Journal articles on the topic 'Null frames'
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1
Ilarslan, Kazim, and Emilija Nešović. "On Bishop frame of a null Cartan curve in Minkowski space-time." International Journal of Geometric Methods in Modern Physics 15, no. 08 (June 22, 2018): 1850142. http://dx.doi.org/10.1142/s0219887818501426.
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In this paper, we define the Bishop frame of a null Cartan curve in Minkowski space-time [Formula: see text]. We obtain the Bishop’s frame equations of a null Cartan curve which lies in the timelike hyperplane of [Formula: see text]. We show that a null Cartan cubic lying in the timelike hyperplane of [Formula: see text] has two Bishop frames, one of which coincides with its Cartan frame. We also derive the Bishop’s frame equation of the null Cartan curve which has the third Cartan curvature [Formula: see text]. As an application, we find a solution of the null Betchov-Da Rios vortex filament equation in terms of a null Cartan curve and its Bishop frame, which generates a timelike Hasimoto surface.
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Lutey, Matt, Mohammad Kabir Hassan, and Dave Rayome. "An Application of Can Slim Investing in the Dow Jones Benchmark." Asian Journal of Economic Modelling 6, no. 3 (May 24, 2018): 274–86. http://dx.doi.org/10.18488/journal.8.2018.63.274.286.
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This paper provides an alternative view of the popular CAN SLIM investing strategy by modifying and weighting the criterion. The modified criterion is used to build a portfolio in each of three overlapping time frames. The results of the study are compared to a Dow Jones Industrial Average benchmark over the same time frame and is evaluated on a risk adjusted basis. The study finds that the system outperforms the market on a risk adjusted basis in all three time frames and holds a high R Squared for each timeframe. The null hypothesis for the majority of this paper is to test whether the mean returns of the strategy are significantly different from zero on a monthly basis. This is tested over three overlapping timeframes of five years, ten years and sixteen years respectively. A further hypothesis is tested for the 2008-2009 timeframe and is whether the mean excess returns of the strategy are significantly different from zero when compared to the Dow Jones benchmark. This paper finds that the null hypothesis is rejected over all time frames with strong evidence. An exception is the 16-year time frame where the null is rejected with weak evidence.
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López, Rafael, Željka Milin Šipuš, Ljiljana Primorac Gajčić, and Ivana Protrka. "Involutes of Pseudo-Null Curves in Lorentz–Minkowski 3-Space." Mathematics 9, no. 11 (May 31, 2021): 1256. http://dx.doi.org/10.3390/math9111256.
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In this paper, we analyze involutes of pseudo-null curves in Lorentz–Minkowski 3-space. Pseudo-null curves are spacelike curves with null principal normals, and their involutes can be defined analogously as for the Euclidean curves, but they exhibit properties that cannot occur in Euclidean space. The first result of the paper is that the involutes of pseudo-null curves are null curves, more precisely, null straight lines. Furthermore, a method of reconstruction of a pseudo-null curve from a given null straight line as its involute is provided. Such a reconstruction process in Euclidean plane generates an evolute of a curve, however it cannot be applied to a straight line. In the case presented, the process is additionally affected by a choice of different null frames that every null curve allows (in this case, a null straight line). Nevertheless, we proved that for different null frames, the obtained pseudo-null curves are congruent. Examples that verify presented results are also given.
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Grbović, Milica, and Emilija Nešović. "On the Bishop frames of pseudo null and null Cartan curves in Minkowski 3-space." Journal of Mathematical Analysis and Applications 461, no. 1 (May 2018): 219–33. http://dx.doi.org/10.1016/j.jmaa.2018.01.014.
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Ertuğ Gürbüz, Nevin. "The variation of the electric field along optic fiber for null Cartan and pseudo-null frames." International Journal of Geometric Methods in Modern Physics 18, no. 08 (May 12, 2021): 2150122. http://dx.doi.org/10.1142/s021988782150122x.
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In this paper, we introduce new frame and new transformation associated with combined Korteweg–de Vries–modified Korteweg–de Vries (KdV–mKdV) equation, the mKdV and the KdV equations with respect to the null Cartan frame in Minkowski 3-space. Direction of the state of polarization of monochromatic linear polarized light wave traveling in the optic fiber is given by the direction of electric field vector. We show that the electric field vector [Formula: see text] can be expressed as a linear combination of null Cartan frame apparatus using this new transformation in Minkowski 3-space. Later, we study rotation of the polarization plane along optic fiber according to null Cartan frame and Frenet frame of pseudo-null curve in Minkowski 3-space. Finally, we obtain Lorentz force equations via null and pseudo null electromagnetic curves.
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ILARSLAN, Kazim, Ali UCUM, Emilija NESOVIC, and Nihal KILIC ASLAN. "Mannheim B-curve couples in Minkowski 3-space." Tamkang Journal of Mathematics 51, no. 3 (September 25, 2020): 219–32. http://dx.doi.org/10.5556/j.tkjm.51.2020.3059.
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In this paper, we define null Cartan and pseudo null Mannheim curves in Minkowski 3-space according to their Bishop frames. We obtain the necessary and the sufficient conditions for pseudo null curves to be Mannheim B-curves in terms of their Bishop curvatures. We prove that there are no null Cartan curves in Minkowski 3-space which are Mannheim B-curves, by considering the cases when their Mannheim B-mate curves are spacelike, timelike, null Cartan and pseudo null curves. Finally, we give some examples of pseudo null Mannheim B-curve pairs.
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Grbovic, Milica, Kazim Ilarslan, and Emilija Nesovic. "On generalized null Mannheim curves in Minkowski space-time." Publications de l'Institut Math?matique (Belgrade) 99, no. 113 (2016): 77–98. http://dx.doi.org/10.2298/pim1613077g.
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We define generalized null Mannheim curves in Minkowski space-time and characterize them and their generalized Mannheim mate curves in terms of curvature functions, and obtain relations between their frames. We provide examples of such curves.
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Azak, Ayşe Zeynep, Murat Tosun, and Melek Masal. "Null parallel p-equidistant b-scrolls." Boletim da Sociedade Paranaense de Matemática 32, no. 2 (September 11, 2014): 23. http://dx.doi.org/10.5269/bspm.v32i2.20119.
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In this paper, null parallel p-equidistant B-scrolls are defined in 3-dimensional Minkowski space R_1^3 . We prove necessary and sufficient conditions for these B-scrolls to be equivalent of their Cartan frames. The relations between matrices of the shape operators and the algebraic invariants (Gauss, mean curvatures, principal curvatures) of these B-scrolls are shown. Besides we give the relations between second Gauss curvatures, mean curvatures and the distribution parameters of non-developable null parallel p-equidistant B-scrolls. Finally, an example is given related to the null parallel p-equidistant B-scrolls in R_1^3.
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Grbović, Milica, and Emilija Nešović. "On Bäcklund transformation and vortex filament equation for pseudo null curves in Minkowski 3-space." International Journal of Geometric Methods in Modern Physics 13, no. 06 (June 15, 2016): 1650077. http://dx.doi.org/10.1142/s0219887816500778.
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In this paper, we introduce Bäcklund transformation of a pseudo null curve in Minkowski 3-space as a transformation mapping a pseudo null helix to another pseudo null helix congruent to the given one. We also give the sufficient conditions for a transformation between two pseudo null curves in the Minkowski 3-space such that these curves have equal constant torsions. By using the Da Rios vortex filament equation, based on localized induction approximation (LIA), we derive the vortex filament equation for a pseudo null curve and prove that the evolution equation for the torsion is the viscous Burger’s equation. As an application, we show that pseudo null curves and their Frenet frames generate solutions of the Da Rios vortex filament equation.
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Qian, Jinhua, Xueshan Fu, and Seoung Dal Jung. "Darboux Associated Curves of a Null Curve on Pseudo-Riemannian Space Forms." Mathematics 8, no. 3 (March 11, 2020): 395. http://dx.doi.org/10.3390/math8030395.
