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Sample records for analyse gene circuit

  1. Automatic design of digital synthetic gene circuits.

    Directory of Open Access Journals (Sweden)

    Mario A Marchisio

    2011-02-01

    Full Text Available De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology and a corresponding tool for in silico automatic design. For a given truth table that specifies a circuit's input-output relations, our algorithm generates and ranks several possible circuit schemes without the need for any optimization. Logic behavior is reproduced by the action of regulatory factors and chemicals on the promoters and on the ribosome binding sites of biological Boolean gates. Simulations of circuits with up to four inputs show a faithful and unequivocal truth table representation, even under parametric perturbations and stochastic noise. A comparison with already implemented circuits, in addition, reveals the potential for simpler designs with the same function. Therefore, we expect the method to help both in devising new circuits and in simplifying existing solutions.

  2. Automatic design of digital synthetic gene circuits.

    Science.gov (United States)

    Marchisio, Mario A; Stelling, Jörg

    2011-02-01

    De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology and a corresponding tool for in silico automatic design. For a given truth table that specifies a circuit's input-output relations, our algorithm generates and ranks several possible circuit schemes without the need for any optimization. Logic behavior is reproduced by the action of regulatory factors and chemicals on the promoters and on the ribosome binding sites of biological Boolean gates. Simulations of circuits with up to four inputs show a faithful and unequivocal truth table representation, even under parametric perturbations and stochastic noise. A comparison with already implemented circuits, in addition, reveals the potential for simpler designs with the same function. Therefore, we expect the method to help both in devising new circuits and in simplifying existing solutions.

  3. Digital and analog gene circuits for biotechnology.

    Science.gov (United States)

    Roquet, Nathaniel; Lu, Timothy K

    2014-05-01

    Biotechnology offers the promise of valuable chemical production via microbial processing of renewable and inexpensive substrates. Thus far, static metabolic engineering strategies have enabled this field to advance industrial applications. However, the industrial scaling of statically engineered microbes inevitably creates inefficiencies due to variable conditions present in large-scale microbial cultures. Synthetic gene circuits that dynamically sense and regulate different molecules can resolve this issue by enabling cells to continuously adapt to variable conditions. These circuits also have the potential to enable next-generation production programs capable of autonomous transitioning between steps in a bioprocess. Here, we review the design and application of two main classes of dynamic gene circuits, digital and analog, for biotechnology. Within the context of these classes, we also discuss the potential benefits of digital-analog interconversion, memory, and multi-signal integration. Though synthetic gene circuits have largely been applied for cellular computation to date, we envision that utilizing them in biotechnology will enhance the efficiency and scope of biochemical production with living cells.

  4. Rett syndrome: genes, synapses, circuits and therapeutics

    Directory of Open Access Journals (Sweden)

    Abhishek eBanerjee

    2012-05-01

    Full Text Available Development of the nervous system proceeds through a set of complex checkpoints which arise from a combination of sequential gene expression and early neural activity sculpted by the environment. Genetic and environmental insults lead to neurodevelopmental disorders which encompass a large group of diseases that result from anatomical and physiological abnormalities during maturation and development of brain circuits. Rett syndrome (RTT is a postnatal neurological disorder of genetic origin, caused by mutations in the X-linked gene MECP2. It features neuropsychiatric abnormalities like motor dysfunctions and mild to severe cognitive impairment. This review discusses several key questions and attempts to evaluate recently developed animal models, cell-type specific function of MeCP2, defects in neural circuit plasticity and possible therapeutic strategies. Finally, we also discuss how genes, proteins and overlapping signaling pathways affect the molecular etiology of apparently unrelated neuropsychiatric disorders, an understanding of which can offer novel therapeutic strategies.

  5. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism.

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    Parikshak, Neelroop N; Luo, Rui; Zhang, Alice; Won, Hyejung; Lowe, Jennifer K; Chandran, Vijayendran; Horvath, Steve; Geschwind, Daniel H

    2013-11-21

    Genetic studies have identified dozens of autism spectrum disorder (ASD) susceptibility genes, raising two critical questions: (1) do these genetic loci converge on specific biological processes, and (2) where does the phenotypic specificity of ASD arise, given its genetic overlap with intellectual disability (ID)? To address this, we mapped ASD and ID risk genes onto coexpression networks representing developmental trajectories and transcriptional profiles representing fetal and adult cortical laminae. ASD genes tightly coalesce in modules that implicate distinct biological functions during human cortical development, including early transcriptional regulation and synaptic development. Bioinformatic analyses suggest that translational regulation by FMRP and transcriptional coregulation by common transcription factors connect these processes. At a circuit level, ASD genes are enriched in superficial cortical layers and glutamatergic projection neurons. Furthermore, we show that the patterns of ASD and ID risk genes are distinct, providing a biological framework for further investigating the pathophysiology of ASD.

  6. Constraint and contingency in multifunctional gene regulatory circuits.

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    Payne, Joshua L; Wagner, Andreas

    2013-01-01

    Gene regulatory circuits drive the development, physiology, and behavior of organisms from bacteria to humans. The phenotypes or functions of such circuits are embodied in the gene expression patterns they form. Regulatory circuits are typically multifunctional, forming distinct gene expression patterns in different embryonic stages, tissues, or physiological states. Any one circuit with a single function can be realized by many different regulatory genotypes. Multifunctionality presumably constrains this number, but we do not know to what extent. We here exhaustively characterize a genotype space harboring millions of model regulatory circuits and all their possible functions. As a circuit's number of functions increases, the number of genotypes with a given number of functions decreases exponentially but can remain very large for a modest number of functions. However, the sets of circuits that can form any one set of functions becomes increasingly fragmented. As a result, historical contingency becomes widespread in circuits with many functions. Whether a circuit can acquire an additional function in the course of its evolution becomes increasingly dependent on the function it already has. Circuits with many functions also become increasingly brittle and sensitive to mutation. These observations are generic properties of a broad class of circuits and independent of any one circuit genotype or phenotype.

  7. Tools and Principles for Microbial Gene Circuit Engineering.

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    Bradley, Robert W; Buck, Martin; Wang, Baojun

    2016-02-27

    Synthetic biologists aim to construct novel genetic circuits with useful applications through rational design and forward engineering. Given the complexity of signal processing that occurs in natural biological systems, engineered microbes have the potential to perform a wide range of desirable tasks that require sophisticated computation and control. Realising this goal will require accurate predictive design of complex synthetic gene circuits and accompanying large sets of quality modular and orthogonal genetic parts. Here we present a current overview of the versatile components and tools available for engineering gene circuits in microbes, including recently developed RNA-based tools that possess large dynamic ranges and can be easily programmed. We introduce design principles that enable robust and scalable circuit performance such as insulating a gene circuit against unwanted interactions with its context, and we describe efficient strategies for rapidly identifying and correcting causes of failure and fine-tuning circuit characteristics.

  8. Rapid, modular and reliable construction of complex mammalian gene circuits.

    Science.gov (United States)

    Guye, Patrick; Li, Yinqing; Wroblewska, Liliana; Duportet, Xavier; Weiss, Ron

    2013-09-01

    We developed a framework for quick and reliable construction of complex gene circuits for genetically engineering mammalian cells. Our hierarchical framework is based on a novel nucleotide addressing system for defining the position of each part in an overall circuit. With this framework, we demonstrate construction of synthetic gene circuits of up to 64 kb in size comprising 11 transcription units and 33 basic parts. We show robust gene expression control of multiple transcription units by small molecule inducers in human cells with transient transfection and stable chromosomal integration of these circuits. This framework enables development of complex gene circuits for engineering mammalian cells with unprecedented speed, reliability and scalability and should have broad applicability in a variety of areas including mammalian cell fermentation, cell fate reprogramming and cell-based assays.

  9. Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology.

    Science.gov (United States)

    Jusiak, Barbara; Cleto, Sara; Perez-Piñera, Pablo; Lu, Timothy K

    2016-07-01

    One of the goals of synthetic biology is to build regulatory circuits that control cell behavior, for both basic research purposes and biomedical applications. The ability to build transcriptional regulatory devices depends on the availability of programmable, sequence-specific, and effective synthetic transcription factors (TFs). The prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR) system, recently harnessed for transcriptional regulation in various heterologous host cells, offers unprecedented ease in designing synthetic TFs. We review how CRISPR can be used to build synthetic gene circuits and discuss recent advances in CRISPR-mediated gene regulation that offer the potential to build increasingly complex, programmable, and efficient gene circuits in the future.

  10. No tradeoff between versatility and robustness in gene circuit motifs

    Science.gov (United States)

    Payne, Joshua L.

    2016-05-01

    Circuit motifs are small directed subgraphs that appear in real-world networks significantly more often than in randomized networks. In the Boolean model of gene circuits, most motifs are realized by multiple circuit genotypes. Each of a motif's constituent circuit genotypes may have one or more functions, which are embodied in the expression patterns the circuit forms in response to specific initial conditions. Recent enumeration of a space of nearly 17 million three-gene circuit genotypes revealed that all circuit motifs have more than one function, with the number of functions per motif ranging from 12 to nearly 30,000. This indicates that some motifs are more functionally versatile than others. However, the individual circuit genotypes that constitute each motif are less robust to mutation if they have many functions, hinting that functionally versatile motifs may be less robust to mutation than motifs with few functions. Here, I explore the relationship between versatility and robustness in circuit motifs, demonstrating that functionally versatile motifs are robust to mutation despite the inherent tradeoff between versatility and robustness at the level of an individual circuit genotype.

  11. Frequency domain analysis of noise in autoregulated gene circuits

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    Simpson, Michael L.; Cox, Chris D.; Sayler, Gary S.

    2003-01-01

    We describe a frequency domain technique for the analysis of intrinsic noise within negatively autoregulated gene circuits. This approach is based on the transfer function around the feedback loop (loop transmission) and the equivalent noise bandwidth of the system. The loop transmission, T, is shown to be a determining factor of the dynamics and the noise behavior of autoregulated gene circuits, and this T-based technique provides a simple and flexible method for the analysis of noise arising from any source within the gene circuit. We show that negative feedback not only reduces the variance of the noise in the protein concentration, but also shifts this noise to higher frequencies where it may have a negligible effect on the noise behavior of following gene circuits within a cascade. This predicted effect is demonstrated through the exact stochastic simulation of a two-gene cascade. The analysis elucidates important aspects of gene circuit structure that control functionality, and may provide some insights into selective pressures leading to this structure. The resulting analytical relationships have a simple form, making them especially useful as synthetic gene circuit design equations. With the exception of the linearization of Hill kinetics, this technique is general and may be applied to the analysis or design of networks of higher complexity. This utility is demonstrated through the exact stochastic simulation of an autoregulated two-gene cascade operating near instability. PMID:12671069

  12. Frequency domain analysis of noise in autoregulated gene circuits

    OpenAIRE

    Simpson, Michael L.; Cox, Chris D.; Sayler, Gary S.

    2003-01-01

    We describe a frequency domain technique for the analysis of intrinsic noise within negatively autoregulated gene circuits. This approach is based on the transfer function around the feedback loop (loop transmission) and the equivalent noise bandwidth of the system. The loop transmission, T, is shown to be a determining factor of the dynamics and the noise behavior of autoregulated gene circuits, and this T-based technique provides a simple and flexible method for the analysis of noise arisin...

  13. Effects of cell cycle noise on excitable gene circuits

    CERN Document Server

    Veliz-Cuba, Alan; Bennett, Matthew R; Josić, Krešimir; Ott, William

    2016-01-01

    We assess the impact of cell cycle noise on gene circuit dynamics. For bistable genetic switches and excitable circuits, we find that transitions between metastable states most likely occur just after cell division and that this concentration effect intensifies in the presence of transcriptional delay. We explain this concentration effect with a 3-states stochastic model. For genetic oscillators, we quantify the temporal correlations between daughter cells induced by cell division. Temporal correlations must be captured properly in order to accurately quantify noise sources within gene networks.

  14. Hox genes: choreographers in neural development, architects of circuit organization.

    Science.gov (United States)

    Philippidou, Polyxeni; Dasen, Jeremy S

    2013-10-02

    The neural circuits governing vital behaviors, such as respiration and locomotion, are comprised of discrete neuronal populations residing within the brainstem and spinal cord. Work over the past decade has provided a fairly comprehensive understanding of the developmental pathways that determine the identity of major neuronal classes within the neural tube. However, the steps through which neurons acquire the subtype diversities necessary for their incorporation into a particular circuit are still poorly defined. Studies on the specification of motor neurons indicate that the large family of Hox transcription factors has a key role in generating the subtypes required for selective muscle innervation. There is also emerging evidence that Hox genes function in multiple neuronal classes to shape synaptic specificity during development, suggesting a broader role in circuit assembly. This Review highlights the functions and mechanisms of Hox gene networks and their multifaceted roles during neuronal specification and connectivity.

  15. Photonic gene circuits by optically addressable siRNA-Au nanoantennas.

    Science.gov (United States)

    Lee, Somin Eunice; Sasaki, Darryl Y; Park, Younggeun; Xu, Ren; Brennan, James S; Bissell, Mina J; Lee, Luke P

    2012-09-25

    The precise perturbation of gene circuits and the direct observation of signaling pathways in living cells are essential for both fundamental biology and translational medicine. Current optogenetic technology offers a new paradigm of optical control for cells; however, this technology relies on permanent genomic modifications with light-responsive genes, thus limiting dynamic reconfiguration of gene circuits. Here, we report precise control of perturbation and reconfiguration of gene circuits in living cells by optically addressable siRNA-Au nanoantennas. The siRNA-Au nanoantennas fulfill dual functions as selectively addressable optical receivers and biomolecular emitters of small interfering RNA (siRNA). Using siRNA-Au nanoantennas as optical inputs to existing circuit connections, photonic gene circuits are constructed in living cells. We show that photonic gene circuits are modular, enabling subcircuits to be combined on-demand. Photonic gene circuits open new avenues for engineering functional gene circuits useful for fundamental bioscience, bioengineering, and medical applications.

  16. Engineering robust and tunable spatial structures with synthetic gene circuits.

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    Kong, Wentao; Blanchard, Andrew E; Liao, Chen; Lu, Ting

    2017-01-25

    Controllable spatial patterning is a major goal for the engineering of biological systems. Recently, synthetic gene circuits have become promising tools to achieve the goal; however, they need to possess both functional robustness and tunability in order to facilitate future applications. Here we show that, by harnessing the dual signaling and antibiotic features of nisin, simple synthetic circuits can direct Lactococcus lactis populations to form programmed spatial band-pass structures that do not require fine-tuning and are robust against environmental and cellular context perturbations. Although robust, the patterns are highly tunable, with their band widths specified by the external nisin gradient and cellular nisin immunity. Additionally, the circuits can direct cells to consistently generate designed patterns, even when the gradient is driven by structured nisin-producing bacteria and the patterning cells are composed of multiple species. A mathematical model successfully reproduces all of the observed patterns. Furthermore, the circuits allow us to establish predictable structures of synthetic communities and controllable arrays of cellular stripes and spots in space. This study offers new synthetic biology tools to program spatial structures. It also demonstrates that a deep mining of natural functionalities of living systems is a valuable route to build circuit robustness and tunability.

  17. A positive feedback-based gene circuit to increase the production of a membrane protein

    Directory of Open Access Journals (Sweden)

    Gennis Robert B

    2010-05-01

    Full Text Available Abstract Background Membrane proteins are an important class of proteins, playing a key role in many biological processes, and are a promising target in pharmaceutical development. However, membrane proteins are often difficult to produce in large quantities for the purpose of crystallographic or biochemical analyses. Results In this paper, we demonstrate that synthetic gene circuits designed specifically to overexpress certain genes can be applied to manipulate the expression kinetics of a model membrane protein, cytochrome bd quinol oxidase in E. coli, resulting in increased expression rates. The synthetic circuit involved is an engineered, autoinducer-independent variant of the lux operon activator LuxR from V. fischeri in an autoregulatory, positive feedback configuration. Conclusions Our proof-of-concept experiments indicate a statistically significant increase in the rate of production of the bd oxidase membrane protein. Synthetic gene networks provide a feasible solution for the problem of membrane protein production.

  18. Modular construction of mammalian gene circuits using TALE transcriptional repressors.

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    Li, Yinqing; Jiang, Yun; Chen, He; Liao, Weixi; Li, Zhihua; Weiss, Ron; Xie, Zhen

    2015-03-01

    An important goal of synthetic biology is the rational design and predictable implementation of synthetic gene circuits using standardized and interchangeable parts. However, engineering of complex circuits in mammalian cells is currently limited by the availability of well-characterized and orthogonal transcriptional repressors. Here, we introduce a library of 26 reversible transcription activator-like effector repressors (TALERs) that bind newly designed hybrid promoters and exert transcriptional repression through steric hindrance of key transcriptional initiation elements. We demonstrate that using the input-output transfer curves of our TALERs enables accurate prediction of the behavior of modularly assembled TALER cascade and switch circuits. We also show that TALER switches using feedback regulation exhibit improved accuracy for microRNA-based HeLa cancer cell classification versus HEK293 cells. Our TALER library is a valuable toolkit for modular engineering of synthetic circuits, enabling programmable manipulation of mammalian cells and helping elucidate design principles of coupled transcriptional and microRNA-mediated post-transcriptional regulation.

  19. Decreasing the stochasticity of mammalian gene expression by a synthetic gene circuit

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    Nevozhay, Dmitry; Zal, Tomasz; Balazsi, Gabor

    2012-02-01

    Gene therapy and functional genetic studies usually require precisely controlled and uniform gene expression in a population of cells for reliable level of protein production. Due to this requirement, stochastic gene expression is perceived as undesirable in these fields and ideally has to be minimized. The number of approaches for decreasing gene expression stochasticity in mammalian cells is limited. This creates an unmet need to develop new gene expression systems for this purpose. Based on earlier synthetic constructs in yeast, we developed and assessed a negative feedback-based mammalian gene circuit, with uniform and low level of stochasticity in gene expression at different levels of induction. In addition, this new synthetic construct enables highly precise gene expression control in mammalian cells, due to the linear dependence of gene expression on the inducer concentration applied to the system. This mammalian gene expression circuit has potential applicability for the development of new treatment modalities in gene therapy and research tools in functional genetics. In addition, this work creates a roadmap for moving synthetic gene circuits from microbes into mammalian cells.

  20. Genome engineering using a synthetic gene circuit in Bacillus subtilis.

    Science.gov (United States)

    Jeong, Da-Eun; Park, Seung-Hwan; Pan, Jae-Gu; Kim, Eui-Joong; Choi, Soo-Keun

    2015-03-31

    Genome engineering without leaving foreign DNA behind requires an efficient counter-selectable marker system. Here, we developed a genome engineering method in Bacillus subtilis using a synthetic gene circuit as a counter-selectable marker system. The system contained two repressible promoters (B. subtilis xylA (Pxyl) and spac (Pspac)) and two repressor genes (lacI and xylR). Pxyl-lacI was integrated into the B. subtilis genome with a target gene containing a desired mutation. The xylR and Pspac-chloramphenicol resistant genes (cat) were located on a helper plasmid. In the presence of xylose, repression of XylR by xylose induced LacI expression, the LacIs repressed the Pspac promoter and the cells become chloramphenicol sensitive. Thus, to survive in the presence of chloramphenicol, the cell must delete Pxyl-lacI by recombination between the wild-type and mutated target genes. The recombination leads to mutation of the target gene. The remaining helper plasmid was removed easily under the chloramphenicol absent condition. In this study, we showed base insertion, deletion and point mutation of the B. subtilis genome without leaving any foreign DNA behind. Additionally, we successfully deleted a 2-kb gene (amyE) and a 38-kb operon (ppsABCDE). This method will be useful to construct designer Bacillus strains for various industrial applications.

  1. Optogenetic dissection of neuronal circuits in zebrafish using viral gene transfer and the Tet system

    Directory of Open Access Journals (Sweden)

    Peixin Zhu

    2009-12-01

    Full Text Available The conditional expression of transgenes at high levels in sparse and specific populations of neurons is important for high-resolution optogenetic analyses of neuronal circuits. We explored two complementary methods, viral gene delivery and the iTet-Off system, to express transgenes in the brain of zebrafish. High-level gene expression in neurons was achieved by Sindbis and Rabies viruses. The Tet system produced strong and specific gene expression that could be modulated conveniently by doxycycline. Moreover, transgenic lines showed expression in distinct, sparse and stable populations of neurons that appeared to be subsets of the neurons targeted by the promoter driving the Tet activator. The Tet system therefore provides the opportunity to generate libraries of diverse expression patterns similar to gene trap approaches or the thy-1 promoter in mice, but with the additional possibility to pre-select cell types of interest. In transgenic lines expressing channelrhodopsin-2, action potential firing could be precisely controlled by two-photon stimulation at low laser power, presumably because the expression levels of the Tet-controlled genes were high even in adults. In channelrhodopsin-2-expressing larvae, optical stimulation with a single blue LED evoked distinct swimming behaviors including backward swimming. These approaches provide new opportunities for the optogenetic dissection of neuronal circuit structure and function.

  2. Impact of the cell division cycle on gene circuits

    Science.gov (United States)

    Bierbaum, Veronika; Klumpp, Stefan

    2015-12-01

    In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle.

  3. Should genes with missing data be excluded from phylogenetic analyses?

    Science.gov (United States)

    Jiang, Wei; Chen, Si-Yun; Wang, Hong; Li, De-Zhu; Wiens, John J

    2014-11-01

    Phylogeneticists often design their studies to maximize the number of genes included but minimize the overall amount of missing data. However, few studies have addressed the costs and benefits of adding characters with missing data, especially for likelihood analyses of multiple loci. In this paper, we address this topic using two empirical data sets (in yeast and plants) with well-resolved phylogenies. We introduce varying amounts of missing data into varying numbers of genes and test whether the benefits of excluding genes with missing data outweigh the costs of excluding the non-missing data that are associated with them. We also test if there is a proportion of missing data in the incomplete genes at which they cease to be beneficial or harmful, and whether missing data consistently bias branch length estimates. Our results indicate that adding incomplete genes generally increases the accuracy of phylogenetic analyses relative to excluding them, especially when there is a high proportion of incomplete genes in the overall dataset (and thus few complete genes). Detailed analyses suggest that adding incomplete genes is especially helpful for resolving poorly supported nodes. Given that we find that excluding genes with missing data often decreases accuracy relative to including these genes (and that decreases are generally of greater magnitude than increases), there is little basis for assuming that excluding these genes is necessarily the safer or more conservative approach. We also find no evidence that missing data consistently bias branch length estimates.

  4. Gene-gene Interaction Analyses for Atrial Fibrillation

    NARCIS (Netherlands)

    Lin, Honghuang; Mueller-Nurasyid, Martina; Smith, Albert V; Arking, Dan E; Barnard, John; Bartz, Traci M; Lunetta, Kathryn L; Lohman, Kurt; Kleber, Marcus E; Lubitz, Steven A; Geelhoed, Bastiaan; Trompet, Stella; Niemeijer, Maartje N; Kacprowski, Tim; Chasman, Daniel I; Klarin, Derek; Sinner, Moritz F; Waldenberger, Melanie; Meitinger, Thomas; Harris, Tamara B; Launer, Lenore J; Soliman, Elsayed Z; Chen, Lin Y; Smith, Jonathan D; Van Wagoner, David R; Rotter, Jerome I; Psaty, Bruce M; Xie, Zhijun; Hendricks, Audrey E; Ding, Jingzhong; Delgado, Graciela E; Verweij, Niek; van der Harst, Pim; Macfarlane, Peter W; Ford, Ian; Hofman, Albert; Uitterlinden, André; Heeringa, Jan; Franco, Oscar H; Kors, Jan A; Weiss, Stefan; Völzke, Henry; Rose, Lynda M; Natarajan, Pradeep; Kathiresan, Sekar; Kääb, Stefan; Gudnason, Vilmundur; Alonso, Alvaro; Chung, Mina K; Heckbert, Susan R; Benjamin, Emelia J; Liu, Yongmei; März, Winfried; Rienstra, Michiel; Jukema, J Wouter; Stricker, Bruno H; Dörr, Marcus; Albert, Christine M; Ellinor, Patrick T

    2016-01-01

    Atrial fibrillation (AF) is a heritable disease that affects more than thirty million individuals worldwide. Extensive efforts have been devoted to the study of genetic determinants of AF. The objective of our study is to examine the effect of gene-gene interaction on AF susceptibility. We performed

  5. Gene-gene Interaction Analyses for Atrial Fibrillation

    NARCIS (Netherlands)

    H. Lin (Honghuang); M. Mueller-Nurasyid; A.V. Smith (Albert Vernon); D.E. Arking (Dan); J. Barnard (John); T.M. Bartz (Traci M.); K.L. Lunetta (Kathryn); K. Lohman (Kurt); M.E. Kleber (Marcus); S.A. Lubitz (Steven); Geelhoed, B. (Bastiaan); S. Trompet (Stella); M.N. Niemeijer (Maartje); T. Kacprowski (Tim); D.I. Chasman (Daniel); Klarin, D. (Derek); M.F. Sinner (Moritz); M. Waldenberger (Melanie); T. Meitinger (Thomas); T.B. Harris (Tamara); Launer, L.J. (Lenore J.); E.Z. Soliman (Elsayed Z.); L. Chen (Lin); J.D. Smith (Jonathan); D.R. van Wagoner (David); Rotter, J.I. (Jerome I.); B.M. Psaty (Bruce); Xie, Z. (Zhijun); A.E. Hendricks (Audrey E.); Ding, J. (Jingzhong); G.E. Delgado (Graciela E.); N. Verweij (Niek); P. van der Harst (Pim); P.W. MacFarlane (Peter); I. Ford (Ian); A. Hofman (Albert); A.G. Uitterlinden (André); J. Heeringa (Jan); O.H. Franco (Oscar); J.A. Kors (Jan); Weiss, S. (Stefan); H. Völzke (Henry); L.M. Rose (Lynda); Natarajan, P. (Pradeep); S. Kathiresan (Sekar); S. Kääb (Stefan); V. Gudnason (Vilmundur); A. Alonso (Alvaro); M.K. Chung (Mina); S.R. Heckbert (Susan); E.J. Benjamin (Emelia); Y. Liu (Yongmei); W. März (Winfried); S.A. Rienstra; J.W. Jukema (Jan Wouter); B.H.Ch. Stricker (Bruno); M. Dörr (Marcus); C.M. Albert (Christine); P.T. Ellinor (Patrick)

    2016-01-01

    textabstractAtrial fibrillation (AF) is a heritable disease that affects more than thirty million individuals worldwide. Extensive efforts have been devoted to the study of genetic determinants of AF. The objective of our study is to examine the effect of gene-gene interaction on AF susceptibility.

  6. Biologic: Gene circuits and feedback in an introductory physics sequence for biology and premedical students

    CERN Document Server

    Cahn, S B

    2013-01-01

    Two synthetic gene circuits -- the genetic toggle switch and the repressilator -- are analyzed quantitatively and discussed in the context of an educational module on gene circuits and feedback that constitutes the final topic of a year-long introductory physics sequence, aimed at biology and premedical undergraduate students. The genetic toggle switch consists of two genes, each of whose protein product represses the other's expression, while the repressilator consists of three genes, each of whose protein product represses the next gene's expression. Analytic, numerical, and electronic treatments of the genetic toggle switch shows that this gene circuit realizes bistability. A simplified treatment of the repressilator reveals that this circuit can realize sustained oscillations. In both cases, a "phase diagram" is obtained, that specifies the region of parameter space in which bistability or oscillatory behavior, respectively, occurs.

  7. Application of four dyes in gene expression analyses by microarrays

    NARCIS (Netherlands)

    Staal, Y.; van Herwijnen, M.H.M.; van Schooten, F.J.; van Delft, J.H.M.

    2005-01-01

    BACKGROUND: DNA microarrays are widely used in gene expression analyses. To increase throughput and minimize costs without reducing gene expression data obtained, we investigated whether four mRNA samples can be analyzed simultaneously by applying four different fluorescent dyes. RESULTS: Following

  8. A Case Study Analysing the Process of Analogy-Based Learning in a Teaching Unit about Simple Electric Circuits

    Science.gov (United States)

    Paatz, Roland; Ryder, James; Schwedes, Hannelore; Scott, Philip

    2004-01-01

    The purpose of this case study is to analyse the learning processes of a 16-year-old student as she learns about simple electric circuits in response to an analogy-based teaching sequence. Analogical thinking processes are modelled by a sequence of four steps according to Gentner's structure mapping theory (activate base domain, postulate local…

  9. The Increasing Importance of Gene-Based Analyses.

    Directory of Open Access Journals (Sweden)

    Elizabeth T Cirulli

    2016-04-01

    Full Text Available In recent years, genome and exome sequencing studies have implicated a plethora of new disease genes with rare causal variants. Here, I review 150 exome sequencing studies that claim to have discovered that a disease can be caused by different rare variants in the same gene, and I determine whether their methods followed the current best-practice guidelines in the interpretation of their data. Specifically, I assess whether studies appropriately assess controls for rare variants throughout the entire gene or implicated region as opposed to only investigating the specific rare variants identified in the cases, and I assess whether studies present sufficient co-segregation data for statistically significant linkage. I find that the proportion of studies performing gene-based analyses has increased with time, but that even in 2015 fewer than 40% of the reviewed studies used this method, and only 10% presented statistically significant co-segregation data. Furthermore, I find that the genes reported in these papers are explaining a decreasing proportion of cases as the field moves past most of the low-hanging fruit, with 50% of the genes from studies in 2014 and 2015 having variants in fewer than 5% of cases. As more studies focus on genes explaining relatively few cases, the importance of performing appropriate gene-based analyses is increasing. It is becoming increasingly important for journal editors and reviewers to require stringent gene-based evidence to avoid an avalanche of misleading disease gene discovery papers.

  10. Changes in maternal gene expression in olfactory circuits in the immediate postpartum period.

    Directory of Open Access Journals (Sweden)

    Sofija V Canavan

    2011-07-01

    Full Text Available Regulation of maternal behavior in the immediate postpartum period involves neural circuits in reward and homeostasis systems responding to cues from the newborn. Our aim was to assess one specific regulatory mechanism: the role that olfaction plays in the onset and modulation of parenting behavior. We focused on changes in gene expression in olfactory brain regions, examining nine genes found in previous knockout studies to be necessary for maternal behavior. Using a qPCR-based approach, we assessed changes in gene expression in response to exposure to pups in eleven microdissected olfactory brain regions. Over the first postpartum days, all nine genes were detected in all eleven regions (at differing levels and their expression changed in response to pup exposure. As a general trend, five genes (Dbh, Esr1, FosB, Foxb1 and Oxtr were found to decrease their expression in most of the olfactory regions examined, while two genes (Mest and Prlr were found to increase expression. Nos1 and Peg3 levels remained relatively stable except in the accessory olfactory bulb (AOB, where greater than 4 fold increases in expression were observed. The largest magnitude expression changes in this study were found in the AOB, which mediates a variety of olfactory cues that elicit stereotypic behaviors such as mating and aggression as well as some non-pheromone odors. Previous analyses of null mice for the nine genes assessed here have rarely examined olfactory function. Our data suggest that there may be olfactory effects in these null mice which contribute to the observed maternal behavioral phenotypes. Collectively, these data support the hypothesis that olfactory processing is an important sensory regulator of maternal behavior.

  11. Gene set analyses for interpreting microarray experiments on prokaryotic organisms.

    Energy Technology Data Exchange (ETDEWEB)

    Tintle, Nathan; Best, Aaron; Dejongh, Matthew; VanBruggen, Dirk; Heffron, Fred; Porwollik, Steffen; Taylor, Ronald C.

    2008-11-05

    Background: Recent advances in microarray technology have brought with them the need for enhanced methods of biologically interpreting gene expression data. Recently, methods like Gene Set Enrichment Analysis (GSEA) and variants of Fisher’s exact test have been proposed which utilize a priori biological information. Typically, these methods are demonstrated with a priori biological information from the Gene Ontology. Results: Alternative gene set definitions are presented based on gene sets inferred from the SEED: open-source software environment for comparative genome annotation and analysis of microbial organisms. Many of these gene sets are then shown to provide consistent expression across a series of experiments involving Salmonella Typhimurium. Implementation of the gene sets in an analysis of microarray data is then presented for the Salmonella Typhimurium data. Conclusions: SEED inferred gene sets can be naturally defined based on subsystems in the SEED. The consistent expression values of these SEED inferred gene sets suggest their utility for statistical analyses of gene expression data based on a priori biological information

  12. Steady state thermal-hydraulic analyses of the MITICA cooling circuits

    Science.gov (United States)

    Zaupa, M.; Sartori, E.; Dalla Palma, M.; Fellin, F.; Marcuzzi, D.; Pavei, M.; Rizzolo, A.

    2016-02-01

    Megavolt ITER Injector Concept Advancement is the full scale prototype of the heating and current drive neutral beam injectors for ITER, to be built at Consorzio RFX (Padova). The engineering design of its components is challenging: the total heat loads they will be subjected to (expected between 2 and 19 MW), the high heat fluxes (up to 20 MW/m2), and the beam pulse duration up to 1 h, set demanding requirements for reliable active cooling circuits. In support of the design, the thermo-hydraulic behavior of each cooling circuit under steady state condition has been investigated by using one-dimensional models. The final results, obtained considering a number of optimizations for the cooling circuits, show that all the requirements in terms of flow rate, temperature, and pressure drop are properly fulfilled.

  13. Steady state thermal-hydraulic analyses of the MITICA cooling circuits

    Energy Technology Data Exchange (ETDEWEB)

    Zaupa, M., E-mail: matteo.zaupa@igi.cnr.it [Università degli Studi di Padova, Via 8 Febbraio 2, Padova 35122 (Italy); Consorzio RFX, Corso Stati Uniti 4, Padova 35127 (Italy); Sartori, E.; Dalla Palma, M.; Fellin, F.; Marcuzzi, D.; Pavei, M.; Rizzolo, A. [Consorzio RFX, Corso Stati Uniti 4, Padova 35127 (Italy)

    2016-02-15

    Megavolt ITER Injector Concept Advancement is the full scale prototype of the heating and current drive neutral beam injectors for ITER, to be built at Consorzio RFX (Padova). The engineering design of its components is challenging: the total heat loads they will be subjected to (expected between 2 and 19 MW), the high heat fluxes (up to 20 MW/m{sup 2}), and the beam pulse duration up to 1 h, set demanding requirements for reliable active cooling circuits. In support of the design, the thermo-hydraulic behavior of each cooling circuit under steady state condition has been investigated by using one-dimensional models. The final results, obtained considering a number of optimizations for the cooling circuits, show that all the requirements in terms of flow rate, temperature, and pressure drop are properly fulfilled.

  14. Target gene analyses of 39 amelogenesis imperfecta kindreds.

    Science.gov (United States)

    Chan, Hui-Chen; Estrella, Ninna M R P; Milkovich, Rachel N; Kim, Jung-Wook; Simmer, James P; Hu, Jan C-C

    2011-12-01

    Previously, mutational analyses identified six disease-causing mutations in 24 amelogenesis imperfecta (AI) kindreds. We have since expanded the number of AI kindreds to 39, and performed mutation analyses covering the coding exons and adjoining intron sequences for the six proven AI candidate genes [amelogenin (AMELX), enamelin (ENAM), family with sequence similarity 83, member H (FAM83H), WD repeat containing domain 72 (WDR72), enamelysin (MMP20), and kallikrein-related peptidase 4 (KLK4)] and for ameloblastin (AMBN) (a suspected candidate gene). All four of the X-linked AI families (100%) had disease-causing mutations in AMELX, suggesting that AMELX is the only gene involved in the aetiology of X-linked AI. Eighteen families showed an autosomal-dominant pattern of inheritance. Disease-causing mutations were identified in 12 (67%): eight in FAM83H, and four in ENAM. No FAM83H coding-region or splice-junction mutations were identified in three probands with autosomal-dominant hypocalcification AI (ADHCAI), suggesting that a second gene may contribute to the aetiology of ADHCAI. Six families showed an autosomal-recessive pattern of inheritance, and disease-causing mutations were identified in three (50%): two in MMP20, and one in WDR72. No disease-causing mutations were found in 11 families with only one affected member. We conclude that mutation analyses of the current candidate genes for AI have about a 50% chance of identifying the disease-causing mutation in a given kindred.

  15. Parameter estimation and determinability analysis applied to Drosophila gap gene circuits

    Directory of Open Access Journals (Sweden)

    Jaeger Johannes

    2008-09-01

    Full Text Available Abstract Background Mathematical modeling of real-life processes often requires the estimation of unknown parameters. Once the parameters are found by means of optimization, it is important to assess the quality of the parameter estimates, especially if parameter values are used to draw biological conclusions from the model. Results In this paper we describe how the quality of parameter estimates can be analyzed. We apply our methodology to assess parameter determinability for gene circuit models of the gap gene network in early Drosophila embryos. Conclusion Our analysis shows that none of the parameters of the considered model can be determined individually with reasonable accuracy due to correlations between parameters. Therefore, the model cannot be used as a tool to infer quantitative regulatory weights. On the other hand, our results show that it is still possible to draw reliable qualitative conclusions on the regulatory topology of the gene network. Moreover, it improves previous analyses of the same model by allowing us to identify those interactions for which qualitative conclusions are reliable, and those for which they are ambiguous.

  16. A systematic molecular circuit design method for gene networks under biochemical time delays and molecular noises

    Directory of Open Access Journals (Sweden)

    Chang Yu-Te

    2008-11-01

    Full Text Available Abstract Background Gene networks in nanoscale are of nonlinear stochastic process. Time delays are common and substantial in these biochemical processes due to gene transcription, translation, posttranslation protein modification and diffusion. Molecular noises in gene networks come from intrinsic fluctuations, transmitted noise from upstream genes, and the global noise affecting all genes. Knowledge of molecular noise filtering and biochemical process delay compensation in gene networks is crucial to understand the signal processing in gene networks and the design of noise-tolerant and delay-robust gene circuits for synthetic biology. Results A nonlinear stochastic dynamic model with multiple time delays is proposed for describing a gene network under process delays, intrinsic molecular fluctuations, and extrinsic molecular noises. Then, the stochastic biochemical processing scheme of gene regulatory networks for attenuating these molecular noises and compensating process delays is investigated from the nonlinear signal processing perspective. In order to improve the robust stability for delay toleration and noise filtering, a robust gene circuit for nonlinear stochastic time-delay gene networks is engineered based on the nonlinear robust H∞ stochastic filtering scheme. Further, in order to avoid solving these complicated noise-tolerant and delay-robust design problems, based on Takagi-Sugeno (T-S fuzzy time-delay model and linear matrix inequalities (LMIs technique, a systematic gene circuit design method is proposed to simplify the design procedure. Conclusion The proposed gene circuit design method has much potential for application to systems biology, synthetic biology and drug design when a gene regulatory network has to be designed for improving its robust stability and filtering ability of disease-perturbed gene network or when a synthetic gene network needs to perform robustly under process delays and molecular noises.

  17. Parts & pools: a framework for modular design of synthetic gene circuits.

    Science.gov (United States)

    Marchisio, Mario Andrea

    2014-01-01

    Published in 2008, Parts & Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the last years and brought, first, to the development of an algorithm for the automatic design of Boolean gene circuits. This is a remarkable achievement since gene digital circuits have a broad range of applications that goes from biosensors for health and environment care to computational devices. More recently, Parts & Pools was enabled to give a proper formal description of eukaryotic biological circuit components. This was possible by employing a rule-based modeling approach, a technique that permits a faithful calculation of all the species and reactions involved in complex systems such as eukaryotic cells and compartments. In this way, Parts & Pools is currently suitable for the visual and modular design of synthetic gene circuits in yeast and mammalian cells too.

  18. Dissecting differential gene expression within the circadian neuronal circuit of Drosophila

    Science.gov (United States)

    Nagoshi, Emi; Sugino, Ken; Kula, Ela; Okazaki, Etsuko; Tachibana, Taro; Nelson, Sacha; Rosbash, Michael

    2013-01-01

    Behavioral circadian rhythms are controlled by a neuronal circuit consisting of diverse neuronal subgroups. To understand the molecular mechanisms underlying the roles of neuronal subgroups within the Drosophila circadian circuit, we used cell-type specific gene-expression profiling and identified a large number of genes specifically expressed in all clock neurons or in two important subgroups. Moreover, we identified and characterized two circadian genes, which are expressed specifically in subsets of clock cells and affect different aspects of rhythms. The transcription factor Fer2 is expressed in ventral lateral neurons; it is required for the specification of lateral neurons and therefore their ability to drive locomotor rhythms. The Drosophila melanogaster homolog of the vertebrate circadian gene nocturnin is expressed in a subset of dorsal neurons and mediates the circadian light response. The approach should also enable the molecular dissection of many different Drosophila neuronal circuits. PMID:19966839

  19. A framework for scalable parameter estimation of gene circuit models using structural information

    KAUST Repository

    Kuwahara, Hiroyuki

    2013-06-21

    Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. The Author 2013.

  20. [Approach to depressogenic genes from genetic analyses of animal models].

    Science.gov (United States)

    Yoshikawa, Takeo

    2004-01-01

    Human depression or mood disorder is defined as a complex disease, making positional cloning of susceptibility genes a formidable task. We have undertaken genetic analyses of three different animal models for depression, comparing our results with advanced database resources. We first performed quantitative trait loci (QTL) analysis on two mouse models of "despair", namely, the forced swim test (FST) and tail suspension test (TST), and detected multiple chromosomal loci that control immobility time in these tests. Since one QTL detected on mouse chromosome 11 harbors the GABA A receptor subunit genes, we tested these genes for association in human mood disorder patients. We obtained significant associations of the alpha 1 and alpha 6 subunit genes with the disease, particularly in females. This result was striking, because we had previously detected an epistatic interaction between mouse chromosomes 11 and X that regulates immobility time in these animals. Next, we performed genome-wide expression analyses using a rat model of depression, learned helplessness (LH). We found that in the frontal cortex of LH rats, a disease implicated region, the LIM kinase 1 gene (Limk 1) showed greatest alteration, in this case down-regulation. By combining data from the QTL analysis of FST/TST and DNA microarray analysis of mouse frontal cortex, we identified adenylyl cyclase-associated CAP protein 1 (Cap 1) as another candidate gene for depression susceptibility. Both Limk 1 and Cap 1 are key players in the modulation of actin G-F conversion. In summary, our current study using animal models suggests disturbances of GABAergic neurotransmission and actin turnover as potential pathophysiologies for mood disorder.

  1. Comparative Analyses of Phase Noise in 28 nm CMOS LC Oscillator Circuit Topologies: Hartley, Colpitts, and Common-Source Cross-Coupled Differential Pair

    Directory of Open Access Journals (Sweden)

    Ilias Chlis

    2014-01-01

    Full Text Available This paper reports comparative analyses of phase noise in Hartley, Colpitts, and common-source cross-coupled differential pair LC oscillator topologies in 28 nm CMOS technology. The impulse sensitivity function is used to carry out both qualitative and quantitative analyses of the phase noise exhibited by each circuit component in each circuit topology with oscillation frequency ranging from 1 to 100 GHz. The comparative analyses show the existence of four distinct frequency regions in which the three oscillator topologies rank unevenly in terms of best phase noise performance, due to the combined effects of device noise and circuit node sensitivity.

  2. Comparative analyses of phase noise in 28 nm CMOS LC oscillator circuit topologies: Hartley, Colpitts, and common-source cross-coupled differential pair.

    Science.gov (United States)

    Chlis, Ilias; Pepe, Domenico; Zito, Domenico

    2014-01-01

    This paper reports comparative analyses of phase noise in Hartley, Colpitts, and common-source cross-coupled differential pair LC oscillator topologies in 28 nm CMOS technology. The impulse sensitivity function is used to carry out both qualitative and quantitative analyses of the phase noise exhibited by each circuit component in each circuit topology with oscillation frequency ranging from 1 to 100 GHz. The comparative analyses show the existence of four distinct frequency regions in which the three oscillator topologies rank unevenly in terms of best phase noise performance, due to the combined effects of device noise and circuit node sensitivity.

  3. Dynamically Tunable Memory in Two-Component Gene Circuit

    Energy Technology Data Exchange (ETDEWEB)

    Ghim, C; Almaas, E

    2008-09-05

    Cell has the potential to remember the environmental conditions for many (10{sup 7}) generations but stochastic fluctuations set a fundamental limit on the stability of this memory. Here we explicitly take the binding-unbinding of macromolecules into account to propose a novel rationale for the protein-protein interaction in cell physiology. Based on the first-exit time and the corresponding deterministic characterization of various genetic circuits, we show that the reversible binding dynamics may stabilize non-genetically inherited cell states, providing a practical strategy for designing robust epigenetic memory.

  4. A recursive network approach can identify constitutive regulatory circuits in gene expression data

    Science.gov (United States)

    Blasi, Monica Francesca; Casorelli, Ida; Colosimo, Alfredo; Blasi, Francesco Simone; Bignami, Margherita; Giuliani, Alessandro

    2005-03-01

    The activity of the cell is often coordinated by the organisation of proteins into regulatory circuits that share a common function. Genome-wide expression profiles might contain important information on these circuits. Current approaches for the analysis of gene expression data include clustering the individual expression measurements and relating them to biological functions as well as modelling and simulation of gene regulation processes by additional computer tools. The identification of the regulative programmes from microarray experiments is limited, however, by the intrinsic difficulty of linear methods to detect low-variance signals and by the sensitivity of the different approaches. Here we face the problem of recognising invariant patterns of correlations among gene expression reminiscent of regulation circuits. We demonstrate that a recursive neural network approach can identify genetic regulation circuits from expression data for ribosomal and genome stability genes. The proposed method, by greatly enhancing the sensitivity of microarray studies, allows the identification of important aspects of genetic regulation networks and might be useful for the discrimination of the different players involved in regulation circuits. Our results suggest that the constitutive regulatory networks involved in the generic organisation of the cell display a high degree of clustering depending on a modular architecture.

  5. Automatic design of synthetic gene circuits through mixed integer non-linear programming.

    Science.gov (United States)

    Huynh, Linh; Kececioglu, John; Köppe, Matthias; Tagkopoulos, Ilias

    2012-01-01

    Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not deterministic, deliver sub-optimal solutions, and provide no guaranties on convergence or error bounds. Here, we introduce an optimization framework for the problem of part selection in synthetic gene circuits that is based on mixed integer non-linear programming (MINLP), which is a deterministic method that finds the globally optimal solution and guarantees convergence in finite time. Given a synthetic gene circuit, a library of characterized parts, and user-defined constraints, our method can find the optimal selection of parts that satisfy the constraints and best approximates the objective function given by the user. We evaluated the proposed method in the design of three synthetic circuits (a toggle switch, a transcriptional cascade, and a band detector), with both experimentally constructed and synthetic promoter libraries. Scalability and robustness analysis shows that the proposed framework scales well with the library size and the solution space. The work described here is a step towards a unifying, realistic framework for the automated design of biological circuits.

  6. Intra- and interregional coregulation of opioid genes: broken symmetry in spinal circuits.

    Science.gov (United States)

    Kononenko, Olga; Galatenko, Vladimir; Andersson, Malin; Bazov, Igor; Watanabe, Hiroyuki; Zhou, Xing Wu; Iatsyshyna, Anna; Mityakina, Irina; Yakovleva, Tatiana; Sarkisyan, Daniil; Ponomarev, Igor; Krishtal, Oleg; Marklund, Niklas; Tonevitsky, Alex; Adkins, DeAnna L; Bakalkin, Georgy

    2017-01-25

    Regulation of the formation and rewiring of neural circuits by neuropeptides may require coordinated production of these signaling molecules and their receptors that may be established at the transcriptional level. Here, we address this hypothesis by comparing absolute expression levels of opioid peptides with their receptors, the largest neuropeptide family, and by characterizing coexpression (transcriptionally coordinated) patterns of these genes. We demonstrated that expression patterns of opioid genes highly correlate within and across functionally and anatomically different areas. Opioid peptide genes, compared with their receptor genes, are transcribed at much greater absolute levels, which suggests formation of a neuropeptide cloud that covers the receptor-expressed circuits. Surprisingly, we found that both expression levels and the proportion of opioid receptors are strongly lateralized in the spinal cord, interregional coexpression patterns are side-specific, and intraregional coexpression profiles are affected differently by left- and right-side unilateral body injury. We propose that opioid genes are regulated as interconnected components of the same molecular system distributed between distinct anatomic regions. The striking feature of this system is its asymmetric coexpression patterns, which suggest side-specific regulation of selective neural circuits by opioid neurohormones.-Kononenko, O., Galatenko, V., Andersson, M., Bazov, I., Watanabe, H., Zhou, X. W., Iatsyshyna, A., Mityakina, I., Yakovleva, T., Sarkisyan, D., Ponomarev, I., Krishtal, O., Marklund, N., Tonevitsky, A., Adkins, D. L., Bakalkin, G. Intra- and interregional coregulation of opioid genes: broken symmetry in spinal circuits.

  7. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased.

    Science.gov (United States)

    Xi, Zhenxiang; Liu, Liang; Davis, Charles C

    2015-11-01

    The development and application of coalescent methods are undergoing rapid changes. One little explored area that bears on the application of gene-tree-based coalescent methods to species tree estimation is gene informativeness. Here, we investigate the accuracy of these coalescent methods when genes have minimal phylogenetic information, including the implementation of the multilocus bootstrap approach. Using simulated DNA sequences, we demonstrate that genes with minimal phylogenetic information can produce unreliable gene trees (i.e., high error in gene tree estimation), which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods. We demonstrate that this problem can be alleviated by sampling more genes, as is commonly done in large-scale phylogenomic analyses. This applies even when these genes are minimally informative. If gene tree estimation is biased, however, gene-tree-based coalescent analyses will produce inconsistent results, which cannot be remedied by increasing the number of genes. In this case, it is not the gene-tree-based coalescent methods that are flawed, but rather the input data (i.e., estimated gene trees). Along these lines, the commonly used program PhyML has a tendency to infer one particular bifurcating topology even though it is best represented as a polytomy. We additionally corroborate these findings by analyzing the 183-locus mammal data set assembled by McCormack et al. (2012) using ultra-conserved elements (UCEs) and flanking DNA. Lastly, we demonstrate that when employing the multilocus bootstrap approach on this 183-locus data set, there is no strong conflict between species trees estimated from concatenation and gene-tree-based coalescent analyses, as has been previously suggested by Gatesy and Springer (2014).

  8. Are Gene Expression Microarray Analyses Reliable? A Review of Studies of Retinoic Acid Responsive Genes

    Institute of Scientific and Technical Information of China (English)

    Peter J. van der Spek; Andreas Kremer; Lynn Murry; Michael G. Walker

    2003-01-01

    Microarray analyses of gene expression are widely used, but reports of the same analyses by different groups give widely divergent results, and raise questions regarding reproducibility and reliability. We take as an example recent published reports on microarray experiments that were designed to identify retinoic acid responsive genes. These reports show substantial differences in their results. In this article, we review the methodology, results, and potential causes of differences in these applications of microarrays. Finally, we suggest practices to improve the reliability and reproducibility of microarray experiments.

  9. Are Gene Expression Microarray Analyses Reliable? A Review of Studies of Retinoic Acid Responsive Genes

    Institute of Scientific and Technical Information of China (English)

    PeterJ.vanderSpek; AndreasKremer; LynnMurry; MichaelG.Walker

    2003-01-01

    Microarray analyses of gene expression are widely used,but reports of the same analyses by different groups give widely divergent results,and raise questions regarding reproducibility and reliability.We take as an example recent published reports on microarray experiments that were designed to identify retinoic acid responsive genes.These reports show substantial differences in their results.In this article,we review the methodology,results,and potential causes of differences in these applications of microarrays.Finally,we suggest practices to improve the reliability and reproducibility of microarray experiments.

  10. Gene set analyses for interpreting microarray experiments on prokaryotic organisms

    OpenAIRE

    Heffron Fred; Van Bruggen Dirk; DeJongh Matthew; Best Aaron A; Tintle Nathan L; Porwollik Steffen; Taylor Ronald C

    2008-01-01

    Abstract Background Despite the widespread usage of DNA microarrays, questions remain about how best to interpret the wealth of gene-by-gene transcriptional levels that they measure. Recently, methods have been proposed which use biologically defined sets of genes in interpretation, instead of examining results gene-by-gene. Despite a serious limitation, a method based on Fisher's exact test remains one of the few plausible options for gene set analysis when an experiment has few replicates, ...

  11. Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae.

    Science.gov (United States)

    Wang, Meng; Li, Sijin; Zhao, Huimin

    2016-01-01

    The development of high-throughput phenotyping tools is lagging far behind the rapid advances of genotype generation methods. To bridge this gap, we report a new strategy for design, construction, and fine-tuning of intracellular-metabolite-sensing/regulation gene circuits by repurposing bacterial transcription factors and eukaryotic promoters. As proof of concept, we systematically investigated the design and engineering of bacterial repressor-based xylose-sensing/regulation gene circuits in Saccharomyces cerevisiae. We demonstrated that numerous properties, such as induction ratio and dose-response curve, can be fine-tuned at three different nodes, including repressor expression level, operator position, and operator sequence. By applying these gene circuits, we developed a cell sorting based, rapid and robust high-throughput screening method for xylose transporter engineering and obtained a sugar transporter HXT14 mutant with 6.5-fold improvement in xylose transportation capacity. This strategy should be generally applicable and highly useful for evolutionary engineering of proteins, pathways, and genomes in S. cerevisiae.

  12. Genes, circuits, and precision therapies for autism and related neurodevelopmental disorders.

    Science.gov (United States)

    Sahin, Mustafa; Sur, Mriganka

    2015-11-20

    Research in the genetics of neurodevelopmental disorders such as autism suggests that several hundred genes are likely risk factors for these disorders. This heterogeneity presents a challenge and an opportunity at the same time. Although the exact identity of many of the genes remains to be discovered, genes identified to date encode proteins that play roles in certain conserved pathways: protein synthesis, transcriptional and epigenetic regulation, and synaptic signaling. The next generation of research in neurodevelopmental disorders must address the neural circuitry underlying the behavioral symptoms and comorbidities, the cell types playing critical roles in these circuits, and common intercellular signaling pathways that link diverse genes. Results from clinical trials have been mixed so far. Only when we can leverage the heterogeneity of neurodevelopmental disorders into precision medicine will the mechanism-based therapeutics for these disorders start to unlock success.

  13. DNA-energetics-based analyses suggest additional genes in prokaryotes

    Indian Academy of Sciences (India)

    Garima Khandelwal; Jalaj Gupta; B Jayaram

    2012-07-01

    We present here a novel methodology for predicting new genes in prokaryotic genomes on the basis of inherent energetics of DNA. Regions of higher thermodynamic stability were identified, which were filtered based on already known annotations to yield a set of potentially new genes. These were then processed for their compatibility with the stereo-chemical properties of proteins and tripeptide frequencies of proteins in Swissprot data, which results in a reliable set of new genes in a genome. Quite surprisingly, the methodology identifies new genes even in well-annotated genomes. Also, the methodology can handle genomes of any GC-content, size and number of annotated genes.

  14. ANALYSES ON DIFFERENTIALLY EXPRESSED GENES ASSOCIATED WITH HUMAN BREAST CANCER

    Institute of Scientific and Technical Information of China (English)

    MENG Xu-li; DING Xiao-wen; XU Xiao-hong

    2006-01-01

    Objective: To investigate the molecular etiology of breast cancer by way of studying the differential expression and initial function of the related genes in the occurrence and development of breast cancer. Methods: Two hundred and eighty-eight human tumor related genes were chosen for preparation of the oligochips probe. mRNA was extracted from 16 breast cancer tissues and the corresponding normal breast tissues, and cDNA probe was prepared through reverse-transcription and hybridized with the gene chip. A laser focused fluorescent scanner was used to scan the chip. The different gene expressions were thereafter automatically compared and analyzed between the two sample groups. Cy3/Cy5>3.5 meant significant up-regulation. Cy3/Cy5<0.25 meant significant down-regulation. Results: The comparison between the breast cancer tissues and their corresponding normal tissues showed that 84 genes had differential expression in the Chip. Among the differently expressed genes, there were 4 genes with significant down-regulation and 6 with significant up-regulation. Compared with normal breast tissues, differentially expressed genes did partially exist in the breast cancer tissues. Conclusion: Changes in multi-gene expression regulations take place during the occurrence and development of breast cancer; and the research on related genes can help understanding the mechanism of tumor occurrence.

  15. Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression.

    Science.gov (United States)

    Shen, Shensi; Rodrigo, Guillermo; Prakash, Satya; Majer, Eszter; Landrain, Thomas E; Kirov, Boris; Daròs, José-Antonio; Jaramillo, Alfonso

    2015-05-26

    Organisms have different circuitries that allow converting signal molecule levels to changes in gene expression. An important challenge in synthetic biology involves the de novo design of RNA modules enabling dynamic signal processing in live cells. This requires a scalable methodology for sensing, transmission, and actuation, which could be assembled into larger signaling networks. Here, we present a biochemical strategy to design RNA-mediated signal transduction cascades able to sense small molecules and small RNAs. We design switchable functional RNA domains by using strand-displacement techniques. We experimentally characterize the molecular mechanism underlying our synthetic RNA signaling cascades, show the ability to regulate gene expression with transduced RNA signals, and describe the signal processing response of our systems to periodic forcing in single live cells. The engineered systems integrate RNA-RNA interaction with available ribozyme and aptamer elements, providing new ways to engineer arbitrary complex gene circuits.

  16. Genomic Analyses of Bacterial Porin-Cytochrome Gene Clusters

    Directory of Open Access Journals (Sweden)

    Liang eShi

    2014-11-01

    Full Text Available The porin-cytochrome (Pcc protein complex is responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens PCA. The identified and characterized Pcc complex of G. sulfurreducens PCA consists of a porin-like outer-membrane protein, a periplasmic 8-heme c-type cytochrome (c-Cyt and an outer-membrane 12-heme c-Cyt, and the genes encoding the Pcc proteins are clustered in the same regions of genome (i.e., the pcc gene clusters of G. sulfurreducens PCA. A survey of additionally microbial genomes has identified the pcc gene clusters in all sequenced Geobacter spp. and other bacteria from six different phyla, including Anaeromyxobacter dehalogenans 2CP-1, A. dehalogenans 2CP-C, Anaeromyxobacter sp. K, Candidatus Kuenenia stuttgartiensis, Denitrovibrio acetiphilus DSM 12809, Desulfurispirillum indicum S5, Desulfurivibrio alkaliphilus AHT2, Desulfurobacterium thermolithotrophum DSM 11699, Desulfuromonas acetoxidans DSM 684, Ignavibacterium album JCM 16511, and Thermovibrio ammonificans HB-1. The numbers of genes in the pcc gene clusters vary, ranging from two to nine. Similar to the metal-reducing (Mtr gene clusters of other Fe(III-reducing bacteria, such as Shewanella spp., additional genes that encode putative c-Cyts with predicted cellular localizations at the cytoplasmic membrane, periplasm and outer membrane often associate with the pcc gene clusters. This suggests that the Pcc-associated c-Cyts may be part of the pathways for extracellular electron transfer reactions. The presence of pcc gene clusters in the microorganisms that do not reduce solid-phase Fe(III and Mn(IV oxides, such as D. alkaliphilus AHT2 and I. album JCM 16511, also suggests that some of the pcc gene clusters may be involved in extracellular electron transfer reactions with the substrates other than Fe(III and Mn(IV oxides.

  17. Comparative analyses of immunoglobulin genes: surprises and portents.

    Science.gov (United States)

    Flajnik, Martin F

    2002-09-01

    The study of immunoglobulin genes in non-mouse and non-human models has shown that different vertebrate groups have evolved distinct methods of generating antibody diversity. By contrast, the development of T cells in the thymus is quite similar in all of the species that have been examined. The three mechanisms by which B cells uniquely modify their immunoglobulin genes -- somatic hypermutation, gene conversion and class switching -- are increasingly believed to share some fundamental mechanisms, which studies in different vertebrate groups have helped (and will continue to help) to resolve. When these mechanisms are better understood, we should be able to look to the constitutive pathways from which they have evolved and perhaps determine whether the rearrangement of variable, diversity and joining antibody gene segments -- V(D)J recombination -- was superimposed on an existing adaptive immune system.

  18. Classification and expression analyses of homeobox genes from Dictyostelium discoideum

    Indian Academy of Sciences (India)

    Himanshu Mishra; Shweta Saran

    2015-06-01

    Homeobox genes are compared between genomes in an attempt to understand the evolution of animal development. The ability of the protist, Dictyostelium discoideum, to shift between uni- and multicellularity makes this group ideal for studying the genetic changes that may have occurred during this transition. We present here the first genome-wide classification and comparative genomic analysis of the 14 homeobox genes present in D. discoideum. Based on the structural alignment of the homeodomains, they can be broadly divided into TALE and non-TALE classes. When individual homeobox genes were compared with members of known class or family, we could further classify them into 3 groups, namely, TALE, OTHER and NOVEL classes, but no HOX family was found. The 5 members of TALE class could be further divided into PBX, PKNOX, IRX and CUP families; 4 homeobox genes classified as NOVEL did not show any similarity to any known homeobox genes; while the remaining 5 were classified as OTHERS as they did show certain degree of similarity to few known homeobox genes. No unique RNA expression pattern during development of D. discoideum emerged for members of an individual group. Putative promoter analysis revealed binding sites for few homeobox transcription factors among many probable factors.

  19. Rational design of modular circuits for gene transcription: A test of the bottom-up approach

    Directory of Open Access Journals (Sweden)

    Giordano Emanuele

    2010-11-01

    Full Text Available Abstract Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure. Conclusions This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts.

  20. Gene Discovery and Functional Analyses in the Model Plant Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Cai-Ping Feng; John Mundy

    2006-01-01

    The present mini-review describes newer methods and strategies, including transposon and T-DNA insertions,TILLING, Deleteagene, and RNA interference, to functionally analyze genes of interest in the model plant Arabidopsis. The relative advantages and disadvantages of the systems are also discussed.

  1. Gene Discovery and Functional Analyses in the Model Plant Arabidopsis

    DEFF Research Database (Denmark)

    Feng, Cai-ping; Mundy, J.

    2006-01-01

    The present mini-review describes newer methods and strategies, including transposon and T-DNA insertions, TILLING, Deleteagene, and RNA interference, to functionally analyze genes of interest in the model plant Arabidopsis. The relative advantages and disadvantages of the systems are also...

  2. Visualizing changes in circuit activity resulting from denervation and reinnervation using immediate early gene expression.

    Science.gov (United States)

    Temple, Meredith D; Worley, Paul F; Steward, Oswald

    2003-04-01

    We describe a novel strategy to evaluate circuit function after brain injury that takes advantage of experience-dependent immediate early gene (IEG) expression. When normal rats undergo training or are exposed to a novel environment, there is a strong induction of IEG expression in forebrain regions, including the hippocampus. This gene induction identifies the neurons that are engaged during the experience. Here, we demonstrate that experience-dependent IEG induction is diminished after brain injury in young adult rats (120-200 gm), specifically after unilateral lesions of the entorhinal cortex (EC), and then recovers with a time course consistent with reinnervation. In situ hybridization techniques were used to assess the expression of the activity-regulated cytoskeleton-associated protein Arc at various times after the lesion (4, 8, 12, 16, or 30 d). One group of rats was allowed to explore a complex novel environment for 1 hr; control operated animals remained in their home cage. In unoperated animals, exposure to the novel environment induced Arc mRNA levels in most pyramidal neurons in CA1, in many pyramidal neurons in CA3, and in a small number of dentate granule cells. This characteristic pattern of induction was absent at early time points after unilateral EC lesions (4 and 8 d) but recovered progressively at later time points. The recovery of Arc expression occurred with approximately the same time course as the reinnervation of the dentate gyrus as a result of postlesion sprouting. These results document a novel approach for quantitatively assessing activity-regulated gene expression in polysynaptic circuits after trauma.

  3. Microdissection of gonadal tissues for gene expression analyses

    DEFF Research Database (Denmark)

    Jørgensen, Anne; Dalgaard, Marlene Danner; Sonne, Si Brask

    2011-01-01

    Laser microdissection permits isolation of specific cell types from tissue sections or cell cultures. This may be beneficial when investigating the role of specific cells in a complex tissue or organ. In tissues with easily distinguishable morphology, a simple hematoxylin staining is sufficient......, but in most cases a more specific staining is required to identify which cells to microdissect. We have established two staining protocols for frozen sections (1) Oil red O, which stains lipid droplet in fat cells and steroid-producing cells and (2) NBT BCIP, which stains cells expressing an alkaline...... protocols could also be used in other species and for other cell types containing lipid droplets or expressing alkaline phosphatase. Both protocols ensure a morphology that enables microdissection of single cells with RNA quality sufficient for subsequent gene expression analysis. However, RNA yields after...

  4. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events

    OpenAIRE

    Zhaxybayeva, Olga; Gogarten, J. Peter; Charlebois, Robert L.; Doolittle, W Ford; Papke, R Thane

    2006-01-01

    Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between cyanobacteria and other phyla. A novel method of detecting and enumerating potential horizontal gene transfer events within a group of organisms based on analyses of “embedded quartets” allows us to identify phylogenetic signal consistent with a plurality of gene families, as well as to delineate cases of c...

  5. Refined anatomical isolation of functional sleep circuits exhibits distinctive regional and circadian gene transcriptional profiles.

    Science.gov (United States)

    Winrow, Christopher J; Tanis, Keith Q; Rigby, Alison M; Taylor, Rhonda R; Serikawa, Kyle; McWhorter, Mollie; Tokiwa, George Y; Marton, Matthew J; Stone, David J; Koblan, Kenneth S; Renger, John J

    2009-05-19

    Powerful new approaches to study molecular variation in distinct neuronal populations have recently been developed enabling a more precise investigation of the control of neural circuits involved in complex behaviors such as wake and sleep. We applied laser capture microdissection (LCM) to isolate precise brain nuclei from rat CNS at opposing circadian time points associated with wake and sleep. Discrete anatomical and temporal analysis was performed to examine the extent of variation in the transcriptional control associated with both identifiable anatomical nuclei and with light/dark cycle. Precise isolation of specific brain nuclei regulating sleep and arousal, including the LC, SCN, TMN, VTA, and VLPO, demonstrated robust changes in gene expression. Many of these differences were not observed in previous studies where whole brain lysates or gross dissections were used to probe for changes in gene expression. The robust and differential profiles of genomic data obtained from the approaches used herein underscore the requirement for careful anatomical refinement in CNS gene expression studies designed to understand genomic control within behaviorally-linked, but functionally isolated brain nuclei.

