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Sample records for differentiation complex edc-encoded

  1. Immunolocalization of a Histidine-Rich Epidermal Differentiation Protein in the Chicken Supports the Hypothesis of an Evolutionary Developmental Link between the Embryonic Subperiderm and Feather Barbs and Barbules.

    PubMed

    Alibardi, Lorenzo; Holthaus, Karin Brigit; Sukseree, Supawadee; Hermann, Marcela; Tschachler, Erwin; Eckhart, Leopold

    2016-01-01

    The morphogenesis of feathers is a complex process that depends on a tight spatiotemporal regulation of gene expression and assembly of the protein components of mature feathers. Recent comparative genomics and gene transcription studies have indicated that genes within the epidermal differentiation complex (EDC) encode numerous structural proteins of cornifying skin cells in amniotes including birds. Here, we determined the localization of one of these proteins, termed EDMTFH (Epidermal Differentiation Protein starting with a MTF motif and rich in Histidine), which belongs to a group of EDC-encoded proteins rich in aromatic amino acid residues. We raised an antibody against an EDMTFH-specific epitope and performed immunohistochemical investigations by light microscopy and immunogold labeling by electron microscopy of chicken embryos at days 14-18 of development. EDMTFH was specifically present in the subperiderm, a transient layer of the embryonic epidermis, and in barbs and barbules of feathers. In the latter, it partially localized to bundles of so-called feather beta-keratins (corneous beta-proteins, CBPs). Cells of the embryonic periderm, the epidermis proper, and the feather sheath were immunonegative for EDMTFH. The results of this study indicate that EDMTFH may contribute to the unique mechanical properties of feathers and define EDMTFH as a common marker of the subperiderm and the feather barbules. This expression pattern of EDMTFH resembles that of epidermal differentiation cysteine-rich protein (EDCRP) and feather CBPs and is in accordance with the hypothesis that a major part of the cyclically regenerating feather follicle is topologically, developmentally and evolutionarily related to the embryonic subperiderm.

  2. Immunolocalization of a Histidine-Rich Epidermal Differentiation Protein in the Chicken Supports the Hypothesis of an Evolutionary Developmental Link between the Embryonic Subperiderm and Feather Barbs and Barbules

    PubMed Central

    Alibardi, Lorenzo; Holthaus, Karin Brigit; Sukseree, Supawadee; Hermann, Marcela; Tschachler, Erwin

    2016-01-01

    The morphogenesis of feathers is a complex process that depends on a tight spatiotemporal regulation of gene expression and assembly of the protein components of mature feathers. Recent comparative genomics and gene transcription studies have indicated that genes within the epidermal differentiation complex (EDC) encode numerous structural proteins of cornifying skin cells in amniotes including birds. Here, we determined the localization of one of these proteins, termed EDMTFH (Epidermal Differentiation Protein starting with a MTF motif and rich in Histidine), which belongs to a group of EDC-encoded proteins rich in aromatic amino acid residues. We raised an antibody against an EDMTFH-specific epitope and performed immunohistochemical investigations by light microscopy and immunogold labeling by electron microscopy of chicken embryos at days 14–18 of development. EDMTFH was specifically present in the subperiderm, a transient layer of the embryonic epidermis, and in barbs and barbules of feathers. In the latter, it partially localized to bundles of so-called feather beta-keratins (corneous beta-proteins, CBPs). Cells of the embryonic periderm, the epidermis proper, and the feather sheath were immunonegative for EDMTFH. The results of this study indicate that EDMTFH may contribute to the unique mechanical properties of feathers and define EDMTFH as a common marker of the subperiderm and the feather barbules. This expression pattern of EDMTFH resembles that of epidermal differentiation cysteine-rich protein (EDCRP) and feather CBPs and is in accordance with the hypothesis that a major part of the cyclically regenerating feather follicle is topologically, developmentally and evolutionarily related to the embryonic subperiderm. PMID:27936131

  3. A differential model of the complex cell.

    PubMed

    Hansard, Miles; Horaud, Radu

    2011-09-01

    The receptive fields of simple cells in the visual cortex can be understood as linear filters. These filters can be modeled by Gabor functions or gaussian derivatives. Gabor functions can also be combined in an energy model of the complex cell response. This letter proposes an alternative model of the complex cell, based on gaussian derivatives. It is most important to account for the insensitivity of the complex response to small shifts of the image. The new model uses a linear combination of the first few derivative filters, at a single position, to approximate the first derivative filter, at a series of adjacent positions. The maximum response, over all positions, gives a signal that is insensitive to small shifts of the image. This model, unlike previous approaches, is based on the scale space theory of visual processing. In particular, the complex cell is built from filters that respond to the 2D differential structure of the image. The computational aspects of the new model are studied in one and two dimensions, using the steerability of the gaussian derivatives. The response of the model to basic images, such as edges and gratings, is derived formally. The response to natural images is also evaluated, using statistical measures of shift insensitivity. The neural implementation and predictions of the model are discussed.

  4. Paired Pulse Voltammetry for differentiating complex analytes

    PubMed Central

    Jang, Dong Pyo; Kim, Inyong; Chang, Su-Youne; Min, Hoon Ki; Arora, Kanika; Marsh, Michale P.; Hwang, Sun-Chul; Kimble, Christopher J.; Bennet, Kevin E.

    2012-01-01

    Although fast-scan cyclic voltammetry (FSCV) has contributed to important advances in neuroscience research, the technique is encumbered by significant analytical challenges. Confounding factors such as pH change and transient effects at the microelectrode surface make it difficult to discern the analytes represented by complex voltammograms. Here we introduce paired-pulse voltammetry (PPV), that mitigates the confounding factors and simplifies the analytical task. PPV consists of a selected binary waveform with a specific time gap between each of its two comprising pulses, such that each binary wave is repeated, while holding the electrode at a negative potential between the waves. This allows two simultaneous yet very different voltammograms (primary and secondary) to be obtained, each corresponding to the two pulses in the binary waveform. PPV was evaluated in the flow cell to characterize three different analytes, (dopamine, adenosine, and pH changes). The peak oxidation current decreased by approximately 50%, 80%, and 4% for dopamine, adenosine, and pH, in the secondary voltammogram compared with primary voltammogram, respectively. Thus, the influence of pH changes could be virtually eliminated using the difference between the primary and secondary voltammograms in the PPV technique, which discriminates analytes on the basis of their adsorption characteristics to the carbon fiber electrode. These results demonstrate that PPV can be effectively used for differentiating complex analytes. PMID:22299131

  5. Differential transendothelial transport of adiponectin complexes

    PubMed Central

    2014-01-01

    Background Adiponectin’s effects on systemic physiology and cell-specific responses are well-defined, but little is known about how this insulin-sensitizing and anti-inflammatory adipokine reaches its target cells. All molecules face active and passive transport limitations, but adiponectin is particularly noteworthy due to the diverse size range and high molecular weights of its oligomers. Additionally, its metabolic target organs possess a range of endothelial permeability. Methods Full-length recombinant murine adiponectin was produced and oligomer fractions isolated by gel filtration. Adiponectin complex sizes were measured by dynamic light scattering to determine Stokes radii. Transendothelial transport of purified oligomers was quantitatively assessed under a number of different conditions in vitro using murine endothelial cells and in vivo using several mouse models of altered endothelial function. Results Adiponectin oligomers exhibit large transport radii that limit transendothelial transport. Oligomerization is a significant determinant of flux across endothelial monolayers in vitro; low molecular weight adiponectin is preferentially transported. In vivo sampled sera from the heart, liver, and tail vein demonstrated significantly different complex distribution of lower molecular weight oligomers. Pharmacological interventions, such as PPARγ agonist treatment, differentially affect adiponectin plasma clearance and tissue uptake. Exercise induces enhanced adiponectin uptake to oxidative skeletal muscles, wherein adiponectin potently lowers ceramide levels. In total, endothelial barriers control adiponectin transport in a cell- and tissue-specific manner. Conclusions Adiponectin oligomer efficacy in a given tissue may therefore be endothelial transport mediated. Targeting endothelial dysfunction in the metabolic syndrome through exercise and pharmaceuticals may afford an effective approach to increasing adiponectin’s beneficial effects. PMID:24552349

  6. A complex Noether approach for variational partial differential equations

    NASA Astrophysics Data System (ADS)

    Naz, R.; Mahomed, F. M.

    2015-10-01

    Scalar complex partial differential equations which admit variational formulations are studied. Such a complex partial differential equation, via a complex dependent variable, splits into a system of two real partial differential equations. The decomposition of the Lagrangian of the complex partial differential equation in the real domain is shown to yield two real Lagrangians for the split system. The complex Maxwellian distribution, transonic gas flow, Maxwellian tails, dissipative wave and Klein-Gordon equations are considered. The Noether symmetries and gauge terms of the split system that correspond to both the Lagrangians are constructed by the Noether approach. In the case of coupled split systems, the same Noether symmetries are obtained. The Noether symmetries for the uncoupled split systems are different. The conserved vectors of the split system which correspond to both the Lagrangians are compared to the split conserved vectors of the complex partial differential equation for the examples. The split conserved vectors of the complex partial differential equation are the same as the conserved vectors of the split system of real partial differential equations in the case of coupled systems. Moreover a Noether-like theorem for the split system is proved which provides the Noether-like conserved quantities of the split system from knowledge of the Noether-like operators. An interesting result on the split characteristics and the conservation laws is shown as well. The Noether symmetries and gauge terms of the Lagrangian of the split system with the split Noether-like operators and gauge terms of the Lagrangian of the given complex partial differential equation are compared. Folklore suggests that the split Noether-like operators of a Lagrangian of a complex Euler-Lagrange partial differential equation are symmetries of the Lagrangian of the split system of real partial differential equations. This is not the case. They are proved to be the same if the

  7. The increasingly complex regulation of adipocyte differentiation

    PubMed Central

    Poulos, Sylvia P; Dodson, Michael V; Culver, Melinda F

    2015-01-01

    Adipose (AD) tissue development and function relies on the ability of adipocytes to proliferate and differentiate into lipid-containing cells that also have endocrine function. Research suggests that certain conditions can induce AD tissue stem cells to differentiate into various cell types and that the microenvironment of the cell, including the extracellular matrix (ECM), is essential in maintaining cell and tissue function. This review provides an overview of factors involved in the proliferation and differentiation of adipocytes. A brief review of the numerous factors that influence PPARγ, the transcription factor thought to be the master regulator of adipocyte differentiation, provides context of established pathways that regulate adipogenesis. Thought provoking findings from research with hypoxia that is supported by earlier research that vascular development is related to adipogenesis are reviewed. Finally, our understanding of the critical role of the ECM and environment in adipogenesis is discussed and compared with studies that suggest that adipocytes may dedifferentiate and can convert into other cell types. PMID:26645953

  8. Sample Complexity Bounds for Differentially Private Learning

    PubMed Central

    Chaudhuri, Kamalika; Hsu, Daniel

    2013-01-01

    This work studies the problem of privacy-preserving classification – namely, learning a classifier from sensitive data while preserving the privacy of individuals in the training set. In particular, the learning algorithm is required in this problem to guarantee differential privacy, a very strong notion of privacy that has gained significant attention in recent years. A natural question to ask is: what is the sample requirement of a learning algorithm that guarantees a certain level of privacy and accuracy? We address this question in the context of learning with infinite hypothesis classes when the data is drawn from a continuous distribution. We first show that even for very simple hypothesis classes, any algorithm that uses a finite number of examples and guarantees differential privacy must fail to return an accurate classifier for at least some unlabeled data distributions. This result is unlike the case with either finite hypothesis classes or discrete data domains, in which distribution-free private learning is possible, as previously shown by Kasiviswanathan et al. (2008). We then consider two approaches to differentially private learning that get around this lower bound. The first approach is to use prior knowledge about the unlabeled data distribution in the form of a reference distribution chosen independently of the sensitive data. Given such a reference , we provide an upper bound on the sample requirement that depends (among other things) on a measure of closeness between and the unlabeled data distribution. Our upper bound applies to the non-realizable as well as the realizable case. The second approach is to relax the privacy requirement, by requiring only label-privacy – namely, that the only labels (and not the unlabeled parts of the examples) be considered sensitive information. An upper bound on the sample requirement of learning with label privacy was shown by Chaudhuri et al. (2006); in this work, we show a lower bound. PMID:25285183

  9. Differentials on graph complexes II: hairy graphs

    NASA Astrophysics Data System (ADS)

    Khoroshkin, Anton; Willwacher, Thomas; Živković, Marko

    2017-10-01

    We study the cohomology of the hairy graph complexes which compute the rational homotopy of embedding spaces, generalizing the Vassiliev invariants of knot theory. We provide spectral sequences converging to zero whose first pages contain the hairy graph cohomology. Our results yield a way to construct many nonzero hairy graph cohomology classes out of (known) non-hairy classes by studying the cancellations in those sequences. This provide a first glimpse at the tentative global structure of the hairy graph cohomology.

  10. The coquaternion algebra and complex partial differential equations

    NASA Astrophysics Data System (ADS)

    Dimiev, Stancho; Konstantinov, Mihail; Todorov, Vladimir

    2009-11-01

    In this paper we consider the problem of differentiation of coquaternionic functions. Let us recall that coquaternions are elements of an associative non-commutative real algebra with zero divisor, introduced by James Cockle (1849) under the name of split-quaternions or coquaternions. Developing two type complex representations for Cockle algebra (complex and paracomplex ones) we present the problem in a non-commutative form of the δ¯-type holomorphy. We prove that corresponding differentiable coquaternionic functions, smooth and analytic, satisfy PDE of complex, and respectively of real variables. Applications for coquaternionic polynomials are sketched.

  11. Integrator complex plays an essential role in adipose differentiation

    SciTech Connect

    Otani, Yuichiro; Nakatsu, Yusuke; Sakoda, Hideyuki; Fukushima, Toshiaki; Fujishiro, Midori; Kushiyama, Akifumi; Okubo, Hirofumi; Tsuchiya, Yoshihiro; Ohno, Haruya; Takahashi, Shin-Ichiro; Nishimura, Fusanori; Kamata, Hideaki; Katagiri, Hideki; Asano, Tomoichiro

    2013-05-03

    Highlights: •IntS6 and IntS11 are subunits of the Integrator complex. •Expression levels of IntS6 and IntS11 were very low in 3T3-L1 fibroblast. •IntS6 and IntS11 were upregulated during adipose differentiation. •Suppression of IntS6 or IntS11 expression inhibited adipose differentiation. -- Abstract: The dynamic process of adipose differentiation involves stepwise expressions of transcription factors and proteins specific to the mature fat cell phenotype. In this study, it was revealed that expression levels of IntS6 and IntS11, subunits of the Integrator complex, were increased in 3T3-L1 cells in the period when the cells reached confluence and differentiated into adipocytes, while being reduced to basal levels after the completion of differentiation. Suppression of IntS6 or IntS11 expression using siRNAs in 3T3-L1 preadipocytes markedly inhibited differentiation into mature adipocytes, based on morphological findings as well as mRNA analysis of adipocyte-specific genes such as Glut4, perilipin and Fabp4. Although Pparγ2 protein expression was suppressed in IntS6 or IntS11-siRNA treated cells, adenoviral forced expression of Pparγ2 failed to restore the capacity for differentiation into mature adipocytes. Taken together, these findings demonstrate that increased expression of Integrator complex subunits is an indispensable event in adipose differentiation. Although further study is necessary to elucidate the underlying mechanism, the processing of U1, U2 small nuclear RNAs may be involved in cell differentiation steps.

  12. A Change In Nuclear Pore Complex Composition Regulates Cell Differentiation

    PubMed Central

    D’Angelo, Maximiliano A.; Gomez-Cavazos, J. Sebastian; Mei, Arianna; Lackner, Daniel H.; Hetzer, Martin W.

    2011-01-01

    SUMMARY Nuclear pore complexes (NPCs) are built from ~30 different proteins called nucleoporins. Previous studies have shown that several Nups exhibit cell-type-specific expression and that mutations in NPC components result in tissue-specific diseases. Here we show that a specific change in NPC composition is required for both myogenic and neuronal differentiation. The transmembrane nucleoporin Nup210 is absent in proliferating myoblasts and embryonic stem (ES) cells but becomes expressed and incorporated into NPCs during cell differentiation. Preventing Nup210 production by RNAi blocks myogenesis and the differentiation of ES cells into neuroprogenitors. We found that the addition of Nup210 to NPCs does not affect nuclear transport but is required for the induction of genes that are essential for cell differentiation. Our results identify a single change in NPC composition as an essential step in cell differentiation and establish a role for Nup210 in gene expression regulation and cell fate determination. PMID:22264802

  13. Dynamical process of complex systems and fractional differential equations

    NASA Astrophysics Data System (ADS)

    Hara, Hiroaki; Tamura, Yoshiyasu

    2013-10-01

    Behavior of dynamical process of complex systems is investigated. Specifically we analyse two types of ideal complex systems. For analysing the ideal complex systems, we define the response functions describing the internal states to an external force. The internal states are obtained as a relaxation process showing a "power law" distribution, such as scale free behaviors observed in actual measurements. By introducing a hybrid system, the logarithmic time, and double logarithmic time, we show how the "slow relaxation" (SR) process and "super slow relaxation" (SSR) process occur. Regarding the irregular variations of the internal states as an activation process, we calculate the response function to the external force. The behaviors are classified into "power", "exponential", and "stretched exponential" type. Finally we construct a fractional differential equation (FDE) describing the time evolution of these complex systems. In our theory, the exponent of the FDE or that of the power law distribution is expressed in terms of the parameters characterizing the structure of the system.

  14. Major histocompatibility complex differentiation in Sacramento River chinook salmon.

    PubMed

    Kim, T J; Parker, K M; Hedrick, P W

    1999-03-01

    The chinook salmon of the Sacramento River, California, have been reduced to a fraction of their former abundance because of human impact and use of the river system. Here we examine the genetic variation at a major histocompatibility complex class II exon in the four Sacramento chinook salmon runs. Examination of the alleles found in these and other chinook salmon revealed nucleotide patterns consistent with selection for amino acid replacement at the putative antigen-binding sites. We found a significant amount of variation in each of the runs, including the federally endangered winter run. All of the samples were in Hardy-Weinberg proportions. A significant amount of genetic differentiation between runs was revealed by several measures of differentiation. Winter run was the most genetically divergent, while the spring, late-fall, and fall runs were less differentiated.

  15. Major histocompatibility complex differentiation in Sacramento River chinook salmon.

    PubMed Central

    Kim, T J; Parker, K M; Hedrick, P W

    1999-01-01

    The chinook salmon of the Sacramento River, California, have been reduced to a fraction of their former abundance because of human impact and use of the river system. Here we examine the genetic variation at a major histocompatibility complex class II exon in the four Sacramento chinook salmon runs. Examination of the alleles found in these and other chinook salmon revealed nucleotide patterns consistent with selection for amino acid replacement at the putative antigen-binding sites. We found a significant amount of variation in each of the runs, including the federally endangered winter run. All of the samples were in Hardy-Weinberg proportions. A significant amount of genetic differentiation between runs was revealed by several measures of differentiation. Winter run was the most genetically divergent, while the spring, late-fall, and fall runs were less differentiated. PMID:10049927

  16. A change in nuclear pore complex composition regulates cell differentiation.

    PubMed

    D'Angelo, Maximiliano A; Gomez-Cavazos, J Sebastian; Mei, Arianna; Lackner, Daniel H; Hetzer, Martin W

    2012-02-14

    Nuclear pore complexes (NPCs) are built from ∼30 different proteins called nucleoporins or Nups. Previous studies have shown that several Nups exhibit cell-type-specific expression and that mutations in NPC components result in tissue-specific diseases. Here we show that a specific change in NPC composition is required for both myogenic and neuronal differentiation. The transmembrane nucleoporin Nup210 is absent in proliferating myoblasts and embryonic stem cells (ESCs) but becomes expressed and incorporated into NPCs during cell differentiation. Preventing Nup210 production by RNAi blocks myogenesis and the differentiation of ESCs into neuroprogenitors. We found that the addition of Nup210 to NPCs does not affect nuclear transport but is required for the induction of genes that are essential for cell differentiation. Our results identify a single change in NPC composition as an essential step in cell differentiation and establish a role for Nup210 in gene expression regulation and cell fate determination. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Polyion complex libraries possessing naturally occurring differentiation for pattern-based protein discrimination.

    PubMed

    Tomita, Shunsuke; Yoshimoto, Keitaro

    2013-11-14

    Polyion complexes with naturally occurring differentiation of enzymes serve to create receptor libraries with high differentiability and lower synthetic demands for pattern-based protein discrimination.

  18. Complex extracellular matrices promote tissue-specific stem cell differentiation.

    PubMed

    Philp, Deborah; Chen, Silvia S; Fitzgerald, Wendy; Orenstein, Jan; Margolis, Leonid; Kleinman, Hynda K

    2005-02-01

    Most cells in tissues contact an extracellular matrix on at least one surface. These complex mixtures of interacting proteins provide structural support and biological signals that regulate cell differentiation and may be important for stem cell differentiation. In this study, we have grown a rhesus monkey embryonic stem cell line in the presence of various extracellular matrix components in monolayer, in a NASA-developed rotating wall vessel bioreactor in vitro, and subcutaneously in vivo. We find that individual components of the extracellular matrix, such as laminin-1 or collagen I, do not influence the growth or morphology of the cells. In contrast, a basement membrane extract, Matrigel, containing multiple extracellular matrix components, induces the cells within 4 days to form immature glandular- and tubular-like structures, many of which contain a lumen with polarized epithelium and microvilli. Such structures were seen in vitro when the cells were grown in the bioreactor and when the cells were injected into mice. These tubular- and glandular-like structures were polarized epithelia based on immunostaining for laminin and cytokeratin. The cell aggregates and tumors also contained additional mixed populations of cells, including mesenchymal cells and neuronal cells, based on immunostaining with vimentin and neuronal markers. An extract of cartilage, containing multiple cartilage matrix components, promoted chondrogenesis in vivo where alcian blue-stained cartilage nodules could be observed. Some of these nodules stained with von Kossa, indicating that they had formed calcified cartilage. We conclude that extracellular matrices can promote the differentiation of embryonic stem cells into differentiated cells and structures that are similar to the tissue from which the matrix is derived. Such preprogramming of cell differentiation with extracellular matrices may be useful in targeting stem cells to repair specific damaged organs.

  19. Differential physiological roles of ESCRT complexes in Caenorhabditis elegans.

    PubMed

    Kim, Dong-Wan; Sung, Hyun; Shin, Donghyuk; Shen, Haihong; Ahnn, Joohong; Lee, Sun-Kyung; Lee, Sangho

    2011-06-01

    Endosomal sorting complex required for transport (ESCRT) complexes are involved in endosomal trafficking to the lysosome, cytokinesis, and viral budding. Extensive genetic, biochemical, and structural studies on the ESCRT system have been carried out in yeast and mammalian systems. However, the question of how the ESCRT system functions at the whole organism level has not been fully explored. In C. elegans, we performed RNAi experiments to knock-down gene expression of components of the ESCRT system and profiled their effects on protein degradation and endocytosis of YP170, a yolk protein. Targeted RNAi knock-down of ESCRT-I (tsg-101 and vps-28) and ESCRT-III (vps-24, and vps-32.2) components interfered with protein degradation while knock-down of ESCRT-II (vps-25 and vps-36) and ESCRT-III (vps-20 and vps-24) components hampered endocytosis. In contrast, the knockdown of vps-37, another ESCRT-I component, showed no defect in either YP170 uptake or degradation. Depletion of at least one component from each complex - ESCRT-0 (hgrs-1), ESCRT-I (tsg-101, vps-28, and vps-37), ESCRT-II (vps-36), ESCRT-III (vps-24), and Vps4 (vps-4) - resulted in abnormal distribution of embryos in the uterus of worms, possibly due to abnormal ovulation, fertilization, and egglaying. These results suggest differential physiological roles of ESCRT-0, -I, -II, and -III complexes in the context of the whole organism, C. elegans.

  20. Hunting complex differential gene interaction patterns across molecular contexts

    PubMed Central

    Song, Mingzhou; Zhang, Yang; Katzaroff, Alexia J.; Edgar, Bruce A.; Buttitta, Laura

    2014-01-01

    Heterogeneity in genetic networks across different signaling molecular contexts can suggest molecular regulatory mechanisms. Here we describe a comparative chi-square analysis (CPχ2) method, considerably more flexible and effective than other alternatives, to screen large gene expression data sets for conserved and differential interactions. CPχ2 decomposes interactions across conditions to assess homogeneity and heterogeneity. Theoretically, we prove an asymptotic chi-square null distribution for the interaction heterogeneity statistic. Empirically, on synthetic yeast cell cycle data, CPχ2 achieved much higher statistical power in detecting differential networks than alternative approaches. We applied CPχ2 to Drosophila melanogaster wing gene expression arrays collected under normal conditions, and conditions with overexpressed E2F and Cabut, two transcription factor complexes that promote ectopic cell cycling. The resulting differential networks suggest a mechanism by which E2F and Cabut regulate distinct gene interactions, while still sharing a small core network. Thus, CPχ2 is sensitive in detecting network rewiring, useful in comparing related biological systems. PMID:24482443

  1. Optimal control of complex networks based on matrix differentiation

    NASA Astrophysics Data System (ADS)

    Li, Guoqi; Ding, Jie; Wen, Changyun; Pei, Jing

    2016-09-01

    Finding the key node set to be connected to external control sources so as to minimize the energy for controlling a complex network, known as the minimum-energy control problem, is of critical importance but remains open. We address this critical problem where matrix differentiation is involved. To this end, the differentiation of energy/cost function with respect to the input matrix is obtained based on tensor analysis, and the Hessian matrix is compressed from a fourth-order tensor. Normalized projected gradient method (NPGM) normalized projected trust-region method (NPTM) are proposed with established convergence property. We show that NPGM is more computationally efficient than NPTM. Simulation results demonstrate satisfactory performance of the algorithms, and reveal important insights as well. Two interesting phenomena are observed. One is that the key node set tends to divide elementary paths equally. The other is that the low-degree nodes may be more important than hubs from a control point of view, indicating that controlling hub nodes does not help to lower the control energy. These results suggest a way of achieving optimal control of complex networks, and provide meaningful insights for future researches.

  2. A note on the Dirichlet problem for model complex partial differential equations

    NASA Astrophysics Data System (ADS)

    Ashyralyev, Allaberen; Karaca, Bahriye

    2016-08-01

    Complex model partial differential equations of arbitrary order are considered. The uniqueness of the Dirichlet problem is studied. It is proved that the Dirichlet problem for higher order of complex partial differential equations with one complex variable has infinitely many solutions.

  3. On the adaptivity and complexity embedded into differential evolution

    SciTech Connect

    Senkerik, Roman; Pluhacek, Michal; Jasek, Roman; Zelinka, Ivan

    2016-06-08

    This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

  4. A Class of Practically Nowhere Differentiable Functions on the Complex Plane

    ERIC Educational Resources Information Center

    Hetzel, Andrew J.

    2006-01-01

    This note could find classroom use in an introductory course on complex analysis. Using some of the most significant theorems from complex analysis, the main result provides a simple method for transforming many elementary functions (defined on the complex plane) into everywhere continuous functions that are differentiable only on a nowhere dense…

  5. Differential Expression of Cysteine Dioxygenase 1 in Complex Karyotype Liposarcomas

    PubMed Central

    Shaker, Mohammed; Pascarelli, Kara M; Plantinga, Matthew J; Love, Miles A; Lazar, Alexander J; Ingram, Davis R; von Mehren, Margaret; Lev, Dina; Kipling, David; Broccoli, Dominique

    2014-01-01

    Altered cysteine dioxygenase 1 (CDO1) gene expression has been observed in several cancers but has not yet been investigated in liposarcomas. The aim of this study was to evaluate CDO1 expression in a cohort of liposarcomas and to determine its association with clinicopathological features. Existing microarray data indicated variable CDO1 expression in liposarcoma subtypes. CDO1 mRNA from a larger cohort of liposarcomas was quantified by real time-PCR, and CDO1 protein expression was determined by immunohistochemistry (IHC) in more than 300 tumor specimens. Well-differentiated liposarcomas (WDLSs) had significantly higher CDO1 gene expression and protein levels than dedifferentiated liposarcomas (DDLSs) (P < 0.001). Location of the tumor was not predictive of the expression level of CDO1 mRNA in any histological subtype of liposarcoma. Recurrent tumors did not show any difference in CDO1 expression when compared to primary tumors. CDO1 expression was upregulated as human mesenchymal stem cells (hMSCs) undergo differentiation into mature adipocytes. Our results suggest that CDO1 is a marker of liposarcoma progression and adipogenic differentiation. PMID:24741338

  6. How females become complex: cell differentiation in the gametophyte.

    PubMed

    Kägi, Christina; Gross-Hardt, Rita

    2007-12-01

    In contrast to animals, gametes in plants form a separate haploid generation, the gametophyte. The female gametophyte of flowering plants consists of just four different cell types that play distinct roles in the reproductive process. Differentiation of the distinct cell fates is tightly controlled and appears to follow regional cues that are arranged along a polar axis. Mutant analysis suggests that important aspects of gametophyte patterning are gametophytically regulated. Additionally, structural and molecular changes following misspecification indicate that the female gametophyte is a remarkably versatile structure with enormous respecification potential. Recently, new tools have been developed that open fascinating possibilities to access and analyze those processes that ultimately ensure successful fertilization.

  7. Effects of differential habitat warming on complex communities.

    PubMed

    Tunney, Tyler D; McCann, Kevin S; Lester, Nigel P; Shuter, Brian J

    2014-06-03

    Food webs unfold across a mosaic of micro and macro habitats, with each habitat coupled by mobile consumers that behave in response to local environmental conditions. Despite this fundamental characteristic of nature, research on how climate change will affect whole ecosystems has overlooked (i) that climate warming will generally affect habitats differently and (ii) that mobile consumers may respond to this differential change in a manner that may fundamentally alter the energy pathways that sustain ecosystems. This reasoning suggests a powerful, but largely unexplored, avenue for studying the impacts of climate change on ecosystem functioning. Here, we use lake ecosystems to show that predictable behavioral adjustments to local temperature differentials govern a fundamental structural shift across 54 food webs. Data show that the trophic pathways from basal resources to a cold-adapted predator shift toward greater reliance on a cold-water refuge habitat, and food chain length increases, as air temperatures rise. Notably, cold-adapted predator behavior may substantially drive this decoupling effect across the climatic range in our study independent of warmer-adapted species responses (for example, changes in near-shore species abundance and predator absence). Such modifications reflect a flexible food web architecture that requires more attention from climate change research. The trophic pathway restructuring documented here is expected to alter biomass accumulation, through the regulation of energy fluxes to predators, and thus potentially threatens ecosystem sustainability in times of rapid environmental change.

  8. Effects of differential habitat warming on complex communities

    PubMed Central

    Tunney, Tyler D.; McCann, Kevin S.; Lester, Nigel P.; Shuter, Brian J.

    2014-01-01

    Food webs unfold across a mosaic of micro and macro habitats, with each habitat coupled by mobile consumers that behave in response to local environmental conditions. Despite this fundamental characteristic of nature, research on how climate change will affect whole ecosystems has overlooked (i) that climate warming will generally affect habitats differently and (ii) that mobile consumers may respond to this differential change in a manner that may fundamentally alter the energy pathways that sustain ecosystems. This reasoning suggests a powerful, but largely unexplored, avenue for studying the impacts of climate change on ecosystem functioning. Here, we use lake ecosystems to show that predictable behavioral adjustments to local temperature differentials govern a fundamental structural shift across 54 food webs. Data show that the trophic pathways from basal resources to a cold-adapted predator shift toward greater reliance on a cold-water refuge habitat, and food chain length increases, as air temperatures rise. Notably, cold-adapted predator behavior may substantially drive this decoupling effect across the climatic range in our study independent of warmer-adapted species responses (for example, changes in near-shore species abundance and predator absence). Such modifications reflect a flexible food web architecture that requires more attention from climate change research. The trophic pathway restructuring documented here is expected to alter biomass accumulation, through the regulation of energy fluxes to predators, and thus potentially threatens ecosystem sustainability in times of rapid environmental change. PMID:24843178

  9. E-Index for Differentiating Complex Dynamic Traits

    PubMed Central

    Qi, Jiandong; Sun, Jianfeng; Wang, Jianxin

    2016-01-01

    While it is a daunting challenge in current biology to understand how the underlying network of genes regulates complex dynamic traits, functional mapping, a tool for mapping quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs), has been applied in a variety of cases to tackle this challenge. Though useful and powerful, functional mapping performs well only when one or more model parameters are clearly responsible for the developmental trajectory, typically being a logistic curve. Moreover, it does not work when the curves are more complex than that, especially when they are not monotonic. To overcome this inadaptability, we therefore propose a mathematical-biological concept and measurement, E-index (earliness-index), which cumulatively measures the earliness degree to which a variable (or a dynamic trait) increases or decreases its value. Theoretical proofs and simulation studies show that E-index is more general than functional mapping and can be applied to any complex dynamic traits, including those with logistic curves and those with nonmonotonic curves. Meanwhile, E-index vector is proposed as well to capture more subtle differences of developmental patterns. PMID:27064292

  10. Differentiating morphology, form, and meaning: neural correlates of morphological complexity.

    PubMed

    Bozic, Mirjana; Marslen-Wilson, William D; Stamatakis, Emmanuel A; Davis, Matthew H; Tyler, Lorraine K

    2007-09-01

    The role of morphological structure in word recognition raises issues about the nature and structure of the language system. One major issue is whether morphological factors provide an independent principle for lexical organization and processing, or whether morphological effects can be reduced to the joint contribution of form and meaning. The independence of form, meaning, and morphological structure can be directly investigated using derivationally complex words, because derived words can share form but need not share meaning (e.g., archer-arch). We used an event-related functional magnetic resonance imaging paradigm to investigate priming between pairs of words that potentially shared a stem, where this link was either semantically transparent (e.g., bravely-brave) or opaque (e.g., archer-arch). These morphologically related pairs were contrasted with identity priming (e.g., mist-mist) and priming for pairs of words that shared only form (e.g., scandal-scan) or meaning (e.g., accuse-blame). Morphologically related words produced significantly reduced activation in left frontal regions, whether the pairs were semantically transparent or opaque. The effect was not found for any of the control conditions (identity, form, or meaning). Morphological effects were observed separately from processing form and meaning and we propose that they reflect segmentation of complex derived words, a process triggered by surface morphological structure of complex words.

  11. Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference.

    PubMed

    Warren, R M; Gey van Pittius, N C; Barnard, M; Hesseling, A; Engelke, E; de Kock, M; Gutierrez, M C; Chege, G K; Victor, T C; Hoal, E G; van Helden, P D

    2006-07-01

    Differentiation of members of the Mycobacterium tuberculosis complex by conventional mycobacteriological methods is time consuming, making surveillance of species-specific disease difficult. A two-step, multiplex polymerase chain reaction (PCR) method based on genomic regions of difference (RD1, RD1(mic), RD2(seal), RD4, RD9 and RD12) was developed for the differentiation of M. canettii, M. tuberculosis, M. africanum, M. microti, M. pinnipedii, M. caprae, M. bovis and M. bovis BCG. The size of the respective multiplex PCR amplification products corresponded to the presence of the different M. tuberculosis complex members. This method allows for rapid differentiation, making it suitable for routine laboratories and surveillance purposes.

  12. Differentiating elements of the soil-vegetation complex

    NASA Technical Reports Server (NTRS)

    Baumgardner, M. F.

    1972-01-01

    The application of remote sensing to study soil-vegetation systems requires quantification and precise location of ground observation data such that they can be correlated with multispectral aerial acquired data. Griddling and sampling of an area for exact identification in a known address on magnetic tape containing multispectral scanner data produces quantitative physico-chemical parameters and the energy which is radiating from within the soil-vegetation complex of an area. Example classifications and spectral mappings of soils made from multispectral scanner data are included.

  13. Linguistic Complexity, Schematic Representations, and Differential Item Functioning for English Language Learners in Math Tests

    ERIC Educational Resources Information Center

    Martiniello, Maria

    2009-01-01

    This article examines nonmathematical linguistic complexity as a source of differential item functioning (DIF) in math word problems for English language learners (ELLs). Specifically, this study investigates the relationship between item measures of linguistic complexity, nonlinguistic forms of representation and DIF measures based on item…

  14. Complex and differential glial responses in Alzheimer's disease and ageing.

    PubMed

    Rodríguez, José J; Butt, Arthur M; Gardenal, Emanuela; Parpura, Vladimir; Verkhratsky, Alexei

    2016-01-01

    Glial cells and their association with neurones are fundamental for brain function. The emergence of complex neurone-glial networks assures rapid information transfer, creating a sophisticated circuitry where both types of neural cells work in concert, serving different activities. All glial cells, represented by astrocytes, oligodendrocytes, microglia and NG2-glia, are essential for brain homeostasis and defence. Thus, glia are key not only for normal central nervous system (CNS) function, but also to its dysfunction, being directly associated with all forms of neuropathological processes. Therefore, the progression and outcome of neurological and neurodegenerative diseases depend on glial reactions. In this review, we provide a concise account of recent data obtained from both human material and animal models demonstrating the pathological involvement of glia in neurodegenerative processes, including Alzheimer's disease (AD), as well as physiological ageing.

  15. Multiplex-PCR for differentiation of Mycobacterium bovis from Mycobacterium tuberculosis complex.

    PubMed

    Spositto, F L E; Campanerut, P A Z; Ghiraldi, L D; Leite, C Q F; Hirata, M H; Hirata, R D C; Siqueira, V L D; Cardoso, R Fressatti

    2014-01-01

    We evaluated a multiplex-PCR to differentiate Mycobacterium bovis from M. tuberculosis Complex (MTC) by one step amplification based on simultaneous detection of pncA 169 C > G change in M. bovis and the IS6110 present in MTC species. Our findings showed the proposed multiplex-PCR is a very useful tool for complementation in differentiating M. bovis from other cultured MTC species.

  16. Muscle Lim Protein and Myosin Binding Protein C form a complex regulating muscle differentiation.

    PubMed

    Arvanitis, Demetrios A; Vafiadaki, Elizabeth; Papalouka, Vasiliki; Sanoudou, Despina

    2017-08-31

    Muscle Lim Protein (MLP) is a protein with multiple functional roles in striated muscle physiology and pathophysiology. Herein, we demonstrate that MLP directly binds to slow, fast, and cardiac myosin-binding protein C (MyBP-C) during myogenesis, as shown by yeast two-hybrid, and a range of protein-protein interaction assays. The minimal interacting domains involve MLP inter-LIM and MyBP-C C4. The interaction is sensitive to cytosolic Ca(2+) concentrations changes and to MyBP-C phosphorylation by PKA or CaMKII. Confocal microscopy of differentiating myoblasts showed MLP and MyBP-C colocalization during myoblast differentiation. Suppression of the complex formation with recombinant MyBP-C C4 peptide overexpression, inhibited myoblast differentiation by 65%. Suppression of both MLP and MyBP-C expression in myoblasts by siRNA revealed negative synergistic effects on differentiation. The MLP/MyBP-C complex modulates the actin activated myosin II ATPase activity in vitro, which could interfere with sarcomerogenesis and myofilaments assembly during differentiation. Our data demonstrate a critical role of the MLP/MyBP-C complex during early myoblast differentiation. Its absence in muscles with mutations or aberrant expression of MLP or MyBP-C could be directly implicated in the development of cardiac and skeletal myopathies. Copyright © 2017. Published by Elsevier B.V.

  17. A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation

    PubMed Central

    Malinverni, Roberto; Valero, Vanesa; Buschbeck, Marcus

    2014-01-01

    Polycomb proteins play an essential role in maintaining the repression of developmental genes in self-renewing embryonic stem cells. The exact mechanism allowing the derepression of polycomb target genes during cell differentiation remains unclear. Our project aimed to identify Cbx8 binding sites in differentiating mouse embryonic stem cells. Therefore, we used a genome-wide chromatin immunoprecipitation of endogenous Cbx8 coupled to direct massive parallel sequencing (ChIP-Seq). Our analysis identified 171 high confidence peaks. By crossing our data with previously published microarray analysis, we show that several differentiation genes transiently recruit Cbx8 during their early activation. Depletion of Cbx8 partially impairs the transcriptional activation of these genes. Both interaction analysis, as well as chromatin immunoprecipitation experiments support the idea that activating Cbx8 acts in the context of an intact PRC1 complex. Prolonged gene activation results in eviction of PRC1 despite persisting H3K27me3 and H2A ubiquitination. The composition of PRC1 is highly modular and changes when embryonic stem cells commit to differentiation. We further demonstrate that the exchange of Cbx7 for Cbx8 is required for the effective activation of differentiation genes. Taken together, our results establish a function for a Cbx8-containing complex in facilitating the transition from a Polycomb-repressed chromatin state to an active state. As this affects several key regulatory differentiation genes this mechanism is likely to contribute to the robust execution of differentiation programs. PMID:25500566

  18. The Painlevé test for nonlinear system of differential equations with complex chaotic behavior

    NASA Astrophysics Data System (ADS)

    Tsegel’nik, V.

    2017-01-01

    The Painlevé-analysis was performed for solutions of nonlinear third-order autonomous system of differential equations with quadratic nonlinearities on their right-hand sides. At certain values of two constant parameters incorporated into the system, the latter exhibits complex chaotic behavior. When the parameters attain the values corresponding to complex chaotic behavior, the system was found not to possess the Painlevé property.

  19. The value of electrocardiography for differential diagnosis in wide QRS complex tachycardia.

    PubMed

    Sousa, Pedro A; Pereira, Salomé; Candeias, Rui; de Jesus, Ilídio

    2014-03-01

    Correct diagnosis in wide QRS complex tachycardia remains a challenge. Differential diagnosis between ventricular and supraventricular tachycardia has important therapeutic and prognostic implications, and although data from clinical history and physical examination may suggest a particular origin, it is the 12-lead surface electrocardiogram that usually enables this differentiation. Since 1978, various electrocardiographic criteria have been proposed for the differential diagnosis of wide complex tachycardias, particularly the presence of atrioventricular dissociation, and the axis, duration and morphology of QRS complexes. Despite the wide variety of criteria, diagnosis is still often difficult, and errors can have serious consequences. To reduce such errors, several differential diagnosis algorithms have been proposed since 1991. However, in a small percentage of wide QRS tachycardias the diagnosis remains uncertain and in these the wisest decision is to treat them as ventricular tachycardias. The authors' objective was to review the main electrocardiographic criteria and differential diagnosis algorithms of wide QRS tachycardia. Copyright © 2012 Sociedade Portuguesa de Cardiologia. Published by Elsevier España. All rights reserved.

  20. Value Differentiation in Adolescence: The Role of Age and Cultural Complexity

    ERIC Educational Resources Information Center

    Daniel, Ella; Schiefer, David; Mollering, Anna; Benish-Weisman, Maya; Boehnke, Klaus; Knafo, Ariel

    2012-01-01

    Living in complex social worlds, individuals encounter discordant values across life contexts, potentially resulting in different importance of values across contexts. Value differentiation is defined here as the degree to which values receive different importance depending on the context in which they are considered. Early and mid-adolescents (N…

  1. The Impact of Mitochondrial Complex Inhibition on mESC Differentiation

    EPA Science Inventory

    The Impact of Mitochondrial Complex Inhibition on mESC Differentiation JE Royland, SH Warren, S Jeffay, MR Hoopes, HP Nichols, ES Hunter U.S. Environmental Protection Agency, Integrated Systems Toxicology Division, Research Triangle Park, NC The importance of mitochondrial funct...

  2. The Impact of Mitochondrial Complex Inhibition on mESC Differentiation

    EPA Science Inventory

    The Impact of Mitochondrial Complex Inhibition on mESC Differentiation JE Royland, SH Warren, S Jeffay, MR Hoopes, HP Nichols, ES Hunter U.S. Environmental Protection Agency, Integrated Systems Toxicology Division, Research Triangle Park, NC The importance of mitochondrial funct...

  3. Value Differentiation in Adolescence: The Role of Age and Cultural Complexity

    ERIC Educational Resources Information Center

    Daniel, Ella; Schiefer, David; Mollering, Anna; Benish-Weisman, Maya; Boehnke, Klaus; Knafo, Ariel

    2012-01-01

    Living in complex social worlds, individuals encounter discordant values across life contexts, potentially resulting in different importance of values across contexts. Value differentiation is defined here as the degree to which values receive different importance depending on the context in which they are considered. Early and mid-adolescents (N…

  4. Exosome complex orchestrates developmental signaling to balance proliferation and differentiation during erythropoiesis

    PubMed Central

    McIver, Skye C; Katsumura, Koichi R; Davids, Elsa; Liu, Peng; Kang, Yoon-A; Yang, David; Bresnick, Emery H

    2016-01-01

    Since the highly conserved exosome complex mediates the degradation and processing of multiple classes of RNAs, it almost certainly controls diverse biological processes. How this post-transcriptional RNA-regulatory machine impacts cell fate decisions and differentiation is poorly understood. Previously, we demonstrated that exosome complex subunits confer an erythroid maturation barricade, and the erythroid transcription factor GATA-1 dismantles the barricade by transcriptionally repressing the cognate genes. While dissecting requirements for the maturation barricade in Mus musculus, we discovered that the exosome complex is a vital determinant of a developmental signaling transition that dictates proliferation/amplification versus differentiation. Exosome complex integrity in erythroid precursor cells ensures Kit receptor tyrosine kinase expression and stem cell factor/Kit signaling, while preventing responsiveness to erythropoietin-instigated signals that promote differentiation. Functioning as a gatekeeper of this developmental signaling transition, the exosome complex controls the massive production of erythroid cells that ensures organismal survival in homeostatic and stress contexts. DOI: http://dx.doi.org/10.7554/eLife.17877.001 PMID:27543448

  5. Unravelling personalized dysfunctional gene network of complex diseases based on differential network model.

    PubMed

    Yu, Xiangtian; Zeng, Tao; Wang, Xiangdong; Li, Guojun; Chen, Luonan

    2015-06-13

    In the conventional analysis of complex diseases, the control and case samples are assumed to be of great purity. However, due to the heterogeneity of disease samples, many disease genes are even not always consistently up-/down-regulated, leading to be under-estimated. This problem will seriously influence effective personalized diagnosis or treatment. The expression variance and expression covariance can address such a problem in a network manner. But, these analyses always require multiple samples rather than one sample, which is generally not available in clinical practice for each individual. To extract the common and specific network characteristics for individual patients in this paper, a novel differential network model, e.g. personalized dysfunctional gene network, is proposed to integrate those genes with different features, such as genes with the differential gene expression (DEG), genes with the differential expression variance (DEVG) and gene-pairs with the differential expression covariance (DECG) simultaneously, to construct personalized dysfunctional networks. This model uses a new statistic-like measurement on differential information, i.e., a differential score (DEVC), to reconstruct the differential expression network between groups of normal and diseased samples; and further quantitatively evaluate different feature genes in the patient-specific network for each individual. This DEVC-based differential expression network (DEVC-net) has been applied to the study of complex diseases for prostate cancer and diabetes. (1) Characterizing the global expression change between normal and diseased samples, the differential gene networks of those diseases were found to have a new bi-coloured topological structure, where their non hub-centred sub-networks are mainly composed of genes/proteins controlling various biological processes. (2) The differential expression variance/covariance rather than differential expression is new informative sources, and can

  6. Differentiating Types of Wide-Complex Tachycardia to Determine Appropriate Treatment in the Emergency Department.

    PubMed

    deSouza, Ian S; Peterson, Alanna C; Marill, Keith A

    2015-07-01

    Wide-complex tachycardia is a rare disease entity among patients presenting to the emergency department. However, due to its potential life-threatening nature, emergency clinicians must know how to assess and manage this condition. Wide-complex tachycardia encompasses a range of cardiac dysrhythmias, some of which can be difficult to distinguish and may require specific treatment approaches. This review summarizes the etiology and pathophysiology of wide-complex tachycardia, describes the differential diagnosis, and presents an evidence-based approach to identification of the different types of tachycardias through the use of a thorough history and physical examination, vagal maneuvers, electrocardiography, and adenosine. The treatment options and disposition for patients with various wide-complex tachycardias are also discussed, with attention to special circumstances and select controversial/contemporary topics.

  7. Differentiating inclusion complexes from host molecules by tapping-mode atomic force microscopy.

    PubMed Central

    Muñoz-Botella, S; Martin, M A; del Castillo, B; Vázquez, L

    1996-01-01

    Tapping-mode atomic force microscopy imaging under different cantilever vibration amplitudes has been used to differentiate the host beta-cyclodextrin nanotubes from retinal/beta-cyclodextrin inclusion complex nanotubes. It was observed that both compounds were deformed differently by the applied probe force because of their different local rigidity. This change in the elasticity properties can be explained as a consequence of the inclusion process. This method shows that tapping-mode atomic force microscopy is an useful tool to map soft sample elasticity properties and to distinguish inclusion complexes from their host molecules on the basis of their different mechanical response. Images FIGURE 1 FIGURE 2 FIGURE 3 PMID:8804591

  8. Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex.

    PubMed

    Hansson, Bengt; Ljungqvist, Marcus; Illera, Juan-Carlos; Kvist, Laura

    2014-01-01

    Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward

  9. Stimulation of preadipocyte differentiation by steroid through targeting of an HDAC1 complex.

    PubMed

    Wiper-Bergeron, Nadine; Wu, Dongmei; Pope, Louise; Schild-Poulter, Caroline; Haché, Robert J G

    2003-05-01

    Glucocorticoids potentiate the early steps of preadipocyte differentiation and promote obesity in Cushing's syndrome and during prolonged steroid therapy. We show that glucocorticoids stimulate 3T3 L1 preadipocyte differentiation through a non-transcriptional mechanism mediated through the ligand-binding domain of the glucocorticoid receptor. This enhanced the onset of CCAAT/enhancer binding protein (C/EBPalpha) expression by potentiating its initial transcriptional activation by C/EBPbeta. In the absence of steroid, C/EBPbeta associated with a transcriptional corepressor complex containing mSin3A and histone deacetylase 1 (HDAC1), but lacking HDAC2 and RbAp46/48. HDAC1/mSin3A were recruited to the C/EBPalpha promoter with C/EBPbeta and promoted the deacetylation of histone H4. Steroid induced the specific depletion of this corepressor by targeting the HDAC1 within the complex for degradation through the 26S proteasome. Treatment with histone deacetylase inhibitors replaced the effects of steroid treatment on preadipocyte differentiation and C/EBPalpha expression, while overexpression of HDAC1 abrogated the stimulatory effects of steroid. Recapitulation of the glucocorticoid effect by progestin treatment in the presence of the progesterone receptor ligand-binding domain suggests a conserved mechanism relevant to many aspects of steroid-mediated differentiation.

  10. The asymptotic limit of an integro-differential equation modelling complex systems

    NASA Astrophysics Data System (ADS)

    Bianca, C.; Ferrara, M.; Guerrini, L.

    2014-12-01

    This paper is devoted to the asymptotic analysis of a mathematical framework that has recently been proposed for modelling complex systems in the applied sciences under the action of an external force field. This framework consists in an integro-differential kinetic equation coupled with a Gaussian isokinetic thermostat. The asymptotic limit obtained here using low-field scaling shows the emergence of diffusive behaviour on a macroscopic scale.

  11. Modulation of basic helix-loop-helix transcription complex formation by Id proteins during neuronal differentiation.

    PubMed

    Jögi, Annika; Persson, Paula; Grynfeld, Anna; Påhlman, Sven; Axelson, Håkan

    2002-03-15

    It is assumed that the Id helix-loop-helix (HLH) proteins act by associating with ubiquitously expressed basic HLH (bHLH) transcription factors, such as E47 and E2-2, which prevents these factors from forming functional hetero- or homodimeric DNA binding complexes. Several tissue-specific bHLH proteins, including HASH-1, dHAND, and HES-1, are important for development of the nervous system. Neuroblastoma tumors are derived from the sympathetic nervous system and exhibit neural crest features. In differentiating neuroblastoma cells, HASH-1 is down-regulated, and there is coincident up-regulation of the transcriptional repressor HES-1, which is known to bind the HASH-1 promoter. We found that the three Id proteins expressed in neuroblastoma cells (Id1, Id2, and Id3) were down-regulated during induced differentiation, indicating that Id proteins help keep the tumor cells in an undifferentiated state. Studying interactions, we noted that all four Id proteins could dimerize with E47 or E2-2, but not with HASH-1 or dHAND. However, the Id proteins did complex with HES-1, and increased levels of Id2 reduced the DNA binding activity of HES-1. Furthermore, HES-1 interfered with Id2/E2-2 complex formation. The ability of Id proteins to affect HES-1 activity is of particular interest in neuronal cells, where regulation of HES-1 is essential for the timing of neuronal differentiation.

  12. Novel splice isoforms of STRADalpha differentially affect LKB1 activity, complex assembly and subcellular localization.

    PubMed

    Marignani, P A; Scott, K D; Bagnulo, R; Cannone, D; Ferrari, E; Stella, A; Guanti, G; Simone, C; Resta, N

    2007-10-01

    STRADalpha is a pseudokinase that forms a heterotrimeric complex with the scaffolding protein MO25 and the tumor suppressor serine threonine protein kinase LKB1. Mutations in the LKB1 gene are responsible for the Peutz-Jeghers Syndrome (PJS) characterized by a predisposition to hamartomatous polyps and hyperpigmentation of the buccal mucosa. Mutations in LKB1 have also been observed in some sporadic tumours unrelated to PJS. The LKB1/STRAD/MO25 complex is involved in the regulation of numerous signaling pathways including metabolism, proliferation and cellular polarity of human intestinal epithelial cells. Cell polarization, together with tissue-restricted transcription, represents the main feature of enterocyte differentiation. Since a full-length STRADalpha transcript has not been identified thus far in these cells, we evaluated the expression of endogenous STRADalpha in five colorectal cancer cell lines characterized by their diverse ability to differentiate in vitro. We report herein the discovery of several novel splice isoforms of STRADalpha that differentially affect the kinase activity, complex assembly, subcellular localization of LKB1 and the activation of the LKB1-dependent AMPK pathway.

  13. Differential functions of WAVE regulatory complex subunits in the regulation of actin-driven processes.

    PubMed

    Litschko, Christof; Linkner, Joern; Brühmann, Stefan; Stradal, Theresia E B; Reinl, Tobias; Jänsch, Lothar; Rottner, Klemens; Faix, Jan

    2017-09-04

    The WAVE regulatory complex (WRC) links upstream Rho-family GTPase signaling to the activation of the ARP2/3 complex in different organisms. WRC-induced and ARP2/3 complex-mediated actin nucleation beneath the plasma membrane is critical for actin assembly in the leading edge to drive efficient cell migration. The WRC is a stable heteropentamer composed of SCAR/WAVE, Abi, Nap, Pir and the small polypeptide Brk1/Hspc300. Functional interference with individual subunits of the complex frequently results in diminished amounts of the remaining polypeptides of the WRC complex, implying the complex to act as molecular entity. However, Abi was also found to associate with mammalian N-WASP, formins, Eps8/SOS1 or VASP, indicating additional functions of individual WRC subunits in eukaryotic cells. To address this issue systematically, we inactivated all WRC subunits, either alone or in combination with VASP in Dictyostelium cells and quantified the protein content of the remaining subunits in respective WRC knockouts. The individual mutants displayed highly differential phenotypes concerning various parameters, including cell morphology, motility, cytokinesis or multicellular development, corroborating the view of additional roles for individual subunits, beyond their established function in WRC-mediated Arp2/3 complex activation. Finally, our data uncover the interaction of the actin polymerase VASP with WRC-embedded Abi to mediate VASP accumulation in cell protrusions, driving efficient cell migration. Copyright © 2017 Elsevier GmbH. All rights reserved.

  14. Differential Many-Body Cooperativity in Electronic Spectra of Oligonuclear Transition-Metal Complexes.

    PubMed

    Chmela, Jiří; Harding, Michael E; Matioszek, Dimitri; Anson, Christopher E; Breher, Frank; Klopper, Wim

    2016-01-04

    In computational chemistry, non-additive and cooperative effects can be defined in terms of a (differential) many-body expansion of the energy or any other physical property of the molecular system of interest. One-body terms describe energies or properties of the subsystems, two-body terms describe non-additive but pairwise contributions and three-body as well as higher-order terms can be interpreted as a measure for cooperativity. In the present article, this concept is applied to the analysis of ultraviolet/visible (UV/Vis) spectra of homotrinuclear transition-metal complexes by means of a many-body expansion of the change in the spectrum induced by replacing each of the three transition-metal ions by another transition-metal ion to yield a different homotrinuclear transition-metal complex. Computed spectra for the triangulo-complexes [M3 {Si(mt(Me) )3}2] (M=Pd/Pt, mt(Me) =methimazole) and tritopic triphenylene-based N-heterocyclic carbene Rh/Ir complexes illustrate the concept, showing large and small differential three-body cooperativity, respectively. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Genetic and Ecotypic Differentiation in a Californian Plant Polyploid Complex (Grindelia, Asteraceae)

    PubMed Central

    Moore, Abigail J.; Moore, William L.; Baldwin, Bruce G.

    2014-01-01

    Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae). We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey. PMID:24755840

  16. Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae).

    PubMed

    Moore, Abigail J; Moore, William L; Baldwin, Bruce G

    2014-01-01

    Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae). We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey.

  17. Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus

    PubMed Central

    Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S.

    2016-01-01

    Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites. PMID:27588023

  18. Genetic differentiation in the Agave deserti (Agavaceae) complex of the Sonoran desert.

    PubMed

    Navarro-Quezada, A; González-Chauvet, R; Molina-Freaner, F; Eguiarte, L E

    2003-03-01

    The Agave deserti complex, comprising A. deserti, A. cerulata and A. subsimplex, represents a group of species and subspecies with a near allopatric distribution and clear differences in morphology. Genetic differentiation and taxonomic status with respect to spatial distribution of 14 populations of the complex were analyzed in an effort to understand the evolution and speciation process within the genus. Allelic frequencies, levels of genetic variation, expected heterozygosity (H(S)), proportion of polymorphic loci (P), and genetic differentiation (theta and Nei's genetic distance) were estimated using 41 putative RAPD loci. All three species show high levels of genetic variation (H(S)=0.12-0.29, P=63.4-95.1), and low genetic differentiation between populations and species (theta populations=0.14+/-0.02 (SE); G(st)=0.11+/-0.02). Accordingly, gene flow among populations was estimated as high by three different methods (N(m)=2.91-6.14). Nei's genetic distances between the three species were low compared to the values obtained from other Agavaceae, and there was no clear correlation with taxonomic divisions. In a UPGMA analysis, A. subsimplex and A. cerulata formed exclusive monospecific clusters, whereas the A. deserti populations appear in more than one cluster together with other species. The results were consistent with a pattern of genetic isolation by distance.

  19. TDP-43 regulates the microprocessor complex activity during in vitro neuronal differentiation.

    PubMed

    Di Carlo, Valerio; Grossi, Elena; Laneve, Pietro; Morlando, Mariangela; Dini Modigliani, Stefano; Ballarino, Monica; Bozzoni, Irene; Caffarelli, Elisa

    2013-12-01

    TDP-43 (TAR DNA-binding protein 43) is an RNA-binding protein implicated in RNA metabolism at several levels. Even if ubiquitously expressed, it is considered as a neuronal activity-responsive factor and a major signature for neurological pathologies, making the comprehension of its activity in the nervous system a very challenging issue. TDP-43 has also been described as an accessory component of the Drosha-DGCR8 (DiGeorge syndrome critical region gene 8) microprocessor complex, which is crucially involved in basal and tissue-specific RNA processing events. In the present study, we exploited in vitro neuronal differentiation systems to investigate the TDP-43 demand for the microprocessor function, focusing on both its canonical microRNA biosynthetic activity and its alternative role as a post-transcriptional regulator of gene expression. Our findings reveal a novel role for TDP-43 as an essential factor that controls the stability of Drosha protein during neuronal differentiation, thus globally affecting the production of microRNAs. We also demonstrate that TDP-43 is required for the Drosha-mediated regulation of Neurogenin 2, a master gene orchestrating neurogenesis, whereas post-transcriptional control of Dgcr8, another Drosha target, resulted to be TDP-43-independent. These results implicate a previously uncovered contribution of TDP-43 in regulating the abundance and the substrate specificity of the microprocessor complex and provide new insights into TDP-43 as a key player in neuronal differentiation.

  20. Engineering complex tissue-like microgel arrays for evaluating stem cell differentiation

    PubMed Central

    Guermani, Enrico; Shaki, Hossein; Mohanty, Soumyaranjan; Mehrali, Mehdi; Arpanaei, Ayyoob; Gaharwar, Akhilesh K.; Dolatshahi-Pirouz, Alireza

    2016-01-01

    Development of tissue engineering scaffolds with native-like biology and microarchitectures is a prerequisite for stem cell mediated generation of off-the-shelf-tissues. So far, the field of tissue engineering has not full-filled its grand potential of engineering such combinatorial scaffolds for engineering functional tissues. This is primarily due to the many challenges associated with finding the right microarchitectures and ECM compositions for optimal tissue regeneration. Here, we have developed a new microgel array to address this grand challenge through robotic printing of complex stem cell-laden microgel arrays. The developed microgel array platform consisted of various microgel environments that where composed of native-like cellular microarchitectures resembling vascularized and bone marrow tissue architectures. The feasibility of our array system was demonstrated through localized cell spreading and osteogenic differentiation of human mesenchymal stem cells (hMSCs) into complex tissue-like structures. In summary, we have developed a tissue-like microgel array for evaluating stem cell differentiation within complex and heterogeneous cell microenvironments. We anticipate that the developed platform will be used for high-throughput identification of combinatorial and native-like scaffolds for tissue engineering of functional organs. PMID:27465860

  1. Genetic Differentiation and Relationships of Populations in the Cycas balansae Complex (Cycadaceae) and its Conservation Implications

    PubMed Central

    XIAO, LONG-QIAN; GONG, XUN

    2006-01-01

    • Background and Aims The Cycas balansae complex is arguably a controversial group with regard to species delineation. Some taxonomists recognize a single polymorphic species while others distinguish five narrowly defined ones. The unresolved taxonomy has the potential to bring about significant problems for species conservation. Thus, an investigation to examine the genetic diversity and differentiation in the C. balansae complex was performed to determine the relationship of populations and to test whether the morphologically defined segregations represent genetically distinct units. • Methods Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity in the C. balansae complex with a sample of 158 individuals from all extant populations in China. • Key Results ISSR markers revealed low genetic diversity in all populations studied (HE and HO averaged 0·0639 and 0·0798 at the population level, respectively). Phenetic analysis showed that the C. balansae complex grouped into five clusters closely corresponding to the narrowly defined C. balansae, C. parvula, C. shiwandashanica, C. tanqingii and C. simplicipinna. • Conclusions ISSR data suggest that the C. balansae complex has evolved into five genetically distinct units. These might be derived from a relatively widespread common ancestor through multiple vicariant events including geographical isolation resulting from the collision of the Indian plate with the Eurasian plate and from Pleistocene glaciations. In conservation, attention should be paid to each genetic unit. PMID:16517547

  2. Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

    PubMed Central

    Jones, Rebecca C; Steane, Dorothy A; Lavery, Martyn; Vaillancourt, René E; Potts, Brad M

    2013-01-01

    Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive “intergrade” populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (FST = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a “cryptic genetic entity” that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes. PMID:23403692

  3. Differentiation of flavonoid glycoside isomers by using metal complexation and electrospray ionization mass spectrometry.

    PubMed

    Pikulski, Michael; Brodbelt, Jennifer S

    2003-12-01

    The elucidation of flavonoid isomers is accomplished by electrospray ionization tandem mass spectrometry (ESI-MS/MS) via formation and collisional activated dissociation (CAD) of metal/flavonoid complexes containing an auxiliary ligand. Addition of a metal salt and a suitable neutral auxiliary ligand to flavonoids in solution results in the formation of [M(II) (flavonoid-H) ligand]+ complexes by ESI which, upon collisional activated dissociation, often result in more distinctive fragmentation patterns than observed for conventional protonated or deprotonated flavonoids. Previously, 2,2'-bipyridine was used as an auxiliary ligand, and now we compare and explore the use of alternative pyridyl ligands, including 4,7-diphenyl-1,10-phenanthroline. Using this technique, three groups of flavonoid glycoside isomers are differentiated, including glycosides of apigenin, quercetin, and luteolin.

  4. Characterization of latex-antineoplastic drug complexes by differential scanning calorimetry and microphotography.

    PubMed

    Gallardo, V; Ruiz, M A; Morales, E; Zouaki, J; Campos, J; Conejo-García, A; Gallo, M A; Espinosa, A

    2006-12-01

    Choline kinase inhibitors have recently been identified as potentially useful antitumoral agents. Here we determine the best conditions for obtaining drug-polymer complexes with 5-fluorouracil (5-FU), and JCR791B, a new drug representing a significant advance in the development of new molecules to inhibit tumour proliferation. As polymers we used the cellulose derivatives Aquacoat and Aquateric. The variables in the adsorption process measured were time to adsorbent-adsorbate equilibrium, pH and concentration. The drug-polymer complexes were characterized by differential scanning calorimetry and microphotography. Our results show that adsorption of 5-FU and JCR was similar with both polymers although slightly greater with Aquacoat. The chemical structure of the drug and its solubility in water and oil are fundamental characteristics that determine the performance of polymers as drug carriers able to provide controlled release.

  5. Magnetic Exchange Couplings in Heterodinuclear Complexes Based on Differential Local Spin Rotations.

    PubMed

    Joshi, Rajendra P; Phillips, Jordan J; Peralta, Juan E

    2016-04-12

    We analyze the performance of a new method for the calculation of magnetic exchange coupling parameters for the particular case of heterodinuclear transition metals complexes of Cu, Ni, and V. This method is based on a generalized perturbative approach which uses differential local spin rotations via formal Lagrange multipiers (Phillips, J. J.; Peralta, J. E. J. Chem. Phys. 2013, 138, 174115). The reliability of the calculated couplings has been assessed by comparing with results from traditional energy differences with different density functional approximations and with experimental values. Our results show that this method to calculate magnetic exchange couplings can be reliably used for heteronuclear transition metal complexes, and at the same time, that it is independent from the different mapping schemes used in energy difference methods.

  6. Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes

    PubMed Central

    Yesudhas, Dhanusha; Anwar, Muhammad Ayaz; Panneerselvam, Suresh; Durai, Prasannavenkatesh; Shah, Masaud; Choi, Sangdun

    2016-01-01

    The octamer-binding transcription factor 4 (Oct4) and sex-determining region Y (SRY)-box 2 (Sox2) proteins induce various transcriptional regulators to maintain cellular pluripotency. Most Oct4/Sox2 complexes have either 0 base pairs (Oct4/Sox20bp) or 3 base pairs (Oct4/Sox23bp) separation between their DNA-binding sites. Results from previous biochemical studies have shown that the complexes separated by 0 base pairs are associated with a higher pluripotency rate than those separated by 3 base pairs. Here, we performed molecular dynamics (MD) simulations and calculations to determine the binding free energy and per-residue free energy for the Oct4/Sox20bp and Oct4/Sox23bp complexes to identify structural differences that contribute to differences in induction rate. Our MD simulation results showed substantial differences in Oct4/Sox2 domain movements, as well as secondary-structure changes in the Oct4 linker region, suggesting a potential reason underlying the distinct efficiencies of these complexes during reprogramming. Moreover, we identified key residues and hydrogen bonds that potentially facilitate protein-protein and protein-DNA interactions, in agreement with previous experimental findings. Consequently, our results confess that differential spacing of the Oct4/Sox2 DNA binding sites can determine the magnitude of transcription of the targeted genes during reprogramming. PMID:26790000

  7. Treatment with at Homeopathic Complex Medication Modulates Mononuclear Bone Marrow Cell Differentiation

    PubMed Central

    Cesar, Beatriz; Abud, Ana Paula R.; de Oliveira, Carolina C.; Cardoso, Francolino; Bernardi, Raffaello Popa Di; Guimarães, Fernando S. F.; Gabardo, Juarez; de Freitas Buchi, Dorly

    2011-01-01

    A homeopathic complex medication (HCM), with immunomodulatory properties, is recommended for patients with depressed immune systems. Previous studies demonstrated that the medication induces an increase in leukocyte number. The bone marrow microenvironment is composed of growth factors, stromal cells, an extracellular matrix and progenitor cells that differentiate into mature blood cells. Mice were our biological model used in this research. We now report in vivo immunophenotyping of total bone marrow cells and ex vivo effects of the medication on mononuclear cell differentiation at different times. Cells were examined by light microscopy and cytokine levels were measured in vitro. After in vivo treatment with HCM, a pool of cells from the new marrow microenvironment was analyzed by flow cytometry to detect any trend in cell alteration. The results showed decreases, mainly, in CD11b and TER-119 markers compared with controls. Mononuclear cells were used to analyze the effects of ex vivo HCM treatment and the number of cells showing ring nuclei, niche cells and activated macrophages increased in culture, even in the absence of macrophage colony-stimulating factor. Cytokines favoring stromal cell survival and differentiation in culture were induced in vitro. Thus, we observe that HCM is immunomodulatory, either alone or in association with other products. PMID:19736221

  8. Fractal Dimension as a Diagnostic Tool of Complex Endometrial Hyperplasia and Well-differentiated Endometrioid Carcinoma.

    PubMed

    Bikou, Olga; Delides, Alexander; Drougou, Aggeliki; Nonni, Afroditi; Patsouris, Efstratios; Pavlakis, Kitty

    Fractal dimension (FD) is widely used in medicine and biology as a tool for defining features of structure. This study aimed to compare pathological endometrium (simple-complex hyperplasia and endometrial carcinoma), as well as the endometrial changes, during the phases of the menstrual cycle. The main goal was the objective measurement of fractal dimension and to refrain from subjective evaluation. Two thousand cases of endometrial tissue from patients who underwent dilatation and curettage (D&C) were reviewed. Out of these, 137 cases were eligible for the study. In each case, immunohistochemistry with cytokeratin Ae1/AE3 was performed in order to simplify the evaluation of the FD. Endometria with carcinoma, simple or complex hyperplasia showed significant differences only in the immunohistochemically stained fractal dimensions. As expected, significant differences were also found between atrophic and secretory endometrium and carcinoma. FD is an objective, rapid and simple procedure for the differential diagnosis between complex hyperplasia and endometrial adenocarcinoma. Copyright © 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  9. A Ubiquitin Ligase Complex Regulates Caspase Activation During Sperm Differentiation in Drosophila

    PubMed Central

    Arama, Eli; Bader, Maya; Rieckhof, Gabrielle E; Steller, Hermann

    2007-01-01

    In both insects and mammals, spermatids eliminate their bulk cytoplasm as they undergo terminal differentiation. In Drosophila, this process of dramatic cellular remodeling requires apoptotic proteins, including caspases. To gain further insight into the regulation of caspases, we screened a large collection of sterile male flies for mutants that block effector caspase activation at the onset of spermatid individualization. Here, we describe the identification and characterization of a testis-specific, Cullin-3–dependent ubiquitin ligase complex that is required for caspase activation in spermatids. Mutations in either a testis-specific isoform of Cullin-3 (Cul3Testis), the small RING protein Roc1b, or a Drosophila orthologue of the mammalian BTB-Kelch protein Klhl10 all reduce or eliminate effector caspase activation in spermatids. Importantly, all three genes encode proteins that can physically interact to form a ubiquitin ligase complex. Roc1b binds to the catalytic core of Cullin-3, and Klhl10 binds specifically to a unique testis-specific N-terminal Cullin-3 (TeNC) domain of Cul3Testis that is required for activation of effector caspase in spermatids. Finally, the BIR domain region of the giant inhibitor of apoptosis–like protein dBruce is sufficient to bind to Klhl10, which is consistent with the idea that dBruce is a substrate for the Cullin-3-based E3-ligase complex. These findings reveal a novel role of Cullin-based ubiquitin ligases in caspase regulation. PMID:17880263

  10. Monocyte-to-macrophage differentiation: synthesis and secretion of a complex extracellular matrix.

    PubMed

    Chang, Mary Y; Chan, Christina K; Braun, Kathleen R; Green, Pattie S; O'Brien, Kevin D; Chait, Alan; Day, Anthony J; Wight, Thomas N

    2012-04-20

    Although monocyte- and macrophage-derived molecules are known to promote extracellular matrix (ECM) disruption and destabilization, it is less appreciated that they also synthesize molecules contributing to ECM formation, stabilization, and function. We have identified and characterized the synthesis of proteoglycans and related proteins, some not previously known to be associated with macrophages. Proteoglycan extracts of [(35)S]sulfate- and (35)S-trans amino acid-radiolabeled culture media from THP-1 monocytes induced to differentiate by treatment with phorbol myristate acetate revealed three major proteins of ~25, 90, and 100 kDa following chondroitin ABC lyase digestion. The 25-kDa protein was predominant for monocytes, whereas the 90- and 100-kDa proteins were predominant for macrophages. Tandem mass spectrometry identified (i) the 25-kDa core protein as serglycin, (ii) the 90-kDa core protein as inter-α-inhibitor heavy chain 2 (IαIHC2), and (iii) the 100-kDa core as amyloid precursor-like protein 2 (APLP2). Differentiation was also associated with (i) a >500-fold increase in mRNA for TNF-stimulated gene-6, an essential cofactor for heavy chain-mediated matrix stabilization; (ii) a >800-fold increase in mRNA for HAS2, which is responsible for hyaluronan synthesis; and (iii) a 3-fold increase in mRNA for versican, which interacts with hyaluronan. Biochemical evidence is also presented for an IαIHC2-APLP2 complex, and immunohistochemical staining of human atherosclerotic lesions demonstrates similar staining patterns for APLP2 and IαIHC2 with macrophages, whereas serglycin localizes to the underlying glycosaminoglycan-rich region. These findings indicate that macrophages synthesize many of the molecules participating in ECM formation and function, suggesting a novel role for these molecules in the differentiation of macrophages in the development of atherosclerosis.

  11. Vital roles of mTOR complex 2 in Notch-driven thymocyte differentiation and leukemia.

    PubMed

    Lee, Keunwook; Nam, Ki Taek; Cho, Sung Hoon; Gudapati, Prathyusha; Hwang, Yoonha; Park, Do-Sim; Potter, Ross; Chen, Jin; Volanakis, Emmanuel; Boothby, Mark

    2012-04-09

    Notch plays critical roles in both cell fate decisions and tumorigenesis. Notch receptor engagement initiates signaling cascades that include a phosphatidylinositol 3-kinase/target of rapamycin (TOR) pathway. Mammalian TOR (mTOR) participates in two distinct biochemical complexes, mTORC1 and mTORC2, and the relationship between mTORC2 and physiological outcomes dependent on Notch signaling is unknown. In this study, we report contributions of mTORC2 to thymic T-cell acute lymphoblastic leukemia (T-ALL) driven by Notch. Conditional deletion of Rictor, an essential component of mTORC2, impaired Notch-driven proliferation and differentiation of pre-T cells. Furthermore, NF-κB activity depended on the integrity of mTORC2 in thymocytes. Active Akt restored NF-κB activation, a normal rate of proliferation, and differentiation of Rictor-deficient pre-T cells. Strikingly, mTORC2 depletion lowered CCR7 expression in thymocytes and leukemic cells, accompanied by decreased tissue invasion and delayed mortality in T-ALL driven by Notch. Collectively, these findings reveal roles for mTORC2 in promoting thymic T cell development and T-ALL and indicate that mTORC2 is crucial for Notch signaling to regulate Akt and NF-κB.