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In this work, the Darboux associated curves of a null curve on pseudo-Riemannian space forms, i.e., de-Sitter space, hyperbolic space and a light-like cone in Minkowski 3-space are defined. The relationships of such partner curves are revealed including the relationship of their Frenet frames and the curvatures. Furthermore, the Darboux associated curves of k-type null helices are characterized and the conclusion that a null curve and its self-associated curve share the same Darboux associated curve is obtained.
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Trogrlić, B., A. Harapin, and A. Mihanović. "The null configuration model in limit load analysis of steel space frames." Materialwissenschaft und Werkstofftechnik 42, no. 5 (May 2011): 417–28. http://dx.doi.org/10.1002/mawe.201100801.
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Qian, Jinhua, Xueqian Tian, and Young Ho Kim. "Normal Partner Curves of a Pseudo Null Curve on Dual Space Forms." Mathematics 8, no. 6 (June 5, 2020): 919. http://dx.doi.org/10.3390/math8060919.
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In this work, a kind of normal partner curves of a pseudo null curve on dual space forms is defined and studied. The Frenet frames and curvatures of a pseudo null curve and its associate normal curve on de-Sitter space, its associate normal curve on hyperbolic space, are related by some particular function and the angles between their tangent vector fields, respectively. Meanwhile, the relationships between the normal partner curves of a pseudo null curve are revealed. Last but not least, some examples are given and their graphs are plotted by the aid of a software programme.
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Liu, Tongchang, and Donghe Pei. "Mixed-type curves and the lightcone frame in Minkowski 3-space." International Journal of Geometric Methods in Modern Physics 17, no. 06 (May 2020): 2050088. http://dx.doi.org/10.1142/s0219887820500887.
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In this paper, we study mixed-type curves in Minkowski 3-space. Mixed-type curves are regular curves, and there are both non-lightlike points and lightlike points in a mixed-type curve. For non-lightlike curves and null curves in Minkowski 3-space, we can study them by a Frenet frame or a Cartan frame, respectively. But for mixed-type curves, the two frames will not work. As far as we know, no one has yet given a frame to study them in Minkowski 3-space. So, we give the lightcone frame in order to provide a tool for studying this type curves in mathematical and physical research. As an application of the lightcone frame, we define an evolute of a mixed-type curve. We also give some examples to show the evolutes.
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Kayama, Yuhko, and Yuriko Oshima-Takane. "The acquisition of argument structures of intransitive and transitive verbs in Japanese: The role of parental input." First Language 42, no. 1 (December 7, 2021): 144–67. http://dx.doi.org/10.1177/01427237211059970.
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The present study investigated the role of morphosyntactic information in the acquisition of transitive and intransitive verb argument structures (VAS) in the Japanese language, which allows massive omissions of arguments and case markers. In particular, we investigated how the ‘variation sets’ proposed by Küntay and Slobin work in Japanese. Longitudinal interaction data from three Japanese-speaking mother–child pairs were collected at five different times between the ages of 0;10 and 3;01. Children’s acquisition of VAS and mothers’ use of verbs were examined, including morphologically related verbs in a variety of sentence frames with null and overt arguments. The results indicate that all three mothers showed an increase in overt arguments in different syntactic roles as well as lexical given arguments around the time that children started uttering words. However, the use of a variety of sentence frames with null and overt arguments was not uniform among the mothers, and such individual differences were related to the acquisition of VAS among children. These findings support the role of ‘variation sets’ in the acquisition of VAS in Japanese and suggest that the availability of morphosyntactic information in the input helps children to reconstruct VAS.
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Souza, Luiz Antonio Farani de, Leandro Vanalli, and Arthur Bueno de Luz. "Numerical-Computational Model for Nonlinear Analysis of Frames with Semirigid Connection." Mathematical Problems in Engineering 2020 (September 3, 2020): 1–11. http://dx.doi.org/10.1155/2020/3613892.
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A numerical-computational model for static analysis of plane frames with semirigid connections and geometric nonlinear behavior is presented. The set of nonlinear equations governing the structural system is solved by the Potra–Pták method in an incremental procedure, with order of cubic convergence, combined with the linear arc-length path-following technique. The algorithm pseudo-code is presented, and the finite element corotational method is used for the discretization of the structures. The equilibrium paths with load and displacement limit points are obtained. The semirigidity is simulated by a linear connection element of null length, which considers the axial, tangential, and rotational stiffness. Nonlinear analyses of 2D frame structures are carried out with the free Scilab program. The results show that the Potra–Pták procedure can decrease the number of iterations and the computing time in comparison with the standard and modified Newton–Raphson iterative schemes. Also, the simulations show that the connection flexibility has a strong influence on the nonlinear behavior and stability of the structural systems.
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Wild, Phillip. "A SPECTRAL-BASED CUSUM TEST OF EVOLUTIONARY CHANGE." Macroeconomic Dynamics 6, no. 3 (June 2002): 385–407. http://dx.doi.org/10.1017/s1365100599990089.
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We develop a test of evolutionary change that incorporates a null hypothesis of homogeneity, which encompasses time invariance in the variance and autocovariance structure of residuals from estimated econometric relationships. The test framework is based on examining whether shifts in spectral decomposition between two frames of data are significant. Rejection of the null hypothesis will point not only to weak nonstationarity but to shifts in the structure of the second-order moments of the limiting distribution of the random process. This would indicate that the second-order properties of any underlying attractor set has changed in a statistically significant way, pointing to the presence of evolutionary change. A demonstration of the test's applicability to a real-world macroeconomic problem is accomplished by applying the test to the Australian Building Society Deposits (ABSD) model.
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Ishikawa, Naoki, Yasuhiro Ohishi, and Kaori Maeda. "Nulls in the Air: Passive and Low-Complexity QoS Estimation Method for a Large-Scale Wi-Fi Network Based on Null Function Data Frames." IEEE Access 7 (2019): 28581–91. http://dx.doi.org/10.1109/access.2019.2902182.
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Turakulov, Zafar Y., and Alisher T. Muminov. "Electromagnetic Field with Constraints and Papapetrou Equation." Zeitschrift für Naturforschung A 61, no. 3-4 (April 1, 2006): 146–52. http://dx.doi.org/10.1515/zna-2006-3-407.
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It is shown that a geometric optical description of the electromagnetic wave with respect to its polarization in a curved space-time can be obtained straightforwardly from the classical variational principle for the electromagnetic field. For this purpose the entire functional space of electromagnetic fields must be reduced to its subspace of locally plane monochromatic waves. We have formulated the constraints under which this can be achieved. These constraints introduce variables of another kind which specify a field of local frames associated with the wave. They contain some congruence with null-curves. The Lagrangian for constrained electromagnetic fields contains variables of two kinds, namely a congruence of null-curves and the field itself. This in turn yields two kinds of Euler- Lagrange equations. The equations of the first kind are trivial due to the constraints imposed. The variation of the curves yields the Papapetrou equations for a classical massless particle with helicity 1
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Marmolejo-Ramos, Fernando, and Denis Cousineau. "Perspectives on the Use of Null Hypothesis Statistical Testing. Part I: The Mighty Frames of Scientific and Statistical Inference." Educational and Psychological Measurement 77, no. 3 (October 6, 2016): 471–74. http://dx.doi.org/10.1177/0013164416667986.
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Tomich, Mladen, Adam Griffith, Christine A. Herfst, Jane L. Burns, and Christian D. Mohr. "Attenuated Virulence of a Burkholderia cepacia Type III Secretion Mutant in a Murine Model of Infection." Infection and Immunity 71, no. 3 (March 2003): 1405–15. http://dx.doi.org/10.1128/iai.71.3.1405-1415.2003.