  6. Validation of endogenous normalizing genes for expression analyses in adult human testis and germ cell neoplasms

    DEFF Research Database (Denmark)

    Svingen, T; Jørgensen, Anne; Rajpert-De Meyts, E

    2014-01-01

    The measurement of gene expression levels in cells and tissues typically depends on a suitable point of reference for inferring biological relevance. For quantitative (or real-time) RT-PCR assays, the method of choice is often to normalize gene expression data to an endogenous gene that is stably...... expressed across the samples analysed: a so-called normalizing or housekeeping gene. Although this is a valid strategy, the identification of stable normalizing genes has proved challenging and a gene showing stable expression across all cells or tissues is unlikely to exist. Therefore, it is necessary...

  7. p53 activated by AND gate genetic circuit under radiation and hypoxia for targeted cancer gene therapy.

    Science.gov (United States)

    Ding, Miao; Li, Rong; He, Rong; Wang, Xingyong; Yi, Qijian; Wang, Weidong

    2015-09-01

    Radio-activated gene therapy has been developed as a novel therapeutic strategy against cancer; however, expression of therapeutic gene in peritumoral tissues will result in unacceptable toxicity to normal cells. To restrict gene expression in targeted tumor mass, we used hypoxia and radiation tolerance features of tumor cells to develop a synthetic AND gate genetic circuit through connecting radiation sensitivity promoter cArG6 , heat shock response elements SNF1, HSF1 and HSE4 with retroviral vector plxsn. Their construction and dynamic activity process were identified through downstream enhanced green fluorescent protein and wtp53 expression in non-small cell lung cancer A549 cells and in a nude mice model. The result showed that AND gate genetic circuit could be activated by lower required radiation dose (6 Gy) and after activated, AND gate could induce significant apoptosis effects and growth inhibition of cancer cells in vitro and in vivo. The radiation- and hypoxia-activated AND gate genetic circuit, which could lead to more powerful target tumoricidal activity represented a promising strategy for both targeted and effective gene therapy of human lung adenocarcinoma and low dose activation character of the AND gate genetic circuit implied that this model could be further exploited to decrease side-effects of clinical radiation therapy.

  8. LOD score exclusion analyses for candidate disease susceptibility genes using case-parents design

    Institute of Scientific and Technical Information of China (English)

    DENG Hongwen; GAO Guimin

    2006-01-01

    The focus of almost all the association studies of candidate genes is to test for their importance. We recently developed a LOD score approach that can be used to test against the importance of candidate genes for complex diseases and quantitative traits in random samples. As a complementary method to regular association analyses, our LOD score approach is powerful but still affected by the population admixture, though it is more conservative. To control the confounding effect of population heterogeneity, we develop here a LOD score exclusion analysis using case-parents design, the basic design of the transmission disequilibrium test (TDT) approach that is immune to population admixture. In the analysis, specific genetic effects and inheritance models at candidate genes can be analyzed and if a LOD score is ≤ - 2.0, the locus can be excluded from having an effect larger than that specified. Simulations show that this approach has reasonable power to exclude a candidate gene having small genetic effects if it is not a disease susceptibility locus (DSL) with sample size often employed in TDT studies. Similar to association analyses with the TDT in nuclear families, our exclusion analyses are generally not affected by population admixture. The exclusion analyses may be implemented to rule out candidate genes with no or minor genetic effects as supplemental analyses for the TDT. The utility of the approach is illustrated with an application to test the importance of vitamin D receptor (VDR) gene underlying the differential risk to osteoporosis.

  9. The Core Mouse Response to Infection by Neospora Caninum Defined by Gene Set Enrichment Analyses

    Science.gov (United States)

    Ellis, John; Goodswen, Stephen; Kennedy, Paul J; Bush, Stephen

    2012-01-01

    In this study, the BALB/c and Qs mouse responses to infection by the parasite Neospora caninum were investigated in order to identify host response mechanisms. Investigation was done using gene set (enrichment) analyses of microarray data. GSEA, MANOVA, Romer, subGSE and SAM-GS were used to study the contrasts Neospora strain type, Mouse type (BALB/c and Qs) and time post infection (6 hours post infection and 10 days post infection). The analyses show that the major signal in the core mouse response to infection is from time post infection and can be defined by gene ontology terms Protein Kinase Activity, Cell Proliferation and Transcription Initiation. Several terms linked to signaling, morphogenesis, response and fat metabolism were also identified. At 10 days post infection, genes associated with fatty acid metabolism were identified as up regulated in expression. The value of gene set (enrichment) analyses in the analysis of microarray data is discussed. PMID:23012496

  10. Iterative experiment design guides the characterization of a light-inducible gene expression circuit.

    Science.gov (United States)

    Ruess, Jakob; Parise, Francesca; Milias-Argeitis, Andreas; Khammash, Mustafa; Lygeros, John

    2015-06-30

    Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.

  11. Association and interaction analyses of eight genes under asthma linkage peaks

    DEFF Research Database (Denmark)

    Ferreira, M.A.R.; Zhao, Z.Z.; Thomsen, S.F.;

    2009-01-01

    Background: Linkage studies have implicated the 2q33, 9p21, 11q13 and 20q13 regions in the regulation of allergic disease. The aim of this study was to test genetic variants in candidate genes from these regions for association with specific asthma traits. Methods: Ninety-five single nucleotide...... polymorphisms (SNP) located in eight genes (CD28, CTLA4, ICOS, ADAM23, ADAMTSL1, MS4A2, CDH26 and HRH3) were genotyped in > 5000 individuals from Australian (n = 1162), Dutch (n = 99) and Danish (n = 303) families. Traits tested included doctor-diagnosed asthma, atopy, airway obstruction, total serum...... immunoglobulin (Ig) E levels and eosinophilia. Association was tested using both multivariate and univariate methods, with gene-wide thresholds for significance determined through simulation. Gene-by-gene and gene-by-environment analyses were also performed. Results: There was no overall evidence for association...

  12. Analyse des raisonnements d’élèves sur les circuits en courant continu et les lois de Kirchhoff

    OpenAIRE

    2013-01-01

    Une méthode de recherche de type qualitatif nous a permis d’analyser les raisonnements d’élèves québécois du collégial professionnel (17 à 21 ans) en technologies de génie électrique. Nous avons identifié leurs raisonnements en les mobilisant sur des problèmes nécessitant le recours aux notions d’intensité et de tension électriques. Nous avons utilisé des moyens classiques tels le questionnaire papier-crayon et l’entretien semi-dirigé pour mettre en évidence leurs raisonnements. L’analyse dém...

  13. A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila.

    Science.gov (United States)

    Saito, Kuniaki; Inagaki, Sachi; Mituyama, Toutai; Kawamura, Yoshinori; Ono, Yukiteru; Sakota, Eri; Kotani, Hazuki; Asai, Kiyoshi; Siomi, Haruhiko; Siomi, Mikiko C

    2009-10-29

    PIWI-interacting RNAs (piRNAs) silence retrotransposons in Drosophila germ lines by associating with the PIWI proteins Argonaute 3 (AGO3), Aubergine (Aub) and Piwi. piRNAs in Drosophila are produced from intergenic repetitive genes and piRNA clusters by two systems: the primary processing pathway and the amplification loop. The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner. However, primary piRNA processing remains elusive. Here we analysed piRNA processing in a Drosophila ovarian somatic cell line where Piwi, but not Aub or AGO3, is expressed; thus, only the primary piRNAs exist. In addition to flamenco, a Piwi-specific piRNA cluster, traffic jam (tj), a large Maf gene, was determined as a new piRNA cluster. piRNAs arising from tj correspond to the untranslated regions of tj messenger RNA and are sense-oriented. piRNA loading on to Piwi may occur in the cytoplasm. zucchini, a gene encoding a putative cytoplasmic nuclease, is required for tj-derived piRNA production. In tj and piwi mutant ovaries, somatic cells fail to intermingle with germ cells and Fasciclin III is overexpressed. Loss of tj abolishes Piwi expression in gonadal somatic cells. Thus, in gonadal somatic cells, tj gives rise simultaneously to two different molecules: the TJ protein, which activates Piwi expression, and piRNAs, which define the Piwi targets for silencing.

  14. Comparative evolutionary analyses of beta globin gene in eutherian, dinosaurian and neopterygii taxa

    Directory of Open Access Journals (Sweden)

    Gauri Awasthi, Garima Srivastava & Aparup Das

    2011-03-01

    Full Text Available Background & objectives: Comparative genomics and evolutionary analyses of conserved genes have enabled usto understand the complexity of genomes of closely related species. For example: -globin gene present inhuman hemoglobin is one such gene that has experienced many genetic changes in many related taxa andproduced more than 600 variants. One of the variant, HBS causes sickle-cell anemia in humans but offersprotection against severe malaria due to Plasmodium falciparum. In the present study, we characterized andperformed evolutionary comparative analyses of the -globin gene in different related and unrelated taxa tohave a comprehensive view of its evolution.Methods: DNA and protein sequences of -globin gene were downloaded from NCBI and characterized in detailin nine eutherian (Homo sapiens, Pan troglodytes, Macaca mulatta, Mus musculus, Rattus norvegicus, Bostaurus, Canis familiaris, Equus caballus, Oryctolagus cuniculus, a dinosaurian (Gallus gallus and a neopterygii(Danio rerio taxa. Three more eutherian (Papio anubis, Ovis aries and Sus scrofa taxa were included for ananalysis at the protein level but not included at the gene level owing to lack of genomic information. Computationaland phylogenetic analyses were performed using evolutionary comparative approach.Results: Results of comparative and phylogenetic analyses revealed less conservation of genetic architecture of-globin compared to its protein architecture in all eutherian taxa. Both dinosaurian and neopterygii taxa servedas outgroups and varied at gene and protein levels.Interpretation & conclusion: Most remarkably, all primates from eutherian taxa including P. anubis showedonly nine codon position differences and an absolute similarity between H. sapiens and P. troglodytes. Absoluteconservation of coding region in Equus caballus (horse was observed. The results were discussed with aninference on the role of evolutionary forces in maintaining such close similarities

  15. Genome-wide identification and expression analyses of cytochrome P450 genes in mulberry (Morus notabilis)

    Institute of Scientific and Technical Information of China (English)

    Bi Ma; Yiwei Luo; Ling Jia; Xiwu Qi; Qiwei Zeng; Zhonghuai Xiang; Ningjia He

    2014-01-01

    Cytochrome P450s play critical roles in the biosyn-thesis of physiological y important compounds in plants. These compounds often act as defense toxins to prevent herbivory. In the present study, a total of 174 P450 genes of mulberry (Morus notabilis C.K.Schn) were identified based on bioinfor-matics analyses. These mulberry P450 genes were divided into nine clans and 47 families and were found to be expressed in a tissue-preferential manner. These genes were compared to the P450 genes in Arabidopsis thaliana. Families CYP80, CYP92, CYP728, CYP733, CYP736, and CYP749 were found to exist in mulberry, and they may play important roles in the biosynthesis of mulberry secondary metabolites. Analyses of the functional and metabolic pathways of these genes indicated that mulberry P450 genes may participate in the metabolism of lipids, other secondary metabolites, xenobiotics, amino acids, cofactors, vitamins, terpenoids, and polyketides. These results provide a foundation for understanding of the structures and biological functions of mulberry P450 genes.

  16. Genes that affect brain structure and function identified by rare variant analyses of Mendelian neurologic disease

    Science.gov (United States)

    Karaca, Ender; Harel, Tamar; Pehlivan, Davut; Jhangiani, Shalini N.; Gambin, Tomasz; Akdemir, Zeynep Coban; Gonzaga-Jauregui, Claudia; Erdin, Serkan; Bayram, Yavuz; Campbell, Ian M.; Hunter, Jill V.; Atik, Mehmed M.; Van Esch, Hilde; Yuan, Bo; Wiszniewski, Wojciech; Isikay, Sedat; Yesil, Gozde; Yuregir, Ozge O.; Bozdogan, Sevcan Tug; Aslan, Huseyin; Aydin, Hatip; Tos, Tulay; Aksoy, Ayse; De Vivo, Darryl C.; Jain, Preti; Geckinli, B. Bilge; Sezer, Ozlem; Gul, Davut; Durmaz, Burak; Cogulu, Ozgur; Ozkinay, Ferda; Topcu, Vehap; Candan, Sukru; Cebi, Alper Han; Ikbal, Mevlit; Gulec, Elif Yilmaz; Gezdirici, Alper; Koparir, Erkan; Ekici, Fatma; Coskun, Salih; Cicek, Salih; Karaer, Kadri; Koparir, Asuman; Duz, Mehmet Bugrahan; Kirat, Emre; Fenercioglu, Elif; Ulucan, Hakan; Seven, Mehmet; Guran, Tulay; Elcioglu, Nursel; Yildirim, Mahmut Selman; Aktas, Dilek; Alikaşifoğlu, Mehmet; Ture, Mehmet; Yakut, Tahsin; Overton, John D.; Yuksel, Adnan; Ozen, Mustafa; Muzny, Donna M.; Adams, David R.; Boerwinkle, Eric; Chung, Wendy K.; Gibbs, Richard A.; Lupski, James R

    2015-01-01

    Development of the human nervous system involves complex interactions between fundamental cellular processes and requires a multitude of genes, many of which remain to be associated with human disease. We applied whole exome sequencing to 128 mostly consanguineous families with neurogenetic disorders that often included brain malformations. Rare variant analyses for both single nucleotide variant (SNV) and copy number variant (CNV) alleles allowed for identification of 45 novel variants in 43 known disease genes, 41 candidate genes, and CNVs in 10 families, with an overall potential molecular cause identified in >85% of families studied. Among the candidate genes identified, we found PRUNE, VARS, and DHX37 in multiple families, and homozygous loss of function variants in AGBL2, SLC18A2, SMARCA1, UBQLN1, and CPLX1. Neuroimaging and in silico analysis of functional and expression proximity between candidate and known disease genes allowed for further understanding of genetic networks underlying specific types of brain malformations. PMID:26539891

  17. Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells.

    Science.gov (United States)

    Ede, Christopher; Chen, Ximin; Lin, Meng-Yin; Chen, Yvonne Y

    2016-05-20

    Inducible transcription systems play a crucial role in a wide array of synthetic biology circuits. However, the majority of inducible promoters are constructed from a limited set of tried-and-true promoter parts, which are susceptible to common shortcomings such as high basal expression levels (i.e., leakiness). To expand the toolbox for regulated mammalian gene expression and facilitate the construction of mammalian genetic circuits with precise functionality, we quantitatively characterized a panel of eight core promoters, including sequences with mammalian, viral, and synthetic origins. We demonstrate that this selection of core promoters can provide a wide range of basal gene expression levels and achieve a gradient of fold-inductions spanning 2 orders of magnitude. Furthermore, commonly used parts such as minimal CMV and minimal SV40 promoters were shown to achieve robust gene expression upon induction, but also suffer from high levels of leakiness. In contrast, a synthetic promoter, YB_TATA, was shown to combine low basal expression with high transcription rate in the induced state to achieve significantly higher fold-induction ratios compared to all other promoters tested. These behaviors remain consistent when the promoters are coupled to different genetic outputs and different response elements, as well as across different host-cell types and DNA copy numbers. We apply this quantitative understanding of core promoter properties to the successful engineering of human T cells that respond to antigen stimulation via chimeric antigen receptor signaling specifically under hypoxic environments. Results presented in this study can facilitate the design and calibration of future mammalian synthetic biology systems capable of precisely programmed functionality.

  18. Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes

    NARCIS (Netherlands)

    Qiu, Y.L.; Dombrovska, O.; Lee, J.; Li, L.; Whitlock, B.A.; Bernasconi-Quadroni, F.; Rest, J.S.; Davis, C.C.; Borsch, T.; Hilu, K.W.; Renner, S.S.; Soltis, D.E.; Soltis, P.E.; Zanis, M.J.; Cannone, J.J.; Powell, M.; Savolainen, V.; Chatrou, L.W.; Chase, M.W.

    2005-01-01

    DNA sequences of nine genes (plastid: atpB, matK, and rbcL; mitochondrial: atp1, matR, mtSSU, and mtLSU; nuclear: 18S and 26S rDNAs) from 100 species of basal angiosperms and gymnosperms were analyzed using parsimony, Bayesian, and maximum likelihood methods. All of these analyses support the follow

  19. In Vitro Global Gene Expression Analyses Support the Ethnopharmacological Use of Achyranthes aspera

    Directory of Open Access Journals (Sweden)

    Pochi R. Subbarayan

    2013-01-01

    Full Text Available Achyranthes aspera (family Amaranthaceae is known for its anticancer properties. We have systematically validated the in vitro and in vivo anticancer properties of this plant. However, we do not know its mode of action. Global gene expression analyses may help decipher its mode of action. In the absence of identified active molecules, we believe this is the best approach to discover the mode of action of natural products with known medicinal properties. We exposed human pancreatic cancer cell line MiaPaCa-2 (CRL-1420 to 34 μg/mL of LE for 24, 48, and 72 hours. Gene expression analyses were performed using whole human genome microarrays (Agilent Technologies, USA. In our analyses, 82 (54/28 genes passed the quality control parameter, set at FDR ≤ 0.01 and FC of ≥±2. LE predominantly affected pathways of immune response, metabolism, development, gene expression regulation, cell adhesion, cystic fibrosis transmembrane conductance regulation (CFTR, and chemotaxis (MetaCore tool (Thomson Reuters, NY. Disease biomarker enrichment analysis identified LE regulated genes involved in Vasculitis—inflammation of blood vessels. Arthritis and pancreatitis are two of many etiologies for vasculitis. The outcome of disease network analysis supports the medicinal use of A. aspera, viz, to stop bleeding, as a cure for pancreatic cancer, as an antiarthritic medication, and so forth.

  20. Comparative transcriptomic analyses of differentially expressed genes in transgenic melatonin biosynthesis ovine HIOMT gene in switchgrass

    Directory of Open Access Journals (Sweden)

    Shan Yuan

    2016-11-01

    Full Text Available Melatonin serves pleiotropic functions in prompting plant growth and resistance to various stresses. The accurate biosynthetic pathway of melatonin remains elusive in plant species, while the N-acetyltransferase and O-methyltransferase were considered to be the last two key enzymes during its biosynthesis. To investigate the biosynthesis and metabolic pathway of melatonin in plants, the RNA-seq profile of overexpression of the ovine HIOMT was analyzed and compared with the previous transcriptome of transgenic oAANAT gene in switchgrass, a model plant for cellulosic ethanol production. A total of 946, 405 and 807 differentially expressed unigenes were observed in AANAT vs. control, HIOMT vs. control, and AANAT vs. HIOMT, respectively. The significantly upregulated (F-box/kelch-repeat protein, zinc finger BED domain-containing protein-3 genes were consistent with enhanced phenotypes of shoot, stem and root growth in transgenic oHIOMT switchgrass. Early flowering in overexpression of oHIOMT switchgrass involved in the regulation of flowering-time genes (APETALA2. Several stress resistant related genes (SPX domain-containing membrane protein, copper transporter 1, late blight resistance protein homolog R1A-6 OS etc. were specifically and significantly upregulated in transgenic oHIOMT only, while metabolism-related genes (phenylalanine-4-hydroxylase, tyrosine decarboxylase 1, protein disulfide-isomerase and galactinol synthase 2 etc. were significantly upregulated in transgenic oAANAT only. These results provide new sights into the biosynthetic and physiological functional networks of melatonin in plants.

  1. Polymorphism Analyses of Hepatitis B Virus X Gene in Hepatocellular Carcinoma Patients from Southern China

    Institute of Scientific and Technical Information of China (English)

    Ping'an ZHU; Deming TAN; Zhongtian PENG; Fei LIU; Lin SONG

    2007-01-01

    Chronic hepatitis B virus (HBV) infection is one of the major causes of hepatocellular carcinoma (HCC), and the HBV X (HBx) gene plays a critical role in the molecular pathogenesis of HBV-related HCC. We have investigated whether there are particular HBx gene mutations associated with HCC in patients from southern China. The HBx gene was examined in 51 paraffin-embedded tumor tissue samples from patients with HCC and 25 serum samples from the HBV carrier by nested polymerase chain reaction (PCR), single-stranded conformational polymorphism and heteroduplex analysis. The HBx genes with potentially important mutations from tumor tissue samples were cloned, sequenced and aligned with the published HBx gene sequence. HBV genotypes in tumor tissue samples were analyzed by nested PCR.Analyses of HBx gene polymorphism showed that 31.3% of HBx gene fragments in tumor tissue samples had a special pattern. A common deletion at nt 382-400 of the HBx gene accompanied by 29 point mutations was detected in four randomly selected tumor tissue samples with this pattern which caused a frame-shift in the HBx open reading frame with a new stop codon at nt 1818, resulting in an HBx polypeptide chain truncated at the C end in these cases. Among the four randomly selected samples, three were HBV genotype B, and one was not detected by our present assay. In another tumor tissue sample, amplification of the full-length HBx gene yielded a shorter fragment. Sequencing of this fragment revealed a 264 bp deletion between nt 1577 and 1840 of the HBV gene. These results suggest that HBx gene mutation occurs frequently in HCC samples, and the deletion at nt 382-400 of the HBx gene might play a role in carcinogenesis of HCC in southern China.

  2. Identification of therapeutic targets for Alzheimer's disease via differentially expressed gene and weighted gene co-expression network analyses.

    Science.gov (United States)

    Jia, Yujie; Nie, Kun; Li, Jing; Liang, Xinyue; Zhang, Xuezhu

    2016-11-01

    In order to investigate the pathogenic targets and associated biological process of Alzheimer's disease in the present study, mRNA expression profiles (GSE28146) and microRNA (miRNA) expression profiles (GSE16759) were downloaded from the Gene Expression Omnibus database. In GSE28146, eight control samples, and Alzheimer's disease samples comprising seven incipient, eight moderate, seven severe Alzheimer's disease samples, were included. The Affy package in R was used for background correction and normalization of the raw microarray data. The differentially expressed genes (DEGs) and differentially expressed miRNAs were identified using the Limma package. In addition, mRNAs were clustered using weighted gene correlation network analysis, and modules found to be significantly associated with the stages of Alzheimer's disease were screened out. The Database for Annotation, Visualization, and Integrated Discovery was used to perform Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. The target genes of the differentially expressed miRNAs were identified using the miRWalk database. Compared with the control samples, 175,59 genes and 90 DEGs were identified in the incipient, moderate and severe Alzheimer's disease samples, respectively. A module, which contained 1,592 genes was found to be closely associated with the stage of Alzheimer's disease and biological processes. In addition, pathways associated with Alzheimer's disease and other neurological diseases were found to be enriched in those genes. A total of 139 overlapped genes were identified between those genes and the DEGs in the three groups. From the miRNA expression profiles, 189 miRNAs were found differentially expressed in the samples from patients with Alzheimer's disease and 1,647 target genes were obtained. In addition, five overlapped genes were identified between those 1,647 target genes and the 139 genes, and these genes may be important pathogenic targets for Alzheimer

  3. GeneChip analyses point to novel pathogenetic mechanisms in mantle cell lymphoma.

    Science.gov (United States)

    Vater, Inga; Wagner, Florian; Kreuz, Markus; Berger, Hilmar; Martín-Subero, José I; Pott, Christiane; Martinez-Climent, Jose A; Klapper, Wolfram; Krause, Kristina; Dyer, Martin J S; Gesk, Stefan; Harder, Lana; Zamo, Alberto; Dreyling, Martin; Hasenclever, Dirk; Arnold, Norbert; Siebert, Reiner

    2009-02-01

    The translocation t(11;14)(q13;q32) is the genetic hallmark of mantle cell lymphoma (MCL) but is not sufficient for inducing lymphomagenesis. Here we performed genome-wide 100K GeneChip Mapping in 26 t(11;14)-positive MCL and six MCL cell lines. Partial uniparental disomy (pUPD) was shown to be a recurrent chromosomal event not only in MCL cell lines but also in primary MCL. Remarkably, pUPD affected recurrent targets of deletion like 11q, 13q and 17p. Moreover, we identified 12 novel regions of recurrent gain and loss as well as 12 high-level amplifications and eight homozygously deleted regions hitherto undescribed in MCL. Interestingly, GeneChip analyses identified different genes, encoding proteins involved in microtubule dynamics, such as MAP2, MAP6 and TP53, as targets for chromosomal aberration in MCL. Further investigation, including mutation analyses, fluorescence in situ hybridisation as well as epigenetic and expression studies, revealed additional aberrations frequently affecting these genes. In total, 19 of 20 MCL cases, which were subjected to genetic and epigenetic analyses, and five of six MCL cell lines harboured at least one aberration in MAP2, MAP6 or TP53. These findings provide evidence that alterations of microtubule dynamics might be one of the critical events in MCL lymphomagenesis contributing to chromosomal instability.

  4. Functional evolution of ADAMTS genes: Evidence from analyses of phylogeny and gene organization

    Directory of Open Access Journals (Sweden)

    Van Meir Erwin G

    2005-02-01

    Full Text Available Abstract Background The ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs proteins are a family of metalloproteases with sequence similarity to the ADAM proteases, that contain the thrombospondin type 1 sequence repeat motifs (TSRs common to extracellular matrix proteins. ADAMTS proteins have recently gained attention with the discovery of their role in a variety of diseases, including tissue and blood disorders, cancer, osteoarthritis, Alzheimer's and the genetic syndromes Weill-Marchesani syndrome (ADAMTS10, thrombotic thrombocytopenic purpura (ADAMTS13, and Ehlers-Danlos syndrome type VIIC (ADAMTS2 in humans and belted white-spotting mutation in mice (ADAMTS20. Results Phylogenetic analysis and comparison of the exon/intron organization of vertebrate (Homo, Mus, Fugu, chordate (Ciona and invertebrate (Drosophila and Caenorhabditis ADAMTS homologs has elucidated the evolutionary relationships of this important gene family, which comprises 19 members in humans. Conclusions The evolutionary history of ADAMTS genes in vertebrate genomes has been marked by rampant gene duplication, including a retrotransposition that gave rise to a distinct ADAMTS subfamily (ADAMTS1, -4, -5, -8, -15 that may have distinct aggrecanase and angiogenesis functions.

  5. Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus

    Directory of Open Access Journals (Sweden)

    Rousvoal Sylvie

    2008-08-01

    Full Text Available Abstract Background Brown algae are plant multi-cellular organisms occupying most of the world coasts and are essential actors in the constitution of ecological niches at the shoreline. Ectocarpus siliculosus is an emerging model for brown algal research. Its genome has been sequenced, and several tools are being developed to perform analyses at different levels of cell organization, including transcriptomic expression analyses. Several topics, including physiological responses to osmotic stress and to exposure to contaminants and solvents are being studied in order to better understand the adaptive capacity of brown algae to pollution and environmental changes. A series of genes that can be used to normalise expression analyses is required for these studies. Results We monitored the expression of 13 genes under 21 different culture conditions. These included genes encoding proteins and factors involved in protein translation (ribosomal protein 26S, EF1alpha, IF2A, IF4E and protein degradation (ubiquitin, ubiquitin conjugating enzyme or folding (cyclophilin, and proteins involved in both the structure of the cytoskeleton (tubulin alpha, actin, actin-related proteins and its trafficking function (dynein, as well as a protein implicated in carbon metabolism (glucose 6-phosphate dehydrogenase. The stability of their expression level was assessed using the Ct range, and by applying both the geNorm and the Normfinder principles of calculation. Conclusion Comparisons of the data obtained with the three methods of calculation indicated that EF1alpha (EF1a was the best reference gene for normalisation. The normalisation factor should be calculated with at least two genes, alpha tubulin, ubiquitin-conjugating enzyme or actin-related proteins being good partners of EF1a. Our results exclude actin as a good normalisation gene, and, in this, are in agreement with previous studies in other organisms.

  6. Evolutionary genetic analyses of MEF2C gene: implications for learning and memory in Homo sapiens.

    Science.gov (United States)

    Kalmady, Sunil V; Venkatasubramanian, Ganesan; Arasappa, Rashmi; Rao, Naren P

    2013-02-01

    MEF2C facilitates context-dependent fear conditioning (CFC) which is a salient aspect of hippocampus-dependent learning and memory. CFC might have played a crucial role in human evolution because of its advantageous influence on survival of species. In this study, we analyzed 23 orthologous mammalian gene sequences of MEF2C gene to examine the evidence for positive selection on this gene in Homo sapiens using Phylogenetic Analysis by Maximum Likelihood (PAML) and HyPhy software. Both PAML Bayes Empirical Bayes (BEB) and HyPhy Fixed Effects Likelihood (FEL) analyses supported significant positive selection on 4 codon sites in H. sapiens. Also, haplotter analysis revealed significant ongoing positive selection on this gene in Central European population. The study findings suggest that adaptive selective pressure on this gene might have influenced human evolution. Further research on this gene might unravel the potential role of this gene in learning and memory as well as its pathogenetic effect in certain hippocampal disorders with evolutionary basis like schizophrenia.

  7. Integrated Analyses of Gene Expression Profiles Digs out Common Markers for Rheumatic Diseases.

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    Lan Wang

    Full Text Available Rheumatic diseases have some common symptoms. Extensive gene expression studies, accumulated thus far, have successfully identified signature molecules for each rheumatic disease, individually. However, whether there exist shared factors across rheumatic diseases has yet to be tested.We collected and utilized 6 public microarray datasets covering 4 types of representative rheumatic diseases including rheumatoid arthritis, systemic lupus erythematosus, ankylosing spondylitis, and osteoarthritis. Then we detected overlaps of differentially expressed genes across datasets and performed a meta-analysis aiming at identifying common differentially expressed genes that discriminate between pathological cases and normal controls. To further gain insights into the functions of the identified common differentially expressed genes, we conducted gene ontology enrichment analysis and protein-protein interaction analysis.We identified a total of eight differentially expressed genes (TNFSF10, CX3CR1, LY96, TLR5, TXN, TIA1, PRKCH, PRF1, each associated with at least 3 of the 4 studied rheumatic diseases. Meta-analysis warranted the significance of the eight genes and highlighted the general significance of four genes (CX3CR1, LY96, TLR5, and PRF1. Protein-protein interaction and gene ontology enrichment analyses indicated that the eight genes interact with each other to exert functions related to immune response and immune regulation.The findings support that there exist common factors underlying rheumatic diseases. For rheumatoid arthritis, systemic lupus erythematosus, ankylosing spondylitis and osteoarthritis diseases, those common factors include TNFSF10, CX3CR1, LY96, TLR5, TXN, TIA1, PRKCH, and PRF1. In-depth studies on these common factors may provide keys to understanding the pathogenesis and developing intervention strategies for rheumatic diseases.

  8. Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

    Science.gov (United States)

    Yin, Wei; Wang, Zong-ji; Li, Qi-ye; Lian, Jin-ming; Zhou, Yang; Lu, Bing-zheng; Jin, Li-jun; Qiu, Peng-xin; Zhang, Pei; Zhu, Wen-bo; Wen, Bo; Huang, Yi-jun; Lin, Zhi-long; Qiu, Bi-tao; Su, Xing-wen; Yang, Huan-ming; Zhang, Guo-jie; Yan, Guang-mei; Zhou, Qi

    2016-01-01

    Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. PMID:27708285

  9. Mitogenomic analyses propose positive selection in mitochondrial genes for high-altitude adaptation in galliform birds.

    Science.gov (United States)

    Zhou, Taicheng; Shen, Xuejuan; Irwin, David M; Shen, Yongyi; Zhang, Yaping

    2014-09-01

    Galliform birds inhabit very diverse habitats, including plateaus that are above 3000 m in altitude. At high altitude, lower temperature and hypoxia are two important factors influencing survival. Mitochondria, as the ultimate oxygen transductor, play an important role in aerobic respiration through oxidative phosphorylation (OXPHOS). We analyzed the mitochondrial genomes of six high-altitude phasianidae birds and sixteen low-altitude relatives in an attempt to determine the role of mitochondrial genes in high-altitude adaptation. We reconstructed the phylogenetic relationships of these phasianidae birds and relatives and found at least four lineages that independently occupied this high-altitude habitat. Selective analyses revealed significant evidence for positive selection in the genes ND2, ND4, and ATP6 in three of the high-altitude lineages. This result strongly suggests that adaptive evolution of mitochondrial genes played a critical role during the independent acclimatization to high altitude by galliform birds.

  10. Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study

    KAUST Repository

    Fan, M.

    2015-03-29

    Parameter estimation is a challenging computational problemin the reverse engineering of biological systems. Because advances in biotechnology have facilitated wide availability of time-series gene expression data, systematic parameter esti- mation of gene circuitmodels fromsuch time-series mRNA data has become an importantmethod for quantitatively dissecting the regulation of gene expression. By focusing on themodeling of gene circuits, we examine here the perform- ance of three types of state-of-the-art parameter estimation methods: population-basedmethods, onlinemethods and model-decomposition-basedmethods. Our results show that certain population-basedmethods are able to generate high- quality parameter solutions. The performance of thesemethods, however, is heavily dependent on the size of the param- eter search space, and their computational requirements substantially increase as the size of the search space increases. In comparison, onlinemethods andmodel decomposition-basedmethods are computationally faster alternatives and are less dependent on the size of the search space. Among other things, our results show that a hybrid approach that augments computationally fastmethods with local search as a subsequent refinement procedure can substantially increase the qual- ity of their parameter estimates to the level on par with the best solution obtained fromthe population-basedmethods whilemaintaining high computational speed. These suggest that such hybridmethods can be a promising alternative to themore commonly used population-basedmethods for parameter estimation of gene circuit models when limited prior knowledge about the underlying regulatorymechanismsmakes the size of the parameter search space vastly large. © The Author 2015. Published by Oxford University Press.

  11. Transcriptional Profiling of Newly Generated Dentate Granule Cells Using TU Tagging Reveals Pattern Shifts in Gene Expression during Circuit Integration1,2

    Science.gov (United States)

    Chatzi, Christina; Shen, Rongkun; Goodman, Richard H.

    2016-01-01

    Abstract Despite representing only a small fraction of hippocampal granule cells, adult-generated newborn granule cells have been implicated in learning and memory (Aimone et al., 2011). Newborn granule cells undergo functional maturation and circuit integration over a period of weeks. However, it is difficult to assess the accompanying gene expression profiles in vivo with high spatial and temporal resolution using traditional methods. Here we used a novel method [“thiouracil (TU) tagging”] to map the profiles of nascent mRNAs in mouse immature newborn granule cells compared with mature granule cells. We targeted a nonmammalian uracil salvage enzyme, uracil phosphoribosyltransferase, to newborn neurons and mature granule cells using retroviral and lentiviral constructs, respectively. Subsequent injection of 4-TU tagged nascent RNAs for analysis by RNA sequencing. Several hundred genes were significantly enhanced in the retroviral dataset compared with the lentiviral dataset. We compared a selection of the enriched genes with steady-state levels of mRNAs using quantitative PCR. Ontology analysis revealed distinct patterns of nascent mRNA expression, with newly generated immature neurons showing enhanced expression for genes involved in synaptic function, and neural differentiation and development, as well as genes not previously associated with granule cell maturation. Surprisingly, the nascent mRNAs enriched in mature cells were related to energy homeostasis and metabolism, presumably indicative of the increased energy demands of synaptic transmission and their complex dendritic architecture. The high spatial and temporal resolution of our modified TU-tagging method provides a foundation for comparison with steady-state RNA analyses by traditional transcriptomic approaches in defining the functional roles of newborn neurons. PMID:27011954

  12. Microarray analyses of glucocorticoid and vitamin D3 target genes in differentiating cultured human podocytes.

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    Xiwen Cheng

    Full Text Available Glomerular podocytes are highly differentiated epithelial cells that are key components of the kidney filtration units. Podocyte damage or loss is the hallmark of nephritic diseases characterized by severe proteinuria. Recent studies implicate that hormones including glucocorticoids (ligand for glucocorticoid receptor and vitamin D3 (ligand for vitamin D receptor protect or promote repair of podocytes from injury. In order to elucidate the mechanisms underlying hormone-mediated podocyte-protecting activity from injury, we carried out microarray gene expression studies to identify the target genes and corresponding pathways in response to these hormones during podocyte differentiation. We used immortalized human cultured podocytes (HPCs as a model system and carried out in vitro differentiation assays followed by dexamethasone (Dex or vitamin D3 (VD3 treatment. Upon the induction of differentiation, multiple functional categories including cell cycle, organelle dynamics, mitochondrion, apoptosis and cytoskeleton organization were among the most significantly affected. Interestingly, while Dex and VD3 are capable of protecting podocytes from injury, they only share limited target genes and affected pathways. Compared to VD3 treatment, Dex had a broader and greater impact on gene expression profiles. In-depth analyses of Dex altered genes indicate that Dex crosstalks with a broad spectrum of signaling pathways, of which inflammatory responses, cell migration, angiogenesis, NF-κB and TGFβ pathways are predominantly altered. Together, our study provides new information and identifies several new avenues for future investigation of hormone signaling in podocytes.

  13. Limited clinical relevance of mitochondrial DNA mutation and gene expression analyses in ovarian cancer

    Directory of Open Access Journals (Sweden)

    Rachinger Andrea

    2008-10-01

    Full Text Available Abstract Background In recent years, numerous studies have investigated somatic mutations in mitochondrial DNA in various tumours. The observed high mutation rates might reflect mitochondrial deregulation; consequently, mutation analyses could be clinically relevant. The purpose of this study was to determine if mutations in the mitochondrial D-loop region and/or the level of mitochondrial gene expression could influence the clinical course of human ovarian carcinomas. Methods We sequenced a 1320-base-pair DNA fragment of the mitochondrial genome (position 16,000-750 in 54 cancer samples and in 44 corresponding germline control samples. In addition, six transcripts (MT-ATP6, MT-CO1, MT-CYB, MT-ND1, MT-ND6, and MT-RNR1 were quantified in 62 cancer tissues by real-time RT-PCR. Results Somatic mutations in the D-loop sequence were found in 57% of ovarian cancers. Univariate analysis showed no association between mitochondrial DNA mutation status or mitochondrial gene expression and any of the examined clinicopathologic parameters. A multivariate logistic regression model revealed that the expression of the mitochondrial gene RNR1 might be used as a predictor of tumour sensitivity to chemotherapy. Conclusion In contrast to many previously published papers, our study indicates rather limited clinical relevance of mitochondrial molecular analyses in ovarian carcinomas. These discrepancies in the clinical utility of mitochondrial molecular tests in ovarian cancer require additional large, well-designed validation studies.

  14. COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses

    Science.gov (United States)

    Moretto, Marco; Sonego, Paolo; Dierckxsens, Nicolas; Brilli, Matteo; Bianco, Luca; Ledezma-Tejeida, Daniela; Gama-Castro, Socorro; Galardini, Marco; Romualdi, Chiara; Laukens, Kris; Collado-Vides, Julio; Meysman, Pieter; Engelen, Kristof

    2016-01-01

    COLOMBOS is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. Compared to the previous version it has more than doubled in size, both in terms of species and data available. The manually curated condition annotation has been overhauled as well, giving more complete information about samples’ experimental conditions and their differences. Functionality-wise cross-species analyses now enable users to analyse expression data for all species simultaneously, and identify candidate genes with evolutionary conserved expression behaviour. All the expression-based query tools have undergone a substantial improvement, overcoming the limit of enforced co-expression data retrieval and instead enabling the return of more complex patterns of expression behaviour. COLOMBOS is freely available through a web application at http://colombos.net/. The complete database is also accessible via REST API or downloadable as tab-delimited text files. PMID:26586805

  15. A combination of transcriptome and methylation analyses reveals embryologically-relevant candidate genes in MRKH patients

    Directory of Open Access Journals (Sweden)

    Riess Olaf

    2011-05-01

    Full Text Available Abstract Background The Mayer-Rokitansky-Küster-Hauser (MRKH syndrome is present in at least 1 out of 4,500 female live births and is the second most common cause for primary amenorrhea. It is characterized by vaginal and uterine aplasia in an XX individual with normal secondary characteristics. It has long been considered a sporadic anomaly, but familial clustering occurs. Several candidate genes have been studied although no single factor has yet been identified. Cases of discordant monozygotic twins suggest that the involvement of epigenetic factors is more likely. Methods Differences in gene expression and methylation patterns of uterine tissue between eight MRKH patients and eight controls were identified using whole-genome microarray analyses. Results obtained by expression and methylation arrays were confirmed by qRT-PCR and pyrosequencing. Results We delineated 293 differentially expressed and 194 differentially methylated genes of which nine overlap in both groups. These nine genes are mainly embryologically relevant for the development of the female genital tract. Conclusion Our study used, for the first time, a combined whole-genome expression and methylation approach to reveal the etiology of the MRKH syndrome. The findings suggest that either deficient estrogen receptors or the ectopic expression of certain HOXA genes might lead to abnormal development of the female reproductive tract. In utero exposure to endocrine disruptors or abnormally high maternal hormone levels might cause ectopic expression or anterior transformation of HOXA genes. It is, however, also possible that different factors influence the anti-Mullerian hormone promoter activity during embryological development causing regression of the Müllerian ducts. Thus, our data stimulate new research directions to decipher the pathogenic basis of MRKH syndrome.

  16. In silico phylogenetic and virulence gene profile analyses of avian pathogenic Escherichia coli genome sequences

    Directory of Open Access Journals (Sweden)

    Thaís C.G. Rojas

    2014-02-01

    Full Text Available Avian pathogenic Escherichia coli (APEC infections are responsible for significant losses in the poultry industry worldwide. A zoonotic risk has been attributed to APEC strains because they present similarities to extraintestinal pathogenic E. coli (ExPEC associated with illness in humans, mainly urinary tract infections and neonatal meningitis. Here, we present in silico analyses with pathogenic E. coli genome sequences, including recently available APEC genomes. The phylogenetic tree, based on multi-locus sequence typing (MLST of seven housekeeping genes, revealed high diversity in the allelic composition. Nevertheless, despite this diversity, the phylogenetic tree was able to cluster the different pathotypes together. An in silico virulence gene profile was also determined for each of these strains, through the presence or absence of 83 well-known virulence genes/traits described in pathogenic E. coli strains. The MLST phylogeny and the virulence gene profiles demonstrated a certain genetic similarity between Brazilian APEC strains, APEC isolated in the United States, UPEC (uropathogenic E. coli and diarrheagenic strains isolated from humans. This correlation corroborates and reinforces the zoonotic potential hypothesis proposed to APEC.

  17. Gene set based association analyses for the WSSV resistance of Pacific white shrimp Litopenaeus vannamei

    Science.gov (United States)

    Yu, Yang; Liu, Jingwen; Li, Fuhua; Zhang, Xiaojun; Zhang, Chengsong; Xiang, Jianhai

    2017-01-01

    White Spot Syndrome Virus (WSSV) is regarded as a virus with the strongest pathogenicity to shrimp. For the threshold trait such as disease resistance, marker assisted selection (MAS) was considered to be a more effective approach. In the present study, association analyses of single nucleotide polymorphisms (SNPs) located in a set of immune related genes were conducted to identify markers associated with WSSV resistance. SNPs were detected by bioinformatics analysis on RNA sequencing data generated by Illimina sequencing platform and Roche 454 sequencing technology. A total of 681 SNPs located in the exons of immune related genes were selected as candidate SNPs. Among these SNPs, 77 loci were genotyped in WSSV susceptible group and resistant group. Association analysis was performed based on logistic regression method under an additive and dominance model in GenABEL package. As a result, five SNPs showed associations with WSSV resistance at a significant level of 0.05. Besides, SNP-SNP interaction analysis was conducted. The combination of SNP loci in TRAF6, Cu/Zn SOD and nLvALF2 exhibited a significant effect on the WSSV resistance of shrimp. Gene expression analysis revealed that these SNPs might influence the expression of these immune-related genes. This study provides a useful method for performing MAS in shrimp. PMID:28094323

  18. Integrative analyses shed new light on human ribosomal protein gene regulation

    Science.gov (United States)

    Li, Xin; Zheng, Yiyu; Hu, Haiyan; Li, Xiaoman

    2016-01-01

    Ribosomal protein genes (RPGs) are important house-keeping genes that are well-known for their coordinated expression. Previous studies on RPGs are largely limited to their promoter regions. Recent high-throughput studies provide an unprecedented opportunity to study how human RPGs are transcriptionally modulated and how such transcriptional regulation may contribute to the coordinate gene expression in various tissues and cell types. By analyzing the DNase I hypersensitive sites under 349 experimental conditions, we predicted 217 RPG regulatory regions in the human genome. More than 86.6% of these computationally predicted regulatory regions were partially corroborated by independent experimental measurements. Motif analyses on these predicted regulatory regions identified 31 DNA motifs, including 57.1% of experimentally validated motifs in literature that regulate RPGs. Interestingly, we observed that the majority of the predicted motifs were shared by the predicted distal and proximal regulatory regions of the same RPGs, a likely general mechanism for enhancer-promoter interactions. We also found that RPGs may be differently regulated in different cells, indicating that condition-specific RPG regulatory regions still need to be discovered and investigated. Our study advances the understanding of how RPGs are coordinately modulated, which sheds light to the general principles of gene transcriptional regulation in mammals. PMID:27346035

  19. Cloning and expression analyses of the anthocyanin biosynthetic genes in mulberry plants.

    Science.gov (United States)

    Qi, Xiwu; Shuai, Qin; Chen, Hu; Fan, Li; Zeng, Qiwei; He, Ningjia

    2014-10-01

    Anthocyanins are natural food colorants produced by plants that play important roles in their growth and development. Mulberry fruits are rich in anthocyanins, which are the most important active components of mulberry and have many potentially beneficial effects on human health. The study of anthocyanin biosynthesis will bring benefits for quality improvement and industrial exploration of mulberry fruits. In the present study, nine putative genes involved in anthocyanin biosynthesis in mulberry plants were identified and cloned. Sequence analysis revealed that the mulberry anthocyanin biosynthetic genes were conserved and had counterparts in other plants. Spatial transcriptional analysis showed detectable expression of eight of these genes in different tissues. The results of expression and UPLC analyses in two mulberry cultivars with differently colored fruit indicated that anthocyanin concentrations correlated with the expression levels of genes associated with anthocyanin biosynthesis including CHS1, CHI, F3H1, F3'H1, and ANS during the fruit ripening process. The present studies provide insight into anthocyanin biosynthesis in mulberry plants and may facilitate genetic engineering for improvement of the anthocyanin content in mulberry fruit.

  20. Comparisons of power of statistical methods for gene-environment interaction analyses.

    Science.gov (United States)

    Ege, Markus J; Strachan, David P

    2013-10-01

    Any genome-wide analysis is hampered by reduced statistical power due to multiple comparisons. This is particularly true for interaction analyses, which have lower statistical power than analyses of associations. To assess gene-environment interactions in population settings we have recently proposed a statistical method based on a modified two-step approach, where first genetic loci are selected by their associations with disease and environment, respectively, and subsequently tested for interactions. We have simulated various data sets resembling real world scenarios and compared single-step and two-step approaches with respect to true positive rate (TPR) in 486 scenarios and (study-wide) false positive rate (FPR) in 252 scenarios. Our simulations confirmed that in all two-step methods the two steps are not correlated. In terms of TPR, two-step approaches combining information on gene-disease association and gene-environment association in the first step were superior to all other methods, while preserving a low FPR in over 250 million simulations under the null hypothesis. Our weighted modification yielded the highest power across various degrees of gene-environment association in the controls. An optimal threshold for step 1 depended on the interacting allele frequency and the disease prevalence. In all scenarios, the least powerful method was to proceed directly to an unbiased full interaction model, applying conventional genome-wide significance thresholds. This simulation study confirms the practical advantage of two-step approaches to interaction testing over more conventional one-step designs, at least in the context of dichotomous disease outcomes and other parameters that might apply in real-world settings.

  1. Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data.

    Science.gov (United States)

    Schrader, Alexandra; Meyer, Katharina; Walther, Neele; Stolz, Ailine; Feist, Maren; Hand, Elisabeth; von Bonin, Frederike; Evers, Maurits; Kohler, Christian; Shirneshan, Katayoon; Vockerodt, Martina; Klapper, Wolfram; Szczepanowski, Monika; Murray, Paul G; Bastians, Holger; Trümper, Lorenz; Spang, Rainer; Kube, Dieter

    2016-07-26

    To discover new regulatory pathways in B lymphoma cells, we performed a combined analysis of experimental, clinical and global gene expression data. We identified a specific cluster of genes that was coherently expressed in primary lymphoma samples and suppressed by activation of the B cell receptor (BCR) through αIgM treatment of lymphoma cells in vitro. This gene cluster, which we called BCR.1, includes numerous cell cycle regulators. A reduced expression of BCR.1 genes after BCR activation was observed in different cell lines and also in CD10+ germinal center B cells. We found that BCR activation led to a delayed entry to and progression of mitosis and defects in metaphase. Cytogenetic changes were detected upon long-term αIgM treatment. Furthermore, an inverse correlation of BCR.1 genes with c-Myc co-regulated genes in distinct groups of lymphoma patients was observed. Finally, we showed that the BCR.1 index discriminates activated B cell-like and germinal centre B cell-like diffuse large B cell lymphoma supporting the functional relevance of this new regulatory circuit and the power of guided clustering for biomarker discovery.

  2. Experimental measurements and mathematical modeling of biological noise arising from transcriptional and translational regulation of basic synthetic gene circuits.

    Science.gov (United States)

    Bandiera, Lucia; Pasini, Alice; Pasotti, Lorenzo; Zucca, Susanna; Mazzini, Giuliano; Magni, Paolo; Giordano, Emanuele; Furini, Simone

    2016-04-21

    The small number of molecules, unevenly distributed within an isogenic cell population, makes gene expression a noisy process, and strategies have evolved to deal with this variability in protein concentration and to limit its impact on cellular behaviors. As translational efficiency has a major impact on biological noise, a possible strategy to control noise is to regulate gene expression processes at the post-transcriptional level. In this study, fluctuations in the concentration of a green fluorescent protein were compared, at the single cell level, upon transformation of an isogenic bacterial cell population with synthetic gene circuits implementing either a transcriptional or a post-transcriptional control of gene expression. Experimental measurements showed that protein variability is lower under post-transcriptional control, when the same average protein concentrations are compared. This effect is well reproduced by stochastic simulations, supporting the hypothesis that noise reduction is due to the control mechanism acting on the efficiency of translation. Similar strategies are likely to play a role in noise reduction in natural systems and to be useful for controlling noise in synthetic biology applications.

  3. Using mice to model Obsessive Compulsive Disorder: From genes to circuits.

    Science.gov (United States)

    Ahmari, Susanne E

    2016-05-03

    Obsessive Compulsive Disorder (OCD) is a severe, chronic, and highly prevalent psychiatric disorder that affects between 1.5% and 3% of people worldwide. Despite its severity, high prevalence, and clear societal cost, current OCD therapies are only partially effective. In order to ultimately develop improved treatments for this severe mental illness, we need further research to gain an improved understanding of the pathophysiology that underlies obsessions and compulsions. Though studies in OCD patients can provide some insight into the disease process, studies in humans are inherently limited in their ability to dissect pathologic processes because of their non-invasive nature. The recent development of strategies for genetic and circuit-specific manipulation in rodent models finally allows us to identify the molecular, cellular, and circuit events that lead to abnormal repetitive behaviors and affect dysregulation relevant to OCD. This review will highlight recent studies in mouse model systems that have used transgenic and optogenetic tools in combination with classic pharmacology and behavioral techniques to advance our understanding of these pathologic processes.

  4. Characterization and expression analyses of the H⁺-pyrophosphatase gene in rye.

    Science.gov (United States)

    Wang, Chang-Shui; Jiang, Qian-Tao; Ma, Jian; Wang, Xiu-Ying; Wang, Ji-Rui; Chen, Guo-Yue; Qi, Peng-Fei; Peng, Yuan-Ying; Lan, Xiu-Jin; Zheng, You-Liang; Wei, Yu-Ming

    2016-09-01

    The H⁺-pyrophosphatase (H⁺-PPase) gene plays an important role in maintaining intracellular proton gradients. Here, we characterized the full-length complementary DNA (cDNA) and DNA of the H⁺-PPase gene ScHP1 in rye (Secale cereale L. 'Qinling'). We determined the subcellular localization of this gene and predicted the corresponding protein structure. We analysed the evolutionary relationship between ScHP1 and H⁺-PPase genes in other species, and did real-time quantitative polymerase chain reaction to explore the expression patterns of ScHP1 in rye plants subjected to N, P and K deprivation and to cold, high-salt and drought stresses. ScHP1 cDNA included a 2289 bp open reading frame (ORF) encoding 762 amino acid residues with 14 transmembrane domains. The genomic ScHP1 DNA was 4354 bp and contained eight exons and seven introns. ScHP1 was highly homologous with other members of the H⁺-PPase gene family. When the full-length ORF was inserted into the expression vector pA7-YFP, the fluorescent microscopy revealed that ScHP1-YFP fusion protein was located in the plasma membrane. Rye plants that were subjected to N deprivation, cold and high-salt stresses, ScHP1 expression was higher in the leaves than roots. Conversely, plants subjected to P and K deprivation and drought stress, ScHP1 expression was higher in the roots than leaves. Under all the investigated stress conditions, expression of ScHP1 was lower in the stem than in the leaves and roots. Our results imply that ScHP1 functions under abiotic stress response.

  5. Characterization and expression analyses of the H ⁺ -pyrophosphatase gene in rye

    Indian Academy of Sciences (India)

    CHANG-SHUI WANG; QIAN-TAO JIANG; JIAN MA; XIU-YING WANG; JI-RUI WANG; GUO-YUE CHEN; PENG-FEI QI; YUAN-YING PENG; XIU-JIN LAN; YOU-LIANG ZHENG; YU-MING WEI

    2016-09-01

    The H+-pyrophosphatase (H⁺-PPase) gene plays an important role in maintaining intracellular proton gradients. Here, we characterized the full-length complementary DNA (cDNA) and DNA of the H⁺ -PPase gene ScHP1 in rye (Secale cereale L. ‘Qinling’). We determined the subcellular localization of this gene and predicted the corresponding protein structure. We analysed the evolutionary relationship between ScHP1 and H⁺ − PPase genes in other species, and did real-time quantitative polymerase chain reaction to explore the expression patterns of ScHP1 in rye plants subjected to N, P and K deprivation and to cold, high-salt and drought stresses. ScHP1 cDNA included a 2289 bp open reading frame (ORF) encoding 762 amino acid residues with 14 transmembrane domains. The genomic ScHP1 DNA was 4354 bp and contained eight exons and seven introns.ScHP1 was highly homologous with other members of the H⁺ -PPase gene family. When the full-length ORF was inserted into the expression vector pA7-YFP, the fluorescent microscopy revealed that ScHP1-YFP fusion protein was located in the plasma membrane. Rye plants that were subjected to N deprivation, cold and high-salt stresses, ScHP1 expression was higher in the leaves than roots. Conversely, plants subjected to P and K deprivation and drought stress,ScHP1 expression was higher in the roots than leaves. Under all the investigated stress conditions, expression of ScHP1 was lower in the stem than in the leaves and roots. Our results imply that ScHP1 functions under abiotic stress response.

  6. Prevalence of Tobacco mosaic virus in Iran and Evolutionary Analyses of the Coat Protein Gene.

    Science.gov (United States)

    Alishiri, Athar; Rakhshandehroo, Farshad; Zamanizadeh, Hamid-Reza; Palukaitis, Peter

    2013-09-01

    The incidence and distribution of Tobacco mosaic virus (TMV) and related tobamoviruses was determined using an enzyme-linked immunosorbent assay on 1,926 symptomatic horticultural crops and 107 asymptomatic weed samples collected from 78 highly infected fields in the major horticultural crop-producing areas in 17 provinces throughout Iran. The results were confirmed by host range studies and reverse transcription-polymerase chain reaction. The overall incidence of infection by these viruses in symptomatic plants was 11.3%. The coat protein (CP) gene sequences of a number of isolates were determined and disclosed to be a high identity (up to 100%) among the Iranian isolates. Phylogenetic analysis of all known TMV CP genes showed three clades on the basis of nucleotide sequences with all Iranian isolates distinctly clustered in clade II. Analysis using the complete CP amino acid sequence showed one clade with two subgroups, IA and IB, with Iranian isolates in both subgroups. The nucleotide diversity within each sub-group was very low, but higher between the two clades. No correlation was found between genetic distance and geographical origin or host species of isolation. Statistical analyses suggested a negative selection and demonstrated the occurrence of gene flow from the isolates in other clades to the Iranian population.

  7. Prevalence of Tobacco mosaic virus in Iran and Evolutionary Analyses of the Coat Protein Gene

    Directory of Open Access Journals (Sweden)

    Athar Alishiri

    2013-09-01

    Full Text Available The incidence and distribution of Tobacco mosaic virus (TMV and related tobamoviruses was determined using an enzyme-linked immunosorbent assay on 1,926 symptomatic horticultural crops and 107 asymptomatic weed samples collected from 78 highly infected fields in the major horticultural crop-producing areas in 17 provinces throughout Iran. The results were confirmed by host range studies and reverse transcription-polymerase chain reaction. The overall incidence of infection by these viruses in symptomatic plants was 11.3%. The coat protein (CP gene sequences of a number of isolates were determined and disclosed to be a high identity (up to 100% among the Iranian isolates. Phylogenetic analysis of all known TMV CP genes showed three clades on the basis of nucleotide sequences with all Iranian isolates distinctly clustered in clade II. Analysis using the complete CP amino acid sequence showed one clade with two subgroups, IA and IB, with Iranian isolates in both subgroups. The nucleotide diversity within each sub-group was very low, but higher between the two clades. No correlation was found between genetic distance and geographical origin or host species of isolation. Statistical analyses suggested a negative selection and demonstrated the occurrence of gene flow from the isolates in other clades to the Iranian population.

  8. Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

    Directory of Open Access Journals (Sweden)

    Lionikas Arimantas

    2012-11-01

    Full Text Available Abstract Background We have recently identified a number of Quantitative Trait Loci (QTL contributing to the 2-fold muscle weight difference between the LG/J and SM/J mouse strains and refined their confidence intervals. To facilitate nomination of the candidate genes responsible for these differences we examined the transcriptome of the tibialis anterior (TA muscle of each strain by RNA-Seq. Results 13,726 genes were expressed in mouse skeletal muscle. Intersection of a set of 1061 differentially expressed transcripts with a mouse muscle Bayesian Network identified a coherent set of differentially expressed genes that we term the LG/J and SM/J Regulatory Network (LSRN. The integration of the QTL, transcriptome and the network analyses identified eight key drivers of the LSRN (Kdr, Plbd1, Mgp, Fah, Prss23, 2310014F06Rik, Grtp1, Stk10 residing within five QTL regions, which were either polymorphic or differentially expressed between the two strains and are strong candidates for quantitative trait genes (QTGs underlying muscle mass. The insight gained from network analysis including the ability to make testable predictions is illustrated by annotating the LSRN with knowledge-based signatures and showing that the SM/J state of the network corresponds to a more oxidative state. We validated this prediction by NADH tetrazolium reductase staining in the TA muscle revealing higher oxidative potential of the SM/J compared to the LG/J strain (p Conclusion Thus, integration of fine resolution QTL mapping, RNA-Seq transcriptome information and mouse muscle Bayesian Network analysis provides a novel and unbiased strategy for nomination of muscle QTGs.

  9. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain.

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    Rajini Sreenivasan

    Full Text Available BACKGROUND: Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs. METHODOLOGY/PRINCIPAL FINDINGS: We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs, 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and 'rest-of-body' from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4 has previously been implicated in reproduction in mice, were all strongly expressed in the gonads. CONCLUSIONS/SIGNIFICANCE: We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar

  10. Utilization of inherent miRNAs in functional analyses of Toxoplasma gondii genes.

    Science.gov (United States)

    Crater, Anna K; Manni, Emad; Ananvoranich, Sirinart

    2015-01-01

    MicroRNAs (miRNAs) are crucial genetic effectors partaking in numerous mechanisms of gene regulation in eukaryotic organisms. Recent discoveries of miRNA in Toxoplasma gondii, an intracellular obligate parasite of the phylum Apicomplexa, suggested possible roles of T. gondii miRNAs (Tg-miRNAs) in the post-transcriptional gene regulation and in the cell biology of the parasite. To gain a better understanding of the involvement of Tg-miRNAs in regulating the parasite gene expression, a dual luciferase reporter system was used in the examination and evaluation of the effects of endogenous Tg-miRNAs, their mimics and inhibitors. A Renilla luciferase (Rnluc) transcript was engineered to carry independent binding sites of two abundant species, namely Tg-miR-60a and Tg-miR-4a, so that the expression of Rnluc was silenced in a sequence specific manner by Tg-miR-60a and Tg-miR-4a. Notably, Tg-miR-60a, but not Tg-miR-4a, caused the levels of Rnluc transcripts to decrease. These findings strongly suggested that T. gondii employs the Tg-miRNA species-specific mode of silencing actions: transcript degradation by Tg-miR-60a, and translational suppression by Tg-miR-4a. Herein we developed a genetic system that exploits and directs the most abundant Tg-miR-60a for loss-of-function analyses in T. gondii. As a proof of principle, we showed that when the binding sites for Tg-miR-60a were introduced into the parasite transcripts via homologous recombination at the locus of (i) DEAD-box RNA helicase (TgHoDI), or (ii) lactate dehydrogenase isoform 1 (TgLDH1), the expression levels of the selected genes can be altered. It was thus proven that inherit Tg-miR-60a could be directed and used to assist in the loss-of-function analyses.

  11. An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors

    Directory of Open Access Journals (Sweden)

    Azuaje Francisco

    2006-06-01

    Full Text Available Abstract Background The analysis of large-scale gene expression data is a fundamental approach to functional genomics and the identification of potential drug targets. Results derived from such studies cannot be trusted unless they are adequately designed and reported. The purpose of this study is to assess current practices on the reporting of experimental design and statistical analyses in gene expression-based studies. Methods We reviewed hundreds of MEDLINE-indexed papers involving gene expression data analysis, which were published between 2003 and 2005. These papers were examined on the basis of their reporting of several factors, such as sample size, statistical power and software availability. Results Among the examined papers, we concentrated on 293 papers consisting of applications and new methodologies. These papers did not report approaches to sample size and statistical power estimation. Explicit statements on data transformation and descriptions of the normalisation techniques applied prior to data analyses (e.g. classification were not reported in 57 (37.5% and 104 (68.4% of the methodology papers respectively. With regard to papers presenting biomedical-relevant applications, 41(29.1 % of these papers did not report on data normalisation and 83 (58.9% did not describe the normalisation technique applied. Clustering-based analysis, the t-test and ANOVA represent the most widely applied techniques in microarray data analysis. But remarkably, only 5 (3.5% of the application papers included statements or references to assumption about variance homogeneity for the application of the t-test and ANOVA. There is still a need to promote the reporting of software packages applied or their availability. Conclusion Recently-published gene expression data analysis studies may lack key information required for properly assessing their design quality and potential impact. There is a need for more rigorous reporting of important experimental

  12. bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses.

    Science.gov (United States)

    Jézéquel, Pascal; Frénel, Jean-Sébastien; Campion, Loïc; Guérin-Charbonnel, Catherine; Gouraud, Wilfried; Ricolleau, Gabriel; Campone, Mario

    2013-01-01

    We recently developed a user-friendly web-based application called bc-GenExMiner (http://bcgenex.centregauducheau.fr), which offered the possibility to evaluate prognostic informativity of genes in breast cancer by means of a 'prognostic module'. In this study, we develop a new module called 'correlation module', which includes three kinds of gene expression correlation analyses. The first one computes correlation coefficient between 2 or more (up to 10) chosen genes. The second one produces two lists of genes that are most correlated (positively and negatively) to a 'tested' gene. A gene ontology (GO) mining function is also proposed to explore GO 'biological process', 'molecular function' and 'cellular component' terms enrichment for the output lists of most correlated genes. The third one explores gene expression correlation between the 15 telomeric and 15 centromeric genes surrounding a 'tested' gene. These correlation analyses can be performed in different groups of patients: all patients (without any subtyping), in molecular subtypes (basal-like, HER2+, luminal A and luminal B) and according to oestrogen receptor status. Validation tests based on published data showed that these automatized analyses lead to results consistent with studies' conclusions. In brief, this new module has been developed to help basic researchers explore molecular mechanisms of breast cancer. DATABASE URL: http://bcgenex.centregauducheau.fr

  13. Genomic and in silico analyses of CRBN gene and thalidomide embryopathy in humans.

    Science.gov (United States)

    Vianna, Fernanda Sales Luiz; Kowalski, Thayne Woycinck; Tovo-Rodrigues, Luciana; Tagliani-Ribeiro, Alice; Godoy, Bibiane Armiliato; Fraga, Lucas Rosa; Sanseverino, Maria Teresa Vieira; Hutz, Mara Helena; Schuler-Faccini, Lavínia

    2016-12-01

    Thalidomide causes Thalidomide Embryopathy (TE), but is largely used to treat several conditions. Investigations with Cereblon, a thalidomide target protein encoded by CRBN gene, have helped to understand thalidomide therapeutic and teratogenic properties. We sequenced CRBN-thalidomide binding region in 38 TE individuals and 136 Brazilians without congenital anomalies, and performed in silico analyses. Eight variants were identified, seven intronic and one in 3'UTR. TE individuals had rare variants in higher frequency than the non-affected group (p=0.04). The genotype rs1620675 CC was related to neurological anomalies in TE individuals (p=0.004). Bioinformatics analysis suggested this genotype leads to potential alterations in splicing sites and binding to transcription factors. Comparison of the Cereblon-thalidomide binding domains in mammals demonstrated that CRBN is highly conserved across species. All the variants require evaluation in functional assays in order to understand their role in Cereblon-thalidomide binding and complex interactions that lead to TE.

  14. Performance analysis of electrical circuits /PANE/

    Science.gov (United States)

    Johnson, K. L.; Steinberg, L. L.

    1968-01-01

    Automated statistical and worst case computer program has been designed to perform dc and ac steady circuit analyses. The program determines the worst case circuit performance by solving circuit equations.

  15. Systems mechanobiology: tension-inhibited protein turnover is sufficient to physically control gene circuits.

    Science.gov (United States)

    Dingal, P C Dave P; Discher, Dennis E

    2014-12-02

    Mechanotransduction pathways convert forces that stress and strain structures within cells into gene expression levels that impact development, homeostasis, and disease. The levels of some key structural proteins in the nucleus, cytoskeleton, or extracellular matrix have been recently reported to scale with tissue- and cell-level forces or mechanical properties such as stiffness, and so the mathematics of mechanotransduction becomes important to understand. Here, we show that if a given structural protein positively regulates its own gene expression, then stresses need only inhibit degradation of that protein to achieve stable, mechanosensitive gene expression. This basic use-it-or-lose-it module is illustrated by application to meshworks of nuclear lamin A, minifilaments of myosin II, and extracellular matrix collagen fibers—all of which possess filamentous coiled-coil/supercoiled structures. Past experiments not only suggest that tension suppresses protein degradation mediated and/or initiated by various enzymes but also that transcript levels vary with protein levels because key transcription factors are regulated by these structural proteins. Coupling between modules occurs within single cells and between cells in tissue, as illustrated during embryonic heart development where cardiac fibroblasts make collagen that cardiomyocytes contract. With few additional assumptions, the basic module has sufficient physics to control key structural genes in both development and disease.