  12. Differential responses of IGF-I molecular complexes to military operational field training.

    PubMed

    Nindl, Bradley C; Castellani, John W; Young, Andrew J; Patton, John F; Khosravi, M Javad; Diamandi, Anastasia; Montain, Scott J

    2003-09-01

    Insulin-like growth factor (IGF) I and IGF binding proteins (IGFBPs) modulate metabolic activity and tissue repair and are influenced by nutritional status. IGF-I circulates in free, ternary [IGF-I + IGFBP-3 + acid labile subunit (ALS)], and binary (IGF-I + IGFBP) molecular complexes, and the relative proportions regulate IGF-I extravascular shifting and bioavailability. This study examined the hypothesis that sustained physical activity and sleep deprivation superimposed on a short-term energy deficit would alter the IGFBP concentrations and alter the proportions of IGF-I circulating in ternary vs. binary molecular complexes. Components of the IGF-I system (total and free IGF-I; IGFBP-1, -3, and ALS; nonternary IGF-I and IGFBP-3), biomarkers of metabolic and nutritional status (transferrin, ferritin, prealbumin, glucose, free fatty acids, glycerol, beta-hydroxybutyrate), and body composition were measured in 12 men (22 +/- 3 yr, 87 +/- 8 kg, 183 +/- 7 cm, 20 +/- 5% body fat) on days 1, 3, and 4 during a control and experimental (Exp) period. During Exp, subjects performed prolonged work (energy expenditure of approximately 4500 kcal/day) with caloric (1600 kcal/day) and sleep (6.2 h total) restriction. IGF-I and IGFBP-3 were measured by immunoassay before and after immunoaffinity depletion of ALS-based complexes (i.e., ternary complex removal). Exp produced losses in body mass (-3.0%), lowered total IGF-I (-24%), free IGF-I (-42%), IGFBP-3 (-6%), nonternary IGF-I (-27%), and IGFBP-3 (-16%), and increased IGFBP-1 (256%). No Exp effects were observed for ALS. No changes were observed in the proportion of IGF-I circulating in free ( approximately 1.2%), ternary ( approximately 87.4%), or nonternary ( approximately 11.4%) molecular complexes. During Exp, glucose concentrations were lower on day 3, but days 1 and 4 were statistically similar. In conclusion, during a short-term energy deficit in young, healthy men, 1). IGF-I system components differentially respond

  13. 2D NMR Barcoding and Differential Analysis of Complex Mixtures for Chemical Identification: The Actaea Triterpenes

    PubMed Central

    2015-01-01

    The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ−δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652

  14. Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes.

    PubMed

    Hellman, Lance M; Yin, Liusong; Wang, Yuan; Blevins, Sydney J; Riley, Timothy P; Belden, Orrin S; Spear, Timothy T; Nishimura, Michael I; Stern, Lawrence J; Baker, Brian M

    2016-05-01

    Measurements of thermal stability by circular dichroism (CD) spectroscopy have been widely used to assess the binding of peptides to MHC proteins, particularly within the structural immunology community. Although thermal stability assays offer advantages over other approaches such as IC50 measurements, CD-based stability measurements are hindered by large sample requirements and low throughput. Here we demonstrate that an alternative approach based on differential scanning fluorimetry (DSF) yields results comparable to those based on CD for both class I and class II complexes. As they require much less sample, DSF-based measurements reduce demands on protein production strategies and are amenable for high throughput studies. DSF can thus not only replace CD as a means to assess peptide/MHC thermal stability, but can complement other peptide-MHC binding assays used in screening, epitope discovery, and vaccine design. Due to the physical process probed, DSF can also uncover complexities not observed with other techniques. Lastly, we show that DSF can also be used to assess peptide/MHC kinetic stability, allowing for a single experimental setup to probe both binding equilibria and kinetics. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Differentiating Obstructive from Central and Complex Sleep Apnea Using an Automated Electrocardiogram-Based Method

    PubMed Central

    Thomas, Robert Joseph; Mietus, Joseph E.; Peng, Chung-Kang; Gilmartin, Geoffrey; Daly, Robert W.; Goldberger, Ary L.; Gottlieb, Daniel J.

    2007-01-01

    . Differentiating obstructive from central and complex sleep apnea using an automated electrocardiogram-based method. SLEEP 2007;30(12):1756-1769. PMID:18246985

  16. Phenotypic differentiation in love song traits among sibling species of the Lutzomyia longipalpis complex in Brazil.

    PubMed

    Vigoder, Felipe M; Souza, Nataly A; Brazil, Reginaldo P; Bruno, Rafaela V; Costa, Pietra L; Ritchie, Michael G; Klaczko, Louis B; Peixoto, Alexandre A

    2015-05-28

    Brazilian populations of Lutzomyia longipalpis may constitute a complex of cryptic species, and this report investigates the distribution and number of potential sibling species. One of the main differences observed among Brazilian populations is the type of acoustic signal produced by males during copulation. These copulation song differences seem to be evolving faster than neutral molecular markers and have been suggested to contribute to insemination failure observed in crosses between these sibling species. In previous studies, two main types of copulation songs were found, burst-type and pulse-type. The latter type can, in turn, be further subdivided into five different patterns. We recorded male song from 13 new populations of the L. longipalpis complex from Brazil and compared the songs with 12 already available. Out of these 25 populations, 16 produce burst-type and 9 produce pulse-type songs. We performed a principal component analysis in these two main groups separately and an additional discriminant analysis in the pulse-type group. The pulse-type populations showed a clear separation between the five known patterns with a high correspondence of individuals to their correct group, confirming the differentiation between them. The distinctiveness of the burst-type subgroups was much lower than that observed among the pulse-type groups and no clear population structure was observed. This suggests that the burst-type populations represent a single species. Overall, our results are consistent with the existence in Brazil of at least six species of the L. longipalpis complex, one with a wide distribution comprising all the populations with burst-type songs, and five more closely related allopatric siblings with different pulse-type song patterns and more restricted distribution ranges.

  17. Analysis of E-box DNA binding during myeloid differentiation reveals complexes that contain Mad but not Max.

    PubMed Central

    Ryan, K M; Birnie, G D

    1997-01-01

    It has been shown that during myeloid differentiation the levels of mad1 mRNA are induced before the loss of c-Myc protein. This suggests that inactivation of the differentiation-blocking activity of c-Myc might not occur primarily through the loss of Myc protein, but through an increase in the levels of its antagonist, Mad1. To investigate this question we have analysed the levels of mad1 mRNA during differentiation of myeloid leukaemic HL60 cells. Although levels of mad1 mRNA were moderately increased after induction with phorbol ester, we also found that differentiation could be achieved with other inducers without any concomitant up-regulation of mad1 mRNA. In addition, analysis of E-box DNA binding revealed that, although Myc-Max complexes were lost rapidly after differentiation induction, formation of Mad1-containing complexes only occurred during the later stages of the differentiation programme. Further analysis of these Mad-containing complexes revealed that they were also unlikely to have the capacity to antagonize c-Myc function, as they did not contain Max. Therefore these data suggest that an increase in the levels of mad1 mRNA or the formation of a Mad-Max complex are unlikely to be essential or determining events for myeloid differentiation. In addition, the discovery of DNA-binding complexes that contain Mad1, but not Max, opens up this transcription factor network to include other Max-like proteins or proteins of an unrelated nature. PMID:9224632

  18. Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems

    NASA Astrophysics Data System (ADS)

    Cerbino, Roberto; Cicuta, Pietro

    2017-09-01

    Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.

  19. Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems.

    PubMed

    Cerbino, Roberto; Cicuta, Pietro

    2017-09-21

    Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.

  20. Morphological and AFLP-based Differentiation within the Taxonomical Complex Section Caninae (subgenus Rosa)

    PubMed Central

    De Cock, Katrien; Vander Mijnsbrugge, Kristine; Breyne, Peter; Van Bockstaele, Erik; Van Slycken, Jos

    2008-01-01

    Background and Aims The taxonomical structure of the polymorphic subgenus Rosa section Caninae is highly complex due to the combination of some unusual features: the unique polyploid chromosomal constitution, the heterogamic canina meiosis, the ability to hybridize interspecifically, and the predominantly matroclinal inheritance. Although most taxonomists agree on the subdivision of the section into three morphologically well-defined groups (Rubigineae, Vestitae, and Caninae), they disagree on the existence of smaller groups such as Tomentellae. The aim was to gain insight in the taxonomical structure and investigate the interpopulation differentiation of the polymorphic section Caninae by analysing morphological and AFLP-based characters of the seven most common Belgian dog-rose taxa. Methods The intersubsectional and -specific relationships within the dog-roses were examined using morphological and molecular-genetic markers. AFLP data were analysed with basic descriptive genetic statistics because of the lack of Hardy–Weinberg equilibrium due to the polyploid genetic structure and heterogamic meiosis. Key Results Both the morphological and AFLP-based analyses supported the subdivision of the dog-roses in three well-defined though partly overlapping groups, Rubigineae, Vestitae and Caninae. However, it was not possible to distinguish between the morphologically well-defined taxa within the same subsection using AFLP-based data. In addition, the results suggested a high similarity of Rosa balsamica with subsection Caninae taxa. Small-scale geographical AFLP-based differentiation was observed within several dog-rose taxa. Surprisingly, individuals sampled at one locality and belonging to morphologically distinct dog-rose taxa displayed higher genetic similarities in comparison to their congeners sampled at different localities. Conclusions The hybridogenic character of the dog-roses was reflected in the vague boundaries between the subsections and on the species

  1. Differentiation of complex lipid isomers by radical-directed dissociation mass spectrometry.

    PubMed

    Pham, Huong T; Ly, Tony; Trevitt, Adam J; Mitchell, Todd W; Blanksby, Stephen J

    2012-09-04

    Contemporary lipidomics protocols are dependent on conventional tandem mass spectrometry for lipid identification. This approach is extremely powerful for determining lipid class and identifying the number of carbons and the degree of unsaturation of any acyl-chain substituents. Such analyses are however, blind to isomeric variants arising from different carbon-carbon bonding motifs within these chains including double bond position, chain branching, and cyclic structures. This limitation arises from the fact that conventional, low energy collision-induced dissociation of even-electron lipid ions does not give rise to product ions from intrachain fragmentation of the fatty acyl moieties. To overcome this limitation, we have applied radical-directed dissociation (RDD) to the study of lipids for the first time. In this approach, bifunctional molecules that contain a photocaged radical initiator and a lipid-adducting group, such as 4-iodoaniline and 4-iodobenzoic acid, are used to form noncovalent complexes (i.e., adduct ions) with a lipid during electrospray ionization. Laser irradiation of these complexes at UV wavelengths (266 nm) cleaves the carbon-iodine bond to liberate a highly reactive phenyl radical. Subsequent activation of the nascent radical ions results in RDD with significant intrachain fragmentation of acyl moieties. This approach provides diagnostic fragments that are associated with the double bond position and the positions of chain-branching in glycerophospholipids, sphingomyelins and triacylglycerols and thus can be used to differentiate isomeric lipids differing only in such motifs. RDD is demonstrated for well-defined lipid standards and also reveals lipid structural diversity in olive oil and human very-low density lipoprotein.

  2. Differential proteolytic activation of factor VIII-von Willebrand factor complex by thrombin

    SciTech Connect

    Hill-Eubanks, D.C.; Parker, C.G.; Lollar, P. )

    1989-09-01

    Blood coagulation factor VIII (fVIII) is a plasma protein that is decreased or absent in hemophilia A. It is isolated as a mixture of heterodimers that contain a variably sized heavy chain and a common light chain. Thrombin catalyzes the activation of fVIII in a reaction that is associated with cleavages in both types of chain. The authors isolated a serine protease from Bothrops jararacussu snake venom that catalyzes thrombin-like heavy-chain cleavage but not light-chain cleavage in porcine fVIII as judged by NaDodSO{sub 4}/PAGE and N-terminal sequence analysis. Using a plasma-free assay of the ability of activated {sup 125}I-fVIII to function as a cofactor in the activation of factor X by factor IXa, they found that fVIII is activated by the venom enzyme. The venom enzyme-activated fVIII was isolated in stable form by cation-exchange HPLC. von Willebrand factor inhibited venom enzyme-activated fVIII but not thrombin-activated fVIII. These results suggest that the binding of fVIII to von Willebrand factor depends on the presence of an intact light chain and that activated fVIII must dissociate from von Willebrand factor to exert its cofactor effect. Thus, proteolytic activation of fVIII-von Willebrand factor complex appears to be differentially regulated by light-chain cleavage to dissociate the complex and heavy-chain cleavage to activate the cofactor function.

  3. Deconvolution of complex differential scanning calorimetry profiles for protein transitions under kinetic control.

    PubMed

    Toledo-Núñez, Citlali; Vera-Robles, L Iraís; Arroyo-Maya, Izlia J; Hernández-Arana, Andrés

    2016-09-15

    A frequent outcome in differential scanning calorimetry (DSC) experiments carried out with large proteins is the irreversibility of the observed endothermic effects. In these cases, DSC profiles are analyzed according to methods developed for temperature-induced denaturation transitions occurring under kinetic control. In the one-step irreversible model (native → denatured) the characteristics of the observed single-peaked endotherm depend on the denaturation enthalpy and the temperature dependence of the reaction rate constant, k. Several procedures have been devised to obtain the parameters that determine the variation of k with temperature. Here, we have elaborated on one of these procedures in order to analyze more complex DSC profiles. Synthetic data for a heat capacity curve were generated according to a model with two sequential reactions; the temperature dependence of each of the two rate constants involved was determined, according to the Eyring's equation, by two fixed parameters. It was then shown that our deconvolution procedure, by making use of heat capacity data alone, permits to extract the parameter values that were initially used. Finally, experimental DSC traces showing two and three maxima were analyzed and reproduced with relative success according to two- and four-step sequential models.

  4. Identification and comparative analysis of the epidermal differentiation complex in snakes

    PubMed Central

    Brigit Holthaus, Karin; Mlitz, Veronika; Strasser, Bettina; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

    2017-01-01

    The epidermis of snakes efficiently protects against dehydration and mechanical stress. However, only few proteins of the epidermal barrier to the environment have so far been identified in snakes. Here, we determined the organization of the Epidermal Differentiation Complex (EDC), a cluster of genes encoding protein constituents of cornified epidermal structures, in snakes and compared it to the EDCs of other squamates and non-squamate reptiles. The EDC of snakes displays shared synteny with that of the green anole lizard, including the presence of a cluster of corneous beta-protein (CBP)/beta-keratin genes. We found that a unique CBP comprising 4 putative beta-sheets and multiple cysteine-rich EDC proteins are conserved in all snakes and other squamates investigated. Comparative genomics of squamates suggests that the evolution of snakes was associated with a gene duplication generating two isoforms of the S100 fused-type protein, scaffoldin, the origin of distinct snake-specific EDC genes, and the loss of other genes that were present in the EDC of the last common ancestor of snakes and lizards. Taken together, our results provide new insights into the evolution of the skin in squamates and a basis for the characterization of the molecular composition of the epidermis in snakes. PMID:28345630

  5. Differential Transmembrane Domain GXXXG Motif Pairing Impacts Major Histocompatibility Complex (MHC) Class II Structure*

    PubMed Central

    Dixon, Ann M.; Drake, Lisa; Hughes, Kelly T.; Sargent, Elizabeth; Hunt, Danielle; Harton, Jonathan A.; Drake, James R.

    2014-01-01

    Major histocompatibility complex (MHC) class II molecules exhibit conformational heterogeneity, which influences their ability to stimulate CD4 T cells and drive immune responses. Previous studies suggest a role for the transmembrane domain of the class II αβ heterodimer in determining molecular structure and function. Our previous studies identified an MHC class II conformer that is marked by the Ia.2 epitope. These Ia.2+ class II conformers are lipid raft-associated and able to drive both tyrosine kinase signaling and efficient antigen presentation to CD4 T cells. Here, we establish that the Ia.2+ I-Ak conformer is formed early in the class II biosynthetic pathway and that differential pairing of highly conserved transmembrane domain GXXXG dimerization motifs is responsible for formation of Ia.2+ versus Ia.2− I-Ak class II conformers and controlling lipid raft partitioning. These findings provide a molecular explanation for the formation of two distinct MHC class II conformers that differ in their inherent ability to signal and drive robust T cell activation, providing new insight into the role of MHC class II in regulating antigen-presenting cell-T cell interactions critical to the initiation and control of multiple aspects of the immune response. PMID:24619409

  6. Laser thermal therapy monitoring using complex differential variance in optical coherence tomography.

    PubMed

    Lo, William C Y; Uribe-Patarroyo, Néstor; Nam, Ahhyun S; Villiger, Martin; Vakoc, Benjamin J; Bouma, Brett E

    2017-01-01

    Conventional thermal therapy monitoring techniques based on temperature are often invasive, limited by point sampling, and are indirect measures of tissue injury, while techniques such as magnetic resonance and ultrasound thermometry are limited by their spatial resolution.  The visualization of the thermal coagulation zone at high spatial resolution is particularly critical to the precise delivery of thermal energy to epithelial lesions. In this work, an integrated thulium laser thermal therapy monitoring system was developed based on complex differential variance (CDV), which enables the 2D visualization of the dynamics of the thermal coagulation process at high spatial and temporal resolution with an optical frequency domain imaging system. With proper calibration to correct for noise, the CDV-based technique was shown to accurately delineate the thermal coagulation zone, which is marked by the transition from high CDV upon heating to a significantly reduced CDV once the tissue is coagulated, in 3 different tissue types ex vivo: skin, retina, and esophagus. The ability to delineate thermal lesions in multiple tissue types at high resolution opens up the possibility of performing microscopic image-guided procedures in a vast array of epithelial applications ranging from dermatology, ophthalmology, to gastroenterology and beyond. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Differentiating the mTOR inhibitors everolimus and sirolimus in the treatment of tuberous sclerosis complex.

    PubMed

    MacKeigan, Jeffrey P; Krueger, Darcy A

    2015-12-01

    Tuberous sclerosis complex (TSC) is a genetic autosomal dominant disorder characterized by benign tumor-like lesions, called hamartomas, in multiple organ systems, including the brain, skin, heart, kidneys, and lung. These hamartomas cause a diverse set of clinical problems based on their location and often result in epilepsy, learning difficulties, and behavioral problems. TSC is caused by mutations within the TSC1 or TSC2 genes that inactivate the genes' tumor-suppressive function and drive hamartomatous cell growth. In normal cells, TSC1 and TSC2 integrate growth signals and nutrient inputs to downregulate signaling to mammalian target of rapamycin (mTOR), an evolutionarily conserved serine-threonine kinase that controls cell growth and cell survival. The molecular connection between TSC and mTOR led to the clinical use of allosteric mTOR inhibitors (sirolimus and everolimus) for the treatment of TSC. Everolimus is approved for subependymal giant cell astrocytomas and renal angiomyolipomas in patients with TSC. Sirolimus, though not approved for TSC, has undergone considerable investigation to treat various aspects of the disease. Everolimus and sirolimus selectively inhibit mTOR signaling with similar molecular mechanisms, but with distinct clinical profiles. This review differentiates mTOR inhibitors in TSC while describing the molecular mechanisms, pathogenic mutations, and clinical trial outcomes for managing TSC.

  8. Identification and comparative analysis of the epidermal differentiation complex in snakes.

    PubMed

    Holthaus, Karin Brigit; Mlitz, Veronika; Strasser, Bettina; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

    2017-03-27

    The epidermis of snakes efficiently protects against dehydration and mechanical stress. However, only few proteins of the epidermal barrier to the environment have so far been identified in snakes. Here, we determined the organization of the Epidermal Differentiation Complex (EDC), a cluster of genes encoding protein constituents of cornified epidermal structures, in snakes and compared it to the EDCs of other squamates and non-squamate reptiles. The EDC of snakes displays shared synteny with that of the green anole lizard, including the presence of a cluster of corneous beta-protein (CBP)/beta-keratin genes. We found that a unique CBP comprising 4 putative beta-sheets and multiple cysteine-rich EDC proteins are conserved in all snakes and other squamates investigated. Comparative genomics of squamates suggests that the evolution of snakes was associated with a gene duplication generating two isoforms of the S100 fused-type protein, scaffoldin, the origin of distinct snake-specific EDC genes, and the loss of other genes that were present in the EDC of the last common ancestor of snakes and lizards. Taken together, our results provide new insights into the evolution of the skin in squamates and a basis for the characterization of the molecular composition of the epidermis in snakes.

  9. Laser thermal therapy monitoring using complex differential variance in optical coherence tomography

    PubMed Central

    Lo, William C. Y.; Uribe-Patarroyo, Néstor; Nam, Ahhyun S.; Villiger, Martin; Vakoc, Benjamin J.; Bouma, Brett E.

    2016-01-01

    Conventional thermal therapy monitoring techniques based on temperature are often invasive, limited by point sampling, and are indirect measures of tissue injury, while techniques such as magnetic resonance and ultrasound thermometry are limited by their spatial resolution. The visualization of the thermal coagulation zone at high spatial resolution is particularly critical to the precise delivery of thermal energy to epithelial lesions. In this work, an integrated thulium laser thermal therapy monitoring system was developed based on complex differential variance (CDV), which enables the 2D visualization of the dynamics of the thermal coagulation process at high spatial and temporal resolution with an optical frequency domain imaging system. With proper calibration to correct for noise, the CDV-based technique was shown to accurately delineate the thermal coagulation zone, which is marked by the transition from high CDV upon heating to a significantly reduced CDV once the tissue is coagulated, in 3 different tissue types ex vivo: skin, retina, and esophagus. The ability to delineate thermal lesions in multiple tissue types at high resolution opens up the possibility of performing microscopic image-guided procedures in a vast array of epithelial applications ranging from dermatology, ophthalmology, to gastroenterology and beyond. PMID:27623742

  10. Differentiating the mTOR inhibitors everolimus and sirolimus in the treatment of tuberous sclerosis complex

    PubMed Central

    MacKeigan, Jeffrey P.; Krueger, Darcy A.

    2015-01-01

    Tuberous sclerosis complex (TSC) is a genetic autosomal dominant disorder characterized by benign tumor-like lesions, called hamartomas, in multiple organ systems, including the brain, skin, heart, kidneys, and lung. These hamartomas cause a diverse set of clinical problems based on their location and often result in epilepsy, learning difficulties, and behavioral problems. TSC is caused by mutations within the TSC1 or TSC2 genes that inactivate the genes' tumor-suppressive function and drive hamartomatous cell growth. In normal cells, TSC1 and TSC2 integrate growth signals and nutrient inputs to downregulate signaling to mammalian target of rapamycin (mTOR), an evolutionarily conserved serine-threonine kinase that controls cell growth and cell survival. The molecular connection between TSC and mTOR led to the clinical use of allosteric mTOR inhibitors (sirolimus and everolimus) for the treatment of TSC. Everolimus is approved for subependymal giant cell astrocytomas and renal angiomyolipomas in patients with TSC. Sirolimus, though not approved for TSC, has undergone considerable investigation to treat various aspects of the disease. Everolimus and sirolimus selectively inhibit mTOR signaling with similar molecular mechanisms, but with distinct clinical profiles. This review differentiates mTOR inhibitors in TSC while describing the molecular mechanisms, pathogenic mutations, and clinical trial outcomes for managing TSC. PMID:26289591

  11. Tuning the electrical properties of the heart by differential trafficking of KATP ion channel complexes

    PubMed Central

    Arakel, Eric C.; Brandenburg, Sören; Uchida, Keita; Zhang, Haixia; Lin, Yu-Wen; Kohl, Tobias; Schrul, Bianca; Sulkin, Matthew S.; Efimov, Igor R.; Nichols, Colin G.; Lehnart, Stephan E.; Schwappach, Blanche

    2014-01-01

    ABSTRACT The copy number of membrane proteins at the cell surface is tightly regulated. Many ion channels and receptors present retrieval motifs to COPI vesicle coats and are retained in the early secretory pathway. In some cases, the interaction with COPI is prevented by binding to 14-3-3 proteins. However, the functional significance of this antagonism between COPI and 14-3-3 in terminally differentiated cells is unknown. Here, we show that ATP-sensitive K+ (KATP) channels, which are composed of Kir6.2 and SUR1 subunits, are stalled in the Golgi complex of ventricular, but not atrial, cardiomyocytes. Upon sustained β-adrenergic stimulation, which leads to activation of protein kinase A (PKA), SUR1-containing channels reach the plasma membrane of ventricular cells. We show that PKA-dependent phosphorylation of the C-terminus of Kir6.2 decreases binding to COPI and, thereby, silences the arginine-based retrieval signal. Thus, activation of the sympathetic nervous system releases this population of KATP channels from storage in the Golgi and, hence, might facilitate the adaptive response to metabolic challenges. PMID:24569881

  12. Mammalian target of rapamycin complex 1 is involved in differentiation of regenerating myofibers in vivo.

    PubMed

    Miyabara, Elen H; Conte, Talita C; Silva, Meiricris T; Baptista, Igor L; Bueno, Carlos; Fiamoncini, Jarlei; Lambertucci, Rafael H; Serra, Carmen S; Brum, Patricia C; Pithon-Curi, Tania; Curi, Rui; Aoki, Marcelo S; Oliveira, Antonio C; Moriscot, Anselmo S

    2010-11-01

    This work was undertaken to provide further insight into the role of mammalian target of rapamycin complex 1 (mTORC1) in skeletal muscle regeneration, focusing on myofiber size recovery. Rats were treated or not with rapamycin, an mTORC1 inhibitor. Soleus muscles were then subjected to cryolesion and analyzed 1, 10, and 21 days later. A decrease in soleus myofiber cross-section area on post-cryolesion days 10 and 21 was accentuated by rapamycin, which was also effective in reducing protein synthesis in these freeze-injured muscles. The incidence of proliferating satellite cells during regeneration was unaltered by rapamycin, although immunolabeling for neonatal myosin heavy chain (MHC) was weaker in cryolesion+rapamycin muscles than in cryolesion-only muscles. In addition, the decline in tetanic contraction of freeze-injured muscles was accentuated by rapamycin. This study indicates that mTORC1 plays a key role in the recovery of muscle mass and the differentiation of regenerating myofibers, independently of necrosis and satellite cell proliferation mechanisms.

  13. Myofibroblast differentiation and its functional properties are inhibited by nicotine and e-cigarette via mitochondrial OXPHOS complex III

    PubMed Central

    Lei, Wei; Lerner, Chad; Sundar, Isaac K.; Rahman, Irfan

    2017-01-01

    Nicotine is the major stimulant in tobacco products including e-cigarettes. Fibroblast to myofibroblast differentiation is a key process during wound healing and is dysregulated in lung diseases. The role of nicotine and e-cigarette derived nicotine on cellular functions including profibrotic response and other functional aspects is not known. We hypothesized that nicotine and e-cigarettes affect myofibroblast differentiation, gel contraction, and wound healing via mitochondria stress through nicotinic receptor-dependent mechanisms. To test the hypothesis, we exposed human lung fibroblasts with various doses of nicotine and e-cigarette condensate and determined myofibroblast differentiation, mitochondrial oxidative phosphorylation (OXPHOS), wound healing, and gel contraction at different time points. We found that both nicotine and e-cigarette inhibit myofibroblast differentiation as shown by smooth muscle actin and collagen type I, alpha 1 abundance. Nicotine and e-cigarette inhibited OXPHOS complex III accompanied by increased MitoROS, and this effect was augmented by complex III inhibitor antimycin A. These mitochondrial associated effects by nicotine resulted in inhibition of myofibroblast differentiation. These effects were associated with inhibition of wound healing and gel contraction suggesting that nicotine is responsible for dysregulated repair during injurious responses. Thus, our data suggest that nicotine causes dysregulated repair by inhibition of myofibroblast differentiation via OXPHOS pathway. PMID:28256533

  14. Differentiation of Species Combined into the Burkholderia cepacia Complex and Related Taxa on the Basis of Their Fatty Acid Patterns

    PubMed Central

    Krejčí, Eva; Kroppenstedt, Reiner M.

    2006-01-01

    Using the established commercial system Sherlock (MIDI, Inc.), cellular fatty acid methyl ester analysis for differentiation among Burkholderia cepacia complex species was proven. The identification key based on the diagnostic fatty acids is able to discern phenotypically related Ralstonia pickettii and Pandoraea spp. and further distinguish Burkholderia pyrrocinia, Burkholderia ambifaria, and Burkholderia vietnamiensis. PMID:16517920

  15. Mof-associated complexes have overlapping and unique roles in regulating pluripotency in embryonic stem cells and during differentiation.

    PubMed

    Ravens, Sarina; Fournier, Marjorie; Ye, Tao; Stierle, Matthieu; Dembele, Doulaye; Chavant, Virginie; Tora, Làszlò

    2014-06-04

    The histone acetyltransferase (HAT) Mof is essential for mouse embryonic stem cell (mESC) pluripotency and early development. Mof is the enzymatic subunit of two different HAT complexes, MSL and NSL. The individual contribution of MSL and NSL to transcription regulation in mESCs is not well understood. Our genome-wide analysis show that i) MSL and NSL bind to specific and common sets of expressed genes, ii) NSL binds exclusively at promoters, iii) while MSL binds in gene bodies. Nsl1 regulates proliferation and cellular homeostasis of mESCs. MSL is the main HAT acetylating H4K16 in mESCs, is enriched at many mESC-specific and bivalent genes. MSL is important to keep a subset of bivalent genes silent in mESCs, while developmental genes require MSL for expression during differentiation. Thus, NSL and MSL HAT complexes differentially regulate specific sets of expressed genes in mESCs and during differentiation.

  16. Differentiation in the Trochulus hispidus complex and related taxa (Pulmonata: Hygromiidae): morphology, ecology and their relation to phylogeography

    PubMed Central

    Duda, Michael; Kruckenhauser, Luise; Sattmann, Helmut; Harl, Josef; Jaksch, Katharina; Haring, Elisabeth

    2014-01-01

    In this study we investigated the morphology and ecology of representatives of the taxonomically ambiguous genus Trochulus. The main focus was on the T. hispidus complex, which comprises several genetically highly divergent mitochondrial clades, as determined in a parallel molecular genetic study. We analysed shell morphology and anatomical traits and asked whether the clades are differentiated in these characters. In addition, the related species T. oreinos and T. striolatus were investigated and compared with the T. hispidus complex. Finally, we compared the ecological requirements of the taxa. Among the genetic clades of the T. hispidus complex there was no clear morphological differentiation and geographic populations could not be distinguished based on their morphology. The investigated characters of the genital anatomy did not allow discrimination of any of the T. hispidus clades and were not even diagnostic for the group as a whole. The morphotype of T. sericeus is present in all clades and thus cannot be assigned to a genetic group or any specific population. Thus, our morphological data do not provide evidence that any of the mitochondrial T. hispidus clades represent separate species. Concerning interspecific delimitation, the T. hispidus complex was clearly differentiated from T. striolatus and T. oreinos by shell morphological and anatomical characters, e.g. sculpture of shell surface and details of the penis. Finally, the habitat of T. oreinos is different from those of the other two species. In contrast to the lack of correspondence between genetic and morphological differentiation within the T. hispidus complex, related species display intraspecific morphological differentiation corresponding with mitochondrial clades: within T. striolatus there was a slight morphological differentiation between the subspecies T. s. striolatus, T. s. juvavensis and T. s. danubialis. The two subspecies of T. oreinos could be discriminated by a small but consistent

  17. Differentiation in the Trochulus hispidus complex and related taxa (Pulmonata: Hygromiidae): morphology, ecology and their relation to phylogeography.

    PubMed

    Duda, Michael; Kruckenhauser, Luise; Sattmann, Helmut; Harl, Josef; Jaksch, Katharina; Haring, Elisabeth

    2014-11-01

    In this study we investigated the morphology and ecology of representatives of the taxonomically ambiguous genus Trochulus. The main focus was on the T. hispidus complex, which comprises several genetically highly divergent mitochondrial clades, as determined in a parallel molecular genetic study. We analysed shell morphology and anatomical traits and asked whether the clades are differentiated in these characters. In addition, the related species T. oreinos and T. striolatus were investigated and compared with the T. hispidus complex. Finally, we compared the ecological requirements of the taxa. Among the genetic clades of the T. hispidus complex there was no clear morphological differentiation and geographic populations could not be distinguished based on their morphology. The investigated characters of the genital anatomy did not allow discrimination of any of the T. hispidus clades and were not even diagnostic for the group as a whole. The morphotype of T. sericeus is present in all clades and thus cannot be assigned to a genetic group or any specific population. Thus, our morphological data do not provide evidence that any of the mitochondrial T. hispidus clades represent separate species. Concerning interspecific delimitation, the T. hispidus complex was clearly differentiated from T. striolatus and T. oreinos by shell morphological and anatomical characters, e.g. sculpture of shell surface and details of the penis. Finally, the habitat of T. oreinos is different from those of the other two species. In contrast to the lack of correspondence between genetic and morphological differentiation within the T. hispidus complex, related species display intraspecific morphological differentiation corresponding with mitochondrial clades: within T. striolatus there was a slight morphological differentiation between the subspecies T. s. striolatus, T. s. juvavensis and T. s. danubialis. The two subspecies of T. oreinos could be discriminated by a small but consistent

  18. Detection and differentiation of neutral organic compounds by 19F NMR with a tungsten calix[4]arene imido complex.

    PubMed

    Zhao, Yanchuan; Swager, Timothy M

    2013-12-18

    Fluorinated tungsten calix[4]arene imido complexes were synthesized and used as receptors to detect and differentiate neutral organic compounds. It was found that the binding of specific neutral organic molecules to the tungsten centers induces an upfield shift of the fluorine atom appended on the arylimido group, the extent of which is highly dependent on electronic and steric properties. We demonstrate that the specific bonding and size-selectivity of calix[4]arene tungsten-imido complex combined with (19)F NMR spectroscopy is a powerful new method for the analysis of complex mixtures.

  19. CRISPR screen identifies the NCOR/HDAC3 complex as a major suppressor of differentiation in rhabdomyosarcoma

    PubMed Central

    Phelps, Michael P.; Bailey, Jenna N.; Vleeshouwer-Neumann, Terra

    2016-01-01

    Dysregulated gene expression resulting from abnormal epigenetic alterations including histone acetylation and deacetylation has been demonstrated to play an important role in driving tumor growth and progression. However, the mechanisms by which specific histone deacetylases (HDACs) regulate differentiation in solid tumors remains unclear. Using pediatric rhabdomyosarcoma (RMS) as a paradigm to elucidate the mechanism blocking differentiation in solid tumors, we identified HDAC3 as a major suppressor of myogenic differentiation from a high-efficiency Clustered regularly interspaced short palindromic repeats (CRISPR)-based phenotypic screen of class I and II HDAC genes. Detailed characterization of the HDAC3-knockout phenotype in vitro and in vivo using a tamoxifen-inducible CRISPR targeting strategy demonstrated that HDAC3 deacetylase activity and the formation of a functional complex with nuclear receptor corepressors (NCORs) were critical in restricting differentiation in RMS. The NCOR/HDAC3 complex specifically functions by blocking myoblast determination protein 1 (MYOD1)-mediated activation of myogenic differentiation. Interestingly, there was also a transient up-regulation of growth-promoting genes upon initial HDAC3 targeting, revealing a unique cancer-specific response to the forced transition from a neoplastic state to terminal differentiation. Our study applied modifications of CRISPR/CRISPR-associated endonuclease 9 (Cas9) technology to interrogate the function of essential cancer genes and pathways and has provided insights into cancer cell adaptation in response to altered differentiation status. Because current pan-HDAC inhibitors have shown disappointing results in clinical trials of solid tumors, therapeutic targets specific to HDAC3 function represent a promising option for differentiation therapy in malignant tumors with dysregulated HDAC3 activity. PMID:27956629

  20. The Lsm1-7-Pat1 complex promotes viral RNA translation and replication by differential mechanisms.

    PubMed

    Jungfleisch, Jennifer; Chowdhury, Ashis; Alves-Rodrigues, Isabel; Tharun, Sundaresan; Díez, Juana

    2015-08-01

    The Lsm1-7-Pat1 complex binds to the 3' end of cellular mRNAs and promotes 3' end protection and 5'-3' decay. Interestingly, this complex also specifically binds to cis-acting regulatory sequences of viral positive-strand RNA genomes promoting their translation and subsequent recruitment from translation to replication. Yet, how the Lsm1-7-Pat1 complex regulates these two processes remains elusive. Here, we show that Lsm1-7-Pat1 complex acts differentially in these processes. By using a collection of well-characterized lsm1 mutant alleles and a system that allows the replication of Brome mosaic virus (BMV) in yeast we show that the Lsm1-7-Pat1 complex integrity is essential for both, translation and recruitment. However, the intrinsic RNA-binding ability of the complex is only required for translation. Consistent with an RNA-binding-independent function of the Lsm1-7-Pat1 complex on BMV RNA recruitment, we show that the BMV 1a protein, the sole viral protein required for recruitment, interacts with this complex in an RNA-independent manner. Together, these results support a model wherein Lsm1-7-Pat1 complex binds consecutively to BMV RNA regulatory sequences and the 1a protein to promote viral RNA translation and later recruitment out of the host translation machinery to the viral replication complexes.

  1. A-type Lamins Form Distinct Filamentous Networks with Differential Nuclear Pore Complex Associations.

    PubMed

    Xie, Wei; Chojnowski, Alexandre; Boudier, Thomas; Lim, John S Y; Ahmed, Sohail; Ser, Zheng; Stewart, Colin; Burke, Brian

    2016-10-10

    The nuclear lamina is a universal feature of metazoan nuclear envelopes (NEs) [1]. In mammalian cells, it appears as a 10-30 nm filamentous layer at the nuclear face of the inner nuclear membrane (INM) and is composed primarily of A- and B-type lamins, members of the intermediate filament family [2]. While providing structural integrity to the NE, the lamina also represents an important signaling and regulatory platform [3]. Two A-type lamin isoforms, lamins A and C (LaA and LaC), are expressed in most adult human cells. Encoded by a single gene, these proteins are largely identical, diverging only in their C-terminal tail domains. By contrast with that of LaC, the unique LaA tail undergoes extensive processing, including farnesylation and endo-proteolysis [4, 5]. However, functional differences between LaA and LaC are still unclear. Compounding this uncertainty, the structure of the lamina remains ill defined. In this study, we used BioID, an in vivo proximity-labeling method to identify differential interactors of A-type lamins [6]. One of these, Tpr, a nuclear pore complex (NPC) protein, is highlighted by its selective association with LaC. By employing superresolution microscopy, we demonstrate that this Tpr association is mirrored in enhanced interaction of LaC with NPCs. Further superresolution studies visualizing both endogenous A- and B-type lamins have allowed us to construct a nanometer-scale model of the mammalian nuclear lamina. Our data indicate that different A- and B-type lamin species assemble into separate filament networks that together form an extended composite structure at the nuclear periphery providing attachment sites for NPCs, thereby regulating their distribution.

  2. Cyclin-dependent kinase complexes in developing maize endosperm: evidence for differential expression and functional specialization.

    PubMed

    Dante, Ricardo A; Sabelli, Paolo A; Nguyen, Hong N; Leiva-Neto, João T; Tao, Yumin; Lowe, Keith S; Hoerster, George J; Gordon-Kamm, William J; Jung, Rudolf; Larkins, Brian A

    2014-02-01

    Endosperm development in maize (Zea mays L.) and related cereals comprises a cell proliferation stage followed by a period of rapid growth coupled to endoreduplication. Regulation of the cell cycle in developing endosperm is poorly understood. We have characterized various subunits of cyclin-dependent kinase (CDK) complexes, master cell cycle regulators in all eukaryotes. A-, B-, and D-type cyclins as well as A- and B-type cyclin-dependent kinases were characterized with respect to their RNA and protein expression profiles. Two main patterns were identified: one showing expression throughout endosperm development, and another characterized by a sharp down-regulation with the onset of endoreduplication. Cyclin CYCB1;3 and CYCD2;1 proteins were distributed in the cytoplasm and nucleus of cells throughout the endosperm, while cyclin CYCD5 protein was localized in the cytoplasm of peripheral cells. CDKB1;1 expression was strongly associated with cell proliferation. Expression and cyclin-binding patterns suggested that CDKA;1 and CDKA;3 are at least partially redundant. The kinase activity associated with the cyclin CYCA1 was highest during the mitotic stage of development, while that associated with CYCB1;3, CYCD2;1 and CYCD5 peaked at the mitosis-to-endoreduplication transition. A-, B- and D-type cyclins were more resistant to proteasome-dependent degradation in endoreduplicating than in mitotic endosperm extracts. These results indicated that endosperm development is characterized by differential expression and activity of specific cyclins and CDKs, and suggested that endoreduplication is associated with reduced cyclin proteolysis via the ubiquitin-proteasome pathway.

  3. Recent Positive Selection in Genes of the Mammalian Epidermal Differentiation Complex Locus

    PubMed Central

    Goodwin, Zane A.; de Guzman Strong, Cristina

    2017-01-01

    The epidermal differentiation complex (EDC) is the most rapidly evolving locus in the human genome compared to that of the chimpanzee. Yet the EDC genes that are undergoing positive selection across mammals and in humans are not known. We sought to identify the positively selected genetic variants and determine the evolutionary events of the EDC using mammalian-wide and clade-specific branch- and branch-site likelihood ratio tests and a genetic algorithm (GA) branch test. Significant non-synonymous substitutions were found in filaggrin, SPRR4, LELP1, and S100A2 genes across 14 mammals. By contrast, we identified recent positive selection in SPRR4 in primates. Additionally, the GA branch test discovered lineage-specific evolution for distinct EDC genes occurring in each of the nodes in the 14-mammal phylogenetic tree. Multiple instances of positive selection for FLG, TCHHL1, SPRR4, LELP1, and S100A2 were noted among the primate branch nodes. Branch-site likelihood ratio tests further revealed positive selection in specific sites in SPRR4, LELP1, filaggrin, and repetin across 14 mammals. However, in addition to continuous evolution of SPRR4, site-specific positive selection was also found in S100A11, KPRP, SPRR1A, S100A7L2, and S100A3 in primates and filaggrin, filaggrin2, and S100A8 in great apes. Very recent human positive selection was identified in the filaggrin2 L41 site that was present in Neanderthal. Together, our results identifying recent positive selection in distinct EDC genes reveal an underappreciated evolution of epidermal skin barrier function in primates and humans. PMID:28119736

  4. Recent Positive Selection in Genes of the Mammalian Epidermal Differentiation Complex Locus.

    PubMed

    Goodwin, Zane A; de Guzman Strong, Cristina

    2016-01-01

    The epidermal differentiation complex (EDC) is the most rapidly evolving locus in the human genome compared to that of the chimpanzee. Yet the EDC genes that are undergoing positive selection across mammals and in humans are not known. We sought to identify the positively selected genetic variants and determine the evolutionary events of the EDC using mammalian-wide and clade-specific branch- and branch-site likelihood ratio tests and a genetic algorithm (GA) branch test. Significant non-synonymous substitutions were found in filaggrin, SPRR4, LELP1, and S100A2 genes across 14 mammals. By contrast, we identified recent positive selection in SPRR4 in primates. Additionally, the GA branch test discovered lineage-specific evolution for distinct EDC genes occurring in each of the nodes in the 14-mammal phylogenetic tree. Multiple instances of positive selection for FLG, TCHHL1, SPRR4, LELP1, and S100A2 were noted among the primate branch nodes. Branch-site likelihood ratio tests further revealed positive selection in specific sites in SPRR4, LELP1, filaggrin, and repetin across 14 mammals. However, in addition to continuous evolution of SPRR4, site-specific positive selection was also found in S100A11, KPRP, SPRR1A, S100A7L2, and S100A3 in primates and filaggrin, filaggrin2, and S100A8 in great apes. Very recent human positive selection was identified in the filaggrin2 L41 site that was present in Neanderthal. Together, our results identifying recent positive selection in distinct EDC genes reveal an underappreciated evolution of epidermal skin barrier function in primates and humans.

  5. Tolerance and autoimmunity to erythroid differentiation (B-G) major histocompatibility complex alloantigens of the chicken

    PubMed Central

    1982-01-01

    Hematopoietic chimeras were produced at four different stages of ontogeny between two allogeneic strains of chickens. All chimeras produced by parabiosis at day 12 of embryogenesis and the majority (83%) of the ones produced at day 15 by intravenous injection of allogeneic stem cells remained healthy, chimeric, and specifically tolerant at both the humoral and cell-mediated level throughout a long examination period. Chimeras generated at day 17 of embryogenesis demonstrated specific unresponsiveness at the cell-mediated level but produced specific anti-donor alloantibodies directed against erythrocyte-associated major histocompatibility complex (MHC) (B-G) antigens. These chimeras and a minority (17%) of the chimeras generated at day 15 of embryogenesis developed severe antibody-mediated autoimmune hemolytic anemia after the 5th mo of age and succumbed to massive bursal lymphomas and metastases by the 10th mo of age. The immunological and pathological characteristics of these birds appear to reflect an autoimmune state rather than one of tolerance. Erythroid chimeras generated at day 21 of ontogenic development displayed normal levels of GVH reactivity. These birds were eventually able to eliminate the chimeric state and remained healthy until deliberately killed. These results show that there is a critical period in embryogenesis during which the induction of allogeneic erythrocytic chimerism leads to the development, in adult life, of severe autoimmune anemia, B cell lymphomas, and death. B-G MHC antigens are erythroid differentiation antigens of the chicken. Polymorphic determinants on B-G antigens appear to be important cross-reactive determinants (with environmental bacteria), against which a high background immunity exists. Evidence is presented that the immune response to B-G antigens is responsible for the development of autoimmunity and other pathological events that follow and that tolerance to class I MHC antigens (B-F antigens) shared by lymphocytes

  6. Differential virulence and disease progression following Mycobacterium tuberculosis complex infection of the common marmoset (Callithrix jacchus).

    PubMed

    Via, Laura E; Weiner, Danielle M; Schimel, Daniel; Lin, Philana Ling; Dayao, Emmanuel; Tankersley, Sarah L; Cai, Ying; Coleman, M Teresa; Tomko, Jaime; Paripati, Praveen; Orandle, Marlene; Kastenmayer, Robin J; Tartakovsky, Michael; Rosenthal, Alexander; Portevin, Damien; Eum, Seok Yong; Lahouar, Saher; Gagneux, Sebastien; Young, Douglas B; Flynn, Joanne L; Barry, Clifton E

    2013-08-01

    Existing small-animal models of tuberculosis (TB) rarely develop cavitary disease, limiting their value for assessing the biology and dynamics of this highly important feature of human disease. To develop a smaller primate model with pathology similar to that seen in humans, we experimentally infected the common marmoset (Callithrix jacchus) with diverse strains of Mycobacterium tuberculosis of various pathogenic potentials. These included recent isolates of the modern Beijing lineage, the Euro-American X lineage, and M. africanum. All three strains produced fulminant disease in this animal with a spectrum of progression rates and clinical sequelae that could be monitored in real time using 2-deoxy-2-[(18)F]fluoro-d-glucose (FDG) positron emission tomography (PET)/computed tomography (CT). Lesion pathology at sacrifice revealed the entire spectrum of lesions observed in human TB patients. The three strains produced different rates of progression to disease, various extents of extrapulmonary dissemination, and various degrees of cavitation. The majority of live births in this species are twins, and comparison of results from siblings with different infecting strains allowed us to establish that the infection was highly reproducible and that the differential virulence of strains was not simply host variation. Quantitative assessment of disease burden by FDG-PET/CT provided an accurate reflection of the pathology findings at necropsy. These results suggest that the marmoset offers an attractive small-animal model of human disease that recapitulates both the complex pathology and spectrum of disease observed in humans infected with various M. tuberculosis strain clades.

  7. Differential Virulence and Disease Progression following Mycobacterium tuberculosis Complex Infection of the Common Marmoset (Callithrix jacchus)

    PubMed Central

    Via, Laura E.; Weiner, Danielle M.; Schimel, Daniel; Lin, Philana Ling; Dayao, Emmanuel; Tankersley, Sarah L.; Cai, Ying; Coleman, M. Teresa; Tomko, Jaime; Paripati, Praveen; Orandle, Marlene; Kastenmayer, Robin J.; Tartakovsky, Michael; Rosenthal, Alexander; Portevin, Damien; Eum, Seok Yong; Lahouar, Saher; Gagneux, Sebastien; Young, Douglas B.; Flynn, JoAnne L.

    2013-01-01

    Existing small-animal models of tuberculosis (TB) rarely develop cavitary disease, limiting their value for assessing the biology and dynamics of this highly important feature of human disease. To develop a smaller primate model with pathology similar to that seen in humans, we experimentally infected the common marmoset (Callithrix jacchus) with diverse strains of Mycobacterium tuberculosis of various pathogenic potentials. These included recent isolates of the modern Beijing lineage, the Euro-American X lineage, and M. africanum. All three strains produced fulminant disease in this animal with a spectrum of progression rates and clinical sequelae that could be monitored in real time using 2-deoxy-2-[18F]fluoro-d-glucose (FDG) positron emission tomography (PET)/computed tomography (CT). Lesion pathology at sacrifice revealed the entire spectrum of lesions observed in human TB patients. The three strains produced different rates of progression to disease, various extents of extrapulmonary dissemination, and various degrees of cavitation. The majority of live births in this species are twins, and comparison of results from siblings with different infecting strains allowed us to establish that the infection was highly reproducible and that the differential virulence of strains was not simply host variation. Quantitative assessment of disease burden by FDG-PET/CT provided an accurate reflection of the pathology findings at necropsy. These results suggest that the marmoset offers an attractive small-animal model of human disease that recapitulates both the complex pathology and spectrum of disease observed in humans infected with various M. tuberculosis strain clades. PMID:23716617

  8. Separating the effects of habitat area, fragmentation and matrix resistance on genetic differentiation in complex landscapes

    Treesearch

    Samuel A. Cushman; Andrew J. Shirk; Erin L. Landguth

    2012-01-01

    Little is known about how variation in landscape mosaics affects genetic differentiation. The goal of this paper is to quantify the relative importance of habitat area and configuration, as well as the contrast in resistance between habitat and non-habitat, on genetic differentiation. We hypothesized that habitat configuration would be more influential than habitat...

  9. Linear ubiquitin chain assembly complex coordinates late thymic T-cell differentiation and regulatory T-cell homeostasis

    PubMed Central

    Teh, Charis E.; Lalaoui, Najoua; Jain, Reema; Policheni, Antonia N.; Heinlein, Melanie; Alvarez-Diaz, Silvia; Sheridan, Julie M.; Rieser, Eva; Deuser, Stefanie; Darding, Maurice; Koay, Hui-Fern; Hu, Yifang; Kupresanin, Fiona; O'Reilly, Lorraine A.; Godfrey, Dale I.; Smyth, Gordon K.; Bouillet, Philippe; Strasser, Andreas; Walczak, Henning; Silke, John; Gray, Daniel H. D.

    2016-01-01

    The linear ubiquitin chain assembly complex (LUBAC) is essential for innate immunity in mice and humans, yet its role in adaptive immunity is unclear. Here we show that the LUBAC components HOIP, HOIL-1 and SHARPIN have essential roles in late thymocyte differentiation, FOXP3+ regulatory T (Treg)-cell development and Treg cell homeostasis. LUBAC activity is not required to prevent TNF-induced apoptosis or necroptosis but is necessary for the transcriptional programme of the penultimate stage of thymocyte differentiation. Treg cell-specific ablation of HOIP causes severe Treg cell deficiency and lethal immune pathology, revealing an ongoing requirement of LUBAC activity for Treg cell homeostasis. These data reveal stage-specific requirements for LUBAC in coordinating the signals required for T-cell differentiation. PMID:27857075

  10. Linear ubiquitin chain assembly complex coordinates late thymic T-cell differentiation and regulatory T-cell homeostasis.

    PubMed

    Teh, Charis E; Lalaoui, Najoua; Jain, Reema; Policheni, Antonia N; Heinlein, Melanie; Alvarez-Diaz, Silvia; Sheridan, Julie M; Rieser, Eva; Deuser, Stefanie; Darding, Maurice; Koay, Hui-Fern; Hu, Yifang; Kupresanin, Fiona; O'Reilly, Lorraine A; Godfrey, Dale I; Smyth, Gordon K; Bouillet, Philippe; Strasser, Andreas; Walczak, Henning; Silke, John; Gray, Daniel H D

    2016-11-18

    The linear ubiquitin chain assembly complex (LUBAC) is essential for innate immunity in mice and humans, yet its role in adaptive immunity is unclear. Here we show that the LUBAC components HOIP, HOIL-1 and SHARPIN have essential roles in late thymocyte differentiation, FOXP3(+) regulatory T (Treg)-cell development and Treg cell homeostasis. LUBAC activity is not required to prevent TNF-induced apoptosis or necroptosis but is necessary for the transcriptional programme of the penultimate stage of thymocyte differentiation. Treg cell-specific ablation of HOIP causes severe Treg cell deficiency and lethal immune pathology, revealing an ongoing requirement of LUBAC activity for Treg cell homeostasis. These data reveal stage-specific requirements for LUBAC in coordinating the signals required for T-cell differentiation.

  11. Identification and Ultrastructural Characterization of a Novel Nuclear Degradation Complex in Differentiating Lens Fiber Cells

    PubMed Central

    Costello, M. Joseph; Brennan, Lisa A.; Gilliland, Kurt O.; Johnsen, Sönke; Kantorow, Marc

    2016-01-01

    An unresolved issue in structural biology is how the encapsulated lens removes membranous organelles to carry out its role as a transparent optical element. In this ultrastructural study, we establish a mechanism for nuclear elimination in the developing chick lens during the formation of the organelle-free zone. Day 12–15 chick embryo lenses were examined by high-resolution confocal light microscopy and thin section transmission electron microscopy (TEM) following fixation in 10% formalin and 4% paraformaldehyde, and then processing for confocal or TEM as described previously. Examination of developing fiber cells revealed normal nuclei with dispersed chromatin and clear nucleoli typical of cells in active ribosome production to support protein synthesis. Early signs of nuclear degradation were observed about 300 μm from the lens capsule in Day 15 lenses where the nuclei display irregular nuclear stain and prominent indentations that sometimes contained a previously undescribed macromolecular aggregate attached to the nuclear envelope. We have termed this novel structure the nuclear excisosome. This complex by confocal is closely adherent to the nuclear envelope and by TEM appears to degrade the outer leaflet of the nuclear envelope, then the inner leaflet up to 500 μm depth. The images suggest that the nuclear excisosome separates nuclear membrane proteins from lipids, which then form multilamellar assemblies that stain intensely in confocal and in TEM have 5 nm spacing consistent with pure lipid bilayers. The denuded nucleoplasm then degrades by condensation and loss of structure in the range 600 to 700 μm depth producing pyknotic nuclear remnants. None of these stages display any classic autophagic vesicles or lysosomes associated with nuclei. Uniquely, the origin of the nuclear excisosome is from filopodial-like projections of adjacent lens fiber cells that initially contact, and then appear to fuse with the outer nuclear membrane. These filopodial

  12. Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae)

    PubMed Central

    Emadzade, Khatere; Jang, Tae-Soo; Macas, Jiří; Kovařík, Ales; Novák, Petr; Parker, John; Weiss-Schneeweiss, Hanna

    2014-01-01

    Background and Aims Chromosomal evolution, including numerical and structural changes, is a major force in plant diversification and speciation. This study addresses genomic changes associated with the extensive chromosomal variation of the Mediterranean Prospero autumnale complex (Hyacinthaceae), which includes four diploid cytotypes each with a unique combination of chromosome number (x = 5, 6, 7), rDNA loci and genome size. Methods A new satellite repeat PaB6 has previously been identified, and monomers were reconstructed from next-generation sequencing (NGS) data of P. autumnale cytotype B6B6 (2n = 12). Monomers of all other Prospero cytotypes and species were sequenced to check for lineage-specific mutations. Copy number, restriction patterns and methylation levels of PaB6 were analysed using Southern blotting. PaB6 was localized on chromosomes using fluorescence in situ hybridization (FISH). Key Results The monomer of PaB6 is 249 bp long, contains several intact and truncated vertebrate-type telomeric repeats and is highly methylated. PaB6 is exceptional because of its high copy number and unprecedented variation among diploid cytotypes, ranging from 104 to 106 copies per 1C. PaB6 is always located in pericentromeric regions of several to all chromosomes. Additionally, two lineages of cytotype B7B7 (x = 7), possessing either a single or duplicated 5S rDNA locus, differ in PaB6 copy number; the ancestral condition of a single locus is associated with higher PaB6 copy numbers. Conclusions Although present in all Prospero species, PaB6 has undergone differential amplification only in chromosomally variable P. autumnale, particularly in cytotypes B6B6 and B5B5. These arose via independent chromosomal fusions from x = 7 to x = 6 and 5, respectively, accompanied by genome size increases. The copy numbers of satellite DNA PaB6 are among the highest in angiosperms, and changes of PaB6 are exceptionally dynamic in this group of closely related cytotypes of a single

  13. Kinetic differentiation between enzyme inactivation involving complex-formation with the inactivator and that involving a conformation-change step.

    PubMed Central

    Liu, C; Tsou, C L

    1992-01-01

    It has been suggested that the complexing type of inactivation in which the inactivator binds reversibly with the enzyme before inactivation cannot be differentiated kinetically from that a slow enzyme conformation change is involved as a first step [Rakitzis (1986) J. Theor. Biol. 122, 247-249]. The kinetics of the substrate reaction during modification of enzyme activity previously described [Tsou (1988) Adv. Enzymol. Relat. Areas Mol. Biol. 61, 381-436] have now been applied to this problem and equations derived to show that the slow-conformational-change type can be differentiated from the complexing type by plotting the final concentration of product formed, [P]infinity, against the reciprocal of inactivator concentration. The reaction of hexokinase with 2-chloromercuri-4-nitrophenol has been shown to involve a conformational change of the enzyme before inactivation. PMID:1546965

  14. Does the mitochondrial transcription-termination complex play an essential role in controlling differential transcription of the mitochondrial DNA?

    PubMed

    Selwood, S P; Chrzanowska-Lightowlers, Z M; Lightowlers, R N

    2000-02-01

    The mechanism of mitochondrial transcription is well documented although the method of regulation remains obscure. The mitochondrial transcription-termination complex, mTERF, holds a key position in determining the fate of heavy-strand promotor-initiated transcripts and has been suggested as a candidate in the regulation of mitochondrial DNA (mtDNA) transcription. We report here the first example of a modulation of mTERF-complex binding activity concomitant with a differential mtDNA transcription rate. We suggest that these observations are indicative of a method of intra-organellar transcriptional fine tuning.

  15. An unusual congenital hepatic cyst in an adolescent and review of differential diagnoses of complex liver cysts

    PubMed Central

    Bryce, Yolanda; Wood, Beverly; Baron, Peter; Gibbs, Liliane

    2008-01-01

    The diagnosis of a simple hepatic cyst is not difficult, but diagnostic confusion occurs when atypical features such as intracystic debris or extremely large size are present. In children, simple liver cysts are described as small, asymptomatic, and rarely hemorrhagic. We report an adolescent male presenting with an unusually large hepatic cyst that did not have typical imaging characteristics. The imaging findings and histology are displayed along with the differential diagnoses of complex liver cysts. PMID:22470600

  16. Differential diagnosis of hyperkalemia: an update to a complex problem

    PubMed Central

    Eleftheriadis, T; Leivaditis, K; Antoniadi, G; Liakopoulos, V

    2012-01-01

    Hyperkalemia is a relative common and sometimes life threatening electorlyte disorder. Although its symptomatic treatment is relatively easy, since precise therapeutic algorithms are available, its differential diagnosis is more complicated. The present review aims to unfold the differential diagnosis of hypekalemia using a pathophysiological, albeit clinically useful, approach. The basic elements of potassium homeostasis are provided, the causes of hyperkalemia are categorized and analysed and finally the required for the diferrential diagnosis laboratory tests are mentioned. PMID:23935306

  17. The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis.

    PubMed

    Gao, Jie; Buckley, Shannon M; Cimmino, Luisa; Guillamot, Maria; Strikoudis, Alexandros; Cang, Yong; Goff, Stephen P; Aifantis, Iannis

    2015-11-27

    Little is known on post-transcriptional regulation of adult and embryonic stem cell maintenance and differentiation. Here we characterize the role of Ddb1, a component of the CUL4-DDB1 ubiquitin ligase complex. Ddb1 is highly expressed in multipotent hematopoietic progenitors and its deletion leads to abrogation of both adult and fetal hematopoiesis, targeting specifically transiently amplifying progenitor subsets. However, Ddb1 deletion in non-dividing lymphocytes has no discernible phenotypes. Ddb1 silencing activates Trp53 pathway and leads to significant effects on cell cycle progression and rapid apoptosis. The abrogation of hematopoietic progenitor cells can be partially rescued by simultaneous deletion of Trp53. Conversely, depletion of DDB1 in embryonic stem cell (ESC) leads to differentiation albeit negative effects on cell cycle and apoptosis. Mass spectrometry reveals differing protein interactions between DDB1 and distinct DCAFs, the substrate recognizing components of the E3 complex, between cell types. Our studies identify CUL4-DDB1 complex as a novel post-translational regulator of stem and progenitor maintenance and differentiation.

  18. The CUL4-DDB1 ubiquitin ligase complex controls adult and embryonic stem cell differentiation and homeostasis

    PubMed Central

    Gao, Jie; Buckley, Shannon M; Cimmino, Luisa; Guillamot, Maria; Strikoudis, Alexandros; Cang, Yong; Goff, Stephen P; Aifantis, Iannis

    2015-01-01

    Little is known on post-transcriptional regulation of adult and embryonic stem cell maintenance and differentiation. Here we characterize the role of Ddb1, a component of the CUL4-DDB1 ubiquitin ligase complex. Ddb1 is highly expressed in multipotent hematopoietic progenitors and its deletion leads to abrogation of both adult and fetal hematopoiesis, targeting specifically transiently amplifying progenitor subsets. However, Ddb1 deletion in non-dividing lymphocytes has no discernible phenotypes. Ddb1 silencing activates Trp53 pathway and leads to significant effects on cell cycle progression and rapid apoptosis. The abrogation of hematopoietic progenitor cells can be partially rescued by simultaneous deletion of Trp53. Conversely, depletion of DDB1 in embryonic stem cell (ESC) leads to differentiation albeit negative effects on cell cycle and apoptosis. Mass spectrometry reveals differing protein interactions between DDB1 and distinct DCAFs, the substrate recognizing components of the E3 complex, between cell types. Our studies identify CUL4-DDB1 complex as a novel post-translational regulator of stem and progenitor maintenance and differentiation. DOI: http://dx.doi.org/10.7554/eLife.07539.001 PMID:26613412

  19. Neuropilin-1 forms complexes with vascular endothelial growth factor receptor-2 during megakaryocytic differentiation of UT-7/TPO cells

    SciTech Connect

    Ohsaka, Akimichi; Hirota-Komatsu, Satoko; Shibata, Miki; Komatsu, Norio

    2009-12-25

    We investigated whether the gene expression of vascular endothelial growth factor (VEGF) and its receptors (VEGFR and neuropilin-1 [NRP-1]) could be specifically regulated during the megakaryocytic differentiation of human thrombopoietin (TPO)-dependent UT-7/TPO cells. Undifferentiated UT-7/TPO cells expressed a functional VEGFR-2, leading to VEGF binding and VEGF{sub 165}-induced tyrosine phosphorylation, cell proliferation, and apoptosis inhibition. The megakaryocytic differentiation of UT-7/TPO cells on treatment with phorbol myristate acetate (PMA) was accompanied by a marked up-regulation of NRP-1 mRNA and protein expression and by an increase in VEGF-binding activity, which was mainly mediated by VEGFR-2. VEGF{sub 165} promoted the formation of complexes containing NRP-1 and VEGFR-2 in undifferentiated UT-7/TPO cells in a dose-dependent manner. Unlike human umbilical vein endothelial cells, PMA-differentiated UT-7/TPO cells exhibited complex formation between NRP-1 and VEGFR-2 even in the absence of VEGF{sub 165}. These findings suggest that NRP-1-VEGFR-2-complex formation may contribute to effective cellular functions mediated by VEGF{sub 165} in megakaryocytic cells.

  20. Complexity and hemispheric abilities: evidence for a differential impact on semantics and phonology.

    PubMed

    Tremblay, Tania; Monetta, Laura; Joanette, Yves

    2009-02-01

    The main goal of this study was to determine whether the phonological and semantic processing of words are similarly influenced by an increase in processing complexity. Thirty-six French-speaking young adults performed both semantic and phonological word judgment tasks, using a divided visual field procedure. The phonological complexity of words was controlled by varying their transparency, while semantic complexity was manipulated through prototypicality. As expected, processing complexity modulated semantic and phonological processing differently. The results revealed that an increase in processing complexity lessened the left-hemisphere advantage in semantics, but reinforced it in phonology. It is therefore suggested that right-hemisphere collaboration in complex language processing is profitable only when the particular kind of processing is not strongly lateralized to the left-hemisphere. The results are discussed from the perspective of interhemispheric collaboration.

  1. Phenotypic differentiation of the Solidago virgaurea complex along an elevational gradient: Insights from a common garden experiment and population genetics.

    PubMed

    Hirano, Masaaki; Sakaguchi, Shota; Takahashi, Koichi

    2017-09-01

    Plant species distributed along wide elevational or latitudinal gradients show phenotypic variation due to their heterogeneous habitats. This study investigated whether phenotypic variation in populations of the Solidago virgaurea complex along an elevational gradient is caused by genetic differentiation. A common garden experiment was based on seeds collected from nine populations of the S. virgaurea complex growing at elevations from 1,597 m to 2,779 m a.s.l. on Mt. Norikura in central Japan. Population genetic analyses with microsatellite markers were used to infer the genetic structure and levels of gene flow between populations. Leaf mass per area was lower, while leaf nitrogen and chlorophyll concentrations were greater for higher elevations at which seeds were originally collected. For reproductive traits, plants derived from higher elevations had larger flower heads on shorter stems and flowering started earlier. These elevational changes in morphology were consistent with the clines in the field, indicating that phenotypic variation along the elevational gradient would have been caused by genetic differentiation. However, population genetic analysis using 16 microsatellite loci suggested an extremely low level of genetic differentiation of neutral genes among the nine populations. Analysis of molecular variance also indicated that most genetic variation was partitioned into individuals within a population, and the genetic differentiation among the populations was not significant. This study suggests that genome regions responsible for adaptive traits may differ among the populations despite the existence of gene flow and that phenotypic variation of the S. virgaurea complex along the elevational gradient is maintained by strong selection pressure.

  2. Complex interplays in immune T-cell differentiation and developmental fate determination.

    PubMed

    Duc, Huynh Thien

    2011-08-01

    Aspects relevant to immune T-cell differentiation and fate determination have been examined and discussed in the context of transcription factors, initiating cytokines in association with cognate antigen activation. It appears that the differentiation optional program, in light of recent results related to genetic as well as epigenetic mechanisms, is not predetermined and irreversibly fixed; rather, there is some degree of flexibility allowing the manipulation of remodeling the already differentiated effector cell subsets/lineages. From the progress obtained it will be possible, in the near future, to tailor and obtain various well-defined and efficient immune effector cell subsets/cell lineages for translational applications in autoimmunity, infectious diseases, graft rejection as well as cancer in safe conditions.

  3. Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

    PubMed Central

    Vijay, Nagarjun; Bossu, Christen M.; Poelstra, Jelmer W.; Weissensteiner, Matthias H.; Suh, Alexander; Kryukov, Alexey P.; Wolf, Jochen B. W.

    2016-01-01

    Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge. PMID:27796282

  4. Hematopoietic Stem Cell Differentiation Regulated by a Single Ubiquitin Ligase: Substrate Complex

    PubMed Central

    Reavie, Linsey; Gatta, Giusy Della; Crusio, Kelly; Aranda-Orgilles, Beatriz; Buckley, Shannon M.; Thompson, Benjamin; Lee, Eugine; Gao, Jie; Bredemeyer, Andrea L.; Helmink, Beth A.; Zavadil, Jiri; Sleckman, Barry P.; Palomero, Teresa; Ferrando, Adolfo; Aifantis, Iannis

    2009-01-01

    Hematopoietic stem cell (HSC) differentiation is regulated by cell-intrinsic and extrinsic cues. In addition to transcriptional regulation, post-translational regulation may also control HSC differentiation. To test this hypothesis, we visualized ubiquitin-regulated protein stability of a single transcription factor, c-Myc. The stability of c-Myc protein was instructive of HSC quiescence and c-Myc protein abundance was controlled by the ubiquitin ligase Fbw7. Fine changes in stability of c-Myc protein regulated the HSC “gene expression signature”. Using whole genome genomic approaches, we identified specific regulators of HSC function that are directly controlled by c-Myc binding, however adult HSCs and embryonic stem cells sense and interpret distinctly c-Myc regulated gene expression. These studies show a ubiquitin ligase substrate pair can orchestrate the molecular program of HSC differentiation. PMID:20081848

  5. Regulation of hematopoietic stem cell differentiation by a single ubiquitin ligase-substrate complex.

    PubMed

    Reavie, Linsey; Della Gatta, Giusy; Crusio, Kelly; Aranda-Orgilles, Beatriz; Buckley, Shannon M; Thompson, Benjamin; Lee, Eugine; Gao, Jie; Bredemeyer, Andrea L; Helmink, Beth A; Zavadil, Jiri; Sleckman, Barry P; Palomero, Teresa; Ferrando, Adolfo; Aifantis, Iannis

    2010-03-01

    Hematopoietic stem cell (HSC) differentiation is regulated by cell-intrinsic and cell-extrinsic cues. In addition to transcriptional regulation, post-translational regulation may also control HSC differentiation. To test this hypothesis, we visualized the ubiquitin-regulated protein stability of a single transcription factor, c-Myc. The stability of c-Myc protein was indicative of HSC quiescence, and c-Myc protein abundance was controlled by the ubiquitin ligase Fbw7. Fine changes in the stability of c-Myc protein regulated the HSC gene-expression signature. Using whole-genome genomic approaches, we identified specific regulators of HSC function directly controlled by c-Myc binding; however, adult HSCs and embryonic stem cells sensed and interpreted c-Myc-regulated gene expression in distinct ways. Our studies show that a ubiquitin ligase-substrate pair can orchestrate the molecular program of HSC differentiation.

  6. Mutations in the Chromosomal Passenger Complex and the Condensin Complex Differentially Affect Synaptonemal Complex Disassembly and Metaphase I Configuration in Drosophila Female Meiosis

    PubMed Central

    Resnick, Tamar D.; Dej, Kimberley J.; Xiang, Youbin; Hawley, R. Scott; Ahn, Caroline; Orr-Weaver, Terry L.

    2009-01-01

    Production of haploid gametes relies on the specially regulated meiotic cell cycle. Analyses of the role of essential mitotic regulators in meiosis have been hampered by a shortage of appropriate alleles in metazoans. We characterized female-sterile alleles of the condensin complex component dcap-g and used them to define roles for condensin in Drosophila female meiosis. In mitosis, the condensin complex is required for sister-chromatid resolution and contributes to chromosome condensation. In meiosis, we demonstrate a role for dcap-g in disassembly of the synaptonemal complex and for proper retention of the chromosomes in a metaphase I-arrested state. The chromosomal passenger complex also is known to have mitotic roles in chromosome condensation and is required in some systems for localization of the condensin complex. We used the QA26 allele of passenger component incenp to investigate the role of the passenger complex in oocyte meiosis. Strikingly, in incenpQA26 mutants maintenance of the synaptonemal complex is disrupted. In contrast to the dcap-g mutants, the incenp mutation leads to a failure of paired homologous chromosomes to biorient, such that bivalents frequently orient toward only one pole in prometaphase and metaphase I. We show that incenp interacts genetically with ord, suggesting an important functional relationship between them in meiotic chromosome dynamics. The dcap-g and incenp mutations cause maternal effect lethality, with embryos from mutant mothers arrested in the initial mitotic divisions. PMID:19104074

  7. Mutations in the chromosomal passenger complex and the condensin complex differentially affect synaptonemal complex disassembly and metaphase I configuration in Drosophila female meiosis.

    PubMed

    Resnick, Tamar D; Dej, Kimberley J; Xiang, Youbin; Hawley, R Scott; Ahn, Caroline; Orr-Weaver, Terry L

    2009-03-01

    Production of haploid gametes relies on the specially regulated meiotic cell cycle. Analyses of the role of essential mitotic regulators in meiosis have been hampered by a shortage of appropriate alleles in metazoans. We characterized female-sterile alleles of the condensin complex component dcap-g and used them to define roles for condensin in Drosophila female meiosis. In mitosis, the condensin complex is required for sister-chromatid resolution and contributes to chromosome condensation. In meiosis, we demonstrate a role for dcap-g in disassembly of the synaptonemal complex and for proper retention of the chromosomes in a metaphase I-arrested state. The chromosomal passenger complex also is known to have mitotic roles in chromosome condensation and is required in some systems for localization of the condensin complex. We used the QA26 allele of passenger component incenp to investigate the role of the passenger complex in oocyte meiosis. Strikingly, in incenp(QA26) mutants maintenance of the synaptonemal complex is disrupted. In contrast to the dcap-g mutants, the incenp mutation leads to a failure of paired homologous chromosomes to biorient, such that bivalents frequently orient toward only one pole in prometaphase and metaphase I. We show that incenp interacts genetically with ord, suggesting an important functional relationship between them in meiotic chromosome dynamics. The dcap-g and incenp mutations cause maternal effect lethality, with embryos from mutant mothers arrested in the initial mitotic divisions.

  8. The complexity of bone architecture: A tool to differentiate bone diseases

    NASA Astrophysics Data System (ADS)

    Saparin, Peter I.; Gowin, Wolfgang; Kurths, Jürgen; Felsenberg, Dieter

    2000-02-01

    We introduce a generalization of symbolic dynamics to analyze two-dimensional objects and propose measures of complexity to quantify the structure of symbol encoded images. This technique is applied to evaluate the architecture of human cancellous bone by analyzing computed tomography images of vertebrae acquired from specimens and in vivo. The pixels of the preprocessed images are encoded using a mixture of static and dynamic encoding. The architecture of encoded cancellous bone is evaluated as a whole using measures of complexity. A set of new parameters are introduced to quantify the different aspects of structure: complexity and degree of disorder of the architecture as a whole, or spatial arrangements of hard or soft elements of the bone separately. It is found that the complexity of the bone structure relates to its density exponentially. Normal bone has a complex ordered structure, while the architecture during the initial stage of bone loss is characterized by lower complexity and a maximal level of disorder. Increased bone loss leads again to ordered structure, however, its complexity is minimal. This phenomenon was observed in a series of osteoporotic specimens as well as in vivo in patients treated with fluor, and hormone replacement therapy. We found that different bone diseases demonstrate distinctive features captured by the measurements of complexity of the bone's structural composition. It is shown that the application of the proposed technique leads to new insights for understanding of the bone's response on medical treatment and provide important additional information for the diagnostics of bone diseases.

  9. Differential susceptibility of mitochondrial complex II to inhibition by oxaloacetate in brain and heart.

    PubMed

    Stepanova, Anna; Shurubor, Yevgeniya; Valsecchi, Federica; Manfredi, Giovanni; Galkin, Alexander

    2016-09-01

    Mitochondrial Complex II is a key mitochondrial enzyme connecting the tricarboxylic acid (TCA) cycle and the electron transport chain. Studies of complex II are clinically important since new roles for this enzyme have recently emerged in cell signalling, cancer biology, immune response and neurodegeneration. Oxaloacetate (OAA) is an intermediate of the TCA cycle and at the same time is an inhibitor of complex II with high affinity (Kd~10(-8)M). Whether or not OAA inhibition of complex II is a physiologically relevant process is a significant, but still controversial topic. We found that complex II from mouse heart and brain tissue has similar affinity to OAA and that only a fraction of the enzyme in isolated mitochondrial membranes (30.2±6.0% and 56.4±5.6% in the heart and brain, respectively) is in the free, active form. Since OAA could bind to complex II during isolation, we established a novel approach to deplete OAA in the homogenates at the early stages of isolation. In heart, this treatment significantly increased the fraction of free enzyme, indicating that OAA binds to complex II during isolation. In brain the OAA-depleting system did not significantly change the amount of free enzyme, indicating that a large fraction of complex II is already in the OAA-bound inactive form. Furthermore, short-term ischemia resulted in a dramatic decline of OAA in tissues, but it did not change the amount of free complex II. Our data show that in brain OAA is an endogenous effector of complex II, potentially capable of modulating the activity of the enzyme.