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ABSTRACT Type III secretion systems are utilized by a number of gram-negative bacterial pathogens to deliver virulence-associated proteins into host cells. Using a PCR-based approach, we identified homologs of type III secretion genes in the gram-negative bacterium Burkholderia cepacia, an important pulmonary pathogen in immunocompromised patients and patients with cystic fibrosis. One of the genes, designated bscN, encodes a member of a family of ATP-binding proteins believed to generate energy driving virulence protein secretion. Genetic dissection of the regions flanking the bscN gene revealed a locus consisting of at least 10 open reading frames, predicted to encode products with significant homology to known type III secretion proteins in other bacteria. A defined null mutation was generated in the bscN gene, and the null strain and wild-type parent strain were examined by use of a murine model of B. cepacia infection. Quantitative bacteriological analysis of the lungs and spleens of infected C57BL/6 mice revealed that the bscN null strain was attenuated in virulence compared to the parent strain, with significantly lower bacterial recovery from the lungs and spleens at 3 days postinfection. Moreover, histopathological changes, including an inflammatory cell infiltrate, were more pronounced in the lungs of mice infected with the wild-type parent strain than in those of mice infected with the isogenic bscN mutant. These results implicate type III secretion as an important determinant in the pathogenesis of B. cepacia.
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Lukić, Branko, Kosta Jovanović, Leon Žlajpah, and Tadej Petrič. "Online Cartesian Compliance Shaping of Redundant Robots in Assembly Tasks." Machines 11, no. 1 (December 28, 2022): 35. http://dx.doi.org/10.3390/machines11010035.
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This paper presents a universal approach to shaping the mechanical properties of the interaction between a collaborative robot and its environment through an end-effector Cartesian compliance shaping. More specifically, the focus is on the class of kinematically redundant robots, for which a novel redundancy reconfiguration scheme for online optimization of the Cartesian compliance of the end-effector is presented. The null-space reconfiguration aims to enable the more efficient and versatile use of collaborative robots, including robots with passive compliant joints. The proposed approach is model-based and gradient-based to enable real-time computation and reconfiguration of the robot for Cartesian compliance while ensuring accurate position tracking. The optimization algorithm combines two coordinate frames: the global (world) coordinate frame commonly used for end-effector trajectory tracking; and the coordinate frame fixed to the end-effector in which optimization is computed. Another attractive feature of the approach is the bound on the magnitude of the interaction force in contact tasks. The results are validated on a torque-controlled 7-DOF KUKA LWR robot emulating joint compliance in a quasi-static experiment (the robot exerts a force on an external object) and a peg-in-hole experiment emulating an assembly task.
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Duan, Chunxia. "Deep Learning-Based Multitarget Motion Shadow Rejection and Accurate Tracking for Sports Video." Complexity 2021 (June 10, 2021): 1–11. http://dx.doi.org/10.1155/2021/5973531.
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The effect is tested in various specific scenes of sports videos to complete the multitarget motion multitarget tracking detection application applicable to various specific scenes within sports videos. In this paper, deep neural networks are applied to sports video multitarget motion shadow suppression and accurate tracking to improve tracking performance. After the target frame selection is determined, the tracker uses an optical flow method to estimate the limits of the target sports video multitarget motion based on the sports video multitarget motion of the target object between frames. The detector first scans each sports video image frame one by one, observing the previously discovered and learned image frame subregions one by one until the current moment that is highly like the target to be tracked. The preprocessed remote sensing images are converted into grayscale images, the histogram is normalized, and the appropriate height threshold is selected in combination with the regional growth function to realize the rejection of sports video multitarget motion shadow and establish the sports video multitarget network model. The distance and direction of the precise target displacement are determined by frequency-domain vectors and null domain vectors, and the target action judgment mechanism is formed by decision learning. Finally, comparing with other shadow rejection and precision tracking algorithms, the proposed algorithm achieves greater advantages in terms of accuracy and time consumption.
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Navascués, María A., and Peter R. Massopust. "Fractal convolution: A new operation between functions." Fractional Calculus and Applied Analysis 22, no. 3 (June 26, 2019): 619–43. http://dx.doi.org/10.1515/fca-2019-0035.
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Abstract In this paper, we define an internal binary operation between functions called fractal convolution that when applied to a pair of mappings generates a fractal function. This is done by means of a suitably defined iterated function system. We study in detail this operation in 𝓛p spaces and in sets of continuous functions in a way that is different from the previous work of the authors. We develop some properties of the operation and its associated sets. The lateral convolutions with the null function provide linear operators whose characteristics are explored. The last part of the article deals with the construction of convolved fractals bases and frames in Banach and Hilbert spaces of functions.
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COPP, ANDREW J., and ELIZABETH M. C. FISHER. "Abstracts of papers presented at the fifteenth Genetics Society's Mammalian Genetics and Development Workshop held at the Institute of Child Health, University College London on 22 and 23 November 2004." Genetical Research 86, no. 3 (December 2005): 233–41. http://dx.doi.org/10.1017/s0016672305007895.
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The Transforming growth factor-β (TGF-β) family control diverse cellular processes and specify cell-fate/differentiation during embryogenesis in vertebrates and invertebrates. Mutations disrupting TGF-β signalling lead to developmental abnormalities and a range of diseases such as cancer. Nodal is a major TGF-β signal, responsible for gastrulation in embryogenesis. Arkadia (Akd) was discovered by mouse gene-trap mutagenesis and encodes a nuclear E3 ubiquitin ligase. Akd allows the Nodal signal to reach its maximum level and Akd-null mice lack mammalian organiser (MO) and mesendodermal tissues. Although Akd RNA is ubiquitously expressed, Akd-null mice lose a subset of Nodal-dependent functions. The specificity of Akd function is therefore most likely to be regulated post-transcriptionally or by co-factors. Akd possesses differentially spliced 5′ untranslated regions (UTRs) and large 3′ UTR. We have employed bioinformatics and developed a reporter system to address Akd post-transcriptional regulation. Akd RNA may initiate from different promoters and 5′ UTR differential splicing, upstream AUGs (uAUGs) and open-reading frames upstream (uORFs) may regulate protein translation. 5′ and 3′ UTRs can interact to either destabilise or decrease translational efficiency of RNA. The nature of this interaction is cell-type and signal level dependent. These data may represent mechanisms by which translational control of Arkadia is achieved and ultimately how TGF-β/Nodal signalling is regulated during embryogenesis.
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Cauthen, Angela N., Corrie C. Brown, and Katherine R. Spindler. "In Vitro and In Vivo Characterization of a Mouse Adenovirus Type 1 Early Region 3 Null Mutant." Journal of Virology 73, no. 10 (October 1, 1999): 8640–46. http://dx.doi.org/10.1128/jvi.73.10.8640-8646.1999.
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ABSTRACT Previous attempts to construct a mouse adenovirus type 1 early region 3 (E3) null mutant by initiator codon mutagenesis were unsuccessful because one of the E3 proteins, gp11K, is synthesized as a fusion protein from a late viral mRNA (A. N. Cauthen and K. R. Spindler, Virology 259:119–128, 1999). Therefore, a different mutagenesis strategy was employed that inserted termination codons into all three reading frames of the E3 proteins. This strategy produced a mutant, pmE314, that was null for the expression of E3 proteins as determined by immunoprecipitation with E3-specific antisera. This mutant grew as well as wild-type (wt) virus in both 3T6 mouse fibroblasts and mouse brain microvascular endothelial cells. However, the 50% lethal dose for pmE314 in adult NIH Swiss outbred mice was approximately 6 log units higher than that of wt virus, indicating that pmE314 was less virulent in mice. In situ hybridization experiments revealed that the absence of the E3 proteins did not alter the tropism of the mutant virus from that of wt virus. When the histopathology was evaluated, the characteristics of the pmE314 infection at both doses administered were strikingly different from those exhibited by wt virus. The central nervous system of wt-infected mice exhibited damage to the endothelium and recruitment of inflammatory cells, whereas the central nervous system of pmE314-infected mice showed no inflammatory response and only mild signs of endothelial damage.
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Mo, Chun-Hui, and Christof Koch. "Modeling Reverse-Phi Motion-Selective Neurons in Cortex: Double Synaptic-Veto Mechanism." Neural Computation 15, no. 4 (April 1, 2003): 735–59. http://dx.doi.org/10.1162/08997660360581886.