  16. Haplotype analyses of DNA repair gene polymorphisms and their role in ulcerative colitis.

    Directory of Open Access Journals (Sweden)

    Avinash Bardia

    Full Text Available Ulcerative colitis (UC is a major clinical form of inflammatory bowel disease. UC is characterized by mucosal inflammation limited to the colon, always involving the rectum and a variable extent of the more proximal colon in a continuous manner. Genetic variations in DNA repair genes may influence the extent of repair functions, DNA damage, and thus the manifestations of UC. This study thus evaluated the role of polymorphisms of the genes involved in DNA repair mechanisms. A total of 171 patients and 213 controls were included. Genotyping was carried out by ARMS PCR and PCR-RFLP analyses for RAD51, XRCC3 and hMSH2 gene polymorphisms. Allelic and genotypic frequencies were computed in both control & patient groups and data was analyzed using appropriate statistical tests. The frequency of 'A' allele of hMSH2 in the UC group caused statistically significant increased risk for UC compared to controls (OR 1.64, 95% CI 1.16-2.31, p = 0.004. Similarly, the CT genotype of XRCC3 gene was predominant in the UC group and increased the risk for UC by 1.75 fold compared to controls (OR 1.75, 95% CI 1.15-2.67, p = 0.03, further confirming the risk of 'T' allele in UC. The GC genotype frequency of RAD51 gene was significantly increased (p = 0.02 in the UC group (50.3% compared to controls (38%. The GC genotype significantly increased the risk for UC compared to GG genotype by 1.73 fold (OR 1.73, 95% CI 1.14-2.62, p = 0.02 confirming the strong association of 'C' allele with UC. Among the controls, the SNP loci combination of hMSH2:XRCC3 were in perfect linkage. The GTC and ACC haplotypes were found to be predominant in UC than controls with a 2.28 and 2.93 fold significant increase risk of UC.

  17. Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses

    Directory of Open Access Journals (Sweden)

    van Wieringen Wessel N

    2012-05-01

    Full Text Available Abstract Background An increasing number of genomic studies interrogating more than one molecular level is published. Bioinformatics follows biological practice, and recent years have seen a surge in methodology for the integrative analysis of genomic data. Often such analyses require knowledge of which elements of one platform link to those of another. Although important, many integrative analyses do not or insufficiently detail the matching of the platforms. Results We describe, illustrate and discuss six matching procedures. They are implemented in the R-package sigaR (available from Bioconductor. The principles underlying the presented matching procedures are generic, and can be combined to form new matching approaches or be applied to the matching of other platforms. Illustration of the matching procedures on a variety of data sets reveals how the procedures differ in the use of the available data, and may even lead to different results for individual genes. Conclusions Matching of data from multiple genomics platforms is an important preprocessing step for many integrative bioinformatic analysis, for which we present six generic procedures, both old and new. They have been implemented in the R-package sigaR, available from Bioconductor.

  18. Comparative sequence analyses of the neurotoxin complex genes in Clostridium botulinum serotypes A, B, E, and F

    Directory of Open Access Journals (Sweden)

    Ajay K. Singh

    2012-09-01

    Full Text Available Neurotoxin complex (NTC genes are arranged in two known hemagglutinin (HA and open reading frame X (ORFX clusters. NTC genes have been analyzed in four serotypes A, B, E and F of Clostridium botulinum causing human botulism. Analysis of amino acid sequences of NT genes demonstrated significant differences among subtypes and four serotypes. Phylogram tree of NT genes reveals that serotypes A1 and B1 are much closer compared to serotype E1 and F1. However, non-toxic non-hemagglutinin (NTNH gene is highly conserved among four serotypes. Analysis of phylogram tree of NTNH gene reveals that serotypes A and F are more closely related compared to serotype B and E. Additionally, sequences of HAs and ORFX genes are very divergent but these genes are specific in subtypes and serotypes of Clostridium botulinum. Information derived from sequence analyses of NTC has direct implication in development of detection tools and therapeutic countermeasures for botulism.

  19. Variable salinity responses of 12 alfalfa genotypes and comparative expression analyses of salt-response genes

    Science.gov (United States)

    Sandhu, Devinder; Cornacchione, Monica V.; Ferreira, Jorge F. S.; Suarez, Donald L.

    2017-01-01

    Twelve alfalfa genotypes that were selected for biomass under salinity, differences in Na and Cl concentrations in shoots and K/Na ratio were evaluated in this long-term salinity experiment. The selected plants were cloned to reduce genetic variability within each genotype. Salt tolerance (ST) index of the genotypes ranged from 0.39 to 1. The most salt-tolerant genotypes SISA14-1 (G03) and AZ-90ST (G10), the top performers for biomass, exhibited the least effect on shoot number and height. SISA14-1 (G03) accumulated low Na and Cl under salinity. Most genotypes exhibited a net reduction in shoot Ca, Mg, P, Fe, and Cu, while Mn and Zn increased under salinity. Salinity reduced foliar area and stomatal conductance; while net photosynthetic rate and transpiration were not affected. Interestingly, salinity increased chlorophyll and antioxidant capacity in most genotypes; however neither parameter correlated well to ST index. Salt-tolerant genotypes showed upregulation of the SOS1, SOS2, SOS3, HKT1, AKT1, NHX1, P5CS1, HSP90.7, HSP81.2, HSP71.1, HSPC025, OTS1, SGF29 and SAL1 genes. Gene expression analyses allowed us to classify genotypes based on their ability to regulate different components of the salt tolerance mechanism. Pyramiding different components of the salt tolerance mechanism may lead to superior salt-tolerant alfalfa genotypes. PMID:28225027

  20. Parentage versus two-generation analyses for estimating pollen-mediated gene flow in plant populations.

    Science.gov (United States)

    Burczyk, Jaroslaw; Koralewski, Tomasz E

    2005-07-01

    Assessment of contemporary pollen-mediated gene flow in plants is important for various aspects of plant population biology, genetic conservation and breeding. Here, through simulations we compare the two alternative approaches for measuring pollen-mediated gene flow: (i) the NEIGHBORHOOD model--a representative of parentage analyses, and (ii) the recently developed TWOGENER analysis of pollen pool structure. We investigate their properties in estimating the effective number of pollen parents (N(ep)) and the mean pollen dispersal distance (delta). We demonstrate that both methods provide very congruent estimates of N(ep) and delta, when the methods' assumptions considering the shape of pollen dispersal curve and the mating system follow those used in data simulations, although the NEIGHBORHOOD model exhibits generally lower variances of the estimates. The violations of the assumptions, especially increased selfing or long-distance pollen dispersal, affect the two methods to a different degree; however, they are still capable to provide comparable estimates of N(ep). The NEIGHBORHOOD model inherently allows to estimate both self-fertilization and outcrossing due to the long-distance pollen dispersal; however, the TWOGENER method is particularly sensitive to inflated selfing levels, which in turn may confound and suppress the effects of distant pollen movement. As a solution we demonstrate that in case of TWOGENER it is possible to extract the fraction of intraclass correlation that results from outcrossing only, which seems to be very relevant for measuring pollen-mediated gene flow. The two approaches differ in estimation precision and experimental efforts but they seem to be complementary depending on the main research focus and type of a population studied.

  1. Experimental and theoretical analyses of gate oxide and junction reliability for 4H-SiC MOSFET under short-circuit operation

    Science.gov (United States)

    An, Junjie; Namai, Masaki; Iwamuro, Noriyuki

    2016-12-01

    In this study, the experimental evaluation and numerical analysis of the short-circuit capability of the 1200 V SiC MOSFET with a thin gate oxide layer were carried out. Two different failures, including the gate oxide breakdown and thermal runaway of the device caused by the high gate electric field and elevated lattice temperature, were initially investigated and their critical temperature points for two failure modes were accurately extrapolated by solving the thermal diffusion equation; the obtained results are in good agreement with simulation results. It was confirmed that short-circuit robustness depends not only on thermal properties of the material but also on dimensional parameters of the device and that the heat is the dominant factor that causes device failure during short-circuit transient.

  2. Coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites for the detection of BCR/ABL fusion gene

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xueping [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Wang, Li [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Department of Medical Laboratory, Chongqing Emergency Medical Center (Chongqing The Fourth Hospital), Chongqing, 400016 (China); Sheng, Shangchun [The No.2 Peoples' Hospital of Yibin, Sichuan, 644000 (China); Wang, Teng; Yang, Juan [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Xie, Guoming, E-mail: guomingxie@cqmu.edu.cn [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China); Feng, Wenli, E-mail: fengwlcqmu@sina.com [Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016 (China)

    2015-08-19

    This article described a novel method by coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites (GS/PANI/AuNPs) for highly sensitive and specific detection of BCR/ABL fusion gene (bcr/abl) in chronic myeloid leukemia (CML). DNA circuit known as catalyzed hairpin assembly (CHA) is enzyme-free and can be simply operated to achieve exponential amplification, which has been widely employed in biosensing. However, application of CHA has been hindered by the need of specially redesigned sequences for each single-stranded DNA input. Herein, a transducer hairpin (HP) was designed to obtain a universal DNA circuit with favorable signal-to-background ratio. To further improve signal amplification, GS/PANI/AuNPs with excellent conductivity and enlarged effective area were introduced into this DNA circuit. Consequently, by combining the advantages of CHA and GS/PANI/AuNPs, bcr/abl could be detected in a linear range from 10 pM to 20 nM with a detection limit of 1.05 pM. Moreover, this protocol showed excellent specificity, good stability and was successfully applied for the detection of real sample, which demonstrated its great potential in clinical application. - Highlights: • A transducer hairpin was designed to improve the versatility of DNA circuit. • GS/PANI/AuNPs were introduced to the DNA circuit for further signal amplification. • The established biosensor displayed high sensitivity and good specificity.

  3. Gene and pathway level analyses of germline DNA-repair gene variants and prostate cancer susceptibility using the iCOGS-genotyping array

    DEFF Research Database (Denmark)

    Saunders, Edward J; Dadaev, Tokhir; Leongamornlert, Daniel A

    2016-01-01

    BACKGROUND: Germline mutations within DNA-repair genes are implicated in susceptibility to multiple forms of cancer. For prostate cancer (PrCa), rare mutations in BRCA2 and BRCA1 give rise to moderately elevated risk, whereas two of B100 common, low-penetrance PrCa susceptibility variants...... identified so far by genome-wide association studies implicate RAD51B and RAD23B. METHODS: Genotype data from the iCOGS array were imputed to the 1000 genomes phase 3 reference panel for 21 780 PrCa cases and 21 727 controls from the Prostate Cancer Association Group to Investigate Cancer Associated...... Alterations in the Genome (PRACTICAL) consortium. We subsequently performed single variant, gene and pathway-level analyses using 81 303 SNPs within 20 Kb of a panel of 179 DNA-repair genes. RESULTS: Single SNP analyses identified only the previously reported association with RAD51B. Gene-level analyses using...

  4. GeneCAT--novel webtools that combine BLAST and co-expression analyses

    DEFF Research Database (Denmark)

    Mutwil, Marek; Obro, Jens; Willats, William G T

    2008-01-01

    The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second......, the high-throughput Map-O-Matic tool matches co-expression pattern of multiple query genes to genes present in user-defined subdatabases, and can therefore be used for gene mapping in forward genetic screens. Third, Rosetta combines co-expression analysis with BLAST and can be used to find 'true' gene...... orthologs in the plant model organisms Arabidopsis thaliana and Hordeum vulgare (Barley). GeneCAT is equipped with expression data for the model plant A. thaliana, and first to introduce co-expression mining tools for the monocot Barley. GeneCAT is available at http://genecat.mpg.de....

  5. Integrative analyses identify osteopontin, LAMB3 and ITGB1 as critical pro-metastatic genes for lung cancer.

    Directory of Open Access Journals (Sweden)

    Xiao-Min Wang

    Full Text Available OBJECTIVE: To explore the key regulatory genes associated with lung cancer in order to reduce its occurrence and progress through silencing these key genes. METHODS: To identify the key regulatory genes involved in lung cancer, we performed a combination of gene array and bioinformatics analyses to compare gene transcription profiles in 3 monoclonal cell strains with high, medium or low metastatic abilities, which were separated from the SPC-A-1sci and SPC-A-1 cell lines by limiting dilution monoclone assay. We then analyzed those genes' biological activities by knocking down their expression in SPC-A-1sci cells using siRNA and lenti-viral shRNA vectors, followed by determinations of the invasion and migration capabilities of the resulting cell lines in vitro as well as their potential for inducing occurrence and metastasis of lung cancer in vivo. To examine the clinical relevance of these findings, we analyzed the expression levels of the identified genes in human lung cancer tissues (n = 135 and matched adjacent normal tissues by immunohistochemical (IHC staining. RESULTS: Three monoclonal cell strains characterized with high, medium or low metastatic abilities were successfully selected. Gene array and bioinformatics analyses implied that osteopontin, LAMB3 and ITGB1 were key genes involved in lung cancer. Knockdown of these genes suppressed human lung cancer cell invasion and metastasis in vitro and in vivo. Clinical sample analyses indicated that osteopontin, LAMB3 and ITGB1 protein expression levels were higher in lung cancer patients, compared to non-cancerous adjacent tissues, and correlated with lymphatic metastasis. CONCLUSIONS: We confirmed that osteopontin, LAMB3 and ITGB1 played important roles in the occurrence and metastasis of lung cancer, thus provided important clues to understanding the molecular mechanism of metastasis and contributing to the therapeutic treatment of lung cancer.

  6. Algebraic circuits

    CERN Document Server

    Lloris Ruiz, Antonio; Parrilla Roure, Luis; García Ríos, Antonio

    2014-01-01

    This book presents a complete and accurate study of algebraic circuits, digital circuits whose performance can be associated with any algebraic structure. The authors distinguish between basic algebraic circuits, such as Linear Feedback Shift Registers (LFSRs) and cellular automata, and algebraic circuits, such as finite fields or Galois fields. The book includes a comprehensive review of representation systems, of arithmetic circuits implementing basic and more complex operations, and of the residue number systems (RNS). It presents a study of basic algebraic circuits such as LFSRs and cellular automata as well as a study of circuits related to Galois fields, including two real cryptographic applications of Galois fields.

  7. Analyses of single nucleotide polymorphisms in selected nutrient-sensitive genes in weight-regain prevention

    DEFF Research Database (Denmark)

    Larsen, Lesli Hingstrup; Ängquist, Lars Henrik; Vimaleswaran, Karani S

    2012-01-01

    Differences in the interindividual response to dietary intervention could be modified by genetic variation in nutrient-sensitive genes.......Differences in the interindividual response to dietary intervention could be modified by genetic variation in nutrient-sensitive genes....

  8. Differential and correlation analyses of microarray gene expression data in the CEPH Utah families

    DEFF Research Database (Denmark)

    Tan, Qihua; Zhao, Jinghua; Li, Shuxia;

    2008-01-01

    The widespread microarray technology capable of analyzing global gene expression at the level of transcription is expanding its application not only in medicine but also in studies on basic biology. This paper presents our analysis on microarray gene expression data in the CEPH Utah families...... focusing on the demographic characteristics such as age and sex on differential gene expression patterns. Our results show that the differential gene expression pattern between age groups is dominated by down-regulated transcriptional activities in the old subjects. Functional analysis on age......-regulated genes identifies cell-cell signaling as an important functional category implicated in human aging. Sex-dependent gene expression is characterized by genes that may escape X-inactivation and, most interestingly, such a pattern is not affected by the aging process. Analysis on sibship correlation on gene...

  9. QUANTITATIVE RT-PCR ANALYSES OF FIVE EVOLUTIONARY CONSERVED GENES IN ALLIGATOR BRAINS DURING DEVELOPMENT

    Science.gov (United States)

    Wilson, Sarah M.; Zhu, Tianli; Khanna, Rajesh; Pritz, Michael B.

    2011-01-01

    Gene expression was investigated in the major brain subdivisions (telencephalon, diencephalon, midbrain and hindbrain) in a representative reptile, Alligator mississipiensis, during the later stages of embryonic development. The following genes were examined: voltage-gated sodium channel isoforms: NaV1.1 and NaV1.2; synaptic vesicle 2a (SV2a); synaptophysin; and calbindin 2. With the exception of synaptophysin, which was only expressed in the telencephalon, all genes were expressed in all brain regions sampled at the time periods examined. For NaV1.1, gene expression varied according to brain area sampled. When compared with NaV1.1, the pattern of NaV1.2 gene expression differed appreciably. The gene expression of SV2a was the most robust of any of the genes examined. Of the other genes examined, although differences were noted, no statistically significant changes were found either between brain part or time interval. Although limited, the present analysis is the first quantitative mRNA gene expression study in any reptile during development. Together with future experiments of a similar nature, the present gene expression results should determine which genes are expressed in major brain areas at which times during development in Alligator. When compared with other amniotes, these results will prove useful for determining how gene expression during development influences adult brain structure. PMID:22379598

  10. Rapid discrimination of Acinetobacter baumannii international clone II lineage by pyrosequencing SNP analyses of bla(OXA-51-like) genes.

    Science.gov (United States)

    Matsui, Mari; Suzuki, Satowa; Suzuki, Masato; Arakawa, Yoshichika; Shibayama, Keigo

    2013-08-01

    We found that Acinetobacter baumannii international clone II generally possesses unique GTA sequence at nucleotide positions 106-108 in the bla(OXA-51-like) genes. We exploited this to develop an easy and rapid method for discrimination of international clone II from other A. baumannii by employing pyrosequencing analyses of single nucleotide polymorphisms.

  11. Nucleotide and phylogenetic analyses of the Chlamydia trachomatis ompA gene indicates it is a hotspot for mutation

    Science.gov (United States)

    Background: Serovars of the human pathogen Chlamydia trachomatis occupy one of three specific tissue niches. Genomic analyses indicate that the serovars have a phylogeny congruent with their pathobiology and have an average substitution rate of less than one nucleotide per kilobase. The ompA gene, h...

  12. Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Shan Goh

    Full Text Available BACKGROUND: Genes essential for bacterial growth are of particular scientific interest. Many putative essential genes have been identified or predicted in several species, however, little is known about gene expression requirement stringency, which may be an important aspect of bacterial physiology and likely a determining factor in drug target development. METHODOLOGY/PRINCIPAL FINDINGS: Working from the premise that essential genes differ in absolute requirement for growth, we describe silencing of putative essential genes in E. coli to obtain a titration of declining growth rates and transcript levels by using antisense peptide nucleic acids (PNA and expressed antisense RNA. The relationship between mRNA decline and growth rate decline reflects the degree of essentiality, or stringency, of an essential gene, which is here defined by the minimum transcript level for a 50% reduction in growth rate (MTL(50. When applied to four growth essential genes, both RNA silencing methods resulted in MTL(50 values that reveal acpP as the most stringently required of the four genes examined, with ftsZ the next most stringently required. The established antibacterial targets murA and fabI were less stringently required. CONCLUSIONS: RNA silencing can reveal stringent requirements for gene expression with respect to growth. This method may be used to validate existing essential genes and to quantify drug target requirement.

  13. Prediction and validation of gene-disease associations using methods inspired by social network analyses.

    Directory of Open Access Journals (Sweden)

    U Martin Singh-Blom

    Full Text Available Correctly identifying associations of genes with diseases has long been a goal in biology. With the emergence of large-scale gene-phenotype association datasets in biology, we can leverage statistical and machine learning methods to help us achieve this goal. In this paper, we present two methods for predicting gene-disease associations based on functional gene associations and gene-phenotype associations in model organisms. The first method, the Katz measure, is motivated from its success in social network link prediction, and is very closely related to some of the recent methods proposed for gene-disease association inference. The second method, called Catapult (Combining dATa Across species using Positive-Unlabeled Learning Techniques, is a supervised machine learning method that uses a biased support vector machine where the features are derived from walks in a heterogeneous gene-trait network. We study the performance of the proposed methods and related state-of-the-art methods using two different evaluation strategies, on two distinct data sets, namely OMIM phenotypes and drug-target interactions. Finally, by measuring the performance of the methods using two different evaluation strategies, we show that even though both methods perform very well, the Katz measure is better at identifying associations between traits and poorly studied genes, whereas Catapult is better suited to correctly identifying gene-trait associations overall [corrected].

  14. Isolation, characterization, and expression analyses of plant elicitor peptides (pep) genes in maize

    Science.gov (United States)

    PROPEP1, PROPEP 2, and PROPEP3 genes appear to have roles in a feedback loop that amplifies defense signaling pathways initiated by pathogens. We present evidence to support the role of peptides derived from PROPEP genes as endogenous elicitors that are generated in response to pathogens. The preval...

  15. Association analyses of depression and genes in the hypothalamus-pituitary-adrenal axis

    DEFF Research Database (Denmark)

    Buttenschøn, Henrietta Nørmølle; Krogh, Jesper; Nielsen, Marit Nyholm;

    2016-01-01

    OBJECTIVE: Dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis has been reported in depression. The aim was to investigate the potential association between depression and seven genes regulating or interfering with the HPA axis, including the gene encoding angiotensin converting enzyme...

  16. Combining phylogenetic and syntenic analyses for understanding the evolution of TCP ECE genes in eudicots.

    Science.gov (United States)

    Citerne, Hélène L; Le Guilloux, Martine; Sannier, Julie; Nadot, Sophie; Damerval, Catherine

    2013-01-01

    TCP ECE genes encode transcription factors which have received much attention for their repeated recruitment in the control of floral symmetry in core eudicots, and more recently in monocots. Major duplications of TCP ECE genes have been described in core eudicots, but the evolutionary history of this gene family is unknown in basal eudicots. Reconstructing the phylogeny of ECE genes in basal eudicots will help set a framework for understanding the functional evolution of these genes. TCP ECE genes were sequenced in all major lineages of basal eudicots and Gunnera which belongs to the sister clade to all other core eudicots. We show that in these lineages they have a complex evolutionary history with repeated duplications. We estimate the timing of the two major duplications already identified in the core eudicots within a timeframe before the divergence of Gunnera and after the divergence of Proteales. We also use a synteny-based approach to examine the extent to which the expansion of TCP ECE genes in diverse eudicot lineages may be due to genome-wide duplications. The three major core-eudicot specific clades share a number of collinear genes, and their common evolutionary history may have originated at the γ event. Genomic comparisons in Arabidopsis thaliana and Solanumlycopersicum highlight their separate polyploid origin, with syntenic fragments with and without TCP ECE genes showing differential gene loss and genomic rearrangements. Comparison between recently available genomes from two basal eudicots Aquilegiacoerulea and Nelumbonucifera suggests that the two TCP ECE paralogs in these species are also derived from large-scale duplications. TCP ECE loci from basal eudicots share many features with the three main core eudicot loci, and allow us to infer the makeup of the ancestral eudicot locus.

  17. Difference-Equation/Flow-Graph Circuit Analysis

    Science.gov (United States)

    Mcvey, I. M.

    1988-01-01

    Numerical technique enables rapid, approximate analyses of electronic circuits containing linear and nonlinear elements. Practiced in variety of computer languages on large and small computers; for circuits simple enough, programmable hand calculators used. Although some combinations of circuit elements make numerical solutions diverge, enables quick identification of divergence and correction of circuit models to make solutions converge.

  18. Complementation analyses of Sinorhizobium meliloti nifA mutant with different originated nifA genes

    Institute of Scientific and Technical Information of China (English)

    YAO Zhenhua; R(U)VERG Silvia; WANG Yiping; ZOU Huasong; TIAN Zhexian; DAI Xiaomi; BECKER Anke; LI Jian; YAN Haiqin; XIAO Yan; ZHU Jiabi; YU Guanqiao

    2006-01-01

    A previous work inferred that the nifA gene of Enterobacter cloacae did not restore the symbiotic phenotype of Sinorhizobium meliloti nifA mutant. In the present study, two nifA genes of Bradyrhizobium japonicum and Mesorhizobium huakuii also did not restore the symbiotic phenotype of S.meliloti nifA mutant. In whole genomic microarray experiments, 238 genes were found to be differentially expressed after S. meliloti nifA had been constitutively expressed in its nifA mutant. In contrast,only 20, 7 and 9 genes changed their transcriptional levels when expressing B. japonium, M. huakuii and Enterobacter cloacae nifA genes in Sm nifA mutant,separately. These genes were classified into several functional groups including house keeping, energy and central intermediary metabolism, transport systems and symbiosis. Interestingly, the genes that of nifH operons showed high expression levels in the presence of either B. japonium or M. huakuii NifA,which was confirmed by subsequent lacZ fusion experiments.

  19. Selection of suitable reference genes for RT-qPCR analyses in cyanobacteria.

    Directory of Open Access Journals (Sweden)

    Filipe Pinto

    Full Text Available Cyanobacteria are a group of photosynthetic prokaryotes that have a diverse morphology, minimal nutritional requirements and metabolic plasticity that has made them attractive organisms to use in biotechnological applications. The use of these organisms as cell factories requires the knowledge of their physiology and metabolism at a systems level. For the quantification of gene transcripts real-time quantitative polymerase chain reaction (RT-qPCR is the standard technique. However, to obtain reliable RT-qPCR results the use and validation of reference genes is mandatory. Towards this goal we have selected and analyzed twelve candidate reference genes from three morphologically distinct cyanobacteria grown under routinely used laboratory conditions. The six genes exhibiting less variation in each organism were evaluated in terms of their expression stability using geNorm, NormFinder and BestKeeper. In addition, the minimum number of reference genes required for normalization was determined. Based on the three algorithms, we provide a list of genes for cyanobacterial RT-qPCR data normalization. To our knowledge, this is the first work on the validation of reference genes for cyanobacteria constituting a valuable starting point for future works.

  20. Validation of Reference Genes for Transcriptional Analyses in Pleurotus ostreatus by Using Reverse Transcription-Quantitative PCR.

    Science.gov (United States)

    Castanera, Raúl; López-Varas, Leticia; Pisabarro, Antonio G; Ramírez, Lucía

    2015-06-15

    Recently, the lignin-degrading basidiomycete Pleurotus ostreatus has become a widely used model organism for fungal genomic and transcriptomic analyses. The increasing interest in this species has led to an increasing number of studies analyzing the transcriptional regulation of multigene families that encode extracellular enzymes. Reverse transcription (RT) followed by real-time PCR is the most suitable technique for analyzing the expression of gene sets under multiple culture conditions. In this work, we tested the suitability of 13 candidate genes for their use as reference genes in P. ostreatus time course cultures for enzyme production. We applied three different statistical algorithms and obtained a combination of stable reference genes for optimal normalization of RT-quantitative PCR assays. This reference index can be used for future transcriptomic analyses and validation of transcriptome sequencing or microarray data. Moreover, we analyzed the expression patterns of a laccase and a manganese peroxidase (lacc10 and mnp3, respectively) in lignocellulose and glucose-based media using submerged, semisolid, and solid-state fermentation. By testing different normalization strategies, we demonstrate that the use of nonvalidated reference genes as internal controls leads to biased results and misinterpretations of the biological responses underlying expression changes.

  1. Molecular cloning and functional analyses of low-temperature induced genes from Ammopiptanthus mongolicus

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Studies on the cold-responsive genes and cold signaling of woody species drop far behind in comparison to herbaceous plants.Due to similar lignified structure,perennial characteristic,and enhanced tolerance,it seems much easier to find strongly antifreeze genes and obtain effective results in transgenic woody plants.In this study,Ammopiptanthus mongolicus,an evergreen,broadleaf and cold-resist leguminous shrub growing in the desert of Inner Mongolia,was used as a material for low-temperature induced gene is...

  2. Cloning and analysing of 5‘ flanking region of Xenopus organizer gene noggin

    Institute of Scientific and Technical Information of China (English)

    TAOQINHUA; JINGYANG; 等

    1999-01-01

    Xenopus organizer specific gene noggin possesses nearly all the characterestic properties of the action of organizer to specify the embryonic body acis.To analyze how the maternal inherited factors control its expression pattern,we cloned the 5' regulatory region of noggin gene.The 1.5 kb upstream sequense could direct reporter gene to express in vivo and data from deletion analysis indicated that a 229 base pair fragmet is essential for activating noggin expression.We further demonstrated that the response elements within this regulatory region were indeed under the control of growth factor activin and Wnt signaling pathway components.

  3. Historical divergence and gene flow: coalescent analyses of mitochondrial, autosomal and sex-linked loci in Passerina buntings.

    Science.gov (United States)

    Carling, Matthew D; Lovette, Irby J; Brumfield, Robb T

    2010-06-01

    Quantifying the role of gene flow during the divergence of closely related species is crucial to understanding the process of speciation. We collected DNA sequence data from 20 loci (one mitochondrial, 13 autosomal, and six sex-linked) for population samples of Lazuli Buntings (Passerina amoena) and Indigo Buntings (Passerina cyanea) (Aves: Cardinalidae) to test explicitly between a strict allopatric speciation model and a model in which divergence occurred despite postdivergence gene flow. Likelihood ratio tests of coalescent-based population genetic parameter estimates indicated a strong signal of postdivergence gene flow and a strict allopatric speciation model was rejected. Analyses of partitioned datasets (mitochondrial, autosomal, and sex-linked) suggest the overall gene flow patterns are driven primarily by autosomal gene flow, as there is no evidence of mitochondrial gene flow and we were unable to reject an allopatric speciation model for the sex-linked data. This pattern is consistent with either a parapatric divergence model or repeated periods of allopatry with gene flow occurring via secondary contact. These results are consistent with the low fitness of female avian hybrids under Haldane's rule and demonstrate that sex-linked loci likely are important in the initial generation of reproductive isolation, not just its maintenance.

  4. Analyses of the complete genome and gene expression of chloroplast of sweet potato [Ipomoea batata].

    Science.gov (United States)

    Yan, Lang; Lai, Xianjun; Li, Xuedan; Wei, Changhe; Tan, Xuemei; Zhang, Yizheng

    2015-01-01

    Sweet potato [Ipomoea batatas (L.) Lam] ranks among the top seven most important food crops cultivated worldwide and is hexaploid plant (2n=6x=90) in the Convolvulaceae family with a genome size between 2,200 to 3,000 Mb. The genomic resources for this crop are deficient due to its complicated genetic structure. Here, we report the complete nucleotide sequence of the chloroplast (cp) genome of sweet potato, which is a circular molecule of 161,303 bp in the typical quadripartite structure with large (LSC) and small (SSC) single-copy regions separated by a pair of inverted repeats (IRs). The chloroplast DNA contains a total of 145 genes, including 94 protein-encoding genes of which there are 72 single-copy and 11 double-copy genes. The organization and structure of the chloroplast genome (gene content and order, IR expansion/contraction, random repeating sequences, structural rearrangement) of sweet potato were compared with those of Ipomoea (L.) species and some basal important angiosperms, respectively. Some boundary gene-flow and gene gain-and-loss events were identified at intra- and inter-species levels. In addition, by comparing with the transcriptome sequences of sweet potato, the RNA editing events and differential expressions of the chloroplast functional-genes were detected. Moreover, phylogenetic analysis was conducted based on 77 protein-coding genes from 33 taxa and the result may contribute to a better understanding of the evolution progress of the genus Ipomoea (L.), including phylogenetic relationships, intraspecific differentiation and interspecific introgression.

  5. Genome-Wide Association Analyses Point to Candidate Genes for Electric Shock Avoidance in Drosophila melanogaster.

    Science.gov (United States)

    Appel, Mirjam; Scholz, Claus-Jürgen; Müller, Tobias; Dittrich, Marcus; König, Christian; Bockstaller, Marie; Oguz, Tuba; Khalili, Afshin; Antwi-Adjei, Emmanuel; Schauer, Tamas; Margulies, Carla; Tanimoto, Hiromu; Yarali, Ayse

    2015-01-01

    Electric shock is a common stimulus for nociception-research and the most widely used reinforcement in aversive associative learning experiments. Yet, nothing is known about the mechanisms it recruits at the periphery. To help fill this gap, we undertook a genome-wide association analysis using 38 inbred Drosophila melanogaster strains, which avoided shock to varying extents. We identified 514 genes whose expression levels and/ or sequences co-varied with shock avoidance scores. We independently scrutinized 14 of these genes using mutants, validating the effect of 7 of them on shock avoidance. This emphasizes the value of our candidate gene list as a guide for follow-up research. In addition, by integrating our association results with external protein-protein interaction data we obtained a shock avoidance-associated network of 38 genes. Both this network and the original candidate list contained a substantial number of genes that affect mechanosensory bristles, which are hair-like organs distributed across the fly's body. These results may point to a potential role for mechanosensory bristles in shock sensation. Thus, we not only provide a first list of candidate genes for shock avoidance, but also point to an interesting new hypothesis on nociceptive mechanisms.

  6. Citrus plastid-related gene profiling based on expressed sequence tag analyses

    Directory of Open Access Journals (Sweden)

    Tercilio Calsa Jr.

    2007-01-01

    Full Text Available Plastid-related sequences, derived from putative nuclear or plastome genes, were searched in a large collection of expressed sequence tags (ESTs and genomic sequences from the Citrus Biotechnology initiative in Brazil. The identified putative Citrus chloroplast gene sequences were compared to those from Arabidopsis, Eucalyptus and Pinus. Differential expression profiling for plastid-directed nuclear-encoded proteins and photosynthesis-related gene expression variation between Citrus sinensis and Citrus reticulata, when inoculated or not with Xylella fastidiosa, were also analyzed. Presumed Citrus plastome regions were more similar to Eucalyptus. Some putative genes appeared to be preferentially expressed in vegetative tissues (leaves and bark or in reproductive organs (flowers and fruits. Genes preferentially expressed in fruit and flower may be associated with hypothetical physiological functions. Expression pattern clustering analysis suggested that photosynthesis- and carbon fixation-related genes appeared to be up- or down-regulated in a resistant or susceptible Citrus species after Xylella inoculation in comparison to non-infected controls, generating novel information which may be helpful to develop novel genetic manipulation strategies to control Citrus variegated chlorosis (CVC.

  7. Visualising the cross-level relationships between pathological and physiological processes and gene expression: analyses of haematological diseases.

    Directory of Open Access Journals (Sweden)

    Masahiro Ono

    Full Text Available The understanding of pathological processes is based on the comparison between physiological and pathological conditions, and transcriptomic analysis has been extensively applied to various diseases for this purpose. However, the way in which the transcriptomic data of pathological cells relate to the transcriptomes of normal cellular counterparts has not been fully explored, and may provide new and unbiased insights into the mechanisms of these diseases. To achieve this, it is necessary to develop a method to simultaneously analyse components across different levels, namely genes, normal cells, and diseases. Here we propose a multidimensional method that visualises the cross-level relationships between these components at three different levels based on transcriptomic data of physiological and pathological processes, by adapting Canonical Correspondence Analysis, which was developed in ecology and sociology, to microarray data (CCA on Microarray data, CCAM. Using CCAM, we have analysed transcriptomes of haematological disorders and those of normal haematopoietic cell differentiation. First, by analysing leukaemia data, CCAM successfully visualised known relationships between leukaemia subtypes and cellular differentiation, and their characteristic genes, which confirmed the relevance of CCAM. Next, by analysing transcriptomes of myelodysplastic syndromes (MDS, we have shown that CCAM was effective in both generating and testing hypotheses. CCAM showed that among MDS patients, high-risk patients had transcriptomes that were more similar to those of both haematopoietic stem cells (HSC and megakaryocyte-erythroid progenitors (MEP than low-risk patients, and provided a prognostic model. Collectively, CCAM reveals hidden relationships between pathological and physiological processes and gene expression, providing meaningful clinical insights into haematological diseases, and these could not be revealed by other univariate and multivariate methods

  8. Visualising the cross-level relationships between pathological and physiological processes and gene expression: analyses of haematological diseases.

    Science.gov (United States)

    Ono, Masahiro; Tanaka, Reiko J; Kano, Manabu; Sugiman, Toshio

    2013-01-01

    The understanding of pathological processes is based on the comparison between physiological and pathological conditions, and transcriptomic analysis has been extensively applied to various diseases for this purpose. However, the way in which the transcriptomic data of pathological cells relate to the transcriptomes of normal cellular counterparts has not been fully explored, and may provide new and unbiased insights into the mechanisms of these diseases. To achieve this, it is necessary to develop a method to simultaneously analyse components across different levels, namely genes, normal cells, and diseases. Here we propose a multidimensional method that visualises the cross-level relationships between these components at three different levels based on transcriptomic data of physiological and pathological processes, by adapting Canonical Correspondence Analysis, which was developed in ecology and sociology, to microarray data (CCA on Microarray data, CCAM). Using CCAM, we have analysed transcriptomes of haematological disorders and those of normal haematopoietic cell differentiation. First, by analysing leukaemia data, CCAM successfully visualised known relationships between leukaemia subtypes and cellular differentiation, and their characteristic genes, which confirmed the relevance of CCAM. Next, by analysing transcriptomes of myelodysplastic syndromes (MDS), we have shown that CCAM was effective in both generating and testing hypotheses. CCAM showed that among MDS patients, high-risk patients had transcriptomes that were more similar to those of both haematopoietic stem cells (HSC) and megakaryocyte-erythroid progenitors (MEP) than low-risk patients, and provided a prognostic model. Collectively, CCAM reveals hidden relationships between pathological and physiological processes and gene expression, providing meaningful clinical insights into haematological diseases, and these could not be revealed by other univariate and multivariate methods. Furthermore, CCAM

  9. Genome-Wide Gene Expression Profile Analyses Identify CTTN as a Potential Prognostic Marker in Esophageal Cancer

    OpenAIRE

    2014-01-01

    Aim Esophageal squamous cell carcinoma (ESCC) is one of the most common fatal malignances of the digestive tract. Its prognosis is poor mainly due to the lack of reliable markers for early detection and prognostic prediction. Here we aim to identify the molecules involved in ESCC carcinogenesis and those as potential markers for prognosis and as new molecular therapeutic targets. Methods We performed genome-wide gene expression profile analyses of 10 primary ESCCs and their adjacent normal ti...

  10. Genome-Wide Identification and Validation of Reference Genes in Infected Tomato Leaves for Quantitative RT-PCR Analyses.

    Directory of Open Access Journals (Sweden)

    Oliver A Müller

    Full Text Available The Gram-negative bacterium Xanthomonas campestris pv. vesicatoria (Xcv causes bacterial spot disease of pepper and tomato by direct translocation of type III effector proteins into the plant cell cytosol. Once in the plant cell the effectors interfere with host cell processes and manipulate the plant transcriptome. Quantitative RT-PCR (qRT-PCR is usually the method of choice to analyze transcriptional changes of selected plant genes. Reliable results depend, however, on measuring stably expressed reference genes that serve as internal normalization controls. We identified the most stably expressed tomato genes based on microarray analyses of Xcv-infected tomato leaves and evaluated the reliability of 11 genes for qRT-PCR studies in comparison to four traditionally employed reference genes. Three different statistical algorithms, geNorm, NormFinder and BestKeeper, concordantly determined the superiority of the newly identified reference genes. The most suitable reference genes encode proteins with homology to PHD finger family proteins and the U6 snRNA-associated protein LSm7. In addition, we identified pepper orthologs and validated several genes as reliable normalization controls for qRT-PCR analysis of Xcv-infected pepper plants. The newly identified reference genes will be beneficial for future qRT-PCR studies of the Xcv-tomato and Xcv-pepper pathosystems, as well as for the identification of suitable normalization controls for qRT-PCR studies of other plant-pathogen interactions, especially, if related plant species are used in combination with bacterial pathogens.

  11. Combinatory microarray and SuperSAGE analyses identify pairing-dependently transcribed genes in Schistosoma mansoni males, including follistatin.

    Directory of Open Access Journals (Sweden)

    Silke Leutner

    2013-11-01

    Full Text Available BACKGROUND: Schistosomiasis is a disease of world-wide importance and is caused by parasitic flatworms of the genus Schistosoma. These parasites exhibit a unique reproduction biology as the female's sexual maturation depends on a constant pairing-contact to the male. Pairing leads to gonad differentiation in the female, and even gene expression of some gonad-associated genes is controlled by pairing. In contrast, no morphological changes have been observed in males, although first data indicated an effect of pairing also on gene transcription in males. METHODOLOGY/PRINCIPAL FINDINGS: To investigate the influence of pairing on males, we performed a combinatory approach applying SuperSAGE and microarray hybridization, generating the most comprehensive data-set on differential transcription available to date. Of 6,326 sense transcripts detected by both analyses, 29 were significantly differentially transcribed. Besides mutual confirmation, the two methods complemented each other as shown by data comparison and real-time PCR, which revealed a number of genes with consistent regulation across all methods. One of the candidate genes, follistatin of S. mansoni (SmFst was characterized in more detail by in situ hybridization and yeast two-hybrid (Y2H interaction analyses with potential binding partners. CONCLUSIONS/SIGNIFICANCE: Beyond confirming previously hypothesized differences in metabolic processes between pairing-experienced (EM and pairing-unexperienced males (UM, our data indicate that neuronal processes are involved in male-female interaction but also TGFβ-signaling. One candidate revealing significant down-regulation in EM was the TGFβ-pathway controlling molecule follistatin (SmFst. First functional analyses demonstrated SmFst interaction with the S. mansoni TGFβ-receptor agonists inhibin/activin (SmInAct and bone morphogenic protein (SmBMP, and all molecules colocalized in the testes. This indicates a yet unknown role of the TGF

  12. EDGAR 2.0: an enhanced software platform for comparative gene content analyses.

    Science.gov (United States)

    Blom, Jochen; Kreis, Julian; Spänig, Sebastian; Juhre, Tobias; Bertelli, Claire; Ernst, Corinna; Goesmann, Alexander

    2016-07-01

    The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports a quick and user-friendly survey of evolutionary relationships between microbial genomes and simplifies the process of obtaining new biological insights into their differential gene content. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio.

  13. Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses

    Directory of Open Access Journals (Sweden)

    Igor R. Costa

    2014-12-01

    Full Text Available Essential amino acids (EAA consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS and betaine-homocysteine S-methyltransferase (BHMT diverged from the expected Tree of Life (ToL relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.

  14. Evidence of a major gene from Bayesian segregation analyses of liability to osteochondral diseases in pigs

    NARCIS (Netherlands)

    Kadarmideen, H.N.; Janss, L.L.G.

    2005-01-01

    Bayesian segregation analyses were used to investigate the mode of inheritance of osteochondral lesions (osteochondrosis, OC) in pigs. Data consisted of 1163 animals with OC and their pedigrees included 2891 animals. Mixed-inheritance threshold models (MITM) and several variants of MITM, in conjunct

  15. Re-engineering adenovirus vector systems to enable high-throughput analyses of gene function.

    Science.gov (United States)

    Stanton, Richard J; McSharry, Brian P; Armstrong, Melanie; Tomasec, Peter; Wilkinson, Gavin W G

    2008-12-01

    With the enhanced capacity of bioinformatics to interrogate extensive banks of sequence data, more efficient technologies are needed to test gene function predictions. Replication-deficient recombinant adenovirus (Ad) vectors are widely used in expression analysis since they provide for extremely efficient expression of transgenes in a wide range of cell types. To facilitate rapid, high-throughput generation of recombinant viruses, we have re-engineered an adenovirus vector (designated AdZ) to allow single-step, directional gene insertion using recombineering technology. Recombineering allows for direct insertion into the Ad vector of PCR products, synthesized sequences, or oligonucleotides encoding shRNAs without requirement for a transfer vector Vectors were optimized for high-throughput applications by making them "self-excising" through incorporating the I-SceI homing endonuclease into the vector removing the need to linearize vectors prior to transfection into packaging cells. AdZ vectors allow genes to be expressed in their native form or with strep, V5, or GFP tags. Insertion of tetracycline operators downstream of the human cytomegalovirus major immediate early (HCMV MIE) promoter permits silencing of transgenes in helper cells expressing the tet repressor thus making the vector compatible with the cloning of toxic gene products. The AdZ vector system is robust, straightforward, and suited to both sporadic and high-throughput applications.

  16. Identification and expression analyses of the alanine aminotransferase (AlaAT) gene family in poplar seedlings

    Science.gov (United States)

    Xu, Zhiru; Ma, Jing; Qu, Chunpu; Hu, Yanbo; Hao, Bingqing; Sun, Yan; Liu, Zhongye; Yang, Han; Yang, Chengjun; Wang, Hongwei; Li, Ying; Liu, Guanjun

    2017-01-01

    Alanine aminotransferase (AlaAT, E.C.2.6.1.2) catalyzes the reversible conversion of pyruvate and glutamate to alanine and α-oxoglutarate. The AlaAT gene family has been well studied in some herbaceous plants, but has not been well characterized in woody plants. In this study, we identified four alanine aminotransferase homologues in Populus trichocarpa, which could be classified into two subgroups, A and B. AlaAT3 and AlaAT4 in subgroup A encode AlaAT, while AlaAT1 and AlaAT2 in subgroup B encode glutamate:glyoxylate aminotransferase (GGAT), which catalyzes the reaction of glutamate and glyoxylate to α-oxoglutarate and glycine. Four AlaAT genes were cloned from P. simonii × P. nigra. PnAlaAT1 and PnAlaAT2 were expressed predominantly in leaves and induced by exogenous nitrogen and exhibited a diurnal fluctuation in leaves, but was inhibited in roots. PnAlaAT3 and PnAlaAT4 were mainly expressed in roots, stems and leaves, and was induced by exogenous nitrogen. The expression of PnAlaAT3 gene could be regulated by glutamine or its related metabolites in roots. Our results suggest that PnAlaAT3 gene may play an important role in nitrogen metabolism and is regulated by glutamine or its related metabolites in the roots of P. simonii × P. nigra. PMID:28378825

  17. GENE EXPRESSION IN THE TESTES OF NORMOSPERMIC VERSUS TERATOSPERMIC DOMESTIC CATS USING HUMAN CDNA MICROARRAY ANALYSES

    Science.gov (United States)

    GENE EXPRESSION IN THE TESTES OF NORMOSPERMIC VERSUS TERATOSPERMIC DOMESTIC CATS USING HUMAN cDNA MICROARRAY ANALYSESB.S. Pukazhenthi1, J. C. Rockett2, M. Ouyang3, D.J. Dix2, J.G. Howard1, P. Georgopoulos4, W.J. J. Welsh3 and D. E. Wildt11Department of Reproductiv...

  18. Gene expression array analyses predict increased proto-oncogene expression in MMTV induced mammary tumors.

    Science.gov (United States)

    Popken-Harris, Pamela; Kirchhof, Nicole; Harrison, Ben; Harris, Lester F

    2006-08-01

    Exogenous infection by milk-borne mouse mammary tumor viruses (MMTV) typically induce mouse mammary tumors in genetically susceptible mice at a rate of 90-95% by 1 year of age. In contrast to other transforming retroviruses, MMTV acts as an insertional mutagen and under the influence of steroid hormones induces oncogenic transformation after insertion into the host genome. As these events correspond with increases in adjacent proto-oncogene transcription, we used expression array profiling to determine which commonly associated MMTV insertion site proto-oncogenes were transcriptionally active in MMTV induced mouse mammary tumors. To verify our gene expression array results we developed real-time quantitative RT-PCR assays for the common MMTV insertion site genes found in RIII/Sa mice (int-1/wnt-1, int-2/fgf-3, int-3/Notch 4, and fgf8/AIGF) as well as two genes that were consistently up regulated (CCND1, and MAT-8) and two genes that were consistently down regulated (FN1 and MAT-8) in the MMTV induced tumors as compared to normal mammary gland. Finally, each tumor was also examined histopathologically. Our expression array findings support a model whereby just one or a few common MMTV insertions into the host genome sets up a dominant cascade of events that leave a characteristic molecular signature.

  19. Mutational analyses of the BRAF, KRAS, and PIK3CA genes in oral squamous cell carcinoma

    Science.gov (United States)

    Bruckman, Karl C.; Schönleben, Frank; Qiu, Wanglong; Woo, Victoria L.; Su, Gloria H.

    2010-01-01

    OBJECTIVES The development of oral squamous cell carcinoma (OSCC) is a complex, multistep process. To date, numerous oncogenes and tumor-suppressor genes have been implicated in oral carcinogenesis. Of particular interest in this regard are genes involved in cell cycling and apoptosis, such BRAF, KRAS, and PIK3CA genes. STUDY DESIGN Mutations of BRAF, KRAS, and PIK3CA were evaluated by direct genomic sequencing of exons 1 of KRAS, 11 and 15 of BRAF, and 9 and 20 of PIK3CA in OSCC specimens. RESULTS Both BRAF and KRAS mutations were detected with a mutation frequency of 2% (1/42). PIK3CA mutations were detected at 3% (1/35). CONCLUSIONS This is the first report implicating BRAF mutation in OSCC. Our study supports that mutations in the BRAF, KRAS, and PIK3CA genes make at least a minor contribution to OSCC tumorigenesis, and pathway-specific therapies targeting these two pathways should be considered for OSCC in a subset of patients with these mutations. PMID:20813562

  20. The Pectin Methylesterase Gene Complement of Phytophthora sojae: Structural and Functional Analyses, and the Evolutionary Relationships with Its Oomycete Homologs.

    Science.gov (United States)

    Horowitz, Brent B; Ospina-Giraldo, Manuel D

    2015-01-01

    Phytophthora sojae is an oomycete pathogen that causes the disease known as root and stem rot in soybean plants, frequently leading to massive economic damage. Additionally, P. sojae is increasingly being utilized as a model for phytopathogenic oomycete research. Despite the economic and scientific importance of P. sojae, the mechanism by which it penetrates the host roots is not yet fully understood. It has been found that oomycetes are not capable of penetrating the cell wall solely through mechanical force, suggesting that alternative factors facilitate breakdown of the host cell wall. Pectin methylesterases have been suggested to be important for Phytophthora pathogenicity, but no data exist on their role in the P. sojae infection process. We have scanned the newly revised version of the annotated P. sojae genome for the presence of putative pectin methylesterases genes and conducted a sequence analysis of all gene models found. We also searched for potential regulatory motifs in the promoter region of the proposed P. sojae models, and investigated the gene expression levels throughout the early course of infection on soybean plants. We found that P. sojae contains a large repertoire of pectin methylesterase-coding genes and that most of these genes display similar motifs in the promoter region, indicating the possibility of a shared regulatory mechanism. Phylogenetic analyses confirmed the evolutionary relatedness of the pectin methylesterase-coding genes within and across Phytophthora spp. In addition, the gene duplication events that led to the emergence of this gene family appear to have occurred prior to many speciation events in the genus Phytophthora. Our results also indicate that the highest levels of expression occurred in the first 24 hours post inoculation, with expression falling after this time. Our study provides evidence that pectin methylesterases may be important for the early action of the P. sojae infection process.

  1. PCR-RFLP analyses for studying the diversity of GH and Pit-1 genes in Slovak Simmental cattle

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    Anna Trakovická

    2013-10-01

    Full Text Available The aim of this study was evaluation of growth hormone (GH and specific pituitary transcription factor (Pit-1 genes diversity in population of 353 Slovak Simmental cows. The analyses were based on single nucleotide polymorphisms GH/AluI and Pit-1/HinfI detections. A polymorphic site of GH gene (AluI has been linked to differences in circulating metabolites, metabolic hormones and milk yield. Bovine Pit-1 is responsible for pituitary development and hormone secreting gene expression, including GH gene. The Pit-1/HinfI locus was associated with growth, milk production and reproduction performance in cattle. Samples of genomic DNA were analyzed by PCR-RFLP method. Digestion of GH gene PCR products with restriction enzyme AluI revealed allele L and V with frequency 0.695 and 0.305, respectively. The digested Pit-1 gene PCR products with enzyme HinfI revealed alleles A (0.249 and B (0.751. Dominant genotypes were for GH gene heterozygous LV (0.47 and for Pit-1 gene homozygous BB (0.56 animals. The observed heterozygosity, effective allele numbers and polymorphism information content of GH/AluI and Pit-1/HinfI bovine loci population were 0.42/0.37, 1.73/1.59 and 0.33/0.30, respectively. The median polymorphic information content of loci was also transferred to the higher observed homozygosity in population (0.58/0.63. Keywords: cattle, growth hormone, leptin, PCR, Pit-1, polymorphism.

  2. Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses

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    Ryan Joseph F

    2011-01-01

    Full Text Available Abstract Background Mutations in the Otopetrin 1 gene (Otop1 in mice and fish produce an unusual bilateral vestibular pathology that involves the absence of otoconia without hearing impairment. The encoded protein, Otop1, is the only functionally characterized member of the Otopetrin Domain Protein (ODP family; the extended sequence and structural preservation of ODP proteins in metazoans suggest a conserved functional role. Here, we use the tools of sequence- and cytogenetic-based comparative genomics to study the Otop1 and the Otop2-Otop3 genes and to establish their genomic context in 25 vertebrates. We extend our evolutionary study to include the gene mutated in Usher syndrome (USH subtype 1G (Ush1g, both because of the head-to-tail clustering of Ush1g with Otop2 and because Otop1 and Ush1g mutations result in inner ear phenotypes. Results We established that OTOP1 is the boundary gene of an inversion polymorphism on human chromosome 4p16 that originated in the common human-chimpanzee lineage more than 6 million years ago. Other lineage-specific evolutionary events included a three-fold expansion of the Otop genes in Xenopus tropicalis and of Ush1g in teleostei fish. The tight physical linkage between Otop2 and Ush1g is conserved in all vertebrates. To further understand the functional organization of the Ushg1-Otop2 locus, we deduced a putative map of binding sites for CCCTC-binding factor (CTCF, a mammalian insulator transcription factor, from genome-wide chromatin immunoprecipitation-sequencing (ChIP-seq data in mouse and human embryonic stem (ES cells combined with detection of CTCF-binding motifs. Conclusions The results presented here clarify the evolutionary history of the vertebrate Otop and Ush1g families, and establish a framework for studying the possible interaction(s of Ush1g and Otop in developmental pathways.

  3. Sample matching by inferred agonal stress in gene expression analyses of the brain

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    Bunney William E

    2007-09-01

    Full Text Available Abstract Background Gene expression patterns in the brain are strongly influenced by the severity and duration of physiological stress at the time of death. This agonal effect, if not well controlled, can lead to spurious findings and diminished statistical power in case-control comparisons. While some recent studies match samples by tissue pH and clinically recorded agonal conditions, we found that these indicators were sometimes at odds with observed stress-related gene expression patterns, and that matching by these criteria still sometimes results in identifying case-control differences that are primarily driven by residual agonal effects. This problem is analogous to the one encountered in genetic association studies, where self-reported race and ethnicity are often imprecise proxies for an individual's actual genetic ancestry. Results We developed an Agonal Stress Rating (ASR system that evaluates each sample's degree of stress based on gene expression data, and used ASRs in post hoc sample matching or covariate analysis. While gene expression patterns are generally correlated across different brain regions, we found strong region-region differences in empirical ASRs in many subjects that likely reflect inter-individual variabilities in local structure or function, resulting in region-specific vulnerability to agonal stress. Conclusion Variation of agonal stress across different brain regions differs between individuals, revealing a new level of complexity for gene expression studies of brain tissues. The Agonal Stress Ratings quantitatively assess each sample's extent of regulatory response to agonal stress, and allow a strong control of this important confounder.

  4. MAGIA2: from miRNA and genes expression data integrative analysis to microRNA–transcription factor mixed regulatory circuits (2012 update)

    Science.gov (United States)

    Bisognin, Andrea; Sales, Gabriele; Coppe, Alessandro; Bortoluzzi, Stefania; Romualdi, Chiara

    2012-01-01

    MAGIA2 (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post-transcriptional regulators of several key biological and pathological processes. As miRNAs act prevalently through target degradation, their expression profiles are expected to be inversely correlated to those of the target genes. Low specificity of target prediction algorithms makes integration approaches an interesting solution for target prediction refinement. MAGIA2 performs this integrative approach supporting different association measures, multiple organisms and almost all target predictions algorithms. Nevertheless, miRNAs activity should be viewed as part of a more complex scenario where regulatory elements and their interactors generate a highly connected network and where gene expression profiles are the result of different levels of regulation. The updated MAGIA2 tries to dissect this complexity by reconstructing mixed regulatory circuits involving either miRNA or transcription factor (TF) as regulators. Two types of circuits are identified: (i) a TF that regulates both a miRNA and its target and (ii) a miRNA that regulates both a TF and its target. PMID:22618880

  5. MAGIA²: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update).

    Science.gov (United States)

    Bisognin, Andrea; Sales, Gabriele; Coppe, Alessandro; Bortoluzzi, Stefania; Romualdi, Chiara

    2012-07-01

    MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post-transcriptional regulators of several key biological and pathological processes. As miRNAs act prevalently through target degradation, their expression profiles are expected to be inversely correlated to those of the target genes. Low specificity of target prediction algorithms makes integration approaches an interesting solution for target prediction refinement. MAGIA(2) performs this integrative approach supporting different association measures, multiple organisms and almost all target predictions algorithms. Nevertheless, miRNAs activity should be viewed as part of a more complex scenario where regulatory elements and their interactors generate a highly connected network and where gene expression profiles are the result of different levels of regulation. The updated MAGIA(2) tries to dissect this complexity by reconstructing mixed regulatory circuits involving either miRNA or transcription factor (TF) as regulators. Two types of circuits are identified: (i) a TF that regulates both a miRNA and its target and (ii) a miRNA that regulates both a TF and its target.

  6. Selective Manipulation of Neural Circuits.

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    Park, Hong Geun; Carmel, Jason B

    2016-04-01

    Unraveling the complex network of neural circuits that form the nervous system demands tools that can manipulate specific circuits. The recent evolution of genetic tools to target neural circuits allows an unprecedented precision in elucidating their function. Here we describe two general approaches for achieving circuit specificity. The first uses the genetic identity of a cell, such as a transcription factor unique to a circuit, to drive expression of a molecule that can manipulate cell function. The second uses the spatial connectivity of a circuit to achieve specificity: one genetic element is introduced at the origin of a circuit and the other at its termination. When the two genetic elements combine within a neuron, they can alter its function. These two general approaches can be combined to allow manipulation of neurons with a specific genetic identity by introducing a regulatory gene into the origin or termination of the circuit. We consider the advantages and disadvantages of both these general approaches with regard to specificity and efficacy of the manipulations. We also review the genetic techniques that allow gain- and loss-of-function within specific neural circuits. These approaches introduce light-sensitive channels (optogenetic) or drug sensitive channels (chemogenetic) into neurons that form specific circuits. We compare these tools with others developed for circuit-specific manipulation and describe the advantages of each. Finally, we discuss how these tools might be applied for identification of the neural circuits that mediate behavior and for repair of neural connections.

  7. A general model for binary cell fate decision gene circuits with degeneracy: indeterminacy and switch behavior in the absence of cooperativity.

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    Mircea Andrecut

    Full Text Available BACKGROUND: The gene regulatory circuit motif in which two opposing fate-determining transcription factors inhibit each other but activate themselves has been used in mathematical models of binary cell fate decisions in multipotent stem or progenitor cells. This simple circuit can generate multistability and explains the symmetric "poised" precursor state in which both factors are present in the cell at equal amounts as well as the resolution of this indeterminate state as the cell commits to either cell fate characterized by an asymmetric expression pattern of the two factors. This establishes the two alternative stable attractors that represent the two fate options. It has been debated whether cooperativity of molecular interactions is necessary to produce such multistability. PRINCIPAL FINDINGS: Here we take a general modeling approach and argue that this question is not relevant. We show that non-linearity can arise in two distinct models in which no explicit interaction between the two factors is assumed and that distinct chemical reaction kinetic formalisms can lead to the same (generic dynamical system form. Moreover, we describe a novel type of bifurcation that produces a degenerate steady state that can explain the metastable state of indeterminacy prior to cell fate decision-making and is consistent with biological observations. CONCLUSION: The general model presented here thus offers a novel principle for linking regulatory circuits with the state of indeterminacy characteristic of multipotent (stem cells.

  8. A General Model for Binary Cell Fate Decision Gene Circuits with Degeneracy: Indeterminacy and Switch Behavior in the Absence of Cooperativity

    Science.gov (United States)

    Andrecut, Mircea; Halley, Julianne D.; Winkler, David A.; Huang, Sui

    2011-01-01

    Background The gene regulatory circuit motif in which two opposing fate-determining transcription factors inhibit each other but activate themselves has been used in mathematical models of binary cell fate decisions in multipotent stem or progenitor cells. This simple circuit can generate multistability and explains the symmetric “poised” precursor state in which both factors are present in the cell at equal amounts as well as the resolution of this indeterminate state as the cell commits to either cell fate characterized by an asymmetric expression pattern of the two factors. This establishes the two alternative stable attractors that represent the two fate options. It has been debated whether cooperativity of molecular interactions is necessary to produce such multistability. Principal Findings Here we take a general modeling approach and argue that this question is not relevant. We show that non-linearity can arise in two distinct models in which no explicit interaction between the two factors is assumed and that distinct chemical reaction kinetic formalisms can lead to the same (generic) dynamical system form. Moreover, we describe a novel type of bifurcation that produces a degenerate steady state that can explain the metastable state of indeterminacy prior to cell fate decision-making and is consistent with biological observations. Conclusion The general model presented here thus offers a novel principle for linking regulatory circuits with the state of indeterminacy characteristic of multipotent (stem) cells. PMID:21625586

  9. Genome-wide association analyses identify SPOCK as a key novel gene underlying age at menarche.

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    Yao-Zhong Liu

    2009-03-01

    Full Text Available For females, menarche is a most significant physiological event. Age at menarche (AAM is a trait with high genetic determination and is associated with major complex diseases in women. However, specific genes for AAM variation are largely unknown. To identify genetic factors underlying AAM variation, a genome-wide association study (GWAS examining about 380,000 SNPs was conducted in 477 Caucasian women. A follow-up replication study was performed to validate our major GWAS findings using two independent Caucasian cohorts with 854 siblings and 762 unrelated subjects, respectively, and one Chinese cohort of 1,387 unrelated subjects--all females. Our GWAS identified a novel gene, SPOCK (Sparc/Osteonectin, CWCV, and Kazal-like domains proteoglycan, which had seven SNPs associated with AAM with genome-wide false discovery rate (FDR q<0.05. Six most significant SNPs of the gene were selected for validation in three independent replication cohorts. All of the six SNPs were replicated in at least one cohort. In particular, SNPs rs13357391 and rs1859345 were replicated both within and across different ethnic groups in all three cohorts, with p values of 5.09 x 10(-3 and 4.37 x 10(-3, respectively, in the Chinese cohort and combined p values (obtained by Fisher's method of 5.19 x 10(-5 and 1.02 x 10(-4, respectively, in all three replication cohorts. Interestingly, SPOCK can inhibit activation of MMP-2 (matrix metalloproteinase-2, a key factor promoting endometrial menstrual breakdown and onset of menstrual bleeding. Our findings, together with the functional relevance, strongly supported that the SPOCK gene underlies variation of AAM.

  10. Association and mutation analyses of 16p11.2 autism candidate genes.

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    Ravinesh A Kumar

    Full Text Available BACKGROUND: Autism is a complex childhood neurodevelopmental disorder with a strong genetic basis. Microdeletion or duplication of a approximately 500-700-kb genomic rearrangement on 16p11.2 that contains 24 genes represents the second most frequent chromosomal disorder associated with autism. The role of common and rare 16p11.2 sequence variants in autism etiology is unknown. METHODOLOGY/PRINCIPAL FINDINGS: To identify common 16p11.2 variants with a potential role in autism, we performed association studies using existing data generated from three microarray platforms: Affymetrix 5.0 (777 families, Illumina 550 K (943 families, and Affymetrix 500 K (60 families. No common variants were identified that were significantly associated with autism. To look for rare variants, we performed resequencing of coding and promoter regions for eight candidate genes selected based on their known expression patterns and functions. In total, we identified 26 novel variants in autism: 13 exonic (nine non-synonymous, three synonymous, and one untranslated region and 13 promoter variants. We found a significant association between autism and a coding variant in the seizure-related gene SEZ6L2 (12/1106 autism vs. 3/1161 controls; p = 0.018. Sez6l2 expression in mouse embryos was restricted to the spinal cord and brain. SEZ6L2 expression in human fetal brain was highest in post-mitotic cortical layers, hippocampus, amygdala, and thalamus. Association analysis of SEZ6L2 in an independent sample set failed to replicate our initial findings. CONCLUSIONS/SIGNIFICANCE: We have identified sequence variation in at least one candidate gene in 16p11.2 that may represent a novel genetic risk factor for autism. However, further studies are required to substantiate these preliminary findings.

  11. Phenotypic profiling and gene expression analyses for aromatic and volatile compounds in Chamoes (Cucumis melo).

    Science.gov (United States)

    Lee, Jeongyeo; Kim, Min Keun; Hwang, Seung Hwan; Kim, Jungeun; Ahn, Jong Moon; Min, Sung Ran; Park, Sang Un; Lim, Soon Sung; Kim, HyeRan

    2014-05-01

    Gotgam chamoe (GgC), a native oriental melon in Korea, is known to possess the aroma of a dried persimmon, an agronomic relevance for melon breeding program. The volatile compounds and the transcript levels of aromatic compound genes in cultivar (Ohbokggul chamoe [OC]) and GgC were profiled. A total of 62 volatile compounds were identified and quantified. Twenty-eight volatile compounds were specific to either the OC or the GgC. The amounts of volatile alcohol, saturated hydrocarbon, and unsaturated hydrocarbon compounds were 2.2, 2.7, and 1.1 times higher in OC, respectively. The amounts of ketone volatiles were 1.2 times higher in GgC, whereas the total amounts of esters were similar. In the shikimate pathway, transcriptional patterns with the fruit parts were different between the two chamoes for CmDAHPS, CmDHD/SDH, and CmEPSPS. The expression levels of all six genes investigated, especially CmCS, were highest in the peel of both chamoes compared to the other parts. The transcript levels of the aromatic amino acid biosynthesis genes demonstrate that phenylalanine and tyrosine are present more in edible parts of the chamoe, while tryptophan may be accumulated low in the chamoe. In addition, phenylalanine and tryptophan are synthesized more in GgC than the OC.

  12. Comprehensive Comparative Genomic and Transcriptomic Analyses of the Legume Genes Controlling the Nodulation Process.

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    Qiao, Zhenzhen; Pingault, Lise; Nourbakhsh-Rey, Mehrnoush; Libault, Marc

    2016-01-01

    Nitrogen is one of the most essential plant nutrients and one of the major factors limiting crop productivity. Having the goal to perform a more sustainable agriculture, there is a need to maximize biological nitrogen fixation, a feature of legumes. To enhance our understanding of the molecular mechanisms controlling the interaction between legumes and rhizobia, the symbiotic partner fixing and assimilating the atmospheric nitrogen for the plant, researchers took advantage of genetic and genomic resources developed across different legume models (e.g., Medicago truncatula, Lotus japonicus, Glycine max, and Phaseolus vulgaris) to identify key regulatory protein coding genes of the nodulation process. In this study, we are presenting the results of a comprehensive comparative genomic analysis to highlight orthologous and paralogous relationships between the legume genes controlling nodulation. Mining large transcriptomic datasets, we also identified several orthologous and paralogous genes characterized by the induction of their expression during nodulation across legume plant species. This comprehensive study prompts new insights into the evolution of the nodulation process in legume plant and will benefit the scientific community interested in the transfer of functional genomic information between species.

