the ordinal level amongst species of 14 and 15 families across 10 and 11 dipteran and lepidopteran superfamilies, respectively. Sequencing the ND3 amplicons as an example of all the loci confirmed detection of population-level variation. This supported finding multiple population haplotypes from the publicly available sequences. Concatenation of the sequences also confirmed that higher population resolution is achieved than for the individual genes. Although as-yet untested in a biosecurity situation, this method is a relatively simple, off-the-shelf means to characterise populations. This makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for unprepared species-specific research and development.

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SANYAL, DULAL CHANDRA, and BIJAN SARKAR. "A THEORETICAL FRAMEWORK RELATING TO EXPONENTIALLY FREQUENCY-DEPENDENT SELECTION MODEL IN POLLAK'S SENSE." International Journal of Biomathematics 02, no. 02 (June 2009): 179–96. http://dx.doi.org/10.1142/s1793524509000571.

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Allowing the exponentially frequency-dependent fitnesses and taking into consideration the viability effect on the fertility model, a deterministic mathematical model of selection in a one-locus two-allele genetic system has been developed in such a way that equilibrium frequencies of the three genotypes are the same as those of optimizing the mean fertility of the population. Under the consideration of both exponentially increasing and decreasing nature environments in the sense of viability and fertility selections to be opposite, degenerate optimization points have been calculated by verifying whether those equilibrium points are Kuhn–Tucker points or not. The Hadeler–Liberman symmetric fertility model has also been accounted for derivation of all sets of frequencies of this type. Assuming the Fundamental Theorem of Natural Selection, a mathematical expression has been derived to show the variation of mean fertility with generation.

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Meyer, Richard. "The R1162 Mob Proteins Can Promote Conjugative Transfer from Cryptic Origins in the Bacterial Chromosome." Journal of Bacteriology 191, no. 5 (December 12, 2008): 1574–80. http://dx.doi.org/10.1128/jb.01471-08.

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ABSTRACT The mobilization proteins of the broad-host-range plasmid R1162 can initiate conjugative transfer of a plasmid from a 19-bp locus that is partially degenerate in sequence. Such loci are likely to appear by chance in the bacterial chromosome and could act as cryptic sites for transfer of chromosomal DNA when R1162 is present. The R1162-dependent transfer of chromosomal DNA, initiated from one such potential site in Pectobacterium atrosepticum, is shown here. A second active site was identified in Escherichia coli, where it is also shown that large amounts of DNA are transferred. This transfer probably reflects the combined activity of the multiple cryptic origins in the chromosome. Transfer of chromosomal DNA due to the presence of a plasmid in the cytoplasm describes a previously unrecognized potential for the exchange of bacterial DNA.

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44

Odehnal, Boris. "Distance Product Cubics." KoG, no. 24 (2020): 29–40. http://dx.doi.org/10.31896/k.24.3.

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The locus of points that determine a constant product of their distances to the sides of a triangle is a cubic curve in the projectively closed Euclidean triangle plane. In this paper, algebraic and geometric properties of these distance product cubics shall be studied. These cubics span a pencil of cubics that contains only one rational and non-degenerate cubic curve which is known as the Bataille acnodal cubic determined by the product of the actual trilinear coordinates of the centroid of the base triangle. Each triangle center defines a distance product cubic. It turns out that only a small number of triangle centers share their distance product cubic with other centers. All distance product cubics share the real points of inflection which lie on the line at infinity. The cubics' dual curves, their Hessians, and especially those distance product cubics that are defined by particular triangle centers shall be studied.

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45

Miller, William G., Emma Yee, and James L. Bono. "Complete Genome Sequencing of Four Arcobacter Species Reveals a Diverse Suite of Mobile Elements." Genome Biology and Evolution 12, no. 2 (February 1, 2020): 3850–56. http://dx.doi.org/10.1093/gbe/evaa014.

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Abstract Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Genome sequencing of the poultry isolate Arcobacter cibarius H743 and the Arcobacter acticola, Arcobacter pacificus, and Arcobacter porcinus type strains identified a large number and variety of insertion sequences. This study presents an analysis of these A. acticola, A. cibarius, A. pacificus, and A. porcinus IS elements. The four genomes sequenced here contain 276 complete and degenerate IS elements, representing 13 of the current 29 prokaryotic IS element families. Expansion of the analysis to include 15 other previously sequenced Arcobacter spp. added 73 complete and degenerate IS elements. Several of these IS elements were identified in two or more Arcobacter species, suggesting movement by horizontal gene transfer between the arcobacters. These IS elements are putatively associated with intragenomic deletions and inversions, and tentative movement of antimicrobial resistance genes. The A. cibarius strain H743 megaplasmid contains multiple IS elements common to the chromosome and, unusually, a complete ribosomal RNA locus, indicating that larger scale genomic rearrangements, potentially resulting from IS element-mediated megaplasmid cointegration and resolution may be occurring within A. cibarius and possibly other arcobacters. The presence of such a large and varied suite of mobile elements could have profound effects on Arcobacter biology and evolution.