  10. Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells.

    PubMed

    Koludrovic, Dana; Laurette, Patrick; Strub, Thomas; Keime, Céline; Le Coz, Madeleine; Coassolo, Sebastien; Mengus, Gabrielle; Larue, Lionel; Davidson, Irwin

    2015-10-01

    MIcrophthalmia-associated Transcription Factor (MITF) regulates melanocyte and melanoma physiology. We show that MITF associates the NURF chromatin-remodelling factor in melanoma cells. ShRNA-mediated silencing of the NURF subunit BPTF revealed its essential role in several melanoma cell lines and in untransformed melanocytes in vitro. Comparative RNA-seq shows that MITF and BPTF co-regulate overlapping gene expression programs in cell lines in vitro. Somatic and specific inactivation of Bptf in developing murine melanoblasts in vivo shows that Bptf regulates their proliferation, migration and morphology. Once born, Bptf-mutant mice display premature greying where the second post-natal coat is white. This second coat is normally pigmented by differentiated melanocytes derived from the adult melanocyte stem cell (MSC) population that is stimulated to proliferate and differentiate at anagen. An MSC population is established and maintained throughout the life of the Bptf-mutant mice, but these MSCs are abnormal and at anagen, give rise to reduced numbers of transient amplifying cells (TACs) that do not express melanocyte markers and fail to differentiate into mature melanin producing melanocytes. MSCs display a transcriptionally repressed chromatin state and Bptf is essential for reactivation of the melanocyte gene expression program at anagen, the subsequent normal proliferation of TACs and their differentiation into mature melanocytes.

  11. Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells

    PubMed Central

    Koludrovic, Dana; Laurette, Patrick; Strub, Thomas; Keime, Céline; Le Coz, Madeleine; Coassolo, Sebastien; Mengus, Gabrielle; Larue, Lionel; Davidson, Irwin

    2015-01-01

    MIcrophthalmia-associated Transcription Factor (MITF) regulates melanocyte and melanoma physiology. We show that MITF associates the NURF chromatin-remodelling factor in melanoma cells. ShRNA-mediated silencing of the NURF subunit BPTF revealed its essential role in several melanoma cell lines and in untransformed melanocytes in vitro. Comparative RNA-seq shows that MITF and BPTF co-regulate overlapping gene expression programs in cell lines in vitro. Somatic and specific inactivation of Bptf in developing murine melanoblasts in vivo shows that Bptf regulates their proliferation, migration and morphology. Once born, Bptf-mutant mice display premature greying where the second post-natal coat is white. This second coat is normally pigmented by differentiated melanocytes derived from the adult melanocyte stem cell (MSC) population that is stimulated to proliferate and differentiate at anagen. An MSC population is established and maintained throughout the life of the Bptf-mutant mice, but these MSCs are abnormal and at anagen, give rise to reduced numbers of transient amplifying cells (TACs) that do not express melanocyte markers and fail to differentiate into mature melanin producing melanocytes. MSCs display a transcriptionally repressed chromatin state and Bptf is essential for reactivation of the melanocyte gene expression program at anagen, the subsequent normal proliferation of TACs and their differentiation into mature melanocytes. PMID:26440048

  12. Solving Second-Order Ordinary Differential Equations without Using Complex Numbers

    ERIC Educational Resources Information Center

    Kougias, Ioannis E.

    2009-01-01

    Ordinary differential equations (ODEs) is a subject with a wide range of applications and the need of introducing it to students often arises in the last year of high school, as well as in the early stages of tertiary education. The usual methods of solving second-order ODEs with constant coefficients, among others, rely upon the use of complex…

  13. Solving Second-Order Ordinary Differential Equations without Using Complex Numbers

    ERIC Educational Resources Information Center

    Kougias, Ioannis E.

    2009-01-01

    Ordinary differential equations (ODEs) is a subject with a wide range of applications and the need of introducing it to students often arises in the last year of high school, as well as in the early stages of tertiary education. The usual methods of solving second-order ODEs with constant coefficients, among others, rely upon the use of complex…

  14. Landscape complexity differentially benefits generalist fourth, over specialized third, trophic level natural enemies

    USDA-ARS?s Scientific Manuscript database

    The differential loss of higher trophic levels in the face of natural habitat loss can result in the disruption of important ecosystem services such as pollination and biological control. Landscape- level conservation biological control aims to mitigate these negative impacts by conserving or resto...

  15. Mof-associated complexes have overlapping and unique roles in regulating pluripotency in embryonic stem cells and during differentiation

    PubMed Central

    Ravens, Sarina; Fournier, Marjorie; Ye, Tao; Stierle, Matthieu; Dembele, Doulaye; Chavant, Virginie; Tora, Làszlò

    2014-01-01

    The histone acetyltransferase (HAT) Mof is essential for mouse embryonic stem cell (mESC) pluripotency and early development. Mof is the enzymatic subunit of two different HAT complexes, MSL and NSL. The individual contribution of MSL and NSL to transcription regulation in mESCs is not well understood. Our genome-wide analysis show that i) MSL and NSL bind to specific and common sets of expressed genes, ii) NSL binds exclusively at promoters, iii) while MSL binds in gene bodies. Nsl1 regulates proliferation and cellular homeostasis of mESCs. MSL is the main HAT acetylating H4K16 in mESCs, is enriched at many mESC-specific and bivalent genes. MSL is important to keep a subset of bivalent genes silent in mESCs, while developmental genes require MSL for expression during differentiation. Thus, NSL and MSL HAT complexes differentially regulate specific sets of expressed genes in mESCs and during differentiation. DOI: http://dx.doi.org/10.7554/eLife.02104.001 PMID:24898753

  16. On obtaining spectrally accurate solutions of linear differential equations with complex interfaces using the immersed interface method

    NASA Astrophysics Data System (ADS)

    Ray, Sudipta; Saha, Sandeep

    2016-11-01

    Numerical solution of engineering problems with interfacial discontinuities requires exact implementation of the jump conditions else the accuracy deteriorates significantly; particularly, achieving spectral accuracy has been limited due to complex interface geometry and Gibbs phenomenon. We adopt a novel implementation of the immersed-interface method that satisfies the jump conditions at the interfaces exactly, in conjunction with the Chebyshev-collocation method. We consider solutions to linear second order ordinary and partial differential equations having a discontinuity in their zeroth and first derivatives across an interface traced by a complex curve. The solutions obtained demonstrate the ability of the proposed method to achieve spectral accuracy for discontinuous solutions across tortuous interfaces. The solution methodology is illustrated using two model problems: (i) an ordinary differential equation with jump conditions forced by an infinitely differentiable function, (ii) Poisson's equation having a discontinuous solution across interfaces that are ellipses of varying aspect ratio. The use of more polynomials in the direction of the major axis than the minor axis of the ellipse increases the convergence rate of the solution.

  17. Jmjd2c facilitates the assembly of essential enhancer-protein complexes at the onset of embryonic stem cell differentiation

    PubMed Central

    Harman, Jennifer L.; Karimlou, Donja; Weavers, Lauren; Fritsch, Lauriane; Bou-Kheir, Tony; Bell, Emma; del Valle Torres, Ignacio; Niakan, Kathy K.; Fisher, Cynthia; Joshi, Onkar; Stunnenberg, Hendrik G.; Curry, Edward; Ait-Si-Ali, Slimane; Jørgensen, Helle F.

    2017-01-01

    Jmjd2 H3K9 demethylases cooperate in promoting mouse embryonic stem cell (ESC) identity. However, little is known about their importance at the exit of ESC pluripotency. Here, we reveal that Jmjd2c facilitates this process by stabilising the assembly of mediator-cohesin complexes at lineage-specific enhancers. Functionally, we show that Jmjd2c is required in ESCs to initiate appropriate gene expression programs upon somatic multi-lineage differentiation. In the absence of Jmjd2c, differentiation is stalled at an early post-implantation epiblast-like stage, while Jmjd2c-knockout ESCs remain capable of forming extra-embryonic endoderm derivatives. Dissection of the underlying molecular basis revealed that Jmjd2c is re-distributed to lineage-specific enhancers during ESC priming for differentiation. Interestingly, Jmjd2c-bound enhancers are co-occupied by the H3K9-methyltransferase G9a (also known as Ehmt2), independently of its H3K9-modifying activity. Loss of Jmjd2c abrogates G9a recruitment and further destabilises loading of the mediator and cohesin components Med1 and Smc1a at newly activated and poised enhancers in ESC-derived epiblast-like cells. These findings unveil Jmjd2c and G9a as novel enhancer-associated factors, and implicate Jmjd2c as a molecular scaffold for the assembly of essential enhancer-protein complexes with an impact on timely gene activation. PMID:28087629

  18. Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity.

    PubMed

    Chen, Lu; Bush, Stephen J; Tovar-Corona, Jaime M; Castillo-Morales, Atahualpa; Urrutia, Araxi O

    2014-06-01

    What at the genomic level underlies organism complexity? Although several genomic features have been associated with organism complexity, in the case of alternative splicing, which has long been proposed to explain the variation in complexity, no such link has been established. Here, we analyzed over 39 million expressed sequence tags available for 47 eukaryotic species with fully sequenced genomes to obtain a comparable index of alternative splicing estimates, which corrects for the distorting effect of a variable number of transcripts per species--an important obstacle for comparative studies of alternative splicing. We find that alternative splicing has steadily increased over the last 1,400 My of eukaryotic evolution and is strongly associated with organism complexity, assayed as the number of cell types. Importantly, this association is not explained as a by-product of covariance between alternative splicing with other variables previously linked to complexity including gene content, protein length, proteome disorder, and protein interactivity. In addition, we found no evidence to suggest that the relationship of alternative splicing to cell type number is explained by drift due to reduced N(e) in more complex species. Taken together, our results firmly establish alternative splicing as a significant predictor of organism complexity and are, in principle, consistent with an important role of transcript diversification through alternative splicing as a means of determining a genome's functional information capacity.

  19. Complex I assembly into supercomplexes determines differential mitochondrial ROS production in neurons and astrocytes

    PubMed Central

    Le Douce, Juliette; Logan, Angela; James, Andrew M.; Bonvento, Gilles; Murphy, Michael P.; Bolaños, Juan P.

    2016-01-01

    Neurons depend on oxidative phosphorylation for energy generation, whereas astrocytes do not, a distinctive feature that is essential for neurotransmission and neuronal survival. However, any link between these metabolic differences and the structural organization of the mitochondrial respiratory chain is unknown. Here, we investigated this issue and found that, in neurons, mitochondrial complex I is predominantly assembled into supercomplexes, whereas in astrocytes the abundance of free complex I is higher. The presence of free complex I in astrocytes correlates with the severalfold higher reactive oxygen species (ROS) production by astrocytes compared with neurons. Using a complexomics approach, we found that the complex I subunit NDUFS1 was more abundant in neurons than in astrocytes. Interestingly, NDUFS1 knockdown in neurons decreased the association of complex I into supercomplexes, leading to impaired oxygen consumption and increased mitochondrial ROS. Conversely, overexpression of NDUFS1 in astrocytes promoted complex I incorporation into supercomplexes, decreasing ROS. Thus, complex I assembly into supercomplexes regulates ROS production and may contribute to the bioenergetic differences between neurons and astrocytes. PMID:27799543

  20. Cilium transition zone proteome reveals compartmentalization and differential dynamics of ciliopathy complexes

    PubMed Central

    Moreira-Leite, Flavia; Varga, Vladimir; Gull, Keith

    2016-01-01

    The transition zone (TZ) of eukaryotic cilia and flagella is a structural intermediate between the basal body and the axoneme that regulates ciliary traffic. Mutations in genes encoding TZ proteins (TZPs) cause human inherited diseases (ciliopathies). Here, we use the trypanosome to identify TZ components and localize them to TZ subdomains, showing that the Bardet-Biedl syndrome complex (BBSome) is more distal in the TZ than the Meckel syndrome (MKS) complex. Several of the TZPs identified here have human orthologs. Functional analysis shows essential roles for TZPs in motility, in building the axoneme central pair apparatus and in flagellum biogenesis. Analysis using RNAi and HaloTag fusion protein approaches reveals that most TZPs (including the MKS ciliopathy complex) show long-term stable association with the TZ, whereas the BBSome is dynamic. We propose that some Bardet-Biedl syndrome and MKS pleiotropy may be caused by mutations that impact TZP complex dynamics. PMID:27519801

  1. A complex of iron and nucleic acid catabolites is a signal that triggers differentiation in a freshwater protozoan

    PubMed Central

    Smith-Somerville, Harriett E.; Hardman, John K.; Timkovich, Russell; Ray, William J.; Rose, Karen E.; Ryals, Phillip E.; Gibbons, Sandra H.; Buhse, Howard E.

    2000-01-01

    The polymorphic ciliated protozoan Tetrahymena vorax can undergo differentiation from the microstomal form, which normally feeds on bacteria and other particulate matter, into the macrostomal cell type, which is capable of ingesting prey ciliates. The process is triggered by exposure of the microstome to an inducer contained in stomatin, an exudate of the prey. To establish the identity of the signal, stomatin was fractionated by combinations of cation exchange, HPLC, and TLC, and the fractions were assayed for biological activity. Although no single active fraction of purified inducer was obtained, all fractions with activity contained ferrous iron and the nucleic acid catabolites hypoxanthine (6-oxypurine) and uracil (2,4-dioxopyrimidine), probably in a chelated form. The activity of synthetic complexes containing these three components is equivalent to stomatin. These results indicate a role for ferrous iron and its potential in chelated form to signal differentiation in certain protozoa and, perhaps, in other organisms as well. PMID:10860998

  2. Proteasome involvement in a complex cascade mediating SigT degradation during differentiation of Streptomyces coelicolor.

    PubMed

    Mao, Xu-Ming; Ren, Ni-Ni; Sun, Ning; Wang, Feng; Zhou, Ri-Cheng; Tang, Yi; Li, Yong-Quan

    2014-02-14

    In Streptomyces coelicolor, the ECF sigma factor SigT negatively regulates cell differentiation, and is degraded by ClpP protease in a dual positive feedback manner. Here we further report that the proteasome is required for degradation of SigT, but not for degradation of its anti-sigma factor RstA, and RstA can protect SigT from degradation independent of the proteasome. Meanwhile, deletion of the proteasome showed reduced production of secondary metabolites, and the fermentation medium from wild type could promote SigT degradation. Furthermore, overexpression of redD or actII-orf4 in the proteasome-deficiency mutant resulted in SigT degradation and over-production of both undecylprodigiosin and actinorhodin. Therefore the proteasome is required for SigT degradation by affecting the production of secondary metabolites during cell differentiation.

  3. Differential effects of transforming growth factors on localization of adhesion complex proteins following corneal epithelial cell wounding.

    PubMed

    Gassner, H L; Esco, M; Smithson, M W; Kurpakus, M A

    1997-04-01

    The differential effects of transforming growth factor (TGF) alpha, beta 1 and beta 2 on the de novo localization of heparan sulfate proteoglycan, collagen type VII and laminin-1 to the adhesion complex were analyzed using an in vitro model of corneal epithelial cell wound healing. Bovine corneal explants were maintained in culture media containing either no growth factor or 1, 5, or 10 ng/ml TGF alpha, TGF beta 1 or TGF beta 2. After 24 or 48 hours in culture, cryostat sections of explants were processed for immunofluorescence microscopy using antibodies directed against heparan sulfate proteoglycan, collagen type VII or laminin-1. A comparison of antibody labeling patterns and relative fluorescence intensity of antibody labeling to controls suggested that TGF alpha inhibits the spatial polarization of proteins into the reforming adhesion complex during early stages of wound healing. Both TGF beta 1 and beta 2 enhanced the linear localization of the three proteins to the site of the reforming adhesion complex. However, in our model TGF beta isoforms did not have identical functions. TGF beta 2 accelerated the temporal localization of collagen type VII to the adhesion complex, an effect which was not observed with TGF beta 1. TGF beta, but not TGF alpha, may play an important role in corneal epithelial cell wound healing by accelerating the reformation of the adhesion complex and subsequent epithelial cell-extracellular matrix adhesion.

  4. Genetic diversity and differentiation in Camellia reticulata (Theaceae) polyploid complex revealed by ISSR and ploidy.

    PubMed

    Wang, B-Y; Ruan, Z-Y

    2012-03-06

    Camellia reticulata is a well-known ornamental and oil plant that is endemic to southwest China. This species shows three cell ploidies, i.e., diploidy, tetraploidy and hexaploidy. We made the first investigation of genetic diversity and differentiation of natural populations of C. reticulata, and 114 individuals from 6 populations were sampled. Cytogeography results showed that ploidy is invariable within populations and evenly distributed. A relatively high level of genetic diversity was found in C. reticulata, both at the species level (PPB = 88.89%; H = 0.2809; I = 0.4278) and at the population level (mean PPB = 42.13%; mean H = 0.14; mean I = 0.21). We found a relatively low degree of differentiation among ploidies (G(ST) = 0.2384; AMOVA = 10.26%) and a relatively high degree of differentiation among populations (G(CS) = 0.3807; AMOVA = 48.75%). The high genetic diversity can be explained by its biological character, wide distribution and ploidies, and the special genetic structure can be ascribed to polyploid origin from hybridization with different Camellia spp. This information will be useful for the introduction, conservation and further studies of C. reticulata and related species.

  5. [Value of aVR lead four steps algorithm on differential diagnosis of wide QRS complex tachycardia].

    PubMed

    Lin, Tao; Ma, Yi-tong; Muhu, Yati; Tang, Bao-peng; Hou, Yue-mei; Zhang, Yan-yi

    2011-01-01

    The aVR lead four steps is a new algorithm for differential diagnosis of wide QRS complex tachycardia (WCT). The study explores the clinical value of this new algorithm on differential diagnosis of WCT. Application of aVR lead four steps to analysis the electrocardiogram of patients with WCT proved by electrophysiological study. Every step's accuracy rate, sensitivity and specificity to differential diagnosis of ventricular tachycardia (VT) were calculated. The first step diagnosed VT according to presence of an initial R wave in the aVR lead. The second step diagnosed VT according to width of an initial r or q wave > 40 ms in the aVR lead. The third step diagnosed VT according to notching on the initial downstroke of a predominantly negative QRS complex in the aVR lead. The fourth step diagnosis VT according to ventricular activation-velocity ratio (Vi/Vt) in the aVR lead, Vi/Vt ≤ 1 suggested VT. Results derived from aVR lead four steps algorithm were compared with results derived from Brugada and Vereckei four steps algorithm. A total of 113 patients with WCT were analyzed (31 supraventricular tachycardia, SVT and 82 ventricular tachycardia, VT). The accuracy rate of differential diagnosis VT is 91.2%, sensitivity is 90.2% and specificity is 77.4%. The accuracy and sensitivity of the aVR lead four steps algorithm for differential diagnosis of WCT were superior to the Brugada Vereckei four steps algorithm (P < 0.05). The specificity of the Vereckei four steps algorithm was superior to aVR lead and Brugada four steps algorithm (P < 0.05), while the specificity of the aVR lead four steps algorithm was similar as Brugada four steps algorithm (P > 0.05). The aVR lead four steps algorithm is associated with excellent accuracy rate, sensitivity for differential diagnosis of WCT. This algorithm is simple and could be easily learned and applied by physician.

  6. Three RNA binding proteins form a complex to promote differentiation of germline stem cell lineage in Drosophila.

    PubMed

    Chen, Di; Wu, Chan; Zhao, Shaowei; Geng, Qing; Gao, Yu; Li, Xin; Zhang, Yang; Wang, Zhaohui

    2014-11-01

    In regenerative tissues, one of the strategies to protect stem cells from genetic aberrations, potentially caused by frequent cell division, is to transiently expand the stem cell daughters before further differentiation. However, failure to exit the transit amplification may lead to overgrowth, and the molecular mechanism governing this regulation remains vague. In a Drosophila mutagenesis screen for factors involved in the regulation of germline stem cell (GSC) lineage, we isolated a mutation in the gene CG32364, which encodes a putative RNA-binding protein (RBP) and is designated as tumorous testis (tut). In tut mutant, spermatogonia fail to differentiate and over-amplify, a phenotype similar to that in mei-P26 mutant. Mei-P26 is a TRIM-NHL tumor suppressor homolog required for the differentiation of GSC lineage. We found that Tut binds preferentially a long isoform of mei-P26 3'UTR, and is essential for the translational repression of mei-P26 reporter. Bam and Bgcn are both RBPs that have also been shown to repress mei-P26 expression. Our genetic analyses indicate that tut, bam, or bgcn is required to repress mei-P26 and to promote the differentiation of GSCs. Biochemically, we demonstrate that Tut, Bam, and Bgcn can form a physical complex in which Bam holds Tut on its N-terminus and Bgcn on its C-terminus. Our in vivo and in vitro evidence illustrate that Tut acts with Bam, Bgcn to accurately coordinate proliferation and differentiation in Drosophila germline stem cell lineage.

  7. Three RNA Binding Proteins Form a Complex to Promote Differentiation of Germline Stem Cell Lineage in Drosophila

    PubMed Central

    Zhao, Shaowei; Geng, Qing; Gao, Yu; Li, Xin; Zhang, Yang; Wang, Zhaohui

    2014-01-01

    In regenerative tissues, one of the strategies to protect stem cells from genetic aberrations, potentially caused by frequent cell division, is to transiently expand the stem cell daughters before further differentiation. However, failure to exit the transit amplification may lead to overgrowth, and the molecular mechanism governing this regulation remains vague. In a Drosophila mutagenesis screen for factors involved in the regulation of germline stem cell (GSC) lineage, we isolated a mutation in the gene CG32364, which encodes a putative RNA-binding protein (RBP) and is designated as tumorous testis (tut). In tut mutant, spermatogonia fail to differentiate and over-amplify, a phenotype similar to that in mei-P26 mutant. Mei-P26 is a TRIM-NHL tumor suppressor homolog required for the differentiation of GSC lineage. We found that Tut binds preferentially a long isoform of mei-P26 3′UTR, and is essential for the translational repression of mei-P26 reporter. Bam and Bgcn are both RBPs that have also been shown to repress mei-P26 expression. Our genetic analyses indicate that tut, bam, or bgcn is required to repress mei-P26 and to promote the differentiation of GSCs. Biochemically, we demonstrate that Tut, Bam, and Bgcn can form a physical complex in which Bam holds Tut on its N-terminus and Bgcn on its C-terminus. Our in vivo and in vitro evidence illustrate that Tut acts with Bam, Bgcn to accurately coordinate proliferation and differentiation in Drosophila germline stem cell lineage. PMID:25412508

  8. DIFFERENTIATION OF THE JUNCTIONAL COMPLEX OF SURFACE CELLS IN THE DEVELOPING FUNDULUS BLASTODERM

    PubMed Central

    Lentz, Thomas L.; Trinkaus, J. P.

    1971-01-01

    The structure of the junctional complex between surface cells was investigated in blastula, mid gastrula, late gastrula, and early embryo of the teleost fish Fundulus heteroclitus. In blastulae, the intercellular complex is simple and consists of an apical region where the adjacent membranes are closely apposed (40–60 A) and in places touch, an intermediate zone with a wider intercellular space (> 100 A), and incipient desmosomes. In gastrulae, there are frequent points of fusion of membranes along the apical zone of the complex. Dilatations and an increased number of desmosomes in different stages of development are found along the intermediate zone. In mid gastrula, a close or gap junction with an intercellular space of 20 A occurs below the level of the desmosomes. In late gastrula, the gap junction is reduced in extent and desmosomes are better developed. In the early embryo, the basic organization of the complex is the same, although the deeply situated close junctions are no longer apparent and desmosomes and their associated system of filaments are well developed. At this time, the junctional complex is comparable to that of many epithelia and consists of an apical zonula occludens, a short zonula adherens, and deeply situated maculae adherentes. PMID:5545331

  9. Differential evolution based on the node degree of its complex network: Initial study

    NASA Astrophysics Data System (ADS)

    Skanderova, Lenka; Zelinka, Ivan

    2016-06-01

    In this paper is reported our progress in the synthesis of two partially different areas of research: complex networks and evolutionary computation. Ideas and results reported and mentioned here are based on our previous results and experiments. The main core of our participation is an evolutionary algorithm performance improvement by means of complex network use. Complex network is related to the evolutionary dynamics and reflect it. We report here our latest results as well as propositions on further research that is in process in our group (http://navy.cs.vsb.cz/). Only the main ideas and results are reported here, for more details it is recommended to read related literature of our previous research and results.

  10. A (Not Really) Complex Method for Finding Solutions to Linear Differential Equations. Modules and Monographs in Undergraduate Mathematics and Its Applications Project. UMAP Unit 497.

    ERIC Educational Resources Information Center

    Uebelacker, James W.

    This module considers ordinary linear differential equations with constant coefficients. The "complex method" used to find solutions is discussed, with numerous examples. The unit includes both problem sets and an exam, with answers provided for both. (MP)

  11. Bound anions differentially stabilize multiprotein complexes in the absence of bulk solvent.

    PubMed

    Han, Linjie; Hyung, Suk-Joon; Mayers, Jonathan J S; Ruotolo, Brandon T

    2011-07-27

    The combination of ion mobility separation with mass spectrometry is an emergent and powerful structural biology tool, capable of simultaneously assessing the structure, topology, dynamics, and composition of large protein assemblies within complex mixtures. An integral part of the ion mobility-mass spectrometry measurement is the ionization of intact multiprotein complexes and their removal from bulk solvent. This process, during which a substantial portion of protein structure and organization is likely to be preserved, imposes a foreign environment on proteins that may cause structural rearrangements to occur. Thus, a general means must be identified to stabilize protein structures in the absence of bulk solvent. Our approach to this problem involves the protection of protein complex structure through the addition of salts in solution prior to desorption/ionization. Anionic components of the added salts bind to the complex either in solution or during the electrospray process, and those that remain bound in the gas phase tend to have high gas phase acidities. The resulting 'shell' of counterions is able to carry away excess energy from the protein complex ion upon activation and can result in significant structural stabilization of the gas-phase protein assembly overall. By using ion mobility-mass spectrometry, we observe both the dissociation and unfolding transitions for four tetrameric protein complexes bound to populations of 12 different anions using collisional activation. The data presented here quantifies, for the first time, the influence of a large range of counterions on gas-phase protein structure and allows us to rank and classify counterions as structure stabilizers in the absence of bulk solvent. Our measurements indicate that tartrate, citrate, chloride, and nitrate anions are among the strongest stabilizers of gas-phase protein structure identified in this screen. The rank order determined by our data is substantially different when compared to

  12. Writing Development in Four Genres from Grades Three to Seven: Syntactic Complexity and Genre Differentiation

    ERIC Educational Resources Information Center

    Beers, Scott F.; Nagy, William E.

    2011-01-01

    Two measures of syntactic complexity, clauses per T-unit and words per clause, were used to examine differences among four genres of text--narrative, descriptive, compare/contrast, and persuasive--written by the same two cohorts (83 students in grades three and five and 96 students in grades five and seven) on two occasions 2 years apart as part…

  13. Differential regulation of adhesion complex turnover by ROCK1 and ROCK2.

    PubMed

    Lock, Frances E; Ryan, Katie R; Poulter, Natalie S; Parsons, Maddy; Hotchin, Neil A

    2012-01-01

    ROCK1 and ROCK2 are serine/threonine kinases that function downstream of the small GTP-binding protein RhoA. Rho signalling via ROCK regulates a number of cellular functions including organisation of the actin cytoskeleton, cell adhesion and cell migration. In this study we use RNAi to specifically knockdown ROCK1 and ROCK2 and analyse their role in assembly of adhesion complexes in human epidermal keratinocytes. We observe that loss of ROCK1 inhibits signalling via focal adhesion kinase resulting in a failure of immature adhesion complexes to form mature stable focal adhesions. In contrast, loss of ROCK2 expression results in a significant reduction in adhesion complex turnover leading to formation of large, stable focal adhesions. Interestingly, loss of either ROCK1 or ROCK2 expression significantly impairs cell migration indicating both ROCK isoforms are required for normal keratinocyte migration. ROCK1 and ROCK2 have distinct and separate roles in adhesion complex assembly and turnover in human epidermal keratinocytes.

  14. Differential Disadvantage of Anglophone Weak Readers Due to English Orthographic Complexity and Cognitive Processing Weakness

    ERIC Educational Resources Information Center

    Galletly, Susan A.; Knight, Bruce Allen

    2011-01-01

    The highly regular orthographies (spelling systems) of many nations expedite literacy development, and their children experience a rapid transition from early literacy (learning to read and write) to sophisticated literacy (reading and writing to learn). In contrast, English orthographic complexity impedes literacy development, particularly for…

  15. Writing Development in Four Genres from Grades Three to Seven: Syntactic Complexity and Genre Differentiation

    ERIC Educational Resources Information Center

    Beers, Scott F.; Nagy, William E.

    2011-01-01

    Two measures of syntactic complexity, clauses per T-unit and words per clause, were used to examine differences among four genres of text--narrative, descriptive, compare/contrast, and persuasive--written by the same two cohorts (83 students in grades three and five and 96 students in grades five and seven) on two occasions 2 years apart as part…

  16. Differential proteomic profiling unveils new molecular mechanisms associated with mitochondrial complex III deficiency

    PubMed Central

    Morán, María; López-Bernardo, Elia; Cadenas, Susana; Hidalgo, Beatriz; Sánchez, Ricardo; Seneca, Sara; Arenas, Joaquín; Martín, Miguel A.; Ugalde, Cristina

    2014-01-01

    We have analyzed the cellular pathways and metabolic adaptations that take place in primary skin fibroblasts from patients with mutations in BCS1L, a major genetic cause of mitochondrial complex III enzyme deficiency. Mutant fibroblasts exhibited low oxygen consumption rates and intracellular ATP levels, indicating that the main altered molecular event probably is a limited respiration-coupled ATP production through the OXPHOS system. Two-dimensional DIGE and MALDI-TOF/TOF mass spectrometry analyses unambiguously identified 39 proteins whose expression was significantly altered in complex III-deficient fibroblasts. Extensive statistical and cluster analyses revealed a protein profile characteristic for the BCS1L mutant fibroblasts that included alterations in energy metabolism, cell signaling and gene expression regulation, cytoskeleton formation and maintenance, and intracellular stress responses. The physiological validation of the predicted functional adaptations of human cultured fibroblasts to complex III deficiency confirmed the up-regulation of glycolytic enzyme activities and the accumulation of branched-chain among other amino acids, suggesting the activation of anaerobic glycolysis and cellular catabolic states, in particular protein catabolism, together with autophagy as adaptive responses to mitochondrial respiratory chain dysfunction and ATP deficiency. Our data point to an overall metabolic and genetic reprogramming that could contribute to explain the clinical manifestations of complex III deficiency in patients. PMID:25239759

  17. Differential Relations between Facets of Complex Problem Solving and Students' Immigration Background

    ERIC Educational Resources Information Center

    Sonnleitner, Philipp; Brunner, Martin; Keller, Ulrich; Martin, Romain

    2014-01-01

    Whereas the assessment of complex problem solving (CPS) has received increasing attention in the context of international large-scale assessments, its fairness in regard to students' cultural background has gone largely unexplored. On the basis of a student sample of 9th-graders (N = 299), including a representative number of immigrant students (N…

  18. Differential triazole sensitivity among members of the Fusarium graminearum species complex infecting barley grains in Brazil

    USDA-ARS?s Scientific Manuscript database

    Fusarium head blight (FHB) is an important disease of small grains and is caused mainly by members of the Fusarium graminearum species complex (FGSC). Barley growers in Brazil rely on fungicides, especially triazoles, to suppress the disease and limit mycotoxin contamination of grain. Information on...

  19. Differential Relations between Facets of Complex Problem Solving and Students' Immigration Background

    ERIC Educational Resources Information Center

    Sonnleitner, Philipp; Brunner, Martin; Keller, Ulrich; Martin, Romain

    2014-01-01

    Whereas the assessment of complex problem solving (CPS) has received increasing attention in the context of international large-scale assessments, its fairness in regard to students' cultural background has gone largely unexplored. On the basis of a student sample of 9th-graders (N = 299), including a representative number of immigrant students (N…

  20. Differential response of continental stock complexes of Atlantic salmon (Salmo salar) to the Atlantic Multidecadal Oscillation

    NASA Astrophysics Data System (ADS)

    Friedland, Kevin D.; Shank, Burton V.; Todd, Christopher D.; McGinnity, Philip; Nye, Janet A.

    2014-05-01

    Atlantic salmon, Salmo salar, in the North Atlantic are managed as a set of population complexes distributed in North America and Europe. In recent years, these complexes have experienced reduced marine survival and many populations within the complexes are at risk, especially those at the southern ends of the species amphi-Atlantic range. Atlantic salmon is an anadromous fish dividing its life history between residence in freshwater and the marine environment. The freshwater portion of the life history includes spawning and the rearing of juveniles where in-river production has tended to be relatively stable, whereas the first year at sea, termed the post-smolt year, is characterized by more variable rates of mortality. Although their habitats are widely separated geographically along the North Atlantic seaboards, strong recruitment coherence exists between North American and European stock complexes. This recruitment coherence is correlated with ocean temperature variation associated with the Atlantic Multidecadal Oscillation (AMO). The North Atlantic Oscillation (NAO) appears to be relatively unimportant as a driver of salmon abundance. The mechanism determining the link between AMO-related thermal variation and abundance appears to differ fundamentally for the two continental stock groupings. Whereas ocean climate variability during the first springtime months of juvenile salmon migration to sea appears to be important to the survival of North American stocks, summer climate variation appears to be central to adult recruitment variation for European stocks. This contrast in seasonal effects appears to be related to the varying roles of predation pressure and size-related mortality on the continental stock complexes. The anticipated warming due to global climate change will impose thermal conditions on salmon populations outside historical context and challenge the ability of many populations to persist.

  1. Differential expression in normal-adenoma-carcinoma sequence suggests complex molecular carcinogenesis in colon.

    PubMed

    Lee, Seungkoo; Bang, Seunghyun; Song, Kyuyoung; Lee, Inchul

    2006-10-01

    The majority of colon cancers develop from pre-existing adenomas. We analyzed the expression profiles in the sequence of normal colon crypts, adenomas and early-stage carcinomas using microdissected cells from tubular adenomas with foci of malignant transformation. Differentially expressed genes were detected between normal-adenoma and adenoma-carcinoma, and were grouped according to the patterns of expression changes in the sequence. Down-regulated genes in the sequence included PLA2G2A, TSPAN1, PDCD4, FCGBP, AATK, EPLIN, FABP1, AGR2, MTUS1, TSC1, galectin 4 and MT1F. PLA2G2A has been shown to suppress colon tumorigenesis in mice, but the pathobiological role in humans has been controversial. Our data showed continuous down-regulation of PLA2G2A in the sequence supporting an implication in human colon cancer. Tumor suppressor and/ or proapoptotic activities have also been reported in other genes. Up-regulated genes included ribosomal proteins, IER3 and TPR. TGF-beta2 and matrix metalloproteinase 23B were up-regulated in carcinoma but not in adenoma, supporting the pathobiological roles in malignant transformation. Differentially expressed genes partly coincided with those in the adenoma-carcinoma sequence of the stomach, which was published previously, suggesting a partial overlap between the adenoma-carcinoma sequences of the colon and stomach.

  2. Genetic evidence for complexity in ethnic differentiation and history in East Africa.

    PubMed

    Poloni, Estella S; Naciri, Yamama; Bucho, Rute; Niba, Régine; Kervaire, Barbara; Excoffier, Laurent; Langaney, André; Sanchez-Mazas, Alicia

    2009-11-01

    The Afro-Asiatic and Nilo-Saharan language families come into contact in Western Ethiopia. Ethnic diversity is particularly high in the South, where the Nilo-Saharan Nyangatom and the Afro-Asiatic Daasanach dwell. Despite their linguistic differentiation, both populations rely on a similar agripastoralist mode of subsistence. Analysis of mitochondrial DNA extracted from Nyangatom and Daasanach archival sera revealed high levels of diversity, with most sequences belonging to the L haplogroups, the basal branches of the mitochondrial phylogeny. However, in sharp contrast with other Ethiopian populations, only 5% of the Nyangatom and Daasanach sequences belong to haplogroups M and N. The Nyangatom and Daasanach were found to be significantly differentiated, while each of them displays close affinities with some Tanzanian populations. The strong genetic structure found over East Africa was neither associated with geography nor with language, a result confirmed by the analysis of 6711 HVS-I sequences of 136 populations mainly from Africa. Processes of migration, language shift and group absorption are documented by linguists and ethnographers for the Nyangatom and Daasanach, thus pointing to the probably transient and plastic nature of these ethnic groups. These processes, associated with periods of isolation, could explain the high diversity and strong genetic structure found in East Africa.

  3. Differential mobility of pigment-protein complexes in granal and agranal thylakoid membranes of C₃ and C₄ plants.

    PubMed

    Kirchhoff, Helmut; Sharpe, Richard M; Herbstova, Miroslava; Yarbrough, Robert; Edwards, Gerald E

    2013-01-01

    The photosynthetic performance of plants is crucially dependent on the mobility of the molecular complexes that catalyze the conversion of sunlight to metabolic energy equivalents in the thylakoid membrane network inside chloroplasts. The role of the extensive folding of thylakoid membranes leading to structural differentiation into stacked grana regions and unstacked stroma lamellae for diffusion-based processes of the photosynthetic machinery is poorly understood. This study examines, to our knowledge for the first time, the mobility of photosynthetic pigment-protein complexes in unstacked thylakoid regions in the C₃ plant Arabidopsis (Arabidopsis thaliana) and agranal bundle sheath chloroplasts of the C₄ plants sorghum (Sorghum bicolor) and maize (Zea mays) by the fluorescence recovery after photobleaching technique. In unstacked thylakoid membranes, more than 50% of the protein complexes are mobile, whereas this number drops to about 20% in stacked grana regions. The higher molecular mobility in unstacked thylakoid regions is explained by a lower protein-packing density compared with stacked grana regions. It is postulated that thylakoid membrane stacking to form grana leads to protein crowding that impedes lateral diffusion processes but is required for efficient light harvesting of the modularly organized photosystem II and its light-harvesting antenna system. In contrast, the arrangement of the photosystem I light-harvesting complex I in separate units in unstacked thylakoid membranes does not require dense protein packing, which is advantageous for protein diffusion.

  4. Macroorganization of Chlorophyll a/b light-harvesting complex in thylakoids and aggregates: information from circular differential scattering

    SciTech Connect

    Garab, G.; Faludi-Daniel, A.; Sutherland, J.C.; Hind, G.

    1988-04-05

    Circular dichroism (CD) and magnetic circular dichroism (MCD) spectra were recorded for spinach thylakoids and for isolated, aggregated chlorophyll a/b light-harvesting pigment-protein complex, in random and magnetically aligned states of orientation at room and low temperatures. The shape and magnitude of the CD signal of most bands strongly depended on the orientation of the thylakoid membranes or the aggregated pigment-protein complex. In both thylakoids and aggregated light-harvesting complexes, however, the MCD spectra of the two different orientations were almost identical. Random and magnetically aligned samples exhibited anomalous, large CD signals outside the bands of pigment absorbance. Lack of similarity between the corresponding MCD and CD spectra showed that the large CD signals are not produced as a distortion of CD of absorbance by light scattering. Instead, these anomalous spectral features are believed to originate in differential selective scattering of circularly polarized light. The results lead to the conclusion that the light-harvesting pigment-protein complex in thylakoid grana forms a helical macroarray with dimensions commensurate with the wavelengths of the anomalous circular dichroism signals. A hypothesis is put forward suggesting a role for these macrodomains in granal organization.

  5. G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation.

    PubMed

    Ruijtenberg, Suzan; van den Heuvel, Sander

    2015-07-16

    The transition from proliferating precursor cells to post-mitotic differentiated cells is crucial for development, tissue homeostasis, and tumor suppression. To study cell-cycle exit during differentiation in vivo, we developed a conditional knockout and lineage-tracing system for Caenorhabditis elegans. Combined lineage-specific gene inactivation and genetic screening revealed extensive redundancies between previously identified cell-cycle inhibitors and the SWI/SNF chromatin-remodeling complex. Muscle precursor cells missing either SWI/SNF or G1/S inhibitor function could still arrest cell division, while simultaneous inactivation of these regulators caused continued proliferation and a C. elegans tumor phenotype. Further genetic analyses support that SWI/SNF acts in concert with hlh-1 MyoD, antagonizes Polycomb-mediated transcriptional repression, and suppresses cye-1 Cyclin E transcription to arrest cell division of muscle precursors. Thus, SWI/SNF and G1/S inhibitors provide alternative mechanisms to arrest cell-cycle progression during terminal differentiation, which offers insight into the frequent mutation of SWI/SNF genes in human cancers.

  6. Improvement of MALDI-TOF MS profiling for the differentiation of species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex.

    PubMed

    Šedo, Ondrej; Nemec, Alexandr; Křížová, Lenka; Kačalová, Magdaléna; Zdráhal, Zbyněk

    2013-12-01

    MALDI-TOF MS is currently becoming the method of choice for rapid identification of bacterial species in routine diagnostics. Yet, this method suffers from the inability to differentiate reliably between some closely related bacterial species including those of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, namely A. baumannii and Acinetobacter nosocomialis. In the present study, we evaluated a protocol which was different from that used in the Bruker Daltonics identification system (MALDI BioTyper) to improve species identification using a taxonomically precisely defined set of 105 strains representing the four validly named species of the ACB complex. The novel protocol is based on the change in matrix composition from alpha-cyano-4-hydroxycinnamic acid (saturated solution in water:acetonitrile:trifluoroacetic acid, 47.5:50:2.5, v/v) to ferulic acid (12.5mgml(-1) solution in water:acetonitrile:formic acid 50:33:17, v/v), while the other steps of sample processing remain unchanged. Compared to the standard protocol, the novel one extended the range of detected compounds towards higher molecular weight, produced signals with better mass resolution, and allowed the detection of species-specific signals. As a result, differentiation of A. nosocomialis and A. baumannii strains by cluster analysis was improved and 13 A. nosocomialis strains, assigned erroneously or ambiguously by using the standard protocol, were correctly identified.

  7. Self-Complexity and Self-Concept Differentiation - What Have We Been Measuring for the Past 30 Years?

    PubMed

    Pilarska, Aleksandra; Suchańska, Anna

    Research on the relation between the structure of the self-concept and psychological well-being has yielded seemingly inconsistent and even conflicting results. This article presents studies that examined the validity of often-used measures of self-complexity and self-concept differentiation and tested their ability to predict personal identity and active cognitive processing. The findings revealed several conceptual and methodological problems that continue to plague self-structure research, including the conflating of self-concept content and self-concept structure. In short, our data indicated that the commonly used indices of self-complexity and self-concept differentiation cannot be considered pure measures of the underlying dimensions of self-structure. In addition, only weak correlations of the self-structure variables with measures of personal identity and thinking dispositions have been found. Moreover, once the theoretically irrelevant sources of variance were controlled, the effects of the included structural features of the self-concept on the outcomes of interest either did not occur or were less pronounced. Given the above, it seems reasonable to suggest that at least some of the conclusions regarding the adaptive value of self-structural variables drawn from previous research in this field need revision.

  8. PCR-based Methodologies Used to Detect and Differentiate the Burkholderia pseudomallei complex: B. pseudomallei, B. mallei, and B. thailandensis.

    PubMed

    Lowe, Woan; March, Jordon K; Bunnell, Annette J; O'Neill, Kim L; Robison, Richard A

    2014-01-01

    Methods for the rapid detection and differentiation of the Burkholderia pseudomallei complex comprising B. pseudomallei, B. mallei, and B. thailandensis, have been the topic of recent research due to the high degree of phenotypic and genotypic similarities of these species. B. pseudomallei and B. mallei are recognized by the CDC as tier 1 select agents. The high mortality rates of glanders and melioidosis, their potential use as bioweapons, and their low infectious dose, necessitate the need for rapid and accurate detection methods. Although B. thailandensis is generally avirulent in mammals, this species displays very similar phenotypic characteristics to that of B. pseudomallei. Optimal identification of these species remains problematic, due to the difficulty in developing a sensitive, selective, and accurate assay. The development of PCR technologies has revolutionized diagnostic testing and these detection methods have become popular due to their speed, sensitivity, and accuracy. The purpose of this review is to provide a comprehensive overview and evaluation of the advancements in PCR-based detection and differentiation methodologies for the B. pseudomallei complex, and examine their potential uses in diagnostic and environmental testing.

  9. Optimization of complex slater-type functions with analytic derivative methods for describing photoionization differential cross sections.

    PubMed

    Matsuzaki, Rei; Yabushita, Satoshi

    2017-05-05

    The complex basis function (CBF) method applied to various atomic and molecular photoionization problems can be interpreted as an L2 method to solve the driven-type (inhomogeneous) Schrödinger equation, whose driven term being dipole operator times the initial state wave function. However, efficient basis functions for representing the solution have not fully been studied. Moreover, the relation between their solution and that of the ordinary Schrödinger equation has been unclear. For these reasons, most previous applications have been limited to total cross sections. To examine the applicability of the CBF method to differential cross sections and asymmetry parameters, we show that the complex valued solution to the driven-type Schrödinger equation can be variationally obtained by optimizing the complex trial functions for the frequency dependent polarizability. In the test calculations made for the hydrogen photoionization problem with five or six complex Slater-type orbitals (cSTOs), their complex valued expansion coefficients and the orbital exponents have been optimized with the analytic derivative method. Both the real and imaginary parts of the solution have been obtained accurately in a wide region covering typical molecular regions. Their phase shifts and asymmetry parameters are successfully obtained by extrapolating the CBF solution from the inner matching region to the asymptotic region using WKB method. The distribution of the optimized orbital exponents in the complex plane is explained based on the close connection between the CBF method and the driven-type equation method. The obtained information is essential to constructing the appropriate basis sets in future molecular applications. © 2017 Wiley Periodicals, Inc.

  10. Comparative study of differential matrix and extended polar decomposition formalisms for polarimetric characterization of complex tissue-like turbid media.

    PubMed

    Kumar, Satish; Purwar, Harsh; Ossikovski, Razvigor; Vitkin, I Alex; Ghosh, Nirmalya

    2012-10-01

    Development of methodologies for quantification/unique interpretation of the intrinsic polarimetry characteristics of biological tissues are important for various applications involving tissue characterization/diagnosis. A detailed comparative evaluation of the polar decomposition and the differential matrix decomposition of Mueller matrices for extraction/quantification of the intrinsic polarimetry characteristics (with special emphasis on linear retardance δ, optical rotation Ψ and depolarization Δ parameters was performed, because these are the most prominent tissue polarimetry effects) from complex tissue-like turbid media exhibiting simultaneous scattering and polarization effects. The results suggest that for media exhibiting simultaneous linear retardance and optical rotation polarization events, the use of retarder polar decomposition with its associated analysis which assumes sequential occurrence of these effects, results in systematic underestimation of δ and overestimation of Ψ parameters. Analytical relationships between the polarization parameters (δ, Ψ) extracted from both the retarder polar decomposition and the differential matrix decomposition for either simultaneous or sequential occurrence of the linear retardance and optical rotation effects were derived. The self-consistency of both decompositions is validated on experimental Mueller matrices recorded from tissue-simulating phantoms (whose polarization properties are controlled, known a-priori, and exhibited simultaneously) of increasing biological complexity. Additional theoretical validation tests were performed on Monte Carlo-generated Mueller matrices from analogous turbid media exhibiting simultaneous depolarization (Δ), linear retardance (δ) and optical rotation (Ψ) effects. After successful evaluation, the potential advantage of the differential matrix decomposition over the polar decomposition formalism was explored for monitoring of myocardial tissue regeneration following

  11. Snail/Slug-YAP/TAZ Complexes Control Skeletal Stem Cell Self-Renewal and Differentiation

    PubMed Central

    Tang, Yi; Feinberg, Tamar; Keller, Evan T.; Li, Xiao-Yan; Weiss, Stephen J.

    2016-01-01

    Bone marrow-derived skeletal stem/stromal cell (SSC) self-renewal and function are critical to skeletal development, homeostasis and repair. Nevertheless, the mechanisms controlling SSC behavior, particularly bone formation, remain ill-defined. Using knockout mouse models that target the zinc-finger transcription factors, Snail, Slug or Snail and Slug combined, a regulatory axis has been uncovered wherein Snail and Slug cooperatively control SSC self-renewal, osteoblastogenesis and bone formation. Mechanistically, Snail/Slug regulate SSC function by forming complexes with the transcriptional co-activators, YAP and TAZ, in tandem with the inhibition of the Hippo pathway-dependent regulation of YAP/TAZ signaling cascades. In turn, the Snail/Slug-YAP/TAZ axis activates a series of YAP/TAZ/TEAD and Runx2 downstream targets that control SSC homeostasis and osteogenesis. Together, these results demonstrate that SSCs mobilize Snail/Slug-YAP/TAZ complexes to control stem cell function. PMID:27479603

  12. Differential patterns of cortical activation as a function of fluid reasoning complexity.

    PubMed

    Perfetti, Bernardo; Saggino, Aristide; Ferretti, Antonio; Caulo, Massimo; Romani, Gian Luca; Onofrj, Marco

    2009-02-01

    Fluid intelligence (gf) refers to abstract reasoning and problem solving abilities. It is considered a human higher cognitive factor central to general intelligence (g). The regions of the cortex supporting gf have been revealed by recent bioimaging studies and valuable hypothesis on the neural correlates of individual differences have been proposed. However, little is known about the interaction between individual variability in gf and variation in cortical activity following task complexity increase. To further investigate this, two samples of participants (high-IQ, N = 8; low-IQ, N = 10) with significant differences in gf underwent two reasoning (moderate and complex) tasks and a control task adapted from the Raven progressive matrices. Functional magnetic resonance was used and the recorded signal analyzed between and within the groups. The present study revealed two opposite patterns of neural activity variation which were probably a reflection of the overall differences in cognitive resource modulation: when complexity increased, high-IQ subjects showed a signal enhancement in some frontal and parietal regions, whereas low-IQ subjects revealed a decreased activity in the same areas. Moreover, a direct comparison between the groups' activation patterns revealed a greater neural activity in the low-IQ sample when conducting moderate task, with a strong involvement of medial and lateral frontal regions thus suggesting that the recruitment of executive functioning might be different between the groups. This study provides evidence for neural differences in facing reasoning complexity among subjects with different gf level that are mediated by specific patterns of activation of the underlying fronto-parietal network.

  13. Differential inhibition/inactivation of mitochondrial complex I implicates its alteration in malignant cells.

    PubMed

    Ghosh, A; Bera, S; Ghosal, S; Ray, S; Basu, A; Ray, M

    2011-09-01

    Methylglyoxal strongly inhibited mitochondrial respiration of a wide variety of malignant tissues including sarcoma of mice, whereas no such significant effect was noted on mitochondrial respiration of normal tissues with the exception of cardiac cells. This inhibition by methylglyoxal was found to be at the level of mitochondrial complex I (NADH dehydrogenase) of the electron transport chain. L-Lactaldehyde, which is structurally and metabolically related to methylglyoxal, could protect against this inhibition. NADH dehydrogenase of submitochondrial particles of malignant and cardiac cells was inhibited by methylglyoxal. This enzyme of these cells was also inactivated by methylglyoxal. The possible involvement of lysine residue(s) for the activity of NADH dehydrogenase was also investigated by using lysine-specific reagents trinitrobenzenesulfonic acid (TNBS) and pyridoxal 5' phosphate (PP). Inactivation of NADH dehydrogenase by both TNBS and PP convincingly demonstrated the involvement of lysine residue(s) for the activity of the sarcoma and cardiac enzymes, whereas both TNBS and PP failed to inactivate the enzymes of skeletal muscle and liver. Together these studies demonstrate a specific effect of methylglyoxal on mitochondrial complex I of malignant cells and importantly some distinct alteration of this complex in cancer cells.

  14. Differential remodeling of the HIV-1 nucleosome upon transcription activators and SWI/SNF complex binding.

    PubMed

    Angelov, D; Charra, M; Seve, M; Côté, J; Khochbin, S; Dimitrov, S

    2000-09-15

    Here we have examined HIV-1 nucleosome remodeling upon the binding of transcription factors and the SWI/SNF complex using a novel approach. The approach combines UV laser protein-DNA crosslinking, electrophoretic mobility-shift analysis and DNase I protection analysis with immunochemical techniques. It was found that single activator-bound HIV-1 nucleosomes exhibit very weak perturbation in histone NH(2) tail-DNA interactions. However, the simultaneous binding of the transcription activators Sp1, NF-kB1, LEF-1 and USF synergistically increased the release of histone NH(2) tails from nucleosomal DNA. In contrast, the binding of SWI/SNF complex to HIV-1 nucleosome disrupted structured histone domain-DNA contacts, but not histone NH(2) tail-DNA interactions. Stable remodeled nucleosomes, (obtained after detachment of SWI/SNF), displayed identical structural alterations with those bound to SWI/SNF. These results demonstrate a different in vitro remodeling of the HIV-1 nucleosome upon the binding of multiple transcription activators and of SWI/SNF complex. Copyright 2000 Academic Press.

  15. Calculation of photoionization differential cross sections using complex Gauss-type orbitals.

    PubMed

    Matsuzaki, Rei; Yabushita, Satoshi

    2017-09-05

    Accurate theoretical calculation of photoelectron angular distributions for general molecules is becoming an important tool to image various chemical reactions in real time. We show in this article that not only photoionization total cross sections but also photoelectron angular distributions can be accurately calculated using complex Gauss-type orbital (cGTO) basis functions. Our method can be easily combined with existing quantum chemistry techniques including electron correlation effects, and applied to various molecules. The so-called two-potential formula is applied to represent the transition dipole moment from an initial bound state to a final continuum state in the molecular coordinate frame. The two required continuum functions, the zeroth-order final continuum state and the first-order wave function induced by the photon field, have been variationally obtained using the complex basis function method with a mixture of appropriate cGTOs and conventional real Gauss-type orbitals (GTOs) to represent the continuum orbitals as well as the remaining bound orbitals. The complex orbital exponents of the cGTOs are optimized by fitting to the outgoing Coulomb functions. The efficiency of the current method is demonstrated through the calculations of the asymmetry parameters and molecular-frame photoelectron angular distributions of H2+ and H2 . In the calculations of H2 , the static exchange and random phase approximations are employed, and the dependence of the results on the basis functions is discussed. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  16. Petrology of Apollo 11 sample 10071 - A differentiated mini-igneous complex.

    NASA Technical Reports Server (NTRS)

    Drake, M. J.; Weill, D. F.

    1971-01-01

    Sample 10071,33 is a thin section of Apollo 11 ferrobasalt showing an unusual dual texture. The major portion of the sample is very similar to other fine grained Apollo 11 basalts, but the thin section also includes materials with a distinct variolitic texture. The two areas are separated by a sharp boundary and the mineralogy and composition of the two textural types are quite distinct. The mineralogy and chemistry of the variolitic portion show it to be the product of rapid cooling of a liquid, intermediate between the typical Apollo 11 ferrobasalt and the associated Si and K-rich mesostasis. This liquid is the result of fractional crystallization of a magma of composition closely corresponding to the major portion of the 10071 system, followed by crystal-liquid separation. The sample provides strong and direct evidence for igneous differentiation on the lunar surface.

  17. Hydraulic Transients in the Long Diversion-Type Hydropower Station with a Complex Differential Surge Tank

    PubMed Central

    Yu, Xiaodong; Zhang, Jian

    2014-01-01

    Based on the theory of hydraulic transients and the method of characteristics (MOC), a mathematic model of the differential surge tank with pressure-reduction orifices (PROs) and overflow weirs for transient calculation is proposed. The numerical model of hydraulic transients is established using the data of a practical hydropower station; and the probable transients are simulated. The results show that successive load rejection is critical for calculating the maximum pressure in spiral case and the maximum rotating speed of runner when the bifurcated pipe is converging under the surge tank in a diversion-type hydropower station; the pressure difference between two sides of breast wall is large during transient conditions, and it would be more serious when simultaneous load rejections happen after load acceptance; the reasonable arrangement of PROs on breast wall can effectively decrease the pressure difference. PMID:25133213

  18. Hydraulic transients in the long diversion-type hydropower station with a complex differential surge tank.

    PubMed

    Yu, Xiaodong; Zhang, Jian; Zhou, Ling

    2014-01-01

    Based on the theory of hydraulic transients and the method of characteristics (MOC), a mathematic model of the differential surge tank with pressure-reduction orifices (PROs) and overflow weirs for transient calculation is proposed. The numerical model of hydraulic transients is established using the data of a practical hydropower station; and the probable transients are simulated. The results show that successive load rejection is critical for calculating the maximum pressure in spiral case and the maximum rotating speed of runner when the bifurcated pipe is converging under the surge tank in a diversion-type hydropower station; the pressure difference between two sides of breast wall is large during transient conditions, and it would be more serious when simultaneous load rejections happen after load acceptance; the reasonable arrangement of PROs on breast wall can effectively decrease the pressure difference.

  19. Differential diagnosis of Hispanic children referred for autism spectrum disorders: complex issues.

    PubMed

    Overton, Terry; Fielding, Cheryl; Garcia de Alba, Roman

    2007-11-01

    This study examines the decision-making process used for differential diagnosis of a sample of Hispanic children referred for autism spectrum disorders (ASDs). Of the sample of 28 children, 18 were diagnosed with ASDs. Of the 10 children who were not diagnosed with ASDs, 80% were found to have multiple diagnostic labels or comorbidities. Mann-Whitney U analyses determined the differences between the children with the most severe social impairment, children with less severe social impairment and the non-autistic children on several domains commonly used to assess ASDs. These analyses indicated significant differences in some characteristics of the children in the sample. Based on these results, a decision-tree for the diagnosis of children with and without ASDs with comorbid disorders was developed.

  20. Is it a tic or Tourette's? Clues for differentiating simple from more complex tic disorders.

    PubMed

    Evidente, V G

    2000-10-01

    Tics are characterized by sterotyped, purposeless, and irregularly repetitive movements and usually can be classified as chronic motor or vocal tic disorders, transient tic disorders, or Tourette's syndrome. The latter is a complex disorder associated with multiple tics and often accompanied by other conditions, such as ADHD and obsessive-compulsive disorder. Treatment can be difficult, and drug therapy should begin with agents least likely to cause problems for the patient. Education of the patient and family and support from the physician and other care providers are essential elements of effective management.

  1. Role of AKAP 149-PKA-PDE4A complex in cell survival and cell differentiation processes.

    PubMed

    Fernández-Araujo, A; Tobío, A; Alfonso, A; Botana, L M

    2014-08-01

    The cellular localization of A-kinase anchoring proteins (AKAPs), protein kinase A (PKAs) and phosphodiesterases (PDEs) is a key step to the spatiotemporal regulation of the second messenger adenosine 3',5'-cyclic monophosphate (cAMP). In this paper the cellular distribution of the mitochondrial AKAP 149-PKA-PDE4A complex and its implications in the cell death induced by YTX treatment, a known PDE modulator, was studied. K-562 cell line was incubated with YTX for 24 or 48 h. Under these conditions AKAP 149, PKA and type-4A PDE (PDE4A) levels were measured in the cytosol, in the plasma membrane and in the nucleus. Apoptotic hallmarks were also measured after the same conditions. In addition, YTX effect on cell viability was checked after AKAP 149 and PDE4A silencing. The results obtained show a decrease in AKAP 149-PKA-PDE4A levels in cytosol after YTX exposure. 24h after the toxin addition, the complex expression increased in the plasma membrane and after 48 h in the nucleus domain. Furthermore Bcl-2 levels were decreased and the expression of caspase 3 together with caspase 8 activity were increased after 24h of toxin incubation but not after 48 h. These results suggest apoptotic cell death at 24h and a non-apoptotic cell death after 48 h. When AKAP 149 and PDE4A were silenced YTX did not induce cellular death. In summary, AKAP 149-PKA-PDE4A complex localization is related with YTX effect in K-562 cell line. When this complex is mainly located in the plasma membrane apoptosis is activated while when the complex is in the nuclear domain non-apoptotic cellular death or cellular differentiation is activated. Therefore AKAP 149-PKA-PDE4A distribution and integrity have a key role in cellular survival.

  2. Members of the Candida parapsilosis Complex and Candida albicans are Differentially Recognized by Human Peripheral Blood Mononuclear Cells

    PubMed Central

    Estrada-Mata, Eine; Navarro-Arias, María J.; Pérez-García, Luis A.; Mellado-Mojica, Erika; López, Mercedes G.; Csonka, Katalin; Gacser, Attila; Mora-Montes, Héctor M.

    2016-01-01

    The systemic infections caused by members of the Candida parapsilosis complex are currently associated to high morbility and mortality rates, and are considered as relevant as those caused by Candida albicans. Since the fungal cell wall is the first point of contact with the host cells, here we performed a comparison of this organelle in members of the C. parapsilosis complex, and its relevance during interaction with human peripheral blood mononuclear cells (PBMCs). We found that the wall of the C. parapsilosis complex members is similar in composition, but differs to that from C. albicans, with less mannan content and more β-glucan and porosity levels. Furthermore, lectin-based analysis showed increased chitin and β1,3-glucan exposure at the surface of C. parapsilosis sensu lato when compared to C. albicans. Yeast cells of members of the C. parapsilosis complex stimulated more cytokine production by human PBMCs than C. albicans cells; and this significantly changed upon removal of O-linked mannans, indicating this wall component plays a significant role in cytokine stimulation by C. parapsilosis sensu lato. When inner wall components were exposed on the wall surface, C. parapsilosis sensu stricto and C. metapsilosis, but not C. orthopsilosis, stimulated higher cytokine production. Moreover, we found a strong dependency on β1,3-glucan recognition for the members of the C. parapsilosis complex, but not for live C. albicans cells; whereas TLR4 was required for TNFα production by the three members of the complex, and stimulation of IL-6 by C. orthopsilosis. Mannose receptor had a significant role during TNFα and IL-1β stimulation by members of the complex. Finally, we demonstrated that purified N- and O-mannans from either C. parapsilosis sensu lato or C. albicans are capable to block the recognition of these pathogens by human PBMCs. Together; our results suggest that the innate immune recognition of the members of the C. parapsilosis complex is differential

  3. Differential adsorption of complex organic molecules isomers at interstellar ice surfaces

    NASA Astrophysics Data System (ADS)

    Lattelais, M.; Bertin, M.; Mokrane, H.; Romanzin, C.; Michaut, X.; Jeseck, P.; Fillion, J.-H.; Chaabouni, H.; Congiu, E.; Dulieu, F.; Baouche, S.; Lemaire, J.-L.; Pauzat, , F.; Pilmé, J.; Minot, C.; Ellinger, Y.

    2011-08-01

    Context. Over 20 of the ~150 different species detected in the interstellar and circumstellar media have also been identified in icy environments. For most of the species observed so far in the interstellar medium (ISM), the most abundant isomer of a given generic chemical formula is the most stable one (minimum energy principle - MEP) with few exceptions such as, for example, CH3COOH/HCOOCH3 and CH3CH2OH/CH3OCH3, whose formation is thought to occur on the icy mantles of interstellar grains. Aims: We investigate whether differences found in the compositions of molecular ices and the surrounding gas phase could originate from differences between the adsorption of one isomer from that of another at the ice surface. Methods: We performed a coherent and concerted theoretical/experimental study of the adsorption energies of the four molecules mentioned above, i.e. acetic acid (AA)/methyl formate (MF) and ethanol (EtOH)/dimethyl ether (DME) on the surface of water ice at low temperature. The question was first addressed theoretically at LCT using solid state periodic density functional theory (DFT) to represent the organized solid support. The experimental determination of the ice/molecule interaction energies was then carried out independently by two teams at LPMAA and LERMA/LAMAp using temperature programmed desorption (TPD) under an ultra-high vacuum (UHV) between 70 and 160 K. Results: For each pair of isomers, theory and experiments both agree that the most stable isomer (AA or EtOH) interacts more efficiently with the water ice than the higher energy isomer (MF or DME). This differential adsorption can be clearly seen in the different desorption temperatures of the isomers. It is not related to their intrinsic stability but instead to both AA and EtOH producing more and stronger hydrogen bonds with the ice surface. Conclusions: We show that hydrogen bonding may play an important role in the release of organic species from grains and propose that, depending on the

  4. Development of a new MLST scheme for differentiation of Fusarium solani Species Complex (FSSC) isolates.

    PubMed

    Debourgogne, Anne; Gueidan, Cécile; Hennequin, Christophe; Contet-Audonneau, Nelly; de Hoog, Sybren; Machouart, Marie

    2010-09-01

    Fungi belonging to the Fusarium solani Species Complex (FSSC) are well known plant pathogens. In addition to being the causative agent of some superficial infections, FSSC has recently emerged as a group of common opportunistic moulds, mainly in patients with haematological malignancies. Molecular typing methods are essential in order to better understand the epidemiology of such opportunistic agents with the final goal of preventing contamination. A three-locus typing scheme has thus been developed for FSSC; based on polymorphisms in the domains of the ITS, EF-1 alpha, and RPB2 genes. This method is now considered to be a useful reference for phylogenetic and taxonomic studies. In other significant clinical fungi (e.g., Candida sp., Cryptococcus neoformans, and Aspergillus fumigatus), genes coding for metabolic enzymes have been widely used and proven to be very informative for diagnosis and epidemiology. The contribution of these genes has never been evaluated for Fusarium sp. and more specifically for F. solani Species Complex. Here, we have evaluated the contribution of 25 genes for diagnosis and epidemiological purposes. We then report a new five-locus MLST scheme useful for diagnosis and typing of clinical FSSC isolates. The method has been validated on 51 epidemiologically unrelated strains of FSSC and presents a high power of discrimination calculated at 0.991.

  5. Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex.

    PubMed

    Dincă, V; Wiklund, C; Lukhtanov, V A; Kodandaramaiah, U; Norén, K; Dapporto, L; Wahlberg, N; Vila, R; Friberg, M

    2013-10-01

    Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.

  6. Differential identity of Filopodia and Tunneling Nanotubes revealed by the opposite functions of actin regulatory complexes

    PubMed Central

    Delage, Elise; Cervantes, Diégo Cordero; Pénard, Esthel; Schmitt, Christine; Syan, Sylvie; Disanza, Andrea; Scita, Giorgio; Zurzolo, Chiara

    2016-01-01

    Tunneling Nanotubes (TNTs) are actin enriched filopodia-like protrusions that play a pivotal role in long-range intercellular communication. Different pathogens use TNT-like structures as “freeways” to propagate across cells. TNTs are also implicated in cancer and neurodegenerative diseases, making them promising therapeutic targets. Understanding the mechanism of their formation, and their relation with filopodia is of fundamental importance to uncover their physiological function, particularly since filopodia, differently from TNTs, are not able to mediate transfer of cargo between distant cells. Here we studied different regulatory complexes of actin, which play a role in the formation of both these structures. We demonstrate that the filopodia-promoting CDC42/IRSp53/VASP network negatively regulates TNT formation and impairs TNT-mediated intercellular vesicle transfer. Conversely, elevation of Eps8, an actin regulatory protein that inhibits the extension of filopodia in neurons, increases TNT formation. Notably, Eps8-mediated TNT induction requires Eps8 bundling but not its capping activity. Thus, despite their structural similarities, filopodia and TNTs form through distinct molecular mechanisms. Our results further suggest that a switch in the molecular composition in common actin regulatory complexes is critical in driving the formation of either type of membrane protrusion. PMID:28008977

  7. Does aging impair first impression accuracy? Differentiating emotion recognition from complex social inferences.

    PubMed

    Krendl, Anne C; Rule, Nicholas O; Ambady, Nalini

    2014-09-01

    Young adults can be surprisingly accurate at making inferences about people from their faces. Although these first impressions have important consequences for both the perceiver and the target, it remains an open question whether first impression accuracy is preserved with age. Specifically, could age differences in impressions toward others stem from age-related deficits in accurately detecting complex social cues? Research on aging and impression formation suggests that young and older adults show relative consensus in their first impressions, but it is unknown whether they differ in accuracy. It has been widely shown that aging disrupts emotion recognition accuracy, and that these impairments may predict deficits in other social judgments, such as detecting deceit. However, it is unclear whether general impression formation accuracy (e.g., emotion recognition accuracy, detecting complex social cues) relies on similar or distinct mechanisms. It is important to examine this question to evaluate how, if at all, aging might affect overall accuracy. Here, we examined whether aging impaired first impression accuracy in predicting real-world outcomes and categorizing social group membership. Specifically, we studied whether emotion recognition accuracy and age-related cognitive decline (which has been implicated in exacerbating deficits in emotion recognition) predict first impression accuracy. Our results revealed that emotion recognition accuracy did not predict first impression accuracy, nor did age-related cognitive decline impair it. These findings suggest that domains of social perception outside of emotion recognition may rely on mechanisms that are relatively unimpaired by aging.

  8. Smelling in chemically complex environments: an optofluidic Bragg fiber array for differentiation of methanol adulterated beverages.

    PubMed

    Yildirim, Adem; Ozturk, Fahri Emre; Bayindir, Mehmet

    2013-07-02

    A novel optoelectronic nose for analysis of alcohols (ethanol and methanol) in chemically complex environments is reported. The cross-responsive sensing unit of the optoelectronic nose is an array of three distinct hollow-core infrared transmitting photonic band gap fibers, which transmit a specific band of IR light depending on their Bragg mirror structures. The presence of alcohol molecules in the optofluidic core quenches the fiber transmissions if there is an absorption band of the analyte overlapping with the transmission band of the fiber; otherwise they remain unchanged. The cumulative response data of the fiber array enables rapid, reversible, and accurate discrimination of alcohols in chemically complex backgrounds such as beer and fruit juice. In addition, we observed that humidity of the environment has no effect on the response matrix of the optoelectronic nose, which is rarely achieved in gas-sensing applications. Consequently, it can be reliably used in virtually any environment without precalibration for humidity or drying the analytes. Besides the discussed application in counterfeit alcoholic beverages, with its superior sensor parameters, this novel concept proves to be a promising contender for many other applications including food quality control, environmental monitoring, and breath analysis for disease diagnostics.

  9. Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation[OPEN

    PubMed Central

    Pu, Li; Turco, Gina; Morao, Ana Karina; Kim, Dahae

    2016-01-01

    Spatiotemporal regulation of transcription is fine-tuned at multiple levels, including chromatin compaction. Polycomb Repressive Complex 2 (PRC2) catalyzes the trimethylation of Histone 3 at lysine 27 (H3K27me3), which is the hallmark of a repressive chromatin state. Multiple PRC2 complexes have been reported in Arabidopsis thaliana to control the expression of genes involved in developmental transitions and maintenance of organ identity. Here, we show that PRC2 member genes display complex spatiotemporal gene expression patterns and function in root meristem and vascular cell proliferation and specification. Furthermore, PRC2 gene expression patterns correspond with vascular and nonvascular tissue-specific H3K27me3-marked genes. This tissue-specific repression via H3K27me3 regulates the balance between cell proliferation and differentiation. Using enhanced yeast one-hybrid analysis, upstream regulators of the PRC2 member genes are identified, and genetic analysis demonstrates that transcriptional regulation of some PRC2 genes plays an important role in determining PRC2 spatiotemporal activity within a developing organ. PMID:27650334

  10. Molecular differentiation of three closely related members of the mosquito species complex, Anopheles moucheti, by mitochondrial and ribosomal DNA polymorphism.

    PubMed

    Kengne, P; Antonio-Nkondjio, C; Awono-Ambene, H P; Simard, F; Awolola, T S; Fontenille, D

    2007-06-01

    Distinction between members of the equatorial Africa malaria vector Anopheles moucheti (Evans) s.l. (Diptera: Culicidae) has been based mainly on doubtful morphological features. To determine the level of genetic differentiation between the three morphological forms of this complex, we investigated molecular polymorphism in the gene encoding for mitochondrial cytochrome oxidase b (CytB) and in the ribosomal internal transcribed spacers (ITS1 and ITS2). The three genomic regions revealed sequence differences between the three morphological forms similar in degree to the differences shown previously for members of other anopheline species groups or complexes (genetic distance d = 0.047-0.05 for CytB, 0.084-0.166 for ITS1 and 0.03-0.05 for ITS2). Using sequence variation in the ITS1 region, we set up a diagnostic polymerase chain reaction (PCR) for rapid and reliable identification of each subspecies within the An. moucheti complex. Specimens of An. moucheti s.l. collected in Cameroon, the Democratic Republic of Congo (DRC), Uganda and Nigeria were successfully identified, demonstrating the general applicability of this technique.

  11. Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex.

    PubMed

    Balao, F; Tannhäuser, M; Lorenzo, M T; Hedrén, M; Paun, O

    2016-04-01

    Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.

  12. Proteomics-based study on asthenozoospermia: differential expression of proteasome alpha complex.

    PubMed

    Siva, Archana Bharadwaj; Kameshwari, Duvvuri Butchi; Singh, Vaibhav; Pavani, Kadupu; Sundaram, Curam Sreenivasacharlu; Rangaraj, Nandini; Deenadayal, Mamata; Shivaji, Sisinthy

    2010-07-01

    With a view to understand the molecular basis of sperm motility, we have tried to establish the human sperm proteome by two-dimensional PAGE MALDI MS/MS analysis. We report identification of 75 different proteins in the human spermatozoa. Comparative proteome analysis was carried out for asthenozoospermic and normozoospermic patients to understand the molecular basis of sperm motility. Analysis revealed eight proteins (including one unidentified) with altered intensity between the groups. Differential proteins distributed into three functional groups: 'energy and metabolism' (triose-phosphate isomerase, glycerol kinase 2, testis specific isoform and succinyl-CoA:3-ketoacid co-enzyme A transferase 1, mitochondrial precursor); 'movement and organization' (tubulin beta 2C and tektin 1) and 'protein turnover, folding and stress response' (proteasome alpha 3 subunit and heat shock-related 70 kDa protein 2). It was interesting to note that although the proteins falling in the functional group of 'energy and metabolism' are higher in the asthenozoospermic patients, the other two functional groups contain proteins, which are higher in the normozoospermic samples. Validation of results carried out for proteasome alpha 3 subunit by immunoblotting and confocal microscopy, confirmed significant changes in intensity of proteasome alpha 3 subunit in asthenozoospermic samples when compared with normozoospermic controls. Significant positive correlation too was found between proteasome alpha 3 subunit levels and rapid, linear progressive motility of the spermatozoa. In our understanding, this data would contribute appreciably to the presently limited information available about the proteins implicated in human sperm motility.

  13. Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex

    PubMed Central

    Balao, F; Tannhäuser, M; Lorenzo, M T; Hedrén, M; Paun, O

    2016-01-01

    Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers. PMID:26604189

  14. Complex N-glycan number and degree of branching cooperate to regulate cell proliferation and differentiation.

    PubMed

    Lau, Ken S; Partridge, Emily A; Grigorian, Ani; Silvescu, Cristina I; Reinhold, Vernon N; Demetriou, Michael; Dennis, James W

    2007-04-06

    The number of N-glycans (n) is a distinct feature of each glycoprotein sequence and cooperates with the physical properties of the Golgi N-glycan-branching pathway to regulate surface glycoprotein levels. The Golgi pathway is ultrasensitive to hexosamine flux for the production of tri- and tetra-antennary N-glycans, which bind to galectins and form a molecular lattice that opposes glycoprotein endocytosis. Glycoproteins with few N-glycans (e.g., TbetaR, CTLA-4, and GLUT4) exhibit enhanced cell-surface expression with switch-like responses to increasing hexosamine concentration, whereas glycoproteins with high numbers of N-glycans (e.g., EGFR, IGFR, FGFR, and PDGFR) exhibit hyperbolic responses. Computational and experimental data reveal that these features allow nutrient flux stimulated by growth-promoting high-n receptors to drive arrest/differentiation programs by increasing surface levels of low-n glycoproteins. We have identified a mechanism for metabolic regulation of cellular transition between growth and arrest in mammals arising from apparent coevolution of N-glycan number and branching.

