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Sample records for background modifies phenotypes

  1. Strain background modifies phenotypes in the ATP8B1-deficient mouse.

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    Sohela Shah

    Full Text Available BACKGROUND: Mutations in ATP8B1 (FIC1 underlie cases of cholestatic disease, ranging from chronic and progressive (progressive familial intrahepatic cholestasis to intermittent (benign recurrent intrahepatic cholestasis. The ATP8B1-deficient mouse serves as an animal model of human ATP8B1 deficiency. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the effect of genetic background on phenotypes of ATP8B1-deficient and wild-type mice, using C57Bl/6 (B6, 129, and (B6-129 F1 strain backgrounds. B6 background resulted in greater abnormalities in ATP8B1-deficient mice than did 129 and/or F1 background. ATP8B1-deficient pups of B6 background gained less weight. In adult ATP8B1-deficient mice at baseline, those of B6 background had lower serum cholesterol levels, higher serum alkaline phosphatase levels, and larger livers. After challenge with cholate-supplemented diet, these mice exhibited higher serum alkaline phosphatase and bilirubin levels, greater weight loss and larger livers. ATP8B1-deficient phenotypes in mice of F1 and 129 backgrounds are usually similar, suggesting that susceptibility to manifestations of ATP8B1 deficiency may be recessive. We also detected differences in hepatobiliary phenotypes between wild-type mice of differing strains. CONCLUSIONS/SIGNIFICANCE: Our results indicate that the ATP8B1-deficient mouse in a B6 background may be a better model of human ATP8B1 deficiency and highlight the importance of informed background strain selection for mouse models of liver disease.

  2. Strain background modifies phenotypes in the ATP8B1-deficient mouse

    NARCIS (Netherlands)

    Shah, S.; Sanford, U.R.; Vargas, J.C.; Xu, H.; Groen, A.; Paulusma, C.C.; Grenert, J.P.; Pawlikowska, L.; Sen, S.; Oude Elferink, R.P.J.; Bull, L.N.

    2010-01-01

    BACKGROUND: Mutations in ATP8B1 (FIC1) underlie cases of cholestatic disease, ranging from chronic and progressive (progressive familial intrahepatic cholestasis) to intermittent (benign recurrent intrahepatic cholestasis). The ATP8B1-deficient mouse serves as an animal model of human ATP8B1 deficie

  3. Genetic background of phenotypic variation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A noteworthy feature of the living world is its bewildering variability. A key issue in several biological disciplines is the achievement of an understanding of the hereditary basis of this variability. Two opposing, but not necessarily irreconcilable conceptions attempt to explain the underlying mechanism. The gene function paradigm postulates that phenotypic variance is generated by the polymorphism in the coding sequences of genes. However, comparisons of a great number of homologous gene and protein sequences have revealed that they predominantly remained functionally conserved even across distantly related phylogenic taxa. Alternatively, the gene regulation paradigm assumes that differences in the cis-regulatory region of genes do account for phenotype variation within species. An extension of this latter concept is that phenotypic variability is generated by the polyrnorphism in the overall gene expression profiles of gene networks.In other words, the activity of a particular gene is a system property determined both by the cis-regulatory sequences of the given genes and by the other genes of a gene network, whose expressions vary among individuals, too. Novel proponents of gene function paradigm claim that functional genetic variance within the coding sequences of regulatory genes is critical for the generation of morphological polymorphism. Note, however, that these developmental genes play direct regulatory roles in the control of gene expression.

  4. Phenotype of heterozygotes for low-density lipoprotein receptor mutations identified in different background populations

    DEFF Research Database (Denmark)

    Tybjaerg-Hansen, Anne; Jensen, Henrik Kjaerulf; Benn, Marianne

    2005-01-01

    The effect of mutations on phenotype is often overestimated because of ascertainment bias. We determined the effect of background population on cholesterol phenotype associated with specific mutations in the low-density lipoprotein (LDL) receptor and the relative importance of background population...... and type of mutation (LDL receptor [LDLR] or APOB R3500Q) for cholesterol phenotype....