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Reverse-phi motion is the illusory reversal of perceived direction of movement when the stimulus contrast is reversed in successive frames. Livingstone, Tsao, and Conway (2000) showed that direction-selective cells in striate cortex of the alert macaque monkey showed reversed excitatory and inhibitory regions when two different contrast bars were flashed sequentially during a two-bar interaction analysis. While correlation or motion energy models predict the reverse-phi response, it is unclear how neurons can accomplish this. We carried out detailed biophysical simulations of a direction-selective cell model implementing a synaptic shunting scheme. Our results suggest that a simple synaptic-veto mechanism with strong direction selectivity for normal motion cannot account for the observed reverse-phi motion effect. Given the nature of reverse-phi motion, a direct interaction between the ON and OFF pathway, missing in the original shunting-inhibition model, it is essential to account for the reversal of response. We here propose a double synaptic-veto mechanism in which ON excitatory synapses are gated by both delayed ON inhibition at their null side and delayed OFF inhibition at their preferred side. The converse applies to OFF excitatory synapses. Mapping this scheme onto the dendrites of a direction-selective neuron permits the model to respond best to normal motion in its preferred direction and to reverse-phi motion in its null direction. Two-bar interaction maps showed reversed excitation and inhibition regions when two different contrast bars are presented.
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Basrai, Munira A., Victor E. Velculescu, Kenneth W. Kinzler, and Philip Hieter. "NORF5/HUG1 Is a Component of theMEC1-Mediated Checkpoint Response to DNA Damage and Replication Arrest in Saccharomyces cerevisiae." Molecular and Cellular Biology 19, no. 10 (October 1, 1999): 7041–49. http://dx.doi.org/10.1128/mcb.19.10.7041.
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ABSTRACT Analysis of global gene expression in Saccharomyces cerevisiae by the serial analysis of gene expression technique has permitted the identification of at least 302 previously unidentified transcripts from nonannotated open reading frames (NORFs). Transcription of one of these, NORF5/HUG1 (hydroxyurea and UV and gamma radiation induced), is induced by DNA damage, and this induction requires MEC1, a homolog of the ataxia telangiectasia mutated (ATM) gene. DNA damage-specific induction of HUG1, which is independent of the cell cycle stage, is due to the alleviation of repression by the Crt1p-Ssn6p-Tup1p complex. Overexpression of HUG1 is lethal in combination with a mec1 mutation in the presence of DNA damage or replication arrest, whereas a deletion of HUG1 rescues the lethality due to a mec1 null allele. HUG1 is the first example of a NORF with important biological functional properties and defines a novel component of the MEC1checkpoint pathway.
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Xiong, Anming, and Radheshyam K. Jayaswal. "Molecular Characterization of a Chromosomal Determinant Conferring Resistance to Zinc and Cobalt Ions inStaphylococcus aureus." Journal of Bacteriology 180, no. 16 (August 15, 1998): 4024–29. http://dx.doi.org/10.1128/jb.180.16.4024-4029.1998.
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ABSTRACT A DNA fragment conferring resistance to zinc and cobalt ions was isolated from a genomic DNA library of Staphylococcus aureus RN450. The DNA sequence analysis revealed two consecutive open reading frames, designated zntR and zntA. The predicted ZntR and ZntA showed significant homology to members of ArsR and cation diffusion families, respectively. A mutant strain containing the null allele of zntA was more sensitive to zinc and cobalt ions than was the parent strain. The metal-sensitive phenotype of the mutant was complemented by a 2.9-kb DNA fragment containing zntR and zntA. An S. aureus strain harboring multiple copies of zntR andzntA showed an increased resistance to zinc. The resistance to zinc in the wild-type strain was inducible. Transcriptional analysis indicated that zntR and zntA genes were cotranscribed. The zinc uptake studies suggested that thezntA product was involved in the export of zinc ions out of cells.
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Nelson, Scot C., Iulian Corcoja, and Sarah J. Pethybridge. "Cluster: A New Application for Spatial Analysis of Pixelated Data for Epiphytotics." Phytopathology® 107, no. 12 (December 2017): 1556–66. http://dx.doi.org/10.1094/phyto-07-17-0223-r.
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Spatial analysis of epiphytotics is essential to develop and test hypotheses about pathogen ecology, disease dynamics, and to optimize plant disease management strategies. Data collection for spatial analysis requires substantial investment in time to depict patterns in various frames and hierarchies. We developed a new approach for spatial analysis of pixelated data in digital imagery and incorporated the method in a stand-alone desktop application called Cluster. The user isolates target entities (clusters) by designating up to 24 pixel colors as nontargets and moves a threshold slider to visualize the targets. The app calculates the percent area occupied by targeted pixels, identifies the centroids of targeted clusters, and computes the relative compass angle of orientation for each cluster. Users can deselect anomalous clusters manually and/or automatically by specifying a size threshold value to exclude smaller targets from the analysis. Up to 1,000 stochastic simulations randomly place the centroids of each cluster in ranked order of size (largest to smallest) within each matrix while preserving their calculated angles of orientation for the long axes. A two-tailed probability t test compares the mean inter-cluster distances for the observed versus the values derived from randomly simulated maps. This is the basis for statistical testing of the null hypothesis that the clusters are randomly distributed within the frame of interest. These frames can assume any shape, from natural (e.g., leaf) to arbitrary (e.g., a rectangular or polygonal field). Cluster summarizes normalized attributes of clusters, including pixel number, axis length, axis width, compass orientation, and the length/width ratio, available to the user as a downloadable spreadsheet. Each simulated map may be saved as an image and inspected. Provided examples demonstrate the utility of Cluster to analyze patterns at various spatial scales in plant pathology and ecology and highlight the limitations, trade-offs, and considerations for the sensitivities of variables and the biological interpretations of results. The Cluster app is available as a free download for Apple computers at iTunes, with a link to a user guide website.
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Ho, Theresa D., Nara Figueroa-Bossi, Minhua Wang, Sergio Uzzau, Lionello Bossi, and James M. Slauch. "Identification of GtgE, a Novel Virulence Factor Encoded on the Gifsy-2 Bacteriophage of Salmonella enterica Serovar Typhimurium." Journal of Bacteriology 184, no. 19 (October 1, 2002): 5234–39. http://dx.doi.org/10.1128/jb.184.19.5234-5239.2002.
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ABSTRACT The Gifsy-2 temperate bacteriophage of Salmonella enterica serovar Typhimurium contributes significantly to the pathogenicity of strains that carry it as a prophage. Previous studies have shown that Gifsy-2 encodes SodCI, a periplasmic Cu/Zn superoxide dismutase, and at least one additional virulence factor. Gifsy-2 encodes a Salmonella pathogenicity island 2 type III secreted effector protein. Sequence analysis of the Gifsy-2 genome also identifies several open reading frames with homology to those of known virulence genes. However, we found that null mutations in these genes did not individually have a significant effect on the ability of S. enterica serovar Typhimurium to establish a systemic infection in mice. Using deletion analysis, we have identified a gene, gtgE, which is necessary for the full virulence of S. enterica serovar Typhimurium Gifsy-2 lysogens. Together, GtgE and SodCI account for the contribution of Gifsy-2 to S. enterica serovar Typhimurium virulence in the murine model.
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Ueda, Kenji, Ken-Ichi Oinuma, Go Ikeda, Kuniaki Hosono, Yasuo Ohnishi, Sueharu Horinouchi, and Teruhiko Beppu. "AmfS, an Extracellular Peptidic Morphogen in Streptomyces griseus." Journal of Bacteriology 184, no. 5 (March 1, 2002): 1488–92. http://dx.doi.org/10.1128/jb.184.5.1488-1492.2002.