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Rahemi, Alireza, Thomas M. Gradziel, Jose X. Chaparro, Kevin M. Folta, Toktam Taghavi, Reza Fatahi, Ali Ebadi, and Darab Hassani. "Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes." Canadian Journal of Plant Science 95, no. 6 (November 2015): 1145–54. http://dx.doi.org/10.4141/cjps-2015-102.

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Rahemi, A., Gradziel T.M., Chaparro J.X., Folta, K.M., Taghavi, T., Fatahi, R., Ebadi, A. and Hassani, D. 2015. Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145–1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD+EM-Pc1ConsRD and EM-Pc2ConsFD+EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%. Most sequences were similar to cultivated almond (Prunus dulcis) or to the European wild almond (P. webbii). Twenty-six alleles for the first and the second introns were registered in the database in the GenBank. Two sequences of the first and second introns, which were taken from Prunus nairica and had similarity in GenBank, were registered in the database under a common sequence of the first and second intron. Analysis of phylogenetic relationships (dendrograms) among S-alleles from wild almond species as well as S-alleles cluster relations showed most pairs of alleles well supported by bootstrap.

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47

Rose, Timothy M., Jonathan T. Ryan, Emily R. Schultz, Brian W. Raden, and Che-Chung Tsai. "Analysis of 4.3 Kilobases of Divergent Locus B of Macaque Retroperitoneal Fibromatosis-Associated Herpesvirus Reveals a Close Similarity in Gene Sequence and Genome Organization to Kaposi's Sarcoma-Associated Herpesvirus." Journal of Virology 77, no. 9 (May 1, 2003): 5084–97. http://dx.doi.org/10.1128/jvi.77.9.5084-5097.2003.

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ABSTRACT We previously identified retroperitoneal fibromatosis-associated herpesvirus (RFHV) as a simian homolog of Kaposi's sarcoma-associated herpesvirus (KSHV) in a fibroproliferative malignancy of macaques that has similarities to Kaposi's sarcoma. In this report, we cloned 4.3 kb of divergent locus B (DL-B) flanking the DNA polymerase gene from two variants of RFHV from different species of macaque with a consensus degenerate hybrid oligonucleotide primer approach. Within the DL-B region of RFHV, viral homologs of the cellular interleukin-6, dihydrofolate reductase, and thymidylate synthase genes were identified, along with a homolog of the gammaherpesvirus open reading frame (ORF) 10. In addition, a homolog of the KSHV ORF K3, the modulator of immune recognition-1, was identified. Our data show a close similarity in sequence conservation, gene content, and genomic structure between RFHV and KSHV which strongly supports the grouping of these viral species within the same RV-1 rhadinovirus lineage and the hypothesis that RFHV is the macaque homolog of KSHV.

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48

Forbes, Michael S., Barbara A. Thornhill, and Robert L. Chevalier. "Proximal tubular injury and rapid formation of atubular glomeruli in mice with unilateral ureteral obstruction: a new look at an old model." American Journal of Physiology-Renal Physiology 301, no. 1 (July 2011): F110—F117. http://dx.doi.org/10.1152/ajprenal.00022.2011.

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Unilateral ureteral obstruction (UUO), employed extensively as a model of progressive renal interstitial fibrosis, results in rapid parenchymal deterioration. Atubular glomeruli are formed in many renal disorders, but their identification has been limited by labor-intensive available techniques. The formation of atubular glomeruli was therefore investigated in adult male mice subjected to complete UUO under general anesthesia. In this species, the urinary pole of Bowman's capsule is normally lined by tall parietal epithelial cells similar to those of the proximal tubule, and both avidly bind Lotus tetragonolobus lectin. Following UUO, these cells became flattened, lost their affinity for Lotus lectin, and no longer generated superoxide (revealed by nitroblue tetrazolium infusion). Based on Lotus lectin staining, stereological measurements, and serial section analysis, over 80% of glomeruli underwent marked transformation after 14 days of UUO. The glomerulotubular junction became stenotic and atrophic due to cell death by apoptosis and autophagy, with concomitant remodeling of Bowman's capsule to form atubular glomeruli. In this degenerative process, transformed epithelial cells sealing the urinary pole expressed α-smooth muscle actin, vimentin, and nestin. Although atubular glomeruli remained perfused, renin immunostaining was markedly increased along afferent arterioles, and associated maculae densae disappeared. Numerous progressive kidney disorders, including diabetic nephropathy, are characterized by the formation of atubular glomeruli. The rapidity with which glomerulotubular junctions degenerate, coupled with Lotus lectin as a marker of glomerular integrity, points to new investigative uses for the model of murine UUO focusing on mechanisms of epithelial cell injury and remodeling in addition to fibrogenesis.