  5. Destabilizing protein polymorphisms in the genetic background direct phenotypic expression of mutant SOD1 toxicity.

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    Tali Gidalevitz

    2009-03-01

    Full Text Available Genetic background exerts a strong modulatory effect on the toxicity of aggregation-prone proteins in conformational diseases. In addition to influencing the misfolding and aggregation behavior of the mutant proteins, polymorphisms in putative modifier genes may affect the molecular processes leading to the disease phenotype. Mutations in SOD1 in a subset of familial amyotrophic lateral sclerosis (ALS cases confer dominant but clinically variable toxicity, thought to be mediated by misfolding and aggregation of mutant SOD1 protein. While the mechanism of toxicity remains unknown, both the nature of the SOD1 mutation and the genetic background in which it is expressed appear important. To address this, we established a Caenorhabditis elegans model to systematically examine the aggregation behavior and genetic interactions of mutant forms of SOD1. Expression of three structurally distinct SOD1 mutants in C. elegans muscle cells resulted in the appearance of heterogeneous populations of aggregates and was associated with only mild cellular dysfunction. However, introduction of destabilizing temperature-sensitive mutations into the genetic background strongly enhanced the toxicity of SOD1 mutants, resulting in exposure of several deleterious phenotypes at permissive conditions in a manner dependent on the specific SOD1 mutation. The nature of the observed phenotype was dependent on the temperature-sensitive mutation present, while its penetrance reflected the specific combination of temperature-sensitive and SOD1 mutations. Thus, the specific toxic phenotypes of conformational disease may not be simply due to misfolding/aggregation toxicity of the causative mutant proteins, but may be defined by their genetic interactions with cellular pathways harboring mildly destabilizing missense alleles.

  6. Phenotype of heterozygotes for low-density lipoprotein receptor mutations identified in different background populations

    DEFF Research Database (Denmark)

    Tybjaerg-Hansen, Anne; Jensen, Henrik Kjaerulf; Benn, Marianne;

    2005-01-01

    The effect of mutations on phenotype is often overestimated because of ascertainment bias. We determined the effect of background population on cholesterol phenotype associated with specific mutations in the low-density lipoprotein (LDL) receptor and the relative importance of background population...

  7. Modifying factors and phenotypic diversity in Wilson's disease.

    Science.gov (United States)

    Lutsenko, Svetlana

    2014-05-01

    Wilson's disease (WD) is a human disorder of copper homeostasis caused by mutations in the copper-transporting ATPase ATP7B. WD is characterized by copper accumulation, predominantly in the liver and brain, hepatic pathology, and wide differences between patients in the age of onset and the spectrum of symptoms. Several factors contribute to the phenotypic variability of WD. The WD-causing mutations produce a wide range of changes in stability, activity, intracellular localization, and trafficking of ATP7B; the nonpathogenic genetic polymorphisms may contribute to the phenotype. In Atp7b(-/-) mice, a mouse model of WD, an abnormal intracellular distribution of copper in the liver triggers distinct changes in the transcriptome; these mRNA profiles might be used to more specifically define disease progression. The major effect of accumulating copper on lipid metabolism and especially cholesterol homeostasis in mice and humans suggests the importance of fat and cholesterol metabolism as modifying factors in WD.

  8. Can background cosmology hold the key for modified gravity tests?

    CERN Document Server

    Ceron-Hurtado, Juan J; Li, Baojiu

    2016-01-01

    Modified gravity theories are a popular alternative to dark energy as a possible explanation for the observed accelerating cosmic expansion, and their cosmological tests are currently an active research field. Studies in recent years have been increasingly focused on testing these theories in the nonlinear regime, which is computationally demanding. Here we show that, under certain circumstances, a whole class of theories can be ruled out by using background cosmology alone. This is possible because certain classes of models (i) are fundamentally incapable of producing specific background expansion histories, and (ii) said histories are incompatible with local gravity tests. As an example, we demonstrate that a popular class of models, $f(R)$ gravity, would not be viable if observations suggest even a slight deviation of the background expansion history from that of the $\\Lambda$CDM paradigm.

  9. Can background cosmology hold the key for modified gravity tests?

    Science.gov (United States)

    Ceron-Hurtado, Juan J.; He, Jian-hua; Li, Baojiu

    2016-09-01

    Modified gravity theories are a popular alternative to dark energy as a possible explanation for the observed accelerating cosmic expansion, and their cosmological tests are currently an active research field. Studies in recent years have been increasingly focused on testing these theories in the nonlinear regime, which is computationally demanding. Here we show that, under certain circumstances, a whole class of theories can be ruled out by using background cosmology alone. This is possible because certain classes of models (i) are fundamentally incapable of producing specific background expansion histories, and (ii) said histories are incompatible with local gravity tests. As an example, we demonstrate that a popular class of models, f (R ) gravity, would not be viable if observations suggest even a slight deviation of the background expansion history from that of the Λ CDM paradigm.