  13. Candidate Genes for Testicular Cancer Evaluated by In Situ Protein Expression Analyses on Tissue Microarrays

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    Rolf I. Skotheim

    2003-09-01

    Full Text Available By the use of high-throughput molecular technologies, the number of genes and proteins potentially relevant to testicular germ cell tumor (TGCT and other diseases will increase rapidly. In a recent transcriptional profiling, we demonstrated the overexpression of GRB7 and JUP in TGCTs, confirmed the reported overexpression of CCND2. We also have recent evidences for frequent genetic alterations of FHIT and epigenetic alterations of MGMT. To evaluate whether the expression of these genes is related to any clinicopathological variables, we constructed a tissue microarray with 510 testicular tissue cores from 279 patients diagnosed with TGCT, covering various histological subgroups and clinical stages. By immunohistochemistry, we found that JUP, GRB7, CCND2 proteins were rarely present in normal testis, but frequently expressed at high levels in TGCT. Additionally, all premalignant intratubular germ cell neoplasias were JUP-immunopositive. MGMT and FHIT were expressed by normal testicular tissues, but at significantly lower frequencies in TGCT. Except for CCND2, the expressions of all markers were significantly associated with various TGCT subtypes. In summary, we have developed a high-throughput tool for the evaluation of TGCT markers, utilized this to validate five candidate genes whose protein expressions were indeed deregulated in TGCT.

  14. Gene expression profiling and phenotype analyses of S. cerevisiae in response to changing copper reveals six genes with new roles in copper and iron metabolism.

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    van Bakel, Harm; Strengman, Eric; Wijmenga, Cisca; Holstege, Frank C P

    2005-08-11

    Exhaustive microarray time course analyses of Saccharomyces cerevisiae during copper starvation and copper excess reveal new aspects of metal-induced gene regulation. Aside from identifying targets of established copper- and iron-responsive transcription factors, we find that genes encoding mitochondrial proteins are downregulated and that copper-independent iron transport genes are preferentially upregulated, both during prolonged copper deprivation. The experiments also suggest the presence of a small regulatory iron pool that links copper and iron responses. One hundred twenty-eight genes with putative roles in metal metabolism were further investigated by several systematic phenotype screens. Of the novel phenotypes uncovered, hsp12-Delta and arn1-Delta display increased sensitivity to copper, cyc1-Delta and crr1-Delta show resistance to high copper, vma13-Delta exhibits increased sensitivity to iron deprivation, and pep12-Delta results in reduced growth in high copper and low iron. Besides revealing new components of eukaryotic metal trafficking pathways, the results underscore the previously determined intimate links between iron and copper metabolism and mitochondrial and vacuolar function in metal trafficking. The analyses further suggest that copper starvation can specifically lead to downregulation of respiratory function to preserve iron and copper for other cellular processes.

  15. Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli.

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    Yanlong Wang

    Full Text Available We previously screened the novel gene Ds-26-16 from a 4 M salt-stressed Dunaliella salina cDNA library and discovered that this gene conferred salt tolerance to broad-spectrum organisms, including E. coli (Escherichia coli, Haematococcus pluvialis and tobacco. To determine the mechanism of this gene conferring salt tolerance, we studied the proteome of E. coli overexpressing the full-length cDNA of Ds-26-16 using the iTRAQ (isobaric tags for relative and absolute quantification approach. A total of 1,610 proteins were identified, which comprised 39.4% of the whole proteome. Of the 559 differential proteins, 259 were up-regulated and 300 were down-regulated. GO (gene ontology and KEGG (Kyoto encyclopedia of genes and genomes enrichment analyses identified 202 major proteins, including those involved in amino acid and organic acid metabolism, energy metabolism, carbon metabolism, ROS (reactive oxygen species scavenging, membrane proteins and ABC (ATP binding cassette transporters, and peptidoglycan synthesis, as well as 5 up-regulated transcription factors. Our iTRAQ data suggest that Ds-26-16 up-regulates the transcription factors in E. coli to enhance salt resistance through osmotic balance, energy metabolism, and oxidative stress protection. Changes in the proteome were also observed in E. coli overexpressing the ORF (open reading frame of Ds-26-16. Furthermore, pH, nitric oxide and glycerol content analyses indicated that Ds-26-16 overexpression increases nitric oxide content but has no effect on glycerol content, thus confirming that enhanced nitric oxide synthesis via lower intercellular pH was one of the mechanisms by which Ds-26-16 confers salt tolerance to E. coli.

  16. Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm.

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    Alexandra Saudemont

    Full Text Available Echinoderms, which are phylogenetically related to vertebrates and produce large numbers of transparent embryos that can be experimentally manipulated, offer many advantages for the analysis of the gene regulatory networks (GRN regulating germ layer formation. During development of the sea urchin embryo, the ectoderm is the source of signals that pattern all three germ layers along the dorsal-ventral axis. How this signaling center controls patterning and morphogenesis of the embryo is not understood. Here, we report a large-scale analysis of the GRN deployed in response to the activity of this signaling center in the embryos of the Mediterranean sea urchin Paracentrotus lividus, in which studies with high spatial resolution are possible. By using a combination of in situ hybridization screening, overexpression of mRNA, recombinant ligand treatments, and morpholino-based loss-of-function studies, we identified a cohort of transcription factors and signaling molecules expressed in the ventral ectoderm, dorsal ectoderm, and interposed neurogenic ("ciliary band" region in response to the known key signaling molecules Nodal and BMP2/4 and defined the epistatic relationships between the most important genes. The resultant GRN showed a number of striking features. First, Nodal was found to be essential for the expression of all ventral and dorsal marker genes, and BMP2/4 for all dorsal genes. Second, goosecoid was identified as a central player in a regulatory sub-circuit controlling mouth formation, while tbx2/3 emerged as a critical factor for differentiation of the dorsal ectoderm. Finally, and unexpectedly, a neurogenic ectoderm regulatory circuit characterized by expression of "ciliary band" genes was triggered in the absence of TGF beta signaling. We propose a novel model for ectoderm regionalization, in which neural ectoderm is the default fate in the absence of TGF beta signaling, and suggest that the stomodeal and neural subcircuits that we

  17. Resonance circuits for adiabatic circuits

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    C. Schlachta

    2003-01-01

    Full Text Available One of the possible techniques to reduces the power consumption in digital CMOS circuits is to slow down the charge transport. This slowdown can be achieved by introducing an inductor in the charging path. Additionally, the inductor can act as an energy storage element, conserving the energy that is normally dissipated during discharging. Together with the parasitic capacitances from the circuit a LCresonant circuit is formed.

  18. Genetic diversity and population structure of black Dahe pig based on DNA sequences analyses of mitochondrial and nuclear genes.

    Science.gov (United States)

    Tang, Lizhou; Yu, Long; Wang, Junjie; Liu, Chao; Shi, Xiaodong; Ding, Wei; Zhu, Lei; Guo, Songchang

    2016-01-01

    To investigate the genetic diversity and population structure of black Dahe pigs, we collected 175 samples from 5 local populations and sequenced them using a combination of two selected molecular markers for mitochondrial cytochrome b and Major Histocompatibility Complex (MHC) DRB. Overall, the results of AMOVA and phylogenetic tree and gene flow analyses detected high levels of gene flow among the five populations, particularly individual pigs from Dahe town (Pop1) or Yingshang town (Pop2) to other populations (Pop3, Pop4, and Pop5). The genetic diversity analyses showed that the diversity indices of the five populations did not vary significantly, but they were much lower than those of other Chinese pig species. These results suggest that distinct gene flow, unstable population pattern, and lower genetic diversity have been influenced mainly by human introductions for economic ends. These findings provide genetic information that could be used for the preservation and further genetic improvement of the black Dahe pig, as well as an important reference for the evaluation, conservation, and utilization of the genetic resources of this breed.

  19. Nucleotide and phylogenetic analyses of the Chlamydia trachomatis ompA gene indicates it is a hotspot for mutation

    Directory of Open Access Journals (Sweden)

    Brunelle Brian W

    2012-01-01

    Full Text Available Abstract Background Serovars of the human pathogen Chlamydia trachomatis occupy one of three specific tissue niches. Genomic analyses indicate that the serovars have a phylogeny congruent with their pathobiology and have an average substitution rate of less than one nucleotide per kilobase. In contrast, the gene that determines serovar specificity, ompA, has a phylogenetic association that is not congruent with tissue tropism and has a degree of nucleotide variability much higher than other genomic loci. The ompA gene encodes the major surface-exposed antigenic determinant, and the observed nucleotide diversity at the ompA locus is thought to be due to recombination and host immune selection pressure. The possible contribution of a localized increase in mutation rate, however, has not been investigated. Results Nucleotide diversity and phylogenetic relationships of the five constant and four variable domains of the ompA gene, as well as several loci surrounding ompA, were examined for each serovar. The loci flanking the ompA gene demonstrated that nucleotide diversity increased monotonically as ompA is approached and that their gene trees are not congruent with either ompA or tissue tropism. The variable domains of the ompA gene had a very high level of non-synonymous change, which is expected as these regions encode the surface-exposed epitopes and are under positive selection. However, the synonymous changes are clustered in the variable regions compared to the constant domains; if hitchhiking were to account for the increase in synonymous changes, these substitutions should be more evenly distributed across the gene. Recombination also cannot entirely account for this increase as the phylogenetic relationships of the constant and variable domains are congruent with each other. Conclusions The high number of synonymous substitutions observed within the variable domains of ompA appears to be due to an increased mutation rate within this region

  20. Molecular analyses of MADS-box genes trace back to Gymnosperms the invention of fleshy fruits.

    Science.gov (United States)

    Lovisetto, Alessandro; Guzzo, Flavia; Tadiello, Alice; Toffali, Ketti; Favretto, Alessandro; Casadoro, Giorgio

    2012-01-01

    Botanical fruits derive from ovaries and their most important function is to favor seed dispersal. Fleshy fruits do so by attracting frugivorous animals that disperse seeds together with their own excrements (endozoochory). Gymnosperms make seeds but have no ovaries to be transformed into fruits. Many species surround their seeds with fleshy structures and use endozoochory to disperse them. Such structures are functionally fruits and can derive from different anatomical parts. Ginkgo biloba and Taxus baccata fruit-like structures differ in their anatomical origin since the outer seed integument becomes fleshy in Ginkgo, whereas in Taxus, the fleshy aril is formed de novo. The ripening characteristics are different, with Ginkgo more rudimentary and Taxus more similar to angiosperm fruits. MADS-box genes are known to be necessary for the formation of flowers and fruits in Angiosperms but also for making both male and female reproductive structures in Gymnosperms. Here, a series of different MADS-box genes have been shown for the first time to be involved also in the formation of gymnosperm fruit-like structures. Apparently, the same gene types have been recruited in phylogenetically distant species to make fleshy structures that also have different anatomical origins. This finding indicates that the main molecular networks operating in the development of fleshy fruits have independently appeared in distantly related Gymnosperm taxa. Hence, the appearance of the seed habit and the accompanying necessity of seed dispersal has led to the invention of the fruit habit that thus seems to have appeared independently of the presence of flowers.

  1. Genome-wide diet-gene interaction analyses for risk of colorectal cancer.

    Science.gov (United States)

    Figueiredo, Jane C; Hsu, Li; Hutter, Carolyn M; Lin, Yi; Campbell, Peter T; Baron, John A; Berndt, Sonja I; Jiao, Shuo; Casey, Graham; Fortini, Barbara; Chan, Andrew T; Cotterchio, Michelle; Lemire, Mathieu; Gallinger, Steven; Harrison, Tabitha A; Le Marchand, Loic; Newcomb, Polly A; Slattery, Martha L; Caan, Bette J; Carlson, Christopher S; Zanke, Brent W; Rosse, Stephanie A; Brenner, Hermann; Giovannucci, Edward L; Wu, Kana; Chang-Claude, Jenny; Chanock, Stephen J; Curtis, Keith R; Duggan, David; Gong, Jian; Haile, Robert W; Hayes, Richard B; Hoffmeister, Michael; Hopper, John L; Jenkins, Mark A; Kolonel, Laurence N; Qu, Conghui; Rudolph, Anja; Schoen, Robert E; Schumacher, Fredrick R; Seminara, Daniela; Stelling, Deanna L; Thibodeau, Stephen N; Thornquist, Mark; Warnick, Greg S; Henderson, Brian E; Ulrich, Cornelia M; Gauderman, W James; Potter, John D; White, Emily; Peters, Ulrike

    2014-04-01

    Dietary factors, including meat, fruits, vegetables and fiber, are associated with colorectal cancer; however, there is limited information as to whether these dietary factors interact with genetic variants to modify risk of colorectal cancer. We tested interactions between these dietary factors and approximately 2.7 million genetic variants for colorectal cancer risk among 9,287 cases and 9,117 controls from ten studies. We used logistic regression to investigate multiplicative gene-diet interactions, as well as our recently developed Cocktail method that involves a screening step based on marginal associations and gene-diet correlations and a testing step for multiplicative interactions, while correcting for multiple testing using weighted hypothesis testing. Per quartile increment in the intake of red and processed meat were associated with statistically significant increased risks of colorectal cancer and vegetable, fruit and fiber intake with lower risks. From the case-control analysis, we detected a significant interaction between rs4143094 (10p14/near GATA3) and processed meat consumption (OR = 1.17; p = 8.7E-09), which was consistently observed across studies (p heterogeneity = 0.78). The risk of colorectal cancer associated with processed meat was increased among individuals with the rs4143094-TG and -TT genotypes (OR = 1.20 and OR = 1.39, respectively) and null among those with the GG genotype (OR = 1.03). Our results identify a novel gene-diet interaction with processed meat for colorectal cancer, highlighting that diet may modify the effect of genetic variants on disease risk, which may have important implications for prevention.

  2. Gene Sequence Analyses of the Healthy Oral Microbiome in Humans and Companion Animals.

    Science.gov (United States)

    Davis, Eric M

    2016-06-01

    It has long been accepted that certain oral bacterial species are responsible for the development of periodontal disease. However, the focus of microbial and immunological research is shifting from studying the organisms associated with disease to examining the indigenous microbial inhabitants that are present in health. Microbiome refers to the aggregate genetic material of all microorganisms living in, or on, a defined habitat. Recent developments in gene sequence analysis have enabled detection and identification of bacteria from polymicrobial samples, including subgingival plaque. Diversity surveys utilizing this technology have demonstrated that bacterial culture techniques have vastly underestimated the richness and diversity of microorganisms in vivo, since only certain bacteria grow in vitro. Surveys using gene sequence analysis have demonstrated that the healthy oral microbiome is composed of an unexpectedly high number of diverse species, including putative pathogens. These findings support the view that coevolution microorganisms and macroscopic hosts has occurred in which certain microorganisms have adapted to survive in the oral cavity and host immune tolerance has allowed the establishment of a symbiotic relationship in which both parties receive benefits (mutualism). This review describes gene sequence analysis as an increasingly common, culture-independent tool for detecting bacteria in vivo and describes the results of recent oral microbiome diversity surveys of clinically healthy humans, dogs, and cats. Six bacterial phyla consistently dominated the healthy oral microbiome of all 3 host species. Previous hypotheses on etiology of periodontitis are reviewed in light of new scientific findings. Finally, the consideration that clinically relevant periodontal disease occurs when immune tolerance of the symbiotic oral microbiome is altered to a proinflammatory response will be discussed.

  3. Gene expression and functional analyses in brassinosteroid-mediated stress tolerance.

    Science.gov (United States)

    Divi, Uday K; Rahman, Tawhidur; Krishna, Priti

    2016-01-01

    The plant hormone brassinosteroid (BR) plays essential roles in plant growth and development, while also controlling plant stress responses. This dual ability of BR is intriguing from a mechanistic point of view and as a viable solution for stabilizing crop yields under the changing climatic conditions. Here we report a time course analysis of BR responses under both stress and no-stress conditions, the results of which establish that BR incorporates many stress-related features even under no-stress conditions, which are then accompanied by a dynamic stress response under unfavourable conditions. Found within the BR transcriptome were distinct molecular signatures of two stress hormones, abscisic acid and jasmonic acid, which were correlated with enhanced endogenous levels of the two hormones in BR-treated seedlings. The marked presence of genes related to protein metabolism and modification, defence responses and calcium signalling highlights the significance of their associated mechanisms and roles in BR processes. Functional analysis of loss-of-function mutants of a subset of genes selected from the BR transcriptome identified abiotic stress-related roles for ACID PHOSPHATASE5 (ACP5), WRKY33, JACALIN-RELATED LECTIN1-3 (JAC-LEC1-3) and a BR-RESPONSIVE-RECEPTOR-LIKE KINASE (BRRLK). Overall, the results of this study provide a clear link between the molecular changes impacted by BR and its ability to confer broad-range stress tolerance, emphasize the importance of post-translational modification and protein turnover as BR regulatory mechanisms and demonstrate the BR transcriptome as a repertoire of new stress-related regulatory and structural genes.

  4. Genome-wide diet-gene interaction analyses for risk of colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Jane C Figueiredo

    2014-04-01

    Full Text Available Dietary factors, including meat, fruits, vegetables and fiber, are associated with colorectal cancer; however, there is limited information as to whether these dietary factors interact with genetic variants to modify risk of colorectal cancer. We tested interactions between these dietary factors and approximately 2.7 million genetic variants for colorectal cancer risk among 9,287 cases and 9,117 controls from ten studies. We used logistic regression to investigate multiplicative gene-diet interactions, as well as our recently developed Cocktail method that involves a screening step based on marginal associations and gene-diet correlations and a testing step for multiplicative interactions, while correcting for multiple testing using weighted hypothesis testing. Per quartile increment in the intake of red and processed meat were associated with statistically significant increased risks of colorectal cancer and vegetable, fruit and fiber intake with lower risks. From the case-control analysis, we detected a significant interaction between rs4143094 (10p14/near GATA3 and processed meat consumption (OR = 1.17; p = 8.7E-09, which was consistently observed across studies (p heterogeneity = 0.78. The risk of colorectal cancer associated with processed meat was increased among individuals with the rs4143094-TG and -TT genotypes (OR = 1.20 and OR = 1.39, respectively and null among those with the GG genotype (OR = 1.03. Our results identify a novel gene-diet interaction with processed meat for colorectal cancer, highlighting that diet may modify the effect of genetic variants on disease risk, which may have important implications for prevention.

  5. Control of Vibrio fischeri lux gene transcription by a cyclic AMP receptor protein-luxR protein regulatory circuit.

    OpenAIRE

    1988-01-01

    Expression of the Vibrio fischeri luminescence genes (lux genes) requires two transcriptional activators: the V. fischeri luxR gene product with autoinducer and the cyclic AMP (cAMP) receptor protein (CRP) with cAMP. It has been established that autoinducer and the luxR gene product are required for transcriptional activation of the luxICDABE operon, which contains a gene required for autoinducer synthesis and genes required for light emission. However, the role of cAMP-CRP in the induction o...

  6. Integrating genetic, transcriptional, and functional analyses to identify 5 novel genes for atrial fibrillation

    DEFF Research Database (Denmark)

    Sinner, Moritz F; Tucker, Nathan R; Lunetta, Kathryn L;

    2014-01-01

    BACKGROUND: Atrial fibrillation (AF) affects >30 million individuals worldwide and is associated with an increased risk of stroke, heart failure, and death. AF is highly heritable, yet the genetic basis for the arrhythmia remains incompletely understood. METHODS AND RESULTS: To identify new AF......-related genes, we used a multifaceted approach, combining large-scale genotyping in 2 ethnically distinct populations, cis-eQTL (expression quantitative trait loci) mapping, and functional validation. Four novel loci were identified in individuals of European descent near the genes NEURL (rs12415501; relative...... risk [RR]=1.18; 95% confidence interval [CI], 1.13-1.23; P=6.5×10(-16)), GJA1 (rs13216675; RR=1.10; 95% CI, 1.06-1.14; P=2.2×10(-8)), TBX5 (rs10507248; RR=1.12; 95% CI, 1.08-1.16; P=5.7×10(-11)), and CAND2 (rs4642101; RR=1.10; 95% CI, 1.06-1.14; P=9.8×10(-9)). In Japanese, novel loci were identified...

  7. Transcriptome Analyses Reveal Candidate Genes Potentially Involved in Al Stress Response in Alfalfa

    Science.gov (United States)

    Liu, Wenxian; Xiong, Conghui; Yan, Longfeng; Zhang, Zhengshe; Ma, Lichao; Wang, Yanrong; Liu, Yajie; Liu, Zhipeng

    2017-01-01

    Alfalfa is the most extensively cultivated forage legume, yet most alfalfa cultivars are not aluminum tolerant, and the molecular mechanisms underlying alfalfa responses to Al stress are largely unknown. In this study, we aimed to understand how alfalfa responds to Al stress by identifying and analyzing Al-stress-responsive genes in alfalfa roots at the whole-genome scale. The transcriptome changes in alfalfa roots under Al stress for 4, 8, or 24 h were analyzed using Illumina high-throughput sequencing platforms. A total of 2464 differentially expressed genes (DEGs) were identified, and most were up-regulated at early (4 h) and/or late (24 h) Al exposure time points rather than at the middle exposure time point (8 h). Metabolic pathway enrichment analysis demonstrated that the DEGs involved in ribosome, protein biosynthesis, and process, the citrate cycle, membrane transport, and hormonal regulation were preferentially enriched and regulated. Biosynthesis inhibition and signal transduction downstream of auxin- and ethylene-mediated signals occur during alfalfa responses to root growth inhibition. The internal Al detoxification mechanisms play important roles in alfalfa roots under Al stress. These findings provide valuable information for identifying and characterizing important components in the Al signaling network in alfalfa and enhance understanding of the molecular mechanisms underlying alfalfa responses to Al stress. PMID:28217130

  8. Phylogenomic analyses reveal the diversity of laccase-coding genes in Fonsecaea genomes

    Science.gov (United States)

    Feng, Peiying; Weiss, Vinicius Almir; Vicente, Vania Aparecida; Stielow, J. Benjamin; de Hoog, Sybren

    2017-01-01

    The genus Fonsecaea comprises black yeast-like fungi of clinical relevance, including etiologic agents of chromoblastomycosis and cerebral phaeohyphomycosis. Presence of melanin and assimilation of monoaromatic hydrocarbons and alkylbenzenes have been proposed as virulence factors. Multicopper oxidase (MCO) is a family of enzymes including laccases, ferroxidases and ascorbate oxidases which are able to catalyze the oxidation of various aromatic organic compounds with the reduction of molecular oxygen to water. Additionally, laccases are required for the production of fungal melanins, a cell-wall black pigment recognized as a key polymer for pathogenicity and extremotolerance in black yeast-like fungi. Although the activity of laccase enzymes has previously been reported in many wood-rotting fungi, the diversity of laccase genes in Fonsecaea has not yet been assessed. In this study, we identified and characterized laccase-coding genes and determined their genomic location in five clinical and environmental Fonsecaea species. The identification of laccases sensu stricto will provide insights into carbon acquisition strategies as well as melanin production in Fonsecaea. PMID:28187150

  9. Candidate gene analyses of 3-dimensional dentoalveolar phenotypes in subjects with malocclusion

    Science.gov (United States)

    Weaver, Cole A.; Miller, Steven F.; da Fontoura, Clarissa S. G.; Wehby, George L.; Amendt, Brad A.; Holton, Nathan E.; Allareddy, Veeratrishul; Southard, Thomas E.; Moreno Uribe, Lina M.

    2017-01-01

    Introduction Genetic studies of malocclusion etiology have identified 4 deleterious mutations in genes, DUSP6, ARHGAP21, FGF23, and ADAMTS1 in familial Class III cases. Although these variants may have large impacts on Class III phenotypic expression, their low frequency (subjects were digitized with 48 landmarks. The 3-dimensional coordinate data were submitted to a geometric morphometric approach along with principal component analysis to generate continuous phenotypes including symmetric and asymmetric components of dentoalveolar shape variation, fluctuating asymmetry, and size. The subjects were genotyped for 222 single-nucleotide polymorphisms in 82 genes/loci, and phenotpye-genotype associations were tested via multivariate linear regression. Results Principal component analysis of symmetric variation identified 4 components that explained 68% of the total variance and depicted anteroposterior, vertical, and transverse dentoalveolar discrepancies. Suggestive associations (P right discrepancies resulting in midline deviations, unilateral crossbites, and ectopic eruptions. Suggestive associations were found with TBX1 AJUBA, SNAI3 SATB2, TP63, and 1p22.1. Fluctuating asymmetry was associated with BMP3 and LATS1. Associations for SATB2 and BMP3 with asymmetric variations remained significant after the Bonferroni correction (P <0.00022). Suggestive associations were found for centroid size, a proxy for dentoalveolar size variation with 4p16.1 and SNAI1. Conclusions Specific genetic pathways associated with 3-dimensional dentoalveolar phenotypic variation in malocclusions were identified. PMID:28257739

  10. Genetic and functional analyses identify DISC1 as a novel callosal agenesis candidate gene.

    Science.gov (United States)

    Osbun, Nathan; Li, Jiang; O'Driscoll, Mary C; Strominger, Zoe; Wakahiro, Mari; Rider, Eric; Bukshpun, Polina; Boland, Elena; Spurrell, Cailyn H; Schackwitz, Wendy; Pennacchio, Len A; Dobyns, William B; Black, Graeme C M; Sherr, Elliott H

    2011-08-01

    Agenesis of the corpus callosum (AgCC) is a congenital brain malformation that occurs in approximately 1:1,000-1:6,000 births. Several syndromes associated with AgCC have been traced to single gene mutations; however, the majority of AgCC causes remain unidentified. We investigated a mother and two children who all shared complete AgCC and a chromosomal deletion at 1q42. We fine mapped this deletion and show that it includes Disrupted-in-Schizophrenia 1 (DISC1), a gene implicated in schizophrenia and other psychiatric disorders. Furthermore, we report a de novo chromosomal deletion at 1q42.13 to q44, which includes DISC1, in another individual with AgCC. We resequenced DISC1 in a cohort of 144 well-characterized AgCC individuals and identified 20 sequence changes, of which 4 are rare potentially pathogenic variants. Two of these variants were undetected in 768 control chromosomes. One of these is a splice site mutation at the 5' boundary of exon 11 that dramatically reduces full-length mRNA expression of DISC1, but not of shorter forms. We investigated the developmental expression of mouse DISC1 and find that it is highly expressed in the embryonic corpus callosum at a critical time for callosal formation. Taken together our results suggest a significant role for DISC1 in corpus callosum development.

  11. Association and interaction analyses of eight genes under asthma linkage peaks

    DEFF Research Database (Denmark)

    Ferreira, M A R; Zhao, Z Z; Thomsen, S F;

    2009-01-01

    BACKGROUND: Linkage studies have implicated the 2q33, 9p21, 11q13 and 20q13 regions in the regulation of allergic disease. The aim of this study was to test genetic variants in candidate genes from these regions for association with specific asthma traits. METHODS: Ninety-five single nucleotide...... polymorphisms (SNP) located in eight genes (CD28, CTLA4, ICOS, ADAM23, ADAMTSL1, MS4A2, CDH26 and HRH3) were genotyped in >5000 individuals from Australian (n = 1162), Dutch (n = 99) and Danish (n = 303) families. Traits tested included doctor-diagnosed asthma, atopy, airway obstruction, total serum...... after accounting for the number of tests performed. CONCLUSIONS: The individual variants genotyped in the 2q33, 9p21 and 20q13 regions do not explain a large fraction of the variation in the quantitative traits tested or have a major impact on asthma or atopy risk. Our results are consistent with a weak...

  12. Cyanophage diversity, inferred from g20 gene analyses, in the largest natural lake in France, Lake Bourget.

    Science.gov (United States)

    Dorigo, Ursula; Jacquet, Stéphan; Humbert, Jean-François

    2004-02-01

    The genetic diversity of the natural freshwater community of cyanophages and its variations over time have been investigated for the first time in the surface waters of the largest natural lake in France. This was done by random screening of clone libraries for the g20 gene and by denaturing gradient gel electrophoresis (DGGE). Nucleotide sequence analysis revealed 35 distinct cyanomyovirus g20 genotypes among the 47 sequences analyzed. Phylogenetic analyses showed that these sequences fell into seven genetically distinct operational taxonomic units (OTUs). The distances between these OTUs were comparable to those reported between marine clusters. Moreover, some of these freshwater cyanophage sequences were genetically more closely related to marine cyanophage sequences than to other freshwater sequences. Both approaches for the g20 gene (sequencing and DGGE analysis) showed that there was a clear seasonal pattern of variation in the composition of the cyanophage community that could reflect changes in its biological, chemical, and/or physical environment.

  13. Comparative analyses of light-induced anthocyanin accumulation and gene expression between the ray florets and leaves in chrysanthemum.

    Science.gov (United States)

    Hong, Yan; Yang, Li-Wen; Li, Meng-Ling; Dai, Si-Lan

    2016-06-01

    Light is one of the key environmental factors that affect anthocyanin biosynthesis. However, the underlying molecular mechanism remains unclear, and many problems regarding phenotypic change and corresponding gene regulation have not been solved. In the present study, comparative analyses of light-induced anthocyanin accumulation and gene expression between the ray florets and leaves were performed in Chrysanthemum × morifolium 'Purple Reagan'. After contrasting the variations in the flower color phenotype and relative pigment content, as well as expression patterns of structural and regulator genes responsible for anthocyanin biosynthesis and photoreceptor between different plant organs under light and dark conditions, we concluded that (1) both the capitulum and foliage are key organs responding to light for chrysanthemum coloration; (2) compared with flavones, shading makes a greater decrease on the anthocyanins accumulation; (3) most of the structural and regulatory genes in the light-induced anthocyanin pathway specifically express in the ray florets; and (4) CmCHS, CmF3H, CmF3'H, CmANS, CmDFR, Cm3GT, CmMYB5-1, CmMYB6, CmMYB7-1, CmbHLH24, CmCOP1 and CmHY5 are key genes for light-induced anthocyanin biosynthesis in chrysanthemum ray florets, while on the transcriptional level, the expressions of CmPHYA, CmPHYB, CmCRY1a, CmCRY1b and CmCRY2 are insignificantly changed. Moreover, the inferred comprehensive effect of multiple signals on the accumulation of anthocyanins and transmission channel of light signal that exist between the leaves and ray florets were further discussed. These results further our understanding of the relationship between the gene expression and light-induced anthocyanin biosynthesis, and lay foundations for the promotion of the molecular breeding of novel flower colors in chrysanthemums.

  14. Genome-wide gene expression profile analyses identify CTTN as a potential prognostic marker in esophageal cancer.

    Directory of Open Access Journals (Sweden)

    Pei Lu

    Full Text Available AIM: Esophageal squamous cell carcinoma (ESCC is one of the most common fatal malignances of the digestive tract. Its prognosis is poor mainly due to the lack of reliable markers for early detection and prognostic prediction. Here we aim to identify the molecules involved in ESCC carcinogenesis and those as potential markers for prognosis and as new molecular therapeutic targets. METHODS: We performed genome-wide gene expression profile analyses of 10 primary ESCCs and their adjacent normal tissues by cDNA microarrays representing 47,000 transcripts and variants. Candidate genes were then validated by semi quantitative reverse transcription-PCR (RT-PCR, tissue microarrays (TMAs and immunohistochemistry (IHC staining. RESULTS: Using an arbitrary cutoff line of signal log ratio of ≥1.5 or ≤-1.5, we observed 549 up-regulated genes and 766 down-regulated genes in ESCCs compared with normal esophageal tissues. The functions of 302 differentially expressed genes were associated with cell metabolism, cell adhesion and immune response. Several candidate deregulated genes including four overexpressed (CTTN, DMRT2, MCM10 and SCYA26 and two underexpressed (HMGCS2 and SORBS2 were subsequently verified, which can be served as biomarkers for ESCC. Moreover, overexpression of cortactin (CTTN was observed in 126/198 (63.6% of ESCC cases and was significantly associated with lymph node metastasis (P = 0.000, pathologic stage (P = 0.000 and poor survival (P<0.001 of ESCC patients. Furthermore, a significant correlation between CTTN overexpression and shorter disease-specific survival rate was found in different subgroups of ESCC patient stratified by the pathologic stage (P<0.05. CONCLUSION: Our data provide valuable information for establishing molecules as candidates for prognostic and/or as therapeutic targets.

  15. Functional analyses of Src-like adaptor (SLA), a glucocorticoid-regulated gene in acute lymphoblastic leukemia.

    Science.gov (United States)

    Mansha, Muhammad; Carlet, Michela; Ploner, Christian; Gruber, Georg; Wasim, Muhammad; Wiegers, Gerrit Jan; Rainer, Johannes; Geley, Stephan; Kofler, Reinhard

    2010-04-01

    Glucocorticoids (GCs) cause apoptosis and cell cycle arrest in lymphoid cells and are used in the therapy of lymphoid malignancies. SLA (Src-like-adaptor), an inhibitor of T- and B-cell receptor signaling, is a promising candidate derived from expression profiling analyses in children with acute lymphoblastic leukemia (ALL). Over-expression and knock-down experiments in ALL in vitro model revealed that transgenic SLA alone had no effect on survival or cell cycle progression, nor did it affect sensitivity to, or kinetics of, GC-induced apoptosis. Although SLA is a prominent GC response gene, it does not seem to contribute to the anti-leukemic effects of GC.

  16. Analyses of RNA Polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang.

    Science.gov (United States)

    Dacks, Joel B; Marinets, Alexandra; Ford Doolittle, W; Cavalier-Smith, Thomas; Logsdon, John M

    2002-06-01

    The phylogenetic relationships among major eukaryotic protist lineages are largely uncertain. Two significant obstacles in reconstructing eukaryotic phylogeny are long-branch attraction (LBA) effects and poor taxon sampling of free-living protists. We have obtained and analyzed gene sequences encoding the largest subunit of RNA Polymerase II (RPB1) from Naegleria gruberi (a heterolobosean), Cercomonas ATCC 50319 (a cercozoan), and Ochromonas danica (a heterokont); we have also analyzed the RPB1 gene from the nucleomorph (nm) genome of Guillardia theta (a cryptomonad). Using a variety of phylogenetic methods our analysis shows that RPB1s from Giardia intestinalis and Trichomonas vaginalis are probably subject to intense LBA effects. Thus, the deep branching of these taxa on RPB1 trees is questionable and should not be interpreted as evidence favoring their early divergence. Similar effects are discernable, to a lesser extent, with the Mastigamoeba invertens RPB1 sequence. Upon removal of the outgroup and these problematic sequences, analyses of the remaining RPB1s indicate some resolution among major eukaryotic groups. The most robustly supported higher-level clades are the opisthokonts (animals plus fungi) and the red algae plus the cryptomonad nm-the latter result gives added support to the red algal origin of cryptomonad chloroplasts. Clades comprising Dictyostelium discoideum plus Acanthamoeba castellanii (Amoebozoa) and Ochromonas plus Plasmodium falciparum (chromalveolates) are consistently observed and moderately supported. The clades supported by our RPB1 analyses are congruent with other data, suggesting that bona fide phylogenetic relationships are being resolved. Thus, the RPB1 gene has apparently retained some phylogenetically meaningful signal, making it worthwhile to obtain sequences from more diverse protist taxa. Additional RPB1 data, especially in combination with other genes, should provide further resolution of branching orders among protist

  17. Association analyses suggest GPR24 as a shared susceptibility gene for bipolar affective disorder and schizophrenia

    DEFF Research Database (Denmark)

    Severinsen, J E; Als, T D; Binderup, H

    2006-01-01

    Linkage analyses suggest that chromosome 22q12-13 may harbor a shared susceptibility locus for bipolar affective disorder (BPD) and schizophrenia (SZ). In a study of a sample from the Faeroe Islands we have previously reported association between both disorders and microsatellite markers in a 3.6 c...... overall P-values of 0.0009, 0.0054, and 0.0023 were found for haplotypes in BPD, SZ, and combined cases, respectively, and in the Scottish sample overall P-values of 0.0003, 0.0005, and 0.016 were observed for similar groupings. Specific haplotypes showed associations with lowest P-values of 7 x 10...

  18. Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes

    Directory of Open Access Journals (Sweden)

    Zhou Xuguo

    2009-10-01

    Full Text Available Abstract Background Termite lignocellulose digestion is achieved through a collaboration of host plus prokaryotic and eukaryotic symbionts. In the present work, we took a combined host and symbiont metatranscriptomic approach for investigating the digestive contributions of host and symbiont in the lower termite Reticulitermes flavipes. Our approach consisted of parallel high-throughput sequencing from (i a host gut cDNA library and (ii a hindgut symbiont cDNA library. Subsequently, we undertook functional analyses of newly identified phenoloxidases with potential importance as pretreatment enzymes in industrial lignocellulose processing. Results Over 10,000 expressed sequence tags (ESTs were sequenced from the 2 libraries that aligned into 6,555 putative transcripts, including 171 putative lignocellulase genes. Sequence analyses provided insights in two areas. First, a non-overlapping complement of host and symbiont (prokaryotic plus protist glycohydrolase gene families known to participate in cellulose, hemicellulose, alpha carbohydrate, and chitin degradation were identified. Of these, cellulases are contributed by host plus symbiont genomes, whereas hemicellulases are contributed exclusively by symbiont genomes. Second, a diverse complement of previously unknown genes that encode proteins with homology to lignase, antioxidant, and detoxification enzymes were identified exclusively from the host library (laccase, catalase, peroxidase, superoxide dismutase, carboxylesterase, cytochrome P450. Subsequently, functional analyses of phenoloxidase activity provided results that were strongly consistent with patterns of laccase gene expression. In particular, phenoloxidase activity and laccase gene expression are mostly restricted to symbiont-free foregut plus salivary gland tissues, and phenoloxidase activity is inducible by lignin feeding. Conclusion To our knowledge, this is the first time that a dual host-symbiont transcriptome sequencing effort

  19. Glucokinase gene mutations: structural and genotype-phenotype analyses in MODY children from South Italy.

    Directory of Open Access Journals (Sweden)

    Nadia Tinto

    Full Text Available BACKGROUND: Maturity onset diabetes of the young type 2 (or GCK MODY is a genetic form of diabetes mellitus provoked by mutations in the glucokinase gene (GCK. METHODOLOGY/PRINCIPAL FINDINGS: We screened the GCK gene by direct sequencing in 30 patients from South Italy with suspected MODY. The mutation-induced structural alterations in the protein were analyzed by molecular modeling. The patients' biochemical, clinical and anamnestic data were obtained. Mutations were detected in 16/30 patients (53%; 9 of the 12 mutations identified were novel (p.Glu70Asp, p.Phe123Leu, p.Asp132Asn, p.His137Asp, p.Gly162Asp, p.Thr168Ala, p.Arg392Ser, p.Glu290X, p.Gln106_Met107delinsLeu and are in regions involved in structural rearrangements required for catalysis. The prevalence of mutation sites was higher in the small domain (7/12: approximately 59% than in the large (4/12: 33% domain or in the connection (1/12: 8% region of the protein. Mild diabetic phenotypes were detected in almost all patients [mean (SD OGTT = 7.8 mMol/L (1.8] and mean triglyceride levels were lower in mutated than in unmutated GCK patients (p = 0.04. CONCLUSIONS: The prevalence of GCK MODY is high in southern Italy, and the GCK small domain is a hot spot for MODY mutations. Both the severity of the GCK mutation and the genetic background seem to play a relevant role in the GCK MODY phenotype. Indeed, a partial genotype-phenotype correlation was identified in related patients (3 pairs of siblings but not in two unrelated children bearing the same mutation. Thus, the molecular approach allows the physician to confirm the diagnosis and to predict severity of the mutation.

  20. Paternal uniparental disomy 14 and related disorders: placental gene expression analyses and histological examinations.

    Science.gov (United States)

    Kagami, Masayo; Matsuoka, Kentaro; Nagai, Toshiro; Yamanaka, Michiko; Kurosawa, Kenji; Suzumori, Nobuhiro; Sekita, Yoichi; Miyado, Mami; Matsubara, Keiko; Fuke, Tomoko; Kato, Fumiko; Fukami, Maki; Ogata, Tsutomu

    2012-10-01

    Although recent studies in patients with paternal uniparental disomy 14 [upd(14)pat] and other conditions affecting the chromosome 14q32.2 imprinted region have successfully identified underlying epigenetic factors involved in the development of upd(14)pat phenotype, several matters, including regulatory mechanism(s) for RTL1 expression, imprinting status of DIO3 and placental histological characteristics, remain to be elucidated. We therefore performed molecular studies using fresh placental samples from two patients with upd(14)pat. We observed that RTL1 expression level was about five times higher in the placental samples of the two patients than in control placental samples, whereas DIO3 expression level was similar between the placental samples of the two patients and the control placental samples. We next performed histological studies using the above fresh placental samples and formalin-fixed and paraffin-embedded placental samples obtained from a patient with a maternally derived microdeletion involving DLK1, the-IG-DMR, the MEG3-DMR and MEG3. Terminal villi were associated with swollen vascular endothelial cells and hypertrophic pericytes, together with narrowed capillary lumens. DLK1, RTL1 and DIO3 proteins were specifically identified in vascular endothelial cells and pericytes, and the degree of protein staining was well correlated with the expression dosage of corresponding genes. These results suggest that RTL1as-encoded microRNA functions as a repressor of RTL1 expression, and argue against DIO3 being a paternally expressed gene. Furthermore, it is inferred that DLK1, DIO3 and, specially, RTL1 proteins, play a pivotal role in the development of vascular endothelial cells and pericytes.

  1. The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction

    Directory of Open Access Journals (Sweden)

    Hocquette Jean-Francois

    2012-08-01

    validated in the groups of 30 Charolais young bulls slaughtered in year 2, and in the 21 Charolais steers slaughtered in year 1, but not in the group of 19 steers slaughtered in year 2 which differ from the reference group by two factors (gender and year. When the first three groups of animals were analysed together, this subset of genes explained a 4-fold higher proportion of the variability in tenderness than muscle biochemical traits. Conclusion This study underlined the relevance of the GENOTEND chip to identify markers of beef quality, mainly by confirming previous results and by detecting other genes of the heat shock family as potential markers of beef quality. However, it was not always possible to extrapolate the relevance of these markers to all animal groups which differ by several factors (such as gender or environmental conditions of production from the initial population of reference in which these markers were identified.

  2. GATING CIRCUITS

    Science.gov (United States)

    Merrill, L.C.

    1958-10-14

    Control circuits for vacuum tubes are described, and a binary counter having an improved trigger circuit is reported. The salient feature of the binary counter is the application of the input signal to the cathode of each of two vacuum tubes through separate capacitors and the connection of each cathode to ground through separate diodes. The control of the binary counter is achieved in this manner without special pulse shaping of the input signal. A further advantage of the circuit is the simplicity and minimum nuruber of components required, making its use particularly desirable in computer machines.

  3. Metagenomic analyses reveal no differences in genes involved in cellulose degradation under different tillage treatments.

    Science.gov (United States)

    de Vries, Maria; Schöler, Anne; Ertl, Julia; Xu, Zhuofei; Schloter, Michael

    2015-07-01

    Incorporation of plant litter is a frequent agricultural practice to increase nutrient availability in soil, and relies heavily on the activity of cellulose-degrading microorganisms. Here we address the question of how different tillage treatments affect soil microbial communities and their cellulose-degrading potential in a long-term agricultural experiment. To identify potential differences in microbial taxonomy and functionality, we generated six soil metagenomes of conventional (CT) and reduced (RT) tillage-treated topsoil samples, which differed in their potential extracellular cellulolytic activity as well as their microbial biomass. Taxonomic analysis of metagenomic data revealed few differences between RT and CT, and a dominance of Proteobacteria and Actinobacteria, whereas eukaryotic phyla were not prevalent. Prediction of cellulolytic enzymes revealed glycoside hydrolase families 1, 3 and 94, auxiliary activity family 8 and carbohydrate-binding module 2 as the most abundant in soil. These were annotated mainly to the phyla of Proteobacteria, Actinobacteria and Bacteroidetes. These results suggest that the observed higher cellulolytic activity in RT soils can be explained by a higher microbial biomass or changed expression levels but not by shifts in the soil microbiome. Overall, this study reveals the stability of soil microbial communities and cellulolytic gene composition under the investigated tillage treatments.

  4. Fusion gene and splice variant analyses in liquid biopsies of lung cancer patients

    Science.gov (United States)

    Giménez-Capitán, Ana; Karachaliou, Niki; Pérez-Rosado, Ana; Viteri, Santiago; Morales-Espinosa, Daniela; Rosell, Rafael

    2016-01-01

    Obtaining a biopsy of solid tumors requires invasive procedures that strongly limit patient compliance. In contrast, a blood extraction is safe, can be performed at many time points during the course disease and encourages appropriate therapy modifications, potentially improving the patient’s clinical outcome and quality of life. Fusion of the tyrosine kinase genes anaplastic lymphoma kinase (ALK), C-ROS oncogen 1 (ROS 1), rearranged during transfection (RET) and neurotrophic tyrosine kinase 1 (NTRK1) occur in 1–5% of lung adenocarcinomas and constitute therapeutic targets for tyrosine kinase inhibitors. In addition, a MET splicing variant of exon 14, has been reported in 2–4% of lung adenocarcinoma and recent studies suggests that targeted therapies inhibiting MET signaling would be beneficial for patients with this alteration. In this review, we will summarize the new techniques recently developed to detect ALK, RET, ROS and NTRK1 fusions and MET exon 14 splicing variant in liquid biopsy using plasma, serum, circulating tumor cells (CTCs), platelets and exosomes as starting material. PMID:27826534

  5. Converging Findings from Linkage and Association Analyses on Susceptibility Genes for Smoking and Other Addictions

    Science.gov (United States)

    Yang, Jackie (Jiekun); Li, Ming D.

    2016-01-01

    Experimental approaches to genetic studies of complex traits evolve with technological advances. How do discoveries using different approaches advance our knowledge of the genetic architecture underlying complex diseases/traits? Do most of the findings of newer techniques, such as genome-wide association study (GWAS), provide more information than older ones, e.g., genome-wide linkage study? In this review, we address these issues by developing a nicotine dependence (ND) genetic susceptibility map based on the results obtained by the approaches commonly used in recent years, namely, genome-wide linkage, candidate gene association, GWAS, and targeted sequencing. Converging and diverging results from these empirical approaches have elucidated a preliminary genetic architecture of this intractable psychiatric disorder and yielded new hypotheses on ND aetiology. The insights we obtained by putting together results from diverse approaches can be applied to other complex diseases/traits. In sum, developing a genetic susceptibility map and keeping it updated are effective ways to keep track of what we know about a disease/trait and what the next steps might be with new approaches. PMID:27166759

  6. The glutathione peroxidase gene family of Lotus japonicus: characterization of genomic clones, expression analyses and immunolocalization in legumes.

    Science.gov (United States)

    Ramos, Javier; Matamoros, Manuel A; Naya, Loreto; James, Euan K; Rouhier, Nicolas; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

    2009-01-01

    Despite the multiple roles played by antioxidants in rhizobia-legume symbioses, little is known about glutathione peroxidases (GPXs) in legumes. Here the characterization of six GPX genes of Lotus japonicus is reported. Expression of GPX genes was analysed by quantitative reverse transcription-polymerase chain reaction in L. japonicus and Lotus corniculatus plants exposed to various treatments known to generate reactive oxygen and/or nitrogen species. LjGPX1 and LjGPX3 were the most abundantly expressed genes in leaves, roots and nodules. Compared with roots, LjGPX1 and LjGPX6 were highly expressed in leaves and LjGPX3 and LjGPX6 in nodules. In roots, salinity decreased GPX4 expression, aluminium decreased expression of the six genes, and cadmium caused up-regulation of GPX3, GPX4 and GPX5 after 1 h and down-regulation of GPX1, GPX2, GPX4 and GPX6 after 3-24 h. Exposure of roots to sodium nitroprusside (a nitric oxide donor) for 1 h increased the mRNA levels of GPX4 and GPX6 by 3.3- and 30-fold, respectively. Thereafter, the GPX6 mRNA level remained consistently higher than that of the control. Immunogold labelling revealed the presence of GPX proteins in root and nodule amyloplasts and in leaf chloroplasts of L. japonicus and other legumes. Labelling was associated with starch grains. These results underscore the differential regulation of GPX expression in response to cadmium, aluminium and nitric oxide, and strongly support a role for GPX6 and possibly other GPX genes in stress and/or metabolic signalling.

  7. Genome-wide linkage, exome sequencing and functional analyses identify ABCB6 as the pathogenic gene of dyschromatosis universalis hereditaria.

    Directory of Open Access Journals (Sweden)

    Hong Liu

    Full Text Available BACKGROUND: As a genetic disorder of abnormal pigmentation, the molecular basis of dyschromatosis universalis hereditaria (DUH had remained unclear until recently when ABCB6 was reported as a causative gene of DUH. METHODOLOGY: We performed genome-wide linkage scan using Illumina Human 660W-Quad BeadChip and exome sequencing analyses using Agilent SureSelect Human All Exon Kits in a multiplex Chinese DUH family to identify the pathogenic mutations and verified the candidate mutations using Sanger sequencing. Quantitative RT-PCR and Immunohistochemistry was performed to verify the expression of the pathogenic gene, Zebrafish was also used to confirm the functional role of ABCB6 in melanocytes and pigmentation. RESULTS: Genome-wide linkage (assuming autosomal dominant inheritance mode and exome sequencing analyses identified ABCB6 as the disease candidate gene by discovering a coding mutation (c.1358C>T; p.Ala453Val that co-segregates with the disease phenotype. Further mutation analysis of ABCB6 in four other DUH families and two sporadic cases by Sanger sequencing confirmed the mutation (c.1358C>T; p.Ala453Val and discovered a second, co-segregating coding mutation (c.964A>C; p.Ser322Lys in one of the four families. Both mutations were heterozygous in DUH patients and not present in the 1000 Genome Project and dbSNP database as well as 1,516 unrelated Chinese healthy controls. Expression analysis in human skin and mutagenesis interrogation in zebrafish confirmed the functional role of ABCB6 in melanocytes and pigmentation. Given the involvement of ABCB6 mutations in coloboma, we performed ophthalmological examination of the DUH carriers of ABCB6 mutations and found ocular abnormalities in them. CONCLUSION: Our study has advanced our understanding of DUH pathogenesis and revealed the shared pathological mechanism between pigmentary DUH and ocular coloboma.

  8. Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

    Directory of Open Access Journals (Sweden)

    Frederick H. Sheldon

    2013-03-01

    Full Text Available Insertion/deletion (indel mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP and a simple maximum likelihood (ML framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.

  9. Longitudinal Claudin Gene Expression Analyses in Canine Mammary Tissues and Thereof Derived Primary Cultures and Cell Lines

    Science.gov (United States)

    Hammer, Susanne C.; Becker, Annegret; Rateitschak, Katja; Mohr, Annika; Lüder Ripoli, Florenza; Hennecke, Silvia; Junginger, Johannes; Hewicker-Trautwein, Marion; Brenig, Bertram; Ngezahayo, Anaclet; Nolte, Ingo; Murua Escobar, Hugo

    2016-01-01

    Human and canine mammary tumours show partial claudin expression deregulations. Further, claudins have been used for directed therapeutic approaches. However, the development of claudin targeting approaches requires stable claudin expressing cell lines. This study reports the establishment and characterisation of canine mammary tissue derived cell lines, analysing longitudinally the claudin-1, -3, -4 and -7 expressions in original tissue samples, primary cultures and developed cell lines. Primary cultures were derived from 17 canine mammary tissues: healthy, lobular hyperplasia, simple adenoma, complex adenoma, simple tubular carcinoma, complex carcinoma, carcinoma arising in a benign mixed tumour and benign mixed tissue. Cultivation was performed, if possible, until passage 30. Claudin mRNA and protein expressions were analysed by PCR, QuantiGene Plex Assay, immunocytochemistry and immunofluorescence. Further, cytokeratin expression was analysed immunocytochemically. Cultivation resulted in 11 established cell lines, eight showing epithelial character. In five of the early passages the claudin expressions decreased compared to the original tissues. In general, claudin expressions were diminished during cultivation. Three cell lines kept longitudinally claudin, as well as epithelial marker expressions, representing valuable tools for the development of claudin targeted anti-tumour therapies. PMID:27690019

  10. Cloning and functional analyses of a gene from sugar beet up-regulated upon cyst nematode infection.

    Science.gov (United States)

    Samuelian, Suren; Kleine, Michael; Ruyter-Spira, Carolien P; Klein-Lankhorst, René M; Jung, Christian

    2004-01-01

    The cDNA-AFLP technique was used to isolate sugar beet genes up-regulated upon infection with the beet cyst nematode Heterodera schachtii. Hairy root cultures were obtained from resistant plants carrying a Beta procumbens translocation as well as from a non-resistant control. mRNA was isolated from hairy root clones and sugar beet plants infected or not with the beet cyst nematode and 8000 transcript-derived fragments (TDFs) were analysed. One TDF was found to be differentially expressed in both materials and was further investigated. Real-time PCR confirmed that this TDF is specifically up-regulated in resistant sugar beet upon nematode infection and its full-length cDNA was isolated. Sequence analysis suggests that the gene encodes a 317 amino acid polypeptide of unknown function. No homology to any sequence present in the public databases could be detected. To further elucidate its function in resistance to the beet cyst nematode, the cDNA was transformed into hairy roots of susceptible sugar beet under the control of the 35S promoter and hairy root clones were inoculated with nematodes. The number of developing females was significantly reduced in 12 out of 15 clones resulting from independent transgenic events suggesting that the gene can be used for inducing cyst nematode resistance in plants.

  11. Genome-Wide Association and Transcriptome Analyses Reveal Candidate Genes Underlying Yield-determining Traits in Brassica napus

    Science.gov (United States)

    Lu, Kun; Peng, Liu; Zhang, Chao; Lu, Junhua; Yang, Bo; Xiao, Zhongchun; Liang, Ying; Xu, Xingfu; Qu, Cunmin; Zhang, Kai; Liu, Liezhao; Zhu, Qinlong; Fu, Minglian; Yuan, Xiaoyan; Li, Jiana

    2017-01-01

    Yield is one of the most important yet complex crop traits. To improve our understanding of the genetic basis of yield establishment, and to identify candidate genes responsible for yield improvement in Brassica napus, we performed genome-wide association studies (GWAS) for seven yield-determining traits [main inflorescence pod number (MIPN), branch pod number (BPN), pod number per plant (PNP), seed number per pod (SPP), thousand seed weight, main inflorescence yield (MIY), and branch yield], using data from 520 diverse B. napus accessions from two different yield environments. In total, we detected 128 significant single nucleotide polymorphisms (SNPs), 93 of which were revealed as novel by integrative analysis. A combination of GWAS and transcriptome sequencing on 21 haplotype blocks from samples pooled by four extremely high-yielding or low-yielding accessions revealed the differential expression of 14 crucial candiate genes (such as Bna.MYB83, Bna.SPL5, and Bna.ROP3) associated with multiple traits or containing multiple SNPs associated with the same trait. Functional annotation and expression pattern analyses further demonstrated that these 14 candiate genes might be important in developmental processes and biomass accumulation, thus affecting the yield establishment of B. napus. These results provide valuable information for understanding the genetic mechanisms underlying the establishment of high yield in B. napus, and lay the foundation for developing high-yielding B. napus varieties. PMID:28261256

  12. Genetic and molecular analyses of UV radiation-induced mutations in the fem-3 gene of Caenorhabditis elegans

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, P.S.; De Wilde, D.; Dwarakanath, V.N. [Texas Christian Univ., Fort Worth, TX (United States). Dept. of Biology

    1995-06-01

    The utility of a new target gene (fem-3) is described for investigating the molecular nature of mutagenesis in the nematode Caenorhabditis elegans. As a principal attribute, this system allows for the selection, maintenance and molecular analysis of any type of mutation that disrupts the gene, including deletions. In this study, 86 mutant strains were isolated, of which 79 proved to have mutations in fem-3. Twenty of these originally tested as homozygous inviable. Homozygous inviability was expected, as Stewart and coworkers had previously observed that, unlike in other organisms, most UV radiation-induced mutations in C. elegans are chromosomal rearrangements of deficiencies (Mutat. Res 249, 37-54, 1991). However, additional data, including Southern blot analyses on 49 of the strains, indicated that most of the UV radiation-induced fem-3 mutations were not deficiencies, as originally inferred from their homozygous inviability. Instead, the lethals were most likely ``coincident mutations`` in linked, essential genes that were concomitantly induced. As such, they were lost owing to genetic recombination during stock maintenance. As in mammalian cells, yeast and bacteria, the frequency of coincident mutations was much higher than would be predicted by chance. (Author).

  13. Deep sequencing and in silico analyses identify MYB-regulated gene networks and signaling pathways in pancreatic cancer.

    Science.gov (United States)

    Azim, Shafquat; Zubair, Haseeb; Srivastava, Sanjeev K; Bhardwaj, Arun; Zubair, Asif; Ahmad, Aamir; Singh, Seema; Khushman, Moh'd; Singh, Ajay P

    2016-06-29

    We have recently demonstrated that the transcription factor MYB can modulate several cancer-associated phenotypes in pancreatic cancer. In order to understand the molecular basis of these MYB-associated changes, we conducted deep-sequencing of transcriptome of MYB-overexpressing and -silenced pancreatic cancer cells, followed by in silico pathway analysis. We identified significant modulation of 774 genes upon MYB-silencing (p networks by in silico analysis. Further analyses placed genes in our RNA sequencing-generated dataset to several canonical signalling pathways, such as cell-cycle control, DNA-damage and -repair responses, p53 and HIF1α. Importantly, we observed downregulation of the pancreatic adenocarcinoma signaling pathway in MYB-silenced pancreatic cancer cells exhibiting suppression of EGFR and NF-κB. Decreased expression of EGFR and RELA was validated by both qPCR and immunoblotting and they were both shown to be under direct transcriptional control of MYB. These observations were further confirmed in a converse approach wherein MYB was overexpressed ectopically in a MYB-null pancreatic cancer cell line. Our findings thus suggest that MYB potentially regulates growth and genomic stability of pancreatic cancer cells via targeting complex gene networks and signaling pathways. Further in-depth functional studies are warranted to fully understand MYB signaling in pancreatic cancer.

  14. Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

    Directory of Open Access Journals (Sweden)

    Hyun-Seob Song

    2015-03-01

    Full Text Available Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.

  15. Advanced circuit simulation using Multisim workbench

    CERN Document Server

    Báez-López, David; Cervantes-Villagómez, Ofelia Delfina

    2012-01-01

    Multisim is now the de facto standard for circuit simulation. It is a SPICE-based circuit simulator which combines analog, discrete-time, and mixed-mode circuits. In addition, it is the only simulator which incorporates microcontroller simulation in the same environment. It also includes a tool for printed circuit board design.Advanced Circuit Simulation Using Multisim Workbench is a companion book to Circuit Analysis Using Multisim, published by Morgan & Claypool in 2011. This new book covers advanced analyses and the creation of models and subcircuits. It also includes coverage of transmissi

  16. SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data

    Directory of Open Access Journals (Sweden)

    Burmester Gerd-R

    2009-03-01

    repository and a high quality tool for primary analysis of GeneChips. It exploits the MAS5.0/GCOS pairwise comparison algorithm, enables restricted access and user specific sharing. It does not aim for a complete representation of all public arrays but for high quality analysis with stepwise integration of reference signatures for detailed meta-analyses. Development of additional tools like functional annotation networks based on expression information will be future steps towards a systematic biological analysis of expression profiles.

  17. An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa

    Science.gov (United States)

    Battogtokh, D.; Asch, D. K.; Case, M. E.; Arnold, J.; Schüttler, H.-B.

    2002-01-01

    A chemical reaction network for the regulation of the quinic acid (qa) gene cluster of Neurospora crassa is proposed. An efficient Monte Carlo method for walking through the parameter space of possible chemical reaction networks is developed to identify an ensemble of deterministic kinetics models with rate constants consistent with RNA and protein profiling data. This method was successful in identifying a model ensemble fitting available RNA profiling data on the qa gene cluster. PMID:12477937

  18. Interactions among Candidate Genes Selected by Meta-Analyses Resulting in Higher Risk of Ischemic Stroke in a Chinese Population.

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    Man Luo

    Full Text Available Ischemic stroke (IS is a multifactorial disorder caused by both genetic and environmental factors. The combined effects of multiple susceptibility genes might result in a higher risk for IS than a single gene. Therefore, we investigated whether interactions among multiple susceptibility genes were associated with an increased risk of IS by evaluating gene polymorphisms identified in previous meta-analyses, including methylenetetrahydrofolate reductase (MTHFR C677T, beta fibrinogen (FGB, β-FG A455G and T148C, apolipoprotein E (APOE ε2-4, angiotensin-converting enzyme (ACE insertion/deletion (I/D, and endothelial nitric oxide synthase (eNOS G894T. In order to examine these interactions, 712 patients with IS and 774 controls in a Chinese Han population were genotyped using the SNaPshot method, and multifactor dimensionality reduction analysis was used to detect potential interactions among the candidate genes. The results of this study found that ACE I/D and β-FG T148C were significant synergistic contributors to IS. In particular, the ACE DD + β-FG 148CC, ACE DD + β-FG 148CT, and ACE ID + β-FG 148CC genotype combinations resulted in higher risk of IS. After adjusting for potential confounding IS risk factors (age, gender, family history of IS, hypertension history and history of diabetes mellitus using a logistic analysis, a significant correlation between the genotype combinations and IS patients persisted (overall stroke: adjusted odds ratio [OR] = 1.57, 95% confidence interval [CI]: 1.22-2.02, P < 0.001, large artery atherosclerosis subtype: adjusted OR = 1.50, 95% CI: 1.08-2.07, P = 0.016, small-artery occlusion subtype: adjusted OR = 2.04, 95% CI: 1.43-2.91, P < 0.001. The results of this study indicate that the ACE I/D and β-FG T148C combination may result in significantly higher risk of IS in this Chinese population.

  19. Identifying Virulence-Associated Genes Using Transcriptomic and Proteomic Association Analyses of the Plant Parasitic Nematode Bursaphelenchus mucronatus

    Science.gov (United States)

    Zhou, Lifeng; Chen, Fengmao; Pan, Hongyang; Ye, Jianren; Dong, Xuejiao; Li, Chunyan; Lin, Fengling

    2016-01-01

    Bursaphelenchus mucronatus (B. mucronatus) isolates that originate from different regions may vary in their virulence, but their virulence-associated genes and proteins are poorly understood. Thus, we conducted an integrated study coupling RNA-Seq and isobaric tags for relative and absolute quantitation (iTRAQ) to analyse transcriptomic and proteomic data of highly and weakly virulent B. mucronatus isolates during the pathogenic processes. Approximately 40,000 annotated unigenes and 5000 proteins were gained from the isolates. When we matched all of the proteins with their detected transcripts, a low correlation coefficient of r = 0.138 was found, indicating probable post-transcriptional gene regulation involved in the pathogenic processes. A functional analysis showed that five differentially expressed proteins which were all highly expressed in the highly virulent isolate were involved in the pathogenic processes of nematodes. Peroxiredoxin, fatty acid- and retinol-binding protein, and glutathione peroxidase relate to resistance against plant defence responses, while β-1,4-endoglucanase and expansin are associated with the breakdown of plant cell walls. Thus, the pathogenesis of B. mucronatus depends on its successful survival in host plants. Our work adds to the understanding of B. mucronatus’ pathogenesis, and will aid in controlling B. mucronatus and other pinewood nematode species complexes in the future. PMID:27618012

  20. Gene expression analyses of the spatio-temporal relationships of human medulloblastoma subgroups during early human neurogenesis.

    Directory of Open Access Journals (Sweden)

    Cornelia M Hooper

    Full Text Available Medulloblastoma is the most common form of malignant paediatric brain tumour and is the leading cause of childhood cancer related mortality. The four molecular subgroups of medulloblastoma that have been identified - WNT, SHH, Group 3 and Group 4 - have molecular and topographical characteristics suggestive of different cells of origin. Definitive identification of the cell(s of origin of the medulloblastoma subgroups, particularly the poorer prognosis Group 3 and Group 4 medulloblastoma, is critical to understand the pathogenesis of the disease, and ultimately for the development of more effective treatment options. To address this issue, the gene expression profiles of normal human neural tissues and cell types representing a broad neuro-developmental continuum, were compared to those of two independent cohorts of primary human medulloblastoma specimens. Clustering, co-expression network, and gene expression analyses revealed that WNT and SHH medulloblastoma may be derived from distinct neural stem cell populations during early embryonic development, while the transcriptional profiles of Group 3 and Group 4 medulloblastoma resemble cerebellar granule neuron precursors at weeks 10-15 and 20-30 of embryogenesis, respectively. Our data indicate that Group 3 medulloblastoma may arise through abnormal neuronal differentiation, whereas deregulation of synaptic pruning-associated apoptosis may be driving Group 4 tumorigenesis. Overall, these data provide significant new insight into the spatio-temporal relationships and molecular pathogenesis of the human medulloblastoma subgroups, and provide an important framework for the development of more refined model systems, and ultimately improved therapeutic strategies.

  1. Identifying Virulence-Associated Genes Using Transcriptomic and Proteomic Association Analyses of the Plant Parasitic Nematode Bursaphelenchus mucronatus

    Directory of Open Access Journals (Sweden)

    Lifeng Zhou

    2016-09-01

    Full Text Available Bursaphelenchus mucronatus (B. mucronatus isolates that originate from different regions may vary in their virulence, but their virulence-associated genes and proteins are poorly understood. Thus, we conducted an integrated study coupling RNA-Seq and isobaric tags for relative and absolute quantitation (iTRAQ to analyse transcriptomic and proteomic data of highly and weakly virulent B. mucronatus isolates during the pathogenic processes. Approximately 40,000 annotated unigenes and 5000 proteins were gained from the isolates. When we matched all of the proteins with their detected transcripts, a low correlation coefficient of r = 0.138 was found, indicating probable post-transcriptional gene regulation involved in the pathogenic processes. A functional analysis showed that five differentially expressed proteins which were all highly expressed in the highly virulent isolate were involved in the pathogenic processes of nematodes. Peroxiredoxin, fatty acid- and retinol-binding protein, and glutathione peroxidase relate to resistance against plant defence responses, while β-1,4-endoglucanase and expansin are associated with the breakdown of plant cell walls. Thus, the pathogenesis of B. mucronatus depends on its successful survival in host plants. Our work adds to the understanding of B. mucronatus’ pathogenesis, and will aid in controlling B. mucronatus and other pinewood nematode species complexes in the future.