  15. Cryptic diversity and ecosystem functioning: a complex tale of differential effects on decomposition.

    PubMed

    De Meester, N; Gingold, R; Rigaux, A; Derycke, S; Moens, T

    2016-10-01

    Marine ecosystems are experiencing accelerating population and species loss. Some ecosystem functions are decreasing and there is growing interest in the link between biodiversity and ecosystem functioning. The role of cryptic (morphologically identical but genetically distinct) species in this biodiversity-ecosystem functioning link is unclear and has not yet been formally tested. We tested if there is a differential effect of four cryptic species of the bacterivorous nematode Litoditis marina on the decomposition process of macroalgae. Bacterivorous nematodes can stimulate or slow down bacterial activity and modify the bacterial assemblage composition. Moreover, we tested if interspecific interactions among the four cryptic species influence the decomposition process. A laboratory experiment with both mono- and multispecific nematode cultures was conducted, and loss of organic matter and the activity of two key extracellular enzymes for the degradation of phytodetritus were assessed. L. marina mainly influenced qualitative aspects of the decomposition process rather than its overall rate: an effect of the nematodes on the enzymatic activities became manifest, although no clear nematode effect on bulk organic matter weight loss was found. We also demonstrated that species-specific effects on the decomposition process existed. Combining the four cryptic species resulted in high competition, with one dominant species, but without complete exclusion of other species. These interspecific interactions translated into different effects on the decomposition process. The species-specific differences indicated that each cryptic species may play an important and distinct role in ecosystem functioning. Functional differences may result in coexistence among very similar species.

  16. Differential effects of a complex organochlorine mixture on the proliferation of breast cancer cell lines

    SciTech Connect

    Aube, Michel; Larochelle, Christian; Ayotte, Pierre

    2011-04-15

    Organochlorine compounds (OCs) are a group of persistent chemicals that accumulate in fatty tissues with age. Although OCs has been tested individually for their capacity to induce breast cancer cell proliferation, few studies examined the effect of complex mixtures that comprise compounds frequently detected in the serum of women. We constituted such an OC mixture containing 15 different components in environmentally relevant proportions and assessed its proliferative effects in four breast cancer cell lines (MCF-7, T47D, CAMA-1, MDAMB231) and in non-cancerous CV-1 cells. We also determined the capacity of the mixture to modulate cell cycle stage of breast cancer cells and to induce estrogenic and antiandrogenic effects using gene reporter assays. We observed that low concentrations of the mixture (100x10{sup 3} and 50x10{sup 3} dilutions) stimulated the proliferation of MCF-7 cells while higher concentrations (10x10{sup 3} and 5x10{sup 3} dilutions) had the opposite effect. In contrast, the mixture inhibited the proliferation of non-hormone-dependent cell lines. The mixture significantly increased the number of MCF-7 cells entering the S phase, an effect that was blocked by the antiestrogen ICI 182,780. Low concentrations of the mixture also caused an increase in CAMA-1 cell proliferation but only in the presence estradiol and dihydrotestosterone (p<0.05 at the 50x10{sup 3} dilution). DDT analogs and polychlorinated biphenyls all had the capacity to stimulate the proliferation of CAMA-1 cells in the presence of sex steroids. Reporter gene assays further revealed that the mixture and several of its constituents (DDT analogs, aldrin, dieldrin, {beta}-hexachlorocyclohexane, toxaphene) induced estrogenic effects, whereas the mixture and several components (DDT analogs, aldrin, dieldrin and PCBs) inhibited the androgen signaling pathway. Our results indicate that the complex OC mixture increases the proliferation of MCF-7 cells due to its estrogenic potential. The

  17. Differentiation of complex vapor mixtures using versatile DNA-carbon nanotube chemical sensor arrays.

    PubMed

    Kybert, Nicholas J; Lerner, Mitchell B; Yodh, Jeremy S; Preti, George; Johnson, A T Charlie

    2013-03-26

    Vapor sensors based on functionalized carbon nanotubes (NTs) have shown great promise, with high sensitivity conferred by the reduced dimensionality and exceptional electronic properties of the NT. Critical challenges in the development of NT-based sensor arrays for chemical detection include the demonstration of reproducible fabrication methods and functionalization schemes that provide high chemical diversity to the resulting sensors. Here, we outline a scalable approach to fabricating arrays of vapor sensors consisting of NT field effect transistors functionalized with single-stranded DNA (DNA-NT). DNA-NT sensors were highly reproducible, with responses that could be described through equilibrium thermodynamics. Target analytes were detected even in large backgrounds of volatile interferents. DNA-NT sensors were able to discriminate between highly similar molecules, including structural isomers and enantiomers. The sensors were also able to detect subtle variations in complex vapors, including mixtures of structural isomers and mixtures of many volatile organic compounds characteristic of humans.

  18. Familial clustering of congenital deafness, patent ductus arteriosus, Eisenmenger complex, and differential cyanosis: A case report.

    PubMed

    Lin, Ting-Wei; Tseng, Chih-Wei; Huang, Chi-Yao; Wang, Kuo-Yang; Liang, Kae-Woei

    2017-06-01

    Few studies had reported syndromes that include patent ductus arteriosus (PDA) with Eisenmenger syndrome and congenital deafness clustered in male siblings without facial, skeletal, or mental abnormalities. Two brothers, who were deaf and had PDA with Eisenmenger complex, were first seen at our Cardiology clinic at the ages of 25 and 41, respectively. They presented with progressive dyspnea on exertion. Upon physical examination, both brothers had clubbing and/or cyanotic toes, normal fingers, and without facial, skeletal, ophthalmological, or mental abnormalities. Echocardiography and multidetector computed tomography revealed large PDAs in both brothers. Cardiac catheterization showed bidirectional shunting via the PDA. Familial clustering of Eisenmenger PDA and congenital deafness is rare. Further studies are warranted to define possible genetic links.

  19. Transducin Duplicates in the Zebrafish Retina and Pineal Complex: Differential Specialisation after the Teleost Tetraploidisation

    PubMed Central

    Lagman, David; Callado-Pérez, Amalia; Franzén, Ilkin E.

    2015-01-01

    Gene duplications provide raw materials that can be selected for functional adaptations by evolutionary mechanisms. We describe here the results of 350 million years of evolution of three functionally related gene families: the alpha, beta and gamma subunits of transducins, the G protein involved in vision. Early vertebrate tetraploidisations resulted in separate transducin heterotrimers: gnat1/gnb1/gngt1 for rods, and gnat2/gnb3/gngt2 for cones. The teleost-specific tetraploidisation generated additional duplicates for gnb1, gnb3 and gngt2. We report here that the duplicates have undergone several types of subfunctionalisation or neofunctionalisation in the zebrafish. We have found that gnb1a and gnb1b are co-expressed at different levels in rods; gnb3a and gnb3b have undergone compartmentalisation restricting gnb3b to the dorsal and medial retina, however, gnb3a expression was detected only at very low levels in both larvae and adult retina; gngt2b expression is restricted to the dorsal and medial retina, whereas gngt2a is expressed ventrally. This dorsoventral distinction could be an adaptation to protect the lower part of the retina from intense light damage. The ontogenetic analysis shows earlier onset of expression in the pineal complex than in the retina, in accordance with its earlier maturation. Additionally, gnb1a but not gnb1b is expressed in the pineal complex, and gnb3b and gngt2b are transiently expressed in the pineal during ontogeny, thus showing partial temporal subfunctionalisation. These retina-pineal distinctions presumably reflect their distinct functional roles in vision and circadian rhythmicity. In summary, this study describes several functional differences between transducin gene duplicates resulting from the teleost-specific tetraploidisation. PMID:25806532

  20. Transducin duplicates in the zebrafish retina and pineal complex: differential specialisation after the teleost tetraploidisation.

    PubMed

    Lagman, David; Callado-Pérez, Amalia; Franzén, Ilkin E; Larhammar, Dan; Abalo, Xesús M

    2015-01-01

    Gene duplications provide raw materials that can be selected for functional adaptations by evolutionary mechanisms. We describe here the results of 350 million years of evolution of three functionally related gene families: the alpha, beta and gamma subunits of transducins, the G protein involved in vision. Early vertebrate tetraploidisations resulted in separate transducin heterotrimers: gnat1/gnb1/gngt1 for rods, and gnat2/gnb3/gngt2 for cones. The teleost-specific tetraploidisation generated additional duplicates for gnb1, gnb3 and gngt2. We report here that the duplicates have undergone several types of subfunctionalisation or neofunctionalisation in the zebrafish. We have found that gnb1a and gnb1b are co-expressed at different levels in rods; gnb3a and gnb3b have undergone compartmentalisation restricting gnb3b to the dorsal and medial retina, however, gnb3a expression was detected only at very low levels in both larvae and adult retina; gngt2b expression is restricted to the dorsal and medial retina, whereas gngt2a is expressed ventrally. This dorsoventral distinction could be an adaptation to protect the lower part of the retina from intense light damage. The ontogenetic analysis shows earlier onset of expression in the pineal complex than in the retina, in accordance with its earlier maturation. Additionally, gnb1a but not gnb1b is expressed in the pineal complex, and gnb3b and gngt2b are transiently expressed in the pineal during ontogeny, thus showing partial temporal subfunctionalisation. These retina-pineal distinctions presumably reflect their distinct functional roles in vision and circadian rhythmicity. In summary, this study describes several functional differences between transducin gene duplicates resulting from the teleost-specific tetraploidisation.

  1. Thiolate-based dinitrosyl iron complexes: Decomposition and detection and differentiation from S-nitrosothiols.

    PubMed

    Keszler, Agnes; Diers, Anne R; Ding, Zhen; Hogg, Neil

    2017-05-01

    Dinitrosyl iron complexes (DNIC) spontaneously form in aqueous solutions of Fe(II), nitric oxide (NO), and various anions. They exist as an equilibrium between diamagnetic, dimeric (bi-DNIC) and paramagnetic, monomeric (mono-DNIC) forms. Thiolate groups (e.g., on glutathione or protein cysteine residues) are the most biologically relevant anions to coordinate to Fe(II). Low molecular weight DNIC have previously been suggested to be important mediators of NO biology in cells, and emerging literature supports their role in the control of iron-dependent cellular processes. Recently, it was shown that DNIC may be one of the most abundant NO-derived products in cells and may serve as intermediates in the cellular formation of S-nitrosothiols. In this work, we examined the stability of low molecular weight DNIC and investigated issues with their detection in the presence of other NO-dependent metabolites such as S-nitrosothiols. By using spectrophotometric, Electron Paramagnetic Resonance, ozone-based chemiluminesence, and HPLC techniques we established that at neutral pH, bi-DNIC remain stable for hours, whereas excess thiol results in decomposition to form nitrite. NO was also detected during the decomposition, but no S-nitrosothiol formation was observed. Importantly, mercury chloride accelerated the degradation of DNIC; thus, the implications of this finding for the diagnostic use of mercury chloride in the detection of S-nitrosothiols were determined in simple and complex biological systems. We conclude S-nitrosothiol levels may have been substantially overestimated in all methods where mercury chloride has been used. Copyright © 2017. Published by Elsevier Inc.

  2. The Novel mTOR Complex 1/2 Inhibitor P529 Inhibits Human Lung Myofibroblast Differentiation.

    PubMed

    Ferguson, Keith T; Torr, Elizabeth E; Bernau, Ksenija; Leet, Jonathan; Sherris, David; Sandbo, Nathan

    2017-01-11

    Idiopathic pulmonary fibrosis is a progressive and deadly disorder with very few therapeutic options. Palomid 529 (8-(1-hydroxyethyl)-2-methoxy-3-(4-methoxybenzyloxy)-benzo[c]chromen-6-one; P529) is a novel dual inhibitor of mechanistic target of rapamycin complex 1/2 (mTORC1/2). In these studies, we investigated the effect of P529 on TGF-β-dependent signaling and myofibroblast differentiation. TGF-β-induced phosphorylation of the mTORC1 targets, p70 S6 kinase 1 (S6K1) and eukaryotic translation initiation factor 4E binding protein 1 (4E-BP1), were both dose dependently inhibited by P529 in human lung fibroblasts with maximal inhibition occurring between 10-20 µM. mTORC2-mediated phosphorylation of Akt at the S473 site was partially inhibited with a similar dose dependency, as was TGF-β-induced myofibroblast differentiation. Protein levels of TGF-β-induced fibronectin and collagen were similarly decreased by P529. At this dose, there was also inhibition of mRNA transcript levels for Col1 and α-SMA, suggesting inhibition of transcriptional activation. However, there was no effect of P529 on canonical TGF-β-induced Smad signaling, as assessed by receptor-associated Smad2/3 phosphorylation, Smad2/3/4 translocation, or Smad-driven gene expression, as assessed by Smad-binding element driven luciferase. Conversely, activation of mTORC1/2 signaling was dependent on TGF-β type I receptor (ALK5) signaling and on Smad2/3 expression. P529 treatment disrupted TGF-β-induced actin stress fiber formation during myofibroblast differentiation, the deposition of new extracellular fibronectin matrix, and linear wound closure by fibroblasts. Likewise, mTOR knockdown inhibited TGF-β-induced myofibroblast differentiation. In conclusion, P529 inhibits TGF-β-induced myofibroblast differentiation, actin stress fiber formation, and matrix protein expression and deposition. Inhibition of mTORC1/2 by P529 may be a promising approach to inhibit in vivo fibrosis. This article is

  3. Unsplit complex frequency shifted perfectly matched layer for second-order wave equation using auxiliary differential equations.

    PubMed

    Gao, Yingjie; Zhang, Jinhai; Yao, Zhenxing

    2015-12-01

    The complex frequency shifted perfectly matched layer (CFS-PML) can improve the absorbing performance of PML for nearly grazing incident waves. However, traditional PML and CFS-PML are based on first-order wave equations; thus, they are not suitable for second-order wave equation. In this paper, an implementation of CFS-PML for second-order wave equation is presented using auxiliary differential equations. This method is free of both convolution calculations and third-order temporal derivatives. As an unsplit CFS-PML, it can reduce the nearly grazing incidence. Numerical experiments show that it has better absorption than typical PML implementations based on second-order wave equation.

  4. Using a system of differential equations that models cattle growth to uncover the genetic basis of complex traits.

    PubMed

    Freua, Mateus Castelani; Santana, Miguel Henrique de Almeida; Ventura, Ricardo Vieira; Tedeschi, Luis Orlindo; Ferraz, José Bento Sterman

    2017-08-01

    The interplay between dynamic models of biological systems and genomics is based on the assumption that genetic variation of the complex trait (i.e., outcome of model behavior) arises from component traits (i.e., model parameters) in lower hierarchical levels. In order to provide a proof of concept of this statement for a cattle growth model, we ask whether model parameters map genomic regions that harbor quantitative trait loci (QTLs) already described for the complex trait. We conducted a genome-wide association study (GWAS) with a Bayesian hierarchical LASSO method in two parameters of the Davis Growth Model, a system of three ordinary differential equations describing DNA accretion, protein synthesis and degradation, and fat synthesis. Phenotypic and genotypic data were available for 893 Nellore (Bos indicus) cattle. Computed values for parameter k1 (DNA accretion rate) ranged from 0.005 ± 0.003 and for α (constant for energy for maintenance requirement) 0.134 ± 0.024. The expected biological interpretation of the parameters is confirmed by QTLs mapped for k1 and α. QTLs within genomic regions mapped for k1 are expected to be correlated with the DNA pool: body size and weight. Single nucleotide polymorphisms (SNPs) which were significant for α mapped QTLs that had already been associated with residual feed intake, feed conversion ratio, average daily gain (ADG), body weight, and also dry matter intake. SNPs identified for k1 were able to additionally explain 2.2% of the phenotypic variability of the complex ADG, even when SNPs for k1 did not match the genomic regions associated with ADG. Although improvements are needed, our findings suggest that genomic analysis on component traits may help to uncover the genetic basis of more complex traits, particularly when lower biological hierarchies are mechanistically described by mathematical simulation models.

  5. Biased assembly of the nuclear pore complex is required for somatic and germline nuclear differentiation in Tetrahymena.

    PubMed

    Iwamoto, Masaaki; Koujin, Takako; Osakada, Hiroko; Mori, Chie; Kojidani, Tomoko; Matsuda, Atsushi; Asakawa, Haruhiko; Hiraoka, Yasushi; Haraguchi, Tokuko

    2015-05-01

    Ciliates have two functionally distinct nuclei, a somatic macronucleus (MAC) and a germline micronucleus (MIC) that develop from daughter nuclei of the last postzygotic division (PZD) during the sexual process of conjugation. Understanding this nuclear dimorphism is a central issue in ciliate biology. We show, by live-cell imaging of Tetrahymena, that biased assembly of the nuclear pore complex (NPC) occurs immediately after the last PZD, which generates anterior-posterior polarized nuclei: MAC-specific NPCs assemble in anterior presumptive MACs but not in posterior presumptive MICs. MAC-specific NPC assembly in the anterior nuclei occurs much earlier than transport of Twi1p, which is required for MAC genome rearrangement. Correlative light-electron microscopy shows that addition of new nuclear envelope (NE) precursors occurs through the formation of domains of redundant NE, where the outer double membrane contains the newly assembled NPCs. Nocodazole inhibition of the second PZD results in assembly of MAC-specific NPCs in the division-failed zygotic nuclei, leading to failure of MIC differentiation. Our findings demonstrate that NPC type switching has a crucial role in the establishment of nuclear differentiation in ciliates. © 2015. Published by The Company of Biologists Ltd.

  6. Biased assembly of the nuclear pore complex is required for somatic and germline nuclear differentiation in Tetrahymena

    PubMed Central

    Iwamoto, Masaaki; Koujin, Takako; Osakada, Hiroko; Mori, Chie; Kojidani, Tomoko; Matsuda, Atsushi; Asakawa, Haruhiko; Hiraoka, Yasushi; Haraguchi, Tokuko

    2015-01-01

    Ciliates have two functionally distinct nuclei, a somatic macronucleus (MAC) and a germline micronucleus (MIC) that develop from daughter nuclei of the last postzygotic division (PZD) during the sexual process of conjugation. Understanding this nuclear dimorphism is a central issue in ciliate biology. We show, by live-cell imaging of Tetrahymena, that biased assembly of the nuclear pore complex (NPC) occurs immediately after the last PZD, which generates anterior-posterior polarized nuclei: MAC-specific NPCs assemble in anterior presumptive MACs but not in posterior presumptive MICs. MAC-specific NPC assembly in the anterior nuclei occurs much earlier than transport of Twi1p, which is required for MAC genome rearrangement. Correlative light-electron microscopy shows that addition of new nuclear envelope (NE) precursors occurs through the formation of domains of redundant NE, where the outer double membrane contains the newly assembled NPCs. Nocodazole inhibition of the second PZD results in assembly of MAC-specific NPCs in the division-failed zygotic nuclei, leading to failure of MIC differentiation. Our findings demonstrate that NPC type switching has a crucial role in the establishment of nuclear differentiation in ciliates. PMID:25788697

  7. Persistent Complex Bereavement Disorder Symptom Domains Relate Differentially to PTSD and Depression: A Study of War-Exposed Bosnian Adolescents.

    PubMed

    Claycomb, Meredith A; Charak, Ruby; Kaplow, Julie; Layne, Christopher M; Pynoos, Robert; Elhai, Jon D

    2016-10-01

    Persistent Complex Bereavement Disorder (PCBD) is a newly proposed diagnosis placed in the Appendix of the 5th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) as an invitation for further research. To date, no studies have examined the dimensionality of PCBD or explored whether different PCBD criteria domains relate in similar, versus differential, ways to other psychological conditions common to war-exposed bereaved youth, including symptoms of Posttraumatic Stress Disorder (PTSD) and depression. We evaluated the dimensionality of proposed PCBD B and C symptom domains, and their respective relations with measures of PTSD and depression, in 1142 bereaved Bosnian adolescents exposed to the 1992-1995 Bosnian civil war. Instruments included the UCLA PTSD Reaction Index, the Depression Self-Rating Scale, and the UCLA Grief Screening Scale (a prototype measure of PCBD symptoms). We investigated potential differences in grief, PTSD, and depression scores as a function of cause of death. We then examined hypothesized differential relations between PCBD B and C symptom domain subscales and selected external correlates, specifically measures of depression and the four-factor emotional numbing model of PTSD. Results of both analyses provide preliminary evidence of a multidimensional structure for PCBD in this population, in that the PCBD Criterion C subscale score covaried more strongly with each of the four PTSD factors and with depression than did PCBD Criterion B. We conclude by discussing theoretical, methodological, clinical, and policy-related implications linked to the ongoing study of essential features of PCBD.

  8. Polycomb Repressive Complex 2-Mediated Chromatin Repression Guides Effector CD8(+) T Cell Terminal Differentiation and Loss of Multipotency.

    PubMed

    Gray, Simon M; Amezquita, Robert A; Guan, Tianxia; Kleinstein, Steven H; Kaech, Susan M

    2017-04-04

    Understanding immunological memory formation depends on elucidating how multipotent memory precursor (MP) cells maintain developmental plasticity and longevity to provide long-term immunity while other effector cells develop into terminally differentiated effector (TE) cells with limited survival. Profiling active (H3K27ac) and repressed (H3K27me3) chromatin in naive, MP, and TE CD8(+) T cells during viral infection revealed increased H3K27me3 deposition at numerous pro-memory and pro-survival genes in TE relative to MP cells, indicative of fate restriction, but permissive chromatin at both pro-memory and pro-effector genes in MP cells, indicative of multipotency. Polycomb repressive complex 2 deficiency impaired clonal expansion and TE cell differentiation, but minimally impacted CD8(+) memory T cell maturation. Abundant H3K27me3 deposition at pro-memory genes occurred late during TE cell development, probably from diminished transcription factor FOXO1 expression. These results outline a temporal model for loss of memory cell potential through selective epigenetic silencing of pro-memory genes in effector T cells.

  9. Differential Response of Coral Assemblages to Thermal Stress Underscores the Complexity in Predicting Bleaching Susceptibility

    PubMed Central

    Toh, Kok Ben; Ng, Chin Soon Lionel; Cabaitan, Patrick; Tun, Karenne; Goh, Eugene; Afiq-Rosli, Lutfi; Taira, Daisuke; Du, Rosa Celia Poquita; Loke, Hai Xin; Khalis, Aizat; Li, Jinghan; Song, Tiancheng

    2016-01-01

    Coral bleaching events have been predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes is dependent on many factors and an understanding of these underlying drivers is crucial for conservation management. In 2013, a mild bleaching episode ensued in response to elevated sea temperature on the sediment-burdened reefs in Singapore. Surveys of seven sites highlighted variable bleaching susceptibility among coral genera–Pachyseris and Podabacia were the most impacted (31% of colonies of both genera bleached). The most susceptible genera such as Acropora and Pocillopora, which were expected to bleach, did not. Susceptibility varied between less than 6% and more than 11% of the corals bleached, at four and three sites respectively. Analysis of four of the most bleached genera revealed that a statistical model that included a combination of the factors (genus, colony size and site) provided a better explanation of the observed bleaching patterns than any single factor alone. This underscored the complexity in predicting the coral susceptibility to future thermal stress events and the importance of monitoring coral bleaching episodes to facilitate more effective management of coral reefs under climate change. PMID:27438593

  10. Differential Response of Coral Assemblages to Thermal Stress Underscores the Complexity in Predicting Bleaching Susceptibility.

    PubMed

    Chou, Loke Ming; Toh, Tai Chong; Toh, Kok Ben; Ng, Chin Soon Lionel; Cabaitan, Patrick; Tun, Karenne; Goh, Eugene; Afiq-Rosli, Lutfi; Taira, Daisuke; Du, Rosa Celia Poquita; Loke, Hai Xin; Khalis, Aizat; Li, Jinghan; Song, Tiancheng

    2016-01-01

    Coral bleaching events have been predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes is dependent on many factors and an understanding of these underlying drivers is crucial for conservation management. In 2013, a mild bleaching episode ensued in response to elevated sea temperature on the sediment-burdened reefs in Singapore. Surveys of seven sites highlighted variable bleaching susceptibility among coral genera-Pachyseris and Podabacia were the most impacted (31% of colonies of both genera bleached). The most susceptible genera such as Acropora and Pocillopora, which were expected to bleach, did not. Susceptibility varied between less than 6% and more than 11% of the corals bleached, at four and three sites respectively. Analysis of four of the most bleached genera revealed that a statistical model that included a combination of the factors (genus, colony size and site) provided a better explanation of the observed bleaching patterns than any single factor alone. This underscored the complexity in predicting the coral susceptibility to future thermal stress events and the importance of monitoring coral bleaching episodes to facilitate more effective management of coral reefs under climate change.

  11. Identification of Chlamydia trachomatis outer membrane complex proteins by differential proteomics.

    PubMed

    Liu, Xiaoyun; Afrane, Mary; Clemmer, David E; Zhong, Guangming; Nelson, David E

    2010-06-01

    The extracellular chlamydial infectious particle, or elementary body (EB), is enveloped by an intra- and intermolecular cysteine cross-linked protein shell called the chlamydial outer membrane complex (COMC). A few abundant proteins, including the major outer membrane protein and cysteine-rich proteins (OmcA and OmcB), constitute the overwhelming majority of COMC proteins. The identification of less-abundant COMC proteins has been complicated by limitations of proteomic methodologies and the contamination of COMC fractions with abundant EB proteins. Here, we used parallel liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analyses of Chlamydia trachomatis serovar L2 434/Bu EB, COMC, and Sarkosyl-soluble EB fractions to identify proteins enriched or depleted from COMC. All well-described COMC proteins were specifically enriched in the COMC fraction. In contrast, multiple COMC-associated proteins found in previous studies were strongly enriched in the Sarkosyl-soluble fraction, suggesting that these proteins are not COMC components or are not stably associated with COMC. Importantly, we also identified novel proteins enriched in COMC. The list of COMC proteins identified in this study has provided reliable information for further understanding chlamydial protein secretion systems and modeling COMC and EB structures.

  12. Differential predictors of DSM-5 PTSD and ICD-11 complex PTSD among African American women.

    PubMed

    Powers, Abigail; Fani, Negar; Carter, Sierra; Cross, Dorthie; Cloitre, Marylene; Bradley, Bekh

    2017-01-01

    Background: Complex posttraumatic stress disorder (CPTSD) is proposed for inclusion in the ICD-11 as a diagnosis distinct from posttraumatic stress disorder (PTSD), reflecting deficits in affective, self-concept, and relational domains. There remains significant controversy over whether CPTSD provides useful diagnostic information beyond PTSD and other comorbid conditions, such as depression or substance use disorders. Objective: The present study examined differences in psychiatric presentation for three groups: traumatized controls, DSM-5 PTSD subjects, and ICD-11 CPTSD subjects. Method: The sample included 190 African American women recruited from an urban public hospital where rates of trauma exposure are high. PTSD was measured using Clinician Administered PTSD Scale for DSM-5 and CPTSD was measured using clinician administered ICD-Trauma Interview. Psychiatric diagnoses and emotion dysregulation were also assessed. In a subset of women (n = 60), emotion recognition was measured using the Penn Emotion Recognition Task. Results: There were significant differences across groups on current and lifetime major depression (p < .001) and current and lifetime alcohol and substance dependence (p < .05), with CPTSD showing the highest rates of comorbidities. CPTSD women also showed significantly higher levels of childhood abuse and lower rates of adult secure attachment. Multivariate analysis of variance showed significantly more severe PTSD and depression symptoms and, as expected, more severe emotion dysregulation and dissociation, compared to DSM-5 PTSD and traumatized control groups. Individuals with CPTSD also had higher levels of emotion recognition to faces on a computer-based behavioural assessment, which may be related to heightened vigilance toward emotional cues from others. CPTSD women had better facial emotion recognition on a computer-based assessment, which may suggest heightened vigilance toward emotional cues. Conclusions: Our results suggest

  13. Differential association of protein subunits with the human RNase MRP and RNase P complexes.

    PubMed

    Welting, Tim J M; Kikkert, Bastiaan J; van Venrooij, Walther J; Pruijn, Ger J M

    2006-07-01

    RNase MRP is a eukaryotic endoribonuclease involved in nucleolar and mitochondrial RNA processing events. RNase MRP is a ribonucleoprotein particle, which is structurally related to RNase P, an endoribonuclease involved in pre-tRNA processing. Most of the protein components of RNase MRP have been reported to be associated with RNase P as well. In this study we determined the association of these protein subunits with the human RNase MRP and RNase P particles by glycerol gradient sedimentation and coimmunoprecipitation. In agreement with previous studies, RNase MRP sedimented at 12S and 60-80S. In contrast, only a single major peak was observed for RNase P at 12S. The analysis of individual protein subunits revealed that hPop4 (also known as Rpp29), Rpp21, Rpp20, and Rpp25 only sedimented in 12S fractions, whereas hPop1, Rpp40, Rpp38, and Rpp30 were also found in 60-80S fractions. In agreement with their cosedimentation with RNase P RNA in the 12S peak, coimmunoprecipitation with VSV-epitope-tagged protein subunits revealed that hPop4, Rpp21, and in addition Rpp14 preferentially associate with RNase P. These data show that hPop4, Rpp21, and Rpp14 may not be associated with RNase MRP. Furthermore, Rpp20 and Rpp25 appear to be associated with only a subset of RNase MRP particles, in contrast to hPop1, Rpp40, Rpp38, and Rpp30 (and possibly also hPop5), which are probably associated with all RNase MRP complexes. Our data are consistent with a transient association of Rpp20 and Rpp25 with RNase MRP, which may be inversely correlated to its involvement in pre-rRNA processing.

  14. Differential role of lipocalin-2 during immune-complex mediated acute and chronic inflammation

    PubMed Central

    Shashidharamurthy, Rangaiah; Machiah, Deepa; Aitken, Jesse D; Putty, Kalyani; Srinivasan, Gayathri; Chassaing, Benoit; Parkos, Charles A; Selvaraj, Periasamy; Vijay-Kumar, Matam

    2013-01-01

    Objectives Lipocalin-2 (Lcn2) is an innate immune protein expressed by a variety of cells and is highly upregulated during several pathological conditions including immune-complex (IC) mediated inflammatory/autoimmune disorders. However, the function of Lcn2 during IC-mediated inflammation is largely unknown. Therefore our objective was to investigate the role of Lcn2 in IC-mediated diseases. Methods The upregulation of Lcn2 was determined by ELISA in three different mouse models of IC-mediated autoimmune disease: systemic lupus erythematosus, collagen-induced arthritis and serum-induced arthritis. The in vivo role of Lcn2 during IC-mediated inflammation was investigated using Lcn2 knockout (Lcn2KO) mice and their wild type (WT) littermates. Results Lcn2 levels were significantly elevated in all the three autoimmune disease models. Further, in an acute skin inflammation model, Lcn2KO mice demonstrated a 50% reduction in inflammation with histopathological analysis revealing strikingly reduced immune cell infiltration compared to WT mice. Administration of recombinant Lcn2 to Lcn2KO mice restored inflammation to levels observed in WT mice. Neutralization of Lcn2 using a monoclonal antibody significantly reduced inflammation in WT mice. In contrast, Lcn2KO mice developed more severe serum-induced arthritis compared to WT mice. Histological analysis revealed extensive tissue and bone destruction with significantly reduced neutrophil infiltration but considerably more macrophage migration in Lcn2KO mice when compared to WT. Conclusion These results demonstrate that Lcn2 may regulate immune cell recruitment to the site of inflammation, a process essential for the controlled initiation, perpetuation and resolution of inflammatory processes. Thus, Lcn2 may present a promising target in the treatment of IC-mediated inflammatory/autoimmune diseases. PMID:23280250

  15. Differential effects of zinc and magnesium ions on mineralization activity of phosphatidylserine calcium phosphate complexes.

    PubMed

    Wu, Licia N Y; Genge, Brian R; Wuthier, Roy E

    2009-07-01

    Mg(2+) and Zn(2+) are present in the mineral of matrix vesicles (MVs) and biological apatites, and are known to influence the onset and progression of mineral formation by amorphous calcium phosphate (ACP) and hydroxyapatite (HAP). However, neither has been studied systematically for its effect on mineral formation by phosphatidylserine-Ca(2+)-Pi complexes (PS-CPLX), an important constituent of the MV nucleation core. Presented here are studies on the effects of increasing levels of Mg(2+) and Zn(2+) on the process of mineral formation, either when present in synthetic cartilage lymph (SCL), or when incorporated during the formation of PS-CPLX. Pure HAP and PS-CPLX proved to be powerful nucleators, but ACP took much longer to induce mineral formation. In SCL, Mg(2+) and Zn(2+) had significantly different inhibitory effects on the onset and amount of mineral formation; HAP and PS-CPLX were less affected than ACP. Mg(2+) and Zn(2+) caused similar reductions in the rate and length of rapid mineral formation, but Zn(2+) was a more potent inhibitor on a molar basis. When incorporated into PS-CPLX, Mg(2+) and Zn(2+) caused significantly different effects than when present in SCL. Even low, subphysiological levels of Mg(2+) altered the inherent structure of PS-CPLX and markedly reduced its ability to induce and propagate mineral formation. Incorporated Zn(2+) caused significantly less effect, low (<20 microM) levels causing almost no inhibition. Levels of Zn(2+) present in MVs do not appear to inhibit their nucleational activity.

  16. Differential cellular expression of neurotrophins in cortical tubers of the tuberous sclerosis complex.

    PubMed

    Kyin, R; Hua, Y; Baybis, M; Scheithauer, B; Kolson, D; Uhlmann, E; Gutmann, D; Crino, P B

    2001-10-01

    Neurotrophins and their receptors modulate cerebral cortical development. Tubers in the tuberous sclerosis complex (TSC) are characterized histologically by disorganized cortical cytoarchitecture and thus, we hypothesized that expression of neurotrophin mRNAs and proteins might be altered in tubers. Using in situ transcription and mRNA amplification to probe cDNA arrays, we found that neurotrophin-3 (NT3) and trkB mRNA expression were reduced whereas neurotrophin-4 (NT4) and trkC mRNA expression were increased in whole tuber sections. Alterations in mRNA abundance were defined in single microdissected dysplastic neurons (DNs) and giant cells (GCs). NT3 mRNA expression was reduced in GCs and trkB mRNA expression was reduced in DNs. NT4 mRNA expression was increased in DNs and trkC mRNA expression was increased in both DNs and GCs. In three patients, TSC2 locus mutations were confirmed and the mean tuberin mRNA expression levels was reduced across all nine cases. Consistent with these observations, NT3 mRNA expression was reduced but trkC mRNA expression was increased in vitro in human NTera2 neurons (NT2N) transfected with a tuberin antisense construct that reduced tuberin expression. Western analysis of tuber homogenates and computer-assisted densitometry of immunolabeled sections confirmed the neurotrophin mRNA expression data in whole sections and single neurotrophin immunoreactive cells. We conclude that alterations in NT4/trkB and NT3/trkC expression may contribute to tuber formation during brain development as downstream effects of the hamartin and tuberin pathway in TSC.

  17. Differential hypersaline stress response in Zygosaccharomyces rouxii complex yeasts: a physiological and transcriptional study.

    PubMed

    Solieri, Lisa; Vezzani, Veronica; Cassanelli, Stefano; Dakal, Tikam Chand; Pazzini, Jacopo; Giudici, Paolo

    2016-09-01

    The Zygosaccharomyces rouxii complex comprises three distinct lineages of halotolerant yeasts relevant in food processing and spoilage, such as Z. sapae, Z. rouxii and a mosaic group of allodiploid strains. They manifest plastic genome architecture (variation in karyotype, ploidy level and Na(+)/H(+) antiporter-encoding gene copy number), and exhibit diverse tolerances to salt concentrations. Here, we investigated accumulation of compatible osmolytes and transcriptional regulation of Na(+)/H(+) antiporter-encoding ZrSOD genes during salt exposure in strains representative for the lineages, namely Z. sapae ABT301(T) (low salt tolerant), Z. rouxii CBS 732(T) (middle salt tolerant) and allodiploid strain ATCC 42981 (high salt tolerant). Growth curve modelling in 2 M NaCl-containing media supplemented with or without yeast extract as nitrogen source indicates that moderate salt tolerance of CBS 732(T) mainly depends on nitrogen availability rather than intrinsic inhibitory effects of salt. All the strains produce glycerol and not mannitol under salt stress and use two different glycerol balance strategies. ATCC 42981 produces comparatively more glycerol than Z. sapae and Z. rouxii under standard growth conditions and better retains it intracellularly under salt injuries. Conversely, Z. sapae and Z. rouxii enhance glycerol production under salt stress and intracellularly retain glycerol less efficiently than ATCC 42981. Expression analysis shows that, in diploid Z. sapae and allodiploid ATCC 42981, transcription of gene variants ZrSOD2-22/ZrSOD2 and ZrSOD22 is constitutive and salt unresponsive. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Complexity.

    PubMed

    Gómez-Hernández, J Jaime

    2006-01-01

    It is difficult to define complexity in modeling. Complexity is often associated with uncertainty since modeling uncertainty is an intrinsically difficult task. However, modeling uncertainty does not require, necessarily, complex models, in the sense of a model requiring an unmanageable number of degrees of freedom to characterize the aquifer. The relationship between complexity, uncertainty, heterogeneity, and stochastic modeling is not simple. Aquifer models should be able to quantify the uncertainty of their predictions, which can be done using stochastic models that produce heterogeneous realizations of aquifer parameters. This is the type of complexity addressed in this article.

  19. cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility–mass spectrometry

    PubMed Central

    Byrne, Dominic P.; Vonderach, Matthias; Ferries, Samantha; Brownridge, Philip J.; Eyers, Claire E.; Eyers, Patrick A.

    2016-01-01

    cAMP-dependent protein kinase (PKA) is an archetypal biological signaling module and a model for understanding the regulation of protein kinases. In the present study, we combine biochemistry with differential scanning fluorimetry (DSF) and ion mobility–mass spectrometry (IM–MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro. We uncover dynamic, conformationally distinct populations of the PKA catalytic subunit with distinct structural stability and susceptibility to the physiological protein inhibitor PKI. Native MS of reconstituted PKA R2C2 holoenzymes reveals variable subunit stoichiometry and holoenzyme ablation by PKI binding. Finally, we find that although a ‘kinase-dead’ PKA catalytic domain cannot bind to ATP in solution, it interacts with several prominent chemical kinase inhibitors. These data demonstrate the combined power of IM–MS and DSF to probe PKA dynamics and regulation, techniques that can be employed to evaluate other protein-ligand complexes, with broad implications for cellular signaling. PMID:27444646

  20. Heteromeric complexes of heat shock protein 70 (HSP70) family members, including Hsp70B′, in differentiated human neuronal cells

    PubMed Central

    Chow, Ari M.; Mok, Philip; Xiao, Dawn; Khalouei, Sam

    2010-01-01

    Human neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis have been termed “protein misfolding disorders.” Upregulation of heat shock proteins that target misfolded aggregation-prone proteins has been proposed as a potential therapeutic strategy to counter neurodegenerative disorders. The heat shock protein 70 (HSP70) family is well characterized for its cytoprotective effects against cell death and has been implicated in neuroprotection by overexpression studies. HSP70 family members exhibit sequence and structural conservation. The significance of the multiplicity of HSP70 proteins is unknown. In this study, coimmunoprecipitation was employed to determine if association of HSP70 family members occurs, including Hsp70B′ which is present in the human genome but not in mouse and rat. Heteromeric complexes of Hsp70B′, Hsp70, and Hsc70 were detected in differentiated human SH-SY5Y neuronal cells. Hsp70B′ also formed complexes with Hsp40 suggesting a common co-chaperone for HSP70 family members. PMID:20084477

  1. Platelet-derived growth factor receptors form complexes with neuropilin-1 during megakaryocytic differentiation of thrombopoietin-dependent UT-7/TPO cells.

    PubMed

    Ohsaka, Akimichi; Hirota-Komatsu, Satoko; Araki, Marito; Komatsu, Norio

    2015-04-10

    Neuropilin-1 (NRP-1) is involved in angiogenesis, but the role of NRP-1 in megakaryocytopoiesis is not yet fully understood. In this study, we investigated whether thrombopoietin (TPO) regulates the expression of platelet-derived growth factor (PDGF) and its receptors (PDGFRs) on TPO-dependent UT-7/TPO cells and whether PDGFRs and NRP-1 on UT-7/TPO cells form complexes during megakaryocytic differentiation. When UT-7/TPO cells were starved of TPO for 24 h and then stimulated with 5 ng/ml TPO, the expression of PDGF-B, PDGFRα, and PDGFRβ were significantly up-regulated after the addition of TPO. TPO also induced tyrosine phosphorylation of PDGFRα but not PDGFRβ, and promoted the formation of PDGFRαβ heterodimer complexes. Furthermore, megakaryocytic differentiation of UT-7/TPO cells on treatment with phorbol myristate acetate (PMA) was accompanied by a marked up-regulation of PDGFRβ and NRP-1 protein expression, complex formation between PDGFRs and NRP-1, PDGFRαβ heterodimer complexes, and an increase in PDGF-BB-binding activity. Immunocytochemistry confirmed complex formation between PDGFRs and NRP-1 and PDGFRαβ heterodimer complexes in PMA-differentiated UT-7/TPO cells. Our observations suggest that NRP-1 is involved in megakaryocytopoiesis through complex formation with PDGFRs, and that NRP-1-PDGFR-complexes may contribute to effective cellular functions mediated by TPO and PDGF in megakaryocytic cells.

  2. PCR-Based Method To Differentiate the Subspecies of the Mycobacterium tuberculosis Complex on the Basis of Genomic Deletions

    PubMed Central

    Huard, Richard C.; de Oliveira Lazzarini, Luiz Claudio; Butler, W. Ray; van Soolingen, Dick; Ho, John L.

    2003-01-01

    The classical Mycobacterium tuberculosis complex (MtbC) subspecies include Mycobacterium tuberculosis, Mycobacterium africanum (subtypes I and II), Mycobacterium bovis (along with the attenuated M. bovis bacillus Calmette-Guérin [BCG]), and Mycobacterium microti; increasingly recognized MtbC groupings include Mycobacterium bovis subsp. caprae and “Mycobacterium tuberculosis subsp. canettii.” Previous investigations have documented each MtbC subspecies as a source of animal and/or human tuberculosis. However, study of these organisms is hindered by the lack of a single protocol that quickly and easily differentiates all of the MtbC groupings. Towards this end we have developed a rapid, simple, and reliable PCR-based MtbC typing method that makes use of MtbC chromosomal region-of-difference deletion loci. Here, seven primer pairs (which amplify within the loci 16S rRNA, Rv0577, IS1561′, Rv1510, Rv1970, Rv3877/8, and Rv3120) were run in separate but simultaneous reactions. Each primer pair either specifically amplified a DNA fragment of a unique size or failed, depending upon the source mycobacterial DNA. The pattern of amplification products from all of the reactions, visualized by agarose gel electrophoresis, allowed immediate identification either as MtbC composed of M. tuberculosis (or M. africanum subtype II), M. africanum subtype I, M. bovis, M. bovis BCG, M. caprae, M. microti, or “M. canettii” or as a Mycobacterium other than MtbC (MOTT). This MtbC PCR typing panel provides an advanced approach to determine the subspecies of MtbC isolates and to differentiate them from clinically important MOTT species. It has proven beneficial in the management of Mycobacterium collections and may be applied for practical clinical and epidemiological use. PMID:12682155

  3. Differential targeting of the E-Cadherin/β-Catenin complex by gram-positive probiotic lactobacilli improves epithelial barrier function.

    PubMed

    Hummel, Stephanie; Veltman, Katharina; Cichon, Christoph; Sonnenborn, Ulrich; Schmidt, M Alexander

    2012-02-01

    The intestinal ecosystem is balanced by dynamic interactions between resident and incoming microbes, the gastrointestinal barrier, and the mucosal immune system. However, in the context of inflammatory bowel diseases (IBD), where the integrity of the gastrointestinal barrier is compromised, resident microbes contribute to the development and perpetuation of inflammation and disease. Probiotic bacteria have been shown to exert beneficial effects, e.g., enhancing epithelial barrier integrity. However, the mechanisms underlying these beneficial effects are only poorly understood. Here, we comparatively investigated the effects of four probiotic lactobacilli, namely, Lactobacillus acidophilus, L. fermentum, L. gasseri, and L. rhamnosus, in a T84 cell epithelial barrier model. Results of DNA microarray experiments indicating that lactobacilli modulate the regulation of genes encoding in particular adherence junction proteins such as E-cadherin and β-catenin were confirmed by quantitative reverse transcription-PCR (qRT-PCR). Furthermore, we show that epithelial barrier function is modulated by Gram-positive probiotic lactobacilli via their effect on adherence junction protein expression and complex formation. In addition, incubation with lactobacilli differentially influences the phosphorylation of adherence junction proteins and the abundance of protein kinase C (PKC) isoforms such as PKCδ that thereby positively modulates epithelial barrier function. Further insight into the underlying molecular mechanisms triggered by these probiotics might also foster the development of novel strategies for the treatment of gastrointestinal diseases (e.g., IBD).

  4. Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula

    PubMed Central

    Sazzini, Marco; Gnecchi Ruscone, Guido Alberto; Giuliani, Cristina; Sarno, Stefania; Quagliariello, Andrea; De Fanti, Sara; Boattini, Alessio; Gentilini, Davide; Fiorito, Giovanni; Catanoso, Mariagrazia; Boiardi, Luigi; Croci, Stefania; Macchioni, Pierluigi; Mantovani, Vilma; Di Blasio, Anna Maria; Matullo, Giuseppe; Salvarani, Carlo; Franceschi, Claudio; Pettener, Davide; Garagnani, Paolo; Luiselli, Donata

    2016-01-01

    The Italian peninsula has long represented a natural hub for human migrations across the Mediterranean area, being involved in several prehistoric and historical population movements. Coupled with a patchy environmental landscape entailing different ecological/cultural selective pressures, this might have produced peculiar patterns of population structure and local adaptations responsible for heterogeneous genomic background of present-day Italians. To disentangle this complex scenario, genome-wide data from 780 Italian individuals were generated and set into the context of European/Mediterranean genomic diversity by comparison with genotypes from 50 populations. To maximize possibility of pinpointing functional genomic regions that have played adaptive roles during Italian natural history, our survey included also ~250,000 exomic markers and ~20,000 coding/regulatory variants with well-established clinical relevance. This enabled fine-grained dissection of Italian population structure through the identification of clusters of genetically homogeneous provinces and of genomic regions underlying their local adaptations. Description of such patterns disclosed crucial implications for understanding differential susceptibility to some inflammatory/autoimmune disorders, coronary artery disease and type 2 diabetes of diverse Italian subpopulations, suggesting the evolutionary causes that made some of them particularly exposed to the metabolic and immune challenges imposed by dietary and lifestyle shifts that involved western societies in the last centuries. PMID:27582244

  5. Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula.

    PubMed

    Sazzini, Marco; Gnecchi Ruscone, Guido Alberto; Giuliani, Cristina; Sarno, Stefania; Quagliariello, Andrea; De Fanti, Sara; Boattini, Alessio; Gentilini, Davide; Fiorito, Giovanni; Catanoso, Mariagrazia; Boiardi, Luigi; Croci, Stefania; Macchioni, Pierluigi; Mantovani, Vilma; Di Blasio, Anna Maria; Matullo, Giuseppe; Salvarani, Carlo; Franceschi, Claudio; Pettener, Davide; Garagnani, Paolo; Luiselli, Donata

    2016-09-01

    The Italian peninsula has long represented a natural hub for human migrations across the Mediterranean area, being involved in several prehistoric and historical population movements. Coupled with a patchy environmental landscape entailing different ecological/cultural selective pressures, this might have produced peculiar patterns of population structure and local adaptations responsible for heterogeneous genomic background of present-day Italians. To disentangle this complex scenario, genome-wide data from 780 Italian individuals were generated and set into the context of European/Mediterranean genomic diversity by comparison with genotypes from 50 populations. To maximize possibility of pinpointing functional genomic regions that have played adaptive roles during Italian natural history, our survey included also ~250,000 exomic markers and ~20,000 coding/regulatory variants with well-established clinical relevance. This enabled fine-grained dissection of Italian population structure through the identification of clusters of genetically homogeneous provinces and of genomic regions underlying their local adaptations. Description of such patterns disclosed crucial implications for understanding differential susceptibility to some inflammatory/autoimmune disorders, coronary artery disease and type 2 diabetes of diverse Italian subpopulations, suggesting the evolutionary causes that made some of them particularly exposed to the metabolic and immune challenges imposed by dietary and lifestyle shifts that involved western societies in the last centuries.

  6. Active suppression of major histocompatibility complex class II gene expression during differentiation from B cells to plasma cells

    SciTech Connect

    Latron, F.; Maffei, A.; Scarpellino, L.; Bernard, M.; Accolla, R.S. ); Jotterand-Bellomo, M. ); Strominger, J.L. )

    1988-04-01

    Constitutive expression of major histocompatibility complex class II genes is acquired very early in B-cell ontogeny and is maintained up to the B-cell blast stage. Terminal differentiation in plasma cells is, however, accompanied by a loss of class II gene expression. In B cells this gene system is under the control of several loci encoding transacting factors with activator function, one of which, the aIr-1 gene product, operates across species barriers. In this report human class II gene expression is shown to be extinguished in somatic cell hybrids between the human class II-positive B-cell line Raji and the mouse class-II negative plasmacytoma cell line P3-U1. Since all murine chromosomes are retained in these hybrids and no preferential segregation of a specific human chromosome is observed, the results are compatible with the presence of suppressor factors of mouse origin, operating across species barriers and inhibiting class II gene expression. Suppression seems to act at the level of transcription or accumulation of class II-specific mRNA, since no human, and very few murine, class II transcripts are detectable in the hybrids.

  7. Differential recognition of calmodulin-enzyme complexes by a conformation-specific anti-calmodulin monoclonal antibody

    SciTech Connect

    Hansen, R.S.; Beavo, J.A.

    1986-11-05

    An anti-calmodulin monoclonal antibody having an absolute requirement for Ca/sup 2 +/ has been produced from mice immunized with a mixture of calmodulin and calmodulin-binding proteins. Radioimmune assays were developed for the determination of its specificity. The epitope for this antibody resides on the COOH-terminal half of the mammalian protein. Plant calmodulin or toponin C had little reactivity. The apparent affinity of the antibody for calmodulin was increased approximately 60-fold in the presence of heart calmodulin-dependent phosphodiesterase. The presence of heart phosphodiesterase in the radioimmune assay greatly enhanced the sensitivity for calmodulin. The intrinsic calmodulin subunit of phosphorylase kinase and calmodulin which was bound to brain phosphodiesterases was also recognized with high affinity by the antibody. In direct binding experiments, most of the calmodulin-binding proteins studied were unreactive with the antibody. This selectivity allowed purification of heart and two brain calmodulin-dependent cyclic nucleotide phosphodiesterase isozymes on immobilized antibody affinity columns. The data suggest that the binding of ligands to Ca/sup 2 +//calmodulin induce conformation changes in calmodulin which alter reactivity with the anti-calmodulin monoclonal antibody. The differential antibody reactivity toward calmodulin-enzyme complexes indicates that target proteins either induce very different conformations in calmodulin and/or interact with different geometries relative to the antibody binding site. The anti-calmodulin monoclonal antibody should be useful for the purification of other calmodulin-dependent phosphodiesterases as well as isozymes of phosphorylase kinase.

  8. Daily differential expression of melatonin-related genes and clock genes in rat cumulus-oocyte complex: changes after pinealectomy.

    PubMed

    Coelho, L A; Peres, R; Amaral, F G; Reiter, R J; Cipolla-Neto, J

    2015-05-01

    This study investigated the maturational stage (immature and mature ovaries) differences of mRNA expression of melatonin-forming enzymes (Aanat and Asmt), melatonin membrane receptors (Mt1 and Mt2) and putative nuclear (Rorα) receptors, and clock genes (Clock, Bmal1, Per1, Per2, Cry1, Cry2) in cumulus-oocyte complexes (COC) from weaning Wistar rats. We also examined the effects of pinealectomy and of melatonin pharmacological replacement on the daily expression of these genes in COC. qRT-PCR analysis revealed that in oocytes, the mRNA expression of Asmt, Mt2, Clock, Bmal1, Per2, and Cry1 were higher (P < 0.05) in immature ovaries than in the mature ones. In cumulus cells, the same pattern of mRNA expression for Asmt, Aanat, Rorα, Clock, Per1, Cry1, and Cry2 genes was observed. In oocytes, pinealectomy altered the daily mRNA expression profiles of Asmt, Mt1, Mt2, Clock, Per1, Cry1, and Cry2 genes. In cumulus cells, removal of the pineal altered the mRNA expression profiles of Mt1, Mt2, Rorα, Aanat, Asmt, Clock, Bmal1, Per2, Cry1, and Cry2 genes. Melatonin treatment partially or completely re-established the daily mRNA expression profiles of most genes studied. The mRNA expression of melatonin-related genes and clock genes in rat COC varies with the maturational stage of the meiotic cellular cycle in addition to the hour of the day. This suggests that melatonin might act differentially in accordance with the maturational stage of cumulus/oocyte complex. In addition, it seems that circulating pineal melatonin is very important in the design of the daily profile of mRNA expression of COC clock genes and genes related to melatonin synthesis and action. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Differential distribution of proteins expressed in companion cells in the sieve element-companion cell complex of rice plants.

    PubMed

    Fukuda, Akari; Fujimaki, Syu; Mori, Tomoko; Suzui, Nobuo; Ishiyama, Keiki; Hayakawa, Toshihiko; Yamaya, Tomoyuki; Fujiwara, Toru; Yoneyama, Tadakatsu; Hayashi, Hiroaki

    2005-11-01

    Sieve tubes are comprised of sieve elements, enucleated cells that are incapable of RNA and protein synthesis. The proteins in sieve elements are supplied from the neighboring companion cells through plasmodesmata. In rice plants, it was unclear whether or not all proteins produced in companion cells had the same distribution pattern in the sieve element-companion cell complex. In this study, the distribution pattern of four proteins, beta-glucuronidase (GUS), green fluorescent protein (GFP), thioredoxin h (TRXh) and glutathione S-transferase (GST) were analyzed. The foreign proteins GUS and GFP were expressed in transgenic rice plants under the control of the TRXh gene promoter (PTRXh), a companion cell-specific promoter. Analysis of leaf cross-sections of PTRXh-GUS and PTRXh-GFP plants indicated high accumulation of GUS and GFP, respectively, in companion cells rather than in sieve elements. GUS and GFP were also detected in phloem sap collected from leaf sheaths of the transgenic rice plants, suggesting these proteins could enter sieve elements. Relative amounts of GFP and endogenous phloem proteins, TRXh and GST, in phloem sap and total leaf extracts were compared. Compared to TRXh and GST, GFP content was higher in total leaf extracts, but lower in phloem sap, suggesting that GFP accumulated mainly in companion cells rather than in sieve elements. On the other hand, TRXh and GST appeared to accumulate in sieve elements rather than in companion cells. These results indicate the evidence for differential distribution of proteins between sieve elements and companion cells in rice plants.

  10. Structural studies of agar-gelatin complex coacervates by small angle neutron scattering, rheology and differential scanning calorimetry.

    PubMed

    Singh, S Santinath; Aswal, V K; Bohidar, H B

    2007-08-01

    Agar-gelatin complex coacervates are studied by small angle neutron scattering (SANS), rheology (in both flow and temperature scan modes) and differential scanning calorimetry (DSC) in order to probe the microscopic structure of this dense protein-polysaccharide-rich phase. DSC and isochronal temperature sweep (rheology) experiments yielded a characteristic temperature at approximately 35+/-2 degrees C. Rheology data revealed a second characteristic temperature at approximately 75+/-5 degrees C which was absent in DSC thermograms. In the flow mode, shear viscosity (eta) was found to scale with (Carreau model) applied shear rate (gamma ) as: eta(gamma ) approximately (gamma )(-k) with k=1.2+/-0.2 indicating non-Newtonian and shear-thinning features independent of ionic strength. The static structure factor S(q) deduced from SANS data in the low wave vector (0.018 A(-1)

  11. H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-renewal and Differentiation

    PubMed Central

    Hu, Gangqing; Cui, Kairong; Northrup, Daniel; Liu, Chengyu; Wang, Chaochen; Tang, Qingsong; Ge, Kai; Levens, David; Crane-Robinson, Colyn; Zhao, Keji

    2012-01-01

    Summary Chromatin modifications have been implicated in the self-renewal and differentiation of embryonic stem cells (ESCs). However, the function of histone variant H2A.Z in ESCs remains unclear. We show that H2A.Z is highly enriched at promoters and enhancers and is required for both efficient self-renewal and differentiation of murine ESCs. H2A.Z deposition leads to an abnormal nucleosome structure, decreased nucleosome occupancy and increased chromatin accessibility. In self-renewing ESCs, knockdown of H2A.Z compromises OCT4 binding to its target genes and leads to decreased binding of MLL complexes to active genes and of PRC2 complex to repressed genes. During differentiation of ESCs, inhibition of H2A.Z also compromises RA-induced RARα binding, activation of differentiation markers and the repression of pluripotency genes. We propose that H2A.Z mediates such contrasting activities by acting as a ‘general facilitator’ that generates access for a variety of complexes both activating and repressive. PMID:23260488

  12. DNA–PKcs–SIN1 complexation mediates low-dose X-ray irradiation (LDI)-induced Akt activation and osteoblast differentiation

    SciTech Connect

    Xu, Yong; Fang, Shi-ji; Zhu, Li-juan; Zhu, Lun-qing; Zhou, Xiao-zhong

    2014-10-24

    Highlights: • LDI increases ALP activity, promotes type I collagen (Col I)/Runx2 mRNA expression. • LDI induces DNA–PKcs activation, which is required for osteoblast differentiation. • Akt activation mediates LDI-induced ALP activity and Col I/Runx2 mRNA increase. • DNA–PKcs–SIN1 complexation mediates LDI-induced Akt Ser-473 phosphorylation. • DNA–PKcs–SIN1 complexation is important for osteoblast differentiation. - Abstract: Low-dose irradiation (LDI) induces osteoblast differentiation, however the underlying mechanisms are not fully understood. In this study, we explored the potential role of DNA-dependent protein kinase catalytic subunit (DNA–PKcs)–Akt signaling in LDI-induced osteoblast differentiation. We confirmed that LDI promoted mouse calvarial osteoblast differentiation, which was detected by increased alkaline phosphatase (ALP) activity as well as mRNA expression of type I collagen (Col I) and runt-related transcription factor 2 (Runx2). In mouse osteoblasts, LDI (1 Gy) induced phosphorylation of DNA–PKcs and Akt (mainly at Ser-473). The kinase inhibitors against DNA–PKcs (NU-7026 and NU-7441) or Akt (LY294002, perifosine and MK-2206), as well as partial depletion of DNA–PKcs or Akt1 by targeted-shRNA, dramatically inhibited LDI-induced Akt activation and mouse osteoblast differentiation. Further, siRNA-knockdown of SIN1, a key component of mTOR complex 2 (mTORC2), also inhibited LDI-induced Akt Ser-473 phosphorylation as well as ALP activity increase and Col I/Runx2 expression in mouse osteoblasts. Co-immunoprecipitation (Co-IP) assay results demonstrated that LDI-induced DNA–PKcs–SIN1 complexation, which was inhibited by NU-7441 or SIN1 siRNA-knockdown in mouse osteoblasts. In summary, our data suggest that DNA–PKcs–SIN1 complexation-mediated Akt activation (Ser-473 phosphorylation) is required for mouse osteoblast differentiation.

  13. Critical roles of mTOR Complex 1 and 2 for T follicular helper cell differentiation and germinal center responses.

    PubMed

    Yang, Jialong; Lin, Xingguang; Pan, Yun; Wang, Jinli; Chen, Pengcheng; Huang, Hongxiang; Xue, Hai-Hui; Gao, Jimin; Zhong, Xiao-Ping

    2016-09-30

    T follicular helper (Tfh) cells play critical roles for germinal center responses and effective humoral immunity. We report here that mTOR in CD4 T cells is essential for Tfh differentiation. In Mtor(f/f)-Cd4Cre mice, both constitutive and inducible Tfh differentiation is severely impaired, leading to defective germinal center B cell formation and antibody production. Moreover, both mTORC1 and mTORC2 contribute to Tfh and GC B cell development but may do so via distinct mechanisms. mTORC1 mainly promotes CD4 T cell proliferation to reach the cell divisions necessary for Tfh differentiation, while Rictor/mTORC2 regulates Tfh differentiation by promoting Akt activation and TCF1 expression without grossly influencing T cell proliferation. Together, our results reveal crucial but distinct roles for mTORC1 and mTORC2 in CD4 T cells during Tfh differentiation and germinal center responses.

  14. Differential and quantitative molecular analysis of ischemia complexity reduction by isotopic labeling of proteins using a neural embryonic stem cell model.

    PubMed

    Schrattenholz, A; Wozny, W; Klemm, M; Schroer, K; Stegmann, W; Cahill, M A

    2005-03-15

    The analysis of rapid changes of protein expression in living systems in response to insults requires rigorous methods of complexity reduction. To control dynamic pattern of hundreds or even thousands of protein isoforms, we applied a novel method of differential molecular analysis to a cellular model which is suited to study ischemia. Neural derivatives of murine embryonic stem cells were exposed to chemical ischemia. The model was used to obtain starting material for a quantitative differential proteomics analysis. Fractionation of phosphoproteins from these samples and subsequent identification by mass spectrometry of differential proteins provide proof of principle of how novel molecular analytical tools provide new insight into the network of neuroprotective molecular events during specific situations of neuronal stress and related pharmaceutical intervention. Our results indicate a particular role of an isoform of the acidic calcium-independent phospholipase A2 in this type of insult.

  15. Epidermal differentiation complex (locus 1q21) gene expression in head and neck cancer and normal mucosa.

    PubMed

    Tyszkiewicz, Tomasz; Jarzab, Michal; Szymczyk, Cezary; Kowal, Monika; Krajewska, Jolanta; Jaworska, Magdalena; Fraczek, Marcin; Krajewska, Anna; Hadas, Ewa; Swierniak, Michal; Markowski, Jaroslaw; Lange, Dariusz; Poltorak, Stanislaw; Wiench, Malgorzata; Krecicki, Tomasz; Jarzab, Jerzy; Maciejewski, Adam

    2014-01-01

    Epidermal differentiation complex (EDC) comprises a number of genes associated with human skin diseases including psoriasis, atopic dermatitis and hyperkeratosis. These genes have also been linked to numerous cancers, among them skin, gastric, colorectal, lung, ovarian and renal carcinomas. The involvement of EDC components encoding S100 proteins, small proline-rich proteins (SPRRs) and other genes in the tumorigenesis of head and neck squamous cell cancer (HNSCC) has been previously suggested. The aim of the study was to systematically analyze the expression of EDC components on the transcript level in HNSCC. Tissue specimens from 93 patients with HNC of oral cavity and 87 samples from adjacent or distant grossly normal oral mucosawere analyzed. 48 samples (24 tumor and 24 corresponding surrounding tissue) were hybridized to Affymetrix GeneChip Human 1.0 ST Arrays. For validation by quantitative real-time PCR (QPCR) the total RNA from all180 samples collected in the study was analyzed with Real-Time PCR system and fluorescent amplicon specific-probes. Additional set of samples from 14 patients with laryngeal carcinoma previously obtained by HG-U133 Plus 2.0 microarray was also included in the analyses. The expression of analyzed EDC genes was heterogeneous. Two transcripts (S100A1 and S100A4) were significantly down-regulated in oral cancer when compared to normal mucosa (0.69 and 0.36-fold change, respectively), showing an opposite pattern of expression to the remaining S100 genes. Significant up-regulation in tumors was found for S100A11, S100A7, LCE3D, S100A3 and S100A2 genes. The increased expression of S100A7 was subsequently validated by QPCR, confirming significant differences. The remaining EDC genes, including all encoding SPRR molecules, did not show any differences between oral cancer and normal mucosa. The observed differences were also assessed in the independent set of laryngeal cancer samples, confirming the role of S100A3 and LCE3D transcripts in

  16. The CCR4-NOT Complex Mediates Deadenylation and Degradation of Stem Cell mRNAs and Promotes Planarian Stem Cell Differentiation

    PubMed Central

    Solana, Jordi; Gamberi, Chiara; Mihaylova, Yuliana; Grosswendt, Stefanie; Chen, Chen; Lasko, Paul; Rajewsky, Nikolaus; Aboobaker, A. Aziz

    2013-01-01

    Post-transcriptional regulatory mechanisms are of fundamental importance to form robust genetic networks, but their roles in stem cell pluripotency remain poorly understood. Here, we use freshwater planarians as a model system to investigate this and uncover a role for CCR4-NOT mediated deadenylation of mRNAs in stem cell differentiation. Planarian adult stem cells, the so-called neoblasts, drive the almost unlimited regenerative capabilities of planarians and allow their ongoing homeostatic tissue turnover. While many genes have been demonstrated to be required for these processes, currently almost no mechanistic insight is available into their regulation. We show that knockdown of planarian Not1, the CCR4-NOT deadenylating complex scaffolding subunit, abrogates regeneration and normal homeostasis. This abrogation is primarily due to severe impairment of their differentiation potential. We describe a stem cell specific increase in the mRNA levels of key neoblast genes after Smed-not1 knock down, consistent with a role of the CCR4-NOT complex in degradation of neoblast mRNAs upon the onset of differentiation. We also observe a stem cell specific increase in the frequency of longer poly(A) tails in these same mRNAs, showing that stem cells after Smed-not1 knock down fail to differentiate as they accumulate populations of transcripts with longer poly(A) tails. As other transcripts are unaffected our data hint at a targeted regulation of these key stem cell mRNAs by post-transcriptional regulators such as RNA-binding proteins or microRNAs. Together, our results show that the CCR4-NOT complex is crucial for stem cell differentiation and controls stem cell-specific degradation of mRNAs, thus providing clear mechanistic insight into this aspect of neoblast biology. PMID:24367277

  17. The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation.

    PubMed

    Solana, Jordi; Gamberi, Chiara; Mihaylova, Yuliana; Grosswendt, Stefanie; Chen, Chen; Lasko, Paul; Rajewsky, Nikolaus; Aboobaker, A Aziz

    2013-01-01

    Post-transcriptional regulatory mechanisms are of fundamental importance to form robust genetic networks, but their roles in stem cell pluripotency remain poorly understood. Here, we use freshwater planarians as a model system to investigate this and uncover a role for CCR4-NOT mediated deadenylation of mRNAs in stem cell differentiation. Planarian adult stem cells, the so-called neoblasts, drive the almost unlimited regenerative capabilities of planarians and allow their ongoing homeostatic tissue turnover. While many genes have been demonstrated to be required for these processes, currently almost no mechanistic insight is available into their regulation. We show that knockdown of planarian Not1, the CCR4-NOT deadenylating complex scaffolding subunit, abrogates regeneration and normal homeostasis. This abrogation is primarily due to severe impairment of their differentiation potential. We describe a stem cell specific increase in the mRNA levels of key neoblast genes after Smed-not1 knock down, consistent with a role of the CCR4-NOT complex in degradation of neoblast mRNAs upon the onset of differentiation. We also observe a stem cell specific increase in the frequency of longer poly(A) tails in these same mRNAs, showing that stem cells after Smed-not1 knock down fail to differentiate as they accumulate populations of transcripts with longer poly(A) tails. As other transcripts are unaffected our data hint at a targeted regulation of these key stem cell mRNAs by post-transcriptional regulators such as RNA-binding proteins or microRNAs. Together, our results show that the CCR4-NOT complex is crucial for stem cell differentiation and controls stem cell-specific degradation of mRNAs, thus providing clear mechanistic insight into this aspect of neoblast biology.

  18. Mutations within the LINC-HELLP non-coding RNA differentially bind ribosomal and RNA splicing complexes and negatively affect trophoblast differentiation.

    PubMed

    van Dijk, Marie; Visser, Allerdien; Buabeng, Kwadwo M L; Poutsma, Ankie; van der Schors, Roel C; Oudejans, Cees B M

    2015-10-01

    LINC-HELLP, showing chromosomal linkage with the pregnancy-specific HELLP syndrome in Dutch families, reduces differentiation from a proliferative to an invasive phenotype of first-trimester extravillous trophoblasts. Here we show that mutations in LINC-HELLP identified in HELLP families negatively affect this trophoblast differentiation either by inducing proliferation rate or by causing cell cycle exit as shown by a decrease in both proliferation and invasion. As LincRNAs predominantly function through interactions with proteins, we identified the directly interacting proteins using chromatin isolation by RNA purification followed by protein mass spectrometry. We found 22 proteins predominantly clustering in two functional networks, i.e. RNA splicing and the ribosome. YBX1, PCBP1, PCBP2, RPS6 and RPL7 were validated, and binding to these proteins was influenced by the HELLP mutations carried. Finally, we show that the LINC-HELLP transcript levels are significantly upregulated in plasma of women in their first trimester of pregnancy compared with non-pregnant women, whereas this upregulation seems absent in a pilot set of patients later developing pregnancy complications, indicative of its functional significance in vivo.

  19. Erythroid differentiation of mouse erythroleukemia cells results in reorganization of protein-DNA complexes in the mouse beta maj globin promoter but not its distal enhancer.

    PubMed Central

    Reddy, P M; Shen, C K

    1993-01-01

    Dimethyl sulfoxide (DMSO) induction of mouse erythroleukemia (MEL) cells represents a well-defined in vitro system of terminal erythroid differentiation. We have studied the molecular mechanisms of transcriptional activation of the mouse beta maj globin gene during MEL cell differentiation by analyzing nuclear factor-DNA interactions in vivo at the gene's upstream promoter and a distal enhancer, 5'HS-2. Genomic footprinting data indicate that three motifs, CAC, NF-E2/AP1, and GATA-1, of the 5'HS-2 enhancer are bound with nuclear factors in MEL cells both prior to and after DMSO induction. No obvious conformational change of these nuclear factor-DNA complexes could be detected upon terminal differentiation of MEL cells. On the other hand, DMSO induction of MEL cells leads to the formation of specific nuclear factor-DNA complexes at several transcriptional regulatory elements of the mouse beta maj globin upstream promoter. Our genomic footprinting data have interesting implications with respect to the molecular mechanisms of transcriptional regulation and chromatin change of the mouse beta maj globin gene during erythroid differentiation. Images PMID:8423777

  20. Usefulness of the GenoType MTBC Assay for Differentiating Species of the Mycobacterium tuberculosis Complex in Cultures Obtained from Clinical Specimens

    PubMed Central

    Richter, Elvira; Weizenegger, Michael; Fahr, Anne-Marie; Rüsch-Gerdes, Sabine

    2004-01-01

    A novel DNA strip assay, GenoType MTBC, was evaluated for differentiation of Mycobacterium tuberculosis complex species from 77 positive liquid cultures in clinical practice. Species identification (M. tuberculosis [71 strains], Mycobacterium bovis subsp. bovis [5 strains], and Mycobacterium africanum subtype I [1 strain]) results were identical to conventional results. The sensitivity was slightly higher for this test than for the AccuProbe assay. PMID:15365028

  1. MiRNA-Mediated Regulation of the SWI/SNF Chromatin Remodeling Complex Controls Pluripotency and Endodermal Differentiation in Human ESCs.

    PubMed

    Wade, Staton L; Langer, Lee F; Ward, James M; Archer, Trevor K

    2015-10-01

    MicroRNAs and chromatin remodeling complexes represent powerful epigenetic mechanisms that regulate the pluripotent state. miR-302 is a strong inducer of pluripotency, which is characterized by a distinct chromatin architecture. This suggests that miR-302 regulates global chromatin structure; however, a direct relationship between miR-302 and chromatin remodelers has not been established. Here, we provide data to show that miR-302 regulates Brg1 chromatin remodeling complex composition in human embryonic stem cells (hESCs) through direct repression of the BAF53a and BAF170 subunits. With the subsequent overexpression of BAF170 in hESCs, we show that miR-302's inhibition of BAF170 protein levels can affect the expression of genes involved in cell proliferation. Furthermore, miR-302-mediated repression of BAF170 regulates pluripotency by positively influencing mesendodermal differentiation. Overexpression of BAF170 in hESCs led to biased differentiation toward the ectoderm lineage during EB formation and severely hindered directed definitive endoderm differentiation. Taken together, these data uncover a direct regulatory relationship between miR-302 and the Brg1 chromatin remodeling complex that controls gene expression and cell fate decisions in hESCs and suggests that similar mechanisms are at play during early human development.

  2. Ski Regulates Muscle Terminal Differentiation by Transcriptional Activation of Myog in a Complex with Six1 and Eya3*S⃞

    PubMed Central

    Zhang, Hong; Stavnezer, Ed

    2009-01-01

    Overexpression of the Ski pro-oncogene has been shown to induce myogenesis in non-muscle cells, to promote muscle hypertrophy in postnatal mice, and to activate transcription of muscle-specific genes. However, the precise role of Ski in muscle cell differentiation and its underlying molecular mechanism are not fully understood. To elucidate the involvement of Ski in muscle terminal differentiation, two retroviral systems were used to achieve conditional overexpression or knockdown of Ski in satellite cell-derived C2C12 myoblasts. We found that enforced expression of Ski promoted differentiation, whereas loss of Ski severely impaired it. Compromised terminal differentiation in the absence of Ski was likely because of the failure to induce myogenin (Myog) and p21 despite normal expression of MyoD. Chromatin immunoprecipitation and transcriptional reporter experiments showed that Ski occupied the endogenous Myog regulatory region and activated transcription from the Myog regulatory region upon differentiation. Transactivation of Myog was largely dependent on a MEF3 site bound by Six1, not on the binding site of MyoD or MEF2. Activation of the MEF3 site required direct interaction of Ski with Six1 and Eya3 mediated by the evolutionarily conserved Dachshund homology domain of Ski. Our results indicate that Ski is necessary for muscle terminal differentiation and that it exerts this role, at least in part, through its association with Six1 and Eya3 to regulate the Myog transcription. PMID:19008232

  3. Critical roles of mTOR Complex 1 and 2 for T follicular helper cell differentiation and germinal center responses

    PubMed Central

    Yang, Jialong; Lin, Xingguang; Pan, Yun; Wang, Jinli; Chen, Pengcheng; Huang, Hongxiang; Xue, Hai-Hui; Gao, Jimin; Zhong, Xiao-Ping

    2016-01-01

    T follicular helper (Tfh) cells play critical roles for germinal center responses and effective humoral immunity. We report here that mTOR in CD4 T cells is essential for Tfh differentiation. In Mtorf/f-Cd4Cre mice, both constitutive and inducible Tfh differentiation is severely impaired, leading to defective germinal center B cell formation and antibody production. Moreover, both mTORC1 and mTORC2 contribute to Tfh and GC B cell development but may do so via distinct mechanisms. mTORC1 mainly promotes CD4 T cell proliferation to reach the cell divisions necessary for Tfh differentiation, while Rictor/mTORC2 regulates Tfh differentiation by promoting Akt activation and TCF1 expression without grossly influencing T cell proliferation. Together, our results reveal crucial but distinct roles for mTORC1 and mTORC2 in CD4 T cells during Tfh differentiation and germinal center responses. DOI: http://dx.doi.org/10.7554/eLife.17936.001 PMID:27690224

  4. Ephrin B1 regulates bone marrow stromal cell differentiation and bone formation by influencing TAZ transactivation via complex formation with NHERF1.