  10. Image Segmentation in Video Sequences Using Modified Background Subtraction

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    D. W. Chinchkhede

    2012-03-01

    Full Text Available In computer vision, "Background subtraction" is a technique for finding moving objects in a video sequences for example vehicle driving on a freeway. For to detect non stationary (dynamic objects, it is necessary to subtracting current image from a time-averaged background image. There are various background subtraction algorithms for detecting moving vehicles or any moving object(s like pedestrians in urban traffic video sequences. A crude approximation to the task of classifying each pixel on the frame of current image, locate slow-moving objects or in poor image qualities of videos and distinguish shadows from moving objects by using modified background subtraction method. While classifying each pixel on the frame of the current image, it is to be detect the moving object at foreground and background conditional environment that we can classify each pixel using a model of how that pixellooks when it is part of video frame classes. A mixture of Gaussians classification model for each pixel using an unsupervised technique is an efficient, incremental version of Expectation Maximization (EM is used for the purpose. Unlike standard image-averaging approach, this method automatically updates the mixture component for each video frame class according to likelihood of membership; hence slowmoving objects and poor image quality of videos are also being handled perfectly. Our approach identifies and eliminates shadows much more effectively than other techniques like thresholding.

  11. Genetic background modifies nuclear mutant huntingtin accumulation and HD CAG repeat instability in Huntington's disease knock-in mice.

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    Lloret, Alejandro; Dragileva, Ella; Teed, Allison; Espinola, Janice; Fossale, Elisa; Gillis, Tammy; Lopez, Edith; Myers, Richard H; MacDonald, Marcy E; Wheeler, Vanessa C

    2006-06-15

    Genetically precise models of Huntington's disease (HD), Hdh CAG knock-in mice, are powerful systems in which phenotypes associated with expanded HD CAG repeats are studied. To dissect the genetic pathways that underlie such phenotypes, we have generated Hdh(Q111) knock-in mouse lines that are congenic for C57BL/6, FVB/N and 129Sv inbred genetic backgrounds and investigated four Hdh(Q111) phenotypes in these three genetic backgrounds: the intergenerational instability of the HD CAG repeat and the striatal-specific somatic HD CAG repeat expansion, nuclear mutant huntingtin accumulation and intranuclear inclusion formation. Our results reveal increased intergenerational and somatic instability of the HD CAG repeat in C57BL/6 and FVB/N backgrounds compared with the 129Sv background. The accumulation of nuclear mutant huntingtin and the formation of intranuclear inclusions were fastest in the C57BL/6 background, slowest in the 129Sv background and intermediate in the FVB/N background. Inbred strain-specific differences were independent of constitutive HD CAG repeat size and did not correlate with Hdh mRNA levels. These data provide evidence for genetic modifiers of both intergenerational HD CAG repeat instability and striatal-specific phenotypes. Different relative contributions of C57BL/6 and 129Sv genetic backgrounds to the onset of nuclear mutant huntingtin and somatic HD CAG repeat expansion predict that the initiation of each of these two phenotypes is modified by different genes. Our findings set the stage for defining disease-related genetic pathways that will ultimately provide insight into disease mechanism.

  12. GENETIC BACKGROUND BUT NOT METALLOTHIONEIN PHENOTYPE DICTATES SENSITIVITY TO CADMIUM-INDUCED TESTICULAR INJURY IN MICE

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    Genetic Background but not Metallothionein Phenotype Dictates Sensitivity to Cadmium-Induced Testicular Injury in MiceJie Liu1,2, Chris Corton3, David J. Dix4, Yaping Liu1, Michael P. Waalkes2 and Curtis D. Klaassen1 ABSTRACTParenteral administrati...

  13. Genetic Background Strongly Influences the Bone Phenotype of P2X7 Receptor Knockout Mice

    DEFF Research Database (Denmark)

    Syberg, Susanne; Petersen, Solveig; Beck Jensen, Jens-Erik;

    2012-01-01

    The purinergic P2X7 receptor is expressed by bone cells and has been shown to be important in both bone formation and bone resorption. In this study we investigated the importance of the genetic background of the mouse strains on which the P2X7 knock-out models were based by comparing bone status...... littermates. In conclusion, we have shown that the genetic background of P2X7(-/-) mice strongly influences the bone phenotype of the P2X7(-/-) mice and that P2X7 has a more significant regulatory role in bone remodeling than found in previous studies....