  2. How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards.

    Science.gov (United States)

    Streicher, Jeffrey W; Schulte, James A; Wiens, John J

    2016-01-01

    Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g., anoles, basilisks, iguanas, and spiny lizards) but relationships among families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1179 to approximately 2.4 million characters per matrix and approximately 30% to 60% total missing data. We then compared mean branch support for interfamilial relationships under these 15 different sampling strategies for both concatenated (maximum likelihood) and species tree (NJst) approaches (after showing that mean branch support appears to be related to accuracy). We found that both approaches had the highest support when including loci with up to 50% missing taxa (matrices with ~40-55% missing data overall). Thus, our results show that simply excluding all missing data may be highly problematic as the primary guiding principle for the inclusion or exclusion of taxa and genes. The optimal strategy was somewhat different for each approach, a pattern that has not been shown previously. For concatenated analyses, branch support was maximized when including many taxa (44) but fewer characters (1.1 million). For species-tree analyses, branch support was maximized with minimal taxon sampling (16) but many loci (4789 of 4921). We also show that the choice of these sampling

  3. Controllable circuit

    DEFF Research Database (Denmark)

    2010-01-01

    A switch-mode power circuit comprises a controllable element and a control unit. The controllable element is configured to control a current in response to a control signal supplied to the controllable element. The control unit is connected to the controllable element and provides the control...

  4. Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia

    Indian Academy of Sciences (India)

    K H Richau; R L Kudahettige; P Pujic; N P Kudahettige; A Sellstedt

    2013-11-01

    The actinorhizal bacterium Frankia expresses nitrogenase and can therefore convert molecular nitrogen into ammonia and the by-product hydrogen. However, nitrogenase is inhibited by oxygen. Consequently, Frankia and its actinorhizal hosts have developed various mechanisms for excluding oxygen from their nitrogen-containing compartments. These include the expression of oxygen-scavenging uptake hydrogenases, the formation of hopanoid-rich vesicles, enclosed by multi-layered hopanoid structures, the lignification of hyphal cell walls, and the production of haemoglobins in the symbiotic nodule. In this work, we analysed the expression and structure of the so-called uptake hydrogenase (Hup), which catalyses the in vivo dissociation of hydrogen to recycle the energy locked up in this ‘waste’ product. Two uptake hydrogenase syntons have been identified in Frankia: synton 1 is expressed under free-living conditions while synton 2 is expressed during symbiosis. We used qPCR to determine synton 1 hup gene expression in two Frankia strains under aerobic and anaerobic conditions. We also predicted the 3D structures of the Hup protein subunits based on multiple sequence alignments and remote homology modelling. Finally, we performed BLAST searches of genome and protein databases to identify genes that may contribute to the protection of nitrogenase against oxygen in the two Frankia strains. Our results show that in Frankia strain ACN14a, the expression patterns of the large (HupL1) and small (HupS1) uptake hydrogenase subunits depend on the abundance of oxygen in the external environment. Structural models of the membrane-bound hydrogenase subunits of ACN14a showed that both subunits resemble the structures of known [NiFe] hydrogenases (Volbeda et al. 1995), but contain fewer cysteine residues than the uptake hydrogenase of the Frankia DC12 and Eu1c strains. Moreover, we show that all of the investigated Frankia strains have two squalene hopane cyclase genes (shc1 and shc2

  5. Identification of Soybean Genes Involved in Circadian Clock Mechanism and Photoperiodic Control of Flowering Time by In Silico Analyses Flowering Time by In Silico Analyses

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Glycine max is a photoperiodic short-day plant and the practical consequence of the response is latitude and sowing period limitations to commercial crops.Genetic and physiological studies using the model plants Arabidopsis thaliana and rice (Oryza sativa)have uncovered several genes and genetic pathways controlling the process,however information about the corresponding pathways in legumes is scarce.Data mining prediction methodologies,Including multiple sequence alignment,phylogenetic analysis,bioinformatics expression and sequence motif pattern identification were used to identify soybean genes involved In day length perception and photoperiodic flowering induction.We have investigated approximately 330 000 sequences from open-access databases and have identified all bona fide central oscillator genes and circadian photoreceptors from A.thaliana in soybean sequence databases.We propose e working model for the photoperiodic control of flowering time in G.max,based on the identified key components.These results demonstrate the power of comparative genomics between model systems and crop species to elucidate the several aspects of plant physiology and metabolism.

  6. VDBP, CYP27B1, and 25-Hydroxyvitamin D Gene Polymorphism Analyses in a Group of Sicilian Multiple Sclerosis Patients.

    Science.gov (United States)

    Agnello, L; Scazzone, C; Lo Sasso, B; Bellia, C; Bivona, G; Realmuto, S; Brighina, F; Schillaci, R; Ragonese, P; Salemi, G; Ciaccio, Marcello

    2017-04-01

    Multiple sclerosis (MS) is a chronic demyelinating disease of central nervous system regarded as one of the most common causes of neurological disability in young adults. The exact etiology of MS is not yet known, although epidemiological data indicate that both genetic susceptibility and environmental exposure are involved. A poor vitamin D status has been proposed as the most attractive environmental factor. Several evidence have highlighted the importance of mutations in vitamin D-regulating genes for vitamin D status. The purpose of our study was to assess the genetic variants of VDBP and CYP27B1 in MS patients and in a control group. A total of 192 subjects, including 100 MS patients and 92 healthy controls, were genotyped by polymerase chain reaction followed by restriction fragment length polymorphism analyses. Serum 25-hydroxyvitamin D levels were measured in MS patients and controls by high-performance liquid chromatography. We did not observe any statically significant difference in the distribution of genotypic VDBP variants between the study groups. 25(OH)D plasma levels were significantly higher in the control group versus MS patients; MS patients who carried Gc2 showed lower 25(OH)D plasma levels and those who carried Gc1f showed higher levels. We observed only wild-type allele for CYP27B1 mutations analyzed both in MS patients and in the control group. In conclusion, our findings do not support a role of an independent effect of the investigated vitamin D-related gene variants, VDBP and CYP27B1, in the risk of MS.

  7. Genetic analyses for deciphering the status and role of photoperiodic and maturity genes in major Indian soybean cultivars

    Indian Academy of Sciences (India)

    SANJAY GUPTA; VIRENDER SINGH BHATIA; GIRIRAJ KUMAWAT; DEVSHREE THAKUR; GOURAV SINGH; RACHANA TRIPATHI; GYANESH SATPUTE; RAMGOPAL DEVADAS; SAYED MASROOR HUSAIN; SURESH CHAND

    2017-03-01

    Allelic combinations of major photoperiodic (E1, E3, E4) and maturity (E2) genes have extended the adaptation of quantitative photoperiod sensitive soybean crop from its origin (China ∼35◦N latitude) to both north (up to ∼50◦N) and south (up to 40◦S) latitudes, but their allelic status and role in India (6–35◦N) are unknown. Loss of function and hypoactive alleles of these genes are known to confer photoinsensitivity to long days and early maturity. Early maturity has helped to adapt soybean to short growing season of India. We had earlier found that all the Indian cultivars are sensitive to incandescent long day (ILD) and could identify six insensitive accessions through screening 2071 accessions under ILD. Available models for ILD insensitivity suggested that identified insensitive genotypes should be either e3/e4 or e1 (e1-nl or e1-fs) with either e3 or e4. We foundthat one of the insensitive accessions (EC 390977) was of e3/e4 genotype and hybridized it with four ILD sensitive cultivars JS 335, JS 95-60, JS 93-05, NRC 37 and an accession EC 538828. Inheritance studies and marker-based cosegregation analyses confirmed the segregation of E3 and E4 genes and identified JS 93-05 and NRC 37 as E3E3E4E4 and EC 538828 ase3e3E4E4. Further, genotyping through sequencing, derived cleaved amplified polymorphic sequences (dCAPS) and cleaved amplified polymorphic sequences (CAPS) markers identified JS 95-60 with hypoactive e1-as and JS 335 with loss of function e3-fs alleles. Presence of photoperiodic recessive alleles in these two most popular Indian cultivars suggested for their role in conferring early flowering and maturity. This observation could be confirmed in F2 population derived from the cross JS 95-60 × EC 390977, where individuals with e1-as e1-as and e4e4 genotypes could flower 7 and 2.4 days earlier, respectively. Possibility of identification of new alleles or mechanism for ILD insensitivity and use of photoinsensitivity in Indian conditions

  8. Affective Circuits

    DEFF Research Database (Denmark)

    to the intersecting streams of goods, people, ideas, and money as they circulate between African migrants and their kin who remain back home. They also show the complex ways that emotions become entangled in these exchanges. Examining how these circuits operate in domains of social life ranging from child fosterage......Moving between Africa and Europe, the book explores the many ways migrants sustain and rework family ties and intimate relationships at home and abroad. It demonstrates how their quotidian efforts—on such a mass scale—contribute to a broader process of social regeneration. The contributors point...

  9. Parallel phylogenetic analyses using the N, G or Nv gene from a fixed group of VHSV isolates reveal the same overall genetic typing

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Ahrens, Peter; Lorenzen, Niels

    2005-01-01

    Different genetic regions representing the viral phospho-(P), nucleocapsid-(N) or glyco-protein (G) gene have been used for phylogenetic studies of viral haemorrhagic septicaemia virus (VHSV). Since these analyses were performed on different virus isolates using various genomic regions, it has been...

  10. Collective of mechatronics circuit

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1987-02-15

    This book is composed of three parts, which deals with mechatronics system about sensor, circuit and motor. The contents of the first part are photo sensor of collector for output, locating detection circuit with photo interrupts, photo sensor circuit with CdS cell and lamp, interface circuit with logic and LED and temperature sensor circuit. The second part deals with oscillation circuit with crystal, C-R oscillation circuit, F-V converter, timer circuit, stability power circuit, DC amp and DC-DC converter. The last part is comprised of bridge server circuit, deformation bridge server, controlling circuit of DC motor, controlling circuit with IC for PLL and driver circuit of stepping motor and driver circuit of Brushless.

  11. Multi-platform whole-genome microarray analyses refine the epigenetic signature of breast cancer metastasis with gene expression and copy number.

    Directory of Open Access Journals (Sweden)

    Joseph Andrews

    Full Text Available BACKGROUND: We have previously identified genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. These complex epigenetic changes that we observed, along with concurrent karyotype analyses, have led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy are superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes observed in breast cancer metastasis. METHODOLOGY/PRINCIPAL FINDINGS: We undertook simultaneous high-resolution, whole-genome analyses of MDA-MB-468GFP and MDA-MB-468GFP-LN human breast cancer cell lines (an isogenic, paired lymphatic metastasis cell line model using Affymetrix gene expression (U133, promoter (1.0R, and SNP/CNV (SNP 6.0 microarray platforms to correlate data from gene expression, epigenetic (DNA methylation, and combination copy number variant/single nucleotide polymorphism microarrays. Using Partek Software and Ingenuity Pathway Analysis we integrated datasets from these three platforms and detected multiple hypomethylation and hypermethylation events. Many of these epigenetic alterations correlated with gene expression changes. In addition, gene dosage events correlated with the karyotypic differences observed between the cell lines and were reflected in specific promoter methylation patterns. Gene subsets were identified that correlated hyper (and hypo methylation with the loss (or gain of gene expression and in parallel, with gene dosage losses and gains, respectively. Individual gene targets from these subsets were also validated for their methylation, expression and copy number status, and susceptible gene pathways were identified that may indicate how selective advantage drives the processes of tumourigenesis and metastasis. CONCLUSIONS/SIGNIFICANCE: Our approach allows more precisely profiling of functionally relevant epigenetic signatures that are associated with cancer

  12. Investigation of genes encoding calcineurin B-like protein family in legumes and their expression analyses in chickpea (Cicer arietinum L..

    Directory of Open Access Journals (Sweden)

    Mukesh Kumar Meena

    Full Text Available Calcium ion (Ca2+ is a ubiquitous second messenger that transmits various internal and external signals including stresses and, therefore, is important for plants' response process. Calcineurin B-like proteins (CBLs are one of the plant calcium sensors, which sense and convey the changes in cytosolic Ca2+-concentration for response process. A search in four leguminous plant (soybean, Medicago truncatula, common bean and chickpea genomes identified 9 to 15 genes in each species that encode CBL proteins. Sequence analyses of CBL peptides and coding sequences (CDS suggested that there are nine original CBL genes in these legumes and some of them were multiplied during whole genome or local gene duplication. Coding sequences of chickpea CBL genes (CaCBL were cloned from their cDNAs and sequenced, and their annotations in the genome assemblies were corrected accordingly. Analyses of protein sequences and gene structures of CBL family in plant kingdom indicated its diverse origin but showed a remarkable conservation in overall protein structure with appearance of complex gene structure in the course of evolution. Expression of CaCBL genes in different tissues and in response to different stress and hormone treatment were studied. Most of the CaCBL genes exhibited high expression in flowers. Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance. These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

  13. Identification of sexually dimorphic gene expression in brain tissue of the fish Leporinus macrocephalus through mRNA differential display and real time PCR analyses.

    Science.gov (United States)

    Alves-Costa, Fernanda A; Wasko, A P

    2010-03-01

    Differentially expressed genes in males and females of vertebrate species generally have been investigated in gonads and, to a lesser extent, in other tissues. Therefore, we attempted to identify sexually dimorphic gene expression in the brains of adult males and females of Leporinus macrocephalus, a gonochoristic fish species that presents a ZZ/ZW sex determination system, throughout a comparative analysis using differential display reverse transcriptase-PCR and real-time PCR. Four cDNA fragments were characterized, representing candidate genes with differential expression between the samples. Two of these fragments presented no significant identity with previously reported gene sequences. The other two fragments, isolated from male specimens, were associated to the gene that codes for the protein APBA2 (amyloid beta (A4) precursor protein-binding, family A, member 2) and to the Rab 37 gene, a member of the Ras oncogene family. The overexpression of these genes has been associated to a greater production of the beta-amyloid protein which, in turns, is the major factor that leads to Alzheimer's disease, and to the development of brain-tumors, respectively. Quantitative RT-PCR analyses revealed a higher Apba2 gene expression in males, thus validating the previous data on differential display. L. macrocephalus may represent an interesting animal model to the understanding of the function of several vertebrate genes, including those involved in neurodegenerative and cancer diseases.

  14. Rearrangement and junctional-site sequence analyses of T-cell receptor gamma genes in intestinal intraepithelial lymphocytes from murine athymic chimeras.

    Science.gov (United States)

    Whetsell, M; Mosley, R L; Whetsell, L; Schaefer, F V; Miller, K S; Klein, J R

    1991-12-01

    The molecular organization of rearranged T-cell receptor (TCR) gamma genes intraepithelial lymphocytes (IEL) was studied in athymic radiation chimeras and was compared with the organization of gamma gene rearrangements in IEL from thymus-bearing animals by polymerase chain reaction and by sequence analyses of DNA spanning the junction of the variable (V) and joining (J) genes. In both thymus-bearing mice and athymic chimeras, IEL V-J gamma-gene rearrangements occurred for V gamma 1.2, V gamma 2, and V gamma 5 but not for V gamma 3 or V gamma 4. Sequence analyses of cloned V-J polymerase chain reaction-amplified products indicated that in both thymus-bearing mice and athymic chimeras, rearrangement of V gamma 1.2 and V gamma 5 resulted in in-frame as well as out-of-frame genes, whereas nearly all V gamma 2 rearrangements were out of frame from either type of animal. V-segment nucleotide removal occurred in most V gamma 1.2, V gamma 2, and V gamma 5 rearrangements; J-segment nucleotide removal was common in V gamma 1.2 but not in V gamma 2 or V gamma 5 rearrangements. N-segment nucleotide insertions were present in V gamma 1.2, V gamma 2, and V gamma 5 IEL rearrangements in both thymus-bearing mice and athymic chimeras, resulting in a predominant in-frame sequence for V gamma 5 and a predominant out-of-frame sequence for V gamma 2 genes. These findings demonstrate that (i) TCR gamma-gene rearrangement occurs extrathymically in IEL, (ii) rearrangements of TCR gamma genes involve the same V gene regardless of thymus influence; and (iii) the thymus does not determine the degree to which functional or nonfunctional rearrangements occur in IEL.

  15. Commutation circuit for an HVDC circuit breaker

    Science.gov (United States)

    Premerlani, William J.

    1981-01-01

    A commutation circuit for a high voltage DC circuit breaker incorporates a resistor capacitor combination and a charging circuit connected to the main breaker, such that a commutating capacitor is discharged in opposition to the load current to force the current in an arc after breaker opening to zero to facilitate arc interruption. In a particular embodiment, a normally open commutating circuit is connected across the contacts of a main DC circuit breaker to absorb the inductive system energy trapped by breaker opening and to limit recovery voltages to a level tolerable by the commutating circuit components.

  16. Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses

    Directory of Open Access Journals (Sweden)

    Siddaramappa Shivakumara

    2011-11-01

    Full Text Available Abstract Background Pneumonia and myocarditis are the most commonly reported diseases due to Histophilus somni, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in H. somni using traditional methods. Analyses of the genome sequences of several Pasteurellaceae species have provided insights into their biology and evolution. In view of the economic and ecological importance of H. somni, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the Pasteurellaceae. Results The chromosome of strain 2336 (2,263,857 bp contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome, and percentage of sequence (number of genes that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the Pasteurellaceae, several H. somni genes that may encode proteins involved in virulence (e.g., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their

  17. Re-engineering an alphoid(tetO)-HAC-based vector to enable high-throughput analyses of gene function.

    Science.gov (United States)

    Kononenko, Artem V; Lee, Nicholas C O; Earnshaw, William C; Kouprina, Natalay; Larionov, Vladimir

    2013-05-01

    Human artificial chromosome (HAC)-based vectors represent an alternative technology for gene delivery and expression with a potential to overcome the problems caused by the use of viral-based vectors. The recently developed alphoid(tetO)-HAC has an advantage over other HAC vectors because it can be easily eliminated from cells by inactivation of the HAC kinetochore via binding of tTS chromatin modifiers to its centromeric tetO sequences. This provides unique control for phenotypes induced by genes loaded into the alphoid(tetO)-HAC. However, inactivation of the HAC kinetochore requires transfection of cells by a retrovirus vector, a step that is potentially mutagenic. Here, we describe an approach to re-engineering the alphoid(tetO)-HAC that allows verification of phenotypic changes attributed to expression of genes from the HAC without a transfection step. In the new HAC vector, a tTS-EYFP cassette is inserted into a gene-loading site along with a gene of interest. Expression of the tTS generates a self-regulating fluctuating heterochromatin on the alphoid(tetO)-HAC that induces fast silencing of the genes on the HAC without significant effects on HAC segregation. This silencing of the HAC-encoded genes can be readily recovered by adding doxycycline. The newly modified alphoid(tetO)-HAC-based system has multiple applications in gene function studies.

  18. Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana.

    Science.gov (United States)

    Hu, Wei; Hou, Xiaowan; Huang, Chao; Yan, Yan; Tie, Weiwei; Ding, Zehong; Wei, Yunxie; Liu, Juhua; Miao, Hongxia; Lu, Zhiwei; Li, Meiying; Xu, Biyu; Jin, Zhiqiang

    2015-08-20

    Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs) were clustered into four subfamilies. Conserved motif analysis showed that all banana AQPs contained the typical AQP-like or major intrinsic protein (MIP) domain. Gene structure analysis suggested the majority of MaAQPs had two to four introns with a highly specific number and length for each subfamily. Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening. Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress. Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars.

  19. Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana

    Directory of Open Access Journals (Sweden)

    Wei Hu

    2015-08-01

    Full Text Available Aquaporins (AQPs function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs were clustered into four subfamilies. Conserved motif analysis showed that all banana AQPs contained the typical AQP-like or major intrinsic protein (MIP domain. Gene structure analysis suggested the majority of MaAQPs had two to four introns with a highly specific number and length for each subfamily. Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening. Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress. Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars.

  20. Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution.

    Science.gov (United States)

    Sun, Yanxia; Moore, Michael J; Zhang, Shoujun; Soltis, Pamela S; Soltis, Douglas E; Zhao, Tingting; Meng, Aiping; Li, Xiaodong; Li, Jianqiang; Wang, Hengchang

    2016-03-01

    The grade of early-diverging eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging eudicots; IRs ranged from 24.3 to 36.4kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was

  1. Genetic variants and haplotype analyses of the ZBRK1/ZNF350 gene in high-risk non BRCA1/2 French Canadian breast and ovarian cancer families.

    Science.gov (United States)

    Desjardins, Sylvie; Belleau, Pascal; Labrie, Yvan; Ouellette, Geneviève; Bessette, Paul; Chiquette, Jocelyne; Laframboise, Rachel; Lépine, Jean; Lespérance, Bernard; Pichette, Roxane; Plante, Marie; Durocher, Francine

    2008-01-01

    Our current understanding of breast cancer susceptibility involves mutations in the 2 major genes BRCA1 and BRCA2, found in about 25% of high-risk families, as well as few other low penetrance genes such as ATM and CHEK2. Approximately two-thirds of the multiple cases families remain to be explained by mutations in still unknown genes. In a candidate gene approach to identify new genes potentially involved in breast cancer susceptibility, we analyzed genomic variants in the ZBRK1 gene, a co-repressor implicated in BRCA1-mediated repression of GADD45. Direct sequencing of ZBRK1 entire coding region in affected breast cancer individuals from 97 high-risk French Canadian breast/ovarian cancer families and 94 healthy controls led to the identification of 18 genomic variants. Haplotype analyses, using PHASE, COCAPHASE and HaploStats programs, put in evidence 3 specific haplotypes which could potentially modulate breast cancer risk, and among which 2 that are associated with a potential protective effect (p = 0.01135 and p = 0.00268), while another haplotype is over-represented in the case group (p = 0.00143). Further analyses of these haplotypes indicated that a strong component of the observed difference between both groups emerge from the first 5 variants (out of 12 used for haplotype determination). The present study also permitted to determine a set of tagging SNPs that could be useful for subsequent analyses in large scale association studies. Additional studies in large cohorts and other populations will however be needed to further evaluate if common and/or rare ZBRK1 sequence variants and haplotypes could be associated with a modest/intermediate breast cancer risk.

  2. Analog circuit design designing dynamic circuit response

    CERN Document Server

    Feucht, Dennis

    2010-01-01

    This second volume, Designing Dynamic Circuit Response builds upon the first volume Designing Amplifier Circuits by extending coverage to include reactances and their time- and frequency-related behavioral consequences.

  3. Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans

    Directory of Open Access Journals (Sweden)

    Cano Liliana M

    2010-11-01

    Full Text Available Abstract Background Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation. Results We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome. We defined the "plastic secretome" as a subset of the genome that (i encodes predicted secreted proteins, (ii is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only ~3% of P. infestans genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors. Conclusions This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.

  4. Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells.

    Science.gov (United States)

    Francesconi, Mirko; Lehner, Ben

    2015-10-01

    Genome-wide gene expression profiling is a fast, cheap and standardised analysis that provides a high dimensional measurement of the state of a biological sample. In this review we describe computational methods that can be applied to identify and interpret sources of variance in gene expression in whole organisms, organs, tissues or single cells. This allows the identification of constituent cell types and states in complex mixtures, the reconstruction of temporal trajectories of development, differentiation and progression, and the reconstruction of spatial patterning. When applied to genetically variable samples, these methods allow the efficient investigation of how genetic variation influences gene expression and biological processes in space and time.

  5. Likelihood and Bayesian analyses reveal major genes affecting body composition, carcass, meat quality and the number of false teats in a Chinese European pig line

    Directory of Open Access Journals (Sweden)

    Le Roy Pascale

    2003-07-01

    Full Text Available Abstract Segregation analyses were performed using both maximum likelihood – via a Quasi Newton algorithm – (ML-QN and Bayesian – via Gibbs sampling – (Bayesian-GS approaches in the Chinese European Tiameslan pig line. Major genes were searched for average ultrasonic backfat thickness (ABT, carcass fat (X2 and X4 and lean (X5 depths, days from 20 to 100 kg (D20100, Napole technological yield (NTY, number of false (FTN and good (GTN teats, as well as total teat number (TTN. The discrete nature of FTN was additionally considered using a threshold model under ML methodology. The results obtained with both methods consistently suggested the presence of major genes affecting ABT, X2, NTY, GTN and FTN. Major genes were also suggested for X4 and X5 using ML-QN, but not the Bayesian-GS, approach. The major gene affecting FTN was confirmed using the threshold model. Genetic correlations as well as gene effect and genotype frequency estimates suggested the presence of four different major genes. The first gene would affect fatness traits (ABT, X2 and X4, the second one a leanness trait (X5, the third one NTY and the last one GTN and FTN. Genotype frequencies of breeding animals and their evolution over time were consistent with the selection performed in the Tiameslan line.

  6. Integration of Genome-Wide Computation DRE Search, AhR ChIP-chip and Gene Expression Analyses of TCDD-Elicited Responses in the Mouse Liver

    Directory of Open Access Journals (Sweden)

    Matthews Jason

    2011-07-01

    Full Text Available Abstract Background The aryl hydrocarbon receptor (AhR is a ligand-activated transcription factor (TF that mediates responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD. Integration of TCDD-induced genome-wide AhR enrichment, differential gene expression and computational dioxin response element (DRE analyses further elucidate the hepatic AhR regulatory network. Results Global ChIP-chip and gene expression analyses were performed on hepatic tissue from immature ovariectomized mice orally gavaged with 30 μg/kg TCDD. ChIP-chip analysis identified 14,446 and 974 AhR enriched regions (1% false discovery rate at 2 and 24 hrs, respectively. Enrichment density was greatest in the proximal promoter, and more specifically, within ± 1.5 kb of a transcriptional start site (TSS. AhR enrichment also occurred distal to a TSS (e.g. intergenic DNA and 3' UTR, extending the potential gene expression regulatory roles of the AhR. Although TF binding site analyses identified over-represented DRE sequences within enriched regions, approximately 50% of all AhR enriched regions lacked a DRE core (5'-GCGTG-3'. Microarray analysis identified 1,896 number of TCDD-responsive genes (|fold change| ≥ 1.5, P1(t > 0.999. Integrating this gene expression data with our ChIP-chip and DRE analyses only identified 625 differentially expressed genes that involved an AhR interaction at a DRE. Functional annotation analysis of differentially regulated genes associated with AhR enrichment identified overrepresented processes related to fatty acid and lipid metabolism and transport, and xenobiotic metabolism, which are consistent with TCDD-elicited steatosis in the mouse liver. Conclusions Details of the AhR regulatory network have been expanded to include AhR-DNA interactions within intragenic and intergenic genomic regions. Moreover, the AhR can interact with DNA independent of a DRE core suggesting there are alternative mechanisms of AhR-mediated gene regulation.

  7. META-GSA: Combining Findings from Gene-Set Analyses across Several Genome-Wide Association Studies.

    Directory of Open Access Journals (Sweden)

    Albert Rosenberger

    Full Text Available Gene-set analysis (GSA methods are used as complementary approaches to genome-wide association studies (GWASs. The single marker association estimates of a predefined set of genes are either contrasted with those of all remaining genes or with a null non-associated background. To pool the p-values from several GSAs, it is important to take into account the concordance of the observed patterns resulting from single marker association point estimates across any given gene set. Here we propose an enhanced version of Fisher's inverse χ2-method META-GSA, however weighting each study to account for imperfect correlation between association patterns.We investigated the performance of META-GSA by simulating GWASs with 500 cases and 500 controls at 100 diallelic markers in 20 different scenarios, simulating different relative risks between 1 and 1.5 in gene sets of 10 genes. Wilcoxon's rank sum test was applied as GSA for each study. We found that META-GSA has greater power to discover truly associated gene sets than simple pooling of the p-values, by e.g. 59% versus 37%, when the true relative risk for 5 of 10 genes was assume to be 1.5. Under the null hypothesis of no difference in the true association pattern between the gene set of interest and the set of remaining genes, the results of both approaches are almost uncorrelated. We recommend not relying on p-values alone when combining the results of independent GSAs.We applied META-GSA to pool the results of four case-control GWASs of lung cancer risk (Central European Study and Toronto/Lunenfeld-Tanenbaum Research Institute Study; German Lung Cancer Study and MD Anderson Cancer Center Study, which had already been analyzed separately with four different GSA methods (EASE; SLAT, mSUMSTAT and GenGen. This application revealed the pathway GO0015291 "transmembrane transporter activity" as significantly enriched with associated genes (GSA-method: EASE, p = 0.0315 corrected for multiple testing. Similar

  8. [Analyses of the rearrangement of T-cell receptor- and immunoglobulin genes in the diagnosis of lymphoproliferative disorders].

    Science.gov (United States)

    Griesser, D H

    1995-01-01

    Rearrangements are developmentally regulated genetic recombinations in T and B cells which generate functional T cell receptor (TcR) and immunoglobulin genes, respectively. Different variable, sometimes diversity, and joining gene segments which are discontinuously spread out within their chromosomal location in germline configuration, are randomly assembled in individual lymphocytes. These rearrangements can be detected by Southern Blot analysis if more than 5% of a total lymphocyte population in a biopsy specimen carries the same clonal rearrangement. We analyzed DNA from 324 snap-frozen biopsy specimens from lympho-proliferative disorders. None of the 20 reactive lesions and four malignant myelomonocytic tumors had a clonal antigen receptor gene rearrangement. All 117 malignant B cell lymphomas of different subtypes and 95 of 97 malignant T cell lymphomas showed a clonal gene rearrangement. Only two angioimmunoblastic lymphadenopathy(AILD)-type T cell lymphomas did not have immune receptor gene rearrangements. They were morphologically indistinguishable from the other 47 T/AILD lymphomas with clonal rearrangement patterns. In most cases TcR beta and immunoglobulin heavy chain (IgH) gene probes were sufficient for lineage assignment of the clonal T or B lymphocyte population. In 18% of B lymphomas, however, a cross-lineage rearrangement of TcR beta genes, and in 20% of the T cell lymphomas a clonal IgH gene rearrangement was detected. After exclusion of centrocytic, large cell anaplastic lymphomas (LCAL) of B-type, and T/AILD lymphomas which are overrepresented in our study, only 10% of the remaining 147 T and B cell lymphomas had aberrant rearrangements. TcR rearrangements other than those of the beta chain genes were extremely rare in B cell lymphomas, as were Ig kappa rearrangements in T lymphomas. Only two T/AILD lymphomas had IgH and Ig kappa rearrangement in addition to their clonal T cell receptor gene rearrangements. Both samples likely contain a clonal B

  9. Analog circuit design designing waveform processing circuits

    CERN Document Server

    Feucht, Dennis

    2010-01-01

    The fourth volume in the set Designing Waveform-Processing Circuits builds on the previous 3 volumes and presents a variety of analog non-amplifier circuits, including voltage references, current sources, filters, hysteresis switches and oscilloscope trigger and sweep circuitry, function generation, absolute-value circuits, and peak detectors.

  10. Gene co-expression analyses differentiate networks associated with diverse cancers harbouring TP53 missense or null mutations

    Directory of Open Access Journals (Sweden)

    Kathleen Oros Klein

    2016-08-01

    Full Text Available In a variety of solid cancers, missense mutations in the well-established TP53 tumour suppressor gene may lead to presence of a partially-functioning protein molecule, whereas mutations affecting the protein encoding reading frame, often referred to as null mutations, result in the absence of p53 protein. Both types of mutations have been observed in the same cancer type. As the resulting tumour biology may be quite different between these two groups, we used RNA-sequencing data from The Cancer Genome Atlas (TCGA from four different cancers with poor prognosis, namely ovarian, breast, lung and skin cancers, to compare the patterns of co-expression of genes in tumours grouped according to their TP53 missense or null mutation status. We used Weighted Gene Coexpression Network analysis (WGCNA and a new test statistic built on differences between groups in the measures of gene connectivity. For each cancer, our analysis identified a set of genes showing differential coexpression patterns between the TP53 missense- and null mutation-carrying groups that was robust to the choice of the tuning parameter in WGCNA. After comparing these sets of genes across the four cancers, one gene (KIR3DL2 consistently showed differential coexpression patterns between the null and missense groups. KIR3DL2 is known to play an important role in regulating the immune response, which is consistent with our observation that this gene’s strongly-correlated partners implicated many immune-related pathways. Examining mutation-type-related changes in correlations between sets of genes may provide new insight into tumour biology.

  11. Phosphoinositide 5-Phosphate and Phosphoinositide 4-Phosphate Trigger Distinct Specific Responses of Arabidopsis Genes: Genome-Wide Expression Analyses

    OpenAIRE

    2006-01-01

    Phosphoinositide phosphates, PtdInsP, are important components of the cell lipid pool that can function as messengers in diverse cellular processes. Lack of information on downstream targets, however, has impeded our understanding of the potential of lipid-signaling to influence gene activity. Our goals here were to identify genes that altered expression in the presence of two isomeric monophosphate lipid messengers (Phosphoinositide 5-Phosphate, PtdIns(5)P, and Phosphoinositide 4-Phosphate, ...

  12. Microarray analyses of SREBP-1a and SREBP-1c target genes identify new regulatory pathways in muscle.

    OpenAIRE

    Rome, Sophie; Lecomte, Virginie; Meugnier, Emmanuelle; Rieusset, Jennifer; Debard, Cyrille; Euthine, Vanessa; Vidal, Hubert; Lefai, Etienne

    2008-01-01

    International audience; In this study we have identified the target genes of sterol regulatory element binding protein (SREBP)-1a and SREBP-1c in primary cultures of human skeletal muscle cells, using adenoviral vectors expressing the mature nuclear form of human SREBP-1a or SREBP-1c combined with oligonucleotide microarrays. Overexpression of SREBP-1a led to significant changes in the expression of 1,315 genes (655 upregulated and 660 downregulated), whereas overexpression of SREBP-1c modifi...

  13. Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana

    OpenAIRE

    Hu, Wei; Hou, Xiaowan; Huang, Chao; Yan, Yan; Tie, Weiwei; Ding, Zehong; Wei, Yunxie; Liu, Juhua; Miao, Hongxia; Lu, Zhiwei; li, Meiying; Xu, Biyu; Jin, Zhiqiang

    2015-01-01

    Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs) were clustered into four subfamilies. Conserved...

  14. Gene network and familial analyses uncover a gene network involving Tbx5/Osr1/Pcsk6 interaction in the second heart field for atrial septation.

    Science.gov (United States)

    Zhang, Ke K; Xiang, Menglan; Zhou, Lun; Liu, Jielin; Curry, Nathan; Heine Suñer, Damian; Garcia-Pavia, Pablo; Zhang, Xiaohua; Wang, Qin; Xie, Linglin

    2016-03-15

    Atrial septal defects (ASDs) are a common human congenital heart disease (CHD) that can be induced by genetic abnormalities. Our previous studies have demonstrated a genetic interaction between Tbx5 and Osr1 in the second heart field (SHF) for atrial septation. We hypothesized that Osr1 and Tbx5 share a common signaling networking and downstream targets for atrial septation. To identify this molecular networks, we acquired the RNA-Seq transcriptome data from the posterior SHF of wild-type, Tbx5(+/) (-), Osr1(+/-), Osr1(-/-) and Tbx5(+/-)/Osr1(+/-) mutant embryos. Gene set analysis was used to identify the Kyoto Encyclopedia of Genes and Genomes pathways that were affected by the doses of Tbx5 and Osr1. A gene network module involving Tbx5 and Osr1 was identified using a non-parametric distance metric, distance correlation. A subset of 10 core genes and gene-gene interactions in the network module were validated by gene expression alterations in posterior second heart field (pSHF) of Tbx5 and Osr1 transgenic mouse embryos, a time-course gene expression change during P19CL6 cell differentiation. Pcsk6 was one of the network module genes that were linked to Tbx5. We validated the direct regulation of Tbx5 on Pcsk6 using immunohistochemical staining of pSHF, ChIP-quantitative polymerase chain reaction and luciferase reporter assay. Importantly, we identified Pcsk6 as a novel gene associated with ASD via a human genotyping study of an ASD family. In summary, our study implicated a gene network involving Tbx5, Osr1 and Pcsk6 interaction in SHF for atrial septation, providing a molecular framework for understanding the role of Tbx5 in CHD ontogeny.

  15. Expression analyses of the genes harbored by the type 2 diabetes and pediatric BMI associated locus on 10q23

    Directory of Open Access Journals (Sweden)

    Zhao Jianhua

    2012-09-01

    Full Text Available Abstract Background There is evidence that one of the key type 2 diabetes (T2D loci identified by GWAS exerts its influence early on in life through its impact on pediatric BMI. This locus on 10q23 harbors three genes, encoding hematopoietically expressed homeobox (HHEX, insulin-degrading enzyme (IDE and kinesin family member 11 (KIF11, respectively. Methods We analyzed the impact of adipogeneis on the mRNA and protein expression levels of these genes in the human adipocyte Simpson-Golabi-Behmel syndrome (SGBS cell line in order to investigate which could be the culprit gene(s in this region of linkage disequilibrium. Results Following activation of differentiation with a PPARγ ligand, we observed ~20% decrease in IDE, ~40% decrease in HHEX and in excess of 80% decrease in KIF11 mRNA levels when comparing the adipocyte and pre-adipocyte states. We also observed decreases in KIF11 and IDE protein levels, but conversely we observed a dramatic increase in HHEX protein levels. Subsequent time course experiments revealed some marked changes in expression as early as three hours after activation of differentiation. Conclusion Our data suggest that the expression of all three genes at this locus are impacted during SGBS adipogenesis and provides insights in to the possible mechanisms of how the genes at this 10q23 locus could influence both adipocyte differentiation and susceptibility to T2D through insulin resistance.

  16. Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma.

    Directory of Open Access Journals (Sweden)

    Chad J Creighton

    Full Text Available BACKGROUND: The Cancer Genome Atlas (TCGA Network recently comprehensively catalogued the molecular aberrations in 487 high-grade serous ovarian cancers, with much remaining to be elucidated regarding the microRNAs (miRNAs. Here, using TCGA ovarian data, we surveyed the miRNAs, in the context of their predicted gene targets. METHODS AND RESULTS: Integration of miRNA and gene patterns yielded evidence that proximal pairs of miRNAs are processed from polycistronic primary transcripts, and that intronic miRNAs and their host gene mRNAs derive from common transcripts. Patterns of miRNA expression revealed multiple tumor subtypes and a set of 34 miRNAs predictive of overall patient survival. In a global analysis, miRNA:mRNA pairs anti-correlated in expression across tumors showed a higher frequency of in silico predicted target sites in the mRNA 3'-untranslated region (with less frequency observed for coding sequence and 5'-untranslated regions. The miR-29 family and predicted target genes were among the most strongly anti-correlated miRNA:mRNA pairs; over-expression of miR-29a in vitro repressed several anti-correlated genes (including DNMT3A and DNMT3B and substantially decreased ovarian cancer cell viability. CONCLUSIONS: This study establishes miRNAs as having a widespread impact on gene expression programs in ovarian cancer, further strengthening our understanding of miRNA biology as it applies to human cancer. As with gene transcripts, miRNAs exhibit high diversity reflecting the genomic heterogeneity within a clinically homogeneous disease population. Putative miRNA:mRNA interactions, as identified using integrative analysis, can be validated. TCGA data are a valuable resource for the identification of novel tumor suppressive miRNAs in ovarian as well as other cancers.

  17. Conifer R2R3-MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca

    Directory of Open Access Journals (Sweden)

    Grima-Pettenati Jacqueline

    2007-03-01

    Full Text Available Abstract Background Several members of the R2R3-MYB family of transcription factors act as regulators of lignin and phenylpropanoid metabolism during wood formation in angiosperm and gymnosperm plants. The angiosperm Arabidopsis has over one hundred R2R3-MYBs genes; however, only a few members of this family have been discovered in gymnosperms. Results We isolated and characterised full-length cDNAs encoding R2R3-MYB genes from the gymnosperms white spruce, Picea glauca (13 sequences, and loblolly pine, Pinus taeda L. (five sequences. Sequence similarities and phylogenetic analyses placed the spruce and pine sequences in diverse subgroups of the large R2R3-MYB family, although several of the sequences clustered closely together. We searched the highly variable C-terminal region of diverse plant MYBs for conserved amino acid sequences and identified 20 motifs in the spruce MYBs, nine of which have not previously been reported and three of which are specific to conifers. The number and length of the introns in spruce MYB genes varied significantly, but their positions were well conserved relative to angiosperm MYB genes. Quantitative RTPCR of MYB genes transcript abundance in root and stem tissues revealed diverse expression patterns; three MYB genes were preferentially expressed in secondary xylem, whereas others were preferentially expressed in phloem or were ubiquitous. The MYB genes expressed in xylem, and three others, were up-regulated in the compression wood of leaning trees within 76 hours of induction. Conclusion Our survey of 18 conifer R2R3-MYB genes clearly showed a gene family structure similar to that of Arabidopsis. Three of the sequences are likely to play a role in lignin metabolism and/or wood formation in gymnosperm trees, including a close homolog of the loblolly pine PtMYB4, shown to regulate lignin biosynthesis in transgenic tobacco.

  18. Comparative Transcriptomic Analyses by RNA-seq to Elucidate Differentially Expressed Genes in the Muscle of Korean Thoroughbred Horses.

    Science.gov (United States)

    Ghosh, Mrinmoy; Cho, Hyun-Woo; Park, Jeong-Woong; Choi, Jae-Young; Chung, Young-Hwa; Sharma, Neelesh; Singh, Amit Kumar; Kim, Nam Eun; Mongre, Raj Kumar; Huynh, Do; Jiao, Zhang Jiao; Do, Kyoung Tag; Lee, Hak-Kyo; Song, Ki-Duk; Cho, Byung-Wook; Jeong, DongKee

    2016-10-01

    The athletic abilities of the horse serve as a valuable model to understand the physiology and molecular mechanisms of adaptive responses to exercise. We analyzed differentially expressed genes in triceps brachii muscle tissues collected from Eonjena Taeyang and Jigusang Seryeok Thoroughbred horses and their co-expression networks in a large-scale RNA-sequence dataset comparing expression before and after exercise. High-quality horse transcriptome data were generated, with over 22 million 90-bp pair-end reads. By comparing the annotations, we found that MYH3, MPZ, and PDE8B genes in Eonjena Taeyang and PDE8B and KIF18A genes in Jigusang Seryeok were upregulated before exercise. Notably further, we observed that PPP1R27, NDUFA3, TNC, and ANK1 in Eonjena Taeyang and HIF1A, BDNF, ADRB2, OBSCN, and PER3 in Jigusang Seryeok have shown upregulation at the postexercise period. This investigation suggested that genes responsible for metabolism and oxidative phosphorylations associated with endurance and resistance exercise were highly expressed, whereas genes encoding structural proteins were generally suppressed. The expression profile of racehorses at pre- and postexercise will provide credible reference for further studies on biological effects such as responses to stress and adaption of other Thoroughbred horse, which might be useful for selective breeding for improvement of traits in commercial production.

  19. Spliced leader-based analyses reveal the effects of polycyclic aromatic hydrocarbons on gene expression in the copepod Pseudodiaptomus poplesia.

    Science.gov (United States)

    Zhuang, Yunyun; Yang, Feifei; Xu, Donghui; Chen, Hongju; Zhang, Huan; Liu, Guangxing

    2017-02-01

    Polycyclic aromatic hydrocarbons (PAHs) are a group of toxic and carcinogenic pollutants that can adversely affect the development, growth and reproduction of marine organisms including copepods. However, knowledge on the molecular mechanisms regulating the response to PAH exposure in marine planktonic copepods is limited. In this study, we investigated the survival and gene expression of the calanoid copepod Pseudodiaptomus poplesia upon exposure to two PAHs, 1, 2-dimethylnaphthalene (1, 2-NAPH) and pyrene. Acute toxicity responses resulted in 96-h LC50 of 788.98μgL(-1) and 54.68μgL(-1) for 1, 2-NAPH and pyrene, respectively. Using the recently discovered copepod spliced leader as a primer, we constructed full-length cDNA libraries from copepods exposed to sublethal concentrations and revealed 289 unique genes of diverse functions, including stress response genes and novel genes previously undocumented for this species. Eighty-three gene families were specifically expressed in PAH exposure libraries. We further analyzed the expression of seven target genes by reverse transcription-quantitative PCR in a time-course test with three sublethal concentrations. These target genes have primary roles in detoxification, oxidative defense, and signal transduction, and include different forms of glutathione S-transferase (GST), glutathione peroxidases (GPX), peroxiredoxin (PRDX), methylmalonate-semialdehyde dehydrogenase (MSDH) and ras-related C3 botulinum toxin substrate (RAC1). Expression stability of seven candidate reference genes were evaluated and the two most stable ones (RPL15 and RPS20 for 1, 2-NAPH exposure, RPL15 and EF1D for pyrene exposure) were used to normalize the expression levels of the target genes. Significant upregulation was detected in GST-T, GST-DE, GPX4, PRDX6 and RAC1 upon 1, 2-NAPH exposure, and GST-DE and MSDH upon pyrene exposure. These results indicated that the oxidative stress was induced and that signal transduction might be affected by PAH

  20. Evidence from single nucleotide polymorphism analyses of ADVANCE study demonstrates EFNB3 as a hypertension risk gene

    Science.gov (United States)

    Tremblay, Johanne; Wang, Yujia; Raelson, John; Marois-Blanchet, Francois-Christophe; Wu, Zenghui; Luo, Hongyu; Bradley, Edward; Chalmers, John; Woodward, Mark; Harrap, Stephen; Hamet, Pavel; Wu, Jiangping

    2017-01-01

    EPH kinases and their ligands, ephrins (EFNs), have vital and diverse biological functions. We recently reported that Efnb3 gene deletion results in hypertension in female but not male mice. These data suggest that EFNB3 regulates blood pressure in a sex- and sex hormone-dependent way. In the present study, we conducted a human genetic study to assess the association of EFNB3 single nucleotide polymorphisms with human hypertension risks, using 3,448 patients with type 2 diabetes from the ADVANCE study (Action in Diabetes and Vascular Disease: Peterax and Diamicron MR Controlled Evaluation). We have observed significant association between 2 SNPs in the 3′ untranslated region or within the adjacent region just 3′ of the EFNB3 gene with hypertension, corroborating our findings from the mouse model. Thus, our investigation has shown that EFNB3 is a hypertension risk gene in certain individuals. PMID:28272517

  1. A growth curve model with fractional polynomials for analysing incomplete time-course data in microarray gene expression studies

    DEFF Research Database (Denmark)

    Tan, Qihua; Thomassen, Mads; Hjelmborg, Jacob V B

    2011-01-01

    among fractional polynomial models with power terms from a set of fixed values that offer a wide range of curve shapes and suggests a best fitting model. After a limited simulation study, the model has been applied to our human in vivo irritated epidermis data with missing observations to investigate......-course pattern in a gene by gene manner. We introduce a growth curve model with fractional polynomials to automatically capture the various time-dependent expression patterns and meanwhile efficiently handle missing values due to incomplete observations. For each gene, our procedure compares the performances...... time-dependent transcriptional responses to a chemical irritant. Our method was able to identify the various nonlinear time-course expression trajectories. The integration of growth curves with fractional polynomials provides a flexible way to model different time-course patterns together with model...

  2. Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae reveal high level variation of genomic organization and a diversity of transfer RNA gene sets

    Directory of Open Access Journals (Sweden)

    Kong Xiaoyu

    2009-05-01

    Full Text Available Abstract Background It can be seen from the available mollusk mitogenomes that the family Pectinidae exhibits the most variation in genome organization. In this study, comparative mitogenomic analyses were performed for three scallops from the subfamily Chlamydinae (Pectinidae, with the goal of characterizing the degree of variability of mitogenome organization and other characteristics among species from the same subfamily and exploring their possible evolution route. Findings The complete or nearly complete mtDNA sequences of scallop Mimachlamys nobilis (17 935 bp, Mizuhopecten yessoensis (20 964 bp and Chlamys farreri (17 035 bp were determined using long PCR amplification and primer walking sequencing strategy. Highly variable size difference of the three genomes resulted primarily from length and number variations of non-coding regions, and the major difference in gene content of the three scallop species are due to varying tRNA gene sets. Only 21, 16, and 17 tRNA genes were detected in the mitogenomes of M. nobilis, M. yessoensis and C. farreri, respectively. Remarkably, no trnS gene could be identified in any of the three scallops. A newly-detected trnA-like sequence within the mitogenome of M. yessoensis seems to exemplify the functional loss of a tRNA gene, and the duplication of trnD in M. yessoensis raises a fundamental question of whether the retention of the tRNA gene copy of 2-tRNAs is easier than that of 4-tRNAs. Analysis of putative evolutionary pathways of gene rearrangement indicates that transposition of neighboring gene blocks may play an important role in the evolution of mitogenomes in scallops. Parsimonious analysis of the genomic variations implies that the mitogenomes of M. yessoensis and C. farreri are likely to derive independently from a common ancestor that was closely related to M. nobilis. Conclusion Comparative mitogenomic analyses among three species from the subfamily Chlamydinae show that the three genomes

  3. Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors.

    Science.gov (United States)

    Fortes, M R S; Snelling, W M; Reverter, A; Nagaraj, S H; Lehnert, S A; Hawken, R J; DeAtley, K L; Peters, S O; Silver, G A; Rincon, G; Medrano, J F; Islas-Trejo, A; Thomas, M G

    2012-09-01

    Measures of heifer fertility are economically relevant traits for beef production systems and knowledge of candidate genes could be incorporated into future genomic selection strategies. Ten traits related to growth and fertility were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These traits were: BW and hip height adjusted to 205 and 365 d of age, postweaning ADG, yearling assessment of carcass traits (i.e., back fat thickness, intramuscular fat, and LM area), as well as heifer pregnancy and first service conception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous synchronization and AI targeting heifers to calve by 24 mo of age. The BovineSNP50 BeadChip was used to ascertain 53,692 SNP genotypes for ∼802 heifers. Associations of genotypes and phenotypes were performed and SNP effects were estimated for each trait. Minimally associated SNP (P < 0.05) and their effects across the 10 traits formed the basis for an association weight matrix and its derived gene network related to FSC (57.3% success and heritability = 0.06 ± 0.05). These analyses yielded 1,555 important SNP, which inferred genes linked by 113,873 correlations within a network. Specifically, 1,386 SNP were nodes and the 5,132 strongest correlations (|r| ≥ 0.90) were edges. The network was filtered with genes queried from a transcriptome resource created from deep sequencing of RNA (i.e., RNA-Seq) from the hypothalamus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network contained 978 genes connected by 2,560 edges or predicted gene interactions. This hypothalamic gene network was enriched with genes involved in axon guidance, which is a pathway known to influence pulsatile release of LHRH. There were 5 transcription factors with 21 or more connections: ZMAT3, STAT6, RFX4, PLAGL1, and NR6A1 for FSC. The SNP that identified these genes were intragenic and were on chromosomes

  4. Genomic analyses and transcriptional profiles of the glycoside hydrolase family 18 genes of the entomopathogenic fungus Metarhizium anisopliae.

    Science.gov (United States)

    Junges, Ângela; Boldo, Juliano Tomazzoni; Souza, Bárbara Kunzler; Guedes, Rafael Lucas Muniz; Sbaraini, Nicolau; Kmetzsch, Lívia; Thompson, Claudia Elizabeth; Staats, Charley Christian; de Almeida, Luis Gonzaga Paula; de Vasconcelos, Ana Tereza Ribeiro; Vainstein, Marilene Henning; Schrank, Augusto

    2014-01-01

    Fungal chitin metabolism involves diverse processes such as metabolically active cell wall maintenance, basic nutrition, and different aspects of virulence. Chitinases are enzymes belonging to the glycoside hydrolase family 18 (GH18) and 19 (GH19) and are responsible for the hydrolysis of β-1,4-linkages in chitin. This linear homopolymer of N-acetyl-β-D-glucosamine is an essential constituent of fungal cell walls and arthropod exoskeletons. Several chitinases have been directly implicated in structural, morphogenetic, autolytic and nutritional activities of fungal cells. In the entomopathogen Metarhizium anisopliae, chitinases are also involved in virulence. Filamentous fungi genomes exhibit a higher number of chitinase-coding genes than bacteria or yeasts. The survey performed in the M. anisopliae genome has successfully identified 24 genes belonging to glycoside hydrolase family 18, including three previously experimentally determined chitinase-coding genes named chit1, chi2 and chi3. These putative chitinases were classified based on domain organization and phylogenetic analysis into the previously described A, B and C chitinase subgroups, and into a new subgroup D. Moreover, three GH18 proteins could be classified as putative endo-N-acetyl-β-D-glucosaminidases, enzymes that are associated with deglycosylation and were therefore assigned to a new subgroup E. The transcriptional profile of the GH18 genes was evaluated by qPCR with RNA extracted from eight culture conditions, representing different stages of development or different nutritional states. The transcripts from the GH18 genes were detected in at least one of the different M. anisopliae developmental stages, thus validating the proposed genes. Moreover, not all members from the same chitinase subgroup presented equal patterns of transcript expression under the eight distinct conditions studied. The determination of M. anisopliae chitinases and ENGases and a more detailed study concerning the enzymes

  5. Sequence and phylogenetic analyses of the chloroplast 16S rRNA, tufA, and rbcL genes from Bryopsis hypnoides

    Institute of Scientific and Technical Information of China (English)

    L(U) Fang; WANG Guangce

    2011-01-01

    Using shotgun sequencing data,the complete sequences of chloroplast 16S rRNA and tufA genes were acquired from native specimens of Bryopsis hypnoides (Qingdao,China).There are two group Ⅰ introns in the 16S rRNA gene,which is structurally similar to that of Caulerpa sertularioides (Bryopsidales,Chlorophyta).The chloroplast-encoded tufA gene sequence is 1230 bp long,very AT-rich (61.5%),and is similar to previously published 16S rRNA sequences of bryopsidinean algae.Phylogenetic analyses based on chloroplast 16S rRNA and tufA gene sequence data support previous hypotheses that the Bryopsidineae,Halimedineae,and Ostreobidineae are three distinct lineages.These results also confirmed the exclusion of Avrainvillea from the family Udoteaceae.Phylogenetic analyses inferred that the genus Bryopsis as sister to Derbesia; however,this clade lacked robust nodal support.Moreover,the phylogenetic tree inferred from rbcL GenBank sequences,combined with the geographical distributions of Bryopsis species,identified a strongly supportive clade for three differently distributed Asian Bryopsis species.The preliminary results suggesting that these organisms are of distinct regional endemism.

  6. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork

    Directory of Open Access Journals (Sweden)

    Druka Arnis

    2008-11-01

    Full Text Available Abstract Background A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community. Description Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits. Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them. Conclusion By

  7. GLITCH ANALYSIS AND REDUCTION IN DIGITAL CIRCUITS

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    Ronak Shah

    2016-08-01

    Full Text Available Hazard in digital circuits is unnecessary transitions due to gate propagation delay in that circuit. Hazards occur due to uneven delay offered in the path of the various ongoing signals. One of the important reasons for power dissipation in CMOS circuits is the switching activity .This include activities such as spurious pulses, called glitches. Power optimization techniques that concentrate on the reduction of switching power dissipation of a given circuit are called glitch reduction techniques. In this paper, we analyse various Glitch reduction techniques such as Hazard filtering Technique, Balanced Path Technique, Multiple Threshold Technique and Gate Freezing Technique. We also measure the parameters such as noise and delay of the circuits on application of various techniques to check the reliability of different circuits in various situations.

  8. A Singularity in the Kirchhoff's Circuit Equations

    CERN Document Server

    Harsha, N R Sree

    2016-01-01

    Students often have difficulty in understanding qualitatively the behaviour of simple electric circuits. In particular, as different studies have shown, they find multiple batteries connected in multiple loops difficult to analyse. In a recent paper [Phys. Educ. 50 568 (2015)], we showed such an electric circuit, which consists of ideal batteries connected in parallel, that couldn't be solved by the existing circuit analysis methods. In this paper, we shall introduce a new mathematical method of solving simple electric circuits from the solutions of more general circuits and show that the currents, in this particular circuit, take the indeterminate 0/0 form. We shall also present some of the implications of teaching the method. We believe that the description presented in this paper should help the instructors in teaching the behaviour of multiple batteries connected in parallel.

  9. Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation.

    Directory of Open Access Journals (Sweden)

    Young-Jin Park

    Full Text Available Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes and carbohydrate degradation (392 CAZymes, along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi- cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-cellulose biomass related industries further increase the significance of F. velutipes as a new model.

  10. Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation.

    Science.gov (United States)

    Park, Young-Jin; Baek, Jeong Hun; Lee, Seonwook; Kim, Changhoon; Rhee, Hwanseok; Kim, Hyungtae; Seo, Jeong-Sun; Park, Hae-Ran; Yoon, Dae-Eun; Nam, Jae-Young; Kim, Hong-Il; Kim, Jong-Guk; Yoon, Hyeokjun; Kang, Hee-Wan; Cho, Jae-Yong; Song, Eun-Sung; Sung, Gi-Ho; Yoo, Young-Bok; Lee, Chang-Soo; Lee, Byoung-Moo; Kong, Won-Sik

    2014-01-01

    Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.

  11. Pseudomonas community structure and antagonistic potential in the rhizosphere : insights gained by combining phylogenetic and functional gene-based analyses

    NARCIS (Netherlands)

    Costa, Rodrigo; Gomes, Newton C. M.; Kroegerrecklenfort, Ellen; Opelt, Katja; Berg, Gabriele; Smalla, Kornelia

    2007-01-01

    The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in environment

  12. Differential gene expression from genome-wide microarray analyses distinguishes Lohmann Selected Leghorn and Lohmann Brown layers.

    Directory of Open Access Journals (Sweden)

    Christin Habig

    Full Text Available The Lohmann Selected Leghorn (LSL and Lohmann Brown (LB layer lines have been selected for high egg production since more than 50 years and belong to the worldwide leading commercial layer lines. The objectives of the present study were to characterize the molecular processes that are different among these two layer lines using whole genome RNA expression profiles. The hens were kept in the newly developed small group housing system Eurovent German with two different group sizes. Differential expression was observed for 6,276 microarray probes (FDR adjusted P-value <0.05 among the two layer lines LSL and LB. A 2-fold or greater change in gene expression was identified on 151 probe sets. In LSL, 72 of the 151 probe sets were up- and 79 of them were down-regulated. Gene ontology (GO enrichment analysis accounting for biological processes evinced 18 GO-terms for the 72 probe sets with higher expression in LSL, especially those taking part in immune system processes and membrane organization. A total of 32 enriched GO-terms were determined among the 79 down-regulated probe sets of LSL. Particularly, these terms included phosphorus metabolic processes and signaling pathways. In conclusion, the phenotypic differences among the two layer lines LSL and LB are clearly reflected in their gene expression profiles of the cerebrum. These novel findings provide clues for genes involved in economically important line characteristics of commercial laying hens.

  13. Cloning and functional analyses of a gene from sugar beet up-regulated upon cyst nematode infection

    NARCIS (Netherlands)

    Samuelian, S.; Kleine, M.; Spira, C.P.; Klein Lankhorst, R.M.; Jung, C.

    2004-01-01

    The cDNA-AFLP technique was used to isolate sugar beet genes up-regulated upon infection with the beet cyst nematode Heterodera schachtii. Hairy root cultures were obtained from resistant plants carrying a Beta procumbens translocation as well as from a non-resistant control. mRNA was isolated from

  14. Analysing the dhaT gene in Colombian Clostridium sp. (Clostridia 1,3-propanediol-producing strains

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    Diana Milena Quilaguy-Ayure

    2010-04-01

    Full Text Available To analyze the dhaT gene, one of the genes responsible for the 1,3-propanediol (1,3-PD production, in two native Clostridiumstrains. Materials and methods: The dhaT gene was amplified by Polimerase Chain Reaction with specific primers designed fromClostridium butyricum VPI1718 operon. Bioinformatics tools like BLASTN, ORF finder, BLASTP and ClustalW were used to determinethe identity of the sequence and to assign a function. Results: DNA amplification products were obtained from Colombian Clostridium sp.native strains (IBUN 13A and IBUN 158B and the Clostridium butyricum DSM 2478 strain, which were sequenced. According to thebioinformatics analysis of the above sequences, a high degree of similarity was found with the dhaT gene of different bacterial species. Thehighest percentage of identity was obtained with the Clostridium butyricum VPI 1718 strain. Conclusion: knowledge of the physicalstructure of the 1,3-PD operon in native strains opens the way for developing genetic and metabolic engineering strategies for improvingprocesses productivity.

  15. "Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses".

    Science.gov (United States)

    Eveno, Emmanuelle; Collada, Carmen; Guevara, M Angeles; Léger, Valérie; Soto, Alvaro; Díaz, Luis; Léger, Patrick; González-Martínez, Santiago C; Cervera, M Teresa; Plomion, Christophe; Garnier-Géré, Pauline H

    2008-02-01

    The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods: 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher F(ST) values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower F(ST) values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed

  16. Solid-state circuits

    CERN Document Server

    Pridham, G J

    2013-01-01

    Solid-State Circuits provides an introduction to the theory and practice underlying solid-state circuits, laying particular emphasis on field effect transistors and integrated circuits. Topics range from construction and characteristics of semiconductor devices to rectification and power supplies, low-frequency amplifiers, sine- and square-wave oscillators, and high-frequency effects and circuits. Black-box equivalent circuits of bipolar transistors, physical equivalent circuits of bipolar transistors, and equivalent circuits of field effect transistors are also covered. This volume is divided

  17. Simple Autonomous Chaotic Circuits

    Science.gov (United States)

    Piper, Jessica; Sprott, J.

    2010-03-01

    Over the last several decades, numerous electronic circuits exhibiting chaos have been proposed. Non-autonomous circuits with as few as two components have been developed. However, the operation of such circuits relies on the non-ideal behavior of the devices used, and therefore the circuit equations can be quite complex. In this paper, we present two simple autonomous chaotic circuits using only opamps and linear passive components. The circuits each use one opamp as a comparator, to provide a signum nonlinearity. The chaotic behavior is robust, and independent of nonlinearities in the passive components. Moreover, the circuit equations are among the algebraically simplest chaotic systems yet constructed.

  18. Circuit analysis for dummies

    CERN Document Server

    Santiago, John

    2013-01-01

    Circuits overloaded from electric circuit analysis? Many universities require that students pursuing a degree in electrical or computer engineering take an Electric Circuit Analysis course to determine who will ""make the cut"" and continue in the degree program. Circuit Analysis For Dummies will help these students to better understand electric circuit analysis by presenting the information in an effective and straightforward manner. Circuit Analysis For Dummies gives you clear-cut information about the topics covered in an electric circuit analysis courses to help

  19. Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.

    Directory of Open Access Journals (Sweden)

    Manal Helal

    Full Text Available BACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. METHODS: A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. RESULTS: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52% corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578. CONCLUSION: The identification of centroids of 16S rRNA gene sequence clusters using novel distance matrix clustering enables the identification of the most representative sequences for each individual species of Nocardia and allows the quantitation of inter- and intra

  20. Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males.

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    Yao-Zhong Liu

    Full Text Available BACKGROUND: Current genome-wide association studies (GWAS are normally implemented in a univariate framework and analyze different phenotypes in isolation. This univariate approach ignores the potential genetic correlation between important disease traits. Hence this approach is difficult to detect pleiotropic genes, which may exist for obesity and osteoporosis, two common diseases of major public health importance that are closely correlated genetically. PRINCIPAL FINDINGS: To identify such pleiotropic genes and the key mechanistic links between the two diseases, we here performed the first bivariate GWAS of obesity and osteoporosis. We searched for genes underlying co-variation of the obesity phenotype, body mass index (BMI, with the osteoporosis risk phenotype, hip bone mineral density (BMD, scanning approximately 380,000 SNPs in 1,000 unrelated homogeneous Caucasians, including 499 males and 501 females. We identified in the male subjects two SNPs in intron 1 of the SOX6 (SRY-box 6 gene, rs297325 and rs4756846, which were bivariately associated with both BMI and hip BMD, achieving p values of 6.82x10(-7 and 1.47x10(-6, respectively. The two SNPs ranked at the top in significance for bivariate association with BMI and hip BMD in the male subjects among all the approximately 380,000 SNPs examined genome-wide. The two SNPs were replicated in a Framingham Heart Study (FHS cohort containing 3,355 Caucasians (1,370 males and 1,985 females from 975 families. In the FHS male subjects, the two SNPs achieved p values of 0.03 and 0.02, respectively, for bivariate association with BMI and femoral neck BMD. Interestingly, SOX6 was previously found to be essential to both cartilage formation/chondrogenesis and obesity-related insulin resistance, suggesting the gene's dual role in both bone and fat. CONCLUSIONS: Our findings, together with the prior biological evidence, suggest the SOX6 gene's importance in co-regulation of obesity and osteoporosis.

  1. AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Michael Considine

    2015-10-01

    Full Text Available Automated Genomics Analysis (AGA is an interactive program to analyze high-throughput genomic data sets on a variety of platforms. An easy to use, point and click, guided pipeline is implemented to combine, define, and compare datasets, and customize their outputs. In contrast to other automated programs, AGA enables flexible selection of sample groups for comparison from complex sample annotations. Batch correction techniques are also included to further enable the combination of datasets from diverse studies in this comparison. AGA also allows users to save plots, tables and data, and log files containing key portions of the R script run for reproducible analyses. The link between the interface and R supports collaborative research, enabling advanced R users to extend preliminary analyses generated from bioinformatics novices.

  2. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.

    Science.gov (United States)

    Frantz, Laurent A F; Schraiber, Joshua G; Madsen, Ole; Megens, Hendrik-Jan; Cagan, Alex; Bosse, Mirte; Paudel, Yogesh; Crooijmans, Richard P M A; Larson, Greger; Groenen, Martien A M

    2015-10-01

    Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

  3. Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae.

    Science.gov (United States)

    He, Yanxia; Guo, Xianguang; Xiang, Shifei; Li, Jiao; Li, Xiaoqin; Xiang, Hui; He, Jinlei; Chen, Dali; Chen, Jianping

    2016-07-01

    The present work aimed to evaluate 16S rRNA, khe and rpoB gene sequencing for the identification of Klebsiella pneumoniae in comparison with phenotypic methods. Fifteen clinical isolates were examined, which were initially identified as K. pneumoniae subsp. pneumoniae using the automated VITEK 32 system in two hospitals in Enshi City, China. Their identity was further supported by conventional phenotypic methods on the basis of morphological and biochemical characteristics. Using Bayesian phylogenetic analyses and haplotypes network reconstruction, 13 isolates were identified as K. pneumoniae, whereas the other two isolates (K19, K24) were classified as Shigella sp. and Enterobacter sp., respectively. Of the three genes, 16S rRNA and khe gene could discriminate the clinical isolates at the genus level, whereas rpoB could discriminate Klebsiella at the species and even subspecies level. Overall, the gene tree based on rpoB is more compatible with the currently accepted classification of Klebsiella than those based on 16S rRNA and khe genes, showing that rpoB can be a powerful tool for identification of K. pneumoniae isolates. Above all, our study challenges the utility of khe as a species-specific marker for identification of K. pneumoniae.