    PubMed

    Xing, Weirong; Kim, Jonghyun; Wergedal, Jon; Chen, Shin-Tai; Mohan, Subburaman

    2010-02-01

    Mutations of ephrin B1 in humans result in craniofrontonasal syndrome. Because little is known of the role and mechanism of action of ephrin B1 in bone, we examined the function of osteoblast-produced ephrin B1 in vivo and identified the molecular mechanism by which ephrin B1 reverse signaling regulates bone formation. Targeted deletion of the ephrin B1 gene in type 1alpha2 collagen-producing cells resulted in severe calvarial defects, decreased bone size, bone mineral density, and trabecular bone volume, caused by impairment in osterix expression and osteoblast differentiation. Coimmunoprecipitation of the TAZ complex with TAZ-specific antibody revealed a protein complex containing ephrin B1, PTPN13, NHERF1, and TAZ in bone marrow stromal (BMS) cells. Activation of ephrin B1 reverse signaling with soluble EphB2-Fc led to a time-dependent increase in TAZ dephosphorylation and shuttling from cytoplasm to nucleus. Treatment of BMS cells with exogenous EphB2-Fc resulted in a 4-fold increase in osterix expression as determined by Western blotting. Disruption of TAZ expression using specific lentivirus small hairpin RNA (shRNA) decreased TAZ mRNA by 80% and ephrin B1 reverse signaling-mediated increases in osterix mRNA by 75%. Knockdown of NHERF1 expression reduced basal levels of osterix expression by 90% and abolished ephrin B1-mediated induction of osterix expression. We conclude that locally produced ephrin B1 mediates its effects on osteoblast differentiation by a novel molecular mechanism in which activation of reverse signaling leads to dephosphorylation of TAZ and subsequent release of TAZ from the ephrin B1/NHERF1/TAZ complex to translocate to the nucleus to induce expression of the osterix gene and perhaps other osteoblast differentiation genes. Our findings provide strong evidence that ephrin B1 reverse signaling in osteoblasts is critical for BMS cell differentiation and bone formation.

  5. Compromised liver mitochondrial function and complex activity in low feed efficient broilers are associated with higher oxidative stress and differential protein expression.

    PubMed

    Iqbal, M; Pumford, N R; Tang, Z X; Lassiter, K; Ojano-Dirain, C; Wing, T; Cooper, M; Bottje, W

    2005-06-01

    Variations in broiler growth and efficiency have been explained in part by differences in mitochondrial function and biochemistry in broilers. To further our knowledge in this regard, 2 experiments were carried out to determine the relationships of a) mitochondrial function and activities of various electron transport chain (ETC) complexes; b) production of H2O2, a reactive oxygen species (ROS), and its association with protein oxidation; and c) mitochondrial protein expression in liver of a single line male broilers with low or high feed efficiency (FE, n = 5 to 8 per group). Mitochondrial function and complex activities were measured polarographically and spectrophotometrically, respectively. H2O2 was measured fluorimetrically, whereas oxidized protein (carbonyls) and specific mitochondrial proteins were analyzed using Western blots. Mitochondrial function (ETC coupling) and activities of ETC complexes (I, II, III, and IV) were higher in high FE compared with low FE broilers. H2O2 and protein carbonyls were higher in the livers of low FE broilers than in high FE broilers. Whereas the expression of 4 immunoreactive proteins [NAD3 (complex I), subunit VII (complex III), cytochrome c oxidase subunits (COX) II, and COX IVb (complex IV)] were higher in low FE liver mitochondria and 2 proteins [subunit 70 (complex II) and a-ATP synthase (complex V)] were higher in high FE birds, there were no differences between groups in the expression of 18 other mitochondrial proteins. In conclusion, increases in oxidative stress in low FE broilers were caused by or may contribute to differences in mitochondrial function (ETC coupling and complex activities) or the differential expression of steady-state levels of some mitochondrial proteins in the liver. Understanding the role of oxidative stress in Low FE broilers will provide clues in understanding the cellular basis of feed efficiency.

  6. Quantum state-resolved differential cross sections for complex-forming chemical reactions: Asymmetry is the rule, symmetry the exception

    SciTech Connect

    Larrégaray, Pascal Bonnet, Laurent

    2015-10-14

    We argue that statistical theories are generally unable to accurately predict state-resolved differential cross sections for triatomic bimolecular reactions studied in beam experiments, even in the idealized limit where the dynamics are fully chaotic. The basic reason is that quenching of interferences between partial waves is less efficient than intuitively expected, especially around the poles.

  7. Evaluation of the p-nitro-alpha-acetylamino-beta-hydroxypropiophenone differential test for identification of Mycobacterium tuberculosis complex.

    PubMed Central

    Morgan, M A; Doerr, K A; Hempel, H O; Goodman, N L; Roberts, G D

    1985-01-01

    The p-nitro-alpha-acetylamino-beta-hydroxypropiophenone (NAP) differential test for the identification of Mycobacterium tuberculosis recovered from clinical specimens was evaluated by two laboratories and found to be a rapid and accurate procedure with a specificity exceeding 99%. PMID:3921563

  8. The dependance of neuronal reactions of the sensorimotor cortex to a simultaneous complex stimulus upon the level of differentiation of its components.

    PubMed

    Yunatov YuA; Perfil'ev, S N; Cherenkova, L V

    1993-01-01

    The change in the neuronal activity of the sensorimotor area of the cerebral cortex of the cat was investigated in awake animals as a function of the level of differentiation of the components of a simultaneous heteromodal complex stimulus. Two groups of neurons in the sensorimotor cortex were distinguished on the basis of the character of this relationship and a number of other parameters. It was shown that the parameters of the reactions of all neurons recorded to the positive conditional stimulus following the consolidation of the conditioned motoric reaction are established first. Such parameters of the responses as degree of manifestation, intensity, duration, and the length of the latent period changed in the process of development. The reactions of neurons of both groups to inhibitory signals were stabilized only after the consolidation of the differentiation skill. In the process only the pattern of the discharge changed in the neurons of the first group, while in the neurons of the second group, the degree of manifestation of the response, its sign, duration, and length of the latent period could vary. Fluctuations in the level of differentiation following the development of the inhibitory conditioned reactions had an effect only on the responses of the neurons of the second group to the components of the complex.

  9. BM-MSCs and Bio-Oss complexes enhanced new bone formation during maxillary sinus floor augmentation by promoting differentiation of BM-MSCs.

    PubMed

    Zhou, Qian; Yu, Bo-Han; Liu, Wei-Cai; Wang, Zuo-Lin

    2016-08-01

    Bone marrow-derived mesenchymal stem cells (BM-MSCs) have been recognized as a new strategy for maxillary sinus floor elevation. However, little is known concerning the effect of the biomechanical pressure (i.e., sinus pressure, masticatory pressure, and respiration) on the differentiation of BM-MSCs and the formation of new bone during maxillary sinus floor elevation. The differentiation of BM-MSCs into osteoblasts was examined in vitro under cyclic compressive pressure using the Flexcell® pressure system, and by immunohistochemical analysis, qRT-PCR, and Western blot. Micro-CT was used to detect bone formation and allow image reconstruction of the entire maxillary sinus floor elevation area. Differentiation of BM-MSCs into osteoblasts was significantly increased under cyclic compressive pressure. The formation of new bone was enhanced after implantation of the pressured complex of BM-MSCs and Bio-Oss during maxillary sinus floor elevation. The pressured complex of BM-MSCs and Bio-Oss promoted new bone formation and maturation in the rabbit maxillary sinus. Stem cell therapy combined with this tissue engineering technique could be effectively used in maxillary sinus elevation and bone regeneration.

  10. VPS37 isoforms differentially modulate the ternary complex formation of ALIX, ALG-2, and ESCRT-I.

    PubMed

    Okumura, Mayumi; Katsuyama, Angela M; Shibata, Hideki; Maki, Masatoshi

    2013-01-01

    The endosomal sorting complex required for transport (ESCRT) system comprises a series of protein complexes that play essential roles in multivesicular body (MVB) sorting of ubiquitylated membrane proteins, enveloped RNA virus budding, and cytokinesis in mammalian cells. The complex, named ESCRT-I, consists of four subunits (TSG101, VPS28, VPS37, and MVB12). There are four VPS37 isoforms. We have reported that ALIX (an ALG-2-interacting protein and accessory protein in the ESCRT system) is physically linked with TSG101 by ALG-2 in a Ca²⁺-dependent manner, but the role of ALG-2 as an adaptor protein for the ESCRT-I complex remains unknown. To characterize this adaptor function, initially we investigated the binding of ALG-2 to ESCRT-I complexes containing each one of the four different VPS37 isoforms by two approaches: first, Far-Western blot analysis with biotin-labeled ALG-2 probe, and second, a pulldown assay to determine the binding of the four recombinant ESCRT-I complexes to Strep-tagged ALG-2 after co-expression in HEK293T cells. VPS37B and VPS37C appeared to interact with ALG-2 in a stronger manner than TSG101 does. The results of in vitro binding assays using purified recombinant proteins indicated that ALG-2 functions as a Ca²⁺-dependent adaptor protein that bridges ALIX and ESCRT-I to form a ternary complex, ESCRT-I/ALIX/ALG-2.

  11. The polycomb complex protein mes-2/E(z) promotes the transition from developmental plasticity to differentiation in C. elegans embryos.

    PubMed

    Yuzyuk, T; Fakhouri, T H I; Kiefer, J; Mango, S E

    2009-05-01

    We have used expression profiling and in vivo imaging to characterize Caenorhabditis elegans embryos as they transit from a developmentally plastic state to the onset of differentiation. Normally, this transition is accompanied by activation of developmental regulators and differentiation genes, downregulation of early-expressed genes, and large-scale reorganization of chromatin. We find that loss of plasticity and differentiation onset depends on the Polycomb complex protein mes-2/E(Z). mes-2 mutants display prolonged developmental plasticity in response to heterologous developmental regulators. Early-expressed genes remain active, differentiation genes fail to reach wild-type levels, and chromatin retains a decompacted morphology in mes-2 mutants. By contrast, loss of the developmental regulators pha-4/FoxA or end-1/GATA does not prolong plasticity. This study establishes a model by which to analyze developmental plasticity within an intact embryo. mes-2 orchestrates large-scale changes in chromatin organization and gene expression to promote the timely loss of developmental plasticity. Our findings indicate that loss of plasticity can be uncoupled from cell fate specification.

  12. CXCR4 undergoes complex lineage and inducing agent-dependent dissociation of expression and functional responsiveness to SDF-1alpha during myeloid differentiation.

    PubMed

    Gupta, S K; Pillarisetti, K; Aiyar, N

    2001-09-01

    The CXC chemokine SDF-1 and its receptor CXCR4 mediate myelopoiesis, presumably by regulating the homing of hematopoietic progenitor cells. We used the inducible HL-60 cell line as a model system for comparative analysis of CXCR4 expression during differential maturation into the granulocytic or monocytic phenotypes. Five different measures of CXCR4 expression and functional coupling: mRNA and surface expression, SDF-1-mediated [(35)S]GTPgammaS binding, calcium flux, and chemotaxis were examined simultaneously. Granulocytic differentiation with dimethyl sulfoxide induced surface expression of CXCR4 as well as SDF-1-mediated [(35)S]GTPgammaS binding and chemotaxis, whereas calcium flux was attenuated by twofold to threefold in HL-60 cells. Conversely, monocytic differentiation with vitamin D(3) inhibited surface expression and SDF-1-mediated chemotaxis, even as it induced [(35)S]GTPgammaS binding and calcium flux by more than twofold. Sodium butyrate up-regulated all parameters of CXCR4 expression studied. Together, these results demonstrate that CXCR4 expression undergoes complex regulation at multiple checkpoints, with the likely involvement of different G-proteins for signal transduction during cellular differentiation and following activation with SDF-1.

  13. Differential effects of buffer pH on Ca2+-induced ROS emission with inhibited mitochondrial complexes I and III

    PubMed Central

    Lindsay, Daniel P.; Camara, Amadou K. S.; Stowe, David F.; Lubbe, Ryan; Aldakkak, Mohammed

    2015-01-01

    Excessive mitochondrial reactive oxygen species (ROS) emission is a critical component in the etiology of ischemic injury. Complex I and complex III of the electron transport chain are considered the primary sources of ROS emission during cardiac ischemia and reperfusion (IR) injury. Several factors modulate ischemic ROS emission, such as an increase in extra-matrix Ca2+, a decrease in extra-matrix pH, and a change in substrate utilization. Here we examined the combined effects of these factors on ROS emission from respiratory complexes I and III under conditions of simulated IR injury. Guinea pig heart mitochondria were suspended in experimental buffer at a given pH and incubated with or without CaCl2. Mitochondria were then treated with either pyruvate, a complex I substrate, followed by rotenone, a complex I inhibitor, or succinate, a complex II substrate, followed by antimycin A, a complex III inhibitor. H2O2 release rate and matrix volume were compared with and without adding CaCl2 and at pH 7.15, 6.9, or 6.5 with pyruvate + rotenone or succinate + antimycin A to simulate conditions that may occur during in vivo cardiac IR injury. We found a large increase in H2O2 release with high [CaCl2] and pyruvate + rotenone at pH 6.9, but not at pHs 7.15 or 6.5. Large increases in H2O2 release rate also occurred at each pH with high [CaCl2] and succinate + antimycin A, with the highest levels observed at pH 7.15. The increases in H2O2 release were associated with significant mitochondrial swelling, and both H2O2 release and swelling were abolished by cyclosporine A, a desensitizer of the mitochondrial permeability transition pore (mPTP). These results indicate that ROS production by complex I and by complex III is differently affected by buffer pH and Ca2+ loading with mPTP opening. The study suggests that changes in the levels of cytosolic Ca2+ and pH during IR alter the relative amounts of ROS produced at mitochondrial respiratory complex I and complex III. PMID

  14. Adaptive differentiation in seedling traits in a hybrid pine species complex, Pinus densata and its parental species, on the Tibetan Plateau.

    PubMed

    Meng, Jingxiang; Mao, Jian-Feng; Zhao, Wei; Xing, Fangqian; Chen, Xinyu; Liu, Hao; Xing, Zhen; Wang, Xiao-Ru; Li, Yue

    2015-01-01

    Evidence from molecular genetics demonstrates that Pinus densata is a natural homoploid hybrid originating from the parent species Pinus tabuliformis and Pinus yunnanensis, and ecological selection may have played a role in the speciation of P. densata. However, data on differentiation in adaptive traits in the species complex are scarce. In this study, we performed a common garden test on 16 seedling traits to examine the differences between P. densata and its parental species in a high altitude environment. We found that among the 16 analyzed traits, 15 were significantly different among the species. Pinus tabuliformis had much earlier bud set and a relatively higher bud set ratio but poorer seedling growth, and P. yunnanensis had opposite responses for the same traits. P. densata had the greatest fitness with higher viability and growth rates than the parents. The relatively high genetic contribution of seedling traits among populations suggested that within each species the evolutionary background is complex. The correlations between the seedling traits of a population within a species and the environmental factors indicated different impacts of the environment on species evolution. The winter temperature is among the most important climate factors that affected the fitness of the three pine species. Our investigation provides empirical evidence on adaptive differentiation among this pine species complex at seedling stages.

  15. Adaptive Differentiation in Seedling Traits in a Hybrid Pine Species Complex, Pinus densata and Its Parental Species, on the Tibetan Plateau

    PubMed Central

    Meng, Jingxiang; Mao, Jian-Feng; Zhao, Wei; Xing, Fangqian; Chen, Xinyu; Liu, Hao; Xing, Zhen; Wang, Xiao-Ru; Li, Yue

    2015-01-01

    Evidence from molecular genetics demonstrates that Pinus densata is a natural homoploid hybrid originating from the parent species Pinus tabuliformis and Pinus yunnanensis, and ecological selection may have played a role in the speciation of P. densata. However, data on differentiation in adaptive traits in the species complex are scarce. In this study, we performed a common garden test on 16 seedling traits to examine the differences between P. densata and its parental species in a high altitude environment. We found that among the 16 analyzed traits, 15 were significantly different among the species. Pinus tabuliformis had much earlier bud set and a relatively higher bud set ratio but poorer seedling growth, and P. yunnanensis had opposite responses for the same traits. P. densata had the greatest fitness with higher viability and growth rates than the parents. The relatively high genetic contribution of seedling traits among populations suggested that within each species the evolutionary background is complex. The correlations between the seedling traits of a population within a species and the environmental factors indicated different impacts of the environment on species evolution. The winter temperature is among the most important climate factors that affected the fitness of the three pine species. Our investigation provides empirical evidence on adaptive differentiation among this pine species complex at seedling stages. PMID:25757072

  16. Differentiation of frogs from two populations belonging to the Pelophylax esculentus complex by LC-MS/MS comparison of their skin peptidomes.

    PubMed

    Samgina, Tatiana Yu; Artemenko, Konstantin A; Bergquist, Jonas; Trebse, Polonca; Torkar, Gregor; Tolpina, Miriam D; Lebedev, Albert T

    2017-03-01

    LC-MS/MS was applied to establish the composition of the skin peptidome of a Slovenian green frog belonging to the Pelophylax esculentus complex. As this was similar to the peptidome of the Moscow population of Pelophylax ridibundus, it allowed us to identify the Slovenian frog from the Pelophylax esculentus complex as Pelophylax ridibundus. The sequences of six new peptides from the brevinin 2 family are reported for the first time on the basis of manual interpretation of their tandem mass spectra. The structural similarity of the brevinin 2 peptides from the Moscow and Slovenian populations of Pelophylax ridibundus enables peptides from this family to be utilized as biomarkers for Pelophylax ridibundus inter- and intraspecies differentiation, and the proposed approach can be used as an analytical tool for differentiating the corresponding species and populations. The potential biological activities of the novel peptides were estimated by 2D mass mapping. The results allowed us to classify all of the available peptides belonging to the brevinin 2 family. Graphical Abstract Intraspecies identification within the green frog complex.

  17. A dual role for the dREAM/MMB complex in the regulation of differentiation-specific E2F/RB target genes.

    PubMed

    Lee, Hangnoh; Ragusano, Linda; Martinez, Ana; Gill, Jagdip; Dimova, Dessislava K

    2012-06-01

    E2F and RB proteins regulate the expression of genes involved in cell cycle progression, apoptosis, differentiation, and development. Recent studies indicate that they function as part of an evolutionarily conserved multiprotein complex termed dREAM/DREAM/LINC. Here we characterize the role of the Drosophila complex, dREAM, in the regulation of differentiation-specific E2F target genes in actively proliferating cells. These genes are regulated differently from cell cycle-related E2F targets, they do not depend on E2F activation, and E2F/RB repression is maintained throughout the cell cycle. In proliferating cells, their repression is dependent on dREAM. We find that dREAM plays a dual role in their regulation. First, it is required for the stability of the repressive dE2F2/RBF complexes at their promoters during S phase. Second, we find that dREAM is indispensable for both transcriptional repression mechanisms employed at these genes.

  18. Identification of a novel intermediate filament-linked N-cadherin/gamma-catenin complex involved in the establishment of the cytoarchitecture of differentiated lens fiber cells.

    PubMed

    Leonard, Michelle; Chan, Yim; Menko, A Sue

    2008-07-15

    Tissue morphogenesis and maintenance of complex tissue architecture requires a variety of cell-cell junctions. Typically, cells adhere to one another through cadherin junctions, both adherens and desmosomal junctions, strengthened by association with cytoskeletal networks during development. Both beta- and gamma-catenins are reported to link classical cadherins to the actin cytoskeleton, but only gamma-catenin binds to the desmosomal cadherins, which links them to intermediate filaments through its association with desmoplakin. Here we provide the first biochemical evidence that, in vivo, gamma-catenin also mediates interactions between classical cadherins and the intermediate filament cytoskeleton, linked through desmoplakin. In the developing lens, which has no desmosomes, we discovered that vimentin became linked to N-cadherin complexes in a differentiation-state specific manner. This newly identified junctional complex was tissue specific but not unique to the lens. To determine whether in this junction N-cadherin was linked to vimentin through gamma-catenin or beta-catenin we developed an innovative "double" immunoprecipitation technique. This approach made possible, for the first time, the separation of N-cadherin/gamma-catenin from N-cadherin/beta-catenin complexes and the identification of multiple members of each of these isolated protein complexes. The study revealed that vimentin was associated exclusively with N-cadherin/gamma-catenin junctions. Assembly of this novel class of cadherin junctions was coincident with establishment of the unique cytoarchitecture of lens fiber cells. In addition, gamma-catenin had a distinctive localization to the vertices of these hexagonally shaped differentiating lens fiber cells, a region devoid of actin; while beta-catenin co-localized with actin at lateral cell interfaces. We believe this novel vimentin-linked N-cadherin/gamma-catenin junction provides the tensile strength necessary to establish and maintain

  19. Dynamic casting of a graben complex: Syn-sedimentary infill and differential subsidence during the permo-carboniferous; Peace River Embayment, western Canada

    SciTech Connect

    Barclay, J.E. Univ. of Calgary, Alberta ); Krause, F.F. ); Campbell, R.R. Calamity Resources, Calgary, Alberta )

    1991-03-01

    The Carboniferous Stoddart Group and Permian Belloy Formation record infill of a long-lived graben complex in the center of the Peace River Embayment. The Dawson Creek Graben Complex began down-dropping during deposition of the Rundle Group and Golata Formation and reached its maximum during Kiskatinaw time. The overlying Taylor Flat Formation shows graben filling and graben decay; whereas the flat Permian Belloy Formation beds within and beyond graben limits indicate tectonic stability. The complex comprised the larger Fort St. John Graben and satellite Hines Creek, Whitelaw, and Cindy grabens. The grabens consist of kilometer-scale horst and graben blocks bounded by normal faults. The internal blocks subsided at various rates, with differential subsidence occurring in the form of horsts subsiding slower than neighboring grabens. Syn- and post-depositional growth-type normal faults controlled formation and bed thickness, as did inter- and intra-formation unconformities. From these observations, a structural/stratigraphic model can be constructed that explains the complex stratigraphy and depositional interpretations. This model describes a basin dominated by tectonic controls rather than global sea-level events. Syn- and post-sedimentary growth-type block faulting, differential subsidence of fault blocks, sedimentary infill, and unconformity truncation were the major controls on the basin. The model provides an analog to grabens and block-faulted basins of growth-faulted basins occurring elsewhere. The implications of the model to petroleum exploration are that all beds can be correlated by assuming that beds were essentially flat-lying prior to and during faulting. The combination of the block-faulted character and complex facies changes provides many structural and stratigraphic petroleum traps.

  20. Small molecule-based disruption of the Axin/β-catenin protein complex regulates mesenchymal stem cell differentiation.

    PubMed

    Gwak, Jungsug; Hwang, Sun Gwan; Park, Hyung-Soon; Choi, Sang Rak; Park, Sun-Hee; Kim, Hyunjoon; Ha, Nam-Chul; Bae, Sung Jin; Han, Jin-Kwan; Kim, Dong-Eun; Cho, Jeong Woo; Oh, Sangtaek

    2012-01-01

    The Wnt/β-catenin pathway plays important roles in the differentiation of multiple cell types, including mesenchymal stem cells. Using a cell-based chemical screening assay with a synthetic chemical library of 270 000 compounds, we identified the compound SKL2001 as a novel agonist of the Wnt/β-catenin pathway and uncovered its molecular mechanism of action. SKL2001 upregulated β-catenin responsive transcription by increasing the intracellular β-catenin protein level and inhibited the phosphorylation of β-catenin at residues Ser33/37/Thr41 and Ser45, which would mark it for proteasomal degradation, without affecting CK1 and GSK-3β enzyme activities. Biochemical analysis revealed that SKL2001 disrupted the Axin/β-catenin interaction, which is a critical step for CK1- and GSK-3β-mediated phosphorylation of β-catenin at Ser33/37/Thr41 and Ser45. The treatment of mesenchymal stem cells with SKL2001 promoted osteoblastogenesis and suppressed adipocyte differentiation, both of which were accompanied by the activation of Wnt/β-catenin pathway. Our findings provide a new strategy to regulate mesenchymal stem cell differentiation by modulation of the Wnt/β-catenin pathway.

  1. Spin-filtering, giant magnetoresistance, rectifying and negative differential resistance effects in planar four-coordinate Fe complex with graphene nanoribbon electrodes

    NASA Astrophysics Data System (ADS)

    Zhao, P.; Wu, Q. H.; Liu, D. S.; Chen, G.

    2014-01-01

    By using the nonequilibrium Green's function formalism combined with the density functional theory, we have investigated the spin-polarized transport properties of a planar four-coordinate Fe complex sandwiched between two zigzag-edge graphene nanoribbon (ZGNR) electrodes, where the ZGNRs are modulated by external magnetic field. The results show that the system can exhibit perfect dual spin-filtering and spin-rectifying effects at a wide bias range, giant magnetoresistance effect with large magnetoresistance ratio at small bias, and obvious negative differential resistance behavior. The mechanisms are proposed for these phenomena.

  2. Transcriptomic Analysis of Liquid Non-Sporulating Streptomyces coelicolor Cultures Demonstrates the Existence of a Complex Differentiation Comparable to That Occurring in Solid Sporulating Cultures

    PubMed Central

    Yagüe, Paula; Rodríguez-García, Antonio; López-García, María Teresa; Rioseras, Beatriz; Martín, Juan Francisco; Sánchez, Jesús; Manteca, Angel

    2014-01-01

    Streptomyces species produce many clinically relevant secondary metabolites and exhibit a complex development that includes hyphal differentiation and sporulation in solid cultures. Industrial fermentations are usually performed in liquid cultures, conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that no differentiation took place. The aim of this work was to compare the transcriptomes of S. coelicolor growing in liquid and solid cultures, deepening the knowledge of Streptomyces differentiation. Microarrays demonstrated that gene expression in liquid and solid cultures were comparable and data indicated that physiological differentiation was similar for both conditions. Eighty-six percent of all transcripts showed similar abundances in liquid and solid cultures, such as those involved in the biosynthesis of actinorhodin (actVA, actII-4) and undecylprodigiosin (redF); activation of secondary metabolism (absR1, ndsA); genes regulating hydrophobic cover formation (aerial mycelium) (bldB, bldC, bldM, bldN, sapA, chpC, chpD, chpE, chpH, ramA, ramC, ramS); and even some genes regulating early stages of sporulation (wblA, whiG, whiH, whiJ). The two most important differences between transcriptomes from liquid and solid cultures were: first, genes related to secondary metabolite biosynthesis (CDA, CPK, coelichelin, desferrioxamine clusters) were highly up-regulated in liquid but not in solid cultures; and second, genes involved in the final stages of hydrophobic cover/spore maturation (chpF, rdlA, whiE, sfr) were up-regulated in solid but not in liquid cultures. New information was also provided for several non-characterized genes differentially expressed in liquid and solid cultures which might be regulating, at least in part, the metabolic and developmental differences observed between liquid and solid cultures. PMID:24466012

  3. Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures.

    PubMed

    Yagüe, Paula; Rodríguez-García, Antonio; López-García, María Teresa; Rioseras, Beatriz; Martín, Juan Francisco; Sánchez, Jesús; Manteca, Angel

    2014-01-01

    Streptomyces species produce many clinically relevant secondary metabolites and exhibit a complex development that includes hyphal differentiation and sporulation in solid cultures. Industrial fermentations are usually performed in liquid cultures, conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that no differentiation took place. The aim of this work was to compare the transcriptomes of S. coelicolor growing in liquid and solid cultures, deepening the knowledge of Streptomyces differentiation. Microarrays demonstrated that gene expression in liquid and solid cultures were comparable and data indicated that physiological differentiation was similar for both conditions. Eighty-six percent of all transcripts showed similar abundances in liquid and solid cultures, such as those involved in the biosynthesis of actinorhodin (actVA, actII-4) and undecylprodigiosin (redF); activation of secondary metabolism (absR1, ndsA); genes regulating hydrophobic cover formation (aerial mycelium) (bldB, bldC, bldM, bldN, sapA, chpC, chpD, chpE, chpH, ramA, ramC, ramS); and even some genes regulating early stages of sporulation (wblA, whiG, whiH, whiJ). The two most important differences between transcriptomes from liquid and solid cultures were: first, genes related to secondary metabolite biosynthesis (CDA, CPK, coelichelin, desferrioxamine clusters) were highly up-regulated in liquid but not in solid cultures; and second, genes involved in the final stages of hydrophobic cover/spore maturation (chpF, rdlA, whiE, sfr) were up-regulated in solid but not in liquid cultures. New information was also provided for several non-characterized genes differentially expressed in liquid and solid cultures which might be regulating, at least in part, the metabolic and developmental differences observed between liquid and solid cultures.

  4. Role of GenoType(®) Mycobacterium Common Mycobacteria/Additional Species Assay for Rapid Differentiation Between Mycobacterium tuberculosis Complex and Different Species of Non-Tuberculous Mycobacteria.

    PubMed

    Singh, Amresh Kumar; Maurya, Anand Kumar; Umrao, Jyoti; Kant, Surya; Kushwaha, Ram Awadh Singh; Nag, Vijaya Laskshmi; Dhole, Tapan N

    2013-07-01

    Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM) may or may not have same clinical presentations, but the treatment regimens are always different. Laboratory differentiation between MTBC and NTM by routine methods are time consuming and cumbersome to perform. We have evaluated the role of GenoType(®) Mycobacterium common mycobacteria/additional species (CM/AS) assay for differentiation between MTBC and different species of NTM in clinical isolates from tuberculosis (TB) cases. A total of 1080 clinical specimens were collected from January 2010 to June 2012. Diagnosis was performed by Ziehl-Neelsen staining followed by culture in BacT/ALERT 3D system (bioMerieux, France). A total of 219 culture positive clinical isolates (BacT/ALERT(®) MP cultures) were selected for differentiation by p-nitrobenzoic acid (PNB) sensitivity test as and BIO-LINE SD Ag MPT64 TB test considering as the gold standard test. Final identification and differentiation between MTBC and different species of NTM were further confirmed by GenoType(®) Mycobacterium CM/AS assay (Hain Lifescience, Nehren, Germany). Out of 219 BacT/ALERT(®) MP culture positive isolates tested by PNB as 153 MTBC (69.9%) and by GenoType(®) Mycobacterium CM/AS assay as 159 (72.6%) MTBC and remaining 60 (27.4%) were considered as NTM species. The GenoType(®) Mycobacterium CM/AS assay was proved 99.3% sensitive and 98.3% specific for rapid differentiation of MTBC and NTM. The most common NTM species were; Mycobacterium fortuitum 20 (33.3%) among rapid growing mycobacteria and Mycobacterium intracellulare 11 (18.3%) among slow growing mycobacteria. The GenoType(®) Mycobacterium assay makes rapid and accurate identification of NTM species as compared with different phenotypic and molecular diagnostic tool and helps in management of infections caused by different mycobacteria.

  5. Differential inhibition of mitochondrial respiratory complexes by inhalation of combustion smoke and carbon monoxide, in vivo, in the rat brain.

    PubMed

    Lee, Heung M; Hallberg, Lance M; Greeley, George H; Englander, Ella W

    2010-08-01

    Combustion smoke contains gases and particulates, which act via hypoxia and cytotoxicity producing mechanisms to injure cells and tissues. While carbon monoxide (CO) is the major toxicant in smoke, its toxicity is exacerbated in the presence of other compounds. Here, we examined modulations of mitochondrial and cytosolic energy metabolism by inhalation of combustion smoke versus CO, in vivo, in the rat brain. Measurements revealed reduced activities of respiratory chain (RC) complexes, with greater inhibition by smoke than equivalent CO in ambient air. In the case of RC complex IV, inhibition by CO and smoke was similar--suggesting that complex IV inhibition is primarily by the action of CO. In contrast, inhibition of complexes I and III was greater by smoke. Increases in cytosolic lactate dehydrogenase and pyruvate kinase activities accompanied inhibition of RC complexes, likely reflecting compensatory increases in cytosolic energy production. Together, the data provide new insights into the mechanisms of smoke inhalation-induced perturbations of brain energetics, which impact neuronal function and contribute to the development of neuropathologies in survivors of exposures to CO and combustion smoke.

  6. Wide-complex tachycardia: beyond the traditional differential diagnosis of ventricular tachycardia vs supraventricular tachycardia with aberrant conduction.

    PubMed

    Hollowell, Heather; Mattu, Amal; Perron, Andrew D; Holstege, Christopher; Brady, William J

    2005-11-01

    Wide-complex tachycardia (WCT) is defined as a rhythm disturbance with a rate greater than 100 beats/min and a QRS complex duration of 0.12 seconds or more in the adult patient; in the pediatric patient, both rate and QRS complex width are age related. In evaluating this type of tachycardia, there are 2 broad categories usually discussed in the medical literature: ventricular and supraventricular with aberrant intraventricular conduction. There are several other important causes of a WCT encountered in clinical practice, which are less often discussed; these tachycardias often require specific therapies differing from the standard approach to WCT. These tachycardias are diverse; as such, the pathophysiology behind each form of WCT includes toxic, metabolic, and conduction system dysfunction mechanisms.

  7. [Differential diagnosis and treatment of complex renal cysts detected by ultrasound screening of the abdominal cavity organs].

    PubMed

    Ukhal', M I; Ukhal', E M; Kvasha, A N

    2014-01-01

    Ultrasound screening of the abdominal cavity organs was performed in 98 patients, and renal cysts were revealed in 31 patientsare. 11 (26,6%) of 31 patients had renal cysts with complex structure. In 4 patients, complex cysts were located in parapelvic zone, in 7 patients - in different parts of the renal parenchyma. Pharmaco-Doppler sonography and computed tomography with bolus contrast enhancement in 7 patients with complex parenchymal cysts had revealed indirect signs of a malignant process - septums, thickening of the walls of cysts and septums, foci of calcination, increased blood circulation in the thickened renal cyst walls, venous stasis on the periphery of cysts and renal medulla, increasing the density of the thickened walls. Results of morphological studies have confirmed the presence of a malignant process in 5 of these 7 patients. In 4 patients with parapelvic cysts malignant process in ectomized layers was not revealed.

  8. Novel synthetic routes to several new, differentially substituted ruthenium tris(4,4 disubstituted-2,2-bipyridine) complexes.

    PubMed

    Hesek, D; Inoue, Y; Everitt, S R; Ishida, H; Kunieda, M; Drew, M G

    2000-01-24

    The stepwise synthesis of several novel Ru(tris(pp)) complexes (pp = 4,4'-disubstituted-2,2'-bipyridine; substituent = H, Me, chiral ester, or chiral amide) is described, where the pp ligands may be the same, or different, in each complex. All of the complexes detailed have been resolved into their pure delta- and lambda-enantiomers or diastereomers. The complexes, which are prepared starting from RuCl3, contain novel ligand architectures, with a range of chiral esters and amides attached to the 4,4'-positions of the bpy ligands. It was postulated that these chiral groups would be capable of inducing chirality at the metal center, but our investigations have shown this not to be the case, and in all reactions completely racemic products were formed. Resolution by chiral HPLC, and the subsequent characterization of the products through NMR, UV-vis, and circular dichroism (CD) spectroscopy, has been carried out; the characteristics of the CD spectra have been discussed with respect to the electron-donating/ withdrawing ability of the groups at the 4,4'-positions. The X-ray crystal structure of the optically pure complex lambda-[Ru(dmbpy)2(4,4'-bis((R)-(+)-alpha-phenylethylamido)-2,2'-bipyridine)] x 2PF6 x 2CHCl3 was obtained and solved using direct methods. This result, in conjunction with the CD spectra, enabled the complete and unambiguous assignment of the stereocenters of all of the novel Ru(tris(bpy)) complexes prepared in this investigation.

  9. Differential inhibition of the yeast bc1 complex by phenanthrolines and ferroin. Implications for structure and catalytic mechanism.

    PubMed

    Boumans, H; van Gaalen, M C; Grivell, L A; Berden, J A

    1997-07-04

    o-Phenanthroline and m-phenanthroline both inhibit the electron transfer activity of lauryl maltoside-solubilized yeast bc1 complex progressively with time. Pre-steady-state kinetics indicate that these compounds bind to the complex on the intermembrane space side, thereby blocking reduction of cytochrome b via the ubiquinol oxidation site. o-Phenanthroline is additionally capable of chelating an iron atom derived from the Rieske Fe-S cluster, thereby distorting the structure of the Rieske protein. EPR analysis shows that the secondary effect of o-phenanthroline occurs after initial inactivation and that m-phenanthroline, which lacks chelating activity, does not affect the Rieske Fe-S cluster. Spectral analysis shows that the b and c1 cytochromes are still dithionite-reducible after inactivation by o-phenanthroline, indicating that they remain intact. Inactivation by o-phenanthroline can be prevented by the addition of Fe2+. Surprisingly, ferroin, the o-phenanthroline-ferrous sulfate complex, also inhibits the bc1 complex activity. In contrast to o-phenanthroline, this effect is instantaneous. The two types of inhibition are clearly distinguishable by pre-steady-state reduction kinetics. Interestingly, ferroin can only inhibit electron transfer activity by about 50%. This behavior is discussed in relation to the dimeric structure of the bc1 complex, and we conclude that ferroin binds to only one of the two protomers. The rate of inactivation by o-phenanthroline is dependent on the incubation temperature and can be quantitated in terms of the half-life for a certain temperature, the time at which the bc1 activity is reduced to 50%. In contrast to the solubilized form, the bc1 complex in intact mitochondria is insensitive to o-phenanthroline, suggesting that the inactivation rate by o-phenanthroline is dependent on accessibility of the complex to the agent. Reaction with o-phenanthroline is thus a useful technique for study of structural stability of the bc1 complex

  10. Inverse analysis of thermal conductivities in transient non-homogeneous and non-linear heat conductions using BEM based on complex variable differentiation method

    NASA Astrophysics Data System (ADS)

    Yu, XiaoChun; Bai, YuGuang; Cui, Miao; Gao, XiaoWei

    2013-05-01

    This paper presents a new inverse analysis approach to sensitivity analysis and material property identification in transient non-homogeneous and non-linear heat conduction Boundary Element Method (BEM) analysis based on Complex Variable Differentiation Method (CVDM). In this approach, the material properties are taken as the optimization variables, and the sensitivity coefficients are computed by CVDM. The advantages of using CVDM are that the computation of partial derivatives of an implicit function is reduced to function calculation in a complex domain, and the parameter sensitivity coefficients can be determined in a more accurate way than the traditional Finite Difference Method (FDM). Based on BEM and CVDM in evaluation of the sensitivity matrix of heat flux, the parameter such as thermal conductivity can be accurately identified. Six numerical examples are given to demonstrate the potential of the proposed approach. The results indicate that the presented method is efficient for identifying the thermal conductivity with single or multiple parameters.

  11. A dominant-negative clathrin mutant differentially affects trafficking of molecules with distinct sorting motifs in the class II major histocompatibility complex (MHC) pathway.

    PubMed

    Liu, S H; Marks, M S; Brodsky, F M

    1998-03-09

    The role of clathrin in intracellular sorting was investigated by expression of a dominant-negative mutant form of clathrin, termed the hub fragment. Hub inhibition of clathrin-mediated membrane transport was established by demonstrating a block of transferrin internalization and an alteration in the intracellular distribution of the cation-independent mannose-6-phosphate receptor. Hubs had no effect on uptake of FITC-dextran, adaptor distribution, organelle integrity in the secretory pathway, or cell surface expression of constitutively secreted molecules. Hub expression blocked lysosomal delivery of chimeric molecules containing either the tyrosine-based sorting signal of H2M or the dileucine-based sorting signal of CD3gamma, confirming a role for clathrin-coated vesicles (CCVs) in recognizing these signals and sorting them to the endocytic pathway. Hub expression was then used to probe the role of CCVs in targeting native molecules bearing these sorting signals in the context of HLA-DM and the invariant chain (I chain) complexed to HLA-DR. The distribution of these molecules was differentially affected. Accumulation of hubs before expression of the DM dimer blocked DM export from the TGN, whereas hubs had no effect on direct targeting of the DR-I chain complex from the TGN to the endocytic pathway. However, concurrent expression of hubs, such that hubs were building to inhibitory concentrations during DM or DR-I chain expression, caused cell surface accumulation of both complexes. These observations suggest that both DM and DR-I chain are directly transported to the endocytic pathway from the TGN, DM in CCVs, and DR-I chain independent of CCVs. Subsequently, both complexes can appear at the cell surface from where they are both internalized by CCVs. Differential packaging in CCVs in the TGN, mediated by tyrosine- and dileucine-based sorting signals, could be a mechanism for functional segregation of DM from DR-I chain until their intended rendezvous in late

  12. A review of sleepwalking (somnambulism): the enigma of neurophysiology and polysomnography with differential diagnosis of complex partial seizures.

    PubMed

    Hughes, John R

    2007-12-01

    The goal of this report is to review all aspects of sleepwalking (SW), also known as somnambulism. Various factors seem to initiate SW, especially drugs, stress, and sleep deprivation. As an etiology, heredity is important, but other conditions include thyrotoxicosis, stress, and herpes simplex encephalitis. Psychological characteristics of sleepwalkers often include aggression, anxiety, panic disorder, and hysteria. Polysomnographic characteristics emphasize abnormal deep sleep associated with arousal and slow wave sleep fragmentation. In the differential diagnosis, the EEG is important to properly identify a seizure disorder, rather than SW. Associated disorders are Tourette's syndrome, sleep-disordered breathing, and migraine. Various kinds of treatment are discussed, as are legal considerations, especially murder during sleepwalking.

  13. Defining Minimal Binding Regions in Regulator of Presynaptic Morphology 1 (RPM-1) Using Caenorhabditis elegans Neurons Reveals Differential Signaling Complexes.

    PubMed

    Baker, Scott T; Grill, Brock

    2017-02-10

    The intracellular signaling protein regulator of presynaptic morphology 1 (RPM-1) is a conserved regulator of synapse formation and axon termination in Caenorhabditis elegans RPM-1 functions in a ubiquitin ligase complex with the F-box protein FSN-1 and functions through the microtubule binding protein RAE-1. Using a structure-function approach and positive selection for transgenic C. elegans, we explored the biochemical relationship between RPM-1, FSN-1, and RAE-1. This led to the identification of two new domains in RPM-1 that are sufficient for binding to FSN-1, called FSN-1 binding domain 2 (FBD2) and FBD3. Furthermore, we map the RAE-1 binding domain to a much smaller region of RPM-1. Point mutations in RPM-1 that reduce binding to RAE-1 did not affect FSN-1 binding, indicating that RPM-1 utilizes different biochemical mechanisms to bind these molecules. Analysis of RPM-1 protein complexes in the neurons of C. elegans elucidated two further discoveries: FSN-1 binds to RAE-1, and this interaction is not mediated by RPM-1, and RPM-1 binding to FSN-1 and RAE-1 reduces FSN-1·RAE-1 complex formation. These results indicate that RPM-1 uses different mechanisms to recruit FSN-1 and RAE-1 into independent signaling complexes in neurons. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. The Differential Effects of Three Types of Task Planning on the Fluency, Complexity, and Accuracy in L2 Oral Production

    ERIC Educational Resources Information Center

    Ellis, Rod

    2009-01-01

    The main purpose of this article is to review studies that have investigated the effects of three types of planning (rehearsal, pre-task planning, and within-task planning) on the fluency, complexity, and accuracy of L2 performance. All three types of planning have been shown to have a beneficial effect on fluency but the results for complexity…

  15. The Dictyostelium prestalk inducer differentiation-inducing factor-1 (DIF-1) triggers unexpectedly complex global phosphorylation changes

    PubMed Central

    Sugden, Chris; Urbaniak, Michael D.; Araki, Tsuyoshi; Williams, Jeffrey G.

    2015-01-01

    Differentiation-inducing factor-1 (DIF-1) is a polyketide that induces Dictyostelium amoebae to differentiate as prestalk cells. We performed a global quantitative screen for phosphorylation changes that occur within the first minutes after addition of DIF-1, using a triple-label SILAC approach. This revealed a new world of DIF-1–controlled signaling, with changes in components of the MAPK and protein kinase B signaling pathways, components of the actinomyosin cytoskeletal signaling networks, and a broad range of small GTPases and their regulators. The results also provide evidence that the Ca2+/calmodulin–dependent phosphatase calcineurin plays a role in DIF-1 signaling to the DimB prestalk transcription factor. At the global level, DIF-1 causes a major shift in the phosphorylation/dephosphorylation equilibrium toward net dephosphorylation. Of interest, many of the sites that are dephosphorylated in response to DIF-1 are phosphorylated in response to extracellular cAMP signaling. This accords with studies that suggest an antagonism between the two inducers and also with the rapid dephosphorylation of the cAMP receptor that we observe in response to DIF-1 and with the known inhibitory effect of DIF-1 on chemotaxis to cAMP. All MS data are available via ProteomeXchange with identifier PXD001555. PMID:25518940

  16. FfVel1 and FfLae1, components of a velvet-like complex in Fusarium fujikuroi, affect differentiation, secondary metabolism and virulence

    PubMed Central

    Wiemann, Philipp; Brown, Daren W.; Kleigrewe, Karin; Bok, Jin Woo; Keller, Nancy P.; Humpf, Hans-Ulrich; Tudzynski, Bettina

    2010-01-01

    Summary Besides industrially produced gibberellins (GAs), Fusarium fujikuroi is able to produce additional secondary metabolites such as the pigments bikaverin and neurosporaxanthin and the mycotoxins fumonisins and fusarin C. The global regulation of these biosynthetic pathways is only poorly understood. Recently, the velvet complex containing VeA and several other regulatory proteins was shown to be involved in global regulation of secondary metabolism and differentiation in Aspergillus nidulans. Here we report on the characterization of two components of the F. fujikuroi velvet-like complex, FfVel1 and FfLae1. The gene encoding this first reported LaeA ortholog outside the class of Eurotiomycetidae is upregulated in ΔFfvel1 microarray-studies and FfLae1 interacts with FfVel1 in the nucleus. Deletion of Ffvel1 and Fflae1 revealed for the first time that velvet can simultaneously act as positive (GAs, fumonisins and fusarin C) and negative (bikaverin) regulator of secondary metabolism, and that both components affect conidiation and virulence of F. fujikuroi. Furthermore, the velvet-like protein FfVel2 revealed similar functions regarding conidiation, secondary metabolism and virulence as FfVel1. Cross genus complementation studies of velvet complex component mutants between Fusarium, Aspergillus and Penicillium support an ancient origin for this complex which has undergone a divergence in specific functions mediating development and secondary metabolism. PMID:20572938

  17. Endoreduplication mediated by the anaphase-promoting complex activator CCS52A is required for symbiotic cell differentiation in Medicago truncatula nodules.

    PubMed

    Vinardell, Jose Maria; Fedorova, Elena; Cebolla, Angel; Kevei, Zoltan; Horvath, Gabor; Kelemen, Zsolt; Tarayre, Sylvie; Roudier, François; Mergaert, Peter; Kondorosi, Adam; Kondorosi, Eva

    2003-09-01

    In Medicago nodules, endoreduplication cycles and ploidy-dependent cell enlargement occur during the differentiation of bacteroid-containing nitrogen-fixing symbiotic cells. These events are accompanied by the expression of ccs52A, a plant ortholog of the yeast and animal cdh1/srw1/fzr genes, acting as a substrate-specific activator of the anaphase-promoting complex (APC) ubiquitin ligase. Because CCS52A is involved in the transition of mitotic cycles to endoreduplication cycles, we investigated the importance of somatic endoploidy and the role of the M. truncatula ccs52A gene in symbiotic cell differentiation. Transcription analysis and ccs52A promoter-driven beta-glucuronidase activity in transgenic plants showed that ccs52A was dispensable for the mitotic cycles and nodule primordium formation, whereas it was induced before nodule differentiation. The CCS52A protein was present in the nucleus of endoreduplication-competent cells, indicating that it may activate APC constitutively during the endoreduplication cycles. Downregulation of ccs52A in transgenic M. truncatula plants drastically affected nodule development, resulting in lower ploidy, reduced cell size, inefficient invasion, and the maturation of symbiotic cells, accompanied by early senescence and finally the death of both the bacterium and plant cells. Thus, ccs52A expression is essential for the formation of large highly polyploid symbiotic cells, and endoreduplication is an integral part of normal nodule development.

  18. Partial plasma cell differentiation as a mechanism of lost major histocompatibility complex class II expression in diffuse large B-cell lymphoma.

    PubMed

    Wilkinson, Sarah T; Vanpatten, Kristie A; Fernandez, Diane R; Brunhoeber, Patrick; Garsha, Karl E; Glinsmann-Gibson, Betty J; Grogan, Thomas M; Teruya-Feldstein, Julie; Rimsza, Lisa M

    2012-02-09

    Loss of major histocompatibility complex class II (MHC II) expression is associated with poor patient outcome in diffuse large B-cell lymphoma (DLBCL). As MHC II molecules are lost with plasmacytic differentiation in normal cells, we asked whether MHC II loss in DLBCL is associated with an altered differentiation state. We used gene expression profiling, quantum dots, and immunohistochemistry to study the relationship between MHC II and plasma cell markers in DLBCL and plasmablastic lymphoma (PBL). Results demonstrate that MHC II(-) DLBCL immunophenotypically overlap with PBL and demonstrate an inverse correlation between MHC II and plasma cell markers MUM1, PRDM1/Blimp1, and XBP1s. In addition, MHC II expression is significantly higher in germinal center-DLBCL than activated B cell-DLBCL. A minor subset of cases with an unusual pattern of mislocalized punctate MHC II staining and intermediate levels of mRNA is also described. Finally, we show that PBL is negative for MHC II. The results imply a spectrum of MHC II expression that is more frequently diminished in tumors derived from B cells at the later stages of differentiation (with complete loss in PBL). Our observations provide a possible unifying concept that may contribute to the poor outcome reported in all MHC II(-) B-cell tumors.

  19. Diversity and endemism in deglaciated areas: ploidy, relative genome size and niche differentiation in the Galium pusillum complex (Rubiaceae) in Northern and Central Europe.

    PubMed

    Kolár, Filip; Lucanová, Magdalena; Vít, Petr; Urfus, Tomás; Chrtek, Jindrich; Fér, Tomás; Ehrendorfer, Friedrich; Suda, Jan

    2013-06-01

    Plants endemic to areas covered by ice sheets during the last glaciation represent paradigmatic examples of rapid speciation in changing environments, yet very few systems outside the harsh arctic zone have been comprehensively investigated so far. The Galium pusillum aggregate (Rubiaceae) is a challenging species complex that exhibits a marked differentiation in boreal parts of Northern Europe. As a first step towards understanding its evolutionary history in deglaciated regions, this study assesses cytological variation and ecological preferences of the northern endemics and compares the results with corresponding data for species occurring in neighbouring unglaciated parts of Central and Western Europe. DNA flow cytometry was used together with confirmatory chromosome counts to determine ploidy levels and relative genome sizes in 1158 individuals from 181 populations. A formalized analysis of habitat preferences was applied to explore niche differentiation among species and ploidy levels. The G. pusillum complex evolved at diploid and tetraploid levels in Northern Europe, in contrast to the high-polyploid evolution of most other northern endemics. A high level of eco-geographic segregation was observed between different species (particularly along gradients of soil pH and competition) which is unusual for plants in deglaciated areas and most probably contributes to maintaining species integrity. Relative monoploid DNA contents of the species from previously glaciated regions were significantly lower than those of their counterparts from mostly unglaciated Central Europe, suggesting independent evolutionary histories. The aggregate of G. pusillum in Northern Europe represents an exceptional case with a geographically vicariant and ecologically distinct diploid/tetraploid species endemic to formerly glaciated areas. The high level of interspecific differentiation substantially widens our perception of the evolutionary dynamics and speciation rates in the

  20. Diversity and endemism in deglaciated areas: ploidy, relative genome size and niche differentiation in the Galium pusillum complex (Rubiaceae) in Northern and Central Europe

    PubMed Central

    Kolář, Filip; Lučanová, Magdalena; Vít, Petr; Urfus, Tomáš; Chrtek, Jindřich; Fér, Tomáš; Ehrendorfer, Friedrich; Suda, Jan

    2013-01-01

    Background and Aims Plants endemic to areas covered by ice sheets during the last glaciation represent paradigmatic examples of rapid speciation in changing environments, yet very few systems outside the harsh arctic zone have been comprehensively investigated so far. The Galium pusillum aggregate (Rubiaceae) is a challenging species complex that exhibits a marked differentiation in boreal parts of Northern Europe. As a first step towards understanding its evolutionary history in deglaciated regions, this study assesses cytological variation and ecological preferences of the northern endemics and compares the results with corresponding data for species occurring in neighbouring unglaciated parts of Central and Western Europe. Methods DNA flow cytometry was used together with confirmatory chromosome counts to determine ploidy levels and relative genome sizes in 1158 individuals from 181 populations. A formalized analysis of habitat preferences was applied to explore niche differentiation among species and ploidy levels. Key Results The G. pusillum complex evolved at diploid and tetraploid levels in Northern Europe, in contrast to the high-polyploid evolution of most other northern endemics. A high level of eco-geographic segregation was observed between different species (particularly along gradients of soil pH and competition) which is unusual for plants in deglaciated areas and most probably contributes to maintaining species integrity. Relative monoploid DNA contents of the species from previously glaciated regions were significantly lower than those of their counterparts from mostly unglaciated Central Europe, suggesting independent evolutionary histories. Conclusions The aggregate of G. pusillum in Northern Europe represents an exceptional case with a geographically vicariant and ecologically distinct diploid/tetraploid species endemic to formerly glaciated areas. The high level of interspecific differentiation substantially widens our perception of the

  1. Differential generation of superoxide radical by rat phagocytes stimulated with IgA and IgG immune complexes

    SciTech Connect

    Warren, P.A.; Ward, P.A.; Johnson K.J.

    1986-03-01

    Rat glycogen elicited peritoneal neutrophils and bronchoalveolar lavage (BAL) marcophages were stimulated with preformed immune complexes consisting of monoclonal IgG anti-dinitorphenol linked bovine serum albumin (DNP-BSA) or monoclonal IgA anti-DNP-BSA. Superoxide (O/sub 2//sup tau/) was detected using superoxide dismutase inhibitable reduction of ferricytochrome C. Neutrophils (2 x 10/sup 6/) generated small (<2.3 nmole/30 min.) quantities of O/sub 2//sup tau/ when stimulated with IgA-DNP-BAS in the presence or absence of cytochalasin B (1.25 ..mu..g/ml). There was a 4 to 8-fold, dose-dependent increase in O/sub 2//sup tau/ generation by neutrophils stimulated with IgG-DNP-BSA. Cytochalasin B was required to generate this quantity (up to 7.7 nmol/30 min.) of O/sub 2//sup tau/. Whether stimulated with IgG-DNP-BSA or IgA-DNP-BSA, BAL macrophages (5 x 10/sup 5/) generated more O/sub 2//sup tau/ in the absence of cytochalasin B than in its presence. Increased O/sub 2//sup tau/ generation by the immune complex stimulated BAL macrophages was dose-dependent and increased to 6-fold with IgG-DNP-BSA stimulated cells and up to 4-fold with IgA-DNP-BSA stimulated cells. These data corroborate published in vivo studies suggesting that IgA immune complex mediated tissue injury may be mediated by macrophages and not neutrophils. These data also suggest that the mechanisms for immune complex induced O/sub 2//sup tau/ generation may vary depending both on the phagocyte as well as on the stimulus.

  2. Second sphere control of spin state: Differential tuning of axial ligand bonds in ferric porphyrin complexes by hydrogen bonding.

    PubMed

    Mittra, Kaustuv; Sengupta, Kushal; Singha, Asmita; Bandyopadhyay, Sabyasachi; Chatterjee, Sudipta; Rana, Atanu; Samanta, Subhra; Dey, Abhishek

    2016-02-01

    An iron porphyrin with a pre-organized hydrogen bonding (H-Bonding) distal architecture is utilized to avoid the inherent loss of entropy associated with H-Bonding from solvent (water) and mimic the behavior of metallo-enzyme active sites attributed to H-Bonding interactions of active site with the 2nd sphere residues. Resonance Raman (rR) data on these iron porphyrin complexes indicate that H-Bonding to an axial ligand like hydroxide can result in both stronger or weaker Fe(III)-OH bond relative to iron porphyrin complexes. The 6-coordinate (6C) complexes bearing water derived axial ligands, trans to imidazole or thiolate axial ligand with H-Bonding stabilize a low spin (LS) ground state (GS) when a complex without H-Bonding stabilizes a high spin (HS) ground state. DFT calculations reproduce the trend in the experimental data and provide a mechanism of how H-Bonding can indeed lead to stronger metal ligand bonds when the axial ligand donates an H-Bond and lead to weaker metal ligand bonds when the axial ligand accepts an H-Bond. The experimental and computational results explain how a weak Fe(III)-OH bond (due to H-Bonding) can lead to the stabilization of low spin ground state in synthetic mimics and in enzymes containing iron porphyrin active sites. H-Bonding to a water ligand bound to a reduced ferrous active site can only strengthen the Fe(II)-OH2 bond and thus exclusion of water and hydrophilic residues from distal sites of O2 binding/activating heme proteins is necessary to avoid inhibition of O2 binding by water. These results help demonstrate the predominant role played by H-Bonding and subtle changes in its orientation in determining the geometric and electronic structure of iron porphyrin based active sites in nature. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Differential binding partners of the Mis18α/β YIPPEE domains regulates the Mis18 complex recruitment to centromeres

    PubMed Central

    Knippler, Christina M.; Foltz, Daniel R.

    2016-01-01

    The Mis18 complex specifies the site of new CENP-A nucleosome assembly by recruiting the CENP-A specific assembly factor HJURP (Holliday junction recognition protein). The human Mis18 complex consists of Mis18α, Mis18β and Mis18 binding protein 1 (Mis18BP1/hsKNL2). Although Mis18α and Mis18β are highly homologous proteins, we find that their conserved YIPPEE domains mediate distinct interactions that are essential to link new CENP-A deposition to existing centromeres. We find that Mis18α directly interacts with the N-terminus of Mis18BP1; whereas, Mis18β directly interacts with CENP-C during G1 phase, revealing that these proteins have evolved to serve distinct functions in centromeres of higher eukaryotes. The N-terminus of Mis18BP1, containing both the Mis18α and CENP-C binding domains, is necessary and sufficient for centromeric localization. Therefore, the Mis18 complex contains dual CENP-C recognition motifs that are combinatorially required to generate robust centromeric localization that leads to CENP-A deposition. PMID:27239045

  4. Differential effects of lesions of the amygdala and prefrontal cortex on recognizing facial expressions of complex emotions.

    PubMed

    Shaw, P; Bramham, J; Lawrence, E J; Morris, R; Baron-Cohen, S; David, A S

    2005-09-01

    Humans can detect facial expressions of both simple, basic emotions and expressions reflecting more complex states of mind. The latter includes emotional expressions that regulate social interactions ("social expressions" such as looking hostile or friendly) and expressions that reflect the inner thought state of others ("cognitive expressions" such as looking pensive). To explore the neural substrate of this skill, we examined performance on a test of detection of such complex expressions in patients with lesions of the temporal lobe (n = 54) or frontal lobe (n = 31). Of the temporal group, 18 had unilateral focal lesions of the amygdala and of the frontal group, 14 patients had unilateral lesions of the ventromedial prefrontal cortex-two regions held to be pivotal in mediating social cognitive skills. Damage to either the left or right amygdala was associated with impairment in the recognition of both social and cognitive expressions, despite an intact ability to extract information relating to invariant physical attributes. Lesions to all of the right prefrontal cortex-not just the ventromedial portions-led to a specific deficit in recognizing complex social expressions with a negative valence. The deficit in the group with right prefrontal cortical damage may contribute to the disturbances in social behavior associated with such lesions. The results also suggest that the amygdala has a role in processing a wide range of emotional expressions.

  5. Molecular Basis for Differential Recognition of G-Quadruplex versus Double-Helix DNA by Bis-Phenanthroline Metal Complexes.

    PubMed

    Rigo, Riccardo; Bianco, Sara; Musetti, Caterina; Palumbo, Manlio; Sissi, Claudia

    2016-08-19

    1,10-Phenanthroline (Phen) derivatives are attractive ligands to provide metal complexes that are selective for different DNA secondary structures. Herein, we analyze the binding processes of two bis-Phen analogues and their Ni(II) complexes toward double-stranded DNA and telomeric G-quadruplex DNA by calorimetric and spectroscopic techniques. The free ligands can adapt to both DNA arrangements. Conversely, metal ion coordination produces an increase in ligand affinity for the tetrahelical structure, whereas it dramatically decreases binding to double-stranded DNA as a result of distinct binding modes on the two templates. In fact, Ni(II) complexes effectively stack on the G-quadruplex terminals, with an entropic loss counterbalanced by favorable enthalpy changes, whereas they cause a conformational reshaping of the double-helix form with a substantial decrease in the binding free energy. Consistently, no Ni(II) -DNA ionic pair has ever been identified. These results provide a rationale for the selective recognition of distinct DNA arrangements in view of targeted pharmacological applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Differentiation of strains in Mycobacterium tuberculosis complex by DNA sequence polymorphisms, including rapid identification of M. bovis BCG.

    PubMed Central

    Frothingham, R

    1995-01-01

    The Mycobacterium tuberculosis complex includes M. tuberculosis, M. bovis, M. microti, and M. africanum. Seven strains of the M. tuberculosis complex were sequenced in a region of about 300 bp which contains multiple 15-bp tandem repeats and which is part of a 1,551-bp open reading frame. Four distinct sequences were obtained, each defining a sequevar. A sequevar includes the strain or strains with a given sequence. The type strain M. tuberculosis TMC 102 (H37Rv) was designated sequevar MED-G. When compared to MED-G, sequevar LONG had an insertion of one 15-bp tandem repeat and sequevar SHORT had a deletion of one tandem repeat. Sequevar MED-C had a G-->C substitution, coding for the conservative change Ser-->Thr. BanI cuts only sequevar MED-C at the site of the substitution. PCR-restriction enzyme analysis was used to determine the sequevars of 92 M. tuberculosis complex strains. All 23 M. bovis BCG strains belonged to sequevar MED-C. The M. africanum type strain was sequevar SHORT. The remaining 68 strains of M. tuberculosis, M. bovis (not BCG), and M. microti were sequevars LONG (3 strains) or MED-G (65 strains). PCR-restriction enzyme analysis was applied to reference strains and clinical isolates with a worldwide distribution. This method provides rapid, sensitive, and specific identification of the important vaccine strain M. bovis BCG. PMID:7790448

  7. Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part II: Application to Partial Differential Equations

    DOE PAGES

    Pawlowski, Roger P.; Phipps, Eric T.; Salinger, Andrew G.; ...

    2012-01-01

    A template-based generic programming approach was presented in Part I of this series of papers [Sci. Program. 20 (2012), 197–219] that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertaintymore » quantification results for a 3D PDE application.« less

  8. Differential expression of microRNAs and their predicted targets in renal cells exposed to amphotericin B and its complex with copper (II) ions.

    PubMed

    Gola, Joanna Magdalena; Strzałka-Mrozik, Barbara; Kruszniewska-Rajs, Celina; Adamska, Jolanta; Gagoś, Mariusz; Mazurek, Urszula

    2017-09-01

    MicroRNAs (miRNAs) have been reported to regulate essential biological processes, and their expression was shown to be affected by pathological processes and drug-induced toxicity. Amphotericin B (AmB) can cause liver and kidney injury, but a recently developed complex of AmB with copper (II) ions (AmB-Cu(2+)) exhibits a lower toxicity to human renal cells while retaining a high antifungal activity. The aim of our study was to assess AmB-Cu(2+)-induced changes in the miRNA profile of renal cells and examine which biological processes are significantly affected by AmB-Cu(2+). We also aimed to predict whether differentially expressed miRNAs would influence observed changes in the mRNA profile. miRNA and mRNA profiles in normal human renal proximal tubule epithelial cells (RPTEC) treated with AmB-Cu(2+) or AmB were appointed with the use of microarray technology. For differentially expressed mRNAs, the PANTHER overrepresentation binomial test was performed. miRNA target interactions (MTIs) were predicted using the miRTar tool. The mRNA profile was much more strongly affected than the miRNA profile, in both AmB-Cu(2+)- and AmB-treated cells. AmB-Cu(2+) influenced both the miRNA and mRNA profiles much more strongly than AmB. The most affected biological processes were intracellular signal transduction (AmB-Cu(2+)) and signal transduction (AmB). Only a few interactions between differentiating miRNAs and mRNAs were found. Changes in the profiles of genes involved in signal transduction and intracellular signal transduction may not result from interactions with differentially expressed miRNAs. Changes in the miRNA profile suggest the possible influence of tested drugs on the regulation of fibrosis via a miRNA-dependent mechanism.

  9. Heterocellular interaction enhances recruitment of {alpha} and {beta}-catenins and ZO-2 into functional gap-junction complexes and induces gap junction-dependant differentiation of mammary epithelial cells

    SciTech Connect

    Talhouk, Rabih S. Mroue, Rana; Mokalled, Mayssa; Abi-Mosleh, Lina; Nehme, Ralda; Ismail, Ayman; Khalil, Antoine; Zaatari, Mira; El-Sabban, Marwan E.

    2008-11-01

    Gap junctions (GJ) are required for mammary epithelial differentiation. Using epithelial (SCp2) and myoepithelial-like (SCg6) mouse-derived mammary cells, the role of heterocellular interaction in assembly of GJ complexes and functional differentiation ({beta}-casein expression) was evaluated. Heterocellular interaction is critical for {beta}-casein expression, independent of exogenous basement membrane or cell anchoring substrata. Functional differentiation of SCp2, co-cultured with SCg6, is more sensitive to GJ inhibition relative to homocellular SCp2 cultures differentiated by exogenous basement membrane. Connexin (Cx)32 and Cx43 levels were not regulated across culture conditions; however, GJ functionality was enhanced under differentiation-permissive conditions. Immunoprecipitation studies demonstrated association of junctional complex components ({alpha}-catenin, {beta}-catenin and ZO-2) with Cx32 and Cx43, in differentiation conditions, and additionally with Cx30 in heterocellular cultures. Although {beta}-catenin did not shuttle between cadherin and GJ complexes, increased association between connexins and {beta}-catenin in heterocellular cultures was observed. This was concomitant with reduced nuclear {beta}-catenin, suggesting that differentiation in heterocellular cultures involves sequestration of {beta}-catenin in GJ complexes.

  10. Differentiation of the DnaA-oriC subcomplex for DNA unwinding in a replication initiation complex.

    PubMed

    Ozaki, Shogo; Noguchi, Yasunori; Hayashi, Yasuhisa; Miyazaki, Erika; Katayama, Tsutomu

    2012-10-26

    In Escherichia coli, ATP-DnaA multimers formed on the replication origin oriC promote duplex unwinding, which leads to helicase loading. Based on a detailed functional analysis of the oriC sequence motifs, we previously proposed that the left half of oriC forms an ATP-DnaA subcomplex competent for oriC unwinding, whereas the right half of oriC forms a distinct ATP-DnaA subcomplex that facilitates helicase loading. However, the molecular basis for the functional difference between these ATP-DnaA subcomplexes remains unclear. By analyzing a series of novel DnaA mutants, we found that structurally distinct DnaA multimers form on each half of oriC. DnaA AAA+ domain residues Arg-227 and Leu-290 are specifically required for oriC unwinding. Notably, these residues are required for the ATP-DnaA-specific structure of DnaA multimers in complex with the left half of oriC but not for that with the right half. These results support the idea that the ATP-DnaA multimers formed on oriC are not uniform and that they can adopt different conformations. Based on a structural model, we propose that Arg-227 and Leu-290 play a crucial role in inter-ATP-DnaA interaction and are a prerequisite for the formation of unwinding-competent DnaA subcomplexes on the left half of oriC. These residues are not required for the interaction with DnaB, nucleotide binding, or regulatory DnaA-ATP hydrolysis, which further supports their important role in inter-DnaA interaction. The corresponding residues are evolutionarily conserved and are required for unwinding in the initial complexes of Thermotoga maritima, an ancient hyperthermophile. Therefore, our findings suggest a novel and common mechanism for ATP-DnaA-dependent activation of initial complexes.

  11. Geographical differentiation of the Euchiloglanis fish complex (Teleostei: Siluriformes) in the Hengduan Mountain Region, China: Phylogeographic evidence of altered drainage patterns.

    PubMed

    Li, Yanping; Ludwig, Arne; Peng, Zuogang

    2017-02-01

    The uplift of the Tibetan Plateau caused significant ecogeographical changes that had a major impact on the exchange and isolation of regional fauna and flora. Furthermore, Pleistocene glacial oscillations were linked to temporal large-scale landmass and drainage system reconfigurations near the Hengduan Mountain Region and might have facilitated speciation and promoted biodiversity in southwestern China. However, strong biotic evidence supporting this role is lacking. Here, we use the Euchiloglanis fish species complex as a model to demonstrate the compound effects of the Tibetan Plateau uplift and Pleistocene glacial oscillations on species formation in this region. The genetic structure and geographical differentiation of the Euchiloglanis complex in four river systems within the Hengduan Mountain Region were deduced using the cytochrome b (cyt b) gene and 10 microsatellite loci from 360 to 192 individuals, respectively. The results indicated that the populations were divided into four independently evolving lineages, in which the populations from the Qingyi River and Jinsha River formed two sub-lineages. Phylogenetic relationships were structured by geographical isolation, especially near drainage systems. Divergence time estimation analyses showed that the Euchiloglanis complex diverged from its sister clade Pareuchiloglanis sinensis at around 1.3 Million years ago (Ma). Within the Euchiloglanis complex, the divergence time between the Dadu-Yalong and Jinsha-Qingyi River populations occurred at 1.0 Ma. This divergence time was in concordance with recent geological events, including the Kun-Huang Movement (1.2-0.6 Ma) and the lag time (<2.0 Ma) of river incision in the Hengduan Mountain Region. Population expansion signals were detected from mismatched distribution analyses, and the expansion times were concurrent with Pleistocene glacier fluctuations. Therefore, current phylogeographic patterns of the Euchiloglanis fish complex in the Hengduan Mountain

  12. Petrogenesis of alkaline magmas at Minna Bluff, Antarctica: evidence for multi-stage differentiation and complex mixing processes

    NASA Astrophysics Data System (ADS)

    Panter, K. S.; Dunbar, N. W.; Scanlan, M. K.; Wilch, T. I.; Fargo, A. J.; McIntosh, W. C.

    2011-12-01

    Minna Bluff, a 45-km-long peninsula that extends SE into the Ross Ice Shelf from the Mt. Discovery stratovolcano, consists of coalesced late Miocene volcanic centers formed through eruption of alkaline magma compositions in a continental rift setting. Highly silica-undersaturated compositions vary from basanite to phonolite and are exposed in volcanic features ranging from small, primitive, cinder cones to large, evolved domes. Lava compositions are more evolved on the eastern end of Minna Bluff and show an overall age progression to younger, more mafic compositions towards Mt. Discovery. Phenocrysts in lava include amphibole, plagioclase and alkali feldspar, pyroxene, olivine, magnetite and apatite. A notable feature of volcanic rocks at Minna Bluff is the presence of large (up to 5 cm) kaersutite and feldspar megacrysts and deposits that contain abundant comagmatic inclusions (kaersutite-rich) and rare mantle xenoliths. Many lavas exhibit strong disequilibrium textures, mainly expressed by breakdown rims on kaersutite that vary dramatically in thickness from crystal to crystal, but reverse compositional zoning in plagioclase is also common. Kaersutite compositions vary within a single sample and show the same compositional range and similar disequilibrium textures in rocks that vary significantly in bulk composition. The textural and compositional characteristics suggest that, for many, mixing between one or more magmas controlled the final composition of the magmas. We envisage a scenario by which some of the primitive, mantle-derived, fluid-rich magmas rose relatively unimpeded to erupt at the surface, while others stalled at or near the crust-mantle boundary and differentiated. Semi-quantitative thermobarometric results for kaersutite and clinopyroxene indicate maximum P-T-X conditions for crystallization of hydrous magmas at 5-9 kbar, ≧1000°C and ≈3 wt. % equiv. H2O. The P-T estimates closely match geophysical and petrologic geotherm estimates for Moho

  13. Evaluation of a rapid radiometric differentiation test for the Mycobacterium tuberculosis complex by selective inhibition with p-nitro-alpha-acetylamino-beta-hydroxypropiophenone

    SciTech Connect

    Laszlo, A.; Siddiqi, S.H.

    1984-05-01

    This study is an evaluation of a rapid technique for the differentiation of the Mycobacterium tuberculosis complex from other mycobacteria, using p-nitro-alpha-acetylamino-beta- hydroxypropiophenone (NAP) as a selective inhibitory agent. A total of 416 coded cultures, 234 cultures belonging to the M. tuberculosis complex and 182 cultures belonging to 35 other mycobacterial species, were tested in two laboratories for p-nitro-alpha-acetylamino-beta- hydroxypropiophenone inhibition to concentrations of 5 and 10 micrograms of NAP per ml in Middlebrook 7H12 liquid medium. Two testing modes were compared: the indirect, in which a large bacterial inoculum was used from an isolated culture on a solid medium, and the direct, which used a small inoculum from 7H12 medium. A decrease or no increase in daily /sup 14/CO/sub 2/ output as measured by a BACTEC system was considered evidence of inhibition. The data presented show that a concentration of 5 micrograms of NAP per ml can effectively separate the M. tuberculosis complex from other mycobacterial species in 4 to 6 days. The direct test data show that, unlike other conventional biochemical tests, it does not require a heavy inoculum of mycobacteria and can therefore be performed soon after growth is detected by the radiometric method.

  14. Histone chaperones ASF1 and NAP1 differentially modulate removal of active histone marks by LID-RPD3 complexes during NOTCH silencing.

    PubMed

    Moshkin, Yuri M; Kan, Tsung Wai; Goodfellow, Henry; Bezstarosti, Karel; Maeda, Robert K; Pilyugin, Maxim; Karch, Francois; Bray, Sarah J; Demmers, Jeroen A A; Verrijzer, C Peter

    2009-09-24

    Histone chaperones are involved in a variety of chromatin transactions. By a proteomics survey, we identified the interaction networks of histone chaperones ASF1, CAF1, HIRA, and NAP1. Here, we analyzed the cooperation of H3/H4 chaperone ASF1 and H2A/H2B chaperone NAP1 with two closely related silencing complexes: LAF and RLAF. NAP1 binds RPD3 and LID-associated factors (RLAF) comprising histone deacetylase RPD3, histone H3K4 demethylase LID/KDM5, SIN3A, PF1, EMSY, and MRG15. ASF1 binds LAF, a similar complex lacking RPD3. ASF1 and NAP1 link, respectively, LAF and RLAF to the DNA-binding Su(H)/Hairless complex, which targets the E(spl) NOTCH-regulated genes. ASF1 facilitates gene-selective removal of the H3K4me3 mark by LAF but has no effect on H3 deacetylation. NAP1 directs high nucleosome density near E(spl) control elements and mediates both H3 deacetylation and H3K4me3 demethylation by RLAF. We conclude that histone chaperones ASF1 and NAP1 differentially modulate local chromatin structure during gene-selective silencing.

  15. Changes in Search Path Complexity and Length During Learning of a Virtual Water Maze: Age Differences and Differential Associations with Hippocampal Subfield Volumes.