  14. Hand Gesture Recognition Using Modified 1$ and Background Subtraction Algorithms

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    Hazem Khaled

    2015-01-01

    Full Text Available Computers and computerized machines have tremendously penetrated all aspects of our lives. This raises the importance of Human-Computer Interface (HCI. The common HCI techniques still rely on simple devices such as keyboard, mice, and joysticks, which are not enough to convoy the latest technology. Hand gesture has become one of the most important attractive alternatives to existing traditional HCI techniques. This paper proposes a new hand gesture detection system for Human-Computer Interaction using real-time video streaming. This is achieved by removing the background using average background algorithm and the 1$ algorithm for hand’s template matching. Then every hand gesture is translated to commands that can be used to control robot movements. The simulation results show that the proposed algorithm can achieve high detection rate and small recognition time under different light changes, scales, rotation, and background.

  15. The W303 genetic background affects the isw2 delta mutant phenotype in Saccharomyces cerevisiae.

    Science.gov (United States)

    Trachtulcová, P; Frýdlová, I; Janatová, I; Dorosh, A; Hasek, J

    2003-01-01

    We performed detailed phenotypic analysis of the isw2 delta strains of the W303 genetic background and compared its results with those obtained previously in BY-derived genetic background. Shmoolike morphology was observed in the isw2 delta strain of alpha-mating type of the BY strains, but not in its W303-derived counterpart. On the other hand, derepression of a-specific genes in the isw2 delta (MAT alpha) strain was observed in both genetic backgrounds, although to a different extent. Unlike in BY-derived strain hyperactivation of the Ras2/cAMP pathway reduced invasiveness of the isw2 delta strain (MAT alpha) of the W303 background. Sensitivity to Calcofluor White indicating a cell wall-integrity defect was significantly increased in the isw2 delta strains of the W303 background in contrast to BY-derived strains. Our data indicate that the effects of the isw2 deletion strongly depend on the background in which the deletion, is made.

  16. The conditional nature of genetic interactions: the consequences of wild-type backgrounds on mutational interactions in a genome-wide modifier screen.

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    Sudarshan Chari

    Full Text Available The phenotypic outcome of a mutation cannot be simply mapped onto the underlying DNA variant. Instead, the phenotype is a function of the allele, the genetic background in which it occurs and the environment where the mutational effects are expressed. While the influence of genetic background on the expressivity of individual mutations is recognized, its consequences on the interactions between genes, or the genetic network they form, is largely unknown. The description of genetic networks is essential for much of biology; yet if, and how, the topologies of such networks are influenced by background is unknown. Furthermore, a comprehensive examination of the background dependent nature of genetic interactions may lead to identification of novel modifiers of biological processes. Previous work in Drosophila melanogaster demonstrated that wild-type genetic background influences the effects of an allele of scalloped (sd, with respect to both its principal consequence on wing development and its interactions with a mutation in optomotor blind. In this study we address whether the background dependence of mutational interactions is a general property of genetic systems by performing a genome wide dominant modifier screen of the sd(E3 allele in two wild-type genetic backgrounds using molecularly defined deletions. We demonstrate that ~74% of all modifiers of the sd(E3 phenotype are background-dependent due in part to differential sensitivity to genetic perturbation. These background dependent interactions include some with qualitative differences in the phenotypic outcome, as well as instances of sign epistasis. This suggests that genetic interactions are often contingent on genetic background, with flexibility in genetic networks due to segregating variation in populations. Such background dependent effects can substantially alter conclusions about how genes influence biological processes, the potential for genetic screens in alternative wild

  17. Genetic background of nonmutant Piebald-Virol-Glaxo rats does not influence nephronophthisis phenotypes

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    Yengkopiong JP

    2013-02-01

    Full Text Available Jada Pasquale Yengkopiong, Joseph Daniel Wani LakoJohn Garang Memorial University of Science and Technology, Faculty of Science and Technology, Bor, Jonglei State, Republic of South SudanBackground: Nephronophthisis (NPHP, which affects multiple organs, is a hereditary cystic kidney disease (CKD, characterized by interstitial fibrosis and numerous fluid-filled cysts in the kidneys. It is caused by mutations in NPHP genes, which encode for ciliary proteins known as nephrocystins. The disorder affects many people across the world and leads to end-stage renal disease. The aim of this study was to determine if the genetic background of the nonmutant female Piebald-Virol-Glaxo (PVG/Seac-/- rat influences phenotypic inheritance of NPHP from mutant male Lewis polycystic kidney rats.Methods: Mating experiments were performed between mutant Lewis polycystic kidney male rats with CKD and nonmutant PVG and Wistar Kyoto female rats without cystic kidney disease to raise second filial and backcross 1 progeny, respectively. Rats that developed cystic kidneys were identified. Systolic blood pressure was determined in each rat at 12 weeks of age using the tail and cuff method. After euthanasia, blood samples were collected and chemistry was determined. Histological examination of the kidneys, pancreas, and liver of rats with and without cystic kidney disease was performed.Results: It was established that the genetic background of nonmutant female PVG rats did not influence the phenotypic inheritance of the CKD from mutant male Lewis polycystic kidney rats. The disease arose as a result of a recessive mutation in a single gene (second filial generation, CKD = 13, non-CKD = 39, Χ2 = 0.00, P ≥ 0.97; backcross 1 generation, CKD = 67, non-CKD = 72, Χ2 = 0.18, P > 0.05 and inherited as NPHP. The rats with CKD developed larger fluid-filled cystic kidneys, higher systolic blood pressure, and anemia, but there were no extrarenal cysts and disease did not lead to