  4. Solenoid-Simulation Circuit

    Science.gov (United States)

    Simon, R. A.

    1986-01-01

    Electrical properties of solenoids imitated for tests of control circuits. Simulation circuit imitates voltage and current responses of two engine-controlling solenoids. Used in tests of programs of digital engine-control circuits, also provides electronic interface with circuits imitating electrical properties of pressure sensors and linear variable-differential transformers. Produces voltages, currents, delays, and discrete turnon and turnoff signals representing operation of solenoid in engine-control relay. Many such circuits used simulating overall engine circuitry.

  5. Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region

    Directory of Open Access Journals (Sweden)

    Ryan Stephen

    2006-05-01

    Full Text Available Abstract Background The MRP1 gene encodes the 190 kDa multidrug resistance-associated protein 1 (MRP1/ABCC1 and effluxes diverse drugs and xenobiotics. Sequence variations within this gene might account for differences in drug response in different individuals. To facilitate association studies of this gene with diseases and/or drug response, exons and flanking introns of MRP1 were screened for polymorphisms in 142 DNA samples from four different populations. Results Seventy-one polymorphisms, including 60 biallelic single nucleotide polymorphisms (SNPs, ten insertions/deletions (indel and one short tandem repeat (STR were identified. Thirty-four of these polymorphisms have not been previously reported. Interestingly, the STR polymorphism at the 5' untranslated region (5'UTR occurs at high but different frequencies in the different populations. Frequencies of common polymorphisms in our populations were comparable to those of similar populations in HAPMAP or Perlegen. Nucleotide diversity indices indicated that the coding region of MRP1 may have undergone negative selection or recent population expansion. SNPs E10/1299 G>T (R433S and E16/2012 G>T (G671V which occur at low frequency in only one or two of four populations examined were predicted to be functionally deleterious and hence are likely to be under negative selection. Conclusion Through in silico approaches, we identified two rare SNPs that are potentially negatively selected. These SNPs may be useful for studies associating this gene with rare events including adverse drug reactions.

  6. Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts

    Energy Technology Data Exchange (ETDEWEB)

    Hodgson, J. Graeme; Yeh, Ru-Fang; Ray, Amrita; Wang, Nicholas J.; Smirnov, Ivan; Yu, Mamie; Hariono, Sujatmi; Silber, Joachim; Feiler, Heidi S.; Gray, Joe W.; Spellman, Paul T.; Vandenberg, Scott R.; Berger, Mitchel S.; James, C. David

    2009-04-03

    Development of model systems that recapitulate the molecular heterogeneity observed among glioblastoma multiforme (GBM) tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from the Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7 gain/chromosome-10 loss, a poor-prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBM tumors, genomic amplification and overexpression of known GBM oncogenes, such as EGFR, MDM2, CDK6, and MYCN, and novel genes, including NUP107, SLC35E3, MMP1, MMP13, and DDX1. The transcriptional signature of GBMX tumors, which was stable over multiple subcutaneous passages, was defined by overexpression of genes involved in M phase, DNA replication, and chromosome organization (MRC) and was highly similar to the poor-prognosis mitosis and cell-cycle module (MCM) in GBM. Assessment of gene expression in TCGA-derived GBMs revealed overexpression of MRC cancer genes AURKB, BIRC5, CCNB1, CCNB2, CDC2, CDK2, and FOXM1, which form a transcriptional network important for G2/M progression and/or checkpoint activation. Our study supports propagation of GBM tumors as subcutaneous xenografts as a useful approach for sustaining key molecular characteristics of patient tumors, and highlights therapeutic opportunities conferred by this GBMX tumor panel for testing targeted therapeutic strategies for GBM treatment.

  7. Association analyses between brain-expressed fatty-acid binding protein (FABP) genes and schizophrenia and bipolar disorder.

    Science.gov (United States)

    Iwayama, Yoshimi; Hattori, Eiji; Maekawa, Motoko; Yamada, Kazuo; Toyota, Tomoko; Ohnishi, Tetsuo; Iwata, Yasuhide; Tsuchiya, Kenji J; Sugihara, Genichi; Kikuchi, Mitsuru; Hashimoto, Kenji; Iyo, Masaomi; Inada, Toshiya; Kunugi, Hiroshi; Ozaki, Norio; Iwata, Nakao; Nanko, Shinichiro; Iwamoto, Kazuya; Okazaki, Yuji; Kato, Tadafumi; Yoshikawa, Takeo

    2010-03-05

    Deficits in prepulse inhibition (PPI) are a biological marker for psychiatric illnesses such as schizophrenia and bipolar disorder. To unravel PPI-controlling mechanisms, we previously performed quantitative trait loci (QTL) analysis in mice, and identified Fabp7, that encodes a brain-type fatty acid binding protein (Fabp), as a causative gene. In that study, human FABP7 showed genetic association with schizophrenia. FABPs constitute a gene family, of which members FABP5 and FABP3 are also expressed in the brain. These FABP proteins are molecular chaperons for polyunsaturated fatty acids (PUFAs) such as arachidonic and docosahexaenoic acids. Additionally, the involvement of PUFAs has been documented in the pathophysiology of schizophrenia and mood disorders. Therefore in this study, we examined the genetic roles of FABP5 and 3 in schizophrenia (N = 1,900 in combination with controls) and FABP7, 5, and 3 in bipolar disorder (N = 1,762 in the case-control set). Three single nucleotide polymorphisms (SNPs) from FABP7 showed nominal association with bipolar disorder, and haplotypes of the same gene showed empirical associations with bipolar disorder even after correction of multiple testing. We could not perform association studies on FABP5, due to the lack of informative SNPs. FABP3 displayed no association with either disease. Each FABP is relatively small and it is assumed that there are multiple regulatory elements that control gene expression. Therefore, future identification of unknown regulatory elements will be necessary to make a more detailed analysis of their genetic contribution to mental illnesses.

  8. Molecular analyses of TEM genes and their corresponding penicillinase-producing Neisseria gonorrhoeae isolates in Bangkok, Thailand.

    Science.gov (United States)

    Nakayama, Shu-Ichi; Tribuddharat, Chanwit; Prombhul, Sasiprapa; Shimuta, Ken; Srifuengfung, Somporn; Unemo, Magnus; Ohnishi, Makoto

    2012-02-01

    Neisseria gonorrhoeae is a major public health problem globally, especially because the bacterium has developed resistance to most antimicrobials introduced for first-line treatment of gonorrhea. In the present study, 96 N. gonorrhoeae isolates with high-level resistance to penicillin from 121 clinical isolates in Thailand were examined to investigate changes related to their plasmid-mediated penicillin resistance and their molecular epidemiological relationships. A β-lactamase (TEM) gene variant, bla(TEM-135), that may be a precursor in the transitional stage of a traditional bla(TEM-1) gene into an extended-spectrum β-lactamase (ESBL), possibly causing high resistance to all extended-spectrum cephalosporins in N. gonorrhoeae, was identified. Clonal analysis using multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence typing (NG-MAST) revealed the existence of a sexual network among patients from Japan and Thailand. Molecular analysis of the bla(TEM-135) gene showed that the emergence of this allele might not be a rare genetic event and that the allele has evolved in different plasmid backgrounds, which results possibly indicate that it is selected due to antimicrobial pressure. The presence of the bla(TEM-135) allele in the penicillinase-producing N. gonorrhoeae population may call for monitoring for the possible emergence of ESBL-producing N. gonorrhoeae in the future. This study identified a bla(TEM) variant (bla(TEM-135)) that is a possible intermediate precursor for an ESBL, which warrants international awareness.

  9. Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.

    Science.gov (United States)

    Wu, Dong-Dong; Ye, Ling-Qun; Li, Yan; Sun, Yan-Bo; Shao, Yi; Chen, Chunyan; Zhu, Zhu; Zhong, Li; Wang, Lu; Irwin, David M; Zhang, Yong E; Zhang, Ya-Ping

    2015-08-01

    Next-generation RNA sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution.

  10. Molecular phylogenetics of cixiid planthoppers (Hemiptera: Fulgoromorpha): new insights from combined analyses of mitochondrial and nuclear genes.

    Science.gov (United States)

    Ceotto, Paula; Kergoat, Gaël J; Rasplus, Jean-Yves; Bourgoin, Thierry

    2008-08-01

    The planthopper family Cixiidae (Hemiptera: Fulgoromorpha) comprises approximately 160 genera and 2000 species divided in three subfamilies: Borystheninae, Bothriocerinae and Cixiinae, the later with 16 tribes. The current paper represents the first attempt to estimate phylogenetic relationships within Cixiidae based on molecular data. We use a total of 3652bp sequence alignment of four genes: the mitochondrial coding genes Cytochrome c Oxidase subunit 1 (Cox1) and Cytochrome b (Cytb), a portion of the nuclear 18S rDNA and two non-contiguous portions of the nuclear 28S rDNA. The phylogenetic relationships of 72 terminal specimens were reconstructed using both maximum parsimony and Bayesian inference methods. Through the analysis of this empirical dataset, we also provide comparisons among different a priori partitioning strategies and the use of mixture models in a Bayesian framework. Our comparisons suggest that mixture models overcome the benefits obtained by partitioning the data according to codon position and gene identity, as they provide better accuracy in phylogenetic reconstructions. The recovered maximum parsimony and Bayesian inference phylogenies suggest that the family Cixiidae is paraphyletic in respect with Delphacidae. The paraphyly of the subfamily Cixiinae is also recovered by both approaches. In contrast to a morphological phylogeny recently proposed for cixiids, subfamilies Borystheninae and Bothriocerinae form a monophyletic group.

  11. Sequence and stress-response analyses of the DNA mismatch repair gene hexA in Lactococcus lactis.

    Science.gov (United States)

    Ren, J; Park, J H; Dunn, N W; Kim, W S

    2001-10-01

    The DNA mismatch repair gene hexA was identified in Lactococcus lactis by PCR amplification by using a pair of primers homologous to the DNA-binding Dps protein. The gene in its entirety, including the regulatory regions, was sequenced, by using a strategy of chromosomal walking based on two PCR protocols. The open reading frame of 2526 bp was preceded by a strong ribosome-binding site (AGGAAG) and was followed by a potential transcription terminator (hairpin loop structure). The 5' terminus of the hexA mRNA was located 135 bp upstream of the start codon, and putative -10 and -35 regions were identified. The deduced amino acid sequence revealed two motifs, the ATP/GTP-binding site (P-loop) and the "MutS family signature". The hexA promoter was cloned into pMU1327, which contained a promoter-less CAT reporter gene, and the promoter activity was examined under oxidative-stress conditions. It appears that the promoter activity is down-shifted by H2O2 at 4 mM.

  12. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David

    2012-11-20

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C) and salinity (~41 psu) from the mixed layer (~200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea\\'s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.

  13. Gonad RNA-specific qRT-PCR analyses identify genes with potential functions in schistosome reproduction such as SmFz1 and SmFGFRs

    Directory of Open Access Journals (Sweden)

    Steffen eHahnel

    2014-06-01

    Full Text Available In the search for new strategies to fight schistosomiasis, the unique reproductive biology of Schistosoma mansoni has come into the focus of research. The development of the gonads and the ability of egg production are fundamental not only for continuing the life cycle but also for pathogenicity.Previous studies of schistosome biology demonstrated an influence of pairing on gonad development of the female and on gene expression profiles in both genders. Due to the limited access to specific tissues, however, most of these studies were done at the level of whole worms neglecting individual tissues that may be targets of pairing-dependent processes.Recently, we established a protocol allowing the isolation of testes and ovaries from adult S. mansoni. Here, we describe tissue-specific qRT-PCR analyses comparing transcript levels of selected genes on the basis of RNA from gonads and whole worms. Gene expression in ovary and testes was in some cases found to be significantly influenced by pairing, which was not traceable in whole worms. Among the candidate genes identified as regulated by pairing in gonads were the frizzled homolog SmFz1 and the two fibroblast growth factor receptor homologs SmFGFR-A and SmFGFR-B. First functional characterizations were done, including comparative qRT-PCR analyses, in situ-localization experiments, heterologous expression in Xenopus oocytes (SmFGFR-A/B, and inhibitor studies using the Fz/Dvl-pathway inhibitor 3289-8625, or BIBF1120 blocking FGFR-signaling. Besides confirming gonad localization and receptor functions, inhibitor-induced phenotypes were observed in vitro such as decreased egg production as well as drastic effects on gonad differentiation, morphology, embryogenesis, and survival of adult worms.In summary, these results emphasise the usefulness of tissue specific qRT-PCRs for selection of candidate genes with important roles in reproduction, allowing subsequent studies to determine their suitability as

  14. Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison

    Directory of Open Access Journals (Sweden)

    Saville Barry J

    2007-09-01

    Full Text Available Abstract Background Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism, several expressed sequence tag (EST libraries were generated from a variety of U. maydis cell types. In addition to utility in the context of gene identification and structure annotation, the ESTs were analyzed to identify differentially abundant transcripts and to detect evidence of alternative splicing and anti-sense transcription. Results Four cDNA libraries were constructed using RNA isolated from U. maydis diploid teliospores (U. maydis strains 518 × 521 and haploid cells of strain 521 grown under nutrient rich, carbon starved, and nitrogen starved conditions. Using the genome sequence as a scaffold, the 15,901 ESTs were assembled into 6,101 contiguous expressed sequences (contigs; among these, 5,482 corresponded to predicted genes in the MUMDB (MIPS Ustilago maydis database, while 619 aligned to regions of the genome not yet designated as genes in MUMDB. A comparison of EST abundance identified numerous genes that may be regulated in a cell type or starvation-specific manner. The transcriptional response to nitrogen starvation was assessed using RT-qPCR. The results of this suggest that there may be cross-talk between the nitrogen and carbon signalling pathways in U. maydis. Bioinformatic analysis identified numerous examples of alternative splicing and anti-sense transcription. While intron retention was the predominant form of alternative splicing in U. maydis, other varieties were also evident (e.g. exon skipping. Selected instances of both alternative splicing and anti-sense transcription were independently confirmed using RT-PCR. Conclusion Through this work: 1 substantial sequence information has been provided for U. maydis genome annotation; 2 new genes were identified through the discovery of 619

  15. Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes.

    Science.gov (United States)

    Fracchia, Letizia; Dohrmann, Anja B; Martinotti, Maria Giovanna; Tebbe, Christoph C

    2006-08-01

    Bacterial communities are important catalysts in the production of composts. Here, it was analysed whether the diversity of bacteria in finished composts is stable and specific for the production process. Single-strand conformation polymorphism (SSCP) based on polymerase chain reaction amplified partial 16S rRNA genes was used to profile and analyse bacterial communities found in total DNA extracted from finished composts. Different batches of compost samples stored over a period of 12 years and a 1-year-old vermicompost were compared to each other. According to digital image analysis, clear differences could be detected between the profiles from compost and vermicompost. Differences between three different periods of compost storage and between replicate vermicompost windrows were only minor. A total of 41 different 16S rRNA genes were identified from the SSCP profiles by DNA sequencing, with the vast majority related to yet-uncultivated bacteria. Sequences retrieved from compost mainly belonged to the phyla Actinobacteria and Firmicutes. In contrast, vermicompost was dominated by bacteria related to uncultured Chloroflexi, Acidobacteria, Bacteroidetes and Gemmatimonadetes. The differences were underscored with specific gene probes and Southern blot hybridizations. The results confirmed that different substrates and composting processes selected for specific bacterial communities in the finished products. The specificity and consistency of the bacterial communities inhabiting the compost materials suggest that cultivation-independent bacterial community analysis is a potentially useful indicator to characterize the quality of finished composts in regard to production processes and effects of storage conditions.

  16. High-resolution linkage analyses to identify genes that influence Varroa sensitive hygiene behavior in honey bees.

    Science.gov (United States)

    Tsuruda, Jennifer M; Harris, Jeffrey W; Bourgeois, Lanie; Danka, Robert G; Hunt, Greg J

    2012-01-01

    Varroa mites (V. destructor) are a major threat to honey bees (Apis melilfera) and beekeeping worldwide and likely lead to colony decline if colonies are not treated. Most treatments involve chemical control of the mites; however, Varroa has evolved resistance to many of these miticides, leaving beekeepers with a limited number of alternatives. A non-chemical control method is highly desirable for numerous reasons including lack of chemical residues and decreased likelihood of resistance. Varroa sensitive hygiene behavior is one of two behaviors identified that are most important for controlling the growth of Varroa populations in bee hives. To identify genes influencing this trait, a study was conducted to map quantitative trait loci (QTL). Individual workers of a backcross family were observed and evaluated for their VSH behavior in a mite-infested observation hive. Bees that uncapped or removed pupae were identified. The genotypes for 1,340 informative single nucleotide polymorphisms were used to construct a high-resolution genetic map and interval mapping was used to analyze the association of the genotypes with the performance of Varroa sensitive hygiene. We identified one major QTL on chromosome 9 (LOD score = 3.21) and a suggestive QTL on chromosome 1 (LOD = 1.95). The QTL confidence interval on chromosome 9 contains the gene 'no receptor potential A' and a dopamine receptor. 'No receptor potential A' is involved in vision and olfaction in Drosophila, and dopamine signaling has been previously shown to be required for aversive olfactory learning in honey bees, which is probably necessary for identifying mites within brood cells. Further studies on these candidate genes may allow for breeding bees with this trait using marker-assisted selection.

  17. Transcriptomic and proteomic analyses of a Wolbachia-free filarial parasite provide evidence of trans-kingdom horizontal gene transfer.

    Directory of Open Access Journals (Sweden)

    Samantha N McNulty

    Full Text Available Most filarial parasites in the subfamilies Onchocercinae and Dirofilariinae depend on Wolbachia endobacteria to successfully carry out their life cycle. Recently published data indicate that the few Wolbachia-free species in these subfamilies were infected in the distant past and have subsequently shed their endosymbionts. We used an integrated transcriptomic and proteomic analysis of Onchocerca flexuosa to explore the molecular mechanisms that allow worms of this species to survive without a bacterial partner. Roche/454 sequencing of the adult transcriptome produced 16,814 isogroup and 47,252 singleton sequences that are estimated to represent approximately 41% of the complete gene set. Sequences similar to 97 Wolbachia genes were identified from the transcriptome, some of which appear on the same transcripts as sequences similar to nematode genes. Computationally predicted peptides, including those with similarity to Wolbachia proteins, were classified at the domain and pathway levels in order to assess the metabolic capabilities of O. flexuosa and compare against the Wolbachia-dependent model filaria, Brugia malayi. Transcript data further facilitated a shotgun proteomic analysis of O. flexuosa adult worm lysate, resulting in the identification of 1,803 proteins. Three of the peptides detected by mass spectroscopy map to two ABC transport-related proteins from Wolbachia. Antibodies raised to one of the Wolbachia-like peptides labeled a single 38 kDa band on Western blots of O. flexuosa lysate and stained specific worm tissues by immunohistology. Future studies will be required to determine the exact functions of Wolbachia-like peptides and proteins in O. flexuosa and to assess their roles in worm biology.

  18. Hidden circuits and argumentation

    Science.gov (United States)

    Leinonen, Risto; Kesonen, Mikko H. P.; Hirvonen, Pekka E.

    2016-11-01

    Despite the relevance of DC circuits in everyday life and schools, they have been shown to cause numerous learning difficulties at various school levels. In the course of this article, we present a flexible method for teaching DC circuits at lower secondary level. The method is labelled as hidden circuits, and the essential idea underlying hidden circuits is in hiding the actual wiring of DC circuits, but to make their behaviour evident for pupils. Pupils are expected to find out the wiring of the circuit which should enhance their learning of DC circuits. We present two possible ways to utilise hidden circuits in a classroom. First, they can be used to test and enhance pupils’ conceptual understanding when pupils are expected to find out which one of the offered circuit diagram options corresponds to the actual circuit shown. This method aims to get pupils to evaluate the circuits holistically rather than locally, and as a part of that aim this method highlights any learning difficulties of pupils. Second, hidden circuits can be used to enhance pupils’ argumentation skills with the aid of argumentation sheet that illustrates the main elements of an argument. Based on the findings from our co-operating teachers and our own experiences, hidden circuits offer a flexible and motivating way to supplement teaching of DC circuits.

  19. The genetic diversity of genus Bacillus and the related genera revealed by 16S rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey

    Directory of Open Access Journals (Sweden)

    Arzu Coleri Cihan

    2012-03-01

    Full Text Available Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%, the facultative thermophiles (14% and the mesophiles (12%. These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16, Brevibacillus (13, Paenibacillus (1 and Thermoactinomycetes (2 were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4-100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6, B. lichenformis (3, B. subtilis (3, B. agri (3, B. smithii (2, T. vulgaris (2 and finally P. barengoltzii (1. In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies.

  20. Applying genotyping (TILLING and phenotyping analyses to elucidate gene function in a chemically induced sorghum mutant population

    Directory of Open Access Journals (Sweden)

    Franks Cleve

    2008-10-01

    Full Text Available Abstract Background Sorghum [Sorghum bicolor (L. Moench] is ranked as the fifth most important grain crop and serves as a major food staple and fodder resource for much of the world, especially in arid and semi-arid regions. The recent surge in sorghum research is driven by its tolerance to drought/heat stresses and its strong potential as a bioenergy feedstock. Completion of the sorghum genome sequence has opened new avenues for sorghum functional genomics. However, the availability of genetic resources, specifically mutant lines, is limited. Chemical mutagenesis of sorghum germplasm, followed by screening for mutants altered in important agronomic traits, represents a rapid and effective means of addressing this limitation. Induced mutations in novel genes of interest can be efficiently assessed using the technique known as Targeting Induced Local Lesion IN Genomes (TILLING. Results A sorghum mutant population consisting of 1,600 lines was generated from the inbred line BTx623 by treatment with the chemical agent ethyl methanesulfonate (EMS. Numerous phenotypes with altered morphological and agronomic traits were observed from M2 and M3 lines in the field. A subset of 768 mutant lines was analyzed by TILLING using four target genes. A total of five mutations were identified resulting in a calculated mutation density of 1/526 kb. Two of the mutations identified by TILLING and verified by sequencing were detected in the gene encoding caffeic acid O-methyltransferase (COMT in two independent mutant lines. The two mutant lines segregated for the expected brown midrib (bmr phenotype, a trait associated with altered lignin content and increased digestibility. Conclusion TILLING as a reverse genetic approach has been successfully applied to sorghum. The diversity of the mutant phenotypes observed in the field, and the density of induced mutations calculated from TILLING indicate that this mutant population represents a useful resource for members of

  1. Analyses of fugu hoxa2 genes provide evidence for subfunctionalization of neural crest cell and rhombomere cis-regulatory modules during vertebrate evolution.

    Science.gov (United States)

    McEllin, Jennifer A; Alexander, Tara B; Tümpel, Stefan; Wiedemann, Leanne M; Krumlauf, Robb

    2016-01-15

    Hoxa2 gene is a primary player in regulation of craniofacial programs of head development in vertebrates. Here we investigate the evolution of a Hoxa2 neural crest enhancer identified originally in mouse by comparing and contrasting the fugu hoxa2a and hoxa2b genes with their orthologous teleost and mammalian sequences. Using sequence analyses in combination with transgenic regulatory assays in zebrafish and mouse embryos we demonstrate subfunctionalization of regulatory activity for expression in hindbrain segments and neural crest cells between these two fugu co-orthologs. hoxa2a regulatory sequences have retained the ability to mediate expression in neural crest cells while those of hoxa2b include cis-elements that direct expression in rhombomeres. Functional dissection of the neural crest regulatory potential of the fugu hoxa2a and hoxa2b genes identify the previously unknown cis-element NC5, which is implicated in generating the differential activity of the enhancers from these genes. The NC5 region plays a similar role in the ability of this enhancer to mediate reporter expression in mice, suggesting it is a conserved component involved in control of neural crest expression of Hoxa2 in vertebrate craniofacial development.

  2. Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies.

    Science.gov (United States)

    Richart, Casey H; Hayashi, Cheryl Y; Hedin, Marshal

    2016-02-01

    Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.

  3. The circuit designer's companion

    CERN Document Server

    Williams, Tim

    2013-01-01

    The Circuit Designer's Companion covers the theoretical aspects and practices in analogue and digital circuit design. Electronic circuit design involves designing a circuit that will fulfill its specified function and designing the same circuit so that every production model of it will fulfill its specified function, and no other undesired and unspecified function.This book is composed of nine chapters and starts with a review of the concept of grounding, wiring, and printed circuits. The subsequent chapters deal with the passive and active components of circuitry design. These topics are foll

  4. Intuitive analog circuit design

    CERN Document Server

    Thompson, Marc

    2013-01-01

    Intuitive Analog Circuit Design outlines ways of thinking about analog circuits and systems that let you develop a feel for what a good, working analog circuit design should be. This book reflects author Marc Thompson's 30 years of experience designing analog and power electronics circuits and teaching graduate-level analog circuit design, and is the ideal reference for anyone who needs a straightforward introduction to the subject. In this book, Dr. Thompson describes intuitive and ""back-of-the-envelope"" techniques for designing and analyzing analog circuits, including transistor amplifi

  5. Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data

    Directory of Open Access Journals (Sweden)

    Pocock Matthew R

    2008-08-01

    Full Text Available Abstract Background There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. Results Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna

  6. Genomic analyses and expression evaluation of thaumatin-like gene family in the cacao fungal pathogen Moniliophthora perniciosa.

    Science.gov (United States)

    Franco, Sulamita de Freitas; Baroni, Renata Moro; Carazzolle, Marcelo Falsarella; Teixeira, Paulo José Pereira Lima; Reis, Osvaldo; Pereira, Gonçalo Amarante Guimarães; Mondego, Jorge Maurício Costa

    2015-10-30

    Thaumatin-like proteins (TLPs) are found in diverse eukaryotes. Plant TLPs, known as Pathogenicity Related Protein (PR-5), are considered fungal inhibitors. However, genes encoding TLPs are frequently found in fungal genomes. In this work, we have identified that Moniliophthora perniciosa, a basidiomycete pathogen that causes the Witches' Broom Disease (WBD) of cacao, presents thirteen putative TLPs from which four are expressed during WBD progression. One of them is similar to small TLPs, which are present in phytopathogenic basidiomycete, such as wheat stem rust fungus Puccinia graminis. Fungi genomes annotation and phylogenetic data revealed a larger number of TLPs in basidiomycetes when comparing with ascomycetes, suggesting that these proteins could be involved in specific traits of mushroom-forming species. Based on the present data, we discuss the contribution of TLPs in the combat against fungal competitors and hypothesize a role of these proteins in M. perniciosa pathogenicity.

  7. Taxonomic relationships among Turkish water frogs as revealed by phylogenetic analyses using mtDNA gene sequences.

    Science.gov (United States)

    Bülbül, Ufuk; Matsui, Masafumi; Kutrup, Bilal; Eto, Koshiro

    2011-12-01

    We assessed taxonomic relationships among Turkish water frogs through estimation of phylogenetic relationships among 62 adult specimens from 44 distinct populations inhabiting seven main geographical regions of Turkey using 2897 bp sequences of the mitochondrial Cytb, 12S rRNA and 16S rRNA genes with equally-weighted parsimony, likelihood, and Bayesian methods of inference. Monophyletic clade (Clade A) of the northwesternmost (Thrace) samples is identified as Pelophylax ridibundus. The other clade (Clade B) consisted of two monophyletic subclades. One of these contains specimens from southernmost populations that are regarded as an unnamed species. The other subclade consists of two lineages, of which one corresponds to P. caralitanus and another to P. bedriagae. Taxonomic relationships of these two species are discussed and recognition of P. caralitanus as a subspecies of P. bedriagae is proposed.

  8. In vivo biochemical and gene expression analyses of the antioxidant activities and hypocholesterolaemic properties of Tamarindus indica fruit pulp extract.

    Directory of Open Access Journals (Sweden)

    Chor Yin Lim

    Full Text Available BACKGROUND: Tamarindus indica (T. indica is a medicinal plant with many biological activities including anti-diabetic, hypolipidaemic and anti-bacterial activities. A recent study demonstrated the hypolipidaemic effect of T. indica fruit pulp in hamsters. However, the biochemical and molecular mechanisms responsible for these effects have not been fully elucidated. Hence, the aims of this study were to evaluate the antioxidant activities and potential hypocholesterolaemic properties of T. indica, using in vitro and in vivo approaches. METHODOLOGY/PRINCIPAL FINDINGS: The in vitro study demonstrated that T. indica fruit pulp had significant amount of phenolic (244.9 ± 10.1 mg GAE/extract and flavonoid (93.9 ± 2.6 mg RE/g extract content and possessed antioxidant activities. In the in vivo study, hamsters fed with high-cholesterol diet for ten weeks showed elevated serum triglyceride, total cholesterol, HDL-C and LDL-C levels. Administration of T. indica fruit pulp to hypercholesterolaemic hamsters significantly lowered serum triglyceride, total cholesterol and LDL-C levels but had no effect on the HDL-C level. The lipid-lowering effect was accompanied with significant increase in the expression of Apo A1, Abcg5 and LDL receptor genes and significant decrease in the expression of HMG-CoA reductase and Mtp genes. Administration of T. indica fruit pulp to hypercholesterolaemic hamsters also protected against oxidative damage by increasing hepatic antioxidant enzymes, antioxidant activities and preventing hepatic lipid peroxidation. CONCLUSION/SIGNIFICANCE: It is postulated that tamarind fruit pulp exerts its hypocholesterolaemic effect by increasing cholesterol efflux, enhancing LDL-C uptake and clearance, suppressing triglyceride accumulation and inhibiting cholesterol biosynthesis. T. indica fruit pulp has potential antioxidative effects and is potentially protective against diet-induced hypercholesterolaemia.

  9. The NOD-like receptor signalling pathway in Helicobacter pylori infection and related gastric cancer: a case-control study and gene expression analyses.

    Directory of Open Access Journals (Sweden)

    Natalia Castaño-Rodríguez

    Full Text Available BACKGROUND: Currently, it is well established that cancer arises in chronically inflamed tissue. A number of NOD-like receptors (NLRs form inflammasomes, intracellular multiprotein complexes critical for generating mature pro-inflammatory cytokines (IL-1β and IL-18. As chronic inflammation of the gastric mucosa is a consequence of Helicobacter pylori infection, we investigated the role of genetic polymorphisms and expression of genes involved in the NLR signalling pathway in H. pylori infection and related gastric cancer (GC. MATERIALS AND METHODS: Fifty-one genetic polymorphisms were genotyped in 310 ethnic Chinese (87 non-cardia GC cases and 223 controls with functional dyspepsia. In addition, gene expression of 84 molecules involved in the NLR signalling pathway was assessed in THP-1 cells challenged with two H. pylori strains, GC026 (GC and 26695 (gastritis. RESULTS: CARD8-rs11672725, NLRP3-rs10754558, NLRP3-rs4612666, NLRP12-rs199475867 and NLRX1-rs10790286 showed significant associations with GC. On multivariate analysis, CARD8-rs11672725 remained a risk factor (OR: 4.80, 95% CI: 1.39-16.58. Further, NLRP12-rs2866112 increased the risk of H. pylori infection (OR: 2.13, 95% CI: 1.22-3.71. Statistical analyses assessing the joint effect of H. pylori infection and the selected polymorphisms revealed strong associations with GC (CARD8, NLRP3, CASP1 and NLRP12 polymorphisms. In gene expression analyses, five genes encoding NLRs were significantly regulated in H. pylori-challenged cells (NLRC4, NLRC5, NLRP9, NLRP12 and NLRX1. Interestingly, persistent up-regulation of NFKB1 with simultaneous down-regulation of NLRP12 and NLRX1 was observed in H. pylori GC026-challenged cells. Further, NF-κB target genes encoding pro-inflammatory cytokines, chemokines and molecules involved in carcinogenesis were markedly up-regulated in H. pylori GC026-challenged cells. CONCLUSIONS: Novel associations between polymorphisms in the NLR signalling pathway (CARD8

  10. Genomic analyses of metal resistance genes in three plant growth promoting bacteria of legume plants in Northwest mine tailings, China

    Institute of Scientific and Technical Information of China (English)

    Pin Xie; Xiuli Hao; Martin Herzberg; Yantao Luo; Dietrich H.Nies; Gehong Wei

    2015-01-01

    To better understand the diversity of metal resistance genetic determinant from microbes that survived at metal tailings in northwest of China,a highly elevated level of heavy metal containing region,genomic analyses was conducted using genome sequence of three native metal-resistant plant growth promoting bacteria (PGPB).It shows that:Mesorhizobium amorphae CCNWGS0123 contains metal ~nsporters from P-type ATPase,CDF (Cation Diffusion Facilitator),HupE/UreJ and CHR (chromate ion transporter) family involved in copper,zinc,nickel as well as chromate resistance and homeostasis.Meanwhile,the putative CopA/CueO system is expected to mediate copper resistance in Sinorhizobium meliloti CCNWSX0020 while ZntA transporter,assisted with putative CzcD,determines zinc tolerance in Agrobacterium tumefaciens CCNWGS0286.The greenhouse experiment provides the consistent evidence of the plant growth promoting effects of these microbes on their hosts by nitrogen fixation and/or indoleacetic acid (IAA) secretion,indicating a potential in-site phytoremediation usage in the mining tailing regions of China.

  11. Heritability and demographic analyses in the large isolated population of Val Borbera suggest advantages in mapping complex traits genes.

    Directory of Open Access Journals (Sweden)

    Michela Traglia

    Full Text Available BACKGROUND: Isolated populations are a useful resource for mapping complex traits due to shared stable environment, reduced genetic complexity and extended Linkage Disequilibrium (LD compared to the general population. Here we describe a large genetic isolate from the North West Apennines, the mountain range that runs through Italy from the North West Alps to the South. METHODOLOGY/PRINCIPAL FINDINGS: The study involved 1,803 people living in 7 villages of the upper Borbera Valley. For this large population cohort, data from genealogy reconstruction, medical questionnaires, blood, anthropometric and bone status QUS parameters were evaluated. Demographic and epidemiological analyses indicated a substantial genetic component contributing to each trait variation as well as overlapping genetic determinants and family clustering for some traits. CONCLUSIONS/SIGNIFICANCE: The data provide evidence for significant heritability of medical relevant traits that will be important in mapping quantitative traits. We suggest that this population isolate is suitable to identify rare variants associated with complex phenotypes that may be difficult to study in larger but more heterogeneous populations.

  12. Electrical Circuits and Water Analogies

    Science.gov (United States)

    Smith, Frederick A.; Wilson, Jerry D.

    1974-01-01

    Briefly describes water analogies for electrical circuits and presents plans for the construction of apparatus to demonstrate these analogies. Demonstrations include series circuits, parallel circuits, and capacitors. (GS)

  13. Functional analyses of a flavonol synthase - like gene from Camellia nitidissima reveal its roles in flavonoid metabolism during floral pigmentation

    Indian Academy of Sciences (India)

    Xing-Wen Zhou; Zheng-Qi Fan; Yue Chen; Yu-Lin Zhu; Ji-Yuan Li; Heng-Fu Yin

    2013-09-01

    The flavonoids metabolic pathway plays central roles in floral coloration, in which anthocyanins and flavonols are derived from common precursors, dihydroflavonols. Flavonol synthase (FLS) catalyses dihydroflavonols into flavonols, which presents a key branch of anthocyanins biosynthesis. The yellow flower of Camellia nitidissima Chi. is a unique feature within the genus Camellia, which makes it a precious resource for breeding yellow camellia varieties. In this work, we characterized the secondary metabolites of pigments during floral development of C. nitidissima and revealed that accumulation of flavonols correlates with floral coloration. We first isolated CnFLS1 and showed that it is a FLS of C. nitidissima by gene family analysis. Second, expression analysis during floral development and different floral organs indicated that the expression level of CnFLS1 was regulated by developmental cues, which was in agreement with the accumulating pattern of flavonols. Furthermore, over-expression of CnFLS1 in Nicotiana tabacum altered floral colour into white or light yellow, and metabolic analysis showed significant increasing of flavonols and reducing of anthocyanins in transgenic plants. Our work suggested CnFLS1 plays critical roles in yellow colour pigmentation and is potentially a key point of genetic engineering toward colour modification in Camellia.

  14. Synthetic analog and digital circuits for cellular computation and memory

    OpenAIRE

    Purcell, Oliver; Lu, Timothy K.

    2014-01-01

    Biological computation is a major area of focus in synthetic biology because it has the potential to enable a wide range of applications. Synthetic biologists have applied engineering concepts to biological systems in order to construct progressively more complex gene circuits capable of processing information in living cells. Here, we review the current state of computational genetic circuits and describe artificial gene circuits that perform digital and analog computation. We then discuss r...

  15. Cloning and analysizing the up-regulated expression of transthyretin-related gene(LR1) in rat liver regeneration following short interval successive partial hepatectomy

    Institute of Scientific and Technical Information of China (English)

    Cun-Shuan Xu; Yu-Chang Li; Jun-Tang Lin; Hui-Yong Zhang; Yun-Han Zhang

    2003-01-01

    AIM: Cloning and analysizing the up-regulated expressionof transthyretin-related gene following short intervalsuccessive partial hepatectomy (SISPH) to elucidate themechanism of differentiation, division, dedifferentiation andredifferentiation in rat liver regeneration (LR).METHODS: Lobus external sinister and lobus centralissinister, lobus centralis, lobus dexter, lobus candatus wereremoved one by one from rat liver at four different time points4, 36, 36 and 36 hr (total time: 4 hr, 40 hr, 76 hr, 112 hr)respectively. Suppression subtractive hybridization (SSH) wascarried out by using normal rat liver tissue as driver and thetissue following short interval successive partial hepatectomy(SISPH) as tester to construct a highly efficient forward-subtractive cDNA library. After screening, an interested ESTfragment was selected by SSH and primers were designedaccording to the sequence of the EST to clone the full-lengthcDNA fragment using RACE (rapid amplification of cDNAend). Homologous detection was performed between thefull-lenth cDNA and Genbank.RESULTS: Forward suppression subtractive hybridization(FSSH) library between 0 h and 112 h following SISPH wasconstructed and an up-regulated full-length cDNA (namedLR1), which was related with the transthyretin gene, wascloned by rapid amplification of cDNA end. It was suggestedthat the gene is involved in the cellular dedifferentiation inLR following SISPH.CONCLUSION: Some genes were up-regulated in 112 hfollowing SISPH in rat. LR1 is one of these up-regulatedexpression genes which may play an important role in rat LR.

  16. Circuits on Cylinders

    DEFF Research Database (Denmark)

    Hansen, Kristoffer Arnsfelt; Miltersen, Peter Bro; Vinay, V

    2006-01-01

    We consider the computational power of constant width polynomial size cylindrical circuits and nondeterministic branching programs. We show that every function computed by a Pi2 o MOD o AC0 circuit can also be computed by a constant width polynomial size cylindrical nondeterministic branching...... program (or cylindrical circuit) and that every function computed by a constant width polynomial size cylindrical circuit belongs to ACC0....

  17. Electric circuits essentials

    CERN Document Server

    REA, Editors of

    2012-01-01

    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Electric Circuits I includes units, notation, resistive circuits, experimental laws, transient circuits, network theorems, techniques of circuit analysis, sinusoidal analysis, polyph

  18. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations.

    Science.gov (United States)

    Iacchei, Matthew; Ben-Horin, Tal; Selkoe, Kimberly A; Bird, Christopher E; García-Rodríguez, Francisco J; Toonen, Robert J

    2013-07-01

    We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; D(est_Chao) = 0.025) and seven nuclear microsatellites (F(ST) = 0.004, P < 0.001; D(est_Chao) = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F(16,988) = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D(est_Chao), R(2) = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R(2) = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F(ST) and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.

  19. Load testing circuit

    DEFF Research Database (Denmark)

    2009-01-01

    A load testing circuit a circuit tests the load impedance of a load connected to an amplifier. The load impedance includes a first terminal and a second terminal, the load testing circuit comprising a signal generator providing a test signal of a defined bandwidth to the first terminal of the load...

  20. Short-circuit logic

    NARCIS (Netherlands)

    Bergstra, J.A.; Ponse, A.

    2010-01-01

    Short-circuit evaluation denotes the semantics of propositional connectives in which the second argument is only evaluated if the first argument does not suffice to determine the value of the expression. In programming, short-circuit evaluation is widely used. A short-circuit logic is a variant of p

  1. Piezoelectric drive circuit

    Science.gov (United States)

    Treu, Jr., Charles A.

    1999-08-31

    A piezoelectric motor drive circuit is provided which utilizes the piezoelectric elements as oscillators and a Meacham half-bridge approach to develop feedback from the motor ground circuit to produce a signal to drive amplifiers to power the motor. The circuit automatically compensates for shifts in harmonic frequency of the piezoelectric elements due to pressure and temperature changes.

  2. Signal sampling circuit

    NARCIS (Netherlands)

    Louwsma, Simon Minze; Vertregt, Maarten

    2011-01-01

    A sampling circuit for sampling a signal is disclosed. The sampling circuit comprises a plurality of sampling channels adapted to sample the signal in time-multiplexed fashion, each sampling channel comprising a respective track-and-hold circuit connected to a respective analogue to digital converte

  3. Signal sampling circuit

    NARCIS (Netherlands)

    Louwsma, Simon Minze; Vertregt, Maarten

    2010-01-01

    A sampling circuit for sampling a signal is disclosed. The sampling circuit comprises a plurality of sampling channels adapted to sample the signal in time-multiplexed fashion, each sampling channel comprising a respective track-and-hold circuit connected to a respective analogue to digital converte

  4. Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals

    Science.gov (United States)

    Heid, Iris M.; Henneman, Peter; Hicks, Andrew; Coassin, Stefan; Winkler, Thomas; Aulchenko, Yurii S.; Fuchsberger, Christian; Song, Kijoung; Hivert, Marie-France; Waterworth, Dawn M.; Timpson, Nicholas J.; Richards, J. Brent; Perry, John R.B.; Tanaka, Toshiko; Amin, Najaf; Kollerits, Barbara; Pichler, Irene; Oostra, Ben A.; Thorand, Barbara; Frants, Rune R.; Illig, Thomas; Dupuis, Josée; Glaser, Beate; Spector, Tim; Guralnik, Jack; Egan, Josephine M.; Florez, Jose C.; Evans, David M.; Soranzo, Nicole; Bandinelli, Stefania; Carlson, Olga D.; Frayling, Timothy M.; Burling, Keith; Smith, George Davey; Mooser, Vincent; Ferrucci, Luigi; Meigs, James B.; Vollenweider, Peter; van Dijk, Ko Willems; Pramstaller, Peter; Kronenberg, Florian; van Duijn, Cornelia M.

    2009-01-01

    Objective Plasma adiponectin is strongly associated with various components of metabolic syndrome, type 2 diabetes and cardiovascular outcomes. Concentrations are highly heritable and differ between men and women. We therefore aimed to investigate the genetics of plasma adiponectin in men and women. Methods We combined genome-wide association scans of three population-based studies including 4659 persons. For the replication stage in 13795 subjects, we selected the 20 top signals of the combined analysis, as well as the 10 top signals with p-values less than 1.0*10-4 for each the men- and the women-specific analyses. We further selected 73 SNPs that were consistently associated with metabolic syndrome parameters in previous genome-wide association studies to check for their association with plasma adiponectin. Results The ADIPOQ locus showed genome-wide significant p-values in the combined (p=4.3*10-24) as well as in both women- and men-specific analyses (p=8.7*10-17 and p=2.5*10-11, respectively). None of the other 39 top signal SNPs showed evidence for association in the replication analysis. None of 73 SNPs from metabolic syndrome loci exhibited association with plasma adiponectin (p>0.01). Conclusions We demonstrated the ADIPOQ gene as the only major gene for plasma adiponectin, which explains 6.7% of the phenotypic variance. We further found that neither this gene nor any of the metabolic syndrome loci explained the sex differences observed for plasma adiponectin. Larger studies are needed to identify more moderate genetic determinants of plasma adiponectin. PMID:20018283

  5. Rapid microcystis cyanophage gene diversification revealed by long- and short-term genetic analyses of the tail sheath gene in a natural pond.

    Science.gov (United States)

    Kimura, Shigeko; Sako, Yoshihiko; Yoshida, Takashi

    2013-04-01

    Viruses influence the abundance of host populations through virus-mediated host cell lysis. Viruses contribute to the generation and maintenance of host diversity, which also results in viral diversity throughout their coevolution. Here, to determine the phage gene diversification throughout the coevolution of host and phage in a natural environment, we investigated the genetic diversity and temporal changes in Microcystis cyanophage populations using a total of 810 sequences of the Ma-LMM01-type cyanophage tail sheath gene (g91) from 2006 to 2011 in a natural pond. The sequences obtained were highly diverse and assigned to 419 different genotypes (GT1 to GT419) clustered at 100% nucleotide sequence similarity. A maximum-parsimony network showed that the genotypes were largely divided into three sequence groups, which were dominated by major genotypes (more than 24 sequences: GT2, GT53, and GT163 in group I; GT25 in group II; and GT1 in group III). These major genotypes coexisted and oscillated throughout the sampling periods, suggesting that the Microcystis-cyanophage coevolution was partly driven by a negative frequency-dependent selection. Meanwhile, the high viral genetic diversity observed was derived from a large number of the variants of each major and moderately frequent genotype (including 7 to 18 sequences: GT7, GT26, GT56, GT149, and GT182 in group I; GT152 in group II) (1 or 2 nucleotide substitutions). The variants almost always co-occurred with their origin genotypes. This manner of variant emergence suggests that increased contact frequency within a host-phage population promotes rapid coevolution in a form of "arms race."

  6. Gene Expression Analyses during Spontaneous Reversal of Cardiomyopathy in Mice with Repressed Nuclear CUG-BP, Elav-Like Family (CELF) Activity in Heart Muscle.

    Science.gov (United States)

    Dasgupta, Twishasri; Coram, Ryan J; Stillwagon, Samantha J; Ladd, Andrea N

    2015-01-01

    CUG-BP, Elav-like family (CELF) proteins regulate cell type- and developmental stage-specific alternative splicing in the heart. Repression of CELF-mediated splicing activity via expression of a nuclear dominant negative CELF protein in heart muscle was previously shown to induce dysregulation of alternative splicing, cardiac dysfunction, cardiac hypertrophy, and dilated cardiomyopathy in MHC-CELFΔ transgenic mice. A "mild" line of MHC-CELFΔ mice that expresses a lower level of the dominant negative protein exhibits cardiac dysfunction and myopathy at a young age, but spontaneously recovers normal cardiac function and heart size with age despite the persistence of splicing defects. To the best of our knowledge, this was the first example of a genetically induced cardiomyopathy that spontaneously recovers without intervention. In this study, we explored the basis for this recovery. We examined whether a transcriptional program regulated by serum response factor (SRF) that is dysregulated in juvenile MHC-CELFΔ mice is restored in the mild line with age, and evaluated global changes in gene expression by microarray analyses. We found that differences in gene expression between the mild line and wild type hearts are greatly reduced in older animals, including a partial recovery of SRF target gene expression. We did not find evidence of a new compensatory pathway being activated in the mild line with age, and propose that recovery may occur due to developmental stage-specific compatibility of CELF-dependent splice variants with the cellular environment of the cardiomyocyte.

  7. Foxtail millet NF-Y families: genome-wide survey and evolution analyses identified two functional genes important in abiotic stresses

    Directory of Open Access Journals (Sweden)

    Zhi-Juan eFeng

    2015-12-01

    Full Text Available It was reported that Nuclear Factor Y (NF-Y genes were involved in abiotic stress in plants. Foxtail millet (Setaria italica, an elite stress tolerant crop, provided an impetus for the investigation of the NF-Y families in abiotic responses. In the present study, a total of 39 NF-Y genes were identified in foxtail millet. Synteny analyses suggested that foxtail millet NF-Y genes had experienced rapid expansion and strong purifying selection during the process of plant evolution. De novo transcriptome assembly of foxtail millet revealed 11 drought up-regulated NF-Y genes. SiNF-YA1 and SiNF-YB8 were highly activated in leaves and/or roots by drought and salt stresses. Abscisic acid (ABA and H2O2 played positive roles in the induction of SiNF-YA1 and SiNF-YB8 under stress treatments. Transient luciferase (LUC expression assays revealed that SiNF-YA1 and SiNF-YB8 could activate the LUC gene driven by the tobacco (Nicotiana tobacam NtERD10, NtLEA5, NtCAT, NtSOD or NtPOD promoter under normal or stress conditions. Overexpression of SiNF-YA1 enhanced drought and salt tolerance by activating stress-related genes NtERD10 and NtCAT1 and by maintaining relatively stable relative water content (RWC and contents of chlorophyll, superoxide dismutase (SOD, peroxidase (POD, catalase (CAT and malondialdehyde (MDA in transgenic lines under stresses. SiNF-YB8 regulated expression of NtSOD, NtPOD, NtLEA5 and NtERD10 and conferred relatively high RWC and chlorophyll contents and low MDA content, resulting in drought and osmotic tolerance in transgenic lines under stresses. Therefore, SiNF-YA1 and SiNF-YB8 could activate stress-related genes and improve physiological traits, resulting in tolerance to abiotic stresses in plants. All these results will facilitate functional characterization of foxtail millet NF-Ys in future studies.

  8. Foxtail Millet NF-Y Families: Genome-Wide Survey and Evolution Analyses Identified Two Functional Genes Important in Abiotic Stresses.

    Science.gov (United States)

    Feng, Zhi-Juan; He, Guan-Hua; Zheng, Wei-Jun; Lu, Pan-Pan; Chen, Ming; Gong, Ya-Ming; Ma, You-Zhi; Xu, Zhao-Shi

    2015-01-01

    It was reported that Nuclear Factor Y (NF-Y) genes were involved in abiotic stress in plants. Foxtail millet (Setaria italica), an elite stress tolerant crop, provided an impetus for the investigation of the NF-Y families in abiotic responses. In the present study, a total of 39 NF-Y genes were identified in foxtail millet. Synteny analyses suggested that foxtail millet NF-Y genes had experienced rapid expansion and strong purifying selection during the process of plant evolution. De novo transcriptome assembly of foxtail millet revealed 11 drought up-regulated NF-Y genes. SiNF-YA1 and SiNF-YB8 were highly activated in leaves and/or roots by drought and salt stresses. Abscisic acid (ABA) and H2O2 played positive roles in the induction of SiNF-YA1 and SiNF-YB8 under stress treatments. Transient luciferase (LUC) expression assays revealed that SiNF-YA1 and SiNF-YB8 could activate the LUC gene driven by the tobacco (Nicotiana tobacam) NtERD10, NtLEA5, NtCAT, NtSOD, or NtPOD promoter under normal or stress conditions. Overexpression of SiNF-YA1 enhanced drought and salt tolerance by activating stress-related genes NtERD10 and NtCAT1 and by maintaining relatively stable relative water content (RWC) and contents of chlorophyll, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and malondialdehyde (MDA) in transgenic lines under stresses. SiNF-YB8 regulated expression of NtSOD, NtPOD, NtLEA5, and NtERD10 and conferred relatively high RWC and chlorophyll contents and low MDA content, resulting in drought and osmotic tolerance in transgenic lines under stresses. Therefore, SiNF-YA1 and SiNF-YB8 could activate stress-related genes and improve physiological traits, resulting in tolerance to abiotic stresses in plants. All these results will facilitate functional characterization of foxtail millet NF-Ys in future studies.

  9. The carrier-generating analysis of MEMS gyroscope interface circuit

    Directory of Open Access Journals (Sweden)

    GuangMin Yuan

    2014-03-01

    Full Text Available In this paper, the main factors which influence the noise ratio of gyroscope output signal were analysed, according to the MEMS gyro interface circuit technology. A working principle of a carrier in the gyroscope circuit was discussed, the process formula of the carrier amplitude and frequency in the interface circuit of modulation and demodulation was deduced, and the error components lead-in from carrier to gyroscope circuit was distinguished. Several commonly used carrier-generating circuit schemes were analysed and compared, and a carrier-generating program in the interface circuits of the micro-gyroscope was designed, which was applied in a MEMS gyro developed by our laboratory. The measurement results show that the amplitude stability and frequency stability is 1.3 ppm and 12 ppm, respectively, meeting the performance requirements of carrier generating in the MEMS gyro circuit.

  10. The carrier-generating analysis of MEMS gyroscope interface circuit

    Science.gov (United States)

    Yuan, GuangMin; Yuan, Weizheng; Zhu, Xiaobo; Chang, HongLong

    2014-03-01

    In this paper, the main factors which influence the noise ratio of gyroscope output signal were analysed, according to the MEMS gyro interface circuit technology. A working principle of a carrier in the gyroscope circuit was discussed, the process formula of the carrier amplitude and frequency in the interface circuit of modulation and demodulation was deduced, and the error components lead-in from carrier to gyroscope circuit was distinguished. Several commonly used carrier-generating circuit schemes were analysed and compared, and a carrier-generating program in the interface circuits of the micro-gyroscope was designed, which was applied in a MEMS gyro developed by our laboratory. The measurement results show that the amplitude stability and frequency stability is 1.3 ppm and 12 ppm, respectively, meeting the performance requirements of carrier generating in the MEMS gyro circuit.

  11. Reversible Logic Circuit Synthesis

    CERN Document Server

    Shende, V V; Markov, I L; Prasad, A K; Hayes, John P.; Markov, Igor L.; Prasad, Aditya K.; Shende, Vivek V.

    2002-01-01

    Reversible, or information-lossless, circuits have applications in digital signal processing, communication, computer graphics and cryptography. They are also a fundamental requirement for quantum computation. We investigate the synthesis of reversible circuits that employ a minimum number of gates and contain no redundant input-output line-pairs (temporary storage channels). We propose new constructions for reversible circuits composed of NOT, Controlled-NOT, and TOFFOLI gates (the CNT gate library) based on permutation theory. A new algorithm is given to synthesize optimal reversible circuits using an arbitrary gate library. We also describe much faster heuristic algorithms. We also pursue applications of the proposed techniques to the synthesis of quantum circuits.

  12. Comparative in vitro and in silico analyses of variants in splicing regions of BRCA1 and BRCA2 genes and characterization of novel pathogenic mutations.

    Directory of Open Access Journals (Sweden)

    Mara Colombo

    Full Text Available Several unclassified variants (UVs have been identified in splicing regions of disease-associated genes and their characterization as pathogenic mutations or benign polymorphisms is crucial for the understanding of their role in disease development. In this study, 24 UVs located at BRCA1 and BRCA2 splice sites were characterized by transcripts analysis. These results were used to evaluate the ability of nine bioinformatics programs in predicting genetic variants causing aberrant splicing (spliceogenic variants and the nature of aberrant transcripts. Eleven variants in BRCA1 and 8 in BRCA2, including 8 not previously characterized at transcript level, were ascertained to affect mRNA splicing. Of these, 16 led to the synthesis of aberrant transcripts containing premature termination codons (PTCs, 2 to the up-regulation of naturally occurring alternative transcripts containing PTCs, and one to an in-frame deletion within the region coding for the DNA binding domain of BRCA2, causing the loss of the ability to bind the partner protein DSS1 and ssDNA. For each computational program, we evaluated the rate of non-informative analyses, i.e. those that did not recognize the natural splice sites in the wild-type sequence, and the rate of false positive predictions, i.e., variants incorrectly classified as spliceogenic, as a measure of their specificity, under conditions setting sensitivity of predictions to 100%. The programs that performed better were Human Splicing Finder and Automated Splice Site Analyses, both exhibiting 100% informativeness and specificity. For 10 mutations the activation of cryptic splice sites was observed, but we were unable to derive simple criteria to select, among the different cryptic sites predicted by the bioinformatics analyses, those actually used. Consistent with previous reports, our study provides evidences that in silico tools can be used for selecting splice site variants for in vitro analyses. However, the latter

  13. Genes for the Major Structural Components of Thermotogales Species' Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs

    Energy Technology Data Exchange (ETDEWEB)

    Petrus, Amanda K. [Univ. of Connecticut, Storrs, CT (United States); Swithers, Kristen S. [Univ. of Connecticut, Storrs, CT (United States); Ranjit, Chaman R. [Univ. of Connecticut, Storrs, CT (United States); Wu, Si [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Brewer, Heather M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gogarten, J. Peter [Univ. of Connecticut, Storrs, CT (United States); Pasa-Tolic, Ljiljana [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Noll, Kenneth M. [Univ. of Connecticut, Storrs, CT (United States)

    2012-06-29

    The unifying structural characteristic of members of the bacterial order Thermotogales is an unusual cell envelope that includes a loose-fitting sheath around each cell, often called a toga. Only two toga-associated structural proteins have been identified in Thermotoga maritima: the anchor protein OmpA1 (previously termed Ompα) and the porin OmpB (previously termed Ompβ). The gene encoding OmpA (ompA1) was assigned in the genome sequence to TM0477, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. Here we identify the ompB gene as TM0476, determined by LC/MS/MS analysis of the native OmpB protein purified from T. maritima cells. The purified OmpB had β-sheet secondary structure as determined by circular dichroism. Analysis of the sequence of ompB product shows it has porin characteristics including a carboxy terminus anchoring motif and a porin-specific amino acid composition. Orthologs of ompB were found in the genomes of some, but not all, Thermotogales. Those without orthologs have putative analogs. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one to three OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1(TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath.

  14. Feedback in analog circuits

    CERN Document Server

    Ochoa, Agustin

    2016-01-01

    This book describes a consistent and direct methodology to the analysis and design of analog circuits with particular application to circuits containing feedback. The analysis and design of circuits containing feedback is generally presented by either following a series of examples where each circuit is simplified through the use of insight or experience (someone else’s), or a complete nodal-matrix analysis generating lots of algebra. Neither of these approaches leads to gaining insight into the design process easily. The author develops a systematic approach to circuit analysis, the Driving Point Impedance and Signal Flow Graphs (DPI/SFG) method that does not require a-priori insight to the circuit being considered and results in factored analysis supporting the design function. This approach enables designers to account fully for loading and the bi-directional nature of elements both in the feedback path and in the amplifier itself, properties many times assumed negligible and ignored. Feedback circuits a...

  15. Exact Threshold Circuits

    DEFF Research Database (Denmark)

    Hansen, Kristoffer Arnsfelt; Podolskii, Vladimir V.

    2010-01-01

    We initiate a systematic study of constant depth Boolean circuits built using exact threshold gates. We consider both unweighted and weighted exact threshold gates and introduce corresponding circuit classes. We next show that this gives a hierarchy of classes that seamlessly interleave with the ......We initiate a systematic study of constant depth Boolean circuits built using exact threshold gates. We consider both unweighted and weighted exact threshold gates and introduce corresponding circuit classes. We next show that this gives a hierarchy of classes that seamlessly interleave...... with the well-studied corresponding hierarchies defined using ordinary threshold gates. A major open problem in Boolean circuit complexity is to provide an explicit super-polynomial lower bound for depth two threshold circuits. We identify the class of depth two exact threshold circuits as a natural subclass...

  16. Regulatory circuit for responses of nitrogen catabolic gene expression to the GLN3 and DAL80 proteins and nitrogen catabolite repression in Saccharomyces cerevisiae.

    OpenAIRE

    Daugherty, J R; Rai, R; el Berry, H M; Cooper, T. G.

    1993-01-01

    We demonstrate that expression of the UGA1, CAN1, GAP1, PUT1, PUT2, PUT4, and DAL4 genes is sensitive to nitrogen catabolite repression. The expression of all these genes, with the exception of UGA1 and PUT2, also required a functional GLN3 protein. In addition, GLN3 protein was required for expression of the DAL1, DAL2, DAL7, GDH1, and GDH2 genes. The UGA1, CAN1, GAP1, and DAL4 genes markedly increased their expression when the DAL80 locus, encoding a negative regulatory element, was disrupt...

  17. Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation

    DEFF Research Database (Denmark)

    Stegmann, Anders; Hansen, Morten; Wang, Yulan

    2006-01-01

    networks during the differentiation of the small intestinal epithelial cell. In addition we have searched for connections between transcription factors and the villus metabolome. Transcriptome data were generated from mouse small intestinal villus, crypt, and fetal intestinal epithelial cells. Metabolome...... data were generated from crypt and villus cells. Our results show that genes that are upregulated during fetal to adult and crypt to villus differentiation have an overrepresentation of potential hepatocyte nuclear factor (HNF)-4 binding sites in their promoters. Moreover, metabolome analyses by magic...... that are involved in lipid metabolism. Our approach also identifies transcription factors of importance for crypt functions such as DNA replication (E2F) and stem cell maintenance (c-Myc)....

  18. Molecular insights into how a deficiency of amylose affects carbon allocation – carbohydrate and oil analyses and gene expression profiling in the seeds of a rice waxy mutant

    Directory of Open Access Journals (Sweden)

    Zhang Ming-Zhou

    2012-12-01

    Full Text Available Abstract Background Understanding carbon partitioning in cereal seeds is of critical importance to develop cereal crops with enhanced starch yields for food security and for producing specified end-products high in amylose, β-glucan, or fructan, such as functional foods or oils for biofuel applications. Waxy mutants of cereals have a high content of amylopectin and have been well characterized. However, the allocation of carbon to other components, such as β-glucan and oils, and the regulation of the altered carbon distribution to amylopectin in a waxy mutant are poorly understood. In this study, we used a rice mutant, GM077, with a low content of amylose to gain molecular insight into how a deficiency of amylose affects carbon allocation to other end products and to amylopectin. We used carbohydrate analysis, subtractive cDNA libraries, and qPCR to identify candidate genes potentially responsible for the changes in carbon allocation in GM077 seeds. Results Carbohydrate analysis indicated that the content of amylose in GM077 seeds was significantly reduced, while that of amylopectin significantly rose as compared to the wild type BP034. The content of glucose, sucrose, total starch, cell-wall polysaccharides and oil were only slightly affected in the mutant as compared to the wild type. Suppression subtractive hybridization (SSH experiments generated 116 unigenes in the mutant on the wild-type background. Among the 116 unigenes, three, AGP, ISA1 and SUSIBA2-like, were found to be directly involved in amylopectin synthesis, indicating their possible roles in redirecting carbon flux from amylose to amylopectin. A bioinformatics analysis of the putative SUSIBA2-like binding elements in the promoter regions of the upregulated genes indicated that the SUSIBA2-like transcription factor may be instrumental in promoting the carbon reallocation from amylose to amylopectin. Conclusion Analyses of carbohydrate and oil fractions and gene expression

  19. cDNA cloning and expression analyses of phytoene synthase 1, phytoene desaturase and ζ-carotene desaturase genes from Solanum lycopersicum KKU-T34003

    Directory of Open Access Journals (Sweden)

    Krittaya Supathaweewat

    2013-10-01

    Full Text Available We report on the cloning of Psy1, Pds and Zds cDNAs encoding the enzymes responsible for lycopene biosynthesis,namely phytoene synthase 1 (PSY1, phytoene desaturase (PDS and -carotene desaturase (ZDS, respectively, from high-lycopene tomato cultivar, Solanum lycopersicum KKU-T34003. DNA sequence analyses showed that the complete openreading frames of Psy1, Pds and Zds cDNAs were 1,239, 1,752 and 1,767 base pairs in length and encoded proteins of 412,583 and 588 amino acids, respectively. Phylogenetic and the conserved domain analyses suggest that PSY1, PDS and ZDSfrom S. lycopersicum KKU-T34003 potentially have similar structures and biological functions to the corresponding proteinsfrom other plants. Gene expression studies showed that Psy1 was expressed only in the petal and the breaker fruit, whereasthe expressions of Pds and Zds were observed in the petal, the breaker fruit and the leaf. The highest expression level for allgenes was detected in the breaker-stage fruit, suggesting that carotenoid accumulation was developmentally regulated inthe chromoplast-containing tissues.

  20. Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene

    Science.gov (United States)

    Lamendella, R.; Domingo, J.W.S.; Oerther, D.B.; Vogel, J.R.; Stoeckel, D.M.

    2007-01-01

    We evaluated the efficacy, sensitivity, host-specificity, and spatial/temporal dynamics of human- and ruminant-specific 16S rRNA gene Bacteroidetes markers used to assess the sources of fecal pollution in a fecally impacted watershed. Phylogenetic analyses of 1271 fecal and environmental 16S rRNA gene clones were also performed to study the diversity of Bacteroidetes in this watershed. The host-specific assays indicated that ruminant feces were present in 28-54% of the water samples and in all sampling seasons, with increasing frequency in downstream sites. The human-targeted assays indicated that only 3-5% of the water samples were positive for human fecal signals, although a higher percentage of human-associated signals (19-24%) were detected in sediment samples. Phylogenetic analysis indicated that 57% of all water clones clustered with yet-to-be-cultured Bacteroidetes species associated with sequences obtained from ruminant feces, further supporting the prevalence of ruminant contamination in this watershed. However, since several clusters contained sequences from multiple sources, future studies need to consider the potential cosmopolitan nature of these bacterial populations when assessing fecal pollution sources using Bacteroidetes markers. Moreover, additional data is needed in order to understand the distribution of Bacteroidetes host-specific markers and their relationship to water quality regulatory standards. ?? 2006 Federation of European Microbiological Societies.

  1. Sequence analyses of ITS2 and CO1 genes of Paragonimus proliferus obtained in Yunnan province, China and their similarities with those of P. hokuoensis.

    Science.gov (United States)

    Zhou, Ben-Jiang; Yang, Bin-Bin; Doanh, Pham Ngoc; Yang, Zhao-Qing; Xiang, Zheng; Li, Cui-Ying; Shinohara, Akio; Horii, Yoichiro; Nawa, Yukifumi

    2008-05-01

    Among about 50 Paragonimus species, Paragonimus proliferus is a rare species characterized by extremely large metacercariae, most of which are present excysted in the crab hosts. Recently, this species was discovered by us in northern Vietnam as the first record outside of China. DNA sequences of both second internal transcribed spacer region (ITS2) and cytochrome oxidase subunit 1 gene (CO1) genes of the metacercariae and adult worms of P. proliferus of the Vietnamese isolates were identical with those of Paragonimus hokuoensis in the DNA database of the GenBank. To confirm those observations and to clarify the molecular phylogenetic status of P. proliferus, we determined the ITS2 and CO1 sequences of the metacercariae of P. proliferus obtained in Yunnan province, China where the original specimen was discovered. The results show that both ITS2 and CO1 sequences of P. proliferus of the Chinese isolates are identical with those of P. proliferus of the Vietnamese isolates and are also identical with those of P. hokuoensis that appeared in the DNA database (obtained in Yunnan province), suggesting the synonymy of P. hokuoensis with P. proliferus. By phylogenetic tree analyses, all samples of P. proliferus from China and Vietnam together with P. hokuoensis constructed a distinct group within, or very close to, Paragonimus skrjabini complex in both trees.