    PubMed

    Daugherty, Ana M; Bender, Andrew R; Yuan, Peng; Raz, Naftali

    2016-06-01

    Impairment of hippocampus-dependent cognitive processes has been proposed to underlie age-related deficits in navigation. Animal studies suggest a differential role of hippocampal subfields in various aspects of navigation, but that hypothesis has not been tested in humans. In this study, we examined the association between volume of hippocampal subfields and age differences in virtual spatial navigation. In a sample of 65 healthy adults (age 19-75 years), advanced age was associated with a slower rate of improvement operationalized as shortening of the search path over 25 learning trials on a virtual Morris water maze task. The deficits were partially explained by greater complexity of older adults' search paths. Larger subiculum and entorhinal cortex volumes were associated with a faster decrease in search path complexity, which in turn explained faster shortening of search distance. Larger Cornu Ammonis (CA)1-2 volume was associated with faster distance shortening, but not in path complexity reduction. Age differences in regional volumes collectively accounted for 23% of the age-related variance in navigation learning. Independent of subfield volumes, advanced age was associated with poorer performance across all trials, even after reaching the asymptote. Thus, subiculum and CA1-2 volumes were associated with speed of acquisition, but not magnitude of gains in virtual maze navigation.

  16. Complex changes in the apoptotic and cell differentiation programs during initiation of the hair follicle response to chemotherapy.

    PubMed

    Sharova, Tatyana Y; Poterlowicz, Krzysztof; Botchkareva, Natalia V; Kondratiev, Nikita A; Aziz, Ahmar; Spiegel, Jeffrey H; Botchkarev, Vladimir A; Sharov, Andrey A

    2014-12-01

    Chemotherapy has severe side effects in normal rapidly proliferating organs, such as hair follicles, and causes massive apoptosis in hair matrix keratinocytes followed by hair loss. To define the molecular signature of hair follicle response to chemotherapy, human scalp hair follicles cultured ex vivo were treated with doxorubicin (DXR), and global microarray analysis was performed 3 hours after treatment. Microarray data revealed changes in expression of 504 genes in DXR-treated hair follicles versus controls. Among these genes, upregulations of several tumor necrosis factor family of apoptotic receptors (FAS, TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) receptors 1/2), as well as of a large number of keratin-associated protein genes, were seen after DXR treatment. Hair follicle apoptosis induced by DXR was significantly inhibited by either TRAIL-neutralizing antibody or caspase-8 inhibitor, thus suggesting a previously unreported role for TRAIL receptor signaling in mediating DXR-induced hair loss. These data demonstrate that the early phase of the hair follicle response to DXR includes upregulation of apoptosis-associated markers, as well as substantial reorganization of the terminal differentiation programs in hair follicle keratinocytes. These data provide an important platform for further studies toward the design of effective approaches for the management of chemotherapy-induced hair loss.

  17. TCR repertoire analysis by next generation sequencing allows complex differential diagnosis of T cell-related pathology.

    PubMed

    Dziubianau, M; Hecht, J; Kuchenbecker, L; Sattler, A; Stervbo, U; Rödelsperger, C; Nickel, P; Neumann, A U; Robinson, P N; Mundlos, S; Volk, H-D; Thiel, A; Reinke, P; Babel, N

    2013-11-01

    Clonotype analysis is essential for complete characterization of antigen-specific T cells. Moreover, knowledge on clonal identity allows tracking of antigen-specific T cells in whole blood and tissue infiltrates and can provide information on antigenic specificity. Here, we developed a next generation sequencing (NGS)-based platform for the highly quantitative clonotype characterization of T cells and determined requirements for the unbiased characterization of the input material (DNA, RNA, ex vivo derived or cell culture expanded T cells). Thereafter we performed T cell receptor (TCR) repertoire analysis of various specimens in clinical settings including cytomegalovirus (CMV), polyomavirus BK (BKV) reactivation and acute cellular allograft rejection. Our results revealed dynamic nature of virus-specific T cell clonotypes; CMV reactivation was linked to appearance of new highly abundant antigen-specific clonalities. Moreover, analysis of clonotype overlap between BKV-, alloantigen-specific T cell-, kidney allograft- and urine-derived lymphocytes provided hints for the differential diagnosis of allograft dysfunction and enabled appropriate therapy adjustment. We believe that the established approach will provide insights into the regulation of virus-specific/anti-tumor immunity and has high diagnostic potential in the clinical routine. © Copyright 2013 The American Society of Transplantation and the American Society of Transplant Surgeons.

  18. Differential expression of voltage-gated K+ currents in medial septum/diagonal band complex neurons exhibiting distinct firing phenotypes.

    PubMed

    Garrido-Sanabria, Emilio R; Perez-Cordova, Miriam G; Colom, Luis V

    2011-08-01

    The medial septum/diagonal band complex (MSDB) controls hippocampal excitability, rhythms and plastic processes. Medial septal neuronal populations display heterogeneous firing patterns. In addition, some of these populations degenerate during age-related disorders (e.g. cholinergic neurons). Thus, it is particularly important to examine the intrinsic properties of theses neurons in order to create new agents that effectively modulate hippocampal excitability and enhance memory processes. Here, we have examined the properties of voltage-gated, K(+) currents in electrophysiologically-identified neurons. These neurons were taken from young rat brain slices containing the MS/DB complex. Whole-cell, patch recordings of outward currents were obtained from slow firing, fast-spiking, regular-firing and burst-firing neurons. Slow firing neurons showed depolarization-activated K(+) current peaks and densities larger than in other neuronal subtypes. Slow firing total current exhibited an inactivating A-type current component that activates at subthreshold depolarization and was reliably blocked by high concentrations of 4-AP. In addition, slow firing neurons expressed a low-threshold delayed rectifier K(+) current component with slow inactivation and intermediate sensitivity to tetraethylammonium. Fast-spiking neurons exhibited the smaller I(K) and I(A) current densities. Burst and regular firing neurons displayed an intermediate firing phenotype with I(K) and I(A) current densities that were larger than the ones observed in fast-spiking neurons but smaller than the ones observed in slow-firing neurons. In addition, the prevalence of each current differed among electrophysiological groups with slow firing and regular firing neurons expressing mostly I(A) and fast spiking and bursting neurons exhibiting mostly delayer rectifier K(+) currents with only minimal contributions of the I(A). The pharmacological or genetic modulations of these currents constitute an important target

  19. Mutation of a Drosophila gamma tubulin ring complex subunit encoded by discs degenerate-4 differentially disrupts centrosomal protein localization

    PubMed Central

    Barbosa, Vitor; Yamamoto, Rochele R.; Henderson, Daryl S.; Glover, David M.

    2000-01-01

    We have cloned the Drosophila gene discs degenerate-4 (dd4) and find that it encodes a component of the γ-tubulin ring complex (γTuRC) homologous to Spc98 of budding yeast. This provides the first opportunity to study decreased function of a member of the γ-tubulin ring complex, other than γ-tubulin itself, in a metazoan cell. γ-tubulin is no longer at the centrosomes but is dispersed throughout dd4 cells and yet bipolar metaphase spindles do form, although these have a dramatically decreased density of microtubules. Centrosomin (CNN) remains in broad discrete bodies but only at the focused poles of such spindles, whereas Asp (abnormal spindle protein) is always present at the presumptive minus ends of microtubules, whether or not they are focused. This is consistent with the proposed role of Asp in coordinating the nucleation of mitotic microtubule organizing centers. The centrosome associated protein CP190 is partially lost from the spindle poles in dd4 cells supporting a weak interaction with γ-tubulin, and the displaced protein accumulates in the vicinity of chromosomes. Electron microscopy indicates not only that the poles of dd4 cells have irregular amounts of pericentriolar material, but also that they can have abnormal centrioles. In six dd4 cells subjected to serial sectioning centrioles were missing from one of the two poles. This suggests that in addition to its role in nucleating cytoplasmic and spindle microtubules, the γTuRC is also essential to the structure of centrioles and the separation of centrosomes. PMID:11124805

  20. Differential roles of the glycogen-binding domains of beta subunits in regulation of the Snf1 kinase complex.

    PubMed

    Mangat, Simmanjeet; Chandrashekarappa, Dakshayini; McCartney, Rhonda R; Elbing, Karin; Schmidt, Martin C

    2010-01-01

    Members of the AMP-activated protein kinase family, including the Snf1 kinase of Saccharomyces cerevisiae, are activated under conditions of nutrient stress. AMP-activated protein kinases are heterotrimeric complexes composed of a catalytic alpha subunit and regulatory beta and gamma subunits. In this study, the role of the beta subunits in the regulation of Snf1 activity was examined. Yeasts express three isoforms of the AMP-activated protein kinase consisting of Snf1 (alpha), Snf4 (gamma), and one of three alternative beta subunits, either Sip1, Sip2, or Gal83. The Gal83 isoform of the Snf1 complex is the most abundant and was analyzed in the greatest detail. All three beta subunits contain a conserved domain referred to as the glycogen-binding domain. The deletion of this domain from Gal83 results in a deregulation of the Snf1 kinase, as judged by a constitutive activity independent of glucose availability. In contrast, the deletion of this homologous domain from the Sip1 and Sip2 subunits had little effect on Snf1 kinase regulation. Therefore, the different Snf1 kinase isoforms are regulated through distinct mechanisms, which may contribute to their specialized roles in different stress response pathways. In addition, the beta subunits are subjected to phosphorylation. The responsible kinases were identified as being Snf1 and casein kinase II. The significance of the phosphorylation is unclear since the deletion of the region containing the phosphorylation sites in Gal83 had little effect on the regulation of Snf1 in response to glucose limitation.

  1. Using Isomap to differentiate between anthropogenic and natural effects on groundwater dynamics in a complex geological setting

    NASA Astrophysics Data System (ADS)

    Boettcher, Steven; Merz, Christoph; Lischeid, Gunnar

    2015-04-01

    The water budget of many catchments has vastly changed throughout the last decades. Intensified land use and increased water withdrawal for drinking water production and irrigation are likely to intensify pressure on water resources. According to model predictions, changing rainfall intensity, duration and spatial distribution in conjunction with increasing temperatures will worsen the situation in the future. The current water resources management has to adapt to these negative developments and to account for competing demands and threats. Essential for successful management applications is the identification and the quantification of the cause-and-effect chains driving the hydrological behavior of a catchment on the scale of management. It needs to check direction and magnitude of intended effects of measures taken as well as to identify unintended side effects that interact with natural effects in heterogeneous environments (Wood et al., 1988; Bloschl and Sivapalan, 1995). Therefore, these tools have to be able to distinguish between natural and anthropogenic driven impacts, even in complex geological settings like the Pleistocene landscape of North-East Germany. This study presents an approach that utilizes monitoring data to detect and quantitatively describe the predominant processes or factors of an observed hydrological system. The multivariate data analysis involves a non-linear dimension reduction method called Isometric Feature Mapping (Isomap, Tenenbaum et al., 2000) to extract information about the causes for the observed dynamics. Ordination methods like Isomap are used to derive a meaningful low-dimensional representation of a complex, high-dimensional data set. The approach is based on the hypothesis, that the number of processes which explain the variance of the data is relative low although the intensity of the processes varies in time and space. Therefore, the results can be interpreted in reference to the effective hydrological processes which

  2. VERDANDI Is a Direct Target of the MADS Domain Ovule Identity Complex and Affects Embryo Sac Differentiation in Arabidopsis[W

    PubMed Central

    Matias-Hernandez, Luis; Battaglia, Raffaella; Galbiati, Francesca; Rubes, Marco; Eichenberger, Christof; Grossniklaus, Ueli; Kater, Martin M.; Colombo, Lucia

    2010-01-01

    In Arabidopsis thaliana, the three MADS box genes SEEDSTICK (STK), SHATTERPROOF1 (SHP1), and SHP2 redundantly regulate ovule development. Protein interaction studies have shown that a multimeric complex composed of the ovule identity proteins together with the SEPALLATA MADS domain proteins is necessary to determine ovule identity. Despite the extensive knowledge that has become available about these MADS domain transcription factors, little is known regarding the genes that they regulate. Here, we show that STK, SHP1, and SHP2 redundantly regulate VERDANDI (VDD), a putative transcription factor that belongs to the plant-specific B3 superfamily. The vdd mutant shows defects during the fertilization process resulting in semisterility. Analysis of the vdd mutant female gametophytes indicates that antipodal and synergid cell identity and/or differentiation are affected. Our results provide insights into the pathways regulated by the ovule identity factors and the role of the downstream target gene VDD in female gametophyte development. PMID:20581305

  3. Isolation and characterization of human and mouse ZIRTL, a member of the IRT1 family of transporters, mapping within the epidermal differentiation complex.

    PubMed

    Lioumi, M; Ferguson, C A; Sharpe, P T; Freeman, T; Marenholz, I; Mischke, D; Heizmann, C; Ragoussis, J

    1999-12-01

    We report the precise mapping and characterization of ZIRTL (zinc-iron regulated transporter-like) gene, the first mammalian member of an extensive family of divalent metal ion transporters, comprising IRT1 and ZIP1, ZIP2, ZIP3, and ZIP4 in plants and ZRT1 and ZRT2 in yeast. The human gene maps at the telomeric end of the epidermal differentiation complex (EDC), within chromosomal band 1q21, while the mouse gene maps within the mouse EDC, on mouse chromosome 3, between S100A9 and S100A13. The structure of the human gene has been determined, and message was detected in most adult and fetal tissues including the epidermis. The mouse gene is developmentally regulated and found expressed in fetal and adult suprabasal epidermis, osteoblasts, small intestine, and salivary gland.

  4. Lanthanide(III)/actinide(III) differentiation in coordination of azine molecules to tris(cyclopentadienyl) complexes of cerium and uranium.

    PubMed

    Mehdoui, Thouraya; Berthet, Jean-Claude; Thuéry, Pierre; Ephritikhine, Michel

    2004-02-21

    Reaction of azine molecules L with the trivalent metallocenes [M(C5H4R)3](M = Ce, U; R = But, SiMe3) in toluene gave the Lewis base adducts [M(C5H4R)3(L)](L = pyridine, 3-picoline, 3,5-lutidine, 3-chloropyridine, pyridazine, pyrimidine, pyrazine, 3,5-dimethylpyrazine and s-triazine), except in the cases of M = U and L = 3-chloropyridine, pyridazine, pyrazine and s-triazine where oxidation of U(III) was found to occur. In the pairs of analogous compounds of Ce(III) and U(III), i.e.[M(C5H4But)3(L)](L = pyridine, picoline) and [M(C5H4SiMe3)3(L)](L = pyridine, lutidine, pyrimidine and dimethylpyrazine), the M-N and average M-C distances are longer for M = Ce than for M = U; however, within a series of azine adducts of the same metallocene, no significant variation is noted in the M-N and average M-C distances. The equilibria between [M(C5H4R)3], L and [M(C5H4R)3(L)] were studied by 1H NMR spectroscopy. The stability constants of the uranium complexes, KUL, are greater than those of the cerium counterparts, KCeL. The values of KML are much greater for R = SiMe3 than for R = But and a linear correlation is found between the logarithms of KML and the hydrogen-bond basicity pKHB scale of the azines. Thermodynamic parameters indicate that the enthalpy-entropy compensation effect holds for these complexation reactions. Competition reactions of [Ce(C5H4R)3] and [U(C5H4R)3] with L show that the selectivity of L in favour of U(III) increases with the [small pi] donor character of the metallocene and is proportional to the pi accepting ability of the azine molecule, measured by its reduction potential.

  5. A Negative Feedback Loop Controlling bHLH Complexes Is Involved in Vascular Cell Division and Differentiation in the Root Apical Meristem.

    PubMed

    Katayama, Hirofumi; Iwamoto, Kuninori; Kariya, Yuka; Asakawa, Tomohiro; Kan, Toshiyuki; Fukuda, Hiroo; Ohashi-Ito, Kyoko

    2015-12-07

    Controlling cell division and differentiation in meristems is essential for proper plant growth. Two bHLH heterodimers consisting of LONESOME HIGHWAY (LHW) and TARGET OF MONOPTEROS 5 (TMO5)/TMO5-LIKE1 (T5L1) regulate periclinal cell division in vascular cells in the root apical meristem (RAM). In this study, we further investigated the functions of LHW-T5L1, finding that in addition to controlling cell division, this complex regulates xylem differentiation in the RAM via a novel negative regulatory system. LHW-T5L1 upregulated the thermospermine synthase gene ACAULIS5 (ACL5), as well as SUPPRESSOR OF ACAULIS5 LIKE3 (SACL3), which encodes a bHLH protein, in the RAM. The SACL3 promoter sequence contains a conserved upstream open reading frame (uORF), which blocked translation of the main SACL3 ORF in the absence of thermospermine. Thermospermine eliminated the negative effect of uORF and enhanced SACL3 production. Further genetic and molecular biological analyses indicated that ACL5 and SACL3 suppress the function of LHW-T5L1 through a protein-protein interaction between LHW and SACL3. Finally, we showed that a negative feedback loop consisting of LHW-T5L1, ACL5, SACL3, and LHW-SACL3 contributes to maintain RAM size and proper root growth. These findings suggest that a negative feedback loop regulates the LHW-T5L1 output level to coordinate cell division and differentiation in a cell-autonomous manner. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Complex permittivity measurement as a new noninvasive tool for monitoring in vitro tissue engineering and cell signature through the detection of cell proliferation, differentiation, and pretissue formation.

    PubMed

    Bagnaninchi, Pierre-Olivier; Dikeakos, Maria; Veres, Teodor; Tabrizian, Maryam

    2004-12-01

    In in vitro tissue engineering, microporous scaffolds are commonly used to promote cell proliferation and differentiation in three-dimensional structures. Classic measurement methods are particularly time consuming, difficult to handle, and destructive. In this study, a new nondestructive method based on complex permittivity measurement (CPM) is proposed to monitor and track the osteoblast and macrophage differentiation through their morphological variation upon cell attachment and proliferation inside the microporous scaffolds. CPM is performed using a vector network analyzer and a dielectric probe under sterile conditions in a laminar-flow hood. A suitable effective medium approximation (EMA) is applied to fit the data in order to extract the parameters of the different constituents. Our data show that the EMA depolarization factor can be monitored to assess the variation of cell morphology characterizing cell attachment. Discrimination between two batches of scaffolds seeded, respectively, with 2 million and 1 million osteoblast cells is possible; the ratio of their CPM-derived cell volume fractions is in agreement with the ratio of their cell seeding numbers. In addition, cell proliferation inside scaffolds seeded with osteoblasts cultured in alpha minimum essential medium and inside scaffolds seeded with osteoblasts cultured in alpha minimum essential medium supplemented to induce the formation of extracellular matrix is monitored via CPM over several days. CPM-determined cell volume fraction is compared to DNA assay cell counts. Extracellular matrix formation and cell presence was confirmed by scanning electron microscopy. A set of three signature parameters (epsilon'mem, epsilon'cyt, kappa'cyt) characteristic of cell line is extracted from CPM. Distinct signatures are recorded for osteoblasts and macrophages, thus confirming the ability of CPM to discriminate between different cell types. This study demonstrates the potential of CPM as a diagnostic tool to

  7. Antigen-Specific Signaling by a Soluble, Dimeric Peptide/Major Histocompatibility Complex Class II/Fc Chimera Leading to T Helper Cell Type 2 Differentiation

    PubMed Central

    Casares, Sofia; Zong, Cong S.; Radu, Dorel L.; Miller, Alexander; Bona, Constantin A.; Brumeanu, Teodor-Doru

    1999-01-01

    Interaction between a T cell receptor (TCR) and various ligands, i.e., anti-TCR antibodies, superantigens, peptides, or altered peptide ligands in the context of major histocompatibility complex (MHC) molecules can trigger different T helper cell (Th) effector functions. Herein, we studied the T cell response induced by a soluble, dimeric peptide/MHC class II chimera, namely hemagglutinin (HA)110-120/I-Edαβ/Fcγ2a (DEF). We have previously demonstrated that the soluble DEF molecule binds stably and specifically to HA110-120–specific TCRs expressed by a T cell hybridoma. Administration of DEF in vivo induced differentiation of resting and activated peptide-specific T cells toward a Th2 response, as indicated by the increase of interleukin (IL)-4, IL-10, and specific immunoglobulin (Ig)G1 antibodies and decrease of IL-2, specific IgG2a antibodies, and cytotoxic T lymphocyte activity. In contrast to HA110-120 peptide presented by the DEF molecule to T cells, the nominal synthetic peptide induced a predominant Th1 response, and the PR8 virus–derived HA110-120 peptides induced a mixed Th1/Th2 response. Independent of antigen processing, soluble DEF was almost 2 logs more potent in stimulating cognate T cells than the nominal peptide. Polarization of cognate T cells toward the Th2 response occurred upon interaction of soluble DEF with TCR and CD4 molecules followed by early activation of p56lck and ZAP-70 tyrosine kinases, and negative signaling of the signal transducer and activator of transcription (STAT)4 pathway of Th1 differentiation. DEF-like molecules may provide a new tool to study the mechanisms of signaling toward Th2 differentiation and may also provide a potential immunotherapeutic approach to modulate autoreactive T cells toward protective Th2 immune responses. PMID:10449525

  8. Genome-wide analysis of histone methylation reveals chromatin state-based complex regulation of differential gene transcription and function of CD8 memory T cells

    PubMed Central

    Araki, Yasuto; Wang, Zhibin; Zang, Chongzhi; Wood, William H.; Schones, Dustin; Cui, Kairong; Roh, Tae-Young; Lhotsky, Brad; Wersto, Robert P.; Peng, Weiqun; Becker, Kevin G.; Zhao, Keji; Weng, Nan-ping

    2009-01-01

    Summary Memory lymphocytes are characterized by their ability to exhibit a rapid response to the recall antigen, in which differential transcription plays a significant role, yet the underlying mechanism is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in naïve and memory CD8 T cells. We found that a general correlation exists between the levels of gene expression and the levels of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations display four distinct modes: repressive, active, poised, and bivalent, reflecting different functions of these genes. Furthermore, a permissive chromatin state of each gene is established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for memory CD8 T cell function. PMID:19523850

  9. Genetic differentiation among distinct karyomorphs of the wolf fish Hoplias malabaricus species complex (Characiformes, Erythrinidae) and report of unusual hybridization with natural triploidy.

    PubMed

    Utsunomia, R; Alves, J C Pansonato; Paiva, L R S; Silva, G J Costa; Oliveira, C; Bertollo, L A C; Foresti, F

    2014-11-01

    In this study, genetic differentiation between karyomorphs A (2n = 42) and D (2n = 39/40) of the wolf fish Hoplias malabaricus, which is comprised of several cryptic species that present a wide variety of diploid chromosome numbers and sex chromosome systems, resulting in the identification of seven distinct karyomorphs (A-G), was investigated using a combination of molecular and cytogenetic tools. Deep sequence divergences for both karyomorphs were observed and indicate a long period of reproductive isolation between karyomorphs A and D. Additionally, one individual with 61 chromosomes was identified, which, as far as is known, is the first case of natural triploidy resulting from the hybridization between these highly differentiated karyomorphs of H. malabaricus. Molecular and cytogenetic analyses revealed that this allotriploid specimen carries two sets of maternal chromosomes from karyomorph D (2n = 40) and one set of chromosomes from karyomorph A (n = 21). Moreover, ribosomal sites and active nucleolus organizer regions from both parental contributors were found in the triploid hybrid. Considering the significant genetic distances between karyomorphs A and D, one of the primary reasons for the lack of recurrent reports of hybridization in the H. malabaricus species complex may be due to post-zygotic barriers, such as hybrid sterility or unviability.

  10. Evaluation of a simple in-house test to presumptively differentiate Mycobacterium tuberculosis complex from nontuberculous mycobacteria by detection of p-nitrobenzoic acid metabolites.

    PubMed

    Wang, Guirong; Yu, Xia; Liang, Qian; Chen, Suting; Wilson, Stuart; Huang, Hairong

    2013-01-01

    The timely differentiation of Mycobacterium tuberculosis complex (MTC) and non-tubercular mycobacterium (NTM) species is urgently needed in patient care since the routine laboratory method is time consuming and cumbersome. An easy and cheap method which can successfully distinguish MTC from NTM was established and evaluated. 38 mycobacterial type and reference strains and 65 clinical isolates representing 10 species of mycobacterium were included in this study. Metabolites of p-nitrobenzoic acid (PNB) reduction were identified using liquid chromatography and tandem mass spectrometry (LC/MS/MS). A spectrophotometric method was developed to detect these metabolites, which was evaluated on a number of MTC and NTM species. All of the tested NTM species and strains reduced PNB to p-aminobenzoic acid (PABA), while none of the MTC strains showed a similar activity. Spectrophotometric detection of PABA had 100% sensitivity and specificity for MTC and NTM differentiation among the type strains and the clinical isolates tested. PABA was identified as one of the metabolites of PNB reduction. All the tested NTM species metabolized PNB to PABA whereas the MTC members lacked this activity. A simple, specific and cost-effective method based on PABA production was established in order to discriminate MTC from NTM from cultured organisms.

  11. Complexity and differential expression of carbohydrate epitopes associated with L-selectin recognition of high endothelial venules.

    PubMed Central

    Berg, E. L.; Mullowney, A. T.; Andrew, D. P.; Goldberg, J. E.; Butcher, E. C.

    1998-01-01

    Carbohydrate ligands for lymphocyte L-selectin are expressed on high endothelial venules (HEVs) in peripheral lymph nodes and sites of chronic inflammation and mediate the recruitment of lymphocytes from the blood into these tissues. In the mouse, these ligands, collectively termed the peripheral lymph node addressin (PNAd), have been shown to contain fucose, sialic acid, and sulfate and to include several HEV glycoproteins including GlyCAM-1, CD34, and MAdCAM-1. Monoclonal antibody (MAb) MECA-79, which binds a sulfate-dependent epitope, recognizes PNAd in both mouse and man. In humans, only CD34 has been identified among the glycoprotein species that react with MECA-79. Although P-selectin is highly expressed in tonsil HEVs, it was not found to react with MECA-79 or to support L-selectin-mediated lymphocyte rolling. To further characterize human PNAd, MAbs were developed against purified PNAd immunoisolated from human tonsil. MAbs JG-1, JG-5, JG-9, and JG-10, like MECA-79, bind HEVs in human tonsil and react similarly in Western blots, and JG-9 and JG-10 also block lymphocyte rolling on purified PNAd. In addition, by competitive ELISA on purified tonsil PNAd, all MAbs were found to react with overlapping epitopes. However, JG-1, JG-5, JG-9, and JG-10 do not recognize mouse PNAd, and unlike MECA-79, they recognize determinants that are sensitive to neuraminidase. Strikingly, the epitope recognized by JG-1, although abundant in tonsil and peripheral lymph node, is absent from appendix HEVs or HEVs in some samples of chronically inflamed skin, even though these HEVs are MECA-79 reactive. Moreover, although JG-5 and JG-9 react well with tonsil, peripheral lymph node, and inflamed skin HEVs, they react only with occasional endothelial cells in appendix tissues. These findings point to significant diversity in the carbohydrate determinants expressed by HEVs and recognized by L-selectin and demonstrate their differential representation in different sites in vivo. These

  12. Differentiation in stag beetles, Neolucanus swinhoei complex (Coleoptera: Lucanidae): four major lineages caused by periodical Pleistocene glaciations and separation by a mountain range.

    PubMed

    Tsai, Cheng-Lung; Wan, Xia; Yeh, Wen-Bin

    2014-09-01

    Taxonomic debates on Neolucanus swinhoei complex consisting of N. swinhoei, N. doro doro, N. doro horaguchii, and N. euganiae, distributed exclusively in Taiwan, have been ongoing for several decades because of their overlapping morphological characters. To clarify their taxonomic status and phylogeographical history, we analyzed nine morphological characteristics and four molecular amplicons. Phylogenetic inferences based on COI+16S rDNA+wingless showed one eastern and three western lineages, with the latter consisting of one low-hill and two montane lineages. Intermingled DNA sequences from different populations within each lineage, many low FST values, and a high variance component between lineages indicate the possibility of gene flow among populations. However, positive relationships were observed between the genetic divergences of 16S rDNA and its FST values with geographic distance. A divergence estimation based on COI+16S revealed that these beetles might have originated from Asian mainland and differentiated into western and eastern lineages ca. 1Mya, with the differentiation of the western lineages occurring approximately 0.50-0.75Mya. Isolation by mountain ranges and limited flying capability of these beetles as well as populations retreat to and expansion from refugia in response to glaciation cycles have resulted in the current distribution of N. swinhoei complex. Although most morphological characters are variable and undistinguishable, multi-dimensional scaling analysis based on measurable characteristics could recognize hill N. swinhoei as a cluster distinct from the others. However, based on the realities of genetic admixture, shared phylogeographical history and overlapping characteristics, all of these stag beetles should be regarded as Neolucanus swinhoei Bates, 1866. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Differentiation between early rheumatoid and early psoriatic arthritis by the ultrasonographic study of the synovio-entheseal complex of the small joints of the hands.

    PubMed

    Zabotti, Alen; Salvin, Sara; Quartuccio, Luca; De Vita, Salvatore

    2016-01-01

    To determine whether ultrasonographic findings of the synovio-entheseal complex of the hand small joints could be used to differentiate between early rheumatoid and early psoriatic arthritis. Thirty-four early rheumatoid and 26 early psoriatic arthritis patients with a prevalent involvement of the hands were examined with ultrasound (US). All exams were performed at the first visit by evaluating synovitis, peritendon extensor digitorum tendon oedema, enthesitis of the central slip of extensor tendon, flexor tenosynovitis and soft tissue oedema. In the same patient, the two most clinically involved joints, if possible of the same digit, were evaluated. Sixty-eight clinically involved joints were evaluated in 34 early rheumatoid arthritis patients and 52 joints in 26 early psoriatic arthritis patients.Synovitis was significantly more frequently detected in early rheumatoid arthritis compared to early psoriatic arthritis patients (p=0.0001), in 91.1% joints of the former and in 59.6% joints of the latter. At metacarpohalangeal joint, the presence of peritendon extensor digitorum tendon inflammation was observed in 2.5% of the joints in the early rheumatoid arthritis group and in 54.1% of the joints in the early psoriatic arthritis group (p=0.0001). At PIP joints, central slip enthesitis was exclusively observed in EPsA (p=0.0045). When considering the most clinically involved finger per patient, soft tissue oedema was detected almost exclusively in psoriatic arthritis (p=0.0002). The US involvement of synovio-entheseal complex and US extrasynovial features may be helpful in the differential diagnosis between early rheumatoid and early psoriatic arthritis.

  14. Differential recruitment of the hippocampus, medial prefrontal cortex, and the human motion complex during path integration in humans.

    PubMed

    Wolbers, Thomas; Wiener, Jan M; Mallot, Hanspeter A; Büchel, Christian

    2007-08-29

    Path integration, the ability to sense self-motion for keeping track of changes in orientation and position, constitutes a fundamental mechanism of spatial navigation and a keystone for the development of cognitive maps. Whereas animal path integration is predominantly supported by the head-direction, grid, and place cell systems, the neural foundations are not well understood in humans. Here we used functional magnetic resonance imaging and a virtual rendition of a triangle completion paradigm to test whether human path integration recruits a cortical system similar to that of rodents and nonhuman primates. Participants traveled along two legs of a triangle before pointing toward the starting location. In accordance with animal models, stronger right hippocampal activation predicted more accurate updating of the starting location on a trial-by-trial basis. Moreover, between-subjects fluctuations in response consistency were negatively correlated with bilateral hippocampal and medial prefrontal activation, and bilateral recruitment of the human motion complex (hMT+) covaried with individual path integration capability. Given that these effects were absent in a perceptual control task, the present study provides the first evidence that visual path integration is related to the dynamic interplay of self-motion processing in hMT+, higher-level spatial processes in the hippocampus, and spatial working memory in medial prefrontal cortex.

  15. Substance P Differentially Modulates Firing Rate of Solitary Complex (SC) Neurons from Control and Chronic Hypoxia-Adapted Adult Rats

    PubMed Central

    Nichols, Nicole L.; Powell, Frank L.; Dean, Jay B.; Putnam, Robert W.

    2014-01-01

    NK1 receptors, which bind substance P, are present in the majority of brainstem regions that contain CO2/H+-sensitive neurons that play a role in central chemosensitivity. However, the effect of substance P on the chemosensitive response of neurons from these regions has not been studied. Hypoxia increases substance P release from peripheral afferents that terminate in the caudal nucleus tractus solitarius (NTS). Here we studied the effect of substance P on the chemosensitive responses of solitary complex (SC: NTS and dorsal motor nucleus) neurons from control and chronic hypoxia-adapted (CHx) adult rats. We simultaneously measured intracellular pH and electrical responses to hypercapnic acidosis in SC neurons from control and CHx adult rats using the blind whole cell patch clamp technique and fluorescence imaging microscopy. Substance P significantly increased the basal firing rate in SC neurons from control and CHx rats, although the increase was smaller in CHx rats. However, substance P did not affect the chemosensitive response of SC neurons from either group of rats. In conclusion, we found that substance P plays a role in modulating the basal firing rate of SC neurons but the magnitude of the effect is smaller for SC neurons from CHx adult rats, implying that NK1 receptors may be down regulated in CHx adult rats. Substance P does not appear to play a role in modulating the firing rate response to hypercapnic acidosis of SC neurons from either control or CHx adult rats. PMID:24516602

  16. Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex

    PubMed Central

    Miller, Anzy; Ralser, Meryem; Kloet, Susan L.; Loos, Remco; Nishinakamura, Ryuichi; Bertone, Paul; Vermeulen, Michiel

    2016-01-01

    Sall4 is an essential transcription factor for early mammalian development and is frequently overexpressed in cancer. Although it is reported to play an important role in embryonic stem cell (ESC) self-renewal, whether it is an essential pluripotency factor has been disputed. Here, we show that Sall4 is dispensable for mouse ESC pluripotency. Sall4 is an enhancer-binding protein that prevents precocious activation of the neural gene expression programme in ESCs but is not required for maintenance of the pluripotency gene regulatory network. Although a proportion of Sall4 protein physically associates with the Nucleosome Remodelling and Deacetylase (NuRD) complex, Sall4 neither recruits NuRD to chromatin nor influences transcription via NuRD; rather, free Sall4 protein regulates transcription independently of NuRD. We propose a model whereby enhancer binding by Sall4 and other pluripotency-associated transcription factors is responsible for maintaining the balance between transcriptional programmes in pluripotent cells. PMID:27471257

  17. SMA observations of the W3(OH) complex: Dynamical differentiation between W3(H2O) and W3(OH)

    NASA Astrophysics Data System (ADS)

    Qin, Sheng-Li; Schilke, Peter; Wu, Jingwen; Liu, Tie; Wu, Yuefang; Sánchez-Monge, Álvaro; Liu, Ying

    2016-03-01

    We present Submillimeter Array observations of the HCN (3-2) and HCO+ (3-2) molecular lines towards the W3(H2O) and W3(OH) star-forming complexes. Infall and outflow motions in the W3(H2O) have been characterized by observing HCN and HCO+ transitions. High-velocity blue/red-shifted emission, tracing the outflow, show multiple knots, which might originate in episodic and precessing outflows. `Blue-peaked' line profiles indicate that gas is infalling on to the W3(H2O) dust core. The measured large mass accretion rate, 2.3 × 10-3 M⊙ yr-1, together with the small free-fall time-scale, 5 × 103 yr, suggest W3(H2O) is in an early evolutionary stage of the process of formation of high-mass stars. For the W3(OH), a two-layer model fit to the HCN and HCO+ spectral lines and Spizter/Infrared Array Camera (IRAC) images support that the W3(OH) H II region is expanding and interacting with the ambient gas, with the shocked neutral gas being expanding with an expansion time-scale of 6.4 × 103 yr. The observations suggest different kinematical time-scales and dynamical states for the W3(H2O) and W3(OH).

  18. Differential distribution and association of repeat DNA sequences in the lateral element of the synaptonemal complex in rat spermatocytes.

    PubMed

    Hernández-Hernández, Abrahan; Rincón-Arano, Héctor; Recillas-Targa, Félix; Ortiz, Rosario; Valdes-Quezada, Christian; Echeverría, Olga M; Benavente, Ricardo; Vázquez-Nin, Gerardo H

    2008-02-01

    The synaptonemal complex (SC) is an evolutionarily conserved structure that mediates synapsis of homologous chromosomes during meiotic prophase I. Previous studies have established that the chromatin of homologous chromosomes is organized in loops that are attached to the lateral elements (LEs) of the SC. The characterization of the genomic sequences associated with LEs of the SC represents an important step toward understanding meiotic chromosome organization and function. To isolate these genomic sequences, we performed chromatin immunoprecipitation assays in rat spermatocytes using an antibody against SYCP3, a major structural component of the LEs of the SC. Our results demonstrated the reproducible and exclusive isolation of repeat deoxyribonucleic acid (DNA) sequences, in particular long interspersed elements, short interspersed elements, long terminal direct repeats, satellite, and simple repeats. The association of these repeat sequences to the LEs of the SC was confirmed by in situ hybridization of meiotic nuclei shown by both light and electron microscopy. Signals were also detected over the chromatin surrounding SCs and in small loops protruding from the lateral elements into the SC central region. We propose that genomic repeat DNA sequences play a key role in anchoring the chromosome to the protein scaffold of the SC.

  19. THE POLYTYPIC SPECIES REVISITED: GENETIC DIFFERENTIATION AND MOLECULAR PHYLOGENETICS OF THE TIGER SALAMANDER AMBYSTOMA TIGRINUM (AMPHIBIA: CAUDATA) COMPLEX.

    PubMed

    Shaffer, H Bradley; McKnight, Mark L

    1996-02-01

    We present a phylogenetic analysis of the Ambystoma tigrinum complex, based on approximately 840 base pairs of mitochondrial-DNA sequence from the rapidly evolving D-loop and an adjacent intron. Our samples include populations of the continentally distributed species, A. tigrinum, plus all described species of Mexican ambystomatids. Sequence divergence is low, ranging from 0-8.5%, and most phylogenetic groupings are weakly supported statistically. We identified eight reasonably well-defined clades from the United States and Mexico, with the geographically isolated A. californiense from California as the probable sister group to the remaining taxa. Our sequence data are not capable of resolving the relationships among these clades, although the pattern of transitional-site evolution suggests that these eight lineages diverged during a period of rapid cladogenesis. We roughly calibrate a molecular clock and identify a few lineages that significantly deviate from the slow, baseline rate of 0.5-0.75% per million years. Our data also suggest that species boundaries for several U.S. and Mexican species need to be altered and that the concept of a continentally distributed, polytypic tiger salamander is not valid. © 1996 The Society for the Study of Evolution.

  20. Statins in lymphangioleiomyomatosis. Simvastatin and atorvastatin induce differential effects on tuberous sclerosis complex 2-null cell growth and signaling.

    PubMed

    Atochina-Vasserman, Elena N; Goncharov, Dmitry A; Volgina, Alla V; Milavec, Megan; James, Melane L; Krymskaya, Vera P

    2013-11-01

    Mutations of the tumor suppressor genes tuberous sclerosis complex (TSC)1 and TSC2 cause pulmonary lymphangioleiomyomatosis (LAM) and tuberous sclerosis (TS). Current rapamycin-based therapies for TS and LAM have a predominantly cytostatic effect, and disease progression resumes with therapy cessation. Evidence of RhoA GTPase activation in LAM-derived and human TSC2-null cells suggests that 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitor statins can be used as potential adjuvant agents. The goal of this study was to determine which statin (simvastatin or atorvastatin) is more effective in suppressing TSC2-null cell growth and signaling. Simvastatin, but not atorvastatin, showed a concentration-dependent (0.5-10 μM) inhibitory effect on mouse TSC2-null and human LAM-derived cell growth. Treatment with 10 μM simvastatin induced dramatic disruption of TSC2-null cell monolayer and cell rounding; in contrast, few changes were observed in cells treated with the same concentration of atorvastatin. Combined treatment of rapamycin with simvastatin but not with atorvastatin showed a synergistic growth-inhibitory effect on TSC2-null cells. Simvastatin, but not atorvastatin, inhibited the activity of prosurvival serine-threonine kinase Akt and induced marked up-regulation of cleaved caspase-3, a marker of cell apoptosis. Simvastatin, but not atorvastatin, also induced concentration-dependent inhibition of p42/p44 Erk and mTORC1. Thus, our data show growth-inhibitory and proapoptotic effects of simvastatin on TSC2-null cells compared with atorvastatin. These findings have translational significance for combinatorial therapeutic strategies of simvastatin to inhibit TSC2-null cell survival in TS and LAM.

  1. Differential Processing of Nuclear Pore Complex Proteins by Rhinovirus 2A Proteases from Different Species and Serotypes▿

    PubMed Central

    Watters, Kelly; Palmenberg, Ann C.

    2011-01-01

    Human rhinoviruses (HRVs) from the HRV-A, HRV-B, and HRV-C species use encoded proteases, 2Apro and 3Cpro, to process their polyproteins and shut off host cell activities detrimental to virus replication. Reactions attributed to 2Apro include cleavage of eIF4G-I and -II to inhibit cellular mRNA translation and cleavage of select nucleoporin proteins (Nups) within nuclear pore complexes (NPCs) to disrupt karyopherin-dependent nuclear-cytoplasmic transport and signaling. Sequence diversity among 2Apro proteases from different HRV clades, even within species, suggested individual viruses might carry out these processes with unique mechanistic signatures. Six different recombinant 2Apro proteases (A16, A89, B04, B14, Cw12, and Cw24) were compared for their relative substrate preferences and cleavage kinetics using eIF4G from cellular extracts and Nups presented in native (NPC) or recombinant formats. The enzyme panel attacked these substrates with different rates or processing profiles, mimicking the preferences observed during natural infection (A16 and B14). For eIF4G, all 2Apro proteases cleaved at similar sites, but the comparative rates were species specific (HRV-A > HRV-C ≫ HRV-B). For Nup substrates, 5 of the 6 enzymes had unique product profiles (order of Nup selection) or reacted at different sites within Nup62, Nup98, and Nup153. Only A16 and A89 behaved similarly in most assays. Since each type of karyopherin receptor prefers particular Nups or uses a limited cohort of binding motifs within those Nups, the consequences of individual 2Apro avidities could profoundly affect relative viral replication levels, intracellular signaling, or extracellular signaling, all of which are underlying triggers for different host immune responses. PMID:21835805

  2. Differential Efficacy of Ketamine in the Acute versus Chronic Stages of Complex Regional Pain Syndrome in Mice

    PubMed Central

    Tajerian, Maral; Leu, David; Yang, Phillip; Huang, Ting Ting; Kingery, Wade S; Clark, J David

    2015-01-01

    Background Complex regional pain syndrome (CRPS) is a painful, disabling and often chronic condition, where many patients transition from an acute phase with prominent peripheral neurogenic inflammation to a chronic phase with evident central nervous system (CNS) changes. Ketamine is a centrally-acting agent believed to work through blockade of N-methyl-D-aspartate (NMDA) receptors and is being increasingly used for the treatment of refractory CRPS, although the basis for the drug’s effects and efficacy at different stages of the syndrome remain unclear. Methods We used a mouse model of CRPS (n=8–12/group) involving tibia fracture/cast immobilization to test the efficacy of ketamine (2 mg/kg/day; 7 days) or vehicle infusion during acute (3weeks [3w] post-fracture) and chronic (7w post-fracture) stages. Results Acute phase fracture mice displayed elevated limb temperature, edema and nociceptive sensitization that were not reduced by ketamine. Fracture mice treated with ketamine during the chronic phase showed reduced nociceptive sensitization that persisted beyond completion of the infusion. During this chronic phase, ketamine also reduced latent nociceptive sensitization and improved motor function at 18 weeks post-fracture. No side effects of the infusions were identified. These behavioral changes were associated with altered spinal astrocyte activation and expression of pain-related proteins including NMDA receptor 2b (NR2b), Ca2+/calmodulin-dependent protein kinase ii (CaMK2), and brain-derived neurotrophic factor (BNDF). Conclusions Collectively, these results demonstrate that ketamine is efficacious in the chronic, but not acute stages of CRPS, suggesting that the centrally-acting drug is relatively ineffective in early CRPS when peripheral mechanisms are more critical for supporting nociceptive sensitization. PMID:26492479

  3. Genetic differentiation and phylogeography of partially sympatric species complex Rhizophora mucronata Lam. and R. stylosa Griff. using SSR markers.

    PubMed

    Wee, Alison K S; Takayama, Koji; Chua, Jasher L; Asakawa, Takeshi; Meenakshisundaram, Sankararamasubramanian H; Onrizal; Adjie, Bayu; Ardli, Erwin Riyanto; Sungkaew, Sarawood; Malekal, Norhaslinda Binti; Tung, Nguyen Xuan; Salmo, Severino G; Yllano, Orlex Baylen; Saleh, M Nazre; Soe, Khin Khin; Tateishi, Yoichi; Watano, Yasuyuki; Baba, Shigeyuki; Webb, Edward L; Kajita, Tadashi

    2015-03-29

    Mangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers. Our results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow. Our findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting

  4. Abscisic Acid and Gibberellin Differentially Regulate Expression of Genes of the SNF1-Related Kinase Complex in Tomato Seeds1

    PubMed Central

    Bradford, Kent J.; Downie, A. Bruce; Gee, Oliver H.; Alvarado, Veria; Yang, Hong; Dahal, Peetambar

    2003-01-01

    The SNF1/AMP-activated protein kinase subfamily plays central roles in metabolic and transcriptional responses to nutritional or environmental stresses. In yeast (Saccharomyces cerevisiae) and mammals, activating and anchoring subunits associate with and regulate the activity, substrate specificity, and cellular localization of the kinase subunit in response to changing nutrient sources or energy demands, and homologous SNF1-related kinase (SnRK1) proteins are present in plants. We isolated cDNAs corresponding to the kinase (LeSNF1), regulatory (LeSNF4), and localization (LeSIP1 and LeGAL83) subunits of the SnRK1 complex from tomato (Lycopersicon esculentum Mill.). LeSNF1 and LeSNF4 complemented yeast snf1 and snf4 mutants and physically interacted with each other and with LeSIP1 in a glucose-dependent manner in yeast two-hybrid assays. LeSNF4 mRNA became abundant at maximum dry weight accumulation during seed development and remained high when radicle protrusion was blocked by abscisic acid (ABA), water stress, far-red light, or dormancy, but was low or undetected in seeds that had completed germination or in gibberellin (GA)-deficient seeds stimulated to germinate by GA. In leaves, LeSNF4 was induced in response to ABA or dehydration. In contrast, LeSNF1 and LeGAL83 genes were essentially constitutively expressed in both seeds and leaves regardless of the developmental, hormonal, or environmental conditions. Regulation of LeSNF4 expression by ABA and GA provides a potential link between hormonal and sugar-sensing pathways controlling seed development, dormancy, and germination. PMID:12857836

  5. A Differential Genome-Wide Transcriptome Analysis: Impact of Cellular Copper on Complex Biological Processes like Aging and Development

    PubMed Central

    Servos, Jörg; Hamann, Andrea; Grimm, Carolin; Osiewacz, Heinz D.

    2012-01-01

    underlying mechanisms controlling complex biological processes like aging and development. PMID:23152891

  6. Efficient Differentiation of Mycobacterium avium Complex Species and Subspecies by Use of Five-Target Multiplex PCR▿

    PubMed Central

    Shin, Sung Jae; Lee, Byung Soo; Koh, Won-Jung; Manning, Elizabeth J. B.; Anklam, Kelly; Sreevatsan, Srinand; Lambrecht, Randall S.; Collins, Michael T.

    2010-01-01

    Infections caused by the Mycobacterium avium complex (MAC) are on the rise in both human and veterinary medicine. A means of effectively discriminating among closely related yet pathogenetically diverse members of the MAC would enable better diagnosis and treatment as well as further our understanding of the epidemiology of these pathogens. In this study, a five-target multiplex PCR designed to discriminate MAC organisms isolated from liquid culture media was developed. This MAC multiplex was designed to amplify a 16S rRNA gene target common to all Mycobacterium species, a chromosomal target called DT1 that is unique to M. avium subsp. avium serotypes 2 and 3, to M. avium subsp. silvaticum, and to M. intracellulare, and three insertion sequences, IS900, IS901, and IS1311. The pattern of amplification results allowed determination of whether isolates were mycobacteria, whether they were members of the MAC, and whether they belonged to one of three major MAC subspecies, M. avium subsp. paratuberculosis, M. avium subsp. avium, and M. avium subsp. hominissuis. Analytical sensitivity was 10 fg of M. avium subsp. paratuberculosis genomic DNA, 5 to 10 fg of M. avium subsp. avium genomic DNA, and 2 to 5 fg of DNA from other mycobacterial species. Identification accuracy of the MAC multiplex was evaluated by testing 53 bacterial reference strains consisting of 28 different mycobacterial species and 12 nonmycobacterial species. Identification accuracy in a clinical setting was evaluated for 223 clinical MAC isolates independently identified by other methods. Isolate identification agreement between the MAC multiplex and these comparison assays was 100%. The novel MAC multiplex is a rapid, reliable, and simple assay for discrimination of MAC species and subspecies in liquid culture media. PMID:20810779

  7. Differential morphology of the superior olivary complex of Meriones unguiculatus and Monodelphis domestica revealed by calcium-binding proteins.

    PubMed

    Bazwinsky-Wutschke, I; Härtig, W; Kretzschmar, R; Rübsamen, R

    2016-12-01

    In mammals, the superior olivary complex (SOC) of the brainstem is composed of nuclei that integrate afferent auditory originating from both ears. Here, the expression of different calcium-binding proteins in subnuclei of the SOC was studied in distantly related mammals, the Mongolian gerbil (Meriones unguiculatus) and the gray short-tailed opossum (Monodelphis domestica) to get a better understanding of the basal nuclear organization of the SOC. Combined immunofluorescence labeling of the calcium-binding proteins (CaBPs) parvalbumin, calbindin-D28k, and calretinin as well as pan-neuronal markers displayed characteristic distribution patterns highlighting details of neuronal architecture of SOC nuclei. Parvalbumin was found in almost all neurons of SOC nuclei in both species, while calbindin and calretinin were restricted to specific cell types and axonal terminal fields. In both species, calbindin displayed a ubiquitous and mostly selective distribution in neurons of the medial nucleus of trapezoid body (MNTB) including their terminal axonal fields in different SOC targets. In Meriones, calretinin and calbindin showed non-overlapping expression patterns in neuron somata and terminal fields throughout the SOC. In Monodelphis, co-expression of calbindin and calretinin was observed in the MNTB, and hence both CaBPs were also co-localized in terminal fields within the adjacent SOC nuclei. The distribution patterns of CaBPs in both species are discussed with respect to the intrinsic neuronal SOC circuits as part of the auditory brainstem system that underlie the binaural integrative processing of acoustic signals as the basis for localization and discrimination of auditory objects.

  8. The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits.

    PubMed

    Yeo, Seungeun; Hodgkinson, Colin A; Zhou, Zhifeng; Jung, Jeesun; Leung, Ming; Yuan, Qiaoping; Goldman, David

    2016-08-11

    Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL's for complex phenotypes. We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were

  9. Survival, Differentiation, and Neuroprotective Mechanisms of Human Stem Cells Complexed With Neurotrophin-3-Releasing Pharmacologically Active Microcarriers in an Ex Vivo Model of Parkinson’s Disease

    PubMed Central

    Daviaud, Nicolas; Garbayo, Elisa; Sindji, Laurence; Martínez-Serrano, Alberto; Schiller, Paul C.

    2015-01-01

    Stem cell-based regenerative therapies hold great potential for the treatment of degenerative disorders such as Parkinson’s disease (PD). We recently reported the repair and functional recovery after treatment with human marrow-isolated adult multilineage inducible (MIAMI) cells adhered to neurotrophin-3 (NT3) releasing pharmacologically active microcarriers (PAMs) in hemiparkinsonian rats. In order to comprehend this effect, the goal of the present work was to elucidate the survival, differentiation, and neuroprotective mechanisms of MIAMI cells and human neural stem cells (NSCs), both adhering to NT3-releasing PAMs in an ex vivo organotypic model of nigrostriatal degeneration made from brain sagittal slices. It was shown that PAMs led to a marked increase in MIAMI cell survival and neuronal differentiation when releasing NT3. A significant neuroprotective effect of MIAMI cells adhering to PAMs was also demonstrated. NSCs barely had a neuroprotective effect and differentiated mostly into dopaminergic neuronal cells when adhering to PAM-NT3. Moreover, those cells were able to release dopamine in a sufficient amount to induce a return to baseline levels. Reverse transcription-quantitative polymerase chain reaction and enzyme-linked immunosorbent assay analyses identified vascular endothelial growth factor (VEGF) and stanniocalcin-1 as potential mediators of the neuroprotective effect of MIAMI cells and NSCs, respectively. It was also shown that VEGF locally stimulated tissue vascularization, which might improve graft survival, without excluding a direct neuroprotective effect of VEGF on dopaminergic neurons. These results indicate a prospective interest of human NSC/PAM and MIAMI cell/PAM complexes in tissue engineering for PD. Significance Stem cell-based regenerative therapies hold great potential for the treatment of degenerative disorders such as Parkinson’s disease (PD). The present work elucidates and compares the survival, differentiation, and

  10. Differential impact of a complex environment on positive affect in an animal model of individual differences in emotionality.

    PubMed

    Perez-Sepulveda, J A; Flagel, S B; Garcia-Fuster, M J; Slusky, R J; Aldridge, J W; Watson, S; Akil, H

    2013-09-17

    Anhedonia, or the inability to experience positive feelings is a hallmark of depression. However, few animal models have relied on decreased positive affect as an index of susceptibility to depression. Rats emit frequency-modulated ultrasonic vocalizations (USVs), designated as "positive" calls in the 50-kHz range. USVs have been associated with pharmacological activation of motivational reward circuits. Here we utilized selectively-bred rats differing in "emotionality" to ask whether there are associated differences in USVs. Rats bred based on locomotor response to novelty and classified as bred High Responders (bHRs) or bred Low Responders (bLRs) exhibit inborn differences in response to environmental cues, stress responsiveness, and depression-like behavior. These animals also exhibit differences in anxiety-like behavior, which are reversed by exposure to environmental complexity (EC). Finally, these animals exhibit unique profiles of responsiveness to rewarding stimuli accompanied with distinct patterns of dopamine regulation. We investigated whether acute and chronic environmental manipulations impacted USVs in bHRs and bLRs. We found that, relative to bLRs, bHRs emitted significantly more 50-kHz USVs. However, if a bLR is accompanied by another bLR, there is a significant increase in 50-kHZ USVs emitted by this phenotype. bHRs emitted increases in 50-kHZ UVSs upon first exposure to EC, whereas bLRs showed a similar increase only after repeated exposure. bLRs' increase in positive affect after chronic EC was coupled with significant positive correlations between corticosterone levels and c-fos mRNA in the accumbens. Conversely, a decline in the rate of positive calls in bHRs after chronic EC was associated with a negative correlation between corticosterone and accumbens c-fos mRNA. These studies demonstrate that inborn differences in emotionality interact with the environment to influence positive affect and underscore the potential interaction between

  11. Musical rhythm and pitch: a differential effect on auditory dynamics as revealed by the N1/MMN/P3a complex.

    PubMed

    Sebastian Lelo de Larrea-Mancera, E; Rodríguez-Agudelo, Yaneth; Solís-Vivanco, Rodolfo

    2017-04-04

    Music represents a complex form of human cognition. To what extent our auditory system is attuned to music is yet to be clearly understood. Our principal aim was to determine whether the neurophysiological operations underlying pre-attentive auditory change detection (N1enhancement (N1e)/Mismatch Negativity (MMN)) and the subsequent involuntary attentional reallocation (P3a) towards infrequent sound omissions, are influenced by differences in musical content. Specifically, we intended to explore any interaction effects that rhythmic and pitch dimensions of musical organization may have over these processes. Results showed that both the N1e and MMN amplitudes were differentially influenced by rhythm and pitch dimensions. MMN latencies were shorter for musical structures containing both domains. This suggests some neurocognitive independence between pitch and rhythm domains, but also calls for further address on possible interactions between both of them at the level of early, automatic auditory detection. Furthermore, results demonstrate that the N1e reflects basic sensory memory processes. Lastly, we show that the involuntary switch of attention associated with the P3a reflects a general-purpose mechanism not modulated by musical features. Altogether, the N1e/MMN/P3a complex elicited by infrequent sound omissions revealed evidence of musical influence over early stages of auditory perception.

  12. Shared and differentiated motor skill impairments in children with dyslexia and/or attention deficit disorder: From simple to complex sequential coordination

    PubMed Central

    Morin-Moncet, Olivier; Bélanger, Anne-Marie; Beauchamp, Miriam H.; Leonard, Gabriel

    2017-01-01

    Dyslexia and Attention deficit disorder (AD) are prevalent neurodevelopmental conditions in children and adolescents. They have high comorbidity rates and have both been associated with motor difficulties. Little is known, however, about what is shared or differentiated in dyslexia and AD in terms of motor abilities. Even when motor skill problems are identified, few studies have used the same measurement tools, resulting in inconstant findings. The present study assessed increasingly complex gross motor skills in children and adolescents with dyslexia, AD, and with both Dyslexia and AD. Our results suggest normal performance on simple motor-speed tests, whereas all three groups share a common impairment on unimanual and bimanual sequential motor tasks. Children in these groups generally improve with practice to the same level as normal subjects, though they make more errors. In addition, children with AD are the most impaired on complex bimanual out-of-phase movements and with manual dexterity. These latter findings are examined in light of the Multiple Deficit Model. PMID:28542319

  13. Differential involvement of Atg16L1 in Crohn disease and canonical autophagy: analysis of the organization of the Atg16L1 complex in fibroblasts.

    PubMed

    Fujita, Naonobu; Saitoh, Tatsuya; Kageyama, Shun; Akira, Shizuo; Noda, Takeshi; Yoshimori, Tamotsu

    2009-11-20

    A single nucleotide polymorphism in Atg16L1, an autophagy-related gene (ATG), is a risk factor for Crohn disease, a major form of chronic inflammatory bowel disease. However, it is still unknown how the Atg16L1 variant contributes to disease development. The Atg16L1 protein possesses a C-terminal WD repeat domain whose function is entirely unknown, and the Crohn disease-associated mutation (T300A) is within this domain. To elucidate the function of the WD repeat domain, we established an experimental system in which a WD repeat domain mutant of Atg16L1 is stably expressed in Atg16L1-deficient mouse embryonic fibroblasts. Using the system, we show that the Atg16L1 complex forms a dimeric complex and that the total Atg16L1 protein level is strictly maintained, possibly by the ubiquitin proteasome system. Furthermore, we show that an Atg16L1 WD repeat domain deletion and the T300A mutant have little impact on canonical autophagy and autophagy against Salmonella enterica serovar Typhimurium. Therefore, we propose that Atg16L1 T300A is differentially involved in Crohn disease and canonical autophagy.

  14. The VELVET Complex in the Gray Mold Fungus Botrytis cinerea: Impact of BcLAE1 on Differentiation, Secondary Metabolism, and Virulence.

    PubMed

    Schumacher, Julia; Simon, Adeline; Cohrs, Kim C; Traeger, Stefanie; Porquier, Antoine; Dalmais, Bérengère; Viaud, Muriel; Tudzynski, Bettina

    2015-06-01

    Botrytis cinerea, the gray mold fungus, is an important plant pathogen. Field populations are characterized by variability with regard to morphology, the mode of reproduction (conidiation or sclerotia formation), the spectrum of secondary metabolites (SM), and virulence. Natural variation in bcvel1 encoding the ortholog of Aspergillus nidulans VeA, a member of the VELVET complex, was previously shown to affect light-dependent differentiation, the formation of oxalic acid (OA), and virulence. To gain broader insight into the B. cinerea VELVET complex, an ortholog of A. nidulans LaeA, BcLAE1, a putative interaction partner of BcVEL1, was studied. BcVEL1 but not its truncated versions interacts with BcLAE1 and BcVEL2 (VelB ortholog). In accordance with the expected common as well as specific functions of BcVEL1 and BcLAE1, the deletions of both genes result in similar though not identical phenotypes. Both mutants lost the ability to produce OA, to colonize the host tissue, and to form sclerotia. However, mutants differ with regard to aerial hyphae and conidia formation. Genome-wide expression analyses revealed that BcVEL1 and BcLAE1 have common and distinct target genes. Some of the genes that are underexpressed in both mutants, e.g., those encoding SM-related enzymes, proteases, and carbohydrate-active enzymes, may account for their reduced virulence.

  15. Human decidua-derived mesenchymal stem cells differentiate into functional alveolar type II-like cells that synthesize and secrete pulmonary surfactant complexes.

    PubMed

    Cerrada, Alejandro; de la Torre, Paz; Grande, Jesús; Haller, Thomas; Flores, Ana I; Pérez-Gil, Jesús

    2014-01-01

    Lung alveolar type II (ATII) cells are specialized in the synthesis and secretion of pulmonary surfactant, a lipid-protein complex that reduces surface tension to minimize the work of breathing. Surfactant synthesis, assembly and secretion are closely regulated and its impairment is associated with severe respiratory disorders. At present, well-established ATII cell culture models are not available. In this work, Decidua-derived Mesenchymal Stem Cells (DMSCs) have been differentiated into Alveolar Type II- Like Cells (ATII-LCs), which display membranous cytoplasmic organelles resembling lamellar bodies, the organelles involved in surfactant storage and secretion by native ATII cells, and accumulate disaturated phospholipid species, a surfactant hallmark. Expression of characteristic ATII cells markers was demonstrated in ATII-LCs at gene and protein level. Mimicking the response of ATII cells to secretagogues, ATII-LCs were able to exocytose lipid-rich assemblies, which displayed highly surface active capabilities, including faster interfacial adsorption kinetics than standard native surfactant, even in the presence of inhibitory agents. ATII-LCs could constitute a highly useful ex vivo model for the study of surfactant biogenesis and the mechanisms involved in protein processing and lipid trafficking, as well as the packing and storage of surfactant complexes.

  16. Differential domain evolution and complex RNA processing in a family of paralogous EPB41 (protein 4.1) genes facilitates expression of diverse tissue-specific isoforms

    SciTech Connect

    Parra, Marilyn; Gee, Sherry; Chan, Nadine; Ryaboy, Dmitriy; Dubchak, Inna; Narla, Mohandas; Gascard, Philippe D.; Conboy, John G.

    2004-07-15

    The EPB41 (protein 4.1) genes epitomize the resourcefulness of the mammalian genome to encode a complex proteome from a small number of genes. By utilizing alternative transcriptional promoters and tissue-specific alternative pre-mRNA splicing, EPB41, EPB41L2, EPB41L3, and EPB41L1 encode a diverse array of structural adapter proteins. Comparative genomic and transcript analysis of these 140kb-240kb genes indicates several unusual features: differential evolution of highly conserved exons encoding known functional domains, interspersed with unique exons whose size and sequence variations contribute substantially to intergenic diversity: alternative first exons, most of which map far upstream of the coding regions; and complex tissue-specific alternative pre-mRNA splicing that facilitates synthesis of functionally different complements of 4.1 proteins in various cells. Understanding the splicing regulatory networks that control protein 4.1 expression will be critical to a full appreciation of the many roles of 4.1 proteins in normal cell biology and their proposed roles in human cancer.

  17. Shared and differentiated motor skill impairments in children with dyslexia and/or attention deficit disorder: From simple to complex sequential coordination.

    PubMed

    Marchand-Krynski, Marie-Ève; Morin-Moncet, Olivier; Bélanger, Anne-Marie; Beauchamp, Miriam H; Leonard, Gabriel

    2017-01-01

    Dyslexia and Attention deficit disorder (AD) are prevalent neurodevelopmental conditions in children and adolescents. They have high comorbidity rates and have both been associated with motor difficulties. Little is known, however, about what is shared or differentiated in dyslexia and AD in terms of motor abilities. Even when motor skill problems are identified, few studies have used the same measurement tools, resulting in inconstant findings. The present study assessed increasingly complex gross motor skills in children and adolescents with dyslexia, AD, and with both Dyslexia and AD. Our results suggest normal performance on simple motor-speed tests, whereas all three groups share a common impairment on unimanual and bimanual sequential motor tasks. Children in these groups generally improve with practice to the same level as normal subjects, though they make more errors. In addition, children with AD are the most impaired on complex bimanual out-of-phase movements and with manual dexterity. These latter findings are examined in light of the Multiple Deficit Model.

  18. Changes in genome composition of the Friend virus complex in erythroleukemia cells during the course of differentiation induced by dimethyl sulfoxide

    PubMed Central

    Ostertag, W.; Pragnell, I. B.

    1978-01-01

    The Friend spleen focus-forming virus (SFFV) complex released by Friend virus-transformed erythroid cells has been analyzed with respect to changes in the genome composition that may occur during induction of erythropoiesis with dimethyl sulfoxide. It is shown that: (a) There are three types of virus particles, one with buoyant density 1.20 g/ml, one with density 1.17 g/ml (the density of the cloned lymphatic leukemia virus helper component of the complex), and a major fraction that has a density of 1.14 g/ml. (b) Three RNA subunits-35S, 32S, and 30S-have previously been shown to be detectable in the Friend virus complex. The 1.20-g/ml particles contain only 30S RNA, whilst the 1.14- to 1.17-g/ml particles contain a mixture consisting of predominantly 30S and 32S RNA and about 5-10% 35S RNA. (c) Induction of differentiation results in an increase in the 1.14-g/ml particles and 32S RNA. The amount of 30S RNA does not change. (d) Hybridization of the different genomic viral RNAs with full-length virus cDNA shows that the 30S RNA (of induced and uninduced Friend virus) is more closely related to the 32S RNA of the induced Friend virus than to the 32S RNA of the constitutively released Friend virus. (e) The 30S RNA contains SFFV-specific sequences. (f) A hypothesis is presented in which the induction of the new 32S RNA species is related to the increase of SFFV activity and to a specific function of the SFFV during induction of erythropoiesis. Images PMID:277925

  19. Differential inhibition of long interspersed element 1 by APOBEC3 does not correlate with high-molecular-mass-complex formation or P-body association.

    PubMed

    Niewiadomska, Anna Maria; Tian, Chunjuan; Tan, Lindi; Wang, Tao; Sarkis, Phuong Thi Nguyen; Yu, Xiao-Fang

    2007-09-01

    The human cytidine deaminase APOBEC3G (A3G) and other APOBEC3 proteins exhibit differential inhibitory activities against diverse endogenous retroelements and retroviruses, including Vif-deficient human immunodeficiency virus type 1. The potential inhibitory activity of human APOBEC proteins against long interspersed element 1 (LINE-1) has not been fully evaluated. Here, we demonstrate inhibition of LINE-1 by multiple human APOBEC3 cytidine deaminases, including previously unreported activity for A3DE and A3G. More ancient members of APOBEC, cytidine deaminases AID and APOBEC2, had no detectable activity against LINE-1. A3A, which did not form high-molecular-mass (HMM) complexes and interacted poorly with P bodies, was the most potent inhibitor of LINE-1. A3A specifically recognizes LINE-1 RNA but not the other cellular RNAs tested. However, in the presence of LINE-1, A3A became associated with HMM complexes containing LINE-1 RNA. The ability of A3A to recognize LINE-1 RNA required its catalytic domain and was important for its LINE-1 suppression. Although the mechanism of LINE-1 restriction did not seem to involve DNA editing, A3A inhibited the accumulation of nascent LINE-1 DNA, suggesting interference with LINE-1 reverse transcription and/or integration or intracellular movement of LINE-1 ribonucleoprotein. Thus, association with P bodies or cellular HMM complexes could not predict the potency of APOBEC3 anti-LINE-1 activities. The catalytic domain of APOBEC3 proteins may be important for proper folding and target factors such as RNA or protein interaction in addition to cytidine deamination.

  20. Differential induction of Leishmania donovani bi-subunit topoisomerase I-DNA cleavage complex by selected flavones and camptothecin: activity of flavones against camptothecin-resistant topoisomerase I.

    PubMed

    Das, Benu Brata; Sen, Nilkantha; Roy, Amit; Dasgupta, Somdeb Bose; Ganguly, Agneyo; Mohanta, Bikash Chandra; Dinda, Biswanath; Majumder, Hemanta K

    2006-01-01

    Emergence of the bi-subunit topoisomerase I in the kinetoplastid family (Trypanosoma and Leishmania) has brought a new twist in topoisomerase research related to evolution, functional conservation and preferential sensitivities to the specific inhibitors of type IB topoisomerase family. In the present study, we describe that naturally occurring flavones baicalein, luteolin and quercetin are potent inhibitors of the recombinant Leishmania donovani topoisomerase I. These compounds bind to the free enzyme and also intercalate into the DNA at a very high concentration (300 microM) without binding to the minor grove. Here, we show that inhibition of topoisomerase I by these flavones is due to stabilization of topoisomerase I-DNA cleavage complexes, which subsequently inhibit the religation step. Their ability to stabilize the covalent topoisomerase I-DNA complex in vitro and in living cells is similar to that of the known topoisomerase I inhibitor camptothecin (CPT). However, in contrast to CPT, baicalein and luteolin failed to inhibit the religation step when the drugs were added to pre-formed enzyme substrate binary complex. This differential mechanism to induce the stabilization of cleavable complex with topoisomerase I and DNA by these selected flavones and CPT led us to investigate the effect of baicalein and luteolin on CPT-resistant mutant enzyme LdTOP1Delta39LS lacking 1-39 amino acids of the large subunit [B. B. Das, N. Sen, S. B. Dasgupta, A. Ganguly and H. K. Majumder (2005) J. Biol. Chem. 280, 16335-16344]. Baicalein and luteolin stabilize duplex oligonucleotide cleavage with LdTOP1Delta39LS. This observation was further supported by the stabilization of in vivo cleavable complex by baicalein and luteolin with highly CPT-resistant L.donovani strain. Taken together, our data suggest that the interacting amino acid residues of topoisomerase I may be partially overlapping or different for flavones and CPT. This study illuminates new properties of the flavones

  1. Differential induction of Leishmania donovani bi-subunit topoisomerase I–DNA cleavage complex by selected flavones and camptothecin: activity of flavones against camptothecin-resistant topoisomerase I

    PubMed Central

    Das, Benu Brata; Sen, Nilkantha; Roy, Amit; Dasgupta, Somdeb Bose; Ganguly, Agneyo; Mohanta, Bikash Chandra; Dinda, Biswanath; Majumder, Hemanta K.

    2006-01-01

    Emergence of the bi-subunit topoisomerase I in the kinetoplastid family (Trypanosoma and Leishmania) has brought a new twist in topoisomerase research related to evolution, functional conservation and preferential sensitivities to the specific inhibitors of type IB topoisomerase family. In the present study, we describe that naturally occurring flavones baicalein, luteolin and quercetin are potent inhibitors of the recombinant Leishmania donovani topoisomerase I. These compounds bind to the free enzyme and also intercalate into the DNA at a very high concentration (300 µM) without binding to the minor grove. Here, we show that inhibition of topoisomerase I by these flavones is due to stabilization of topoisomerase I–DNA cleavage complexes, which subsequently inhibit the religation step. Their ability to stabilize the covalent topoisomerase I–DNA complex in vitro and in living cells is similar to that of the known topoisomerase I inhibitor camptothecin (CPT). However, in contrast to CPT, baicalein and luteolin failed to inhibit the religation step when the drugs were added to pre-formed enzyme substrate binary complex. This differential mechanism to induce the stabilization of cleavable complex with topoisomerase I and DNA by these selected flavones and CPT led us to investigate the effect of baicalein and luteolin on CPT-resistant mutant enzyme LdTOP1Δ39LS lacking 1–39 amino acids of the large subunit [B. B. Das, N. Sen, S. B. Dasgupta, A. Ganguly and H. K. Majumder (2005) J. Biol. Chem. 280, 16335–16344]. Baicalein and luteolin stabilize duplex oligonucleotide cleavage with LdTOP1Δ39LS. This observation was further supported by the stabilization of in vivo cleavable complex by baicalein and luteolin with highly CPT-resistant L.donovani strain. Taken together, our data suggest that the interacting amino acid residues of topoisomerase I may be partially overlapping or different for flavones and CPT. This study illuminates new properties of the flavones

  2. Recruitment of SWI/SNF Complex Is Required for Transcriptional Activation of the SLC11A1 Gene during Macrophage Differentiation of HL-60 Cells*

    PubMed Central

    Xu, Yong Zhong; Thuraisingam, Thusanth; Marino, Rafael; Radzioch, Danuta

    2011-01-01

    The solute carrier family 11 member 1 (SLC11A1) gene is strictly regulated and exclusively expressed in myeloid lineage cells. However, little is known about the transcriptional regulation of the SLC11A1 gene during myeloid development. In this study, we used HL-60 cells as a model to investigate the regulatory elements/factors involved in the transactivation of the SLC11A1 gene during phorbol 12-myristate 13-acetate (PMA)-induced macrophage differentiation of HL-60 cells. Promoter deletion analysis showed that a 7-base AP-1-like element (TGACTCT) was critical for the responsiveness of the SLC11A1 promoter to PMA. Stimulation by PMA induced the binding of ATF-3 and the recruitment of two components of the SWI/SNF complex, BRG1 and β-actin, to this element in an ATF-3-dependent manner. RNAi-mediated depletion of ATF-3 or BRG1 markedly decreased SLC11A1 gene expression and its promoter activity induced by PMA. Luciferase reporter experiments demonstrated that ATF-3 cooperated with BRG1 and β-actin to activate the SLC11A1 promoter. Furthermore, we showed that PMA can induce the proximal (GT/AC)n repeat sequence to convert to the Z-DNA structure in the SLC11A1 gene promoter, and depletion of BRG1 resulted in a significant decrease of Z-DNA formation. Our results demonstrated that recruitment of the SWI/SNF complex initiated Z-DNA formation and subsequently helped to transactivate the SLC11A1 gene. PMID:21300803

  3. Allelic variation and differential expression of the mSIN3A histone deacetylase complex gene Arid4b promote mammary tumor growth and metastasis.

    PubMed

    Winter, Scott F; Lukes, Luanne; Walker, Renard C; Welch, Danny R; Hunter, Kent W

    2012-05-01

    Accumulating evidence suggests that breast cancer metastatic progression is modified by germline polymorphism, although specific modifier genes have remained largely undefined. In the current study, we employ the MMTV-PyMT transgenic mouse model and the AKXD panel of recombinant inbred mice to identify AT-rich interactive domain 4B (Arid4b; NM_194262) as a breast cancer progression modifier gene. Ectopic expression of Arid4b promoted primary tumor growth in vivo as well as increased migration and invasion in vitro, and the phenotype was associated with polymorphisms identified between the AKR/J and DBA/2J alleles as predicted by our genetic analyses. Stable shRNA-mediated knockdown of Arid4b caused a significant reduction in pulmonary metastases, validating a role for Arid4b as a metastasis modifier gene. ARID4B physically interacts with the breast cancer metastasis suppressor BRMS1, and we detected differential binding of the Arid4b alleles to histone deacetylase complex members mSIN3A and mSDS3, suggesting that the mechanism of Arid4b action likely involves interactions with chromatin modifying complexes. Downregulation of the conserved Tpx2 gene network, which is comprised of many factors regulating cell cycle and mitotic spindle biology, was observed concomitant with loss of metastatic efficiency in Arid4b knockdown cells. Consistent with our genetic analysis and in vivo experiments in our mouse model system, ARID4B expression was also an independent predictor of distant metastasis-free survival in breast cancer patients with ER+ tumors. These studies support a causative role of ARID4B in metastatic progression of breast cancer.

  4. Lu Hf systematics of the ultra-high temperature Napier Metamorphic Complex in Antarctica: Evidence for the early Archean differentiation of Earth's mantle

    NASA Astrophysics Data System (ADS)

    Choi, Sung Hi; Mukasa, Samuel B.; Andronikov, Alexandre V.; Osanai, Yasuhito; Harley, Simon L.; Kelly, Nigel M.