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ABSTRACT The amf gene cluster was previously identified as a regulator for the onset of aerial-mycelium formation in Streptomyces griseus. The nucleotide sequences of amf and its counterparts in other species revealed a conserved gene organization consisting of five open reading frames. A nonsense mutation in amfS, encoding a 43-amino-acid peptide, caused significant blocking of aerial-mycelium formation and streptomycin production, suggesting its role as a regulatory molecule. Extracellular-complementation tests for the aerial-mycelium-deficient phenotype of the amfS mutant demonstrated that AmfS was secreted by the wild-type strain. A null mutation in amfBA, encoding HlyB-like membrane translocators, abolished the extracellular AmfS activity without affecting the wild-type morphology, which suggests that AmfBA is involved not in production but in export of AmfS. A synthetic C-terminal octapeptide partially induced aerial-mycelium formation in the amfS mutant, which suggests that an AmfS derivative, but not AmfS itself, serves as an extracellular morphogen.
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Kwast, Kurt E., Liang-Chuan Lai, Nina Menda, David T. James, Susanne Aref, and Patricia V. Burke. "Genomic Analyses of Anaerobically Induced Genes in Saccharomyces cerevisiae: Functional Roles of Rox1 and Other Factors in Mediating the Anoxic Response." Journal of Bacteriology 184, no. 1 (January 1, 2002): 250–65. http://dx.doi.org/10.1128/jb.184.1.250-265.2002.
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ABSTRACT DNA arrays were used to investigate the functional role of Rox1 in mediating acclimatization to anaerobic conditions in Saccharomyces cerevisiae. Multiple growth conditions for wild-type and rox1 null strains were used to identify open reading frames with a statistically robust response to this repressor. These results were compared to those obtained for a wild-type strain in response to oxygen availability. Transcripts of nearly one-sixth of the genome were differentially expressed (P < 0.05) with respect to oxygen availability, the majority (>65%) being down-regulated under anoxia. Of the anaerobically induced genes, about one-third (106) contain putative Rox1-binding sites in their promoters and were significantly (P < 0.05) up-regulated in the rox1 null strains under aerobiosis. Additional promoter searches revealed that nearly one-third of the anaerobically induced genes contain an AR1 site(s) for the Upc2 transcription factor, suggesting that Upc2 and Rox1 regulate the majority of anaerobically induced genes in S. cerevisiae. Functional analyses indicate that a large fraction of the anaerobically induced genes are involved in cell stress (∼1/3), cell wall maintenance (∼1/8), carbohydrate metabolism (∼1/10), and lipid metabolism (∼1/12), with both Rox1 and Upc2 predominating in the regulation of this latter group and Upc2 predominating in cell wall maintenance. Mapping the changes in expression of functional regulons onto metabolic pathways has provided novel insight into the role of Rox1 and other trans-acting factors in mediating the physiological response of S. cerevisiae to anaerobic conditions.
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Lee, Shee Eun, Sung Heui Shin, Soo Young Kim, Young Ran Kim, Dong Hyeon Shin, Sun Sik Chung, Zang Hee Lee, et al. "Vibrio vulnificus Has the Transmembrane Transcription Activator ToxRS Stimulating the Expression of the Hemolysin GenevvhA." Journal of Bacteriology 182, no. 12 (June 15, 2000): 3405–15. http://dx.doi.org/10.1128/jb.182.12.3405-3415.2000.
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ABSTRACT In an attempt to dissect the virulence regulatory mechanism inVibrio vulnificus, we tried to identify the V. cholerae transmembrane virulence regulator toxRS(toxRS Vc) homologs in V. vulnificus. By comparing the sequences of toxRS ofV. cholerae and V. parahaemolyticus(toxRS Vp), we designed a degenerate primer set targeting well-conserved sequences. Using the PCR product as an authentic probe for Southern blot hybridization, a 1.6-kbBglII-HindIII fragment and a 1.2-kbHindIII fragment containing two complete open reading frames and one partial open reading frame attributable totoxR Vv, toxS Vv, andhtpG Vv were cloned. ToxRVv shared 55.0 and 63.0% sequence homology with ToxRVc and ToxRVp, respectively. ToxSVv was 71.5 and 65.7% homologous to ToxSVc and ToxSVp, respectively. The amino acid sequences of ToxRSVv showed transmembrane and activity domains similar to those observed in ToxRSVc and ToxRSVp. Western blot analysis proved the expression of ToxRVv in V. vulnificus. ToxRSVv enhanced, in an Escherichia coli background, the expression of the V. vulnificushemolysin gene (vvhA) fivefold. ToxRSVv also activated the ToxRVc-regulated ctx promoter incorporated into an E. coli chromosome. AtoxR Vv null mutation decreased hemolysin production. The defect in hemolysin production could be complemented by a plasmid harboring the wild-type gene. ThetoxR Vv mutation also showed a reversed outer membrane protein expression profile in comparison to the isogenic wild-type strain. These results demonstrate that ToxRVv may regulate the virulence expression of V. vulnificus.
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Mullen, Janet R., Vivek Kaliraman, Samer S. Ibrahim, and Steven J. Brill. "Requirement for Three Novel Protein Complexes in the Absence of the Sgs1 DNA Helicase in Saccharomyces cerevisiae." Genetics 157, no. 1 (January 1, 2001): 103–18. http://dx.doi.org/10.1093/genetics/157.1.103.
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Abstract The Saccharomyces cerevisiae Sgs1 protein is a member of the RecQ family of DNA helicases and is required for genome stability, but not cell viability. To identify proteins that function in the absence of Sgs1, a synthetic-lethal screen was performed. We obtained mutations in six complementation groups that we refer to as SLX genes. Most of the SLX genes encode uncharacterized open reading frames that are conserved in other species. None of these genes is required for viability and all SLX null mutations are synthetically lethal with mutations in TOP3, encoding the SGS1-interacting DNA topoisomerase. Analysis of the null mutants identified a pair of genes in each of three phenotypic classes. Mutations in MMS4 (SLX2) and SLX3 generate identical phenotypes, including weak UV and strong MMS hypersensitivity, complete loss of sporulation, and synthetic growth defects with mutations in TOP1. Mms4 and Slx3 proteins coimmunoprecipitate from cell extracts, suggesting that they function in a complex. Mutations in SLX5 and SLX8 generate hydroxyurea sensitivity, reduced sporulation efficiency, and a slow-growth phenotype characterized by heterogeneous colony morphology. The Slx5 and Slx8 proteins contain RING finger domains and coimmunoprecipitate from cell extracts. The SLX1 and SLX4 genes are required for viability in the presence of an sgs1 temperature-sensitive allele at the restrictive temperature and Slx1 and Slx4 proteins are similarly associated in cell extracts. We propose that the MMS4/SLX3, SLX5/8, and SLX1/4 gene pairs encode heterodimeric complexes and speculate that these complexes are required to resolve recombination intermediates that arise in response to DNA damage, during meiosis, and in the absence of SGS1/TOP3.
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Badciong, James C., Jeffery M. Otto, and Gail L. Waring. "The Functions of the Multiproduct and Rapidly Evolving dec-1 Eggshell Gene Are Conserved Between Evolutionarily Distant Species of Drosophila." Genetics 159, no. 3 (November 1, 2001): 1089–102. http://dx.doi.org/10.1093/genetics/159.3.1089.
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Abstract The Drosophila dec-1 gene encodes multiple proteins that are required for female fertility and proper eggshell morphogenesis. Genetic and immunolocalization data suggest that the different DEC-1 proteins are functionally distinct. To identify regions within the proteins with potential biological significance, we cloned and sequenced the D. yakuba and D. virilis dec-1 homologs. Interspecies comparisons of the predicted translation products revealed rapidly evolving sequences punctuated by blocks of conserved amino acids. Despite extensive amino acid variability, the proteins produced by the different dec-1 homologs were functionally interchangeable. The introduction of transgenes containing either the D. yakuba or the D. virilis dec-1 open reading frames into a D. melanogaster DEC-1 protein null mutant was sufficient to restore female fertility and wild-type eggshell morphology. Normal expression and extracellular processing of the DEC-1 proteins was correlated with the phenotypic rescue. The nature of the conserved features highlighted by the evolutionary comparison and the molecular resemblance of some of these features to those found in other extracellular proteins suggests functional correlates for some of the multiple DEC-1 derivatives.