  2. Genetic and biochemical analyses of chromosome and plasmid gene homologues encoding ICL and ArCP domains in Vibrio anguillarum strain 775.

    Science.gov (United States)

    Di Lorenzo, Manuela; Stork, Michiel; Crosa, Jorge H

    2011-08-01

    Anguibactin, the siderophore produced by Vibrio anguillarum 775 is synthesized from 2,3-dihydroxybenzoic acid (DHBA), cysteine and hydroxyhistamine via a nonribosomal peptide synthetase (NRPS) mechanism. Most of the genes encoding anguibactin biosynthetic proteins are harbored by the pJM1 plasmid. In this work we report the identification of a homologue of the plasmid-encoded angB on the chromosome of strain 775. The product of both genes harbor an isochorismate lyase (ICL) domain that converts isochorismic acid to 2,3-dihydro-2,3-dihydroxybenzoic acid, one of the steps of DHBA synthesis. We show in this work that both ICL domains are functional in the production of DHBA in V. anguillarum as well as in E. coli. Substitution by alanine of the aspartic acid residue in the active site of both ICL domains completely abolishes their isochorismate lyase activity in vivo. The two proteins also carry an aryl carrier protein (ArCP) domain. In contrast with the ICL domains only the plasmid encoded ArCP can participate in anguibactin production as determined by complementation analyses and site-directed mutagenesis in the active site of the plasmid encoded protein, S248A. The site-directed mutants, D37A in the ICL domain and S248A in the ArCP domain of the plasmid encoded AngB were also tested in vitro and clearly show the importance of each residue for the domain function and that each domain operates independently.

  3. Robust design of biological circuits: evolutionary systems biology approach.

    Science.gov (United States)

    Chen, Bor-Sen; Hsu, Chih-Yuan; Liou, Jing-Jia

    2011-01-01

    Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter fluctuations and environmental molecular noise from the cellular context in the host cell. Based on evolutionary systems biology algorithm, the design parameters of target gene circuits can evolve to specific values in order to robustly track a desired biologic function in spite of intrinsic and environmental noise. The fitness function is selected to be inversely proportional to the tracking error so that the evolutionary biological circuit can achieve the optimal tracking mimicking the evolutionary process of a gene circuit. Finally, several design examples are given in silico with the Monte Carlo simulation to illustrate the design procedure and to confirm the robust performance of the proposed design method. The result shows that the designed gene circuits can robustly track desired behaviors with minimal errors even with nontrivial intrinsic and external noise.

  4. Regulatory circuit for responses of nitrogen catabolic gene expression to the GLN3 and DAL80 proteins and nitrogen catabolite repression in Saccharomyces cerevisiae.

    Science.gov (United States)

    Daugherty, J R; Rai, R; el Berry, H M; Cooper, T G

    1993-01-01

    We demonstrate that expression of the UGA1, CAN1, GAP1, PUT1, PUT2, PUT4, and DAL4 genes is sensitive to nitrogen catabolite repression. The expression of all these genes, with the exception of UGA1 and PUT2, also required a functional GLN3 protein. In addition, GLN3 protein was required for expression of the DAL1, DAL2, DAL7, GDH1, and GDH2 genes. The UGA1, CAN1, GAP1, and DAL4 genes markedly increased their expression when the DAL80 locus, encoding a negative regulatory element, was disrupted. Expression of the GDH1, PUT1, PUT2, and PUT4 genes also responded to DAL80 disruption, but much more modestly. Expression of GLN1 and GDH2 exhibited parallel responses to the provision of asparagine and glutamine as nitrogen sources but did not follow the regulatory responses noted above for the nitrogen catabolic genes such as DAL5. Steady-state mRNA levels of both genes did not significantly decrease when glutamine was provided as nitrogen source but were lowered by the provision of asparagine. They also did not respond to disruption of DAL80.

  5. Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2010-05-01

    Full Text Available Abstract Background The neonatal bovine mammary fat pad (MFP surrounding the mammary parenchyma (PAR is thought to exert proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones. We used bioinformatics to characterize transcriptomics differences between PAR and MFP from ~65 d old Holstein heifers. Data were mined to uncover potential crosstalk through the analyses of signaling molecules preferentially expressed in one tissue relative to the other. Results Over 9,000 differentially expressed genes (DEG; False discovery rate ≤ 0.05 were found of which 1,478 had a ≥1.5-fold difference between PAR and MFP. Within the DEG highly-expressed in PAR vs. MFP (n = 736 we noted significant enrichment of functions related to cell cycle, structural organization, signaling, and DNA/RNA metabolism. Only actin cytoskeletal signaling was significant among canonical pathways. DEG more highly-expressed in MFP vs. PAR (n = 742 belong to lipid metabolism, signaling, cell movement, and immune-related functions. Canonical pathways associated with metabolism and signaling, particularly immune- and metabolism-related were significantly-enriched. Network analysis uncovered a central role of MYC, TP53, and CTNNB1 in controlling expression of DEG highly-expressed in PAR vs. MFP. Similar analysis suggested a central role for PPARG, KLF2, EGR2, and EPAS1 in regulating expression of more highly-expressed DEG in MFP vs. PAR. Gene network analyses revealed putative inter-tissue crosstalk between cytokines and growth factors preferentially expressed in one tissue (e.g., ANGPTL1, SPP1, IL1B in PAR vs. MFP; ADIPOQ, IL13, FGF2, LEP in MFP vs. PAR with DEG preferentially expressed in the other tissue, particularly transcription factors or pathways (e.g., MYC, TP53, and actin cytoskeletal signaling in PAR vs. MFP; PPARG and LXR/RXR Signaling in MFP vs. PAR. Conclusions Functional analyses underscored a reciprocal influence in

  6. Analog circuit design

    CERN Document Server

    Dobkin, Bob

    2012-01-01

    Analog circuit and system design today is more essential than ever before. With the growth of digital systems, wireless communications, complex industrial and automotive systems, designers are being challenged to develop sophisticated analog solutions. This comprehensive source book of circuit design solutions aids engineers with elegant and practical design techniques that focus on common analog challenges. The book's in-depth application examples provide insight into circuit design and application solutions that you can apply in today's demanding designs. <

  7. Parallelizing quantum circuit synthesis

    OpenAIRE

    Di Matteo, Olivia; Mosca, Michele

    2016-01-01

    Quantum circuit synthesis is the process in which an arbitrary unitary operation is decomposed into a sequence of gates from a universal set, typically one which a quantum computer can implement both efficiently and fault-tolerantly. As physical implementations of quantum computers improve, the need is growing for tools which can effectively synthesize components of the circuits and algorithms they will run. Existing algorithms for exact, multi-qubit circuit synthesis scale exponentially in t...

  8. Regenerative feedback resonant circuit

    Science.gov (United States)

    Jones, A. Mark; Kelly, James F.; McCloy, John S.; McMakin, Douglas L.

    2014-09-02

    A regenerative feedback resonant circuit for measuring a transient response in a loop is disclosed. The circuit includes an amplifier for generating a signal in the loop. The circuit further includes a resonator having a resonant cavity and a material located within the cavity. The signal sent into the resonator produces a resonant frequency. A variation of the resonant frequency due to perturbations in electromagnetic properties of the material is measured.

  9. Analog circuits cookbook

    CERN Document Server

    Hickman, Ian

    2013-01-01

    Analog Circuits Cookbook presents articles about advanced circuit techniques, components and concepts, useful IC for analog signal processing in the audio range, direct digital synthesis, and ingenious video op-amp. The book also includes articles about amplitude measurements on RF signals, linear optical imager, power supplies and devices, and RF circuits and techniques. Professionals and students of electrical engineering will find the book informative and useful.

  10. Timergenerator circuits manual

    CERN Document Server

    Marston, R M

    2013-01-01

    Timer/Generator Circuits Manual is an 11-chapter text that deals mainly with waveform generator techniques and circuits. Each chapter starts with an explanation of the basic principles of its subject followed by a wide range of practical circuit designs. This work presents a total of over 300 practical circuits, diagrams, and tables.Chapter 1 outlines the basic principles and the different types of generator. Chapters 2 to 9 deal with a specific type of waveform generator, including sine, square, triangular, sawtooth, and special waveform generators pulse. These chapters also include pulse gen

  11. CMOS circuits manual

    CERN Document Server

    Marston, R M

    1995-01-01

    CMOS Circuits Manual is a user's guide for CMOS. The book emphasizes the practical aspects of CMOS and provides circuits, tables, and graphs to further relate the fundamentals with the applications. The text first discusses the basic principles and characteristics of the CMOS devices. The succeeding chapters detail the types of CMOS IC, including simple inverter, gate and logic ICs and circuits, and complex counters and decoders. The last chapter presents a miscellaneous collection of two dozen useful CMOS circuits. The book will be useful to researchers and professionals who employ CMOS circu

  12. Electronic devices and circuits

    CERN Document Server

    Pridham, Gordon John

    1968-01-01

    Electronic Devices and Circuits, Volume 1 deals with the design and applications of electronic devices and circuits such as passive components, diodes, triodes and transistors, rectification and power supplies, amplifying circuits, electronic instruments, and oscillators. These topics are supported with introductory network theory and physics. This volume is comprised of nine chapters and begins by explaining the operation of resistive, inductive, and capacitive elements in direct and alternating current circuits. The theory for some of the expressions quoted in later chapters is presented. Th

  13. Circuits and filters handbook

    CERN Document Server

    Chen, Wai-Kai

    2003-01-01

    A bestseller in its first edition, The Circuits and Filters Handbook has been thoroughly updated to provide the most current, most comprehensive information available in both the classical and emerging fields of circuits and filters, both analog and digital. This edition contains 29 new chapters, with significant additions in the areas of computer-aided design, circuit simulation, VLSI circuits, design automation, and active and digital filters. It will undoubtedly take its place as the engineer's first choice in looking for solutions to problems encountered in the design, analysis, and behavi

  14. MOS integrated circuit design

    CERN Document Server

    Wolfendale, E

    2013-01-01

    MOS Integral Circuit Design aims to help in the design of integrated circuits, especially large-scale ones, using MOS Technology through teaching of techniques, practical applications, and examples. The book covers topics such as design equation and process parameters; MOS static and dynamic circuits; logic design techniques, system partitioning, and layout techniques. Also featured are computer aids such as logic simulation and mask layout, as well as examples on simple MOS design. The text is recommended for electrical engineers who would like to know how to use MOS for integral circuit desi

  15. Security electronics circuits manual

    CERN Document Server

    MARSTON, R M

    1998-01-01

    Security Electronics Circuits Manual is an invaluable guide for engineers and technicians in the security industry. It will also prove to be a useful guide for students and experimenters, as well as providing experienced amateurs and DIY enthusiasts with numerous ideas to protect their homes, businesses and properties.As with all Ray Marston's Circuits Manuals, the style is easy-to-read and non-mathematical, with the emphasis firmly on practical applications, circuits and design ideas. The ICs and other devices used in the practical circuits are modestly priced and readily available ty

  16. Protein-Protein Interaction and Pathway Analyses of Top Schizophrenia Genes Reveal Schizophrenia Susceptibility Genes Converge on Common Molecular Networks and Enrichment of Nucleosome (Chromatin) Assembly Genes in Schizophrenia Susceptibility Loci

    OpenAIRE

    Luo, Xiongjian; Huang, Liang; Jia, Peilin; Li, Ming; SU, Bing; Zhao, Zhongming; Gan, Lin

    2013-01-01

    Recent genome-wide association studies have identified many promising schizophrenia candidate genes and demonstrated that common polygenic variation contributes to schizophrenia risk. However, whether these genes represent perturbations to a common but limited set of underlying molecular processes (pathways) that modulate risk to schizophrenia remains elusive, and it is not known whether these genes converge on common biological pathways (networks) or represent different pathways. In addition...

  17. Isolation and selection of suitable reference genes for real-time PCR analyses in the skeletal muscle of the fine flounder in response to nutritional status: assessment and normalization of gene expression of growth-related genes.

    Science.gov (United States)

    Fuentes, Eduardo N; Safian, Diego; Valdés, Juan Antonio; Molina, Alfredo

    2013-08-01

    In the present study, different reference genes were isolated, and their stability in the skeletal muscle of fine flounder subjected to different nutritional states was assessed using geNorm and NormFinder. The combinations between 18S and ActB; Fau and 18S; and Fau and Tubb were chosen as the most stable gene combinations in feeding, long-term fasting and refeeding, and short-term refeeding conditions, respectively. In all periods, ActB was identified as the single least stable gene. Subsequently, the expression of the myosin heavy chain (MYH) and the insulin-like growth factor-I receptor (IGF-IR) was assessed. A large variation in MYH and IGF-IR expression was found depending on the reference gene that was chosen for normalizing the expression of both genes. Using the most stable reference genes, mRNA levels of MYH decreased and IGF-IR increased during fasting, with both returning to basal levels during refeeding. However, the drop in mRNA levels for IGF-IR occurred during short-term refeeding, in contrast with the observed events in the expression of MYH, which occurred during long-term refeeding. The present study highlights the vast differences incurred when using unsuitable versus suitable reference genes for normalizing gene expression, pointing out that normalization without proper validation could result in a bias of gene expression.

  18. Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs.

    Directory of Open Access Journals (Sweden)

    Amanda K Petrus

    Full Text Available The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Ompα and the porin OmpB (or Ompβ. The gene encoding OmpA1 (ompA1 was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant β-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had β-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477 and ompA2 (TM1729, both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath.

  19. Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs

    Energy Technology Data Exchange (ETDEWEB)

    Petrus, Amanda K.; Swithers, Kristen S.; Ranjit, Chaman R.; Wu, Si; Brewer, Heather M.; Gogarten, J Peter; Pasa-Tolic, Ljiljana; Noll, Kenneth M.

    2012-06-29

    The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Ompa) and the porin OmpB (or Ompb). The gene encoding OmpA1 (ompA1) was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant b-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had b-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath.

  20. Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs

    Science.gov (United States)

    Petrus, Amanda K.; Swithers, Kristen S.; Ranjit, Chaman; Wu, Si; Brewer, Heather M.; Gogarten, J. Peter; Pasa-Tolic, Ljiljana; Noll, Kenneth M.

    2012-01-01

    The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Ompα) and the porin OmpB (or Ompβ). The gene encoding OmpA1 (ompA1) was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant β-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had β-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath. PMID:22768259

  1. Kvalitative analyser ..

    DEFF Research Database (Denmark)

    Boolsen, Merete Watt

    bogen forklarer de fundamentale trin i forskningsprocessen og applikerer dem på udvalgte kvalitative analyser: indholdsanalyse, Grounded Theory, argumentationsanalyse og diskursanalyse......bogen forklarer de fundamentale trin i forskningsprocessen og applikerer dem på udvalgte kvalitative analyser: indholdsanalyse, Grounded Theory, argumentationsanalyse og diskursanalyse...

  2. Protein-protein interaction and pathway analyses of top schizophrenia genes reveal schizophrenia susceptibility genes converge on common molecular networks and enrichment of nucleosome (chromatin) assembly genes in schizophrenia susceptibility loci.

    Science.gov (United States)

    Luo, Xiongjian; Huang, Liang; Jia, Peilin; Li, Ming; Su, Bing; Zhao, Zhongming; Gan, Lin

    2014-01-01

    Recent genome-wide association studies have identified many promising schizophrenia candidate genes and demonstrated that common polygenic variation contributes to schizophrenia risk. However, whether these genes represent perturbations to a common but limited set of underlying molecular processes (pathways) that modulate risk to schizophrenia remains elusive, and it is not known whether these genes converge on common biological pathways (networks) or represent different pathways. In addition, the theoretical and genetic mechanisms underlying the strong genetic heterogeneity of schizophrenia remain largely unknown. Using 4 well-defined data sets that contain top schizophrenia susceptibility genes and applying protein-protein interaction (PPI) network analysis, we investigated the interactions among proteins encoded by top schizophrenia susceptibility genes. We found proteins encoded by top schizophrenia susceptibility genes formed a highly significant interconnected network, and, compared with random networks, these PPI networks are statistically highly significant for both direct connectivity and indirect connectivity. We further validated these results using empirical functional data (transcriptome data from a clinical sample). These highly significant findings indicate that top schizophrenia susceptibility genes encode proteins that significantly directly interacted and formed a densely interconnected network, suggesting perturbations of common underlying molecular processes or pathways that modulate risk to schizophrenia. Our findings that schizophrenia susceptibility genes encode a highly interconnected protein network may also provide a novel explanation for the observed genetic heterogeneity of schizophrenia, ie, mutation in any member of this molecular network will lead to same functional consequences that eventually contribute to risk of schizophrenia.

  3. Synchronizing Hyperchaotic Circuits

    DEFF Research Database (Denmark)

    Tamasevicius, Arunas; Cenys, Antanas; Namajunas, Audrius;

    1997-01-01

    Regarding possible applications to secure communications the technique of synchronizing hyperchaotic circuits with a single dynamical variable is discussed. Several specific examples including the fourth-order circuits with two positive Lyapunov exponents as well as the oscillator with a delay line...

  4. A Virtual Circuits Lab

    Science.gov (United States)

    Vick, Matthew E.

    2010-01-01

    The University of Colorado's Physics Education Technology (PhET) website offers free, high-quality simulations of many physics experiments that can be used in the classroom. The Circuit Construction Kit, for example, allows students to safely and constructively play with circuit components while learning the mathematics behind many circuit…

  5. Genetic circuit design automation.

    Science.gov (United States)

    Nielsen, Alec A K; Der, Bryan S; Shin, Jonghyeon; Vaidyanathan, Prashant; Paralanov, Vanya; Strychalski, Elizabeth A; Ross, David; Densmore, Douglas; Voigt, Christopher A

    2016-04-01

    Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits forEscherichia coli(880,000 base pairs of DNA), for which each DNA sequence was built as predicted by the software with no additional tuning. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts), and across all circuits 92% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decision-making, control, sensing, or spatial organization.

  6. Gene expression analyses of essential catch factors in the smooth and striated adductor muscles of larval, juvenile and adult great scallop (Pecten maximus).

    Science.gov (United States)

    Andersen, Øivind; Torgersen, Jacob S; Pagander, Helene H; Magnesen, Thorolf; Johnston, Ian A

    2009-01-01

    The scallop adductor muscle consists of striated fibres responsible for the fast closure of the shells, and smooth fibres able to maintain tension in a prolonged state of contraction called catch. Formation of the force-bearing catch linkages has been demonstrated to be initiated by dephosphorylation of the key catch-regulating factor twitchin by a calcineurin-like phosphatase, while the involvement of other thick filament proteins is uncertain. Here we report on the development of catchability of the adductor smooth muscle in the great scallop (Pecten maximus) by analysing the spatio-temporal gene expression patterns of the myosin regulatory light chain (MLCr), twitchin, myorod and calcineurin using whole mount in situ hybridization and real-time quantitative PCR. The MLCr signal was identified in the retractor and adductor muscles of the pediveliger larvae, and the juvenile and adult scallop displayed abundant mRNA levels of MLCr in the smooth and striated adductor muscles. Twitchin was mainly expressed in the smooth adductor muscle during metamorphosis, whereas the adult striated adductor muscle contained seven-folds higher twitchin mRNA levels compared to the smooth portion. Calcineurin expression predominated in the gonads and in the smooth adductor, and five-folds higher mRNA levels were measured in the smooth than in the striated fibres at the adult stage. In contrast to the other genes examined, the expression of myorod was confined to the smooth adductor muscle suggesting that myorod plays a permissive role in the molluscan catch muscles, which are first required at the vulnerable settlement stage as a component of the predator defence system.

  7. Phylogenetic analyses of influenza A (H1N1)pdm09 hemagglutinin gene during and after the pandemic event in Brazil.

    Science.gov (United States)

    Resende, Paola Cristina; Motta, Fernando Couto; Born, Priscila Silva; Machado, Daniela; Caetano, Braulia Costa; Brown, David; Siqueira, Marilda Mendonça

    2015-12-01

    Pandemic influenza A H1N1 [A(H1N1)pdm09] was first detected in Brazil in May 2009, and spread extensively throughout the country causing a peak of infection during June to August 2009. Since then, it has continued to circulate with a seasonal pattern, causing high rates of morbidity and mortality. Over this period, the virus has continually evolved with the accumulation of new mutations. In this study we analyze the phylogenetic relationship in a collection of 220 A(H1N1)pdm09 hemagglutinin (HA) gene sequences collected during and after the pandemic period (2009 to 2014) in Brazil. In addition, we have looked for evidence of viral polymorphisms associated with severe disease and compared the range of viral variants with the vaccine strain (A/California/7/2009) used throughout this period. The phylogenetic analyses in this study revealed the circulation of at least eight genetic groups in Brazil. Two (G6-pdm and G7-pdm) co-circulated during the pandemic period, showing an early pattern of viral diversification with a low genetic distance from vaccine strain. Other phylogenetic groups, G5, G6 (including 6B, 6C and 6D subgroups), and G7 were found in the subsequent epidemic seasons from 2011 to 2014. These viruses exhibited more amino acid differences from the vaccine strain with several substitutions at the antigenic sites. This is associated with a theoretical decrease in the vaccine efficacy. Furthermore, we observed that the presence of any polymorphism at residue 222 of the HA gene was significantly associated with severe/fatal cases, reinforcing previous reports that described this residue as a potential virulence marker. This study provides new information about the circulation of some viral variants in Brazil, follows up potential genetic markers associated with virulence and allows infer if the efficacy of the current vaccine against more recent A(H1N1)pdm09 strains may be reduced.

  8. Genetic analyses of Pseudomonas aeruginosa isolated from healthy captive snakes: evidence of high inter- and intrasite dissemination and occurrence of antibiotic resistance genes.

    Science.gov (United States)

    Colinon, Céline; Jocktane, Dominique; Brothier, Elisabeth; Rossolini, Gian Maria; Cournoyer, Benoit; Nazaret, Sylvie

    2010-03-01

    Faecal carriage of Pseudomonas aeruginosa was investigated by selective plating and PCR identification test, among healthy captive snakes from zoological and private collections from France as well as from wild snakes from Guinea. P. aeruginosa faecal carriage among captive snakes was high (72 out of 83 individuals), but low among wild specimen (3 out of 23 individuals). Genetic diversity analyses of the isolates, based on SpeI-PFGE profiles, evidenced five dominant clones or clonal complexes spreading among snakes within a site and between sites and persisting over time. Similar clones or clonal complexes were detected from mouth swabs of the owners and from water and preys used to feed the snakes, evidencing various sources of snake colonization and the first cases of P. aeruginosa cross-contamination between snakes and owners. These observations led to the conclusion that P. aeruginosa behaves as an opportunistic species within snakes in captivity and that colonization and dissemination occurs consecutively to processes similar to those identified within the hospital. Antibiotic susceptibility testing showed that most isolates had a wild-type resistance profile except for one persistent clone isolated from both snakes and preys that harboured multiple antimicrobial resistance genes mediated by an integron carrying the qacH, aadB, aadA2 and cmlA10 cassettes, and a tetA(C)-carrying transposon. Biocides or antibiotics used in the zoological garden could have led to the acquisition of this integron.

  9. Deep sequencing and Circos analyses of antibody libraries reveal antigen-driven selection of Ig VH genes during HIV-1 infection.

    Science.gov (United States)

    Xiao, Madelyne; Prabakaran, Ponraj; Chen, Weizao; Kessing, Bailey; Dimitrov, Dimiter S

    2013-12-01

    The vast diversity of antibody repertoires is largely attributed to heavy chain (V(H)) recombination of variable (V), diversity (D) and joining (J) gene segments. We used 454 sequencing information of the variable domains of the antibody heavy chain repertoires from neonates, normal adults and an HIV-1-infected individual, to analyze, with Circos software, the VDJ pairing patterns at birth, adulthood and a time-dependent response to HIV-1 infection. Our comparative analyses of the Ig VDJ repertoires from these libraries indicated that, from birth to adulthood, VDJ recombination patterns remain the same with some slight changes, whereas some V(H) families are selected and preferentially expressed after long-term infection with HIV-1. We also demonstrated that the immune system responds to HIV-1 chronic infection by selectively expanding certain HV families in an attempt to combat infection. Our findings may have implications for understanding immune responses in pathology as well as for development of new therapeutics and vaccines.

  10. High protists diversity in the plankton of sulfurous lakes and lagoons examined by 18s rRNA gene sequence analyses.

    Science.gov (United States)

    Triadó-Margarit, Xavier; Casamayor, Emilio O

    2015-12-01

    Diversity of small protists was studied in sulfidic and anoxic (euxinic) stratified karstic lakes and coastal lagoons by 18S rRNA gene analyses. We hypothesized a major sulfide effect, reducing protist diversity and richness with only a few specialized populations adapted to deal with low-redox conditions and high-sulfide concentrations. However, genetic fingerprinting suggested similar ecological diversity in anoxic and sulfurous than in upper oxygen rich water compartments with specific populations inhabiting euxinic waters. Many of them agreed with genera previously identified by microscopic observations, but also new and unexpected groups were detected. Most of the sequences matched a rich assemblage of Ciliophora (i.e., Coleps, Prorodon, Plagiopyla, Strombidium, Metopus, Vorticella and Caenomorpha, among others) and algae (mainly Cryptomonadales). Unidentified Cercozoa, Fungi, Stramenopiles and Discoba were recurrently found. The lack of GenBank counterparts was higher in deep hypolimnetic waters and appeared differentially allocated in the different taxa, being higher within Discoba and lower in Cryptophyceae. A larger number of populations than expected were specifically detected in the deep sulfurous waters, with unknown ecological interactions and metabolic capabilities.

  11. Approximate circuits for increased reliability

    Energy Technology Data Exchange (ETDEWEB)

    Hamlet, Jason R.; Mayo, Jackson R.

    2015-12-22

    Embodiments of the invention describe a Boolean circuit having a voter circuit and a plurality of approximate circuits each based, at least in part, on a reference circuit. The approximate circuits are each to generate one or more output signals based on values of received input signals. The voter circuit is to receive the one or more output signals generated by each of the approximate circuits, and is to output one or more signals corresponding to a majority value of the received signals. At least some of the approximate circuits are to generate an output value different than the reference circuit for one or more input signal values; however, for each possible input signal value, the majority values of the one or more output signals generated by the approximate circuits and received by the voter circuit correspond to output signal result values of the reference circuit.

  12. Approximate circuits for increased reliability

    Energy Technology Data Exchange (ETDEWEB)

    Hamlet, Jason R.; Mayo, Jackson R.

    2015-08-18

    Embodiments of the invention describe a Boolean circuit having a voter circuit and a plurality of approximate circuits each based, at least in part, on a reference circuit. The approximate circuits are each to generate one or more output signals based on values of received input signals. The voter circuit is to receive the one or more output signals generated by each of the approximate circuits, and is to output one or more signals corresponding to a majority value of the received signals. At least some of the approximate circuits are to generate an output value different than the reference circuit for one or more input signal values; however, for each possible input signal value, the majority values of the one or more output signals generated by the approximate circuits and received by the voter circuit correspond to output signal result values of the reference circuit.

  13. Troubleshooting analog circuits

    CERN Document Server

    Pease, Robert A

    1991-01-01

    Troubleshooting Analog Circuits is a guidebook for solving product or process related problems in analog circuits. The book also provides advice in selecting equipment, preventing problems, and general tips. The coverage of the book includes the philosophy of troubleshooting; the modes of failure of various components; and preventive measures. The text also deals with the active components of analog circuits, including diodes and rectifiers, optically coupled devices, solar cells, and batteries. The book will be of great use to both students and practitioners of electronics engineering. Other

  14. Modern TTL circuits manual

    CERN Document Server

    Marston, R M

    2013-01-01

    Modern TTL Circuits Manual provides an introduction to the basic principles of Transistor-Transistor Logic (TTL). This book outlines the major features of the 74 series of integrated circuits (ICs) and introduces the various sub-groups of the TTL family.Organized into seven chapters, this book begins with an overview of the basics of digital ICs. This text then examines the symbology and mathematics of digital logic. Other chapters consider a variety of topics, including waveform generator circuitry, clocked flip-flop and counter circuits, special counter/dividers, registers, data latches, com

  15. Plasmonic Nanoguides and Circuits

    CERN Document Server

    Bozhevolnyi, Sergey

    2008-01-01

    Modern communication systems dealing with huge amounts of data at ever increasing speed try to utilize the best aspects of electronic and optical circuits. Electronic circuits are tiny but their operation speed is limited, whereas optical circuits are extremely fast but their sizes are limited by diffraction. Waveguide components utilizing surface plasmon (SP) modes were found to combine the huge optical bandwidth and compactness of electronics, and plasmonics thereby began to be considered as the next chip-scale technology. In this book, the authors concentrate on the SP waveguide configurati

  16. Pragmatic circuits frequency domain

    CERN Document Server

    Eccles, William

    2006-01-01

    Pragmatic Circuits: Frequency Domain goes through the Laplace transform to get from the time domain to topics that include the s-plane, Bode diagrams, and the sinusoidal steady state. This second of three volumes ends with a-c power, which, although it is just a special case of the sinusoidal steady state, is an important topic with unique techniques and terminology. Pragmatic Circuits: Frequency Domain is focused on the frequency domain. In other words, time will no longer be the independent variable in our analysis. The two other volumes in the Pragmatic Circuits series include titles on DC

  17. Optoelectronics circuits manual

    CERN Document Server

    Marston, R M

    2013-01-01

    Optoelectronics Circuits Manual covers the basic principles and characteristics of the best known types of optoelectronic devices, as well as the practical applications of many of these optoelectronic devices. The book describes LED display circuits and LED dot- and bar-graph circuits and discusses the applications of seven-segment displays, light-sensitive devices, optocouplers, and a variety of brightness control techniques. The text also tackles infrared light-beam alarms and multichannel remote control systems. The book provides practical user information and circuitry and illustrations.

  18. Circuit analysis with Multisim

    CERN Document Server

    Baez-Lopez, David

    2011-01-01

    This book is concerned with circuit simulation using National Instruments Multisim. It focuses on the use and comprehension of the working techniques for electrical and electronic circuit simulation. The first chapters are devoted to basic circuit analysis.It starts by describing in detail how to perform a DC analysis using only resistors and independent and controlled sources. Then, it introduces capacitors and inductors to make a transient analysis. In the case of transient analysis, it is possible to have an initial condition either in the capacitor voltage or in the inductor current, or bo

  19. Monolithic microwave integrated circuits

    Science.gov (United States)

    Pucel, R. A.

    Monolithic microwave integrated circuits (MMICs), a new microwave technology which is expected to exert a profound influence on microwave circuit designs for future military systems as well as for the commercial and consumer markets, is discussed. The book contains an historical discussion followed by a comprehensive review presenting the current status in the field. The general topics of the volume are: design considerations, materials and processing considerations, monolithic circuit applications, and CAD, measurement, and packaging techniques. All phases of MMIC technology are covered, from design to testing.

  20. Design theory of digital circuits at switch level

    Institute of Scientific and Technical Information of China (English)

    吴训威; F.Prosser

    1996-01-01

    By analysing problems in the traditional design theory of digital circuits it is proposed that both switching variable and signal variable should be adopted for describing the switching state of internal elements and signal in digital circuits respectively.Based on the above viewpoint the switch-signal theory is established.According to the working principle in CMOS circuits,the related design technique at switch level is developed.By using the practical design examples it is shown that the circuits designed at switch level have simpler structures than their counterparts designed at the traditional gate level since the switch transistors are used as construction units in designs.

  1. Note on homological modeling of the electric circuits

    OpenAIRE

    2014-01-01

    Based on a simple example, it is explained how the homological analysis may be applied for modeling of the electric circuits. The homological branch, mesh and nodal analyses are presented. Geometrical interpretations are given.

  2. Solution methods for very highly integrated circuits.

    Energy Technology Data Exchange (ETDEWEB)

    Nong, Ryan; Thornquist, Heidi K.; Chen, Yao; Mei, Ting; Santarelli, Keith R.; Tuminaro, Raymond Stephen

    2010-12-01

    While advances in manufacturing enable the fabrication of integrated circuits containing tens-to-hundreds of millions of devices, the time-sensitive modeling and simulation necessary to design these circuits poses a significant computational challenge. This is especially true for mixed-signal integrated circuits where detailed performance analyses are necessary for the individual analog/digital circuit components as well as the full system. When the integrated circuit has millions of devices, performing a full system simulation is practically infeasible using currently available Electrical Design Automation (EDA) tools. The principal reason for this is the time required for the nonlinear solver to compute the solutions of large linearized systems during the simulation of these circuits. The research presented in this report aims to address the computational difficulties introduced by these large linearized systems by using Model Order Reduction (MOR) to (i) generate specialized preconditioners that accelerate the computation of the linear system solution and (ii) reduce the overall dynamical system size. MOR techniques attempt to produce macromodels that capture the desired input-output behavior of larger dynamical systems and enable substantial speedups in simulation time. Several MOR techniques that have been developed under the LDRD on 'Solution Methods for Very Highly Integrated Circuits' will be presented in this report. Among those presented are techniques for linear time-invariant dynamical systems that either extend current approaches or improve the time-domain performance of the reduced model using novel error bounds and a new approach for linear time-varying dynamical systems that guarantees dimension reduction, which has not been proven before. Progress on preconditioning power grid systems using multi-grid techniques will be presented as well as a framework for delivering MOR techniques to the user community using Trilinos and the Xyce circuit

  3. Latching overcurrent circuit breaker

    Science.gov (United States)

    Moore, M. L.

    1970-01-01

    Circuit breaker consists of a preset current amplitude sensor, and a lamp-photo-resistor combination in a feedback arrangement which energizes a power switching relay. The ac input power is removed from the load at predetermined current amplitudes.

  4. High temperature circuit breaker

    Science.gov (United States)

    Edwards, R. N.; Travis, E. F.

    1970-01-01

    Alternating current circuit breaker is suitable for reliable long-term service at 1000 deg F in the vacuum conditions of outer space. Construction materials are resistant to nuclear radiation and vacuum welding. Service test conditions and results are given.

  5. Overriding Faulty Circuit Breakers

    Science.gov (United States)

    Robbins, Richard L.; Pierson, Thomas E.

    1987-01-01

    Retainer keeps power on in emergency. Simple mechanical device attaches to failed aircraft-type push/pull circuit breaker to restore electrical power temporarily until breaker replaced. Device holds push/pull button in closed position; unnecessary for crewmember to hold button in position by continual finger pressure. Sleeve and plug hold button in, overriding mechanical failure in circuit breaker. Windows in sleeve show button position.

  6. Genome-wide transcriptomic and proteomic analyses of bollworm-infested developing cotton bolls revealed the genes and pathways involved in the insect pest defence mechanism.

    Science.gov (United States)

    Kumar, Saravanan; Kanakachari, Mogilicherla; Gurusamy, Dhandapani; Kumar, Krishan; Narayanasamy, Prabhakaran; Kethireddy Venkata, Padmalatha; Solanke, Amolkumar; Gamanagatti, Savita; Hiremath, Vamadevaiah; Katageri, Ishwarappa S; Leelavathi, Sadhu; Kumar, Polumetla Ananda; Reddy, Vanga Siva

    2016-06-01

    Cotton bollworm, Helicoverpa armigera, is a major insect pest that feeds on cotton bolls causing extensive damage leading to crop and productivity loss. In spite of such a major impact, cotton plant response to bollworm infection is yet to be witnessed. In this context, we have studied the genome-wide response of cotton bolls infested with bollworm using transcriptomic and proteomic approaches. Further, we have validated this data using semi-quantitative real-time PCR. Comparative analyses have revealed that 39% of the transcriptome and 35% of the proteome were differentially regulated during bollworm infestation. Around 36% of significantly regulated transcripts and 45% of differentially expressed proteins were found to be involved in signalling followed by redox regulation. Further analysis showed that defence-related stress hormones and their lipid precursors, transcription factors, signalling molecules, etc. were stimulated, whereas the growth-related counterparts were suppressed during bollworm infestation. Around 26% of the significantly up-regulated proteins were defence molecules, while >50% of the significantly down-regulated were related to photosynthesis and growth. Interestingly, the biosynthesis genes for synergistically regulated jasmonate, ethylene and suppressors of the antagonistic factor salicylate were found to be up-regulated, suggesting a choice among stress-responsive phytohormone regulation. Manual curation of the enzymes and TFs highlighted the components of retrograde signalling pathways. Our data suggest that a selective regulatory mechanism directs the reallocation of metabolic resources favouring defence over growth under bollworm infestation and these insights could be exploited to develop bollworm-resistant cotton varieties.

  7. Kirchhoff voltage law corrected for radiating circuits

    CERN Document Server

    Lara, Vitor

    2014-01-01

    When a circular loop composed by a RLC is put to oscillate, the oscillation will eventually vanish in an exponentially decaying current, even considering superconducting wires, due to the emission of electric and magnetic dipole radiation. In this work we propose a modification on the Kirchhoff voltage law by adding the radiative contributions to the energy loss as an effective resistance, whose value is relatively small when compared to typical resistance value, but fundamental to describe correctly real circuits. We have also analysed the change in the pattern of the radiation spectra emitted by the circuit as we vary both the effective and electrical resistance.

  8. Timing Analysis of Genetic Logic Circuits using D-VASim

    DEFF Research Database (Denmark)

    Baig, Hasan; Madsen, Jan

    A genetic logic circuit is a gene regulator network implemented by re-engineering the DNA of a cell, in order to controlgene expression or metabolic pathways, through a logic combination of external signals, such as chemicals or proteins. As for electroniclogic circuits, timing and propagation...... delay analysis may play a very significant role in the designing of genetic logic circuits. In thisdemonstration, we present the capability of D-VASim (Dynamic Virtual Analyzer and Simulator) to perform the timing and propagationdelay analysis of genetic logic circuits. Using D-VASim, the timing...... and propagation delay analysis of single as well as cascaded geneticlogic circuits can be performed. D-VASim allows user to change the circuit parameters during runtime simulation to observe its effectson circuit’s timing behavior. The results obtained from D-VASim can be used not only to characterize the timing...

  9. Virus-Induced Gene Silencing-Based Functional Analyses Revealed the Involvement of Several Putative Trehalose-6-Phosphate Synthase/Phosphatase Genes in Disease Resistance against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 in Tomato

    Science.gov (United States)

    Zhang, Huijuan; Hong, Yongbo; Huang, Lei; Liu, Shixia; Tian, Limei; Dai, Yi; Cao, Zhongye; Huang, Lihong; Li, Dayong; Song, Fengming

    2016-01-01

    Trehalose and its metabolism have been demonstrated to play important roles in control of plant growth, development, and stress responses. However, direct genetic evidence supporting the functions of trehalose and its metabolism in defense response against pathogens is lacking. In the present study, genome-wide characterization of putative trehalose-related genes identified 11 SlTPSs for trehalose-6-phosphate synthase, 8 SlTPPs for trehalose-6-phosphate phosphatase and one SlTRE1 for trehalase in tomato genome. Nine SlTPSs, 4 SlTPPs, and SlTRE1 were selected for functional analyses to explore their involvement in tomato disease resistance. Some selected SlTPSs, SlTPPs, and SlTRE1 responded with distinct expression induction patterns to Botrytis cinerea and Pseudomonas syringae pv. tomato (Pst) DC3000 as well as to defense signaling hormones (e.g., salicylic acid, jasmonic acid, and a precursor of ethylene). Virus-induced gene silencing-mediated silencing of SlTPS3, SlTPS4, or SlTPS7 led to deregulation of ROS accumulation and attenuated the expression of defense-related genes upon pathogen infection and thus deteriorated the resistance against B. cinerea or Pst DC3000. By contrast, silencing of SlTPS5 or SlTPP2 led to an increased expression of the defense-related genes upon pathogen infection and conferred an increased resistance against Pst DC3000. Silencing of SlTPS3, SlTPS4, SlTPS5, SlTPS7, or SlTPP2 affected trehalose level in tomato plants with or without infection of B. cinerea or Pst DC3000. These results demonstrate that SlTPS3, SlTPS4, SlTPS5, SlTPS7, and SlTPP2 play roles in resistance against B. cinerea and Pst DC3000, implying the importance of trehalose and tis metabolism in regulation of defense response against pathogens in tomato. PMID:27540389

  10. Comparison of NASCAP modelling results with lumped circuit analysis

    Science.gov (United States)

    Stang, D. B.; Purvis, C. K.

    1980-01-01

    Engineering design tools that can be used to predict the development of absolute and differential potentials by realistic spacecraft under geomagnetic substorm conditions are described. Two types of analyses are in use: (1) the NASCAP code, which computes quasistatic charging of geometrically complex objects with multiple surface materials in three dimensions; (2) lumped element equivalent circuit models that are used for analyses of particular spacecraft. The equivalent circuit models require very little computation time, however, they cannot account for effects, such as the formation of potential barriers, that are inherently multidimensional. Steady state potentials of structure and insulation are compared with those resulting from the equivalent circuit model.

  11. Circuit simulation: some humbling thoughts

    Energy Technology Data Exchange (ETDEWEB)

    Wendt, Manfred; /Fermilab

    2006-01-01

    A short, very personal note on circuit simulation is presented. It does neither include theoretical background on circuit simulation, nor offers an overview of available software, but just gives some general remarks for a discussion on circuit simulator needs in context to the design and development of accelerator beam instrumentation circuits and systems.

  12. Analysis and design of a charge pump circuit for high output current applications

    NARCIS (Netherlands)

    Steenwijk, van Gijs; Hoen, Klaas; Wallinga, Hans

    1993-01-01

    A charge pump circuit has been developed that can deliver high currents even for a system supply voltage of 3 V. The circuit consists of capacitances, connected by MOS switches. The influence of the on-resistance of the switches on the circuit's output resistance has been analysed. The switches are

  13. Cellular Signaling Pathways in Insulin Resistance-Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus

    Science.gov (United States)

    Muhammad, Syed Aun; Raza, Waseem; Nguyen, Thanh; Bai, Baogang; Wu, Xiaogang; Chen, Jake

    2017-01-01

    Purpose: Type 2 diabetes mellitus (T2DM) is a chronic and metabolic disorder affecting large set of population of the world. To widen the scope of understanding of genetic causes of this disease, we performed interactive and toxicogenomic based systems biology study to find potential T2DM related genes after cDNA differential analysis. Methods: From the list of 50-differential expressed genes (p < 0.05), we found 9-T2DM related genes using extensive data mapping. In our constructed gene-network, T2DM-related differentially expressed seeder genes (9-genes) are found to interact with functionally related gene signatures (31-genes). The genetic interaction network of both T2DM-associated seeder as well as signature genes generally relates well with the disease condition based on toxicogenomic and data curation. Results: These networks showed significant enrichment of insulin signaling, insulin secretion and other T2DM-related pathways including JAK-STAT, MAPK, TGF, Toll-like receptor, p53 and mTOR, adipocytokine, FOXO, PPAR, P13-AKT, and triglyceride metabolic pathways. We found some enriched pathways that are common in different conditions. We recognized 11-signaling pathways as a connecting link between gene signatures in insulin resistance and T2DM. Notably, in the drug-gene network, the interacting genes showed significant overlap with 13-FDA approved and few non-approved drugs. This study demonstrates the value of systems genetics for identifying 18 potential genes associated with T2DM that are probable drug targets. Conclusions: This integrative and network based approaches for finding variants in genomic data expect to accelerate identification of new drug target molecules for different diseases and can speed up drug discovery outcomes. PMID:28179884

  14. Fractional-order RC and RL circuits

    KAUST Repository

    Radwan, Ahmed Gomaa

    2012-05-30

    This paper is a step forward to generalize the fundamentals of the conventional RC and RL circuits in fractional-order sense. The effect of fractional orders is the key factor for extra freedom, more flexibility, and novelty. The conditions for RC and RL circuits to act as pure imaginary impedances are derived, which are unrealizable in the conventional case. In addition, the sensitivity analyses of the magnitude and phase response with respect to all parameters showing the locations of these critical values are discussed. A qualitative revision for the fractional RC and RL circuits in the frequency domain is provided. Numerical and PSpice simulations are included to validate this study. © Springer Science+Business Media, LLC 2012.

  15. A semiconductor laser excitation circuit

    Energy Technology Data Exchange (ETDEWEB)

    Kaadzunari, O.; Masaty, K.

    1984-03-27

    A semiconductor laser excitation circuit is patented that is designed for operation in a pulsed mode with a high pulse repetition frequency. This circuit includes, in addition to a semiconductor laser, a high speed photodetector, a reference voltage source, a comparator, and a pulse oscillator and modulator. If the circuit is built using standard silicon integrated circuits, its speed amounts to several hundred megahertz, if it is constructed using gallium arsenide integrated circuits, its speed is several gigahertz.

  16. The Mind Grows Circuits

    CERN Document Server

    Panigrahy, Rina

    2012-01-01

    There is a vast supply of prior art that study models for mental processes. Some studies in psychology and philosophy approach it from an inner perspective in terms of experiences and percepts. Others such as neurobiology or connectionist-machines approach it externally by viewing the mind as complex circuit of neurons where each neuron is a primitive binary circuit. In this paper, we also model the mind as a place where a circuit grows, starting as a collection of primitive components at birth and then builds up incrementally in a bottom up fashion. A new node is formed by a simple composition of prior nodes when we undergo a repeated experience that can be described by that composition. Unlike neural networks, however, these circuits take "concepts" or "percepts" as inputs and outputs. Thus the growing circuits can be likened to a growing collection of lambda expressions that are built on top of one another in an attempt to compress the sensory input as a heuristic to bound its Kolmogorov Complexity.

  17. Comprehensive phenotype/genotype analyses of the norepinephrine transporter gene (SLC6A2 in ADHD: relation to maternal smoking during pregnancy.

    Directory of Open Access Journals (Sweden)

    Geeta A Thakur

    Full Text Available OBJECTIVE: Despite strong pharmacological evidence implicating the norepinephrine transporter in ADHD, genetic studies have yielded largely insignificant results. We tested the association between 30 tag SNPs within the SLC6A2 gene and ADHD, with stratification based on maternal smoking during pregnancy, an environmental factor strongly associated with ADHD. METHODS: Children (6-12 years old diagnosed with ADHD according to DSM-IV criteria were comprehensively evaluated with regard to several behavioral and cognitive dimensions of ADHD as well as response to a fixed dose of methylphenidate (MPH using a double-blind placebo controlled crossover trial. Family-based association tests (FBAT, including categorical and quantitative trait analyses, were conducted in 377 nuclear families. RESULTS: A highly significant association was observed with rs36021 (and linked SNPs in the group where mothers smoked during pregnancy. Association was noted with categorical DSM-IV ADHD diagnosis (Z=3.74, P=0.0002, behavioral assessments by parents (CBCL, P=0.00008, as well as restless-impulsive subscale scores on Conners'-teachers (P=0.006 and parents (P=0.006. In this subgroup, significant association was also observed with cognitive deficits, more specifically sustained attention, spatial working memory, planning, and response inhibition. The risk allele was associated with significant improvement of behavior as measured by research staff (Z=3.28, P=0.001, parents (Z=2.62, P=0.009, as well as evaluation in the simulated academic environment (Z=3.58, P=0.0003. CONCLUSIONS: By using maternal smoking during pregnancy to index a putatively more homogeneous group of ADHD, highly significant associations were observed between tag SNPs within SLC6A2 and ADHD diagnosis, behavioral and cognitive measures relevant to ADHD and response to MPH. This comprehensive phenotype/genotype analysis may help to further understand this complex disorder and improve its treatment

  18. VH Replacement Footprint Analyzer-I, a Java-Based Computer Program for Analyses of Immunoglobulin Heavy Chain Genes and Potential VH Replacement Products in Human and Mouse.

    Science.gov (United States)

    Huang, Lin; Lange, Miles D; Zhang, Zhixin

    2014-01-01

    VH replacement occurs through RAG-mediated secondary recombination between a rearranged VH gene and an upstream unrearranged VH gene. Due to the location of the cryptic recombination signal sequence (cRSS, TACTGTG) at the 3' end of VH gene coding region, a short stretch of nucleotides from the previous rearranged VH gene can be retained in the newly formed VH-DH junction as a "footprint" of VH replacement. Such footprints can be used as markers to identify Ig heavy chain (IgH) genes potentially generated through VH replacement. To explore the contribution of VH replacement products to the antibody repertoire, we developed a Java-based computer program, VH replacement footprint analyzer-I (VHRFA-I), to analyze published or newly obtained IgH genes from human or mouse. The VHRFA-1 program has multiple functional modules: it first uses service provided by the IMGT/V-QUEST program to assign potential VH, DH, and JH germline genes; then, it searches for VH replacement footprint motifs within the VH-DH junction (N1) regions of IgH gene sequences to identify potential VH replacement products; it can also analyze the frequencies of VH replacement products in correlation with publications, keywords, or VH, DH, and JH gene usages, and mutation status; it can further analyze the amino acid usages encoded by the identified VH replacement footprints. In summary, this program provides a useful computation tool for exploring the biological significance of VH replacement products in human and mouse.

  19. Chaotic memristive circuit: equivalent circuit realization and dynamical analysis

    Institute of Scientific and Technical Information of China (English)

    Bao Bo-Cheng; Xu Jian-Ping; Zhou Guo-Hua; Ma Zheng-Hua; Zou Ling

    2011-01-01

    In this paper,a practical equivalent circuit of an active flux-controlled memristor characterized by smooth piecewise-quadratic nonlinearity is designed and an experimental chaotic memristive circuit is implemented.The chaotic memristive circuit has an equilibrium set and its stability is dependent on the initial state of the memristor.The initial state-dependent and the circuit parameter-dependent dynamics of the chaotic memristive circuit are investigated via phase portraits,bifurcation diagrams and Lyapunov exponents.Both experimental and simulation results validate the proposed equivalent circuit realization of the active flux-controlled memristor.

  20. Primer printed circuit boards

    CERN Document Server

    Argyle, Andrew

    2009-01-01

    Step-by-step instructions for making your own PCBs at home. Making your own printed circuit board (PCB) might seem a daunting task, but once you master the steps, it's easy to attain professional-looking results. Printed circuit boards, which connect chips and other components, are what make almost all modern electronic devices possible. PCBs are made from sheets of fiberglass clad with copper, usually in multiplelayers. Cut a computer motherboard in two, for instance, and you'll often see five or more differently patterned layers. Making boards at home is relatively easy

  1. Current Conveyor Equivalent Circuits

    Directory of Open Access Journals (Sweden)

    Tejmal S. Rathore

    2012-02-01

    Full Text Available An equivalence between a class of (current conveyor CC II+ and CC II- circuits is established. CC IIequivalent circuit uses one extra element. However, under certain condition, the extra element can be eliminated. As an illustration of the application of this equivalence, minimal first and second order all-pass filters are derived. Incertain cases, it is possible to compensate the effect of the input resistor of CC at port X. At the end, an open problem of realizing an Nth order (N > 2 minimal all-pass filter is stated.

  2. Inrush Current Control Circuit

    Science.gov (United States)

    Cole, Steven W. (Inventor)

    2002-01-01

    An inrush current control circuit having an input terminal connected to a DC power supply and an output terminal connected to a load capacitor limits the inrush current that charges up the load capacitor during power up of a system. When the DC power supply applies a DC voltage to the input terminal, the inrush current control circuit produces a voltage ramp at the load capacitor instead of an abrupt DC voltage. The voltage ramp results in a constant low level current to charge up the load capacitor, greatly reducing the current drain on the DC power supply.

  3. Circuit design for reliability

    CERN Document Server

    Cao, Yu; Wirth, Gilson

    2015-01-01

    This book presents physical understanding, modeling and simulation, on-chip characterization, layout solutions, and design techniques that are effective to enhance the reliability of various circuit units.  The authors provide readers with techniques for state of the art and future technologies, ranging from technology modeling, fault detection and analysis, circuit hardening, and reliability management. Provides comprehensive review on various reliability mechanisms at sub-45nm nodes; Describes practical modeling and characterization techniques for reliability; Includes thorough presentation of robust design techniques for major VLSI design units; Promotes physical understanding with first-principle simulations.

  4. Electronic circuits fundamentals & applications

    CERN Document Server

    Tooley, Mike

    2015-01-01

    Electronics explained in one volume, using both theoretical and practical applications.New chapter on Raspberry PiCompanion website contains free electronic tools to aid learning for students and a question bank for lecturersPractical investigations and questions within each chapter help reinforce learning Mike Tooley provides all the information required to get to grips with the fundamentals of electronics, detailing the underpinning knowledge necessary to appreciate the operation of a wide range of electronic circuits, including amplifiers, logic circuits, power supplies and oscillators. The

  5. Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation

    DEFF Research Database (Denmark)

    Stegmann, Anders; Hansen, Morten; Wang, Yulan;

    2006-01-01

    DNA-binding transcription factors bind to promoters that carry their binding sites. Transcription factors therefore function as nodes in gene regulatory networks. In the present work we used a bioinformatic approach to search for transcription factors that might function as nodes in gene regulatory...

  6. Hepatic gene expression changes in pigs experimentally infected with the lung pathogen Actinobacillus pleuropneumoniae as analysed with an innate immunity focused microarray

    DEFF Research Database (Denmark)

    Skovgaard, Kerstin; Mortensen, Shila; Boye, Mette

    2010-01-01

    response of genes associated with innate immune responses was studied in pigs 14–18 h after intranasal inoculation with Actinobacillus pleuropneumoniae, using innate immune focused microarrays and quantitative real-time PCR (qPCR). The microarray analysis of liver tissue established that 51 genes were...

  7. Spatiotemporal dynamics of distributed synthetic genetic circuits

    Science.gov (United States)

    Kanakov, Oleg; Laptyeva, Tetyana; Tsimring, Lev; Ivanchenko, Mikhail

    2016-04-01

    We propose and study models of two distributed synthetic gene circuits, toggle-switch and oscillator, each split between two cell strains and coupled via quorum-sensing signals. The distributed toggle switch relies on mutual repression of the two strains, and oscillator is comprised of two strains, one of which acts as an activator for another that in turn acts as a repressor. Distributed toggle switch can exhibit mobile fronts, switching the system from the weaker to the stronger spatially homogeneous state. The circuit can also act as a biosensor, with the switching front dynamics determined by the properties of an external signal. Distributed oscillator system displays another biosensor functionality: oscillations emerge once a small amount of one cell strain appears amid the other, present in abundance. Distribution of synthetic gene circuits among multiple strains allows one to reduce crosstalk among different parts of the overall system and also decrease the energetic burden of the synthetic circuit per cell, which may allow for enhanced functionality and viability of engineered cells.

  8. Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p.

    Science.gov (United States)

    Davidsson, Josef; Johansson, Bertil

    2016-03-03

    To ascertain the epigenomic features, i.e., the methylation, non-coding RNA, and gene expression patterns, associated with gain of i(12p) in Pallister-Killian syndrome (PKS), we investigated single cell clones, harboring either disomy 12 or tetrasomy 12p, from a patient with PKS. The i(12p)-positive cells displayed a characteristic expression and methylation signature. Of all the genes on 12p, 13% were overexpressed, including the ATN1, COPS7A, and NECAP1 genes in 12p13.31, a region previously implicated in PKS. However, the median expression fold change (1.3) on 12p was lower than expected by tetrasomy 12p. Thus, partial dosage compensation occurs in cells with i(12p). The majority (89%) of the significantly deregulated genes were not situated on 12p, indicating that global perturbation of gene expression is a key pathogenetic event in PKS. Three genes-ATP6V1G1 in 9q32, GMPS in 3q25.31, and TBX5 in 12q24.21-exhibited concomitant hypermethylation and decreased expression. The i(12p)-positive cells displayed global hypomethylation of gene-poor regions on 12p, a footprint previously associated with constitutional and acquired gains of whole chromosomes as well as with X-chromosome inactivation in females. We hypothesize that this non-genic hypomethylation is associated with chromatin processing that facilitates cellular adaptation to excess genetic material.

  9. Comprehensive transcriptional and functional analyses of melatonin synthesis genes in cassava reveal their novel role in hypersensitive-like cell death

    Science.gov (United States)

    Wei, Yunxie; Hu, Wei; Wang, Qiannan; Liu, Wei; Wu, Chunjie; Zeng, Hongqiu; Yan, Yu; Li, Xiaolin; He, Chaozu; Shi, Haitao

    2016-01-01

    Melatonin is a widely known hormone in animals. Since melatonin was discovered in plants, more and more studies highlight its involvement in a wide range of physiological processes including plant development and stress responses. Many advances have been made in the terms of melatonin-mediated abiotic stress resistance and innate immunity in plants, focusing on model plants such as rice and Arabidopsis. In this study, 7 melatonin synthesis genes were systematically analyzed in cassava. Quantitative real-time PCR showed that all these genes were commonly regulated by melatonin, flg22, Xanthomonas axonopodis pv manihotis (Xam) and hydrogen peroxide (H2O2). Transient expression in Nicotiana benthamiana revealed the subcellular locations and possible roles of these melatonin synthesis genes. Notably, we highlight novel roles of these genes in hypersensitive-like cell death, as confirmed by the results of several physiological parameters. Moreover, transient expression of these genes had significant effects on the transcripts of reactive oxygen species (ROS) accumulation and defense-related genes, and triggered the burst of callose depositions and papillae-associated plant defense, indicating the possible role of them in plant innate immunity. Taken together, this study reveals the comprehensive transcripts and putative roles of melatonin synthesis genes as well as melatonin in immune responses in cassava. PMID:27739451

  10. ESD analog circuits and design

    CERN Document Server

    Voldman, Steven H

    2014-01-01

    A comprehensive and in-depth review of analog circuit layout, schematic architecture, device, power network and ESD design This book will provide a balanced overview of analog circuit design layout, analog circuit schematic development, architecture of chips, and ESD design.  It will start at an introductory level and will bring the reader right up to the state-of-the-art. Two critical design aspects for analog and power integrated circuits are combined. The first design aspect covers analog circuit design techniques to achieve the desired circuit performance. The second and main aspect pres

  11. Quantum secure circuit evaluation

    Institute of Scientific and Technical Information of China (English)

    CHEN Huanhuan; LI Bin; ZHUANG Zhenquan

    2004-01-01

    In order to solve the problem of classical secure circuit evaluation, this paper proposes a quantum approach. In this approach, the method of inserting redundant entangled particles and quantum signature has been employed to strengthen the security of the system. Theoretical analysis shows that our solution is secure against classical and quantum attacks.

  12. Superconducting Quantum Circuits

    NARCIS (Netherlands)

    Majer, J.B.

    2002-01-01

    This thesis describes a number of experiments with superconducting cir- cuits containing small Josephson junctions. The circuits are made out of aluminum islands which are interconnected with a very thin insulating alu- minum oxide layer. The connections form a Josephson junction. The current trough

  13. Bioluminescent bioreporter integrated circuit

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Michael L. (Knoxville, TN); Sayler, Gary S. (Blaine, TN); Paulus, Michael J. (Knoxville, TN)

    2000-01-01

    Disclosed are monolithic bioelectronic devices comprising a bioreporter and an OASIC. These bioluminescent bioreporter integrated circuit are useful in detecting substances such as pollutants, explosives, and heavy-metals residing in inhospitable areas such as groundwater, industrial process vessels, and battlefields. Also disclosed are methods and apparatus for environmental pollutant detection, oil exploration, drug discovery, industrial process control, and hazardous chemical monitoring.

  14. Assessment and validation of a suite of reverse transcription-quantitative PCR reference genes for analyses of density-dependent behavioural plasticity in the Australian plague locust

    Directory of Open Access Journals (Sweden)

    Blondin Laurence

    2011-02-01

    Full Text Available Abstract Background The Australian plague locust, Chortoicetes terminifera, is among the most promising species to unravel the suites of genes underling the density-dependent shift from shy and cryptic solitarious behaviour to the highly active and aggregating gregarious behaviour that is characteristic of locusts. This is because it lacks many of the major phenotypic changes in colour and morphology that accompany phase change in other locust species. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR is the most sensitive method available for determining changes in gene expression. However, to accurately monitor the expression of target genes, it is essential to select an appropriate normalization strategy to control for non-specific variation between samples. Here we identify eight potential reference genes and examine their expression stability at different rearing density treatments in neural tissue of the Australian plague locust. Results Taking advantage of the new orthologous DNA sequences available in locusts, we developed primers for genes encoding 18SrRNA, ribosomal protein L32 (RpL32, armadillo (Arm, actin 5C (Actin, succinate dehydrogenase (SDHa, glyceraldehyde-3P-dehydrogenase (GAPDH, elongation factor 1 alpha (EF1a and annexin IX (AnnIX. The relative transcription levels of these eight genes were then analyzed in three treatment groups differing in rearing density (isolated, short- and long-term crowded, each made up of five pools of four neural tissue samples from 5th instar nymphs. SDHa and GAPDH, which are both involved in metabolic pathways, were identified as the least stable in expression levels, challenging their usefulness in normalization. Based on calculations performed with the geNorm and NormFinder programs, the best combination of two genes for normalization of gene expression data following crowding in the Australian plague locust was EF1a and Arm. We applied their use to studying a target gene

  15. Full-length cloning and phylogenetic analyses of translationally controlled tumour protein and ferritin genes from the Indian white prawn, Fenneropenaeus indicus (H. Milne Edwards)

    Digital Repository Service at National Institute of Oceanography (India)

    Nayak, S.; Ramaiah, N.; Meena, R.M.; Sreepada, R.A.

    Elucidation, through molecular analyses, of bacterial afflictions in commercially important aquaculture- reared shrimps is pivotal for the prevention and/or control of disease outbreaks. In this study, we examined the phylogenetic relatedness...

  16. System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of soybean (Glycine max).

    Science.gov (United States)

    Xu, Yungang; Guo, Maozu; Zou, Quan; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

    2014-01-01

    Cellular interactome, in which genes and/or their products interact on several levels, forming transcriptional regulatory-, protein interaction-, metabolic-, signal transduction networks, etc., has attracted decades of research focuses. However, such a specific type of network alone can hardly explain the various interactive activities among genes. These networks characterize different interaction relationships, implying their unique intrinsic properties and defects, and covering different slices of biological information. Functional gene network (FGN), a consolidated interaction network that models fuzzy and more generalized notion of gene-gene relations, have been proposed to combine heterogeneous networks with the goal of identifying functional modules supported by multiple interaction types. There are yet no successful precedents of FGNs on sparsely studied non-model organisms, such as soybean (Glycine max), due to the absence of sufficient heterogeneous interaction data. We present an alternative solution for inferring the FGNs of soybean (SoyFGNs), in a pioneering study on the soybean interactome, which is also applicable to other organisms. SoyFGNs exhibit the typical characteristics of biological networks: scale-free, small-world architecture and modularization. Verified by co-expression and KEGG pathways, SoyFGNs are more extensive and accurate than an orthology network derived from Arabidopsis. As a case study, network-guided disease-resistance gene discovery indicates that SoyFGNs can provide system-level studies on gene functions and interactions. This work suggests that inferring and modelling the interactome of a non-model plant are feasible. It will speed up the discovery and definition of the functions and interactions of other genes that control important functions, such as nitrogen fixation and protein or lipid synthesis. The efforts of the study are the basis of our further comprehensive studies on the soybean functional interactome at the genome

  17. Cellular Signaling Pathways in Insulin Resistance-Systems Biology Analyses of Microarray Dataset Reveals New Drug Target Gene Signatures of Type 2 Diabetes Mellitus.

    Science.gov (United States)

    Muhammad, Syed Aun; Raza, Waseem; Nguyen, Thanh; Bai, Baogang; Wu, Xiaogang; Chen, Jake

    2017-01-01

    Purpose: Type 2 diabetes mellitus (T2DM) is a chronic and metabolic disorder affecting large set of population of the world. To widen the scope of understanding of genetic causes of this disease, we performed interactive and toxicogenomic based systems biology study to find potential T2DM related genes after cDNA differential analysis. Methods: From the list of 50-differential expressed genes (p new drug target molecules for different diseases and can speed up drug discovery outcomes.

  18. Electronic circuits and systems: A compilation. [including integrated circuits, logic circuits, varactor diode circuits, low pass filters, and optical equipment circuits

    Science.gov (United States)

    1975-01-01

    Technological information is presented electronic circuits and systems which have potential utility outside the aerospace community. Topics discussed include circuit components such as filters, converters, and integrators, circuits designed for use with specific equipment or systems, and circuits designed primarily for use with optical equipment or displays.

  19. Thyroid hormone-regulated gene expression in juvenile mouse liver: identification of thyroid response elements using microarray profiling and in silico analyses

    Directory of Open Access Journals (Sweden)

    Paquette Martin A

    2011-12-01

    Full Text Available Abstract Background Disruption of thyroid hormone signalling can alter growth, development and energy metabolism. Thyroid hormones exert their effects through interactions with thyroid receptors that directly bind thyroid response elements and can alter transcriptional activity of target genes. The effects of short-term thyroid hormone perturbation on hepatic mRNA transcription in juvenile mice were evaluated, with the goal of identifying genes containing active thyroid response elements. Thyroid hormone disruption was induced from postnatal day 12 to 15 by adding goitrogens to dams' drinking water (hypothyroid. A subgroup of thyroid hormone-disrupted pups received intraperitoneal injections of replacement thyroid hormones four hours prior to sacrifice (replacement. An additional group received only thyroid hormones four hours prior to sacrifice (hyperthyroid. Hepatic mRNA was extracted and hybridized to Agilent mouse microarrays. Results Transcriptional profiling enabled the identification of 28 genes that appeared to be under direct thyroid hormone-regulation. The regulatory regions of the genome adjacent to these genes were examined for half-site sequences that resemble known thyroid response elements. A bioinformatics search identified 33 thyroid response elements in the promoter regions of 13 different genes thought to be directly regulated by thyroid hormones. Thyroid response elements found in the promoter regions of Tor1a, 2310003H01Rik, Hect3d and Slc25a45 were further validated by confirming that the thyroid receptor is associated with these sequences in vivo and that it can bind directly to these sequences in vitro. Three different arrangements of thyroid response elements were identified. Some of these thyroid response elements were located far up-stream (> 7 kb of the transcription start site of the regulated gene. Conclusions Transcriptional profiling of thyroid hormone disrupted animals coupled with a novel bioinformatics search

  20. Electronic Circuit Analog of Synthetic Genetic Networks: Revisited

    CERN Document Server

    Hellen, Edward H

    2016-01-01

    Electronic circuits are useful tools for studying potential dynamical behaviors of synthetic genetic networks. The circuit models are complementary to numerical simulations of the networks, especially providing a framework for verification of dynamical behaviors in the presence of intrinsic and extrinsic noise of the electrical systems. Here we present an improved version of our previous design of an electronic analog of genetic networks that includes the 3-gene Repressilator and we show conversions between model parameters and real circuit component values to mimic the numerical results in experiments. Important features of the circuit design include the incorporation of chemical kinetics representing Hill function inhibition, quorum sensing coupling, and additive noise. Especially, we make a circuit design for a systematic change of initial conditions in experiment, which is critically important for studies of dynamical systems' behavior, particularly, when it shows multistability. This improved electronic ...