    2006-06-01

    The Napier Complex of the East Antarctic Craton comprises some of the oldest rocks on Earth (˜ 3.8 billion years old), overprinted by an ultra-high temperature (UHT) metamorphic event near the Archean-Proterozoic boundary. Garnet, orthopyroxene, sapphirine, osumilite, rutile and a whole rock representing a fully equilibrated assemblage from this UHT granulite belt have yielded a Lu-Hf isochron age of 2403 ± 43 Ma, the first ever determined on a UHT mineral assemblage. Preservation of the UHT mineral assemblage in the rock analyzed, without any significant retrogression, suggests rapid cooling with closure likely to have occurred for the Lu-Hf system at post-peak UHT conditions near a temperature of ˜ 800 °C. This mineral-whole rock isochron yields an initial 176Hf/ 177Hf ratio corresponding to an ɛHf value of - 14 ± 1, acquired during UHT metamorphism. Such a low value demonstrates that overall UHT granulites evolved in a low Lu/Hf environment, probably formed when the rocks were first extracted from a highly depleted mantle. Zircon ɛHf values we have measured "see through" the UHT metamorphism and show that the source materials for the magmas that formed the Napier Complex were extremely depleted (> + 5.6 ɛHf at 3.85 Ga) relative to the chondritic uniform reservoir (CHUR). These results also suggest significant depletion of the early Archean mantle, in agreement with the early differentiation of the Earth that the latest core formation models require.

  5. Differential Roles of Protein Complexes NOX1-NOXO1 and NOX2-p47phox in Mediating Endothelial Redox Responses to Oscillatory and Unidirectional Laminar Shear Stress*

    PubMed Central

    Siu, Kin Lung; Gao, Ling; Cai, Hua

    2016-01-01

    The endothelium is exposed to various flow patterns such as vasoprotective unidirectional laminar shear stress (LSS) and atherogenic oscillatory shear stress (OSS). A software-controlled, valve-operated OsciFlow device with parallel chambers was used to apply LSS and OSS to endothelial cells. Although LSS inhibited superoxide over time, OSS time-dependently increased superoxide production from endothelial cells. Immunocytochemical staining revealed that, at resting state, p47phox colocalizes with NOX2, whereas NOXO1 colocalizes with NOX1. RNAi of p47phox had no effects on superoxide or NO production in response to OSS but significantly reduced NO production in LSS, implicating a p47phox-bound NADPH oxidase (NOX) in mediating basal NO production. Indeed, RNAi of p47phox inhibited endothelial nitric oxide synthase (eNOS) serine 1179 phosphorylation, whereas PEG-catalase scavenging of intracellular hydrogen peroxide or RNAi of NOX2 produced similar results, indicating a role of NOX2/p47phox-derived hydrogen peroxide in mediating the basal activity of NO production from eNOS. In contrast, RNAi of NOXO1 resulted in no significant changes in NO and superoxide levels in response to LSS but significantly reduced superoxide while increasing NO in response to OSS. Furthermore, we identified, for the first time, that OSS uncouples eNOS, which was corrected by RNAi of NOXO1. In summary, LSS activates the NOX2-p47phox complex to activate eNOS phosphorylation and NO production. OSS instead activates the NOX1-NOXO1 complex to uncouple eNOS. These results demonstrate differential roles of NOXs in modulating the redox state in response to different shear stresses, which may promote the development of novel therapeutic agents to mimic the protective effects of LSS while inhibiting the injurious effects of OSS. PMID:26826128

  6. Complexity and Productivity Differentiation Models of Metallogenic Indicator Elements in Rocks and Supergene Media Around Daijiazhuang Pb-Zn Deposit in Dangchang County, Gansu Province

    SciTech Connect

    He, Jin-zhong Yao, Shu-zhen; Zhang, Zhong-ping; You, Guan-jin

    2013-03-15

    With the help of complexity indices, we quantitatively studied multifractals, frequency distributions, and linear and nonlinear characteristics of geochemical data for exploration of the Daijiazhuang Pb-Zn deposit. Furthermore, we derived productivity differentiation models of elements from thermodynamics and self-organized criticality of metallogenic systems. With respect to frequency distributions and multifractals, only Zn in rocks and most elements except Sb in secondary media, which had been derived mainly from weathering and alluviation, exhibit nonlinear distributions. The relations of productivity to concentrations of metallogenic elements and paragenic elements in rocks and those of elements strongly leached in secondary media can be seen as linear addition of exponential functions with a characteristic weak chaos. The relations of associated elements such as Mo, Sb, and Hg in rocks and other elements in secondary media can be expressed as an exponential function, and the relations of one-phase self-organized geological or metallogenic processes can be represented by a power function, each representing secondary chaos or strong chaos. For secondary media, exploration data of most elements should be processed using nonlinear mathematical methods or should be transformed to linear distributions before processing using linear mathematical methods.

  7. DELLA signaling mediates stress-induced cell differentiation in Arabidopsis leaves through modulation of anaphase-promoting complex/cyclosome activity.

    PubMed

    Claeys, Hannes; Skirycz, Aleksandra; Maleux, Katrien; Inzé, Dirk

    2012-06-01

    Drought is responsible for considerable yield losses in agriculture due to its detrimental effects on growth. Drought responses have been extensively studied, but mostly on the level of complete plants or mature tissues. However, stress responses were shown to be highly tissue and developmental stage specific, and dividing tissues have developed unique mechanisms to respond to stress. Previously, we studied the effects of osmotic stress on dividing leaf cells in Arabidopsis (Arabidopsis thaliana) and found that stress causes early mitotic exit, in which cells end their mitotic division and start endoreduplication earlier. In this study, we analyzed this phenomenon in more detail. Osmotic stress induces changes in gibberellin metabolism, resulting in the stabilization of DELLAs, which are responsible for mitotic exit and earlier onset of endoreduplication. Consequently, this response is absent in mutants with altered gibberellin levels or DELLA activity. Mitotic exit and onset of endoreduplication do not correlate with an up-regulation of known cell cycle inhibitors but are the result of reduced levels of DP-E2F-LIKE1/E2Fe and UV-B-INSENSITIVE4, both inhibitors of the developmental transition from mitosis to endoreduplication by modulating anaphase-promoting complex/cyclosome activity, which are down-regulated rapidly after DELLA stabilization. This work fits into an emerging view of DELLAs as regulators of cell division by regulating the transition to endoreduplication and differentiation.

  8. Lipin1 Regulates Skeletal Muscle Differentiation through Extracellular Signal-regulated Kinase (ERK) Activation and Cyclin D Complex-regulated Cell Cycle Withdrawal*

    PubMed Central

    Jiang, Weihua; Zhu, Jing; Zhuang, Xun; Zhang, Xiping; Luo, Tao; Esser, Karyn A.; Ren, Hongmei

    2015-01-01

    Lipin1, an intracellular protein, plays critical roles in controlling lipid synthesis and energy metabolism through its enzymatic activity and nuclear transcriptional functions. Several mouse models of skeletal muscle wasting are associated with lipin1 mutation or altered expression. Recent human studies have suggested that children with homozygous null mutations in the LPIN1 gene suffer from rhabdomyolysis. However, the underlying pathophysiologic mechanism is still poorly understood. In the present study we examined whether lipin1 contributes to regulating muscle regeneration. We characterized the time course of skeletal muscle regeneration in lipin1-deficient fld mice after injury. We found that fld mice exhibited smaller regenerated muscle fiber cross-sectional areas compared with wild-type mice in response to injury. Our results from a series of in vitro experiments suggest that lipin1 is up-regulated and translocated to the nucleus during myoblast differentiation and plays a key role in myogenesis by regulating the cytosolic activation of ERK1/2 to form a complex and a downstream effector cyclin D3-mediated cell cycle withdrawal. Overall, our study reveals a previously unknown role of lipin1 in skeletal muscle regeneration and expands our understanding of the cellular and molecular mechanisms underlying skeletal muscle regeneration. PMID:26296887

  9. The Protein Phosphatase-1/Inhibitor-2 Complex Differentially Regulates GSK-3 Dephosphorylation and Increases Sarcoplasmic/Endoplasmic Reticulum Calcium ATPase 2 Levels

    PubMed Central

    King, Taj D.; Gandy, Johanna C.; Bijur, Gautam N.

    2007-01-01

    The ubiquitously expressed protein glycogen synthase kinase-3 (GSK3) is constitutively active, however its activity is markedly diminished following phosphorylation of Ser21 of GSK3α and Ser9 of GSK3β. Although several kinases are known to phosphorylate Ser21/9 of GSK3, for example Akt, relatively much less is known about the mechanisms that cause the dephosphorylation of GSK3 at Ser21/9. In the present study KCl-induced plasma membrane depolarization of SH-SY5Y cells, which increases intracellular calcium concentrations caused a transient decrease in the phosphorylation of Akt at Thr308 and Ser473, and GSK3 at Ser21/9. Overexpression of the selective protein phosphatase-1 inhibitor protein, inhibitor-2, increased basal GSK3 phosphorylation at Ser21/9 and significantly blocked the KCl-induced dephosphorylation of GSK3β, but not GSK3α. The phosphorylation of Akt was not affected by the overexpression of inhibitor-2. GSK3 activity is known to affect sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) levels. Overexpression of inhibitor-2 or treatment of cells with the GSK3 inhibitors lithium and SB216763 increased the levels of SERCA2. These results indicate that the protein phosphatase-1/inhibitor-2 complex differentially regulates GSK3 dephosphorylation induced by KCl and that GSK3 activity regulates SERCA2 levels. PMID:16987514

  10. Evaluation of three real-time PCR assays for differential identification of Mycobacterium tuberculosis complex and nontuberculous mycobacteria species in liquid culture media.

    PubMed

    Jung, Yu Jung; Kim, Ji-Youn; Song, Dong Joon; Koh, Won-Jung; Huh, Hee Jae; Ki, Chang-Seok; Lee, Nam Yong

    2016-06-01

    We evaluated the analytical performance of M. tuberculosis complex (MTBC)/nontuberculous mycobacteria (NTM) PCR assays for differential identification of MTBC and NTM using culture-positive liquid media. Eighty-five type strains and 100 consecutive mycobacterial liquid media cultures (MGIT 960 system) were analyzed by a conventional PCR assay (MTB-ID(®) V3) and three real-time PCR assays (AdvanSure™ TB/NTM real-time PCR, AdvanSure; GENEDIA(®) MTB/NTM Detection Kit, Genedia; Real-Q MTB & NTM kit, Real-Q). The accuracy rates for reference strains were 89.4%, 100%, 98.8%, and 98.8% for the MTB-ID V3, AdvanSure, Genedia, and Real-Q assays, respectively. Cross-reactivity in the MTB-ID V3 assay was mainly attributable to non-mycobacterium Corynebacterineae species. The diagnostic performance was determined using clinical isolates grown in liquid media, and the overall sensitivities for all PCR assays were higher than 95%. In conclusion, the three real-time PCR assays showed better performance in discriminating mycobacterium species and non-mycobacterium Corynebacterineae species than the conventional PCR assay.

  11. Potential of the reversed-inject differential flow modulator for comprehensive two-dimensional gas chromatography in the quantitative profiling and fingerprinting of essential oils of different complexity.

    PubMed

    Cordero, Chiara; Rubiolo, Patrizia; Cobelli, Luigi; Stani, Gianluca; Miliazza, Armando; Giardina, Matthew; Firor, Roger; Bicchi, Carlo

    2015-10-23

    In this study, the first capillary flow technology reverse-inject differential flow modulator was implemented with different column configurations (lengths, diameters and stationary phase coupling) and detector combinations (mass spectrometry--MS and flame ionization detection--FID) to evaluate its potential in the quantitative profiling and fingerprinting of medium-to-highly complex essential oils. In particular, a parallel dual-secondary column dual-detection configuration that has shown to improve the information potential also with thermally modulated GC × GC platforms (MS identification reliability and accurate FID quantitation), was tested. Several system performance parameters (separation measure SGC × GC, modulation ratio MR, separation space used and peak symmetry) were evaluated by analyzing a mixture of volatiles of interest in the flavor and fragrance field. The systems demonstrating the best chromatographic performance were selected for quantitative profiling of lavender and mint essential oils and fingerprinting of vetiver essential oil. Experimental results demonstrate that careful tuning of column dimensions and system configurations yields improved: (a) selectivity; (b) operable carrier gas linear velocities at close-to-optimal values; (c) (2)D separation power by extending the modulation period and (d) handling of overloaded peaks without dramatic losses in resolution and quantitative accuracy.

  12. DELLA Signaling Mediates Stress-Induced Cell Differentiation in Arabidopsis Leaves through Modulation of Anaphase-Promoting Complex/Cyclosome Activity1[W][OA

    PubMed Central

    Claeys, Hannes; Skirycz, Aleksandra; Maleux, Katrien; Inzé, Dirk

    2012-01-01

    Drought is responsible for considerable yield losses in agriculture due to its detrimental effects on growth. Drought responses have been extensively studied, but mostly on the level of complete plants or mature tissues. However, stress responses were shown to be highly tissue and developmental stage specific, and dividing tissues have developed unique mechanisms to respond to stress. Previously, we studied the effects of osmotic stress on dividing leaf cells in Arabidopsis (Arabidopsis thaliana) and found that stress causes early mitotic exit, in which cells end their mitotic division and start endoreduplication earlier. In this study, we analyzed this phenomenon in more detail. Osmotic stress induces changes in gibberellin metabolism, resulting in the stabilization of DELLAs, which are responsible for mitotic exit and earlier onset of endoreduplication. Consequently, this response is absent in mutants with altered gibberellin levels or DELLA activity. Mitotic exit and onset of endoreduplication do not correlate with an up-regulation of known cell cycle inhibitors but are the result of reduced levels of DP-E2F-LIKE1/E2Fe and UV-B-INSENSITIVE4, both inhibitors of the developmental transition from mitosis to endoreduplication by modulating anaphase-promoting complex/cyclosome activity, which are down-regulated rapidly after DELLA stabilization. This work fits into an emerging view of DELLAs as regulators of cell division by regulating the transition to endoreduplication and differentiation. PMID:22535421

  13. The protein phosphatase-1/inhibitor-2 complex differentially regulates GSK3 dephosphorylation and increases sarcoplasmic/endoplasmic reticulum calcium ATPase 2 levels

    SciTech Connect

    King, Taj D.; Gandy, Johanna C.; Bijur, Gautam N. . E-mail: gautam@uab.edu

    2006-11-01

    The ubiquitously expressed protein glycogen synthase kinase-3 (GSK3) is constitutively active, however its activity is markedly diminished following phosphorylation of Ser21 of GSK3{alpha} and Ser9 of GSK3{beta}. Although several kinases are known to phosphorylate Ser21/9 of GSK3, for example Akt, relatively much less is known about the mechanisms that cause the dephosphorylation of GSK3 at Ser21/9. In the present study KCl-induced plasma membrane depolarization of SH-SY5Y cells, which increases intracellular calcium concentrations caused a transient decrease in the phosphorylation of Akt at Thr308 and Ser473, and GSK3 at Ser21/9. Overexpression of the selective protein phosphatase-1 inhibitor protein, inhibitor-2, increased basal GSK3 phosphorylation at Ser21/9 and significantly blocked the KCl-induced dephosphorylation of GSK3{beta}, but not GSK3{alpha}. The phosphorylation of Akt was not affected by the overexpression of inhibitor-2. GSK3 activity is known to affect sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) levels. Overexpression of inhibitor-2 or treatment of cells with the GSK3 inhibitors lithium and SB216763 increased the levels of SERCA2. These results indicate that the protein phosphatase-1/inhibitor-2 complex differentially regulates GSK3 dephosphorylation induced by KCl and that GSK3 activity regulates SERCA2 levels.

  14. Speciation analysis of aluminium(III) in natural waters and biological fluids by complexing with various catechols followed by differential pulse voltammetry detection.

    PubMed

    Liu, Jian; Bi, Shuping; Yang, Li; Gu, Xiaodong; Ma, Pengju; Gan, Ning; Wang, Xianlong; Long, Xiufeng; Zhang, Fuping

    2002-12-01

    The biological effects of aluminium have received much attention in recent years. Speciation of Al is of basic relevance as it concerns its reactivity and bioavailability. A differential pulse voltammetry (DPV) procedure is proposed for speciation analysis of Al(III) in natural waters and biological fluids using six catechols (L-dopa, dopamine, epinephrine, norepinephrine, caffeic acid and o-benzenediol) as electroactive ligands. The decrease of the DPV anodic peak current for each catechol ligand is linear with the increase of Al concentration. This speciation analysis idea is based on the measurement of the complexation capacity, namely, different affinities of Al(III) for catechols and organic ligands under two pH conditions. The labile monomeric Al fraction (mainly inorganic aluminium) is determined at pH 4.6, while the total monomeric Al fraction is determined at pH 8.5. The principle for Al(III) speciation analysis by an electrochemical method is discussed. This sensitive and simple fractionation method is successfully applied to the speciation analysis of Al in natural waters and the results agree well with those of Driscoll's method. The speciation analysis of Al in biological fluids is also explored and the results are compared with those obtained by ultrafiltration and dialysis. Compared with other speciation protocols the electrochemical method possesses some remarkable advantages: rapidity, high sensitivity, cheap instrumentation and a simple operation procedure.

  15. The differential effects of a complex protein drink versus isocaloric carbohydrate drink on performance indices following high-intensity resistance training: a two arm crossover design

    PubMed Central

    2013-01-01

    Background Post-workout nutrient timing and macronutrient selection are essential for recovery, glycogen replenishment and muscle protein synthesis (MPS). Performance repeatability, particularly after strenuous activity, can be influenced by substrate availability, recovery markers and perceived rate of exertion. This study compared the differential effects of a complex protein ready-to-drink beverage (VPX) and isocaloric carbohydrate beverage (iCHO) on performance—agility T-test, push-up test, 40-yard sprint, and rate of perceived exertion (RPE), following high-intensity resistance training (HIRT). Methods In a randomized, double blind two-arm crossover controlled trial, 15 subjects performed a 15–18 minute (2:1 work to rest) HIRT and then immediately drank one of the two treatments. After a 2-hour fast, subjects returned to execute the field tests and report RPE. The protocol was repeated one week later with the other treatment. Results There were no significant main effect differences in the agility T-test (p = 0.83), push-up (p = 0.21) sprint (p = 0.12), average agility RPE (p = 0.83), average push-up RPE (p = 0.81) or average sprint RPE (p = 0.66) between the two trials and the two treatments. The multivariate analysis yielded a cumulative significant interaction effect amongst the three performance variables after consuming VPX (p < 0.01). These results suggest a complex protein beverage is a better post-workout choice compared to an isocaloric carbohydrate beverage for repeated performance for activities that require multiple energy demands and athletic skills; however, this outcome was not observed for each single performance event or RPE. Conclusion When considering the collective physical effects of the agility T-test, push-up and sprint tests, a complex protein beverage may provide a recovery advantage as it relates to repeated-bout performance compared to an iCHO-only beverage. Additional research examining the chronic effects of post

  16. The differentiation of units in the Nevado-Filábride complex (Betic Cordillera, Spain). A revision based on a geochronological study of detrital zircons

    NASA Astrophysics Data System (ADS)

    Santamaría-López, Ángel; Ruiz-Cruz, María Dolores; Sanz de Galdeano, Carlos

    2017-04-01

    of common age populations at 300, 450, 600, 1000 and 2000 Ma in all the studied samples. This similarity of the age populations between samples points to a common source area. According to the results of this work, the similarities existing between U/Pb ages of zircons do not support the tectonic differentiation of the Nevado-Filábride complex. Conversely, it is remarkable the enormous thickness of the petrological succession (more than 5000 m) between the lower and upper samples. This huge volume of sediments should have been deposited in a relatively short period of time, during the Permian to Carboniferous, according to the younger ages of the lower and upper samples.

  17. Comparison of differential pulse and alternating current polarography in the soft-modelling study of the complexation of Cd(II) by the fragment Cys-Gly and by the phytochelatin (gamma-Glu-Cys)2Gly.

    PubMed

    Garrigosa, Anna Maria; Ariño, Cristina; Díaz-Cruz, José Manuel; Esteban, Miquel

    2008-07-01

    A comparison of a differential pulse polarographic with a phase sensitive alternating current polarographic study of the Cd-Cys-Gly and Cd-PC(2) systems [PC(2) being a phytochelatin of general structure (gamma-Glu-Cys)(n)-Gly, with n = 2] has been performed. The chemometric multivariate curve resolution method with alternating least squares was applied in the experimental data analysis. The results obtained by both polarographic techniques have made it possible to find out the formation sequences of the complexes and their final stoichiometries. The alternating current polarograms compared with the differential pulse ones show some differences (a new signal and an important shift of peak potentials), which anyway are consistent with some of the conclusions obtained by differential pulse polarography. This fact implies that although the alternating current polarography results need some corrections before data treatment, they provide extra information that complements the conclusions achieved by differential pulse polarography.

  18. 5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells.

    PubMed

    Poterlowicz, Krzysztof; Yarker, Joanne L; Malashchuk, Igor; Lajoie, Brian R; Mardaryev, Andrei N; Gdula, Michal R; Sharov, Andrey A; Kohwi-Shigematsu, Terumi; Botchkarev, Vladimir A; Fessing, Michael Y

    2017-09-01

    Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and

  19. A Quadruplex Real-Time PCR Assay for the Rapid Detection and Differentiation of the Most Relevant Members of the B. pseudomallei Complex: B. mallei, B. pseudomallei, and B. thailandensis

    PubMed Central

    Lowe, Chinn-Woan; Thiriot, Joseph D.; Heder, Michael J.; March, Jordon K.; Drake, David S.; Lew, Cynthia S.; Bunnell, Annette J.; Moore, Emily S.; O'Neill, Kim L.; Robison, Richard A.

    2016-01-01

    The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively. Although B. thailandensis and B. oklahomensis are generally avirulent, both display similar phenotypic characteristics to that of B. pseudomallei. B. humptydooensis and the Burkholderia clades are genetically similar to the B. pseudomallei complex, and are not associated with disease. Optimal identification of these species remains problematic, and PCR-based methods can resolve issues with B. pseudomallei complex detection and differentiation. Currently, no PCR assay is available that detects the major species of the B. pseudomallei complex. A real-time PCR assay in a multiplex single-tube format was developed to simultaneously detect and differentiate B. mallei, B. pseudomallei, and B. thailandensis, and a common sequence found in B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis. A total of 309 Burkholderia isolates and 5 other bacterial species were evaluated. The assay was 100% sensitive and specific, demonstrated sensitivity beyond culture and GC methods for the isolates tested, and is completed in about an hour with a detection limit between 2.6pg and 48.9pg of gDNA. Bioinformatic analyses also showed the assay is likely 100% specific and sensitive for all 84 fully sequenced B. pseudomallei, B. mallei, B. thailandensis, and B. oklahomensis strains currently available in GenBank. For these reasons, this assay could be a rapid and sensitive tool in the detection and differentiation for those species of the B

  20. Selective control of Pax7 expression by TNF-activated p38α/polycomb repressive complex 2 (PRC2) signaling during muscle satellite cell differentiation.

    PubMed

    Mozzetta, Chiara; Consalvi, Silvia; Saccone, Valentina; Forcales, Sonia V; Puri, Pier Lorenzo; Palacios, Daniela

    2011-01-15

    Muscle regeneration relies on adult muscle stem (satellite) cells. Inflammatory cues released within the regenerative microenvironment, such as TNFα, instruct different components of the satellite cell niche toward specialized tasks by regulating specific subsets of genes in each individual cell type. However, how regeneration cues are deciphered and interpreted by the multitude of cell types within the regenerative environment is unknown. We have recently identified an inflammation-activated signaling, consisting of p38α-mediated recruitment of polycomb repressive complex 2 (PRC2) to the Pax7 promoter, in satellite cells. Here we show that p38α-PRC2 regulation of Pax7 expression is restricted to a discrete stage of satellite cell-mediated regeneration. In activated satellite cells, Pax7 locus shows a "bivalent" chromatin signature, with co-existence of H3-K27(3me) and H3-K4(3me), that appears to confer responsiveness to p38α-PRC2 signaling. p38α activation resolves bivalence to H3-K27(3me) which results in Pax7 repression, while p38α blockade promotes Pax7 expression by preventing PRC2-mediated H3-K27(3me) and leading to relative increase in H3-K4(3me). Interestingly, in satellite cell-derived myotubes Pax7 expression cannot be re-induced by p38α blockade, revealing a post-mitotic resistance of Pax7 gene to inflammatory cues. Likewise, in other cell types, such as muscle-derived fibroblasts, Pax7 locus is constitutively repressed by PRC2 and is unresponsive to p38α signaling. Finally, we show that Pax7 repression in embryonic stem cells is not directed by p38α signaling, although it is mediated by PRC2. This evidence indicates a cell type- and differentiation-stage specific control of Pax7 transcription by the p38α-PRC2.

  1. Murine peptidoglycan recognition proteins PglyrpIalpha and PglyrpIbeta are encoded in the epidermal differentiation complex and are expressed in epidermal and hematopoietic tissues.

    PubMed

    Mathur, Punam; Murray, Beth; Crowell, Thomas; Gardner, Humphrey; Allaire, Normand; Hsu, Yen-Ming; Thill, Greg; Carulli, John P

    2004-06-01

    Peptidoglycan recognition proteins (PGRPs or PGLYRPs) are pattern recognition molecules that are found in insects and mammals and are critical for innate immune responses. PGRPs bind peptidoglycan, a ubiquitous component of bacterial cell walls, and are involved in killing bacteria, degrading peptidoglycan, and initiating host defense reactions. Relatively little is known about the four mammalian PGRPs. In this article, we report the sequences of mouse PglyrpIalpha and PglyrpIbeta and provide details of their expression in wild-type mouse tissues. PglyrpIalpha and PglyrpIbeta are encoded within the epidermal differentiation complex on mouse chromosome 3F. Both genes are expressed in epidermal and hematopoietic tissues. PglyrpIbeta is expressed in each of 16 tissues tested, while PglyrpIalpha expression is limited to fewer tissues, including the lung and spleen as well as several tissues of the digestive system. Both proteins are expressed in epithelial cells throughout the gut, and immunohistochemical staining shows expression in salivary glands, the squamous epithelium of the stomach, and the villi of the jejunum. Immunohistochemical staining further shows expression of both PglyrpIalpha and PglyrpIbeta in macrophages in the spleen. PglyrpIalpha is not expressed in resting RAW264.7 macrophage-like cells, but is induced by stimulation with lipopolysaccharide. PglyrpIbeta is constitutively expressed in RAW264.7 cells and is unaffected by lipopolysaccharide or peptidoglycan stimulation. Computational and experimental data suggest that these proteins are secreted. This work provides a step toward understanding the roles of PglyrpIalpha and PglyrpIbeta in host defense and chronic inflammatory conditions induced by bacteria or their components.

  2. Sex differences in prenatally programmed anxiety behaviour in rats: differential corticotropin-releasing hormone receptor mRNA expression in the amygdaloid complex.

    PubMed

    Brunton, Paula J; Donadio, Márcio V F; Russell, John A

    2011-11-01

    We recently reported that male, but not female, offspring born to mothers exposed to social stress during late gestation show heightened anxiety-type behaviour in adulthood. The amygdala organises anxious behaviour, which involves actions of corticotropin-releasing hormone (CRH). CRH gene expression and/or its release are increased in the amygdala in prenatally stressed (PNS) rats. CRH type 1 receptor (CRH-R1) mediates actions of CRH and urocortin I to promote anxiety-like behaviour, whereas the CRH type 2 receptor (CRH-R2) may mediate anxiolytic actions, through actions of urocortins 2 and 3. Here, using quantitative in situ hybridisation, we investigated whether altered CRH receptor mRNA expression in the amygdaloid nuclei may explain the sex differences in anxiety behaviour in adult male and female PNS rats. CRH-R1 mRNA expression was significantly greater in the central amygdala and basolateral amygdala (BLA) in male PNS rats compared with controls, with no change in the basomedial amygdala (BMA) or medial amygdala (MeA). In PNS females, CRH-R1 mRNA expression was greater than controls only in the MeA. Conversely, CRH-R2 mRNA expression was significantly lower in the BMA of male PNS rats compared with controls, but greater in female PNS rats, with no change in the BLA or MeA in either sex. The ratio of CRH-R1:CRH-R2 mRNA in the amygdaloid nuclei was generally increased in PNS males, but not in the PNS females. In conclusion, sex differences in anxiety-type behaviour in PNS rats may be explained by differential mRNA expression for CRH-R1 (pro-anxiogenic) and CRH-R2 (pro-anxiolytic) in the amygdaloid complex.

  3. Differential regulation of acid sphingomyelinase in macrophages stimulated with oxidized low-density lipoprotein (LDL) and oxidized LDL immune complexes: role in phagocytosis and cytokine release.

    PubMed

    Truman, Jean-Philip; Al Gadban, Mohammed M; Smith, Kent J; Jenkins, Russell W; Mayroo, Nalini; Virella, Gabriel; Lopes-Virella, Maria F; Bielawska, Alicja; Hannun, Yusuf A; Hammad, Samar M

    2012-05-01

    Oxidized low-density lipoprotein (oxLDL) and oxLDL-containing immune complexes (oxLDL-IC) contribute to the formation of lipid-laden macrophages (foam cells). Fcγ receptors mediate uptake of oxLDL-IC, whereas scavenger receptors internalize oxLDL. We have previously reported that oxLDL-IC, but not free oxLDL, activate macrophages and prolong their survival. Sphingomyelin is a major constituent of cell membranes and lipoprotein particles and acid sphingomyelinase (ASMase) hydrolyses sphingomyelin to generate the bioactive lipid ceramide. ASMase exists in two forms: lysosomal (L-ASMase) and secretory (S-ASMase). In this study we examined whether oxLDL and oxLDL-IC regulate ASMase differently, and whether ASMase mediates monocyte/macrophage activation and cytokine release. The oxLDL-IC, but not oxLDL, induced early and consistent release of catalytically active S-ASMase. The oxLDL-IC also consistently stimulated L-ASMase activity, whereas oxLDL induced a rapid transient increase in L-ASMase activity before it steadily declined below baseline. Prolonged exposure to oxLDL increased L-ASMase activity; however, activity remained significantly lower than that induced by oxLDL-IC. Further studies were aimed at defining the function of the activated ASMase. In response to oxLDL-IC, heat-shock protein 70B' (HSP70B') was up-regulated and localized with redistributed ASMase in the endosomal compartment outside the lysosome. Treatment with oxLDL-IC induced the formation and release of HSP70-containing and IL-1β-containing exosomes via an ASMase-dependent mechanism. Taken together, the results suggest that oxLDL and oxLDL-IC differentially regulate ASMase activity, and the pro-inflammatory responses to oxLDL-IC are mediated by prolonged activation of ASMase. These findings may contribute to increased understanding of mechanisms mediating macrophage involvement in atherosclerosis.

  4. [MicroRNA differential expression profile in tuberous sclerosis complex cell line TSC2(-/-) MEFs and normal cell line TSC2(+/+) MEFs].

    PubMed

    Cai, Y; Guo, H; Li, H Z; Wang, W D; Zhang, Y S

    2017-08-18

    Tuberous sclerosis complex (TSC) is a multisystem genetic disorder caused by mutations in the TSC1 and TSC2 genes, but the molecular events contributing to TSC are not well understood. However, little is known about the role of microRNAs in TSC. To explore the microRNA differential expression profile between tuberous sclerosis complex cell line TSC2(-/-) MEFs and normal type cell line TSC2(+/+) MEFs, and to provide new clues to study the mechanism of microRNA function in tuberous sclerosis complex. TSC2(-/-) MEFs and TSC2(+/+) MEFs cell lines were cultured in vitro, each with three samples chosen as the experimental group and the control group respectively. Total RNA was isolated using TRizol and purified with RNeasy mini kit according to manufacturer's instructions. RNA quality and quantity were measured by using nanodrop spectrophotometer and RNA integrity was determined by gel electrophoresis. Total RNAs were extracted by TRizol, followed by RNA quantification and quality control. MicroRNA profiles were analyzed by microarray and the threshold value used to screen up-regulated more than 2-fold change or down-regulated less than 0.5-fold change compared with controls. Real-time PCR was used to validate the reliability of microarray. Cell counting kit-8 (CCK-8) assay was performed to evaluate the proliferation. Fourteen microRNAs, including miR-18a-5p, miR-376c-3p, miR-136-5p, miR-467c-5p, miR-467b-5p, miR-5104, miR-3098-3p, miR-30a-3p, miR-302b-3p, miR-18a-3p, miR-19b-1-5p, miR-19a-5p, miR-20a-5p, miR-155-5p, were up-regulated, while twenty-six microRNAs, including miR-200b-3p, miR-450a-1-3p, miR-542-5p, miR-199b-5p, miR-10a-5p, miR-466c-5p, miR-450a-5p, miR-450b-5p, miR-542-3p, miR-351-5p, miR-322-3p, miR-199a-3p, miR-335-5p, miR-10b-5p, miR-351-3p, miR-155-3p, miR-497a-5p, miR-503-5p, miR-148a-3p, miR-1843a-5p, miR-199a-5p, miR-490-5p, miR-450a-2-3p, miR-322-5p, miR-214-3p, miR-450b-3p, were down-regulated in tuberous sclerosis complex cell line TSC2(-/-) MEFs

  5. THOC5, a member of the mRNA export complex: a novel link between mRNA export machinery and signal transduction pathways in cell proliferation and differentiation.

    PubMed

    Tran, Doan D H; Koch, Alexandra; Tamura, Teruko

    2014-01-10

    Cell growth, differentiation, and commitment to a restricted lineage are guided by a timely expressed set of growth factor/cytokine receptors and their down-stream transcription factor genes. Transcriptional control mechanisms of gene expression during differentiation have been mainly studied by focusing on the cis- and trans-elements in promoters however, the role of mRNA export machinery during differentiation has not been adequately examined. THO (Suppressors of the transcriptional defects of hpr1 delta by overexpression) complex 5 (THOC5) is a member of THO complex which is a subcomplex of the transcription/export complex (TREX). THOC5 is evolutionarily conserved in higher eukaryotes, however the exact roles of THOC5 in transcription and mRNA export are still unclear. In this review, we focus on recently uncovered aspects of the role of THOC5 in signal transduction induced by extracellular stimuli. THOC5 is phosphorylated by several protein kinases at multiple residues upon extracellular stimuli. These include stimulation with growth factors/cytokines/chemokines, or DNA damage reagents. Furthermore, THOC5 is a substrate for several oncogenic tyrosine kinases, suggesting that THOC5 may be involved in cancer development. Recent THOC5 knockout mouse data reveal that THOC5 is an essential element in the maintenance of stem cells and growth factor/cytokine-mediated differentiation/proliferation. Furthermore, depletion of THOC5 influences less than 1% of total mRNA export in the steady state, however it influences more than 90% of growth factor/cytokine induced genes. THOC5, thereby contributes to the 3' processing and/or export of immediate-early genes induced by extracellular stimuli. These studies bring new insight into the link between the mRNA export complex and immediate-early gene response. The data from these studies also suggest that THOC5 may be a useful tool for studying stem cell biology, for modifying the differentiation processes and for cancer therapy.

  6. Differential recruitment of coregulators to the RORA promoter adds another layer of complexity to gene (dys) regulation by sex hormones in autism.

    PubMed

    Sarachana, Tewarit; Hu, Valerie W

    2013-10-11

    Our independent cohort studies have consistently shown the reduction of the nuclear receptor RORA (retinoic acid-related orphan receptor-alpha) in lymphoblasts as well as in brain tissues from individuals with autism spectrum disorder (ASD). Moreover, we have found that RORA regulates the gene for aromatase, which converts androgen to estrogen, and that male and female hormones regulate RORA in opposite directions, with androgen suppressing RORA, suggesting that the sexually dimorphic regulation of RORA may contribute to the male bias in ASD. However, the molecular mechanisms through which androgen and estrogen differentially regulate RORA are still unknown. Here we use functional knockdown of hormone receptors and coregulators with small interfering RNA (siRNA) to investigate their involvement in sex hormone regulation of RORA in human neuronal cells. Luciferase assays using a vector containing various RORA promoter constructs were first performed to identify the promoter regions required for inverse regulation of RORA by male and female hormones. Sequential chromatin immunoprecipitation methods followed by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analyses of RORA expression in hormone-treated SH-SY5Y cells were then utilized to identify coregulators that associate with hormone receptors on the RORA promoter. siRNA-mediated knockdown of interacting coregulators was performed followed by qRT-PCR analyses to confirm the functional requirement of each coregulator in hormone-regulated RORA expression. Our studies demonstrate the direct involvement of androgen receptor (AR) and estrogen receptor (ER) in the regulation of RORA by male and female hormones, respectively, and that the promoter region between -10055 bp and -2344 bp from the transcription start site of RORA is required for the inverse hormonal regulation. We further show that AR interacts with SUMO1, a reported suppressor of AR transcriptional activity, whereas ERα interacts

  7. Differential recruitment of coregulators to the RORA promoter adds another layer of complexity to gene (dys) regulation by sex hormones in autism

    PubMed Central

    2013-01-01

    Background Our independent cohort studies have consistently shown the reduction of the nuclear receptor RORA (retinoic acid-related orphan receptor-alpha) in lymphoblasts as well as in brain tissues from individuals with autism spectrum disorder (ASD). Moreover, we have found that RORA regulates the gene for aromatase, which converts androgen to estrogen, and that male and female hormones regulate RORA in opposite directions, with androgen suppressing RORA, suggesting that the sexually dimorphic regulation of RORA may contribute to the male bias in ASD. However, the molecular mechanisms through which androgen and estrogen differentially regulate RORA are still unknown. Methods Here we use functional knockdown of hormone receptors and coregulators with small interfering RNA (siRNA) to investigate their involvement in sex hormone regulation of RORA in human neuronal cells. Luciferase assays using a vector containing various RORA promoter constructs were first performed to identify the promoter regions required for inverse regulation of RORA by male and female hormones. Sequential chromatin immunoprecipitation methods followed by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analyses of RORA expression in hormone-treated SH-SY5Y cells were then utilized to identify coregulators that associate with hormone receptors on the RORA promoter. siRNA-mediated knockdown of interacting coregulators was performed followed by qRT-PCR analyses to confirm the functional requirement of each coregulator in hormone-regulated RORA expression. Results Our studies demonstrate the direct involvement of androgen receptor (AR) and estrogen receptor (ER) in the regulation of RORA by male and female hormones, respectively, and that the promoter region between −10055 bp and −2344 bp from the transcription start site of RORA is required for the inverse hormonal regulation. We further show that AR interacts with SUMO1, a reported suppressor of AR transcriptional

  8. Stoichiometry of the heparin-Cu2+-glycine mixed-ligand complex according to differential thermal analysis and IR spectroscopy data

    NASA Astrophysics Data System (ADS)

    Feofanova, M. A.; Frantseva, Yu. V.; Zhuravlev, E. V.; Baranova, N. V.; Ryasenskii, S. S.

    2015-02-01

    A method or the synthesis, isolation, and purification of a mixed-ligand complex of heparin with copper and glycine cations was suggested. The complex was studied by elemental, thermal, and spectral analyses. The elemental and crystalline hydrate compositions of the complex were determined and the molecular formula was suggested to be Na3CuHepGly · 2H2O.

  9. Bcl-xL Is Essential for the Survival and Function of Differentiated Neurons in the Cortex That Control Complex Behaviors

    PubMed Central

    Nakamura, Ayumi; Swahari, Vijay; Plestant, Charlotte; Smith, Ikuko; McCoy, Eric; Smith, Spencer; Moy, Sheryl S.; Anton, E. S.

    2016-01-01

    conditionally deleted Bcl-xL in the brain and found that this did not result in widespread apoptosis in the proliferating progenitors. Instead, Bcl-xL deficiency induced apoptosis in a select population of differentiated neurons predominantly in the early postnatal stages. Importantly, these Bcl-xL-dependent neurons are not essential for survival of the organism but instead regulate complex behaviors. Our results show that the selective loss of these Bcl-xL-dependent neurons results in mice exhibiting severe neurobehavioral abnormalities, including self-injurious and risk-taking behaviors, hyperactivity, and learning and memory defects. PMID:27194326

  10. Bcl-xL Is Essential for the Survival and Function of Differentiated Neurons in the Cortex That Control Complex Behaviors.

    PubMed

    Nakamura, Ayumi; Swahari, Vijay; Plestant, Charlotte; Smith, Ikuko; McCoy, Eric; Smith, Spencer; Moy, Sheryl S; Anton, E S; Deshmukh, Mohanish

    2016-05-18

    -xL in the brain and found that this did not result in widespread apoptosis in the proliferating progenitors. Instead, Bcl-xL deficiency induced apoptosis in a select population of differentiated neurons predominantly in the early postnatal stages. Importantly, these Bcl-xL-dependent neurons are not essential for survival of the organism but instead regulate complex behaviors. Our results show that the selective loss of these Bcl-xL-dependent neurons results in mice exhibiting severe neurobehavioral abnormalities, including self-injurious and risk-taking behaviors, hyperactivity, and learning and memory defects. Copyright © 2016 the authors 0270-6474/16/365449-14$15.00/0.

  11. Characteristics of TCR/CD3 complex CD3{varepsilon} chains of regulatory CD4+ T (Treg) lymphocytes: role in Treg differentiation in vitro and impact on Treg in vivo.

    PubMed

    Rojo, Jose M; Ojeda, Gloria; Acosta, Yenny Y; Montes-Casado, Maria; Criado, Gabriel; Portolés, Pilar

    2014-03-01

    Tregs are anergic CD4(+)CD25(+)Foxp3(+) T lymphocytes exerting active suppression to control immune and autoimmune responses. However, the factors in TCR recognition underlying Treg differentiation are unclear. Based on our previous data, we hypothesized that Treg TCR/CD3 antigen receptor complexes might differ from those of CD4(+)CD25(-) Tconv. Expression levels of TCR/CD3, CD3ε,ζ chains, or other molecules involved in antigen signaling and the characteristics of CD3ε chains were analyzed in thymus or spleen Treg cells from normal mice. Tregs had quantitative and qualitatively distinct TCR/CD3 complexes and CD3ε chains. They expressed significantly lower levels of the TCR/CD3 antigen receptor, CD3ε chains, TCR-ζ chain, or the CD4 coreceptor than Tconv. Levels of kinases, adaptor molecules involved in TCR signaling, and early downstream activation pathways were also lower in Tregs than in Tconv. Furthermore, TCR/CD3 complexes in Tregs were enriched in CD3ε chains conserving their N-terminal, negatively charged amino acid residues; this trait is linked to a higher activation threshold. Transfection of mutant CD3ε chains lacking these residues inhibited the differentiation of mature CD4(+)Foxp3(-) T lymphocytes into CD4(+)Foxp3(+) Tregs, and differences in CD3ε chain recognition by antibodies could be used to enrich for Tregs in vivo. Our results show quantitative and qualitative differences in the TCR/CD3 complex, supporting the hyporesponsive phenotype of Tregs concerning TCR/CD3 signals. These differences might reconcile avidity and flexible threshold models of Treg differentiation and be used to implement therapeutic approaches involving Treg manipulation.

  12. Geochemistry of anorthositic differentiated sills in the Archean (~ 2970 Ma) Fiskenæsset Complex, SW Greenland: Implications for parental magma compositions, geodynamic setting, and secular heat flow in arcs

    NASA Astrophysics Data System (ADS)

    Polat, Ali; Fryer, Brian J.; Appel, Peter W. U.; Kalvig, Per; Kerrich, Robert; Dilek, Yildirim; Yang, Zhaoping

    2011-04-01

    The Fiskenæsset Complex, SW Greenland, is one of the best preserved layered Archean intrusions in the world, consisting of an association of ca. 550-meter-thick anorthosite, leucogabbro, gabbro, and ultramafic rocks (dunite, peridotite, pyroxenite, and hornblendite). Despite poly-phase deformation and amphibolite to granulite facies metamorphism, primary cumulate textures and igneous layering are well-preserved in the complex. This study reports new major and trace element data for three variably thick (1 to 5 m) differentiated (dunite, through peridotite, pyroxenite, gabbro leucogabbro, to anorthosite) sequences (Sequences 1, 2 and 3) in the Sinarssuk area of the Fiskenæsset region. On several variation diagrams, samples from these sequences plot along a well-defined liquid line of descent, consistent with in situ fractional crystallization. The average chemical compositions of these sequences are used to constrain their approximate parental magma compositions. Petrographic observations and geochemical data suggest that Sequences 2 and 3 solidified from evolved magmas that underwent olivine fractionation prior to their intrusion. In contrast, Sequence 1 appears to have been derived from a near-primary parental magma (SiO 2 = 43 wt.%, MgO = 20 wt.%, Al 2O 3 = 16 wt.%, CaO = 9.3 wt.%, Ni = 840 ppm, Mg-number = 80). The trace element patterns of this parental magma are comparable to those of Phanerozoic boninites, consistent with a supra-subduction zone geodynamic setting. If the relative thickness of ultramafic layers, the sum of dunite, peridotite and pyroxenite layers, in differentiated sequences is taken as an analog for the original complex emplaced into Archean oceanic crust, the Fiskenæsset Complex might have had a minimum thickness of 1000 m, with a 500 m thick ultramafic unit at the bottom. The thickness of the ultramafic unit in the preserved complex is less than 50 m, suggesting that more than 90% of the original ultramafic unit was either delaminated

  13. A mass spectrometry-based method for differentiation of positional isomers of monosubstituted pyrazine N-oxides using metal ion complexes.

    PubMed

    Butler, Matías; Cabrera, Gabriela M

    2015-01-01

    A series of 11 pairs of substituted pyrazine N-oxides, differing in the substituent position, were examined using electrospray ionization mass spectrometry (ESI-MS) in order to use spectra to assess the differentiation of positional isomers. For each compound, mass spectra were recorded with three different metal cations, namely calcium (II), copper (II) and aluminum (III), with characterization of the observed peaks. Differentiation between regioisomeric N-oxides has been achieved by comparison of the identity and relative intensities of the peaks originating from the adduct ions formed with the metal ions. Principal component analysis (PCA) has been employed to assist in the interpretation of the results obtained with each metal ion, exploring possible trends according to the nature and position of the substituent in the pyrazine N-oxide. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Upregulation of TCF4 expression as a transcriptional target of beta-catenin/p300 complexes during trans-differentiation of endometrial carcinoma cells.

    PubMed

    Saegusa, Makoto; Hashimura, Miki; Kuwata, Takeshi; Hamano, Mieko; Okayasu, Isao

    2005-06-01

    Nuclear stabilization of beta-catenin and its interaction with TCF/LEF factors are key events in transduction of the Wnt/beta-catenin signal pathway. Our previous study indicated that nuclear beta-catenin accumulation provides an initial signal for trans-differentiation toward the squamoid phenotype of endometrial carcinoma (Em Ca) cells in a TCF4-dependent manner, which makes this a possible factor for a positive prognosis. However, little is known about regulation of TCF4 expression in Em Cas. We show here that beta-catenin can directly induce transcription from the TCF4 promoter, the effect being enhanced by the p300 coactivator. In clinical cases, nuclear beta-catenin accumulation was found to frequently overlap with TCF4 immunoreactivity in morules and surrounding glandular carcinoma lesions, showing a significant positive correlation (r = 0.82, P < 0.0001), in contrast to areas of squamous metaplasia (SqM) within Em Cas. In cases with coexistence of two squamoid features in trans-differentiated areas, loss of nuclear beta-catenin and TCF4 immunoreactivity was closely related to change in the morphology from the morular to the SqM phenotype. The TCF4 promoter contains a single consensus TCF-binding site that is critical for activation by beta-catenin. The p300 coactivator, in particular N-terminal residues 1 to 670, appears sufficient to enhance beta-catenin-dependent transcription, again with TCF4-dependence. These findings indicate that a positive feedback loop of TCF4 expression mediated by beta-catenin/p300 may be important for initial steps during trans-differentiation of Em Ca cells. In addition, its downregulation is associated with induction of a more-differentiated squamoid phenotype.

  15. Differential enhancement of dengue virus immune complex infectivity mediated by signaling-competent and signaling-incompetent human Fcgamma RIA (CD64) or FcgammaRIIA (CD32).

    PubMed

    Rodrigo, W W Shanaka I; Jin, Xia; Blackley, Shanley D; Rose, Robert C; Schlesinger, Jacob J

    2006-10-01

    Fcgamma receptor (FcgammaR)-mediated entry of infectious dengue virus immune complexes into monocytes/macrophages is hypothesized to be a key event in the pathogenesis of complicated dengue fever. FcgammaRIA (CD64) and FcgammaRIIA (CD32), which predominate on the surface of such dengue virus-permissive cells, were compared for their influence on the infectivity of dengue 2 virus immune complexes formed with human dengue virus antibodies. A signaling immunoreceptor tyrosine-based activation motif (ITAM) incorporated into the accessory gamma-chain subunit that associates with FcgammaRIA and constitutively in FcgammaRIIA is required for phagocytosis mediated by these receptors. To determine whether FcgammaRIA and FcgammaRIIA activation functions are also required for internalization of infectious dengue virus immune complexes, we generated native and signaling-incompetent versions of each receptor by site-directed mutagenesis of ITAM tyrosine residues. Plasmids designed to express these receptors were transfected into COS-7 cells, and dengue virus replication was measured by plaque assay and flow cytometry. We found that both receptors mediated enhanced dengue virus immune complex infectivity but that FcgammaRIIA appeared to do so far more effectively. Abrogation of FcgammaRIA signaling competency, either by expression without gamma-chain or by coexpression with gamma-chain mutants, was associated with significant impairment of phagocytosis and of dengue virus immune complex infectivity. Abrogation of FcgammaRIIA signaling competency was also associated with equally impaired phagocytosis but had no discernible effect on dengue virus immune complex infectivity. These findings point to fundamental differences between FcgammaRIA and FcgammaRIIA with respect to their immune-enhancing capabilities and suggest that different mechanisms of dengue virus immune complex internalization may operate between these FcgammaRs.

  16. Novel Insights into Interleukin 6 (IL-6) Cis- and Trans-signaling Pathways by Differentially Manipulating the Assembly of the IL-6 Signaling Complex*

    PubMed Central

    Lacroix, Marine; Rousseau, François; Guilhot, Florence; Malinge, Pauline; Magistrelli, Giovanni; Herren, Suzanne; Jones, Simon A.; Jones, Gareth W.; Scheller, Jürgen; Lissilaa, Rami; Kosco-Vilbois, Marie; Johnson, Zoë; Buatois, Vanessa; Ferlin, Walter

    2015-01-01

    The IL-6 signaling complex is described as a hexamer, formed by the association of two IL-6·IL-6 receptor (IL-6R)·gp130 trimers, with gp130 being the signal transducer inducing cis- and trans-mediated signaling via a membrane-bound or soluble form of the IL-6R, respectively. 25F10 is an anti-mouse IL-6R mAb that binds to both membrane-bound IL-6R and soluble IL-6R with the unique property of specifically inhibiting trans-mediated signaling events. In this study, epitope mapping revealed that 25F10 interacts at site IIb of IL-6R but allows the binding of IL-6 to the IL-6R and the recruitment of gp130, forming a trimer complex. Binding of 25F10 to IL-6R prevented the formation of the hexameric complex obligate for trans-mediated signaling, suggesting that the cis- and trans-modes of IL-6 signaling adopt different mechanisms for receptor complex assembly. To study this phenomenon also in the human system, we developed NI-1201, a mAb that targets, in the human IL-6R sequence, the epitope recognized by 25F10 for mice. Interestingly, NI-1201, however, did not selectively inhibit human IL-6 trans-signaling, although both mAbs produced beneficial outcomes in conditions of exacerbated IL-6 as compared with a site I-directed mAb. These findings shed light on the complexity of IL-6 signaling. First, triggering cis- versus trans-mediated IL-6 signaling occurs via distinctive mechanisms for receptor complex assembly in mice. Second, the formation of the receptor complex leading to cis- and trans-signaling biology in mice and humans is different, and this should be taken into account when developing strategies to inhibit IL-6 clinically. PMID:26363066

  17. Novel Insights into Interleukin 6 (IL-6) Cis- and Trans-signaling Pathways by Differentially Manipulating the Assembly of the IL-6 Signaling Complex.

    PubMed

    Lacroix, Marine; Rousseau, François; Guilhot, Florence; Malinge, Pauline; Magistrelli, Giovanni; Herren, Suzanne; Jones, Simon A; Jones, Gareth W; Scheller, Jürgen; Lissilaa, Rami; Kosco-Vilbois, Marie; Johnson, Zoë; Buatois, Vanessa; Ferlin, Walter

    2015-11-06

    The IL-6 signaling complex is described as a hexamer, formed by the association of two IL-6·IL-6 receptor (IL-6R)·gp130 trimers, with gp130 being the signal transducer inducing cis- and trans-mediated signaling via a membrane-bound or soluble form of the IL-6R, respectively. 25F10 is an anti-mouse IL-6R mAb that binds to both membrane-bound IL-6R and soluble IL-6R with the unique property of specifically inhibiting trans-mediated signaling events. In this study, epitope mapping revealed that 25F10 interacts at site IIb of IL-6R but allows the binding of IL-6 to the IL-6R and the recruitment of gp130, forming a trimer complex. Binding of 25F10 to IL-6R prevented the formation of the hexameric complex obligate for trans-mediated signaling, suggesting that the cis- and trans-modes of IL-6 signaling adopt different mechanisms for receptor complex assembly. To study this phenomenon also in the human system, we developed NI-1201, a mAb that targets, in the human IL-6R sequence, the epitope recognized by 25F10 for mice. Interestingly, NI-1201, however, did not selectively inhibit human IL-6 trans-signaling, although both mAbs produced beneficial outcomes in conditions of exacerbated IL-6 as compared with a site I-directed mAb. These findings shed light on the complexity of IL-6 signaling. First, triggering cis- versus trans-mediated IL-6 signaling occurs via distinctive mechanisms for receptor complex assembly in mice. Second, the formation of the receptor complex leading to cis- and trans-signaling biology in mice and humans is different, and this should be taken into account when developing strategies to inhibit IL-6 clinically. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Communication complexity and information complexity

    NASA Astrophysics Data System (ADS)

    Pankratov, Denis

    Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information

  19. Differential salt-induced dissociation of the p53 protein complexes with circular and linear plasmid DNA substrates suggest involvement of a sliding mechanism.

    PubMed

    Šebest, Peter; Brázdová, Marie; Fojta, Miroslav; Pivoňková, Hana

    2015-01-30

    A study of the effects of salt conditions on the association and dissociation of wild type p53 with different ~3 kbp long plasmid DNA substrates (supercoiled, relaxed circular and linear, containing or lacking a specific p53 binding site, p53CON) using immunoprecipitation at magnetic beads is presented. Salt concentrations above 200 mM strongly affected association of the p53 protein to any plasmid DNA substrate. Strikingly different behavior was observed when dissociation of pre-formed p53-DNA complexes in increased salt concentrations was studied. While contribution from the p53CON to the stability of the p53-DNA complexes was detected between 100 and 170 mM KCl, p53 complexes with circular DNAs (but not linear) exhibited considerable resistance towards salt treatment for KCl concentrations as high as 2 M provided that the p53 basic C-terminal DNA binding site (CTDBS) was available for DNA binding. On the contrary, when the CTDBS was blocked by antibody used for immunoprecipitation, all p53-DNA complexes were completely dissociated from the p53 protein in KCl concentrations≥200 mM under the same conditions. These observations suggest: (a) different ways for association and dissociation of the p53-DNA complexes in the presence of the CTDBS; and (b) a critical role for a sliding mechanism, mediated by the C-terminal domain, in the dissociation process.

  20. Differential recall of derived and inflected word forms in working memory: examining the role of morphological information in simple and complex working memory tasks

    PubMed Central

    Service, Elisabet; Maury, Sini

    2015-01-01

    Working memory (WM) has been described as an interface between cognition and action, or a system for access to a limited amount of information needed in complex cognition. Access to morphological information is needed for comprehending and producing sentences. The present study probed WM for morphologically complex word forms in Finnish, a morphologically rich language. We studied monomorphemic (boy), inflected (boy+’s), and derived (boy+hood) words in three tasks. Simple span, immediate serial recall of words, in Experiment 1, is assumed to mainly rely on information in the focus of attention. Sentence span, a dual task combining sentence reading with recall of the last word (Experiment 2) or of a word not included in the sentence (Experiment 3) is assumed to involve establishment of a search set in long-term memory for fast activation into the focus of attention. Recall was best for monomorphemic and worst for inflected word forms with performance on derived words in between. However, there was an interaction between word type and experiment, suggesting that complex span is more sensitive to morphological complexity in derivations than simple span. This was explored in a within-subjects Experiment 4 combining all three tasks. An interaction between morphological complexity and task was replicated. Both inflected and derived forms increased load in WM. In simple span, recall of inflectional forms resulted in form errors. Complex span tasks were more sensitive to morphological load in derived words, possibly resulting from interference from morphological neighbors in the mental lexicon. The results are best understood as involving competition among inflectional forms when binding words from input into an output structure, and competition from morphological neighbors in secondary memory during cumulative retrieval-encoding cycles. Models of verbal recall need to be able to represent morphological as well as phonological and semantic information. PMID:25642181

  1. A Comprehensive Analysis of Chromoplast Differentiation Reveals Complex Protein Changes Associated with Plastoglobule Biogenesis and Remodeling of Protein Systems in Sweet Orange Flesh1[OPEN

    PubMed Central

    Wang, Lun; Deng, Xiuxin

    2015-01-01

    Globular and crystalloid chromoplasts were observed to be region specifically formed in sweet orange (Citrus sinensis) flesh and converted from amyloplasts during fruit maturation, which was associated with the composition of specific carotenoids and the expression of carotenogenic genes. Subsequent isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analyses of purified plastids from the flesh during chromoplast differentiation and senescence identified 1,386 putative plastid-localized proteins, 1,016 of which were quantified by spectral counting. The iTRAQ values reflecting the expression abundance of three identified proteins were validated by immunoblotting. Based on iTRAQ data, chromoplastogenesis appeared to be associated with three major protein expression patterns: (1) marked decrease in abundance of the proteins participating in the translation machinery through ribosome assembly; (2) increase in abundance of the proteins involved in terpenoid biosynthesis (including carotenoids), stress responses (redox, ascorbate, and glutathione), and development; and (3) maintenance of the proteins for signaling and DNA and RNA. Interestingly, a strong increase in abundance of several plastoglobule-localized proteins coincided with the formation of plastoglobules in the chromoplast. The proteomic data also showed that stable functioning of protein import, suppression of ribosome assembly, and accumulation of chromoplast proteases are correlated with the amyloplast-to-chromoplast transition; thus, these processes may play a collective role in chromoplast biogenesis and differentiation. By contrast, the chromoplast senescence process was inferred to be associated with significant increases in stress response and energy supply. In conclusion, this comprehensive proteomic study identified many potentially new plastid-localized proteins and provides insights into the potential developmental and molecular mechanisms underlying chromoplast

  2. The Differential Effects of Two Types of Task Repetition on the Complexity, Accuracy, and Fluency in Computer-Mediated L2 Written Production: A Focus on Computer Anxiety

    ERIC Educational Resources Information Center

    Amiryousefi, Mohammad

    2016-01-01

    Previous task repetition studies have primarily focused on how task repetition characteristics affect the complexity, accuracy, and fluency in L2 oral production with little attention to L2 written production. The main purpose of the study reported in this paper was to examine the effects of task repetition versus procedural repetition on the…

  3. The Differential Effects of Two Types of Task Repetition on the Complexity, Accuracy, and Fluency in Computer-Mediated L2 Written Production: A Focus on Computer Anxiety

    ERIC Educational Resources Information Center

    Amiryousefi, Mohammad

    2016-01-01

    Previous task repetition studies have primarily focused on how task repetition characteristics affect the complexity, accuracy, and fluency in L2 oral production with little attention to L2 written production. The main purpose of the study reported in this paper was to examine the effects of task repetition versus procedural repetition on the…

  4. Comparison of platinum, palladium, and rhodium distributions in some layered intrusions with special reference to the late differentiates (upper zone) of the Bushveld complex, South Africa.

    USGS Publications Warehouse

    Page, N.J.; Von Gruenewaldt, G.; Haffty, J.; Aruscavage, P. J.

    1982-01-01

    The Stillwater, Fiskenaesset and Bushveld complexes have many similarities. The trends of the Pt/(Pt + Pd) and its correlation with Mg/(Mg + Fe2+) are presented. Presumably the Pt/(Pt + Pd) variations are related to changes in major mineral compositions. -K.A.R.

  5. Ancient DNA of the Extinct Lava Shearwater (Puffinus olsoni) from the Canary Islands Reveals Incipient Differentiation within the P. puffinus Complex

    PubMed Central

    Ramirez, Oscar; Illera, Juan Carlos; Rando, Juan Carlos; Gonzalez-Solis, Jacob; Alcover, Josep Antoni; Lalueza-Fox, Carles

    2010-01-01

    Background The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae) the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands. Methodology/Principal Findings We used bones of the two extinct Canary shearwaters (P. olsoni and P. holeae) to obtain genetic data, for use in providing insights into the differentiation process within the genus Puffinus. Although mitochondrial DNA (mtDNA) cytochrome b sequences were successfully retrieved from four Holocene specimens of the extinct Lava shearwater (P. olsoni) from Fuerteventura (Canary Islands), the P. holeae specimens yielded no DNA. Only one haplotype was detected in P. olsoni, suggesting a low genetic diversity within this species. Conclusions The phylogenetic analyses based on the DNA data reveal that: (i) the “Puffinus puffinus complex”, an assemblage of species defined using osteological characteristics (P. puffinus, P. olsoni, P. mauretanicus, P. yelkouan and probably P. holeae), shows unresolved phylogenetic relationships; (ii) despite the differences in body size and proportions, P. olsoni and the extant P. puffinus are sister species. Several hypotheses can be considered to explain the incipient differentiation between P. olsoni and P. puffinus. PMID:21209838

  6. Density functional theory investigations of the homoleptic tris(dithiolene) complexes [M(dddt)(3)](-q) (q = 3, 2 ; M = Nd(3+) and U(3+/4+)) related to lanthanide(III)/actinide(III) differentiation.

    PubMed

    Meskaldji, Samir; Belkhiri, Lotfi; Arliguie, Thérèse; Fourmigué, Marc; Ephritikhine, Michel; Boucekkine, Abdou

    2010-04-05

    The structures of the homoleptic lanthanide and actinide tris(dithiolene) complexes [M(dddt)(3)](q-) (q = 3, M = Nd(3+) and q = 3 or 2, M = U(3+/4+)) have been investigated using relativistic Density Functional Theory (DFT) computations including spin-orbit corrections coupled with the COnductor-like Screening Model (COSMO) for a realistic solvation approach. The dithiolene ligands are known to be very efficient at stabilizing metal high oxidation states. The aim of the work is to explain the peculiar symmetric folding of the three Mdddt metallacycles in these complexes, some of them existing under a polymeric form, in relation with the Ln(III)/An(III) differentiation. In the [M(dddt)(3)(py)](q-) species, where an additional pyridine ligand is linked to the metal center, the Mdddt moieties appear to be almost planar. The study brings to light the occurrence of a M...C=C interaction explaining the Mdddt folding of the [U(dddt)(3)](q-) uranium species, the metal 5f electrons playing a driving role. No such interaction appears in the case of the Nd(III) complex, and the folding of the rather flexible dddt ligands in the polymeric structure of this species should be mainly due to steric effects. Moreover, the analysis of the normal modes of vibration shows that the U(III) complex [U(dddt)(3)](3-), which has not yet been isolated, is thermodynamically stable. It appears that the X-ray characterized U(IV) complex [U(dddt)(3)](2-) should be less stable than the calculated U(III) complex in a polar solvent.

  7. Differential Phosphatidylinositol-3-Kinase-Akt-mTOR Activation by Semliki Forest and Chikungunya Viruses Is Dependent on nsP3 and Connected to Replication Complex Internalization

    PubMed Central

    Biasiotto, Roberta; Eng, Kai; Neuvonen, Maarit; Götte, Benjamin; Rheinemann, Lara; Mutso, Margit; Utt, Age; Varghese, Finny; Balistreri, Giuseppe; Merits, Andres; Ahola, Tero; McInerney, Gerald M.

    2015-01-01

    ABSTRACT Many viruses affect or exploit the phosphatidylinositol-3-kinase (PI3K)-Akt-mammalian target of rapamycin (mTOR) pathway, a crucial prosurvival signaling cascade. We report that this pathway was strongly activated in cells upon infection with the Old World alphavirus Semliki Forest virus (SFV), even under conditions of complete nutrient starvation. We mapped this activation to the hyperphosphorylated/acidic domain in the C-terminal tail of SFV nonstructural protein nsP3. Viruses with a deletion of this domain (SFV-Δ50) but not of other regions in nsP3 displayed a clearly delayed and reduced capacity of Akt stimulation. Ectopic expression of the nsP3 of SFV wild type (nsP3-wt), but not nsP3-Δ50, equipped with a membrane anchor was sufficient to activate Akt. We linked PI3K-Akt-mTOR stimulation to the intracellular dynamics of viral replication complexes, which are formed at the plasma membrane and subsequently internalized in a process blocked by the PI3K inhibitor wortmannin. Replication complex internalization was observed upon infection of cells with SFV-wt and SFV mutants with deletions in nsP3 but not with SFV-Δ50, where replication complexes were typically accumulated at the cell periphery. In cells infected with the closely related chikungunya virus (CHIKV), the PI3K-Akt-mTOR pathway was only moderately activated. Replication complexes of CHIKV were predominantly located at the cell periphery. Exchanging the hypervariable C-terminal tail of nsP3 between SFV and CHIKV induced the phenotype of strong PI3K-Akt-mTOR activation and replication complex internalization in CHIKV. In conclusion, infection with SFV but not CHIKV boosts PI3K-Akt-mTOR through the hyperphosphorylated/acidic domain of nsP3 to drive replication complex internalization. IMPORTANCE SFV and CHIKV are very similar in terms of molecular and cell biology, e.g., regarding replication and molecular interactions, but are strikingly different regarding pathology: CHIKV is a relevant human

  8. Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex.

    PubMed

    Morley, Laura; McNally, Alan; Paszkiewicz, Konrad; Corander, Jukka; Méric, Guillaume; Sheppard, Samuel K; Blom, Jochen; Manning, Georgina

    2015-06-01

    Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation.

  9. Mechanisms Regulating Spermatogonial Differentiation.

    PubMed

    Mecklenburg, Jennifer M; Hermann, Brian P

    Mammalian spermatogenesis is a complex and highly ordered process by which male germ cells proceed through a series of differentiation steps to produce haploid flagellated spermatozoa. Underlying this process is a pool of adult stem cells, the spermatogonial stem cells (SSCs), which commence the spermatogenic lineage by undertaking a differentiation fate decision to become progenitor spermatogonia. Subsequently, progenitors acquire a differentiating spermatogonia phenotype and undergo a series of amplifying mitoses while becoming competent to enter meiosis. After spermatocytes complete meiosis, post-meiotic spermatids must then undergo a remarkable transformation from small round spermatids to a flagellated spermatozoa with extremely compacted nuclei. This chapter reviews the current literature pertaining to spermatogonial differentiation with an emphasis on the mechanisms controlling stem cell fate decisions and early differentiation events in the life of a spermatogonium.

  10. Assessing the Effects of Light on Differentiation and Virulence of the Plant Pathogen Botrytis cinerea: Characterization of the White Collar Complex

    PubMed Central

    Hevia, Montserrat A.; Tudzynski, Paul; Larrondo, Luis F.

    2013-01-01

    Organisms are exposed to a tough environment, where acute daily challenges, like light, can strongly affect several aspects of an individual's physiology, including pathogenesis. While several fungal models have been widely employed to understand the physiological and molecular events associated with light perception, various other agricultural-relevant fungi still remain, in terms of their responsiveness to light, in the dark. The fungus Botrytis cinerea is an aggressive pathogen able to cause disease on a wide range of plant species. Natural B. cinerea isolates exhibit a high degree of diversity in their predominant mode of reproduction. Thus, the majority of naturally occurring strains are known to reproduce asexually via conidia and sclerotia, and sexually via apothecia. Studies from the 1970′s reported on specific developmental responses to treatments with near-UV, blue, red and far-red light. To unravel the signaling machinery triggering development – and possibly also connected with virulence – we initiated the functional characterization of the transcription factor/photoreceptor BcWCL1 and its partner BcWCL2, that form the White Collar Complex (WCC) in B. cinerea. Using mutants either abolished in or exhibiting enhanced WCC signaling (overexpression of both bcwcl1 and bcwcl2), we demonstrate that the WCC is an integral part of the mentioned machinery by mediating transcriptional responses to white light and the inhibition of conidiation in response to this stimulus. Furthermore, the WCC is required for coping with excessive light, oxidative stress and also to achieve full virulence. Although several transcriptional responses are abolished in the absence of bcwcl1, the expression of some genes is still light induced and a distinct conidiation pattern in response to daily light oscillations is enhanced, revealing a complex underlying photobiology. Though overlaps with well-studied fungal systems exist, the light-associated machinery of B. cinerea

  11. Assessing the effects of light on differentiation and virulence of the plant pathogen Botrytis cinerea: characterization of the White Collar Complex.

    PubMed

    Canessa, Paulo; Schumacher, Julia; Hevia, Montserrat A; Tudzynski, Paul; Larrondo, Luis F

    2013-01-01

    Organisms are exposed to a tough environment, where acute daily challenges, like light, can strongly affect several aspects of an individual's physiology, including pathogenesis. While several fungal models have been widely employed to understand the physiological and molecular events associated with light perception, various other agricultural-relevant fungi still remain, in terms of their responsiveness to light, in the dark. The fungus Botrytis cinerea is an aggressive pathogen able to cause disease on a wide range of plant species. Natural B. cinerea isolates exhibit a high degree of diversity in their predominant mode of reproduction. Thus, the majority of naturally occurring strains are known to reproduce asexually via conidia and sclerotia, and sexually via apothecia. Studies from the 1970's reported on specific developmental responses to treatments with near-UV, blue, red and far-red light. To unravel the signaling machinery triggering development--and possibly also connected with virulence--we initiated the functional characterization of the transcription factor/photoreceptor BcWCL1 and its partner BcWCL2, that form the White Collar Complex (WCC) in B. cinerea. Using mutants either abolished in or exhibiting enhanced WCC signaling (overexpression of both bcwcl1 and bcwcl2), we demonstrate that the WCC is an integral part of the mentioned machinery by mediating transcriptional responses to white light and the inhibition of conidiation in response to this stimulus. Furthermore, the WCC is required for coping with excessive light, oxidative stress and also to achieve full virulence. Although several transcriptional responses are abolished in the absence of bcwcl1, the expression of some genes is still light induced and a distinct conidiation pattern in response to daily light oscillations is enhanced, revealing a complex underlying photobiology. Though overlaps with well-studied fungal systems exist, the light-associated machinery of B. cinerea appears more

  12. Subunits of the Plastid ClpPR Protease Complex Have Differential Contributions to Embryogenesis, Plastid Biogenesis, and Plant Development in Arabidopsis[C][W

    PubMed Central

    Kim, Jitae; Rudella, Andrea; Ramirez Rodriguez, Verenice; Zybailov, Boris; Olinares, Paul Dominic B.; van Wijk, Klaas J.

    2009-01-01

    The plastid ClpPR protease complex in Arabidopsis thaliana consists of five catalytic ClpP and four noncatalytic ClpR subunits. An extensive analysis of the CLPR family and CLPP5 is presented to address this complexity. Null alleles for CLPR2 and CLPR4 showed delayed embryogenesis and albino embryos, with seedling development blocked in the cotyledon stage; this developmental block was overcome under heterotrophic conditions, and seedlings developed into small albino to virescent seedlings. By contrast, null alleles for CLPP5 were embryo lethal. Thus, the ClpPR proteins make different functional contributions. To further test for redundancies and functional differences between the ClpR proteins, we overexpressed full-length cDNAs for ClpR1, R2, R3, R4 in clpr1, clpr2 and clpr4 mutants. This showed that overexpression of ClpR3 can complement for the loss of ClpR1, but not for the loss of ClpR2 or ClpR4, indicating that ClpR3 can functionally substitute ClpR1. By contrast, ClpR1, R2 and R4 could not substitute each other. Double mutants of weak CLPR1 and 2 alleles were seedling lethal, showing that a minimum concentration of different ClpR proteins is essential for Clp function. Microscopy and large-scale comparative leaf proteome analyses of a CLPR4 null allele demonstrate a central role of Clp protease in chloroplast biogenesis and protein homeostasis; substrates are discussed. Lack of transcriptional and translational feedback regulation within the CLPPR gene family indicates that regulation of Clp activity occurs through Clp complex assembly and substrate delivery. PMID:19525416

  13. Differential expression of two bc1 complexes in the strict acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation.

    PubMed

    Bruscella, Patrice; Appia-Ayme, Corinne; Levicán, Gloria; Ratouchniak, Jeanine; Jedlicki, Eugenia; Holmes, David S; Bonnefoy, Violaine

    2007-01-01

    Three strains of the strict acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans, including the type strain ATCC 23270, contain a petIIABC gene cluster that encodes the three proteins, cytochrome c1, cytochrome b and a Rieske protein, that constitute a bc1 electron-transfer complex. RT-PCR and Northern blotting show that the petIIABC cluster is co-transcribed with cycA, encoding a cytochrome c belonging to the c4 family, sdrA, encoding a putative short-chain dehydrogenase, and hip, encoding a high potential iron-sulfur protein, suggesting that the six genes constitute an operon, termed the petII operon. Previous results indicated that A. ferrooxidans contains a second pet operon, termed the petI operon, which contains a gene cluster that is similarly organized except that it lacks hip. Real-time PCR and Northern blot experiments demonstrate that petI is transcribed mainly in cells grown in medium containing iron, whereas petII is transcribed in cells grown in media containing sulfur or iron. Primer extension experiments revealed possible transcription initiation sites for the petI and petII operons. A model is presented in which petI is proposed to encode the bc1 complex, functioning in the uphill flow of electrons from iron to NAD(P), whereas petII is suggested to be involved in electron transfer from sulfur (or formate) to oxygen (or ferric iron). A. ferrooxidans is the only organism, to date, to exhibit two functional bc1 complexes.

  14. Differential gear

    SciTech Connect

    Shibuya, K.; Hamada, T.; Masuda, K.; Shimada, K.

    1989-05-02

    A differential gear for permitting a difference in rotational speed between two output shafts is described, the differential gear including an input shaft and two output shafts. The improvement consists of means for limiting the difference in rotational speed between the two output shafts in response to the rotational speed of the input shaft, the rotational speed limiting means comprising a differential casing coupled to the input shaft and adapted to be rotated by the input shaft, a differential pinion shaft radially extending within the differential casing and rotatably mounted at its opposite ends in the differential casing. A plurality of differential pinion gears rotatably mounted on the differential pinion shaft is also included, and also a pair of side gears having a rotational axis common to that of the differential casing, wherein the side gears mesh with the differential pinion gears and the two output shafts are fixed to the side gears, the means for limiting the difference in rotational speed between the two output shafts comprising a weight means radially movable in the differential casing, the weight means limiting the difference in rotational speed between the two output shafts in response to the centrifugal force applied to the weight means, the weight means being slidably mounted on the differential pinion shaft and being biased radially inwardly.

  15. Differential transcript profiling through cDNA-AFLP showed complexity of rutin biosynthesis and accumulation in seeds of a nutraceutical food crop (Fagopyrum spp.)