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Estruch, F., and M. Carlson. "SNF6 encodes a nuclear protein that is required for expression of many genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 10, no. 6 (June 1990): 2544–53. http://dx.doi.org/10.1128/mcb.10.6.2544-2553.1990.
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The SNF6 gene appears to affect transcription from a variety of promoters in Saccharomyces cerevisiae. The gene was cloned, and sequence analysis revealed two completely overlapping open reading frames of 996 and 1092 nucleotides on opposite strands. The SNF6 coding sequence was identified by selective mutagenesis. The predicted 37,604-dalton SNF6 protein is highly charged but overall neutral. A bifunctional SNF6-beta-galactosidase fusion protein was localized in the nucleus, as judged by immunofluorescence microscopy. The N terminus of SNF6 contains a sequence homologous to nuclear localization signals and was sufficient to direct beta-galactosidase to the nucleus. The 5' ends of the SNF6 RNA were heterogeneous and included ends mapping downstream from the first ATG codon. Construction of a frameshift mutation provided evidence that translational initiation at the second ATG yields a partially functional SNF6 product. Null mutations in SNF6 caused a wider range of pleiotropic defects than the previously isolated point mutation, including slow growth. Genetic and molecular evidence suggested that SNF6 is functionally related to the SNF2 and SNF5 genes. These genes may function together to affect transcription.
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Baldi, Mario, and Andrea Vesco. "Blocking Probability in Pipeline Forwarding Networks." Journal of Communications Software and Systems 10, no. 1 (March 21, 2014): 30. http://dx.doi.org/10.24138/jcomss.v10i1.138.
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As multimedia communications continue to grow steadily on the Internet, pipeline forwarding (PF) of packets provides a scalable solution for engineering delay-sensitive traffic while guaranteeing deterministic Quality of Service (QoS) with high resource utilization. In PF networks resource reservation, while ensuring deterministic QoS on a per-flow basis, can result in a not null blocking probability. A reservation request may fails due to enough resources being available but not during the proper time frames. This work analyses blocking probability of reservation requests since it affects the capability of utilizing network resources to carry traffic with deterministic QoS. The blocking probability and, consequently, the achievable network utilization are analytically derived on general topology PF networks as function of the traffic intensity given the traffic matrix and the network routing. The correctness of the blocking models is also assessed by simulation in different scenarios. This work represent a valuable contribution over previous analytical models of the blocking probability as their application to real size scenarios is impractical due to their computation complexity.
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Estruch, F., and M. Carlson. "SNF6 encodes a nuclear protein that is required for expression of many genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 10, no. 6 (June 1990): 2544–53. http://dx.doi.org/10.1128/mcb.10.6.2544.
Full textAbstract:
The SNF6 gene appears to affect transcription from a variety of promoters in Saccharomyces cerevisiae. The gene was cloned, and sequence analysis revealed two completely overlapping open reading frames of 996 and 1092 nucleotides on opposite strands. The SNF6 coding sequence was identified by selective mutagenesis. The predicted 37,604-dalton SNF6 protein is highly charged but overall neutral. A bifunctional SNF6-beta-galactosidase fusion protein was localized in the nucleus, as judged by immunofluorescence microscopy. The N terminus of SNF6 contains a sequence homologous to nuclear localization signals and was sufficient to direct beta-galactosidase to the nucleus. The 5' ends of the SNF6 RNA were heterogeneous and included ends mapping downstream from the first ATG codon. Construction of a frameshift mutation provided evidence that translational initiation at the second ATG yields a partially functional SNF6 product. Null mutations in SNF6 caused a wider range of pleiotropic defects than the previously isolated point mutation, including slow growth. Genetic and molecular evidence suggested that SNF6 is functionally related to the SNF2 and SNF5 genes. These genes may function together to affect transcription.
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Li, Shude D., Dangeruta Kersulyte, Ivan J. D. Lindley, Beena Neelam, Douglas E. Berg, and Jean E. Crabtree. "Multiple Genes in the Left Half of the cagPathogenicity Island of Helicobacter pylori Are Required for Tyrosine Kinase-Dependent Transcription of Interleukin-8 in Gastric Epithelial Cells." Infection and Immunity 67, no. 8 (August 1, 1999): 3893–99. http://dx.doi.org/10.1128/iai.67.8.3893-3899.1999.
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ABSTRACT Helicobacter pylori strains that contain thecag pathogenicity island (PAI) elicit increased synthesis of gastric C-X-C chemokines, promote neutrophilic infiltration into the gastric epithelium, and stimulate the synthesis of interleukin-8 (IL-8) in cultured gastric epithelial cells. To investigate the effects ofcag PAI genes on the transcription of the IL-8 gene, the Kato-3 gastric epithelial cell line was stably transfected with plasmid DNA containing the IL-8 gene promoter fused to a luciferase reporter gene. The resulting reporter cell line, L5F11, was used to monitor the effects of infection in cell culture by H. pylori 26695 and isogenic derivatives with null mutations in genes in thecag PAI on transcription of the IL-8 gene. We found that null mutations in eight open reading frames, including homologs of theAgrobacterium virB9, virB10, andvirB11 genes, in the left half of the cag PAI abrogated the induction of IL-8 gene transcription. Further studies with the L5F11 cell line showed that IL-8 gene transcription induced byH. pylori was blocked by the protein tyrosine kinase inhibitor herbimycin A but not by the protein kinase C inhibitor calphostin C or by the protein kinase G inhibitor KT5823. IL-8 gene transcription in L5F11 cells could also be induced by the cytokine tumor necrosis factor alpha (TNF-α) without exposure to H. pylori. This TNF-α-induced IL-8 transcription was inhibited by the protein kinase A inhibitor H7, which had no significant effect onH. pylori-induced IL-8 transcription. These studies show that multiple genes in the left half of the cag PAI are essential for the transcription of the IL-8 gene in gastric epithelial cells and that this depends on protein tyrosine kinase activation.
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Rochet, Marie-Joëlle, Magali Prigent, Jacques A. Bertrand, André Carpentier, Franck Coppin, Jean-Paul Delpech, Guy Fontenelle, et al. "Ecosystem trends: evidence for agreement between fishers' perceptions and scientific information." ICES Journal of Marine Science 65, no. 6 (May 6, 2008): 1057–68. http://dx.doi.org/10.1093/icesjms/fsn062.
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Abstract Rochet, M-J., Prigent, M., Bertrand, J. A., Carpentier, A., Coppin, F., Delpech, J-P., Fontenelle, G., Foucher, E., Mahé, K., Rostiaux, E., and Trenkel, V. M. 2008. Ecosystem trends: evidence for agreement between fishers' perceptions and scientific information. – ICES Journal of Marine Science, 65: 1057–1068. The results of a survey on fishers' perceptions of recent changes in the eastern English Channel ecosystem carried out in 2006 were compared with fishery and bottom-trawl survey data. A hypothesis-testing framework was used, testing the null hypothesis that fishers' statements were true, which permitted evaluation of both agreement and disagreement. Overall good agreement between fishers' statements and scientific data was found, and both sources suggested that the fish community in the Channel is undergoing large changes, among which are decreases in some commercially important species; in addition, a number of human pressures impact the ecosystem. Fishers had an accurate perception of changes and their time-frames, but not necessarily of their causes. They had a greater power than survey data to detect recent changes, showing that fishers' perceptions have great potential as early warning signals.
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Arvidson, Cindy Grove, Risa Kirkpatrick, Manon T. Witkamp, Jason A. Larson, Christel A. Schipper, Lillian S. Waldbeser, Peadar O’Gaora, Morris Cooper, and Magdalene So. "Neisseria gonorrhoeae Mutants Altered in Toxicity to Human Fallopian Tubes and Molecular Characterization of the Genetic Locus Involved." Infection and Immunity 67, no. 2 (February 1, 1999): 643–52. http://dx.doi.org/10.1128/iai.67.2.643-652.1999.