  1. Behavioral synthesis of asynchronous circuits

    DEFF Research Database (Denmark)

    Nielsen, Sune Fallgaard

    2005-01-01

    This thesis presents a method for behavioral synthesis of asynchronous circuits, which aims at providing a synthesis flow which uses and tranfers methods from synchronous circuits to asynchronous circuits. We move the synchronous behavioral synthesis abstraction into the asynchronous handshake...... is idle. This reduces unnecessary switching activity in the individual functional units and therefore the energy consumption of the entire circuit. A collection of behavioral synthesis algorithms have been developed allowing the designer to perform time and power constrained design space exploration...

  2. The LMT circuit and SPICE

    DEFF Research Database (Denmark)

    Lindberg, Erik; Murali, K.; Tamacevicius, Arunas

    2006-01-01

    The state equations of the LMT circuit are modeled as a dedicated analogue computer circuit and solved by means of PSpice. The nonlinear part of the system is studied. Problems with the PSpice program are presented.......The state equations of the LMT circuit are modeled as a dedicated analogue computer circuit and solved by means of PSpice. The nonlinear part of the system is studied. Problems with the PSpice program are presented....

  3. Diode, transistor & fet circuits manual

    CERN Document Server

    Marston, R M

    2013-01-01

    Diode, Transistor and FET Circuits Manual is a handbook of circuits based on discrete semiconductor components such as diodes, transistors, and FETS. The book also includes diagrams and practical circuits. The book describes basic and special diode characteristics, heat wave-rectifier circuits, transformers, filter capacitors, and rectifier ratings. The text also presents practical applications of associated devices, for example, zeners, varicaps, photodiodes, or LEDs, as well as it describes bipolar transistor characteristics. The transistor can be used in three basic amplifier configuration

  4. Molecular Cloning, Expression of minD Gene from Lactobacillus acidophilus VTCC-B-871 and Analyses to Identify Lactobacillus rhamnosus PN04 from Vietnam Hottuynia cordata Thunb.

    Science.gov (United States)

    Nguyen, Tu Hoang Khue; Doan, Vinh Thi Thanh; Ha, Ly Dieu; Nguyen, Huu Ngoc

    2013-12-01

    The minD gene encoding an inhibitor cell division MinD homolog from Lactobacillus acidophilus VTCC-B-871 was cloned. We showed that there were 97 % homology between minD genes of L. acidophilus VTCC-B-871 and Lactobacillus rhamnosus GG and Lactobacillus rhamnosus Lc705. Based on the analysis of the DNA sequence data from the L. rhamnosus genome project and sequenced minD gene of L. acidophilus VTCC-B-871, a pair of primers was designed to identified the different minD genes from L. acidophilus ATCC 4356, L. rhamnosus ATCC 11443. Besides, the polymerase chain reaction product of minD gene was also obtained in L. rhamnosus PN04, a strain was isolated from Vietnamese Hottuynia cordata Thunb. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of MinD homologs from L. acidophilus VTCC-B-871 with the other strains and compared the predicted three-dimension structure of L. acidophilus VTCC-B-871 MinD with Escherichia coli MinD, there are similarity that showed evolution of these strains. The overexpression of L. acidophilus VTCC-B-871 MinD in E. coli led to cell filamentation in IPTG and morphology changes in different sugar stresses, interestingly. The present study is the first report characterizing the Lactobacilus MinD homolog that will be useful in probiotic field.

  5. De Novo Assembly and Genome Analyses of the Marine-Derived Scopulariopsis brevicaulis Strain LF580 Unravels Life-Style Traits and Anticancerous Scopularide Biosynthetic Gene Cluster

    Science.gov (United States)

    Kumar, Abhishek; Henrissat, Bernard; Arvas, Mikko; Syed, Muhammad Fahad; Thieme, Nils; Benz, J. Philipp; Sørensen, Jens Laurids; Record, Eric; Pöggeler, Stefanie; Kempken, Frank

    2015-01-01

    The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis. PMID:26505484

  6. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae.

    Science.gov (United States)

    Zhao, Lei; Zhang, Ning; Ma, Peng-Fei; Liu, Qi; Li, De-Zhu; Guo, Zhen-Hua

    2013-01-01

    BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.

  7. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae.

    Directory of Open Access Journals (Sweden)

    Lei Zhao

    Full Text Available BEP clade of the grass family (Poaceae is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P E topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.

  8. De Novo Assembly and Genome Analyses of the Marine-Derived Scopulariopsis brevicaulis Strain LF580 Unravels Life-Style Traits and Anticancerous Scopularide Biosynthetic Gene Cluster.

    Science.gov (United States)

    Kumar, Abhishek; Henrissat, Bernard; Arvas, Mikko; Syed, Muhammad Fahad; Thieme, Nils; Benz, J Philipp; Sørensen, Jens Laurids; Record, Eric; Pöggeler, Stefanie; Kempken, Frank

    2015-01-01

    The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis.

  9. Statistical circuit design for yield improvement in CMOS circuits

    Science.gov (United States)

    Kamath, H. J.; Purviance, J. E.; Whitaker, S. R.

    1990-01-01

    This paper addresses the statistical design of CMOS integrated circuits for improved parametric yield. The work uses the Monte Carlo technique of circuit simulation to obtain an unbiased estimation of the yield. A simple graphical analysis tool, the yield factor histogram, is presented. The yield factor histograms are generated by a new computer program called SPICENTER. Using the yield factor histograms, the most sensitive circuit parameters are noted, and their nominal values are changed to improve the yield. Two basic CMOS example circuits, one analog and one digital, are chosen and their designs are 'centered' to illustrate the use of the yield factor histograms for statistical circuit design.

  10. Bioluminescent bioreporter integrated circuit devices and methods for detecting ammonia

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Michael L [Knoxville, TN; Paulus, Michael J [Knoxville, TN; Sayler, Gary S [Blaine, TN; Applegate, Bruce M [West Lafayette, IN; Ripp, Steven A [Knoxville, TN

    2007-04-24

    Monolithic bioelectronic devices for the detection of ammonia includes a microorganism that metabolizes ammonia and which harbors a lux gene fused with a heterologous promoter gene stably incorporated into the chromosome of the microorganism and an Optical Application Specific Integrated Circuit (OASIC). The microorganism is generally a bacterium.

  11. Circuit Bodging: Atari Punk Console

    NARCIS (Netherlands)

    Allen, B.

    2009-01-01

    Circuit bodging is back! Maxwell is proud to present small, simple, but ultimately lovable little circuits to build for your own, personal pleasure. In this edition we are featuring: The Atari Punk Console. The Atari Punk Console (or APC) is a 555 timer IC based noise maker circuit. The original was

  12. cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer Independent.

    Science.gov (United States)

    Huang, Yue; Koues, Olivia I; Zhao, Jiang-Yang; Liu, Regina; Pyfrom, Sarah C; Payton, Jacqueline E; Oltz, Eugene M

    2017-03-21

    Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. We find that only a minor subset of predicted enhancers is required for NEK6 expression. Indeed, an annotated super-enhancer is dispensable for NEK6 overexpression and for maintaining the architecture of a B cell-specific regulatory hub. A CTCF cluster serves as a chromatin and architectural boundary to block communication of the NEK6 regulatory hub with neighboring genes. Our findings emphasize that validation of predicted cis-regulatory circuits and super-enhancers is needed to prioritize transcriptional control elements as therapeutic targets.

  13. Two genetic clusters in swine hemoplasmas revealed by analyses of the 16S rRNA and RNase P RNA genes.

    Science.gov (United States)

    Watanabe, Yusaku; Fujihara, Masatoshi; Obara, Hisato; Nagai, Kazuya; Harasawa, Ryô

    2011-12-01

    Only two hemoplasma species, Eperythrozoon parvum and Mycoplasma suis, have been recognized in pigs. Here we demonstrate the genetic variations among six hemoplasma strains detected from pigs, by analyzing the 16S rRNA and RNase P RNA (rnpB) genes, and propose a novel hemoplasma taxon that has not been described previously. Phylogenetic trees based on the nucleotide sequence of the 16S rRNA gene indicated that these six hemoplasmas were divided into two clusters representing M. suis and a novel taxon. We further examined the primary and secondary structures of the nucleotide sequences of the rnpB gene of the novel taxon, and found it distinct from that of M. suis. In conclusion, we unveiled a genetic cluster distinct from M. suis, suggesting a new swine hemoplasma species or E. parvum. Our findings also suggest that this novel cluster should be included in the genus Mycoplasma.

  14. Subtractive and differential hybridization molecular analyses of Ceratitis capitata XX/XY versus XX embryos to search for male-specific early transcribed genes.

    Science.gov (United States)

    Salvemini, Marco; D'Amato, Rocco; Petrella, Valeria; Ippolito, Domenica; Ventre, Giuseppe; Zhang, Ying; Saccone, Giuseppe

    2014-01-01

    The agricultural pest Ceratitis capitata, also known as the Mediterranean fruit fly or Medfly, is a fruit crop pest of very high economic relevance in different continents. The strategy to separate Ceratitis males from females (sexing) in mass rearing facilities is a useful step before the sterilization and release of male-only flies in Sterile Insect Technique control programs (SIT). The identification of genes having early embryonic male-specific expression, including Y-linked genes, such as the Maleness factor, could help to design novel and improved methods of sexing in combination with transgenesis, aiming to confer conditional female-specific lethality or female-to-male sexual reversal. We used a combination of Suppression Subtractive Hybrydization (SSH), Mirror Orientation Selection (MOS) anddifferential screening hybridization (DSH) techniques to approach the problem of isolating corresponding mRNAs expressed in XX/XY embryos versus XX-only embryos during a narrow developmental window (8-10 hours after egg laying, AEL ). Here we describe a novel strategy we have conceived to obtain relatively large amounts of XX-only embryos staged at 8-10 h AEL and so to extract few micrograms of polyA+ required to apply the complex technical procedure. The combination of these 3 techniques led to the identification of a Y-linked putative gene, CcGm2, sharing high sequence identity to a paralogous gene, CcGm1, localized either on an autosome or on the X chromosome. We propose that CcGm2 is a first interesting putative Y-linked gene which could play a role in sex determination. The function exterted by this gene should be investigated by novel genetic tools, such as CRISPR-CAS9, which will permit to target only the Y-linked paralogue, avoiding to interfere with the autosomal or X-linked paralogue function.

  15. Neuromorphic silicon neuron circuits

    Directory of Open Access Journals (Sweden)

    Giacomo eIndiveri

    2011-05-01

    Full Text Available Hardware implementations of spiking neurons can be extremely useful for a large variety of applications, ranging from high-speed modeling of large-scale neural systems to real-time behaving systems, to bidirectional brain-machine interfaces. The specific circuit solutions used to implement silicon neurons depend on the application requirements. In this paper we describe the most common building blocks and techniques used to implement these circuits, and present an overview of a wide range of neuromorphic silicon neurons, which implement different computational models, ranging from biophysically realistic and conductance based Hodgkin-Huxley models to bi-dimensional generalized adaptive Integrate and Fire models. We compare the different design methodologies used for each silicon neuron design described, and demonstrate their features with experimental results, measured from a wide range of fabricated VLSI chips.

  16. LC-Circuit Calorimetry

    CERN Document Server

    Bossen, Olaf

    2011-01-01

    We present a new type of calorimeter in which we couple an unknown heat capacity with the aid of Peltier elements to an electrical circuit. The use of an electrical inductance and an amplifier in the circuit allows us to achieve autonomous oscillations, and the measurement of the corresponding resonance frequency makes it possible to accurately measure the heat capacity with an intrinsic statistical error that decreases as ~t^{-3/2} with measuring time t, as opposed to a corresponding error ~t^{-1/2} in the conventional alternating current (a.c.) method to measure heat capacities. We have built a demonstration experiment to show the feasibility of the new technique, and we have tested it on a gadolinium sample at its transition to the ferromagnetic state.

  17. Preconditioner Circuit Analysis

    Science.gov (United States)

    2011-09-01

    ground plane and both operational amplifier terminals. The parasitic capacitances are labeled Cp1 and Cp2 in Figure 19. Figure 19. Circuit for...3.69 MHz 3.98pF 55720 5107 OV                                  (17) Cp2 = 1 pF R1 = 5107 Ω R3...circuit. The capacitor would be placed in parallel with RF to cancel the effect of Cp2 and then feedback factor will look purely resistive. Another

  18. System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of soybean (Glycine max.

    Directory of Open Access Journals (Sweden)

    Yungang Xu

    Full Text Available Cellular interactome, in which genes and/or their products interact on several levels, forming transcriptional regulatory-, protein interaction-, metabolic-, signal transduction networks, etc., has attracted decades of research focuses. However, such a specific type of network alone can hardly explain the various interactive activities among genes. These networks characterize different interaction relationships, implying their unique intrinsic properties and defects, and covering different slices of biological information. Functional gene network (FGN, a consolidated interaction network that models fuzzy and more generalized notion of gene-gene relations, have been proposed to combine heterogeneous networks with the goal of identifying functional modules supported by multiple interaction types. There are yet no successful precedents of FGNs on sparsely studied non-model organisms, such as soybean (Glycine max, due to the absence of sufficient heterogeneous interaction data. We present an alternative solution for inferring the FGNs of soybean (SoyFGNs, in a pioneering study on the soybean interactome, which is also applicable to other organisms. SoyFGNs exhibit the typical characteristics of biological networks: scale-free, small-world architecture and modularization. Verified by co-expression and KEGG pathways, SoyFGNs are more extensive and accurate than an orthology network derived from Arabidopsis. As a case study, network-guided disease-resistance gene discovery indicates that SoyFGNs can provide system-level studies on gene functions and interactions. This work suggests that inferring and modelling the interactome of a non-model plant are feasible. It will speed up the discovery and definition of the functions and interactions of other genes that control important functions, such as nitrogen fixation and protein or lipid synthesis. The efforts of the study are the basis of our further comprehensive studies on the soybean functional

  19. Inkjet deposited circuit components

    Science.gov (United States)

    Bidoki, S. M.; Nouri, J.; Heidari, A. A.

    2010-05-01

    All-printed electronics as a means of achieving ultra-low-cost electronic circuits has attracted great interest in recent years. Inkjet printing is one of the most promising techniques by which the circuit components can be ultimately drawn (i.e. printed) onto the substrate in one step. Here, the inkjet printing technique was used to chemically deposit silver nanoparticles (10-200 nm) simply by ejection of silver nitrate and reducing solutions onto different substrates such as paper, PET plastic film and textile fabrics. The silver patterns were tested for their functionality to work as circuit components like conductor, resistor, capacitor and inductor. Different levels of conductivity were achieved simply by changing the printing sequence, inks ratio and concentration. The highest level of conductivity achieved by an office thermal inkjet printer (300 dpi) was 5.54 × 105 S m-1 on paper. Inkjet deposited capacitors could exhibit a capacitance of more than 1.5 nF (parallel plate 45 × 45 mm2) and induction coils displayed an inductance of around 400 µH (planar coil 10 cm in diameter). Comparison of electronic performance of inkjet deposited components to the performance of conventionally etched items makes the technique highly promising for fabricating different printed electronic devices.

  20. Digital integrated circuits

    Science.gov (United States)

    Polasek, P.; Halamik, J.

    1984-05-01

    The term semicustom designed integrated circuits denotes integrated circuits of an all purpose character in which the production of chips is completed by using one to three custom design stencil type exposure masks. This involves in most cases interconnecting masks that are used to devise the circuit function desired by the customer. Silicon plates with an all purpose gate matrix are produced up to the interconnection level and can be kept at this phase in storage, after which a customer's specific demands can be met very expediently. All purpose logic fields containing 200 logic gates on a chip and an all purpose chip to be expanded to 1,000 logic gates are discussed. The technology facilitates the devising of fast gates with a delay of approximately 5 ns and power dissipation of 1 mW. In assembly it will be possible to make use of the entire assortment of the currently used casings with 16, 18, 20, 24, 28 and 40 outlets. In addition to the development of the mentioned technology, a general methodology for design of the mentioned gate fields is currently under way.

  1. Circuit Implementation and Antisynchronization of an Improved Lorenz Chaotic System

    Directory of Open Access Journals (Sweden)

    Li Xiong

    2016-01-01

    Full Text Available An improved Lorenz chaotic system is proposed, making it into a circuit which is easy to be implemented by using some basic electronic components. The antisynchronization error systems can be asymptotically stabilized at the origin with three different methods which are proposed to control the improved Lorenz system. Theoretical analyses and simulation results are given to demonstrate the feasibility and effectiveness of these proposed schemes. Then the hardware circuit for the proposed Lorenz system is implemented by repeated optimization design. Experimental results show that the circuit has good comprehensive performance.

  2. Phylogenetic and In Silico Functional Analyses of Thermostable-Direct Hemolysin and tdh-Related Encoding Genes in Vibrio parahaemolyticus and Other Gram-Negative Bacteria

    Directory of Open Access Journals (Sweden)

    Sushanta K. Bhowmik

    2014-01-01

    Full Text Available Emergence and spread of pandemic strains of Vibrio parahaemolyticus have drawn attention to make detailed study on their genomes. The pathogenicity of V. parahaemolyticus has been associated with thermostable-direct hemolysin (TDH and/or TDH-related hemolysin (TRH. The present study evaluated characteristics of tdh and trh genes, considering the phylogenetic and in silico functional features of V. parahaemolyticus and other bacteria. Fifty-two tdh and trh genes submitted to the GenBank were analyzed for sequence similarity. The promoter sequences of these genes were also analyzed from transcription start point to −35 regions and correlated with amino acid substitution within the coding regions. The phylogenetic analysis revealed that tdh and trh are highly distinct and also differ within the V. parahaemolyticus strains that were isolated from different geographical regions. Promoter sequence analysis revealed nucleotide substitutions and deletions at −18 and −19 positions among the pandemic, prepandemic, and nonpandemic tdh sequences. Many amino acid substitutions were also found within the signal peptide and also in the matured protein region of several TDH proteins as compared to TDH-S protein of pandemic V. parahaemolyticus. Experimental evidences are needed to recognize the importance of substitutions and deletions in the tdh and trh genes.

  3. Anti-obesity effect of radix Angelica sinensis and candidate causative genes in transcriptome analyses of adipose tissues in high-fat diet-induced mice.

    Science.gov (United States)

    Zhong, Tao; Zhang, Hao; Duan, Xiaoyue; Hu, Jiangtao; Wang, Linjie; Li, Li; Zhang, Hongping; Niu, Lili

    2017-01-30

    We have previously reported that radix Angelica sinensis (RAS) suppressed body weight and altered the expression of the fat mass and obesity associated (FTO) gene in mice with high fat diet (HFD)-induced obesity. In the present study we performed RNA sequencing-mediated transcriptome analysis to elucidate the molecular mechanisms underlying the anti-obesogenic effects of RAS in mice. The results revealed that 36 differentially-expressed genes (DEGs) were identified in adipose tissues from the RAS supplementation group (DH) and control group (HC). These 36 DEGs were clustered into 297 functional gene ontology (GO) categories, among which several GO annotations and signaling pathways were associated with lipid homeostasis. Six out of the 36 DEGs were identified to be involved in lipid metabolism, with the APOA2 gene a potential anti-obesogenic influence. The expression pattern revealed by RNA-Seq was identical to the results of quantitative real-time PCR (qPCR). Therefore, RAS supplementation in HFD-induced obese mice was associated with an anti-obesogenic global transcriptomic response. This study provides insight into potential applications of RAS in obesity therapy.

  4. Genetic and biochemical analyses of chromosome and plasmid gene homologues encoding ICL and ArCP domains in Vibrioanguillarum strain 775

    NARCIS (Netherlands)

    Di Lorenzo, M.; Stork, M.; Crosa, J.H.

    2011-01-01

    Anguibactin, the siderophore produced by Vibrio anguillarum 775 is synthesized from 2,3-dihydroxybenzoic acid (DHBA), cysteine and hydroxyhistamine via a nonribosomal peptide synthetase (NRPS) mechanism. Most of the genes encoding anguibactin biosynthetic proteins are harbored by the pJM1 plasmid. I

  5. Phylogenetic and in silico functional analyses of thermostable-direct hemolysin and tdh-related encoding genes in Vibrio parahaemolyticus and other Gram-negative bacteria.

    Science.gov (United States)

    Bhowmik, Sushanta K; Pazhani, Gururaja P; Ramamurthy, Thandavarayan

    2014-01-01

    Emergence and spread of pandemic strains of Vibrio parahaemolyticus have drawn attention to make detailed study on their genomes. The pathogenicity of V. parahaemolyticus has been associated with thermostable-direct hemolysin (TDH) and/or TDH-related hemolysin (TRH). The present study evaluated characteristics of tdh and trh genes, considering the phylogenetic and in silico functional features of V. parahaemolyticus and other bacteria. Fifty-two tdh and trh genes submitted to the GenBank were analyzed for sequence similarity. The promoter sequences of these genes were also analyzed from transcription start point to -35 regions and correlated with amino acid substitution within the coding regions. The phylogenetic analysis revealed that tdh and trh are highly distinct and also differ within the V. parahaemolyticus strains that were isolated from different geographical regions. Promoter sequence analysis revealed nucleotide substitutions and deletions at -18 and -19 positions among the pandemic, prepandemic, and nonpandemic tdh sequences. Many amino acid substitutions were also found within the signal peptide and also in the matured protein region of several TDH proteins as compared to TDH-S protein of pandemic V. parahaemolyticus. Experimental evidences are needed to recognize the importance of substitutions and deletions in the tdh and trh genes.

  6. Effects of intronic mutations in the LDLR gene on pre-mRNA splicing: Comparison of wet-lab and bioinformatics analyses

    NARCIS (Netherlands)

    O.L. Holla; S. Nakken; M. Mattingsdal; T. Ranheim; K.E. Berge; J.C. Defesche; T.P. Leren

    2009-01-01

    Screening for mutations in the low density lipoprotein receptor (LDLR) gene has identified more than 1000 mutations as the cause of familial hypercholesterolemia (FH). In addition, numerous intronic mutations with uncertain effects on pre-mRNA splicing have also been identified. In this study, we ha

  7. Gene Expression Responses to FUS, EWS, and TAF15 Reduction and Stress Granule Sequestration Analyses Identifies FET-Protein Non-Redundant Functions

    DEFF Research Database (Denmark)

    Blechingberg, Jenny; Luo, Yonglun; Bolund, Lars;

    2012-01-01

    in amyotrophic lateral sclerosis, frontotemporal lobar degeneration, and trinucleotide repeat expansion diseases. We here describe a comparative characterization of FET-protein localization and gene regulatory functions. We show that FUS and TAF15 locate to cellular stress granules to a larger extend than EWS...

  8. Changes to the shuttle circuits

    CERN Multimedia

    GS Department

    2011-01-01

    To fit with passengers expectation, there will be some changes to the shuttle circuits as from Monday 10 October. See details on http://cern.ch/ShuttleService (on line on 7 October). Circuit No. 5 is cancelled as circuit No. 1 also stops at Bldg. 33. In order to guarantee shorter travel times, circuit No. 1 will circulate on Meyrin site only and circuit No. 2, with departures from Bldg. 33 and 500, on Prévessin site only. Site Services Section

  9. Quantitative transformation for implementation of adder circuits in physical systems.

    Science.gov (United States)

    Jones, Jeff; Whiting, James G H; Adamatzky, Andrew

    2015-08-01

    Computing devices are composed of spatial arrangements of simple fundamental logic gates. These gates may be combined to form more complex adding circuits and, ultimately, complete computer systems. Implementing classical adding circuits using unconventional, or even living substrates such as slime mould Physarum polycephalum, is made difficult and often impractical by the challenges of branching fan-out of inputs and regions where circuit lines must cross without interference. In this report we explore whether it is possible to avoid spatial propagation, branching and crossing completely in the design of adding circuits. We analyse the input and output patterns of a single-bit full adder circuit. A simple quantitative transformation of the input patterns which considers the total number of bits in the input string allows us to map the respective input combinations to the correct outputs patterns of the full adder circuit, reducing the circuit combinations from a 2:1 mapping to a 1:1 mapping. The mapping of inputs to outputs also shows an incremental linear progression, suggesting its implementation in a range of physical systems. We demonstrate an example implementation, first in simulation, inspired by self-oscillatory dynamics of the acellular slime mould P. polycephalum. We then assess the potential implementation using plasmodium of slime mould itself. This simple transformation may enrich the potential for using unconventional computing substrates to implement digital circuits.

  10. Power system with an integrated lubrication circuit

    Science.gov (United States)

    Hoff, Brian D.; Akasam, Sivaprasad; Algrain, Marcelo C.; Johnson, Kris W.; Lane, William H.

    2009-11-10

    A power system includes an engine having a first lubrication circuit and at least one auxiliary power unit having a second lubrication circuit. The first lubrication circuit is in fluid communication with the second lubrication circuit.

  11. Association and expression analyses of the Ucp2 and Ucp3 gene polymorphisms with body measurement and meat quality traits in Qinchuan cattle

    Indian Academy of Sciences (India)

    YANING WANG; WUCAI YANG; LINSHENG GUI; HONGBAO WANG; LINSEN ZAN

    2016-12-01

    The uncoupling proteins (UCPs) belong to the mitochondrial inner membrane anion carrier superfamily and play an important role in energy homeostasis. Genetic studies have demonstrated that Ucp2 and Ucp3 gene variants are involved in obesity and metabolic syndrome. The aim of this study was to identify associations between polymorphisms of Ucp2 and Ucp3 genes and economically-important traits in Qinchuan cattle. In the present study, one single-nucleotide polymorphism (SNP) in the 5'UTR region (SNP1: g.C-754G) of the Ucp2 gene was identified by direct sequencing of 441 Qinchuan cattle. Two SNPs in exon 3 (SNP2: g.G4877A; SNP3: g.C4902T) of the Ucp3 gene were identified by sequencing and polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) among 441 Qinchuan cattle. Association analysis showed that SNP1 and SNP2 were associated with the meat quality traits (MQTs) including back fat thickness, loin muscle area and intramuscular fat content. SNP3 was found to be associated with part of the body measurement traits (BMTs) which referred to withers height and chest depth. In addition, QTL pyramiding analysis showed that individuals with diplotype P3P3 (GG–GG–CC) exhibited the best performance in terms of back fat thickness, loin muscle area, intramuscular fat content, rump length, hip width, chestdepth and chest circumference. With regard to the G4877A mutation, real time PCR analysis revealed that individuals with AA genotype of the Ucp3 gene expressed higher mRNA levels than those with GG genotype. These results suggest that thediplotype P3P3 (GG–GG–CC) could be used as a molecular marker of the combined genotypes for future selection of body measurement traits and meat quality traits in Qinchuan cattle.

  12. Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth

    Directory of Open Access Journals (Sweden)

    Kema Gert HJ

    2008-11-01

    Full Text Available Abstract Background The ascomycete fungus Cercospora zeae-maydis is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is known about the regulation of pathogenesis in C. zeae-maydis at the molecular level. The objectives of this study were to generate a collection of expressed sequence tags (ESTs from C. zeae-maydis and evaluate their expression during vegetative, infectious, and reproductive growth. Results A total of 27,551 ESTs was obtained from five cDNA libraries constructed from vegetative and sporulating cultures of C. zeae-maydis. The ESTs, grouped into 4088 clusters and 531 singlets, represented 4619 putative unique genes. Of these, 36% encoded proteins similar (E value ≤ 10-05 to characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions and biological processes based on Gene Ontology (GO classification. We identified numerous, previously undescribed genes with potential roles in photoreception, pathogenesis, and the regulation of development as well as Zephyr, a novel, actively transcribed transposable element. Differential expression of selected genes was demonstrated by real-time PCR, supporting their proposed roles in vegetative, infectious, and reproductive growth. Conclusion Novel genes that are potentially involved in regulating growth, development, and pathogenesis were identified in C. zeae-maydis, providing specific targets for characterization by molecular genetics and functional genomics. The EST data establish a foundation for future studies in evolutionary and comparative genomics among species of Cercospora and other groups of plant pathogenic fungi.

  13. Allopolyploid speciation and ongoing backcrossing between diploid progenitor and tetraploid progeny lineages in the Achillea millefolium species complex: analyses of single-copy nuclear genes and genomic AFLP

    Directory of Open Access Journals (Sweden)

    Ehrendorfer Friedrich

    2010-04-01

    Full Text Available Abstract Background In the flowering plants, many polyploid species complexes display evolutionary radiation. This could be facilitated by gene flow between otherwise separate evolutionary lineages in contact zones. Achillea collina is a widespread tetraploid species within the Achillea millefolium polyploid complex (Asteraceae-Anthemideae. It is morphologically intermediate between the relic diploids, A. setacea-2x in xeric and A. asplenifolia-2x in humid habitats, and often grows in close contact with either of them. By analyzing DNA sequences of two single-copy nuclear genes and the genomic AFLP data, we assess the allopolyploid origin of A. collina-4x from ancestors corresponding to A. setacea-2x and A. asplenifolia-2x, and the ongoing backcross introgression between these diploid progenitor and tetraploid progeny lineages. Results In both the ncpGS and the PgiC gene tree, haplotype sequences of the diploid A. setacea-2x and A. asplenifolia-2x group into two clades corresponding to the two species, though lineage sorting seems incomplete for the PgiC gene. In contrast, A. collina-4x and its suspected backcross plants show homeologous gene copies: sequences from the same tetraploid individual plant are placed in both diploid clades. Semi-congruent splits of an AFLP Neighbor Net link not only A. collina-4x to both diploid species, but some 4x individuals in a polymorphic population with mixed ploidy levels to A. setacea-2x on one hand and to A. collina-4x on the other, indicating allopolyploid speciation as well as hybridization across ploidal levels. Conclusions The findings of this study clearly demonstrate the hybrid origin of Achillea collina-4x, the ongoing backcrossing between the diploid progenitor and their tetraploid progeny lineages. Such repeated hybridizations are likely the cause of the great genetic and phenotypic variation and ecological differentiation of the polyploid taxa in Achillea millefolium agg.

  14. Identification and Analyses of miRNA Genes in Allotetraploid Gossypium hirsutum Fiber Cells Based on the Sequenced Diploid G.raimondii Genome

    Institute of Scientific and Technical Information of China (English)

    Qin Li; Xiang Jin; Yu-Xian Zhu

    2012-01-01

    The plant genome possesses a large number of microRNAs (miRNAs) mainly 21-24 nucleotides in length.They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle.Here we sequenced and analyzed ~ 10 million non-coding RNAs (ncRNAs) derived from fiber tissue of the allotetraploid cotton (Gossypium hirsutum) 7 days post-anthesis using ncRNA-seq technology.In terms of distinct reads,24 nt ncRNA is by far the dominant species,followed by 21 nt and 23 nt ncRNAs.Using ab initio prediction,we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D5 genome of the diploid cotton G.raimondii.Of all the 562 predicted miRNAs,22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species.Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes.Among the 463 putative miRNA target genes,most significant up/down-regulation occurred in 10-20 days post-anthesis,indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber developmem.The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.

  15. Memristor based startup circuit for self biased circuits

    Science.gov (United States)

    Das, Mangal; Singh, Amit Kumar; Rathi, Amit; Singhal, Sonal

    2016-04-01

    This paper presents the design of a Memristor based startup circuit for self biased circuits. Memristor has many advantages over conventional CMOS devices such as low leakage current at nanometer scale, easy to manufacture. In this work the switching characteristics of memristor is utilized. First the theoretical equations describing the switching behavior of memristor are investigated. To prove the switching capability of Memristor, a startup circuit based on memristor is proposed which uses series combination of Memristor and capacitor. Proposed circuit is compared with the previously reported MOSFET based startup circuits. Comparison of different circuits was done to validate the results. Simulation results show that memristor based circuit can attain on (I = 12.94 µA) to off state (I = 1 .2 µA) in 25 ns while the MOSFET based startup circuits take on (I = 14.19 µA) to off state (I = 1.4 µA) in more than 90 ns. The benefit comes in terms of area because the number of components used in the circuit are lesser than the conventional startup circuits.

  16. Comparative Gene Expression Analyses Identify Luminal and Basal Subtypes of Canine Invasive Urothelial Carcinoma That Mimic Patterns in Human Invasive Bladder Cancer.

    Science.gov (United States)

    Dhawan, Deepika; Paoloni, Melissa; Shukradas, Shweta; Choudhury, Dipanwita Roy; Craig, Bruce A; Ramos-Vara, José A; Hahn, Noah; Bonney, Patty L; Khanna, Chand; Knapp, Deborah W

    2015-01-01

    More than 160,000 people are expected to die from invasive urothelial carcinoma (iUC) this year worldwide. Research in relevant animal models is essential to improving iUC management. Naturally-occurring canine iUC closely resembles human iUC in histopathology, metastatic behavior, and treatment response, and could provide a relevant model for human iUC. The molecular characterization of canine iUC, however, has been limited. Work was conducted to compare gene expression array results between tissue samples from iUC and normal bladder in dogs, with comparison to similar expression array data from human iUC and normal bladder in the literature. Considerable similarities between enrichment patterns of genes in canine and human iUC were observed. These included patterns mirroring basal and luminal subtypes initially observed in human breast cancer and more recently noted in human iUC. Canine iUC samples also exhibited enrichment for genes involved in P53 pathways, as has been reported in human iUC. This is particularly relevant as drugs targeting these genes/pathways in other cancers could be repurposed to treat iUC, with dogs providing a model to optimize therapy. As part of the validation of the results and proof of principal for evaluating individualized targeted therapy, the overexpression of EGFR in canine bladder iUC was confirmed. The similarities in gene expression patterns between dogs and humans add considerably to the value of naturally-occurring canine iUC as a relevant and much needed animal model for human iUC. Furthermore, the finding of expression patterns that cross different pathologically-defined cancers could allow studies of dogs with iUC to help optimize cancer management across multiple cancer types. The work is also expected to lead to a better understanding of the biological importance of the gene expression patterns, and the potential application of the cross-species comparisons approach to other cancer types as well.

  17. Comparative Gene Expression Analyses Identify Luminal and Basal Subtypes of Canine Invasive Urothelial Carcinoma That Mimic Patterns in Human Invasive Bladder Cancer.

    Directory of Open Access Journals (Sweden)

    Deepika Dhawan

    Full Text Available More than 160,000 people are expected to die from invasive urothelial carcinoma (iUC this year worldwide. Research in relevant animal models is essential to improving iUC management. Naturally-occurring canine iUC closely resembles human iUC in histopathology, metastatic behavior, and treatment response, and could provide a relevant model for human iUC. The molecular characterization of canine iUC, however, has been limited. Work was conducted to compare gene expression array results between tissue samples from iUC and normal bladder in dogs, with comparison to similar expression array data from human iUC and normal bladder in the literature. Considerable similarities between enrichment patterns of genes in canine and human iUC were observed. These included patterns mirroring basal and luminal subtypes initially observed in human breast cancer and more recently noted in human iUC. Canine iUC samples also exhibited enrichment for genes involved in P53 pathways, as has been reported in human iUC. This is particularly relevant as drugs targeting these genes/pathways in other cancers could be repurposed to treat iUC, with dogs providing a model to optimize therapy. As part of the validation of the results and proof of principal for evaluating individualized targeted therapy, the overexpression of EGFR in canine bladder iUC was confirmed. The similarities in gene expression patterns between dogs and humans add considerably to the value of naturally-occurring canine iUC as a relevant and much needed animal model for human iUC. Furthermore, the finding of expression patterns that cross different pathologically-defined cancers could allow studies of dogs with iUC to help optimize cancer management across multiple cancer types. The work is also expected to lead to a better understanding of the biological importance of the gene expression patterns, and the potential application of the cross-species comparisons approach to other cancer types as well.

  18. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  19. Multi-gene phylogenetic analyses of New Zealand coralline algae: Corallinapetra Novaezelandiae gen. et sp. nov. and recognition of the Hapalidiales ord. nov.

    Science.gov (United States)

    Nelson, Wendy A; Sutherland, Judith E; Farr, Tracy J; Hart, Darren R; Neill, Kate F; Kim, Hee Jeong; Yoon, Hwan Su

    2015-06-01

    Coralline red algae from the New Zealand region were investigated in a study focused on documenting regional diversity. We present a multi-gene analysis using sequence data obtained for four genes (nSSU, psaA, psbA, rbcL) from 68 samples. The study revealed cryptic diversity at both genus and species levels, confirming and providing further evidence of problems with current taxonomic concepts in the Corallinophycidae. In addition, a new genus Corallinapetra novaezelandiae gen. et sp. nov. is erected for material from northern New Zealand. Corallinapetra is excluded from all currently recognized families and orders within the Corallinophycidae and thus represents a previously unrecognized lineage within this subclass. We discuss rank in the Corallinophycidae and propose the order Hapalidiales.

  20. Equivalent realisation circuit for a class of non-ideal voltage-controlled memristors

    Directory of Open Access Journals (Sweden)

    Saihu Pan

    2015-12-01

    Full Text Available In this study, an equivalent realisation circuit with off-the-shelf components and devices is proposed, which can be used to equivalently implement a class of non-ideal voltage-controlled memristors. The mathematical models of the equivalent realisation circuit with three function arithmetic circuits are built and their fingerprints are analysed by the pinched hysteresis loops with bipolar periodic voltage stimuli. The numerical simulations are easily verified by experimental measurements, which indicate that when three function arithmetic circuits are linked, the equivalent realisation circuit can realise three non-ideal voltage-controlled memristors with different non-linearities.

  1. The position of tree shrews in the mammalian tree: Comparing multi-gene analyses with phylogenomic results leaves monophyly of Euarchonta doubtful.

    Science.gov (United States)

    Zhou, Xuming; Sun, Fengming; Xu, Shixia; Yang, Guang; Li, Ming

    2015-03-01

    The well-accepted Euarchonta grandorder is a pruned version of Archonta nested within the Euarchontoglires (or Supraprimates) clade. At present, it includes tree shrews (Scandentia), flying lemurs (Dermoptera) and primates (Primates). Here, a phylogenomic dataset containing 1912 exons from 22 representative mammals was compiled to investigate the phylogenetic relationships within this group. Phylogenetic analyses and hypothesis testing suggested that tree shrews can be classified as a sister group to Primates or to Glires or even as a basal clade within Euarchontoglires. Further analyses of both modified and original previously published datasets found that the phylogenetic position of tree shrews is unstable. We also found that two of three exonic indels reported as synapomorphies of Euarchonta in a previous study do not unambiguously support the monophyly of such a clade. Therefore, the monophyly of both Euarchonta and Sundatheria (Dermoptera + Scandentia) are suspect. Molecular dating and divergence rate analyses suggested that the ancestor of Euarchontoglires experienced a rapid divergence, which may cause the unresolved position of tree shrews even using the whole genomic data.

  2. Vertical Distribution of Bacterial Communities in the Indian Ocean as Revealed by Analyses of 16S rRNA and nasA Genes.

    Science.gov (United States)

    Jiang, Xuexia; Jiao, Nianzhi

    2016-09-01

    Bacteria play an important role in the marine biogeochemical cycles. However, research on the bacterial community structure of the Indian Ocean is scarce, particularly within the vertical dimension. In this study, we investigated the bacterial diversity of the pelagic, mesopelagic and bathypelagic zones of the southwestern Indian Ocean (50.46°E, 37.71°S). The clone libraries constructed by 16S rRNA gene sequence revealed that most phylotypes retrieved from the Indian Ocean were highly divergent from those retrieved from other oceans. Vertical differences were observed based on the analysis of natural bacterial community populations derived from the 16S rRNA gene sequences. Based on the analysis of the nasA gene sequences from GenBank database, a pair of general primers was developed and used to amplify the bacterial nitrate-assimilating populations. Environmental factors play an important role in mediating the bacterial communities in the Indian Ocean revealed by canonical correlation analysis.

  3. Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population.

    Science.gov (United States)

    Lee, Daehwan; Cho, Minah; Hong, Woon-Young; Lim, Dajeong; Kim, Hyung-Chul; Cho, Yong-Min; Jeong, Jin-Young; Choi, Bong-Hwan; Ko, Younhee; Kim, Jaebum

    2016-09-01

    Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.

  4. Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population

    Science.gov (United States)

    Lee, Daehwan; Cho, Minah; Hong, Woon-young; Lim, Dajeong; Kim, Hyung-Chul; Cho, Yong-Min; Jeong, Jin-Young; Choi, Bong-Hwan; Ko, Younhee; Kim, Jaebum

    2016-01-01

    Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality. PMID:27640093

  5. Examining new phylogenetic markers to uncover the evolutionary history of early-diverging fungi: comparing MCM7, TSR1 and rRNA genes for single- and multi-gene analyses of the Kickxellomycotina

    NARCIS (Netherlands)

    Tretter, E.D.; Johnson, E.M.; Wang, Y.; Kandel, P.; White, M.M.

    2013-01-01

    The recently recognised protein-coding genes MCM7 and TSR1 have shown significant promise for phylogenetic resolution within the Ascomycota and Basidiomycota, but have remained unexamined within other fungal groups (except for Mucorales). We designed and tested primers to amplify these genes across

  6. Mapping of a chromosome 12 region associated with airway hyperresponsiveness in a recombinant congenic mouse strain and selection of potential candidate genes by expression and sequence variation analyses.

    Directory of Open Access Journals (Sweden)

    Cynthia Kanagaratham

    Full Text Available In a previous study we determined that BcA86 mice, a strain belonging to a panel of AcB/BcA recombinant congenic strains, have an airway responsiveness phenotype resembling mice from the airway hyperresponsive A/J strain. The majority of the BcA86 genome is however from the hyporesponsive C57BL/6J strain. The aim of this study was to identify candidate regions and genes associated with airway hyperresponsiveness (AHR by quantitative trait locus (QTL analysis using the BcA86 strain. Airway responsiveness of 205 F2 mice generated from backcrossing BcA86 strain to C57BL/6J strain was measured and used for QTL analysis to identify genomic regions in linkage with AHR. Consomic mice for the QTL containing chromosomes were phenotyped to study the contribution of each chromosome to lung responsiveness. Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools. One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68 × 10(-3. We confirmed that the genotype of mouse Chromosome 12 is an important determinant of lung responsiveness using a Chromosome 12 substitution strain. Mice with an A/J Chromosome 12 on a C57BL/6J background have an AHR phenotype similar to hyperresponsive strains A/J and BcA86. Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype. Overall, through QTL analysis of a recombinant congenic strain, microarray analysis and coding variant analysis we identified Chromosome 12 and three potential candidate genes to be in linkage with airway responsiveness.

  7. Photonic Integrated Circuits

    Science.gov (United States)

    Krainak, Michael; Merritt, Scott

    2016-01-01

    Integrated photonics generally is the integration of multiple lithographically defined photonic and electronic components and devices (e.g. lasers, detectors, waveguides passive structures, modulators, electronic control and optical interconnects) on a single platform with nanometer-scale feature sizes. The development of photonic integrated circuits permits size, weight, power and cost reductions for spacecraft microprocessors, optical communication, processor buses, advanced data processing, and integrated optic science instrument optical systems, subsystems and components. This is particularly critical for small spacecraft platforms. We will give an overview of some NASA applications for integrated photonics.

  8. Electronic logic circuits

    CERN Document Server

    Gibson, J

    2013-01-01

    Most branches of organizing utilize digital electronic systems. This book introduces the design of such systems using basic logic elements as the components. The material is presented in a straightforward manner suitable for students of electronic engineering and computer science. The book is also of use to engineers in related disciplines who require a clear introduction to logic circuits. This third edition has been revised to encompass the most recent advances in technology as well as the latest trends in components and notation. It includes a wide coverage of application specific integrate

  9. Electronics circuits and systems

    CERN Document Server

    Bishop, Owen

    2011-01-01

    The material in Electronics - Circuits and Systems is a truly up-to-date textbook, with coverage carefully matched to the electronics units of the 2007 BTEC National Engineering and the latest AS and A Level specifications in Electronics from AQA, OCR and WJEC. The material has been organized with a logical learning progression, making it ideal for a wide range of pre-degree courses in electronics. The approach is student-centred and includes: numerous examples and activities; web research topics; Self Test features, highlighted key facts, formulae and definitions. Ea

  10. Linear integrated circuits

    CERN Document Server

    Carr, Joseph

    1996-01-01

    The linear IC market is large and growing, as is the demand for well trained technicians and engineers who understand how these devices work and how to apply them. Linear Integrated Circuits provides in-depth coverage of the devices and their operation, but not at the expense of practical applications in which linear devices figure prominently. This book is written for a wide readership from FE and first degree students, to hobbyists and professionals.Chapter 1 offers a general introduction that will provide students with the foundations of linear IC technology. From chapter 2 onwa

  11. Optoelectronics circuits manual

    CERN Document Server

    Marston, R M

    1999-01-01

    This manual is a useful single-volume guide specifically aimed at the practical design engineer, technician, and experimenter, as well as the electronics student and amateur. It deals with the subject in an easy to read, down to earth, and non-mathematical yet comprehensive manner, explaining the basic principles and characteristics of the best known devices, and presenting the reader with many practical applications and over 200 circuits. Most of the ICs and other devices used are inexpensive and readily available types, with universally recognised type numbers.The second edition

  12. Nano integrated circuit process

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Yung Sup

    2004-02-15

    This book contains nine chapters, which are introduction of manufacture of semiconductor chip, oxidation such as Dry-oxidation, wet oxidation, oxidation model and oxide film, diffusion like diffusion process, diffusion equation, diffusion coefficient and diffusion system, ion implantation, including ion distribution, channeling, multiimplantation and masking and its system, sputtering such as CVD and PVD, lithography, wet etch and dry etch, interconnection and flattening like metal-silicon connection, silicide, multiple layer metal process and flattening, an integrated circuit process, including MOSFET and CMOS.

  13. Electronics circuits and systems

    CERN Document Server

    Bishop, Owen

    2007-01-01

    The material in Electronics - Circuits and Systems is a truly up-to-date textbook, with coverage carefully matched to the electronics units of the 2007 BTEC National Engineering and the latest AS and A Level specifications in Electronics from AQA, OCR and WJEC. The material has been organized with a logical learning progression, making it ideal for a wide range of pre-degree courses in electronics. The approach is student-centred and includes: numerous examples and activities; web research topics; Self Test features, highlighted key facts, formulae and definitions. Each chapter ends with a set

  14. Electric circuits problem solver

    CERN Document Server

    REA, Editors of

    2012-01-01

    Each Problem Solver is an insightful and essential study and solution guide chock-full of clear, concise problem-solving gems. All your questions can be found in one convenient source from one of the most trusted names in reference solution guides. More useful, more practical, and more informative, these study aids are the best review books and textbook companions available. Nothing remotely as comprehensive or as helpful exists in their subject anywhere. Perfect for undergraduate and graduate studies.Here in this highly useful reference is the finest overview of electric circuits currently av

  15. Sequential circuit design for radiation hardened multiple voltage integrated circuits

    Science.gov (United States)

    Clark, Lawrence T.; McIver, III, John K.

    2009-11-24

    The present invention includes a radiation hardened sequential circuit, such as a bistable circuit, flip-flop or other suitable design that presents substantial immunity to ionizing radiation while simultaneously maintaining a low operating voltage. In one embodiment, the circuit includes a plurality of logic elements that operate on relatively low voltage, and a master and slave latches each having storage elements that operate on a relatively high voltage.

  16. Analyses of loss-of-function mutations of the MITF gene suggest that haploinsufficiency is a cause of Waardenburg syndrome type 2A

    Energy Technology Data Exchange (ETDEWEB)

    Nobukuni, Yoshitaka; Watanabe, A.; Takeda, Kazushisa; Skarka, Hana; Tachibana, Masayoshi [National Inst. of Health, Bethesda, MD (United States)

    1996-07-01

    Waardenburg syndrome type 2 (WS2) is a dominantly inherited disorder characterized by a pigmentation anomaly and hearing impairment due to lack of melanocyte. Previous work has linked a subset of families with WS2 (WS2A) to the MITF gene that encodes a transcription factor with a basic-helix-loop-helix-leucine zipper (bHLH-Zip) motif and that is involved in melanocyte differentiation. Several splice-site and missense mutations have been reported in individuals affected with WS2A. In this report, we have identified two novel point mutations in the MITF gene in affected individuals from two different families with WS2A. The two mutations (C760{r_arrow}T and C895{r_arrow}T) create stop codons in exons 7 and 8, respectively. Corresponding mutant alleles predict the truncated proteins lacking HLH-Zip or Zip structure. To understand how these mutations cause WS2 in heterozygotes, we generated mutant MITF cDNAs and used them for DNA-binding and luciferase reporter assays. The mutated MITF proteins lose the DNA-binding activity and fail to transactivate the promoter of tyrosinase, a melanocyte-specific enzyme. However, these mutated proteins do not appear to interfere with the activity of wild-type MITF protein in these assays, indicating that they do not show a dominant-negative effect. These findings suggest that the phenotypes of the two families with WS2A in the present study are caused by loss-of-function mutations in one of the two alleles of the MITF gene, resulting in haploinsufficiency of the MITF protein, the protein necessary for normal development of melanocytes. 37 refs., 4 figs.

  17. Candidate Gene Discovery Procedure after Follow-Up Confirmatory Analyses of Candidate Regions of Interests for Alzheimer’s Disease in the NIMH Sibling Dataset

    Directory of Open Access Journals (Sweden)

    Tesfaye M. Baye

    2008-01-01

    Full Text Available The objective of this research was to develop a procedure to identify candidate genes under linkage peaks confirmed in a follow-up of candidate regions of interests (CRIs identified in our original genome scan in the NIMH Alzheimer’s diseases (AD Initiative families (Blacker et al. [1]. There were six CRIs identified that met the threshold of multipoint lod score (MLS of ≥ 2.0 from the original scan. The most significant peak (MLS = 7.7 was at 19q13, which was attributed to APOE. The remaining CRIs with ‘suggestive’ evidence for linkage were identified at 9q22, 6q27, 14q22, 11q25, and 3p26. We have followed up and narrowed the 9q22 CRI signal using simple tandem repeat (STR markers (Perry et al. [2]. In this confirmatory project, we have followed up the 6q27, 14q22, 11q25, and 3p26 CRIs with a total of 24 additional flanking STRs, reducing the mean interval marker distance (MID in each CRI, and substantially increase in the information content (IC. The linkage signals at 6q27, 14q22 and 11q25 remain ‘suggestive’, indicating that these CRIs are promising and worthy of detailed fine mapping and assessment of candidate genes associated with AD.

  18. [TUB9 polymorphism in the CFTR gene of cystic fibrosis patients, carriers, and healthy donors from the Moscow region. SSCP and restriction analyses].

    Science.gov (United States)

    Amosenko, F A; Trubnikova, I S; Zakhar'ev, V M; Bannikov, V M; Sazonova, M A; Petrova, N V; Kapranov, N I; Kaplinin, V N

    1997-02-01

    Data on the screening of 266 non-delta F508 chromosomes (42 cystic fibrosis patients, 43 carriers, and 48 healthy donors from the Moscow region) for the presence of structural abnormalities within the tenth exon of the CFTR gene conducted by means of the single-stranded conformation polymorphism (SSCP) technique in nonisotope modification are presented. The method used made it possible to detect three SSCP variants, one of which was present in cystic fibrosis patients (23.8%) and carriers (9.3%), but not in healthy donors. Sequencing of the 5 amplified DNA fragments carrying this SSCP variant revealed an A-->G substitution in the 1525-61 position, which indicated the presence of TUB9 polymorphism with allele 1 in the homozygous state in all cases tested. The three SSCP variants described corresponded to the three allelic variants of TUB9 polymorphism as judged by MnlI restriction analysis of the amplified tenth exon sequence. The modified SSCP technique is also suitable for routine screening for the G542X, G55ID, and W1282X point mutations within the CFTR gene. The frequency distribution of polymorphic TUB9 marker alleles across the non-delta F508 chromosomes in the three studied groups were estimated. Homozygotes for the TUB9 allele 1 were shown to have identical GATT-TUB9-M470V haplotypes.

  19. Functional Analyses of the Diels-Alderase Gene sol5 of Ascochyta rabiei and Alternaria solani Indicate that the Solanapyrone Phytotoxins Are Not Required for Pathogenicity.

    Science.gov (United States)

    Kim, Wonyong; Park, Chung-Min; Park, Jeong-Jin; Akamatsu, Hajime O; Peever, Tobin L; Xian, Ming; Gang, David R; Vandemark, George; Chen, Weidong

    2015-04-01

    Ascochyta rabiei and Alternaria solani, the causal agents of Ascochyta blight of chickpea (Cicer arietinum) and early blight of potato (Solanum tuberosum), respectively, produce a set of phytotoxic compounds including solanapyrones A, B, and C. Although both the phytotoxicity of solanapyrones and their universal production among field isolates have been documented, the role of solanapyrones in pathogenicity is not well understood. Here, we report the functional characterization of the sol5 gene, which encodes a Diels-Alderase that catalyzes the final step of solanapyrone biosynthesis. Deletion of sol5 in both Ascochyta rabiei and Alternaria solani completely prevented production of solanapyrones and led to accumulation of the immediate precursor compound, prosolanapyrone II-diol, which is not toxic to plants. Deletion of sol5 did not negatively affect growth rate or spore production in vitro, and led to overexpression of the other solanapyrone biosynthesis genes, suggesting a possible feedback regulation mechanism. Phytotoxicity tests showed that solanapyrone A is highly toxic to several legume species and Arabidopsis thaliana. Despite the apparent phytotoxicity of solanapyrone A, pathogenicity tests showed that solanapyrone-minus mutants of Ascochyta rabiei and Alternaria solani were equally virulent as their corresponding wild-type progenitors, suggesting that solanapyrones are not required for pathogenicity.

  20. Comparative Analyses of the β-Tubulin Gene and Molecular Modeling Reveal Molecular Insight into the Colchicine Resistance in Kinetoplastids Organisms

    Directory of Open Access Journals (Sweden)

    Luis Luis

    2013-01-01

    Full Text Available Differential susceptibility to microtubule agents has been demonstrated between mammalian cells and kinetoplastid organisms such as Leishmania spp. and Trypanosoma spp. The aims of this study were to identify and characterize the architecture of the putative colchicine binding site of Leishmania spp. and investigate the molecular basis of colchicine resistance. We cloned and sequenced the β-tubulin gene of Leishmania (Viannia guyanensis and established the theoretical 3D model of the protein, using the crystallographic structure of the bovine protein as template. We identified mutations on the Leishmania  β-tubulin gene sequences on regions related to the putative colchicine-binding pocket, which generate amino acid substitutions and changes in the topology of this region, blocking the access of colchicine. The same mutations were found in the β-tubulin sequence of kinetoplastid organisms such as Trypanosoma cruzi, T. brucei, and T. evansi. Using molecular modelling approaches, we demonstrated that conformational changes include an elongation and torsion of an α-helix structure and displacement to the inside of the pocket of one β-sheet that hinders access of colchicine. We propose that kinetoplastid organisms show resistance to colchicine due to amino acids substitutions that generate structural changes in the putative colchicine-binding domain, which prevent colchicine access.

  1. 49 CFR 236.13 - Spring switch; selection of signal control circuits through circuit controller.

    Science.gov (United States)

    2010-10-01

    ... circuits through circuit controller. 236.13 Section 236.13 Transportation Other Regulations Relating to...; selection of signal control circuits through circuit controller. The control circuits of signals governing... circuit controller, or through the contacts of relay repeating the position of such circuit...

  2. Quasi-Linear Circuit

    Science.gov (United States)

    Bradley, William; Bird, Ross; Eldred, Dennis; Zook, Jon; Knowles, Gareth

    2013-01-01

    This work involved developing spacequalifiable switch mode DC/DC power supplies that improve performance with fewer components, and result in elimination of digital components and reduction in magnetics. This design is for missions where systems may be operating under extreme conditions, especially at elevated temperature levels from 200 to 300 degC. Prior art for radiation-tolerant DC/DC converters has been accomplished utilizing classical magnetic-based switch mode converter topologies; however, this requires specific shielding and component de-rating to meet the high-reliability specifications. It requires complex measurement and feedback components, and will not enable automatic re-optimization for larger changes in voltage supply or electrical loading condition. The innovation is a switch mode DC/DC power supply that eliminates the need for processors and most magnetics. It can provide a well-regulated voltage supply with a gain of 1:100 step-up to 8:1 step down, tolerating an up to 30% fluctuation of the voltage supply parameters. The circuit incorporates a ceramic core transformer in a manner that enables it to provide a well-regulated voltage output without use of any processor components or magnetic transformers. The circuit adjusts its internal parameters to re-optimize its performance for changes in supply voltage, environmental conditions, or electrical loading at the output

  3. Cloning and function analyses of HDS gene from Artemisia annua%黄花蒿HDS基因的克隆与功能分析

    Institute of Scientific and Technical Information of China (English)

    张祖荣; 廖志华; 彭梅芳

    2012-01-01

    目的 克隆获得黄花蒿MEP途径中必需关键酶——羟甲基丁烯基-4-磷酸合成酶基因(HDS),并进行生物信息学分析和功能互补分析研究.方法 对已知的其他种子植物HDS基因的核苷酸序列进行多重序列比对,选取保守区域设计简并引物,利用同源扩增和cDNA末端快速扩增技术从黄花蒿中获得目的基因;利用BLAST进行序列比对,ORF Finder寻找开放阅读框,并用MEGA3.0中的临位相联法构建进化树.结果 得到1条长2324 bp的HDS cDNA序列,其ORF 框长1854 bp,编码617个氨基酸残基的蛋白;生物信息学分析显示,黄花蒿HDS基因AaHDS与其他种子植物来源的HDS高度同源;功能互补分析表明,AaHDS能互补突变菌株Escherichia coli MG1655 ara<> HDS中缺失的HDS功能,使突变菌株恢复生长,证明AaHDS具有典型的HDS基因功能.结论 首次克隆获得黄花蒿HDS基因,为青蒿素的代谢工程研究提供相应的基础.%Objective To obtain the indispensable key enzyme-hydroxide methyl enylamino 4-cyclodiphosphate synthase (HDS) gene involved in the MEP pathway cloned from Artemisia annua and conduct bioinformatic and functional complementation analysis. Methods To perform multiple sequence alignment for the nucleotide acid sequence of the other reported seed plants' HDS gene, to select conservative areas for designing degenerate primers, and to gain the aim gene from A. Annua through homologous expanding and cDNA bottom speedily expanding technique. To perform sequence alignment using BLAST, to identify open reading frame (ORF) using ORF Finder, and to construct phylogenetic tree using neighbor joining (NJ) ways in MEGA3.0. Results The obtained HDS cDNA sequence was 2 324 bp containing a 1 854 bp ORF and encoding a 617-amino acid protein. Bioinformatic analysis showed that AaHDS was homologous with HDS derived from other seed plant species. Functional complementation analysis indicated that AaHDS could make up the short HDS

  4. Automated Design of Quantum Circuits

    Science.gov (United States)

    Williams, Colin P.; Gray, Alexander G.

    2000-01-01

    In order to design a quantum circuit that performs a desired quantum computation, it is necessary to find a decomposition of the unitary matrix that represents that computation in terms of a sequence of quantum gate operations. To date, such designs have either been found by hand or by exhaustive enumeration of all possible circuit topologies. In this paper we propose an automated approach to quantum circuit design using search heuristics based on principles abstracted from evolutionary genetics, i.e. using a genetic programming algorithm adapted specially for this problem. We demonstrate the method on the task of discovering quantum circuit designs for quantum teleportation. We show that to find a given known circuit design (one which was hand-crafted by a human), the method considers roughly an order of magnitude fewer designs than naive enumeration. In addition, the method finds novel circuit designs superior to those previously known.

  5. Ribozyme-based insulator parts buffer synthetic circuits from genetic context.

    Science.gov (United States)

    Lou, Chunbo; Stanton, Brynne; Chen, Ying-Ja; Munsky, Brian; Voigt, Christopher A

    2012-11-01

    Synthetic genetic programs are built from circuits that integrate sensors and implement temporal control of gene expression. Transcriptional circuits are layered by using promoters to carry the signal between circuits. In other words, the output promoter of one circuit serves as the input promoter to the next. Thus, connecting circuits requires physically connecting a promoter to the next circuit. We show that the sequence at the junction between the input promoter and circuit can affect the input-output response (transfer function) of the circuit. A library of putative sequences that might reduce (or buffer) such context effects, which we refer to as 'insulator parts', is screened in Escherichia coli. We find that ribozymes that cleave the 5' untranslated region (5'-UTR) of the mRNA are effective insulators. They generate quantitatively identical transfer functions, irrespective of the identity of the input promoter. When these insulators are used to join synthetic gene circuits, the behavior of layered circuits can be predicted using a mathematical model. The inclusion of insulators will be critical in reliably permuting circuits to build different programs.

  6. CMOS Nonlinear Signal Processing Circuits

    OpenAIRE

    2010-01-01

    The chapter describes various nonlinear signal processing CMOS circuits, including a high reliable WTA/LTA, simple MED cell, and low-voltage arbitrary order extractor. We focus the discussion on CMOS analog circuit design with reliable, programmable capability, and low voltage operation. It is a practical problem when the multiple identical cells are required to match and realized within a single chip using a conventional process. Thus, the design of high-reliable circuit is indeed needed. Th...

  7. Analog electronic neural network circuits

    Energy Technology Data Exchange (ETDEWEB)

    Graf, H.P.; Jackel, L.D. (AT and T Bell Labs., Holmdel, NJ (USA))

    1989-07-01

    The large interconnectivity and moderate precision required in neural network models present new opportunities for analog computing. This paper discusses analog circuits for a variety of problems such as pattern matching, optimization, and learning. Most of the circuits build so far are relatively small, exploratory designs. The most mature circuits are those for template matching. Chips performing this function are now being applied to pattern recognition problems.

  8. Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1

    Science.gov (United States)

    Feng, Xinxin; An, Yuyan; Zheng, Jie; Sun, Miao; Wang, Liangju

    2016-01-01

    Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA), a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control) were identified by complementary gel-based and gel-free separation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control) and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related genes. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX, and MdUFGT) in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin

  9. Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1.

    Science.gov (United States)

    Feng, Xinxin; An, Yuyan; Zheng, Jie; Sun, Miao; Wang, Liangju

    2016-01-01

    Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA), a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control) were identified by complementary gel-based and gel-free separation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control) and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related genes. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX, and MdUFGT) in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin

  10. Transistor switching and sequential circuits

    CERN Document Server

    Sparkes, John J

    1969-01-01

    Transistor Switching and Sequential Circuits presents the basic ideas involved in the construction of computers, instrumentation, pulse communication systems, and automation. This book discusses the design procedure for sequential circuits. Organized into two parts encompassing eight chapters, this book begins with an overview of the ways on how to generate the types of waveforms needed in digital circuits, principally ramps, square waves, and delays. This text then considers the behavior of some simple circuits, including the inverter, the emitter follower, and the long-tailed pair. Other cha

  11. Unstable oscillators based hyperchaotic circuit

    DEFF Research Database (Denmark)

    Murali, K.; Tamasevicius, A.; G. Mykolaitis, A.;

    1999-01-01

    A simple 4th order hyperchaotic circuit with unstable oscillators is described. The circuit contains two negative impedance converters, two inductors, two capacitors, a linear resistor and a diode. The Lyapunov exponents are presented to confirm hyperchaotic nature of the oscillations in the circ......A simple 4th order hyperchaotic circuit with unstable oscillators is described. The circuit contains two negative impedance converters, two inductors, two capacitors, a linear resistor and a diode. The Lyapunov exponents are presented to confirm hyperchaotic nature of the oscillations...

  12. Cloning and sequence analyses of myostatin gene in Squaliobarbus crriculus%赤眼鳟myostatin基因的克隆与组织表达分析

    Institute of Scientific and Technical Information of China (English)

    邵芳; 郁建锋; 张燕萍; 卢祥云; 徐建荣; 朱斌; 顾志良

    2013-01-01

    Myostatin is a negative regulator of skeletal muscle growth and has a potential application in aquaculture. In order to clone full-length myostatin gene and characterize its tissue expression profile in Squalwbarbus crriculus, RT-PCR and rapid-amplification cDNA ends( RACE) were used to acquire a full-length of 2 214 bp myostatin cDNA, which included a 1 128 bp long complete ORF encoding a 375 amino acid peptide. myostatin gene in S. crriculus consisted of two typical TGF-β protein domains; TGF-β propeptide domain and TGF-p activity domain. Multiple sequence comparison showed that the S. crriculus myostatin had a high homology with Cyprinus carpio at 96. 99%. A homology with other fish at 76% -81% , and a low homology with mammals at 63%. S. crriculus myostatin protein amino acid sequence had a very high homology with other species, especially in the C terminal biologically active region. In the eight examined tissues, the myostatin gene was highly expressed in muscle and brain, followed by in heart, weakly expressed in gill, spleen and intestine, and traced in kidney, and there was no obvious expression in liver. These results suggested that the fish myostatin gene might not only play roles in muscle development but also contribute to other biological functions.%以赤眼鳟(Squaliobarbus crriculus)肌肉总RNA为模板,采用RT-PCR结合RACE方法,获得其myostatin(肌肉生长抑制素)基因全长为2 214 bp的cDNA序列,其包含了1个含有1 128个核苷酸的开放性阅读框(ORF),共编码375个氨基酸.赤眼鳟与其他物种myostatin的特征性一致.其编码区序列与鲤鱼同源性最高,为96.99%,与其他鱼类的同源性为76%~81%,与哺乳类和鸟类的同源性较低,为63%左右.赤眼鳟Myostatin蛋白的氨基酸序列与其他物种同源性较高,尤其在C端生物活性区,高度的保守性反映了该基因受到了高度的进化限制以及功能的重要性.半定量RT-PCR分析表明,myostatin基因在除肝脏

  13. Integrative analyses of hepatic differentially expressed genes and blood biomarkers during the peripartal period between dairy cows overfed or restricted-fed energy prepartum.

    Directory of Open Access Journals (Sweden)

    Khuram Shahzad

    Full Text Available Using published dairy cattle liver transcriptomics dataset along with novel blood biomarkers of liver function, metabolism, and inflammation we have attempted an integrative systems biology approach applying the classical functional enrichment analysis using DAVID, a newly-developed Dynamic Impact Approach (DIA, and an upstream gene network analysis using Ingenuity Pathway Analysis (IPA. Transcriptome data was generated from experiments evaluating the impact of prepartal plane of energy intake [overfed (OF or restricted (RE] on liver of dairy cows during the peripartal period. Blood biomarkers uncovered that RE vs. OF led to greater prepartal liver distress accompanied by a low-grade inflammation and larger proteolysis (i.e., higher haptoglobin, bilirubin, and creatinine.