    PubMed Central

    2012-01-01

    Background Buckwheat, consisting of two cultivated species Fagopyrum tataricum and F. esculentum, is the richest source of flavonoid rutin. Vegetative tissues of both the Fagopyrum species contain almost similar amount of rutin; however, rutin content in seed of F. tataricum are ~50 folds of that in seed of F. esculentum. In order to understand the molecular basis of high rutin content in F. tataricum, differential transcript profiling through cDNA-AFLP has been utilized to decipher what genetic factors in addition to flavonoid structural genes contribute to high rutin content of F. tataricum compared to F. esculentum. Results Differential transcript profiling through cDNA-AFLP in seed maturing stages (inflorescence to seed maturation) with 32 primer combinations generated total of 509 transcript fragments (TDFs). 167 TDFs were then eluted, cloned and sequenced from F. tataricum and F. esculentum. Categorization of TDFs on the basis of their presence/absence (qualitative variation) or differences in the amount of expression (quantitative variation) between both the Fagopyrum species showed that majority of variants are quantitative (64%). The TDFs represented genes controlling different biological processes such as basic and secondary metabolism (33%), regulation (18%), signal transduction (14%), transportation (13%), cellular organization (10%), and photosynthesis & energy (4%). Most of the TDFs except belonging to cellular metabolism showed relatively higher transcript abundance in F. tataricum over F. esculentum. Quantitative RT-PCR analysis of nine TDFs representing genes involved in regulation, metabolism, signaling and transport of secondary metabolites showed that all the tested nine TDFs (Ubiquitin protein ligase, ABC transporter, sugar transporter) except MYB 118 showed significantly higher expression in early seed formation stage (S7) of F. tataricum compared to F. esculentum. qRT-PCR results were found to be consistent with the cDNA-AFLP results

  16. Cell-type specific interaction of Neu differentiation factor (NDF/heregulin) with Neu/HER-2 suggests complex ligand-receptor relationships.

    PubMed Central

    Peles, E; Ben-Levy, R; Tzahar, E; Liu, N; Wen, D; Yarden, Y

    1993-01-01

    The Neu/HER-2 receptor tyrosine kinase is overexpressed in some types of human adenocarcinomas, including tumors of the breast and the ovary. A 44 kDa glycoprotein that elevates tyrosine phosphorylation of Neu has been isolated and named Neu differentiation factor (NDF), or heregulin. Here we show that NDF affects tyrosine phosphorylation of Neu in human tumor cells of breast, colon and neuronal origin, but not in ovarian cells that overexpress the receptor. By using monoclonal antibodies (mAbs) to Neu, we found that the ovarian receptor is immunologically and biochemically similar to the mammary p185neu. Nevertheless, unlike breast-derived Neu, the ovarian protein did not display covalent cross-linking to radiolabeled NDF, and was devoid of ligand-induced association with phosphatidylinositol 3'-kinase. Direct binding analysis showed that NDF binds with high affinity (Kd approximately 10(-9) M) to mammary cells, but its weak association with ovarian cells is probably mediated by heparin-like molecules. Similar to the endogenous receptor, the ectopically overexpressed Neu of mammary cells, but not of ovarian and fibroblastic cells, exhibited elevated levels of NDF-induced phosphorylation and covalent cross-linking of the radiolabeled factor. Taken together, our results imply that NDF binding to cells requires both Neu and an additional cellular component, whose identity is still unknown, but its tissue distribution is more restricted than the expression of the neu gene. Images PMID:8096177

  17. Coxsackievirus and adenovirus receptor (CAR) is expressed in male germ cells and forms a complex with the differentiation factor JAM-C in mouse testis.

    PubMed

    Mirza, Momina; Hreinsson, Julius; Strand, Mona-Lisa; Hovatta, Outi; Söder, Olle; Philipson, Lennart; Pettersson, Ralf F; Sollerbrant, Kerstin

    2006-04-01

    The coxsackievirus and adenovirus receptor (CAR) is a transmembrane protein important for viral binding to target cells. Using RT-PCR, Western analysis, GST pull-down assay and indirect immunofluorescence, it was shown that CAR is expressed in male germ cells from mice, rats, and humans. CAR was detected in round spermatids in the testis as well as in purified, mature spermatozoa. The two membrane-bound isoforms of CAR occupied different subcellular sites in the acrosomal region of the spermatozoa. CAR was exposed on the surface of acrosome-reacted, but not acrosome-intact cells. Two CAR-binding proteins belonging to the ligand-of-numb protein-X (LNX) family also occupied distinct regions in spermatozoa. Finally, co-immunoprecipitation experiments demonstrated an interaction between CAR and JAM-C, a protein required for spermatid differentiation. Together, these findings imply a function for CAR in male fertility. The results also suggest that CAR in spermatozoa is inaccessible to adenovirus-based gene therapy vectors, and that the risk of germ line infection therefore is low.

  18. Differentiation of Staphylococcus argenteus (formerly: Staphylococcus aureus clonal complex 75) by mass spectrometry from S. aureus using the first strain isolated from a wild African great ape.

    PubMed

    Schuster, Dominik; Rickmeyer, Jasmin; Gajdiss, Mike; Thye, Thorsten; Lorenzen, Stephan; Reif, Marion; Josten, Michaele; Szekat, Christiane; Melo, Luís D R; Schmithausen, Ricarda M; Liégeois, Florian; Sahl, Hans-Georg; Gonzalez, Jean-Paul J; Nagel, Michael; Bierbaum, Gabriele

    2017-01-01

    The species Staphylococcus argenteus was separated recently from Staphylococcus aureus (Tong S.Y., F. Schaumburg, M.J. Ellington, J. Corander, B. Pichon, F. Leendertz, S.D. Bentley, J. Parkhill, D.C. Holt, G. Peters, and P.M. Giffard, 2015). The objective of this work was to characterise the genome of a non-human S. argenteus strain, which had been isolated from the faeces of a wild-living western lowland gorilla in Gabon, and analyse the spectrum of this species in matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The full genome sequence revealed a scarcity of virulence genes and absence of resistance genes, indicating a decreased virulence potential compared to S. aureus and the human methicillin-resistant S. argenteus isolate MSHR1132(T). Spectra obtained by MALDI-TOF MS and the analysis of available sequences in the genome databases identified several MALDI-TOF MS signals that clearly differentiate S. argenteus, the closely related Staphylococcus schweitzeri and S. aureus. In conclusion, in the absence of biochemical tests that identify the three species, mass spectrometry should be employed as method of choice. Copyright © 2016 Elsevier GmbH. All rights reserved.

  19. In vitro effects of binuclear (η (6)-p-cymene)ruthenium(II) complex containing bridging bis(nicotinate)-polyethylene glycol ester ligand on differentiation pathways of murine Th lymphocytes activated by T cell mitogen.

    PubMed

    Momcilovic, Miljana; Eichhorn, Thomas; Blazevski, Jana; Schmidt, Harry; Kaluđerović, Goran N; Stosic-Grujicic, Stanislava

    2015-04-01

    T cell differentiation into distinct T helper (Th) subpopulations is crucial in governing acquired immune responses as well as some inflammatory and autoimmune disorders. This study investigated potential of the novel neutral binuclear ruthenium(II) complexes 1-8 with general formula [{RuCl2(η(6)-p-cym)}2μ-(N(∩)N)] (N(∩)N = bis(nicotinate)- and bis(iso-nicotinate)-polyethylene glycol esters; (3-py)COO(CH2CH2O) n CO(3-py) and (4-py)COO(CH2CH2O) n CO(4-py); n = 1-4), as well as [RuCl2(η(6)-p-cym)(nic)] (R1, nic = nicotinate) and [RuCl2(η(6)-p-cym)(inic)] (R2, inic = isonicotinate) as an immunomodulatory agents capable to direct Th cell differentiation. From all investigated complexes, [{RuCl2(η(6)-p-cym)}2μ-{(3-py)COO(CH2CH2O)4CO(3-py)}] (4) was selected for further study because it did not affect splenocyte viability (in concentration up to 50 μM), but significantly reduced secretion of representative Th1 cytokine, IFN-γ induced by T cell mitogen. Besides IFN-γ, 4 inhibited dose dependently expression and production of representative Th17 cytokine, IL-17, in these cells. Otherwise, the production of anti-inflammatory cytokines IL-4 and IL-10 was upregulated. Also, 4 significantly increased CD4(+)CD25(+)FoxP3(+) Treg cell frequency in the activated splenocytes. Moreover, ConA-induced expression of Th1 transcription factors, T-bet and STAT1, as well as of Th17-related protein STAT3 was attenuated upon exposure to 4, while the expression of Th2-related transcription factor GATA3 remained stable. In conclusion, ruthenium(II) complex 4 modulates immune system cell functions in vitro by inhibiting T cell differentiation towards pathogenic Th1/Th17 phenotype and inducing a regulatory phenotype characterized by IL-10 and IL-4 production, which may provide novel therapeutic opportunities for immune-inflammatory and/or autoimmune disorders.

  20. Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study

    PubMed Central

    Blacklock, Kristin; Verkhivker, Gennady M.

    2013-01-01

    Allosteric interactions of the molecular chaperone Hsp90 with a large cohort of cochaperones and client proteins allow for molecular communication and event coupling in signal transduction networks. The integration of cochaperones into the Hsp90 system is driven by the regulatory mechanisms that modulate the progression of the ATPase cycle and control the recruitment of the Hsp90 clientele. In this work, we report the results of computational modeling of allosteric regulation in the Hsp90 complexes with the cochaperones p23 and Aha1. By integrating protein docking, biophysical simulations, modeling of allosteric communications, protein structure network analysis and the energy landscape theory we have investigated dynamics and stability of the Hsp90-p23 and Hsp90-Aha1 interactions in direct comparison with the extensive body of structural and functional experiments. The results have revealed that functional dynamics and allosteric interactions of Hsp90 can be selectively modulated by these cochaperones via specific targeting of the regulatory hinge regions that could restrict collective motions and stabilize specific chaperone conformations. The protein structure network parameters have quantified the effects of cochaperones on conformational stability of the Hsp90 complexes and identified dynamically stable communities of residues that can contribute to the strengthening of allosteric interactions. According to our results, p23-mediated changes in the Hsp90 interactions may provide “molecular brakes” that could slow down an efficient transmission of the inter-domain allosteric signals, consistent with the functional role of p23 in partially inhibiting the ATPase cycle. Unlike p23, Aha1-mediated acceleration of the Hsp90-ATPase cycle may be achieved via modulation of the equilibrium motions that facilitate allosteric changes favoring a closed dimerized form of Hsp90. The results of our study have shown that Aha1 and p23 can modulate the Hsp90-ATPase activity

  1. Ctr9, a Key Component of the Paf1 Complex, Affects Proliferation and Terminal Differentiation in the Developing Drosophila Nervous System

    PubMed Central

    Bahrampour, Shahrzad; Thor, Stefan

    2016-01-01

    The Paf1 protein complex (Paf1C) is increasingly recognized as a highly conserved and broadly utilized regulator of a variety of transcriptional processes. These include the promotion of H3K4 and H3K36 trimethylation, H2BK123 ubiquitination, RNA Pol II transcriptional termination, and also RNA-mediated gene silencing. Paf1C contains five canonical protein components, including Paf1 and Ctr9, which are critical for overall complex integrity, as well as Rtf1, Leo1, and Cdc73/Parafibromin(Hrpt2)/Hyrax. In spite of a growing appreciation for the importance of Paf1C from yeast and mammalian studies, there has only been limited work in Drosophila. Here, we provide the first detailed phenotypic study of Ctr9 function in Drosophila. We found that Ctr9 mutants die at late embryogenesis or early larval life, but can be partly rescued by nervous system reexpression of Ctr9. We observed a number of phenotypes in Ctr9 mutants, including increased neuroblast numbers, increased nervous system proliferation, as well as downregulation of many neuropeptide genes. Analysis of cell cycle and regulatory gene expression revealed upregulation of the E2f1 cell cycle factor, as well as changes in Antennapedia and Grainy head expression. We also found reduction of H3K4me3 modification in the embryonic nervous system. Genome-wide transcriptome analysis points to additional downstream genes that may underlie these Ctr9 phenotypes, revealing gene expression changes in Notch pathway target genes, cell cycle genes, and neuropeptide genes. In addition, we find significant effects on the gene expression of metabolic genes. These findings reveal that Ctr9 is an essential gene that is necessary at multiple stages of nervous system development, and provides a starting point for future studies of the Paf1C in Drosophila. PMID:27520958

  2. Ctr9, a Key Component of the Paf1 Complex, Affects Proliferation and Terminal Differentiation in the Developing Drosophila Nervous System.

    PubMed

    Bahrampour, Shahrzad; Thor, Stefan

    2016-10-13

    The Paf1 protein complex (Paf1C) is increasingly recognized as a highly conserved and broadly utilized regulator of a variety of transcriptional processes. These include the promotion of H3K4 and H3K36 trimethylation, H2BK123 ubiquitination, RNA Pol II transcriptional termination, and also RNA-mediated gene silencing. Paf1C contains five canonical protein components, including Paf1 and Ctr9, which are critical for overall complex integrity, as well as Rtf1, Leo1, and Cdc73/Parafibromin(Hrpt2)/Hyrax. In spite of a growing appreciation for the importance of Paf1C from yeast and mammalian studies, there has only been limited work in Drosophila Here, we provide the first detailed phenotypic study of Ctr9 function in Drosophila We found that Ctr9 mutants die at late embryogenesis or early larval life, but can be partly rescued by nervous system reexpression of Ctr9 We observed a number of phenotypes in Ctr9 mutants, including increased neuroblast numbers, increased nervous system proliferation, as well as downregulation of many neuropeptide genes. Analysis of cell cycle and regulatory gene expression revealed upregulation of the E2f1 cell cycle factor, as well as changes in Antennapedia and Grainy head expression. We also found reduction of H3K4me3 modification in the embryonic nervous system. Genome-wide transcriptome analysis points to additional downstream genes that may underlie these Ctr9 phenotypes, revealing gene expression changes in Notch pathway target genes, cell cycle genes, and neuropeptide genes. In addition, we find significant effects on the gene expression of metabolic genes. These findings reveal that Ctr9 is an essential gene that is necessary at multiple stages of nervous system development, and provides a starting point for future studies of the Paf1C in Drosophila. Copyright © 2016 Bahrampour and Thor.

  3. ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex.

    PubMed

    Rampersad, Sephra N

    2014-01-01

    The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of member species which are of quarantine importance is impacted by a number of factors that negatively affect species identification. Structural information of the rRNA marker may be considered to be a conserved marker which can be used as supplementary information for possible species identification. The difficulty in using ITS rDNA sequences for identification lies in the low level of sequence variation at the intra-specific level and the generation of artificially-induced sequence variation due to errors in polymerization of the ITS array during DNA replication. Type and query ITS sequences were subjected to sequence analyses prior to generation of predicted consensus secondary structures, including the pattern of nucleotide polymorphisms and number of indel haplotypes, GC content, and detection of artificially-induced sequence variation. Data pertaining to structure stability, the presence of conserved motifs in secondary structures and mapping of all sequences onto the consensus C. gloeosporioides sensu stricto secondary structure for ITS1, 5.8S and ITS2 markers was then carried out. Motifs that are evolutionarily conserved among eukaryotes were found for all ITS1, 5.8S and ITS2 sequences. The sequences exhibited conserved features typical of functional rRNAs. Generally, polymorphisms occurred within less conserved regions and were seen as bulges, internal and terminal loops or non-canonical G-U base-pairs within regions of the double stranded helices. Importantly, there were also taxonomic motifs and base changes that were unique to specific taxa and which may be used to support intra-specific identification of members of the C. gloeosporioides sensu lato species complex.

  4. The study of the Bithorax-complex genes in patterning CCAP neurons reveals a temporal control of neuronal differentiation by Abd-B

    PubMed Central

    Moris-Sanz, M.; Estacio-Gómez, A.; Sánchez-Herrero, E.; Díaz-Benjumea, F. J.

    2015-01-01

    ABSTRACT During development, HOX genes play critical roles in the establishment of segmental differences. In the Drosophila central nervous system, these differences are manifested in the number and type of neurons generated by each neuroblast in each segment. HOX genes can act either in neuroblasts or in postmitotic cells, and either early or late in a lineage. Additionally, they can be continuously required during development or just at a specific stage. Moreover, these features are generally segment-specific. Lately, it has been shown that contrary to what happens in other tissues, where HOX genes define domains of expression, these genes are expressed in individual cells as part of the combinatorial codes involved in cell type specification. In this report we analyse the role of the Bithorax-complex genes – Ultrabithorax, abdominal-A and Abdominal-B – in sculpting the pattern of crustacean cardioactive peptide (CCAP)-expressing neurons. These neurons are widespread in invertebrates, express CCAP, Bursicon and MIP neuropeptides and play major roles in controlling ecdysis. There are two types of CCAP neuron: interneurons and efferent neurons. Our results indicate that Ultrabithorax and Abdominal-A are not necessary for specification of the CCAP-interneurons, but are absolutely required to prevent the death by apoptosis of the CCAP-efferent neurons. Furthermore, Abdominal-B controls by repression the temporal onset of neuropeptide expression in a subset of CCAP-efferent neurons, and a peak of ecdysone hormone at the end of larval life counteracts this repression. Thus, Bithorax complex genes control the developmental appearance of these neuropeptides both temporally and spatially. PMID:26276099

  5. SMA OBSERVATIONS OF THE W3(OH) COMPLEX: PHYSICAL AND CHEMICAL DIFFERENTIATION BETWEEN W3(H{sub 2}O) AND W3(OH)

    SciTech Connect

    Qin, Sheng-Li; Schilke, Peter; Sánchez-Monge, Álvaro; Wu, Jingwen; Wu, Yuefang; Liu, Tie; Liu, Ying

    2015-04-10

    We report on the Submillimeter Array (SMA) observations of molecular lines at 270 GHz toward the W3(OH) and W3(H{sub 2}O) complex. Although previous observations already resolved the W3(H{sub 2}O) into two or three sub-components, the physical and chemical properties of the two sources are not well constrained. Our SMA observations clearly resolved the W3(OH) and W3(H{sub 2}O) continuum cores. Taking advantage of the line fitting tool XCLASS, we identified and modeled a rich molecular spectrum in this complex, including multiple CH{sub 3}CN and CH{sub 3}OH transitions in both cores. HDO, C{sub 2}H{sub 5}CN, O{sup 13}CS, and vibrationally excited lines of HCN, CH{sub 3}CN, and CH{sub 3}OCHO were only detected in W3(H{sub 2}O). We calculate gas temperatures and column densities for both cores. The results show that W3(H{sub 2}O) has higher gas temperatures and larger column densities than W3(OH) as previously observed, suggesting physical and chemical differences between the two cores. We compare the molecular abundances in W3(H{sub 2}O) to those in the Sgr B2(N) hot core, the Orion KL hot core, and the Orion Compact Ridge, and discuss the chemical origin of specific species. An east–west velocity gradient is seen in W3(H{sub 2}O), and the extension is consistent with the bipolar outflow orientation traced by water masers and radio jets. A north–south velocity gradient across W3(OH) is also observed. However, with current observations we cannot be assured whether the velocity gradients are caused by rotation, outflow, or radial velocity differences of the sub-components of W3(OH)

  6. Differential but competitive binding of Nogo protein and class i major histocompatibility complex (MHCI) to the PIR-B ectodomain provides an inhibition of cells.

    PubMed

    Matsushita, Haruka; Endo, Shota; Kobayashi, Eiji; Sakamoto, Yuzuru; Kobayashi, Keisuke; Kitaguchi, Kohji; Kuroki, Kimiko; Söderhäll, Arvid; Maenaka, Katsumi; Nakamura, Akira; Strittmatter, Stephen M; Takai, Toshiyuki

    2011-07-22

    Binding of class I MHC molecules (MHCI) to an inhibitory receptor, PIR-B, expressed on B cells and myeloid cells provides constitutive cellular inhibition, thus ensuring peripheral tolerance. Recent unexpected findings pointed to a novel inhibitory role of PIR-B in neurite regeneration through binding to three axonal outgrowth inhibitors of myelin, including Nogo. Thus, it becomes interesting to determine whether the actions of the inhibitory myelin proteins and MHCI could coexist independently or be mutually exclusive as to the PIR-B-mediated immune and neural cell inhibition. Here, we present data supporting the competition of Nogo- and MHCI-mediated inhibition where they coexist. Kinetic analyses of Nogo and MHCI binding to the whole or a part of the recombinant PIR-B ectodomain revealed that PIR-B binds with higher affinity to Nogo than MHCI and that the MHCI binding only occurred with the N-terminal domains of PIR-B, whereas Nogo binding occurred with either the N- or C-terminal ectodomains. Importantly, kinetic tests indicated that the binding to PIR-B of Nogo and MHCI was competitive. Both endogenous and exogenous Nogo intensified the PIR-B-mediated suppression of interleukin-6 release from lipopolysaccharide-stimulated wild-type, but not PIR-B-deficient, cultured mast cells, indicating that PIR-B mediates Nogo-induced inhibition. Thus, we propose a novel mechanism by which PIR-B-mediated regulation is achieved differentially but competitively via MHCI and Nogo in cells of the immune system.

  7. Lack of CAK complex accumulation at DNA damage sites in XP-B and XP-B/CS fibroblasts reveals differential regulation of CAK anchoring to core TFIIH by XPB and XPD helicases during nucleotide excision repair

    PubMed Central

    Zhu, Qianzheng; Wani, Gulzar; Sharma, Nidhi; Wani, Altaf

    2012-01-01

    Transcription factor II H (TFIIH) is composed of core TFIIH and Cdk-activating kinase (CAK) complexes. Besides transcription, TFIIH also participates in nucleotide excision repair (NER), verifying DNA lesions through its helicase components XPB and XPD. The assembly state of TFIIH is known to be affected by truncation mutations in Xeroderma pigmentosum group G/Cockayne syndrome (XP-G/CS). Here, we showed that CAK component MAT1 was rapidly recruited to UV-induced DNA damage sites, co-localizing with core TFIIH component p62, and dispersed from the damage sites upon completion of DNA repair. While the core TFIIH-CAK association remained intact, MAT1 failed to accumulate at DNA damage sites in fibroblasts harboring XP-B or XP-B/CS mutations. Nevertheless, MAT1, XPD and XPC as well as XPG were able to accumulate at damage sites in XP-D fibroblasts, in which the core TFIIH-CAK association also remained intact. Interestingly, XPG recruitment was impaired in XP-B/CS fibroblasts derived from patients with mild phenotype, but persisted in XP-B/CS fibroblasts from severely affected patients resulting in a nonfunctional preincision complex. An examination of steady-state levels of RNA polymerase II (RNAPII) indicated that UV-induced RNAPII phosphorylation was dramatically reduced in XP-B/CS fibroblasts. These results demonstrated that the CAK rapidly disassociates from the core TFIIH upon assembly of nonfunctional preincision complex in XP-B and XP-B/CS cells. The persistency of nonfunctional preincision complex correlates with the severity exhibited by XP-B patients. The results suggest that XPB and XPD helicases differentially regulate the anchoring of CAK to core TFIIH during damage verification step of NER. PMID:23083890

  8. Performance analysis of low-complexity adaptive frequency-domain equalization and MIMO signal processing for compensation of differential mode group delay in mode-division multiplexing communication systems using few-mode fibers

    NASA Astrophysics Data System (ADS)

    Weng, Yi; He, Xuan; Pan, Zhongqi

    2016-02-01

    Mode-division multiplexing (MDM) transmission systems utilizing few-mode fibers (FMF) have been intensively explored to sustain continuous traffic growth. The key challenges of MDM systems are inter-modal crosstalk due to random mode coupling (RMC), and largely-accumulated differential mode group delay (DMGD), whilst hinders mode-demultiplexer implementation. The adaptive multi-input multi-output (MIMO) frequency-domain equalization (FDE) can dynamically compensate DMGD using digital signal processing (DSP) algorithms. The frequency-domain least-mean squares (FD-LMS) algorithm has been universally adopted for high-speed MDM communications, mainly for its relatively low computational complexity. However, longer training sequence is appended for FD-LMS to achieve faster convergence, which incurs prohibitively higher system overhead and reduces overall throughput. In this paper, we propose a fast-convergent single-stage adaptive frequency-domain recursive least-squares (FD-RLS) algorithm with reduced complexity for DMGD compensation at MDM coherent receivers. The performance and complexity comparison of FD-RLS, with signal-PSD-dependent FD-LMS method and conventional FD-LMS approach, are performed in a 3000 km six-mode transmission system with 65 ps/km DMGD. We explore the convergence speed of three adaptive algorithms, including the normalized mean-square-error (NMSE) per fast Fourier transform (FFT) block at 14-30 dB OSNR. The fast convergence of FD-RLS is exploited at the expense of slightly-increased necessary tap numbers for MIMO equalizers, and it can partially save the overhead of training sequence. Furthermore, we demonstrate adaptive FD-RLS can also be used for chromatic dispersion (CD) compensation without increasing the filter tap length, thus prominently reducing the DSP implementation complexity for MDM systems.

  9. Differential activation of brain regions involved with error-feedback and imitation based motor simulation when observing self and an expert's actions in pilots and non-pilots on a complex glider landing task.

    PubMed

    Callan, Daniel E; Terzibas, Cengiz; Cassel, Daniel B; Callan, Akiko; Kawato, Mitsuo; Sato, Masa-Aki

    2013-05-15

    In this fMRI study we investigate neural processes related to the action observation network using a complex perceptual-motor task in pilots and non-pilots. The task involved landing a glider (using aileron, elevator, rudder, and dive brake) as close to a target as possible, passively observing a replay of one's own previous trial, passively observing a replay of an expert's trial, and a baseline do nothing condition. The objective of this study is to investigate two types of motor simulation processes used during observation of action: imitation based motor simulation and error-feedback based motor simulation. It has been proposed that the computational neurocircuitry of the cortex is well suited for unsupervised imitation based learning, whereas, the cerebellum is well suited for error-feedback based learning. Consistent with predictions, pilots (to a greater extent than non-pilots) showed significant differential activity when observing an expert landing the glider in brain regions involved with imitation based motor simulation (including premotor cortex PMC, inferior frontal gyrus IFG, anterior insula, parietal cortex, superior temporal gyrus, and middle temporal MT area) than when observing one's own previous trial which showed significant differential activity in the cerebellum (only for pilots) thought to be concerned with error-feedback based motor simulation. While there was some differential brain activity for pilots in regions involved with both Execution and Observation of the flying task (potential Mirror System sites including IFG, PMC, superior parietal lobule) the majority was adjacent to these areas (Observation Only Sites) (predominantly in PMC, IFG, and inferior parietal loblule). These regions showing greater activity for observation than for action may be involved with processes related to motor-based representational transforms that are not necessary when actually carrying out the task. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. Knockout of the gamma subunit of the AP-1 adaptor complex in the human parasite Trypanosoma cruzi impairs infectivity and differentiation and prevents the maturation and targeting of the major protease cruzipain.

    PubMed

    Moreira, Claudia Maria do Nascimento; Batista, Cassiano Martin; Fernandes, Jessica Chimenes; Kessler, Rafael Luis; Soares, Maurilio José; Fragoso, Stenio Perdigão

    2017-01-01

    The AP-1 Adaptor Complex assists clathrin-coated vesicle assembly in the trans-Golgi network (TGN) of eukaryotic cells. However, the role of AP-1 in the protozoan Trypanosoma cruzi-the Chagas disease parasite-has not been addressed. Here, we studied the function and localization of AP-1 in different T. cruzi life cycle forms, by generating a gene knockout of the large AP-1 subunit gamma adaptin (TcAP1-γ), and raising a monoclonal antibody against TcAP1-γ. Co-localization with a Golgi marker and with the clathrin light chain showed that TcAP1-γ is located in the Golgi, and it may interact with clathrin in vivo, at the TGN. Epimastigote (insect form) parasites lacking TcAP1-γ (TcγKO) have reduced proliferation and differentiation into infective metacyclic trypomastigotes (compared with wild-type parasites). TcγKO parasites have also displayed significantly reduced infectivity towards mammalian cells. Importantly, TcAP1-γ knockout impaired maturation and transport to lysosome-related organelles (reservosomes) of a key cargo-the major cysteine protease cruzipain, which is important for parasite nutrition, differentiation and infection. In conclusion, the defective processing and transport of cruzipain upon AP-1 ablation may underlie the phenotype of TcγKO parasites.

  11. Establishment of in vitro culture system for evaluating dentin-pulp complex regeneration with special reference to the differentiation capacity of BrdU label-retaining dental pulp cells.

    PubMed

    Ida-Yonemochi, Hiroko; Nakatomi, Mitsushiro; Ohshima, Hayato

    2014-09-01

    We have proposed the new hypothesis that dental pulp stem cells play crucial roles in the pulpal healing process following exogenous stimuli in cooperation with progenitors. This study aimed to establish an in vitro culture system for evaluating dentin-pulp complex regeneration with special reference to the differentiation capacity of slow-cycling long-term label-retaining cells (LRCs). Three intraperitoneal injections of BrdU were given to pregnant ICR mice to map LRCs in the mature tissues of born animals. The upper bilateral first molars of 3-week-old mice were extracted and divided into two pieces and cultured for 0, 1, 3, 5 and 7 days using the Trowel's method. We succeeded in establishing an in vitro culture system for evaluating dentin-pulp complex regeneration, where most odontoblasts were occasionally degenerated and lost nestin immunoreactivity because of the separation of cell bodies from cellular processes in the dentin matrix by the beginning of in vitro culture. Numerous dense LRCs mainly resided in the center of the dental pulp associating with blood vessels throughout the experimental periods. On postoperative days 1-3, the periphery of the pulp tissue including the odontoblast layer showed degenerative features. By Day 7, nestin-positive odontoblast-like cells were arranged along the pulp-dentin border and dense LRCs were committed in the odontoblast-like cells. These results suggest that dense LRCs in the center of the dental pulp associating with blood vessels were supposed to be dental pulp stem/progenitor cells possessing regenerative capacity for forming newly differentiated odontoblast-like cells.

  12. Differentiation of the gene clusters encoding botulinum neurotoxin type A complexes in Clostridium botulinum type A, Ab, and A(B) strains.

    PubMed

    Franciosa, Giovanna; Floridi, Francesca; Maugliani, Antonella; Aureli, Paolo

    2004-12-01

    We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of Clostridium botulinum types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the ha33 and/or p47 genes with those of boNT/A PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two C. botulinum type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for C. botulinum type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the boNT/A gene clusters obtained.

  13. Differentiation of the Gene Clusters Encoding Botulinum Neurotoxin Type A Complexes in Clostridium botulinum Type A, Ab, and A(B) Strains

    PubMed Central

    Franciosa, Giovanna; Floridi, Francesca; Maugliani, Antonella; Aureli, Paolo

    2004-01-01

    We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of Clostridium botulinum types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the ha33 and/or p47 genes with those of boNT/A PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two C. botulinum type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for C. botulinum type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the boNT/A gene clusters obtained. PMID:15574917

  14. Differentiation of pulmonary bacterial pathogens in cystic fibrosis by volatile metabolites emitted by their in vitro cultures: Pseudomonas aeruginosa, Staphylococcus aureus, Stenotrophomonas maltophilia and the Burkholderia cepacia complex.

    PubMed

    Dryahina, Kseniya; Sovová, Kristýna; Nemec, Alexandr; Španěl, Patrik

    2016-08-10

    As a contribution to the continuing search for breath biomarkers of lung and airways infection in patients with cystic fibrosis, CF, we have analysed the volatile metabolites released in vitro by Pseudomonas aeruginosa and other bacteria involved in respiratory infections in these patients, i.e. those belonging to the Burkholderia cepacia complex, Staphylococcus aureus or Stenotrophomonas maltophilia. These opportunistic pathogens are generally harmless to healthy people but they may cause serious infections in patients with severe underlying disease or impaired immunity such as CF patients. Volatile organic compounds emitted from the cultures of strains belonging to the above-mentioned four taxa were analysed by selected ion flow tube mass spectrometry. In order to minimize the effect of differences in media composition all strains were cultured in three different liquid media. Multivariate statistical analysis reveals that the four taxa can be well discriminated by the differences in the headspace VOC concentration profiles. The compounds that should be targeted in breath as potential biomarkers of airway infection were identified for each of these taxa of CF pathogens.

  15. SDF2L1, a Component of the Endoplasmic Reticulum Chaperone Complex, Differentially Interacts with α-, β-, and θ-Defensin Propeptides*S⃞

    PubMed Central

    Tongaonkar, Prasad; Selsted, Michael E.

    2009-01-01

    Mammalian defensins are cationic antimicrobial peptides that play a central role in host innate immunity and as regulators of acquired immunity. In animals, three structural defensin subfamilies, designated as α, β, and θ, have been characterized, each possessing a distinctive tridisulfide motif. Mature α- and β-defensins are produced by simple proteolytic processing of their prepropeptide precursors. In contrast, the macrocyclic θ-defensins are formed by the head-to-tail splicing of nonapeptides excised from a pair of prepropeptide precursors. Thus, elucidation of the θ-defensin biosynthetic pathway provides an opportunity to identify novel factors involved in this unique process. We incorporated the θ-defensin precursor, proRTD1a, into a bait construct for a yeast two-hybrid screen that identified rhesus macaque stromal cell-derived factor 2-like protein 1 (SDF2L1), as an interactor. SDF2L1 is a component of the endoplasmic reticulum (ER) chaperone complex, which we found to also interact with α- and β-defensins. However, analysis of the SDF2L1 domain requirements for binding of representative α-, β-, and θ-defensins revealed that α- and β-defensins bind SDF2L1 similarly, but differently from the interactions that mediate binding of SDF2L1 to pro-θ-defensins. Thus, SDF2L1 is a factor involved in processing and/or sorting of all three defensin subfamilies. PMID:19109254

  16. Energy transfer efficiency based on one-and two-photon FRET microscopy differentiates between clustered and random distribution of membrane-bound receptor-ligand complexes

    NASA Astrophysics Data System (ADS)

    Wallrabe, Horst; Elangovan, Masilamani; Burchard, Almut; Barroso, Margarida

    2002-06-01

    We are investigating membrane-based sorting processes in polarized epithelial MDCK cells, which most likely involves membrane microdomains. We have postulated that proteins contained in these microdomains, cluster, and to prove this, we have internalized differently fluorophore labeled pIgA-R ligands in MDCK cells, stably transfected with polymeric IgA receptors (pIgA-R), from opposite plasma membranes. Our previous work showed that these receptor-ligand complexes colocalize in the apical recycling endosome (ARE), underneath the apical plasma membrane. Quantitative one-photon confocal and 2-photon (2-P) FRET microscopy allowed us to calculate energy transfer efficiency (E%). Unquenched donor levels where established based on a novel algorithm, which corrects the FRET contamination of acceptor bleed-through and donor crosstalk. Using different emission filters also confirmed the veracity of the algorithm. 2-P FRET allows the selection of a specific donor wavelength, which does not precipitate acceptor bleed-through, a clear advantage over 1-P confocal microscopy. Results show that E% is independent of acceptor levels, an indication of a clustered distribution, as in random distribution E% rises with increasing acceptor levels. However, E% decreases with increasing donor and donor:acceptor ratio levels, which we have termed 'donor geometric exclusion', where some donors in a cluster block others from interacting with an acceptor. We submit that this is a second indicator for a clustered pattern, because in a random, dispersed situation donors are not likely to be in close proximity to have such an effect. We have developed a model explaining this phenomenon.

  17. Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability.

    PubMed

    Derycke, S; De Meester, N; Rigaux, A; Creer, S; Bik, H; Thomas, W K; Moens, T

    2016-05-01

    Differences in resource use or in tolerances to abiotic conditions are often invoked as potential mechanisms underlying the sympatric distribution of cryptic species. Additionally, the microbiome can provide physiological adaptations of the host to environmental conditions. We determined the intra- and interspecific variability of the microbiomes of three cryptic nematode species of the Litoditis marina species complex that co-occur, but show differences in abiotic tolerances. Roche 454 pyrosequencing of the microbial 16S rRNA gene revealed distinct bacterial communities characterized by a substantial diversity (85-513 OTUs) and many rare OTUs. The core microbiome of each species contained only very few OTUs (2-6), and four OTUs were identified as potentially generating tolerance to abiotic conditions. A controlled experiment in which nematodes from two cryptic species (Pm1 and Pm3) were fed with either an E. coli suspension or a bacterial mix was performed, and the 16S rRNA gene was sequenced using the MiSeq technology. OTU richness was 10-fold higher compared to the 454 data set and ranged between 1118 and 7864. This experiment confirmed the existence of species-specific microbiomes, a core microbiome with few OTUs, and high interindividual variability. The offered food source affected the bacterial community and illustrated different feeding behaviour between the cryptic species, with Pm3 exhibiting a higher degree of selective feeding than Pm1. Morphologically similar species belonging to the same feeding guild (bacterivores) can thus have substantial differences in their associated microbiomes and feeding strategy, which in turn may have important ramifications for biodiversity-ecosystem functioning relationships. © 2016 John Wiley & Sons Ltd.

  18. Differential expression and localization of glycosidic residues in in vitro- and in vivo-matured cumulus-oocyte complexes in equine and porcine species.

    PubMed

    Accogli, Gianluca; Douet, Cécile; Ambruosi, Barbara; Martino, Nicola Antonio; Uranio, Manuel Filioli; Deleuze, Stefan; Dell'Aquila, Maria Elena; Desantis, Salvatore; Goudet, Ghylène

    2014-12-01

    Glycoprotein oligosaccharides play major roles during reproduction, yet their function in gamete interactions is not fully elucidated. Identification and comparison of the glycan pattern in cumulus-oocyte complexes (COCs) from species with different efficiencies of in vitro spermatozoa penetration through the zona pellucida (ZP) could help clarify how oligosaccharides affect gamete interactions. We compared the expression and localization of 12 glycosidic residues in equine and porcine in vitro-matured (IVM) and preovulatory COCs by means of lectin histochemistry. The COCs glycan pattern differed between animals and COC source (IVM versus preovulatory). Among the 12 carbohydrate residues investigated, the IVM COCs from these two species shared: (a) sialo- and βN-acetylgalactosamine (GalNAc)-terminating glycans in the ZP; (b) sialylated and fucosylated glycans in cumulus cells; and (c) GalNAc and N-acetylglucosamine (GlcNAc) glycans in the ooplasm. Differences in the preovulatory COCs of the two species included: (a) sialoglycans and GlcNAc terminating glycans in the equine ZP versus terminal GalNAc and internal GlcNAc in the porcine ZP; (b) terminal galactosides in equine cumulus cells versus terminal GlcNAc and fucose in porcine cohorts; and (c) fucose in the mare ooplasm versus lactosamine and internal GlcNAc in porcine oocyte cytoplasm. Furthermore, equine and porcine cumulus cells and oocytes contributed differently to the synthesis of ZP glycoproteins. These results could be attributed to the different in vitro fertilization efficiencies between these two divergent, large-animal models. © 2014 Wiley Periodicals, Inc.

  19. Differential Gene Expression and Protein Phosphorylation as Factors Regulating the State of the Arabidopsis SNX1 Protein Complexes in Response to Environmental Stimuli

    PubMed Central

    Brumbarova, Tzvetina; Ivanov, Rumen

    2016-01-01

    Endosomal recycling of plasma membrane proteins contributes significantly to the regulation of cellular transport and signaling processes. Members of the Arabidopsis (Arabidopsis thaliana) SORTING NEXIN (SNX) protein family were shown to mediate the endosomal retrieval of transporter proteins in response to external challenges. Our aim is to understand the possible ways through which external stimuli influence the activity of SNX1 in the root. Several proteins are known to contribute to the function of SNX1 through direct protein–protein interaction. We, therefore, compiled a list of all Arabidopsis proteins known to physically interact with SNX1 and employed available gene expression and proteomic data for a comprehensive analysis of the transcriptional and post-transcriptional regulation of this interactome. The genes encoding SNX1-interaction partners showed distinct expression patterns with some, like FAB1A, being uniformly expressed, while others, like MC9 and BLOS1, were expressed in specific root zones and cell types. Under stress conditions known to induce SNX1-dependent responses, two genes encoding SNX1-interacting proteins, MC9 and NHX6, showed major gene-expression variations. We could also observe zone-specific transcriptional changes of SNX1 under iron deficiency, which are consistent with the described role of the SNX1 protein. This suggests that the composition of potential SNX1-containing protein complexes in roots is cell-specific and may be readjusted in response to external stimuli. On the level of post-transcriptional modifications, we observed stress-dependent changes in the phosphorylation status of SNX1, FAB1A, and CLASP. Interestingly, the phosphorylation events affecting SNX1 interactors occur in a pattern which is largely complementary to transcriptional regulation. Our analysis shows that transcriptional and post-transcriptional regulation play distinct roles in SNX1-mediated endosomal recycling under external stress. PMID:27725825

  20. Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles.

    PubMed

    Yao, Yong-Fang; Dai, Qiu-Xia; Li, Jing; Ni, Qing-Yong; Zhang, Ming-Wang; Xu, Huai-Liang

    2014-06-14

    Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even with a low level of neutral variability in some species. However, in small and isolated or bottlenecked populations, balancing selection may be overwhelmed by genetic drift. To estimate microevolutionary forces acting on the isolated rhesus macaque populations, we examined genetic variation at Mhc-DQB1 loci in 119 wild rhesus macaques from five geographically isolated populations in western Sichuan, China, and compared the levels of MHC variation and differentiation among populations with that previously observed at neutral microsatellite markers. 23 Mamu-DQB1 alleles were identified in 119 rhesus macaques in western Sichuan, China. These macaques exhibited relatively high levels of genetic diversity at Mamu-DQB1. The Hanyuan population presented the highest genetic variation, whereas the Heishui population was the lowest. Analysis of molecular variance (AMOVA) and pairwise FST values showed moderate genetic differentiation occurring among the five populations at the Mhc-DQB1 locus. Non-synonymous substitutions occurred at a higher frequency than synonymous substitutions in the peptide binding region. Levels of MHC variation within rhesus macaque populations are concordant with microsatellite variation. On the phylogenetic tree for the rhesus and crab-eating macaques, extensive allele or allelic lineage sharing is observed between the two species. Phylogenetic analyses confirm the apparent trans-species model of evolution of the Mhc-DQB1 genes in these macaques. Balancing selection plays an

  1. Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles

    PubMed Central

    2014-01-01

    Abstracts Background Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even with a low level of neutral variability in some species. However, in small and isolated or bottlenecked populations, balancing selection may be overwhelmed by genetic drift. To estimate microevolutionary forces acting on the isolated rhesus macaque populations, we examined genetic variation at Mhc-DQB1 loci in 119 wild rhesus macaques from five geographically isolated populations in western Sichuan, China, and compared the levels of MHC variation and differentiation among populations with that previously observed at neutral microsatellite markers. Results 23 Mamu-DQB1 alleles were identified in 119 rhesus macaques in western Sichuan, China. These macaques exhibited relatively high levels of genetic diversity at Mamu-DQB1. The Hanyuan population presented the highest genetic variation, whereas the Heishui population was the lowest. Analysis of molecular variance (AMOVA) and pairwise FST values showed moderate genetic differentiation occurring among the five populations at the Mhc-DQB1 locus. Non-synonymous substitutions occurred at a higher frequency than synonymous substitutions in the peptide binding region. Levels of MHC variation within rhesus macaque populations are concordant with microsatellite variation. On the phylogenetic tree for the rhesus and crab-eating macaques, extensive allele or allelic lineage sharing is observed betweenthe two species. Conclusions Phylogenetic analyses confirm the apparent trans-species model of evolution of the Mhc-DQB1 genes in these

  2. Trace Fear Conditioning Differentially Modulates Intrinsic Excitability of Medial Prefrontal Cortex-Basolateral Complex of Amygdala Projection Neurons in Infralimbic and Prelimbic Cortices.

    PubMed

    Song, Chenghui; Ehlers, Vanessa L; Moyer, James R

    2015-09-30

    Neuronal activity in medial prefrontal cortex (mPFC) is critical for the formation of trace fear memory, yet the cellular mechanisms underlying these memories remain unclear. One possibility involves the modulation of intrinsic excitability within mPFC neurons that project to the basolateral complex of amygdala (BLA). The current study used a combination of retrograde labeling and in vitro whole-cell patch-clamp recordings to examine the effect of trace fear conditioning on the intrinsic excitability of layer 5 mPFC-BLA projection neurons in adult rats. Trace fear conditioning significantly enhanced the intrinsic excitability of regular spiking infralimbic (IL) projection neurons, as evidenced by an increase in the number of action potentials after current injection. These changes were also associated with a reduction in spike threshold and an increase in h current. In contrast, trace fear conditioning reduced the excitability of regular spiking prelimbic (PL) projection neurons, through a learning-related decrease of input resistance. Interestingly, the amount of conditioned freezing was (1) positively correlated with excitability of IL-BLA projection neurons after conditioning and (2) negatively correlated with excitability of PL-BLA projection neurons after extinction. Trace fear conditioning also significantly enhanced the excitability of burst spiking PL-BLA projection neurons. In both regions, conditioning-induced plasticity was learning specific (observed in conditioned but not in pseudoconditioned rats), flexible (reversed by extinction), and transient (lasted <10 d). Together, these data suggest that intrinsic plasticity within mPFC-BLA projection neurons occurs in a subregion- and cell-type-specific manner during acquisition, consolidation, and extinction of trace fear conditioning. Significance statement: Frontal lobe-related function is vital for a variety of important behaviors, some of which decline during aging. This study involves a novel

  3. Trace Fear Conditioning Differentially Modulates Intrinsic Excitability of Medial Prefrontal Cortex–Basolateral Complex of Amygdala Projection Neurons in Infralimbic and Prelimbic Cortices

    PubMed Central

    Song, Chenghui; Ehlers, Vanessa L.

    2015-01-01

    Neuronal activity in medial prefrontal cortex (mPFC) is critical for the formation of trace fear memory, yet the cellular mechanisms underlying these memories remain unclear. One possibility involves the modulation of intrinsic excitability within mPFC neurons that project to the basolateral complex of amygdala (BLA). The current study used a combination of retrograde labeling and in vitro whole-cell patch-clamp recordings to examine the effect of trace fear conditioning on the intrinsic excitability of layer 5 mPFC–BLA projection neurons in adult rats. Trace fear conditioning significantly enhanced the intrinsic excitability of regular spiking infralimbic (IL) projection neurons, as evidenced by an increase in the number of action potentials after current injection. These changes were also associated with a reduction in spike threshold and an increase in h current. In contrast, trace fear conditioning reduced the excitability of regular spiking prelimbic (PL) projection neurons, through a learning-related decrease of input resistance. Interestingly, the amount of conditioned freezing was (1) positively correlated with excitability of IL-BLA projection neurons after conditioning and (2) negatively correlated with excitability of PL-BLA projection neurons after extinction. Trace fear conditioning also significantly enhanced the excitability of burst spiking PL-BLA projection neurons. In both regions, conditioning-induced plasticity was learning specific (observed in conditioned but not in pseudoconditioned rats), flexible (reversed by extinction), and transient (lasted <10 d). Together, these data suggest that intrinsic plasticity within mPFC–BLA projection neurons occurs in a subregion- and cell-type-specific manner during acquisition, consolidation, and extinction of trace fear conditioning. SIGNIFICANCE STATEMENT Frontal lobe-related function is vital for a variety of important behaviors, some of which decline during aging. This study involves a novel

  4. Heterogenous graft rejection pathways in class I major histocompatibility complex-disparate combinations and their differential susceptibility to immunomodulation induced by intravenous presensitization with relevant alloantigens

    PubMed Central

    1991-01-01

    The present study investigates the heterogeneity of graft rejection pathways in class I major histocompatibility complex (MHC)-disparate combinations and the susceptibility of each pathway to immunomodulation induced by intravenous presensitization with alloantigens. Depletion of CD8+ T cells was induced by repeated administration of anti-CD8 monoclonal antibody. CD8+ T cell-depleted mice failed to generate anti- allo class I MHC cytotoxic T cell (CTL) responses but exhibited anti- allo class I MHC T cell responses, such as mixed lymphocyte reaction (MLR)/IL-2 production, that were induced by CD4+ T cells. In contrast, donor-specific intravenous presensitization (DSP), as a model of donor- specific transfusion, induced almost complete elimination of CD4+ and CD8+ T cell-mediated MLR/IL-2 production, whereas this regimen did not affect the generation of CTL responses induced by DSP-resistant elements (CD8+ CTL precursors and CD4+ CTL helpers). Prolongation of skin graft survival was not induced by either of the above two regimens alone, but by the combination of these. Prolonged graft survival was obtained irrespective of whether the administration of anti-CD8 antibody capable of eliminating CTL was started before or after DSP. The combination of DSP with injection of anti-CD4 antibody also effectively prolonged graft survival. However, this was the case only when the injection of antibody was started before DSP, because such antibody administration was capable of inhibiting the generation of CTL responses by eliminating DSP-resistant CD4+ CTL helpers. These results indicate that (a) the graft rejection in class I-disparate combinations is induced by CD8+ CTL-involved and -independent pathways that are resistant and susceptible to DSP, respectively; (b) DSP contributes to, but is not sufficient for, the prolongation of graft survival; and (c) the suppression of graft rejection requires an additional treatment for reducing DSP-resistant CTL responses. The results are

  5. The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA

    PubMed Central

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2016-01-01

    Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, andCandida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories. PMID:27074256

  6. Parp2 is required for the differentiation of post-meiotic germ cells: Identification of a spermatid-specific complex containing Parp1, Parp2, TP2 and HSPA2

    SciTech Connect

    Quenet, Delphine; Mark, Manuel; Govin, Jerome; Dorsselear, A. van; Schreiber, Valerie; Khochbin, Saadi; Dantzer, Francoise

    2009-10-01

    Spermiogenesis is a complex male germ cell post-meiotic differentiation process characterized by dramatic changes in chromatin structure and function, including chromatin condensation, transcriptional inhibition and the sequential replacement of histones by transition proteins and protamines. Recent advances, in mammalian cells, suggest a possible role of poly(ADP-ribosyl)ation catalyzed by Parp1 and/or Parp2 in this process. We have recently reported severely compromised spermiogenesis in Parp2-deficient mice characterized by a marked delay in nuclear elongation whose molecular mechanisms remain however unknown. Here, using in vitro protein-protein interaction assays, we show that Parp2 interacts significantly with both the transition protein TP2 and the transition chaperone HSPA2, whereas Parp1 binds weakly to HSPA2. Parp2-TP2 interaction is partly mediated by poly(ADP-ribosyl)ation. Only Parp1 poly(ADP-ribosyl)ates HSPA2. In addition, a detailed analysis of spermatid maturation in Parp2-deficient mice, combining immunohistochemistry and electron microscopic approaches, reveals a loss of spermatids expressing TP2, a defect in chromatin condensation and abnormal formation of the manchette microtubules that, together, contribute to spermatid-specific cell death. In conclusion, we propose both Parps as new participants of a spermatid-specific protein complex involved in genome reorganization throughout spermiogenesis.

  7. Membrane-bound versus soluble major histocompatibility complex Class I-related chain A and major histocompatibility complex Class I-related chain B differential expression: Mechanisms of tumor eradication versus evasion and current drug development strategies.

    PubMed

    Suresh, P K

    2016-01-01

    Major histocompatibility complex Class I-related chain A/chain B (MICA/MICB) is stress-inducible, highly polymorphic ligands whose expression at the transcript level has been detected in all tissues except the central nervous system. However, their restricted protein expression is due to their regulation at the posttranslational level. Its levels are elevated in virally infected and neoplastically transformed cells. Membrane expression of this NKG2DL marks the aberrant cells for elimination by those immune effector cells that express the cognate NKG2D receptor. Among the evasion strategies developed by tumors, the metalloprotease-dependent shedding of MICA/MICB from tumors (either the free or the exosome form) can contribute to the inhibition of cytolysis by the immune effector cells (all NK cells, most NKT cells; γδ CD8+ T cells and αβ CD8+ T cells, as well as some αβ CD4+ T cells). There are micro-RNA clusters that regulate surface expression and shedding. Polymorphic variants can be used as susceptibility/associative markers and can also possibly be used to correlate with tumor survival as well as staging/grading of tumors. Variations in the expression level require quantification of this marker for diagnostic/prognostic and therapeutic purposes. Mechanism-based studies would provide a better tumor-specific understanding of their relative roles in the processes of tumor cell elimination versus growth and progression. Last but not least, conventional, interlaboratory validated assays (for, e.g., antibody-based methods) should be replaced by robust, reproducible, feasible biophysics-based methods using tumor biopsies. Further, correlative DNA polymorphism-based studies can be done using biological fluids (for, e.g., human saliva) that can be sampled by minimally invasive means.

  8. Amplicon DNA melting analysis for the simultaneous detection of Brucella spp and Mycobacterium tuberculosis complex. Potential use in rapid differential diagnosis between extrapulmonary tuberculosis and focal complications of brucellosis.

    PubMed

    Sanjuan-Jimenez, Rocio; Colmenero, Juan D; Bermúdez, Pilar; Alonso, Antonio; Morata, Pilar

    2013-01-01

    Some sites of extrapulmonary tuberculosis and focal complications of brucellosis are very difficult to differentiate clinically, radiologically, and even histopathologically. Conventional microbiological methods for the diagnosis of extrapulmonary tuberculosis and complicated brucellosis not only lack adequate sensitivity, they are also time consuming, which could lead to an unfavourable prognosis. The aim of this work was to develop a multiplex real-time PCR assay based on SYBR Green I to simultaneously detect Brucella spp and Mycobacterium tuberculosis complex and evaluate the efficacy of the technique with different candidate genes. The IS711, bcsp31 and omp2a genes were used for the identification of Brucella spp and the IS6110, senX3-regX3 and cfp31 genes were targeted for the detection of the M. tuberculosis complex. As a result of the different combinations of primers, nine different reactions were evaluated. A test was defined as positive only when the gene combinations were capable of co-amplifying both pathogens in a single reaction tube and showed distinguishable melting temperatures for each microorganism. According to the melting analysis, only three combinations of amplicons (senX3-regX3+bcsp31, senX3-regX3+IS711 and IS6110+IS711) were visible. Detection limits of senX3-regX3+bcsp31 and senX3-regX3+IS711 were of 2 and 3 genome equivalents for M. tuberculosis complex and Brucella while for IS6110+IS711 they were of 200 and 300 genome equivalents, respectively. The three assays correctly identified all the samples, showing negative results for the control patients. The presence of multicopy elements and GC content were the components most influencing the efficiency of the test; this should be taken into account when designing a multiplex-based SYBR Green I assay. In conclusion, multiplex real time PCR assays based on the targets senX3-regX3+bcsp31 and senX3-regX3+IS711 using SYBR Green I are highly sensitive and reproducible. This may therefore be a

  9. Mo-mineralized porphyries are relatively hydrous and differentiated: insights from the Permian-Triassic granitic complex in the Baituyingzi Mo-Cu district, eastern Inner Mongolia, NE China

    NASA Astrophysics Data System (ADS)

    Sun, Yan; Liu, Jianming; Zeng, Qingdong; Wang, Jingbin; Wang, Yuwang; Hu, Ruizhong; Zhou, Lingli; Wu, Guanbin

    2016-12-01

    Mo-Cu mineralization in the Baituyingzi district of eastern Inner Mongolia occurs within a granitic complex. This paper presents and discusses zircon U-Pb ages and whole-rock geochemical and Sr-Nd-Pb isotopic data from the granitic complex as potential indicators for porphyry Mo fertility. The U-Pb ages indicate that five units of the granitic complex were emplaced between 265.2 ± 0.7 and 246.5 ± 1.0 Ma. Constrained by crosscutting dikes, Mo-Cu mineralization was probably related to the Baituyingzi monzogranite porphyry dated at 248.2 ± 0.64 Ma. The intrusions belong to high-K calc-alkaline to shoshonitic series that are characterized by highly fractionated rare earth element (REE) patterns and strong enrichments of large ion lithophile elements, relative to high-field strength elements. Apart from the ˜246-Ma dike that shows negative ɛNd (t) values (-14.9 to -13.1), the intrusions have ɛNd(t) values ranging from -3.9 to 1.0, relatively young depleted mantle model ages (811 to 1183 Ma), 206Pb/204Pb of 18.137-18.335, and 207Pb/204Pb of 15.591-15.625, which are consistent with a juvenile lower crustal origin. Among the intrusions, the ˜248-Ma porphyry and the ˜246-Ma dike show adakite-like characteristics (e.g., Sr/Y = 44.9-185) and listric-shaped REE patterns that indicate amphibole fractionation and a hydrous magma source. However, the porphyry exhibits a higher differentiation index (81.4-91.5) and a steeper REE profile (e.g., LaN/YbN = 25.6-87.0) than those of the ˜246-Ma dike, which suggests that it is highly differentiated. We propose that the complex was generated by the partial melting of juvenile mafic lower crust (containing minor old crustal relicts) that was triggered by collision between the North China Craton and Siberian Craton. As indicated by the Th/Nb, Th/Yb, Ba/Th, and Ba/La ratios of the intrusions, the crust may have been derived from the melting of the fertile mantle wedge that was metasomatized by various amounts of slab-derived fluids

  10. Mo-mineralized porphyries are relatively hydrous and differentiated: insights from the Permian-Triassic granitic complex in the Baituyingzi Mo-Cu district, eastern Inner Mongolia, NE China

    NASA Astrophysics Data System (ADS)

    Sun, Yan; Liu, Jianming; Zeng, Qingdong; Wang, Jingbin; Wang, Yuwang; Hu, Ruizhong; Zhou, Lingli; Wu, Guanbin

    2017-08-01

    Mo-Cu mineralization in the Baituyingzi district of eastern Inner Mongolia occurs within a granitic complex. This paper presents and discusses zircon U-Pb ages and whole-rock geochemical and Sr-Nd-Pb isotopic data from the granitic complex as potential indicators for porphyry Mo fertility. The U-Pb ages indicate that five units of the granitic complex were emplaced between 265.2 ± 0.7 and 246.5 ± 1.0 Ma. Constrained by crosscutting dikes, Mo-Cu mineralization was probably related to the Baituyingzi monzogranite porphyry dated at 248.2 ± 0.64 Ma. The intrusions belong to high-K calc-alkaline to shoshonitic series that are characterized by highly fractionated rare earth element (REE) patterns and strong enrichments of large ion lithophile elements, relative to high-field strength elements. Apart from the ˜246-Ma dike that shows negative ɛNd ( t) values (-14.9 to -13.1), the intrusions have ɛNd( t) values ranging from -3.9 to 1.0, relatively young depleted mantle model ages (811 to 1183 Ma), 206Pb/204Pb of 18.137-18.335, and 207Pb/204Pb of 15.591-15.625, which are consistent with a juvenile lower crustal origin. Among the intrusions, the ˜248-Ma porphyry and the ˜246-Ma dike show adakite-like characteristics (e.g., Sr/Y = 44.9-185) and listric-shaped REE patterns that indicate amphibole fractionation and a hydrous magma source. However, the porphyry exhibits a higher differentiation index (81.4-91.5) and a steeper REE profile (e.g., LaN/YbN = 25.6-87.0) than those of the ˜246-Ma dike, which suggests that it is highly differentiated. We propose that the complex was generated by the partial melting of juvenile mafic lower crust (containing minor old crustal relicts) that was triggered by collision between the North China Craton and Siberian Craton. As indicated by the Th/Nb, Th/Yb, Ba/Th, and Ba/La ratios of the intrusions, the crust may have been derived from the melting of the fertile mantle wedge that was metasomatized by various amounts of slab

  11. Differential games.

    NASA Technical Reports Server (NTRS)

    Varaiya, P. P.

    1972-01-01

    General discussion of the theory of differential games with two players and zero sum. Games starting at a fixed initial state and ending at a fixed final time are analyzed. Strategies for the games are defined. The existence of saddle values and saddle points is considered. A stochastic version of a differential game is used to examine the synthesis problem.

  12. Differentiated Staffing.

    ERIC Educational Resources Information Center

    Allen, Dwight W.; Kline, Lloyd W.

    The traditional educational structure requires the teacher to be part bookkeeper, part clerical assistant, and part psychologist, among other roles, while his salary scale is based on length of service. Differentiated staffing offers ways of changing this pattern. The details of differentiated duties are largely a matter of local option and…

  13. Differentiating Knowledge, Differentiating (Occupational) Practice

    ERIC Educational Resources Information Center

    Hordern, Jim

    2016-01-01

    This paper extends arguments for differentiating knowledge into conceptualisations of occupational practice. It is argued that specialised forms of knowledge and practice require recognition and differentiation in ways that many contemporary approaches to practice theory deny. Drawing on Hager's interpretation of MacIntyre, it is suggested that…

  14. Differentiating Knowledge, Differentiating (Occupational) Practice

    ERIC Educational Resources Information Center

    Hordern, Jim

    2016-01-01

    This paper extends arguments for differentiating knowledge into conceptualisations of occupational practice. It is argued that specialised forms of knowledge and practice require recognition and differentiation in ways that many contemporary approaches to practice theory deny. Drawing on Hager's interpretation of MacIntyre, it is suggested that…

  15. Cognitive Complexity and Interest Crystallization.

    ERIC Educational Resources Information Center

    Winer, Dov; Gati, Itamar

    1986-01-01

    Investigated the relationship between cognitive differentiation and vocational interest crystallization. Results indicated the relationships between measures of cognitive differentiation were generally low, and that interest crystallization was related to between-construct differentiation, but not to the other measures of cognitive complexity.…

  16. Spherical-complex-optical-potential (SCOP) model for electron-monosilane (SiH4) collisions at 30-400 eV: Total (elastic+absorption), momentum transfer, and differential cross sections

    NASA Astrophysics Data System (ADS)

    Jain, Ashok

    1987-02-01

    We report nonempirical quantum mechanical calculations on the total (elastic+absorption), momentum transfer, and differential cross sections for e-SiH4 collisions at intermediate and high energies (30-400 eV). A parameter-free and energy-dependent spherical-complex-optical potential (SCOP) is evaluated for the e-SiH4 system. The real part of the SCOP consists of three local terms, namely static, exchange, and polarization. The static interaction is generated very accurately from near-Hartree-Fock one-center silane wave functions, while the exchange effects are accounted for in the free-electron-gas-exchange (FEGE) model. The polarization potential is evaluated ab initio in a parameter-free approximation of Jain and Thompson. The imaginary term of the total SCOP represents loss of flux due to inelastic channels via an energy-dependent absorption potential calculated from target electron density and short-range static-exchange force in the quasifree model with Pauli blocking [Staszewska et al.; J. Phys. B 16, L281 (1983)]. Two versions of this absorption potential are employed; one with an undistorted density and the other with a polarized density determined approximately from first order target wave functions. The later version is more successful when the final results are compared with experiment. The total SCOP is treated exactly in a partial-wave analysis using the variable-phase approach to yield complex phase shifts. Our final total cross sections compare very well with the only available measurements of Sueoka and Mori. However, below 50 eV, present total cross sections overestimate the experimental data within 10%. The effect of absorption potential is to reduce the elastic cross sections significantly; this reduction is more dramatic in case of the differential cross sections (DCS); for example, the reduced DCS are exposed to more pronounced structure. Interestingly, the e-SiH4 reduced DCS are very close in shape to the corresponding e-Ar cross sections

  17. DIFFERENTIAL ANALYZER

    DOEpatents

    Sorensen, E.G.; Gordon, C.M.

    1959-02-10

    Improvements in analog eomputing machines of the class capable of evaluating differential equations, commonly termed differential analyzers, are described. In general form, the analyzer embodies a plurality of basic computer mechanisms for performing integration, multiplication, and addition, and means for directing the result of any one operation to another computer mechanism performing a further operation. In the device, numerical quantities are represented by the rotation of shafts, or the electrical equivalent of shafts.

  18. Functional Differentiation of Antiporter-Like Polypeptides in Complex I; a Site-Directed Mutagenesis Study of Residues Conserved in MrpA and NuoL but Not in MrpD, NuoM, and NuoN

    PubMed Central

    Sperling, Eva; Górecki, Kamil; Drakenberg, Torbjörn

    2016-01-01

    It has long been known that the three largest subunits in the membrane domain (NuoL, NuoM and NuoN) of complex I are homologous to each other, as well as to two subunits (MrpA and MrpD) from a Na+/H+ antiporter, Mrp. MrpA and NuoL are more similar to each other and the same is true for MrpD and NuoN. This suggests a functional differentiation which was proven experimentally in a deletion strain model system, where NuoL could restore the loss of MrpA, but not that of MrpD and vice versa. The simplest explanation for these observations was that the MrpA and MrpD proteins are not antiporters, but rather single subunit ion channels that together form an antiporter. In this work our focus was on a set of amino acid residues in helix VIII, which are only conserved in NuoL and MrpA (but not in any of the other antiporter-like subunits.) and to compare their effect on the function of these two proteins. By combining complementation studies in B. subtilis and 23Na-NMR, response of mutants to high sodium levels were tested. All of the mutants were able to cope with high salt levels; however, all but one mutation (M258I/M225I) showed differences in the efficiency of cell growth and sodium efflux. Our findings showed that, although very similar in sequence, NuoL and MrpA seem to differ on the functional level. Nonetheless the studied mutations gave rise to interesting phenotypes which are of interest in complex I research. PMID:27391676

  19. The implementation of long-lasting insecticidal bed nets has differential effects on the genetic structure of the African malaria vectors in the Anopheles gambiae complex in Dielmo, Senegal.

    PubMed

    Sougoufara, Seynabou; Sokhna, Cheikh; Diagne, Nafissatou; Doucouré, Souleymane; Sembène, Pape MBacké; Harry, Myriam

    2017-08-15

    Mosquitoes belonging to the Anopheles gambiae complex are the main vectors of malaria in sub-Saharan Africa. Among these, An. gambiae, Anopheles coluzzii and Anopheles arabiensis are the most efficient vectors and are largely distributed in sympatric locations. However, these species present ecological and behavioural differences that impact their vectorial capacity and complicate vector-control efforts, mainly based on long-lasting insecticidal bed nets (LLINs) and indoor residual spraying (IRS). In this study, the genetic structure of these three species in a Senegalese village (Dielmo) was investigated using microsatellite data in samples collected in 2006 before implementation of LLINs, in 2008, when they were introduced, and in 2010, 2 years after the use of LLINs. In this study 611 individuals were included, namely 136 An. coluzzii, 101 An. gambiae, 6 An. coluzzii/An. gambiae hybrids and 368 An. arabiensis. According to the species, the effect of the implementation of LLINs in Dielmo is differentiated. Populations of the sister species An. coluzzii and An. gambiae regularly experienced bottleneck events, but without significant inbreeding. The Fst values suggested in 2006 a breakdown of assortative mating resulting in hybrids, but the introduction of LLINs was followed by a decrease in the number of hybrids. This suggests a decrease in mating success of hybrids, ecological maladaptation, or a lesser probability of mating between species due to a decrease in An. coluzzii population size. By contrast, the introduction of LLINs has favoured the sibling species An. arabiensis. In this study, some spatial and temporal structuration between An. arabiensis populations were detected, especially in 2008, and the higher genetic diversity observed could result from a diversifying selection. This work demonstrates the complexity of the malaria context and shows the need to study the genetic structure of Anopheles populations to evaluate the effectiveness of vector

  20. [Complex system of differentiated prediction of strokes].

    PubMed

    Semak, A E; Misiuk, N S; Adamovich, V I; Plotnikov, Iu V; Khomasuridze, D O

    1987-01-01

    On the basis of the data on 2287 patients with cerebral strokes (CS) and 800 individuals without this disease, and using discriminant and probability methods, the authors have identified 158 supposed risk factors (RF) of CS development. They have also established the specificity of RFs which depends on the nature of CS, as well as ascertained the dependence of informative value of these factors on the size of samples and the degree of percentage reflection by the main demographic indicators of the studied population. RFs are classified as controllable and uncontrollable. The authors have selected 50 risk factors with 2-5 gradations ranging from the normal to the maximal pathology and reflecting various aspects of CS etiopathogenesis. This work has resulted in the creating of a mathematical model of SC development. On the basis of this model and using the Bayes' theorem the authors have developed a system intended for predicting CS and its nature by 50, 25, and 15 RFs which is implemented by means of universal, micro- or minicomputers and tables which make it possible to predict with a 88.8% accuracy the development of CS as well as to determine the most rational individual prophylaxis of threatening stroke which is achieved through an accurate balancing in the system of controllable and uncontrollable RFs.

  1. Erythropoiesis: development and differentiation.

    PubMed

    Dzierzak, Elaine; Philipsen, Sjaak

    2013-04-01

    Through their oxygen delivery function, red blood cells are pivotal to the healthy existence of all vertebrate organisms. These cells are required during all stages of life--embryonic, fetal, neonatal, adolescent, and adult. In the adult, red blood cells are the terminally differentiated end-product cells of a complex hierarchy of hematopoietic progenitors that become progressively restricted to the erythroid lineage. During this stepwise differentiation process, erythroid progenitors undergo enormous expansion, so as to fulfill the daily requirement of ~2 × 10(11) new erythrocytes. How the erythroid lineage is made has been a topic of intense research over the last decades. Developmental studies show that there are two types of red blood cells--embryonic and adult. They develop from distinct hemogenic/hematopoietic progenitors in different anatomical sites and show distinct genetic programs. This article highlights the developmental and differentiation events necessary in the production of hemoglobin-producing red blood cells.

  2. Linear ion trap MS(n) of enzymatically synthesized 13C-labeled fructans revealing differentiating fragmentation patterns of β (1-2) and β (1-6) fructans and providing a tool for oligosaccharide identification in complex mixtures.

    PubMed

    Harrison, Scott; Xue, Hong; Lane, Geoff; Villas-Boas, Silas; Rasmussen, Susanne

    2012-02-07

    Fructans are polymeric carbohydrates, which play important roles as plant reserve carbohydrates and stress protectants, and are beneficial for human health and animal production. Fructans are formed by the addition of β-d-fructofuranosyl units to sucrose, leading to very complex mixtures of 1-kestose based inulins, 6-kestose linked levans, and 6G-kestose derived neoseries inulins and levans in cool season grasses such as Lolium perenne. The identification of isomeric fructan oligomers in chromatographic analysis of crude plant extracts is often hampered by the lack of authentic standards, and unambiguous peak assignment usually requires time-consuming analyses of purified fructan oligomers. We have developed a LC-MS(n) method for the separation and detection of fructan isomers and present here evidence for specific MS(n) fragmentation patterns associated with β 1-2 (inulins) and β 2-6 (levans) fructans. LC-MS(n) analysis of (13)C labeled fructan oligomers produced by L. perenne fructosyltransferases expressed in yeast has enabled us to account for the observed fragmentation patterns in terms of preferential cleavage of the glycosidic bond between O- and fructose C2 in both inulins and levans and to differentiate reducing-end from nonreducing end cross ring cleavages in levans. We propose that higher order MS fragmentation patterns can be used to distinguish between the two major classes of fructan, i.e., inulins and levans, without the need for authentic standards.

  3. Food and social complexity at Çayönü Tepesi, southeastern Anatolia: Stable isotope evidence of differentiation in diet according to burial practice and sex in the early Neolithic.

    PubMed

    Pearson, Jessica; Grove, Matt; Ozbek, Metin; Hongo, Hitomi

    2013-06-01

    The identification of early social complexity and differentiation in early village societies has been approached in the past most notably through the evaluation of rituals and architectural layouts. Such studies could be complemented by an approach that provides data about everyday behaviours of individuals. We took 540 human and animal bone samples for stable carbon and nitrogen isotope analysis from the Neolithic site of Çayönü Tepesi in southeastern Anatolia. The inhabitants at this site chose to bury their dead in two different ways at different times during its occupation: beneath the floors of their houses, but also inside a public mortuary building known as the Skull Building. This variation provides an opportunity using isotope methods to test whether there was evidence for structuring of daily activities (diet in this case) that might serve to reinforce this change in burial practice. We show that when the inhabitants of Çayönü Tepesi changed their architecture and operated different burial practices in conjunction, this coincided with other aspects of behaviour including socially-constituted food consumption practices, which served to reinforce social identities.

  4. Food and social complexity at Çayönü Tepesi, southeastern Anatolia: Stable isotope evidence of differentiation in diet according to burial practice and sex in the early Neolithic

    PubMed Central

    Pearson, Jessica; Grove, Matt; Özbek, Metin; Hongo, Hitomi

    2013-01-01

    The identification of early social complexity and differentiation in early village societies has been approached in the past most notably through the evaluation of rituals and architectural layouts. Such studies could be complemented by an approach that provides data about everyday behaviours of individuals. We took 540 human and animal bone samples for stable carbon and nitrogen isotope analysis from the Neolithic site of Çayönü Tepesi in southeastern Anatolia. The inhabitants at this site chose to bury their dead in two different ways at different times during its occupation: beneath the floors of their houses, but also inside a public mortuary building known as the Skull Building. This variation provides an opportunity using isotope methods to test whether there was evidence for structuring of daily activities (diet in this case) that might serve to reinforce this change in burial practice. We show that when the inhabitants of Çayönü Tepesi changed their architecture and operated different burial practices in conjunction, this coincided with other aspects of behaviour including socially-constituted food consumption practices, which served to reinforce social identities. PMID:24976671

  5. Crustal differentiation

    NASA Astrophysics Data System (ADS)

    Melekhova, E.; Blundy, J.

    2012-12-01

    Few erupted arc magmas are sufficiently primitive to be in equilibrium with mantle wedge peridotite, meaning a significant volume of arc crust must comprise plutonic cumulates formed during differentiation of primitive basalts. This cumulate material is typically not available for petrological study. A notable exception is the Lesser Antilles arc, which is renowned for the exceptional abundance and variety of cumulate xenoliths. Additionally, several Lesser Antilles islands erupt primitive basaltic magmas that are close to being in mantle equilibrium. The abundance of plutonic cumulate xenolith and presence of primitive basalts make the Lesser Antilles an ideal natural laboratory for understanding crust-building processes. Here we evaluate the chemical consequences of basalt differentiation in the mid to lower crust and uppermost mantle (10 to 30 km) by means of experiments on a primitive basalt from St. Vincent. The results were combined with compositional and textural observation of plutonic cumulate xenoliths from the island. Our goal was to constrain the conditions under which basalt differentiation can generate the observed chemical diversity of erupted magmas at St. Vincent and the compositions of minerals in cumulate xenoliths. Our experimental results show that it is possible to produce a wide compositional range of melts by differentiation at different depths and water contents from the same primitive source. The melts provide a close match to the full range of erupted lavas on the island. The cumulate assemblages, however, have a consistently lower pressure origin (6-10 km). They are formed by crystallisation of ascending melts generated in the deep crust. Phencocrysts in the lavas are distinct from those in cumulates, notably in the absence of amphibole. The phenocrysts demonstrably grew in response to crystallisation at very shallow depth, probably in sub-volcanic magma chambers. Thus St. Vincent shows clear evidence for polybaric crustal

  6. Transcriptome Analysis by Illumina High-Throughout Paired-End Sequencing Reveals the Complexity of Differential Gene Expression during In Vitro Plantlet Growth and Flowering in Amaranthus tricolor L.

    PubMed Central

    Liu, Shengcai; Kuang, Huaqin; Lai, Zhongxiong

    2014-01-01

    Amaranthus tricolor L. is a C4 plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, Am. tricolor readily bolts and blooms, degrading leaf quality. A preliminary in vitro flowering study demonstrated that the flowering control pathway in Am. tricolor may differ from that of Arabidopsis. Nevertheless, no transcriptome analysis of the flowering process in Amaranthus has been conducted. To study Am. tricolor floral regulatory mechanisms, we conducted a large-scale transcriptome analysis—based on Illumina HiSeq sequencing of cDNA libraries generated from Am. tricolor at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to in vitro flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for in vitro flowering in Am. tricolor. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from Am. tricolor at YSS, ASS, FBS, and FS; their differential expressions at the various stages indic