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Ehlers, Bernhard, Judit Küchler, Nezlisah Yasmum, Güzin Dural, Sebastian Voigt, Jonas Schmidt-Chanasit, Thomas Jäkel, et al. "Identification of Novel Rodent Herpesviruses, Including the First Gammaherpesvirus of Mus musculus." Journal of Virology 81, no. 15 (May 16, 2007): 8091–100. http://dx.doi.org/10.1128/jvi.00255-07.

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ABSTRACT Rodent herpesviruses such as murine cytomegalovirus (host, Mus musculus), rat cytomegalovirus (host, Rattus norvegicus), and murine gammaherpesvirus 68 (hosts, Apodemus species) are important tools for the experimental study of human herpesvirus diseases. However, alphaherpesviruses, roseoloviruses, and lymphocryptoviruses, as well as rhadinoviruses, that naturally infect Mus musculus (house mouse) and other Old World mice are unknown. To identify hitherto-unknown rodent-associated herpesviruses, we captured M. musculus, R. norvegicus, and 14 other rodent species in several locations in Germany, the United Kingdom, and Thailand. Samples of trigeminal ganglia, dorsal root ganglia, brains, spleens, and other organs, as well as blood, were analyzed with a degenerate panherpesvirus PCR targeting the DNA polymerase (DPOL) gene. Herpesvirus-positive samples were subjected to a second degenerate PCR targeting the glycoprotein B (gB) gene. The sequences located between the partial DPOL and gB sequences were amplified by long-distance PCR and sequenced, resulting in a contiguous sequence of approximately 3.5 kbp. By DPOL PCR, we detected 17 novel betaherpesviruses and 21 novel gammaherpesviruses but no alphaherpesvirus. Of these 38 novel herpesviruses, 14 were successfully analyzed by the complete bigenic approach. Most importantly, the first gammaherpesvirus of Mus musculus was discovered (Mus musculus rhadinovirus 1 [MmusRHV1]). This virus is a member of a novel group of rodent gammaherpesviruses, which is clearly distinct from murine herpesvirus 68-like rodent gammaherpesviruses. Multigenic phylogenetic analysis, using an 8-kbp locus, revealed that MmusRHV1 diverged from the other gammaherpesviruses soon after the evolutionary separation of Epstein-Barr virus-like lymphocryptoviruses from human herpesvirus 8-like rhadinoviruses and alcelaphine herpesvirus 1-like macaviruses.

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Chapeland-Leclerc, Florence, Julien Bouchoux, Abdelhak Goumar, Christiane Chastin, Jean Villard, and Thierry Noël. "Inactivation of the FCY2 Gene Encoding Purine-Cytosine Permease Promotes Cross-Resistance to Flucytosine and Fluconazole in Candida lusitaniae." Antimicrobial Agents and Chemotherapy 49, no. 8 (August 2005): 3101–8. http://dx.doi.org/10.1128/aac.49.8.3101-3108.2005.

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ABSTRACT In a previous work, we described the possible relationship between a defect of purine-cytosine permease and the acquisition of a cross-resistance to the antifungal combination flucytosine (5FC) and fluconazole (FLC) in Candida lusitaniae (T. Noël, F. François, P. Paumard, C. Chastin, D. Brethes, and J. Villard, Antimicrob. Agents Chemother. 47:1275-1284, 2003). Using degenerate PCR and chromosome walking, we cloned two FCY2-like genes in C. lusitaniae. Northern blot analysis revealed that only one gene was expressed; it was named FCY2. The other one behaved as a pseudogene and was named FCY21. In order to better characterize the possible role of FCY2 in cross-resistance to 5FC-FLC, disruption experiments with auxotrophic strain 6936 ura3(D95V) FCY2 with an integrative vector carrying the URA3 gene and a partial sequence of the C. lusitaniae FCY2 gene were undertaken. Southern blot analysis revealed that homologous recombination events occurred in all transformants analyzed at rates of 50% at resident locus FCY2 and 50% at resident locus URA3, resulting in the genotypes ura3 fcy2::URA3 and ura3::URA3 FCY2, respectively. It was then demonstrated that only transformants harboring a disrupted fcy2 gene were resistant to 5FC, susceptible to FLC, and resistant to the 5FC-FLC combination. Finally, complementation experiments with a functional FCY2 gene restored 5FC and FLC susceptibilities to the wild-type levels. The results of this study provide molecular evidence that inactivation of the sole FCY2 gene promotes cross-resistance to the antifungal association 5FC-FLC in C. lusitaniae.

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Journal articles on the topic 'Degeneracy locus'

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