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ABSTRACT In an effort to identify potential cytotoxins expressed byNeisseria gonorrhoeae, we have identified a locus that, when mutated in the gonococcus, results in a significant increase in toxicity of the strain to human fallopian tube organ cultures (HFTOC). This locus, gly1, contains two open reading frames (ORFs) which are likely cotranscribed. ORF1 encodes a polypeptide of 17.8 kDa with a signal sequence that is recognized and processed inEscherichia coli and N. gonorrhoeae. The 15.6-kDa processed polypeptide has been observed in membrane fractions and filtered spent media from cultures of E. coli expressing gly1 and in outer membrane preparations of wild-type N. gonorrhoeae. The gly1 locus is not essential for bacterial survival, and it does not play a detectable role in epithelial cell adhesion, invasion, or intracellular survival. However, agly1 null mutant causes much more damage to fallopian tube tissues than its isogenic wild-type parent. A strain complemented intrans for the gly1 mutation showed a level of toxicity to HFTOC similar to the level elicited by the wild-type parent. Taken together, these results indicate an involvement of the gly1 locus in the toxicity of N. gonorrhoeae to human fallopian tubes.
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Jiang, Hao, and Kathleen E. Kendrick. "Characterization of ssfR andssgA, Two Genes Involved in Sporulation ofStreptomyces griseus." Journal of Bacteriology 182, no. 19 (October 1, 2000): 5521–29. http://dx.doi.org/10.1128/jb.182.19.5521-5529.2000.
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ABSTRACT In the presence of cefoxitin, which inhibits septum formation during sporulation, Streptomyces griseus is unable to sporulate, retaining the sonication sensitivity of nonsporulating hyphae. Cefoxitin- and sonication-resistant mutant SKK2600 was isolated and showed many morphological differences from its parental strain. A 3.6-kb DNA fragment that complemented the mutations of SKK2600 contained two open reading frames (ORFs), either of which could complement SKK2600. One ORF, designated ssfR, encoded a protein containing a potential DNA-binding helix-turn-helix motif close to its N terminus. SsfR is similar to members of a large family of transcriptional regulators, particularly IclR of Escherichia coli. The second ORF was identified as ssgA, a previously described sporulation gene from S. griseus (S. Kawamoto and J. C. Ensign, Actinomycetology 9:136–151, 1995). A point mutation of C to T seven nucleotides upstream of the UGA stop codon of ssfR was responsible for the phenotype of isolated mutant strain SKK2600. Surprisingly, this mutation should not change the primary structure of SsfR. The ssfR andssgA disruption mutants were constructed and showed the “white” mutant phenotype, with some growth medium dependence. In addition, the ssfR null mutant sporulated ectopically in phosphate starvation medium.
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Yeung, C. H., and T. G. Cooper. "Aquaporin AQP11 in the testis: molecular identity and association with the processing of residual cytoplasm of elongated spermatids." REPRODUCTION 139, no. 1 (January 2010): 209–16. http://dx.doi.org/10.1530/rep-09-0298.
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AQP11 is one of the latest aquaporin (AQP) family members found, which differs from the other AQPs by its intracellular localisation and unusual water pore nucleotides with unclear function. Despite the highest mRNA expression among organs having been reported in the testis, the testicular molecule has not been studied in detail. Immunohistochemistry of rat adult testis localised AQP11 to the elongated spermatids (ES) and no other cell types except residual bodies inside Sertoli cells. It was absent from early ES at least until stage 13, and after a first diffuse appearance in the caudal cytoplasm became concentrated in intracellular organelles by stage 17, was strongest in vesicles in the anterior cytoplasm at the final ES stages and appeared in residual bodies. Staining was detected on the distal quarter of the sperm tail only immediately before spermiation. A similar localisation was found in the mouse and developmental profiles for both the open reading frame mRNA and protein expression in 8–50 dpp testis pinpointed its first appearance coinciding with late stage ES. Sequencing of PCR products of testicular Aqp11 containing the open reading frames confirmed a full match with GenBank databases for rat, mouse and human. Western blotting revealed two or more molecular forms with the 26/27 kDa species dominating in the rat/mouse testis and the 33/34 kDa form selectively allocated to the spermatozoa. In view of intracellular vacuolation leading to polycystic kidney in Aqp11-null mice, a possible role of testicular AQP11 in the recycling of surplus cytoplasmic components of the ES and sustaining Sertoli cell capacity in the support of spermatogenesis was discussed.
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Baudin-Baillieu, A., D. Tollervey, C. Cullin, and F. Lacroute. "Functional analysis of Rrp7p, an essential yeast protein involved in pre-rRNA processing and ribosome assembly." Molecular and Cellular Biology 17, no. 9 (September 1997): 5023–32. http://dx.doi.org/10.1128/mcb.17.9.5023.
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During the functional analysis of open reading frames (ORFs) identified during the sequencing of chromosome III of Saccharomyces cerevisiae, the previously uncharacterized ORF YCL031C (now designated RRP7) was deleted. RRP7 is essential for cell viability, and a conditional null allele was therefore constructed, by placing its expression under the control of a regulated GAL promoter. Genetic depletion of Rrp7p inhibited the pre-rRNA processing steps that lead to the production of the 20S pre-rRNA, resulting in reduced synthesis of the 18S rRNA and a reduced ratio of 40S to 60S ribosomal subunits. A screen for multicopy suppressors of the lethality of the GAL::rrp7 allele isolated the two genes encoding a previously unidentified ribosomal protein (r-protein) that is highly homologous to the rat r-protein S27. When present in multiple copies, either gene can suppress the lethality of an RRP7 deletion mutation and can partially restore the ribosomal subunit ratio in Rrp7p-depleted cells. Deletion of both r-protein genes is lethal; deletion of either single gene has an effect on pre-rRNA processing similar to that of Rrp7p depletion. We believe that Rrp7p is required for correct assembly of rpS27 into the preribosomal particle, with the inhibition of pre-rRNA processing appearing as a consequence of this defect.
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Mangialavori Rasia, Eugenia. "Expanding the causative alternation." Current trends in analyzing syntactic variation 31 (December 31, 2017): 104–36. http://dx.doi.org/10.1075/bjl.00005.man.
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Abstract The causative-inchoative alternation has been a subject of much debate. It might also be a case where variation patterns that escape existing typological descriptions provide a new perspective on the problem. We analyze the variability and systematicity of alternative argument structure realizations, together with corresponding aspectual/event properties, by considering three different ways in which change-of-state verbs can be semantically and syntactically construed in Romance. Under the general assumption that the syntactic projection of arguments correlates non-trivially with event structure, we apply a novel theoretical approach to the semantics and syntax of the causative-inchoative alternation. We argue that different verbal heads can be independently combined to yield contrasting verbal configurations, with corresponding event/argument structure properties quite freely. Alongside standard cases such as causative and inchoative frames, we discuss what we call ‘stative-causative constructions’ [SCC], where the initiator appears as the sole argument. The general properties of this additional (third) variant suggest the availability of a null causative (external-argument-selecting) v0 producing original monoargumental structures with corresponding (simpler) event structure. These little-known Spanish data challenge current argument structure theories assuming that the causative v0 necessarily implicates the eventive (BECOME) component, or that the latter figures in the verb’s permanent lexical entry. SCCs provide empirical evidence suggesting that what is commonly described as a basic unaccusative/transitive verb may have unergative uses.
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Saito, Akihiro, Tomonori Shinya, Katsushiro Miyamoto, Tomofumi Yokoyama, Hanae Kaku, Eiichi Minami, Naoto Shibuya, et al. "The dasABC Gene Cluster, Adjacent to dasR, Encodes a Novel ABC Transporter for the Uptake of N,N′-Diacetylchitobiose in Streptomyces coelicolor A3(2)." Applied and Environmental Microbiology 73, no. 9 (March 9, 2007): 3000–3008. http://dx.doi.org/10.1128/aem.02612-06.
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ABSTRACT N,N′-Diacetylchitobiose [(GlcNAc)2] induces the transcription of chitinase (chi) genes in Streptomyces coelicolor A3(2). Physiological studies showed that (GlcNAc)2 addition triggered chi expression and increased the rate of (GlcNAc)2 concentration decline in culture supernatants of mycelia already cultivated with (GlcNAc)2, suggesting that (GlcNAc)2 induced the synthesis of its own uptake system. Four open reading frames (SCO0531, SCO0914, SCO2946, and SCO5232) encoding putative sugar-binding proteins of ABC transporters were found in the genome by probing the 12-bp repeat sequence required for regulation of chi transcription. SCO5232, named dasA, showed transcriptional induction by (GlcNAc)2 and N,N′,N‴-triacetylchitotriose [(GlcNAc)3]. Surface plasmon resonance analysis showed that recombinant DasA protein exhibited the highest affinity for (GlcNAc)2 (equilibrium dissociation constant [KD ] = 3.22 × 10−8). In the dasA-null mutant, the rate of decline of the (GlcNAc)2 concentration in the culture supernatant was about 25% of that in strain M145. The in vitro and in vivo data clearly demonstrated that dasA is involved in (GlcNAc)2 uptake. Upstream and downstream of dasA, the transcriptional regulator gene (dasR) and two putative integral membrane protein genes (dasBC) are located in the opposite and same orientations, respectively. The expression of dasR and dasB, which seemed independent of dasA transcription, was also induced by (GlcNAc)2 and (GlcNAc)3.
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Martínez-Fortún, Jorge, Dylan W. Phillips, and Huw D. Jones. "Potential impact of genome editing in world agriculture." Emerging Topics in Life Sciences 1, no. 2 (November 10, 2017): 117–33. http://dx.doi.org/10.1042/etls20170010.
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Changeable biotic and abiotic stress factors that affect crop growth and productivity, alongside a drive to reduce the unintended consequences of plant protection products, will demand highly adaptive farm management practices as well as access to continually improved seed varieties. The former is limited mainly by cost and, in theory, could be implemented in relatively short time frames. The latter is fundamentally a longer-term activity where genome editing can play a major role. The first targets for genome editing will inevitably be loss-of-function alleles, because these are straightforward to generate. In addition, they are likely to focus on traits under simple genetic control and where the results of modification are already well understood from null alleles in existing gene pools or other knockout or silencing approaches such as induced mutations or RNA interference. In the longer term, genome editing will underpin more fundamental changes in agricultural performance and food quality, and ultimately will merge with the tools and philosophies of synthetic biology to underpin and enable new cellular systems, processes and organisms completely. The genetic changes required for simple allele edits or knockout phenotypes are synonymous with those found naturally in conventional breeding material and should be regulated as such. The more radical possibilities in the longer term will need societal engagement along with appropriate safety and ethical oversight.
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Varré, D’Agostino, Touzet, Gallina, Tamburino, Cantarella, Ubrig, et al. "Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome." International Journal of Molecular Sciences 20, no. 19 (September 26, 2019): 4788. http://dx.doi.org/10.3390/ijms20194788.
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Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions. Based on the relevance of the potato crop worldwide, herewith we report the complete mtDNA sequence of two S. tuberosum cultivars, namely Cicero and Désirée, and a comprehensive study of its expression, based on high-coverage RNA sequencing data. We found that the potato mitogenome has a multi-partite architecture, divided in at least three independent molecules that according to our data should behave as autonomous chromosomes. Inter-cultivar variability was null, while comparative analyses with other species of the Solanaceae family allowed the investigation of the evolutionary history of their mitogenomes. The RNA-seq data revealed peculiarities in transcriptional and post-transcriptional processing of mRNAs. These included co-transcription of genes with open reading frames that are probably expressed, methylation of an rRNA at a position that should impact translation efficiency and extensive RNA editing, with a high proportion of partial editing implying frequent mis-targeting by the editing machinery.
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Hua, Zhaolin, Parvin Fatheddin, and Todd R. Graham. "An Essential Subfamily of Drs2p-related P-Type ATPases Is Required for Protein Trafficking between Golgi Complex and Endosomal/Vacuolar System." Molecular Biology of the Cell 13, no. 9 (September 2002): 3162–77. http://dx.doi.org/10.1091/mbc.e02-03-0172.
Full textAbstract:
The Saccharomyces cerevisiae genome contains five genes encoding P-type ATPases that are potential aminophospholipid translocases (APTs): DRS2, NEO1, and three uncharacterized open reading frames that we have namedDNF1, DNF2, and DNF3 forDRS2/NEO1 family. NEO1 is the only essential gene in APT family and seems to be functionally distinct from the DRS2/DNF genes. The drs2Δdnf1Δ dnf2Δ dnf3Δ quadruple mutant is inviable, although any one member of this group can maintain viability, indicating that there is a substantial functional overlap between the encoded proteins. We have previously implicated Drs2p in clathrin function at the trans-Golgi network. In this study, we constructed strains carrying all possible viable combinations of null alleles from this group and analyzed them for defects in protein transport. The drs2Δdnf1Δ mutant grows slowly, massively accumulates intracellular membranes, and exhibits a substantial defect in the transport of alkaline phosphatase to the vacuole. Transport of carboxypeptidase Y to the vacuole is also perturbed, but to a lesser extent. In addition, the dnf1Δ dnf2Δdnf3Δ mutant exhibits a defect in recycling of GFP-Snc1p in the early endocytic-late secretory pathways. Drs2p and Dnf3p colocalize with the trans-Golgi network marker Kex2p, whereas Dnf1p and Dnf2p seem to localize to the plasma membrane and late exocytic or early endocytic membranes. We propose that eukaryotes express multiple APT subfamily members to facilitate protein transport in multiple pathways.
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O'Donnell, P. T., and S. I. Bernstein. "Molecular and ultrastructural defects in a Drosophila myosin heavy chain mutant: differential effects on muscle function produced by similar thick filament abnormalities." Journal of Cell Biology 107, no. 6 (December 1, 1988): 2601–12. http://dx.doi.org/10.1083/jcb.107.6.2601.
Full textAbstract:
We have determined the molecular defect of the Drosophila melanogaster myosin heavy chain (MHC) mutation Mhc and the mutation's effect on indirect flight muscle, jump muscle, and larval intersegmental muscle. We show that the Mhc1 mutation is essentially a null allele which results in the dominant-flightless and recessive-lethal phenotypes associated with this mutant (Mogami, K., P. T. O'Donnell, S. I. Bernstein, T. R. F. Wright, C. P. Emerson, Jr. 1986. Proc. Natl. Acad. Sci. USA. 83:1393-1397). The mutation is a 101-bp deletion in the MHC gene which removes most of exon 5 and the intron that precedes it. S1 nuclease mapping indicates that mutant transcripts follow two alternative processing pathways. Both pathways result in the production of mature transcripts with altered reading frames, apparently yielding unstable, truncated MHC proteins. Interestingly, the preferred splicing pathway uses the more distal of two available splice donor sites. We present the first ultrastrutural characterization of a completely MHC-null muscle and show that it lacks any discernable thick filaments. Sarcomeres in these muscles are completely disorganized suggesting that thick filaments play a critical role in sarcomere assembly. To understand why the Mhc1 mutation severely disrupts indirect flight muscle and jump muscle function in heterozygotes, but does not seriously affect the function of other muscle types, we examined the muscle ultrastructure of Mhc1/+ heterozygotes. We find that these organisms have a nearly 50% reduction in the number of thick filaments in indirect flight muscle, jump muscle, and larval intersegmental muscle. In addition, aberrantly shaped thick filaments are common in the jump muscle and larval intersegmental muscle. We suggest that the differential sensitivity of muscle function to the Mhc1 mutation is a consequence of the unique myofilament arrays in each of these muscles. The highly variable myofilament array of larval intersegmental muscle makes its function relatively insensitive to changes in thick filament number and morphology. Conversely, the rigid double hexagonal lattice of the indirect flight muscle, and the organized lattice of the jump muscle cannot be perturbed without interfering with the specialized and evolutionarily more complex functions they perform.