  18. Phenotypic variation within European carriers of the Y-chromosomal gr/gr deletion is independent of Y-chromosomal background

    DEFF Research Database (Denmark)

    Krausz, C; Giachini, C; Xue, Y;

    2008-01-01

    BACKGROUND: Previous studies have compared sperm phenotypes between men with partial deletions within the AZFc region of the Y chromosome and non-carriers, with variable results. In this study, a separate question was investigated, the basis of the variation in sperm phenotype within gr/gr deletion...... carriers, which ranges from normozoospermia to azoospermia. Differences in the genes removed by independent gr/gr deletions, the occurrence of subsequent duplications or the presence of linked modifying variants elsewhere on the chromosome have been suggested as possible causal factors. This study set out...... to test these possibilities in a large sample of gr/gr deletion carriers with known phenotypes spanning the complete range. RESULTS: In total, 169 men diagnosed with gr/gr deletions from six centres in Europe and one in Australia were studied. The DAZ and CDY1 copies retained, the presence or absence...

  19. The expression of HSP in human skeletal muscle. Effects of muscle fiber phenotype and training background

    DEFF Research Database (Denmark)

    Folkesson, Mattias; Mackey, Abigail L; Langberg, Henning;

    2013-01-01

    AIM: Exercise-induced adaptations of skeletal muscle are related to training mode and can be muscle fibre type specific. This study aimed to investigate heat shock protein expression in type I and type II muscle fibres in resting skeletal muscle of subjects with different training backgrounds...... HSPs in human skeletal muscle is influenced by muscle fibre phenotype. The fibre type specific expression of HSP70 is influenced by resistance and endurance training whereas those of αB-crystallin and HSP27 are influenced only by endurance training suggesting the existence of a training......-modality specific action on the adaptive processes including heat shock proteins in human skeletal muscle. This article is protected by copyright. All rights reserved....

  20. MutLα heterodimers modify the molecular phenotype of Friedreich ataxia.

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    Vahid Ezzatizadeh

    Full Text Available BACKGROUND: Friedreich ataxia (FRDA, the most common autosomal recessive ataxia disorder, is caused by a dynamic GAA repeat expansion mutation within intron 1 of FXN gene, resulting in down-regulation of frataxin expression. Studies of cell and mouse models have revealed a role for the mismatch repair (MMR MutS-heterodimer complexes and the PMS2 component of the MutLα complex in the dynamics of intergenerational and somatic GAA repeat expansions: MSH2, MSH3 and MSH6 promote GAA repeat expansions, while PMS2 inhibits GAA repeat expansions. METHODOLOGY/PRINCIPAL FINDINGS: To determine the potential role of the other component of the MutLα complex, MLH1, in GAA repeat instability in FRDA, we have analyzed intergenerational and somatic GAA repeat expansions from FXN transgenic mice that have been crossed with Mlh1 deficient mice. We find that loss of Mlh1 activity reduces both intergenerational and somatic GAA repeat expansions. However, we also find that loss of either Mlh1 or Pms2 reduces FXN transcription, suggesting different mechanisms of action for Mlh1 and Pms2 on GAA repeat expansion dynamics and regulation of FXN transcription. CONCLUSIONS/SIGNIFICANCE: Both MutLα components, PMS2 and MLH1, have now been shown to modify the molecular phenotype of FRDA. We propose that upregulation of MLH1 or PMS2 could be potential FRDA therapeutic approaches to increase FXN transcription.

  1. Elevated oxidative membrane damage associated with genetic modifiers of Lyst-mutant phenotypes.

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    Colleen M Trantow

    2010-07-01

    Full Text Available LYST is a large cytosolic protein that influences the biogenesis of lysosome-related organelles, and mutation of the encoding gene, LYST, can cause Chediak-Higashi syndrome. Recently, Lyst-mutant mice were recognized to also exhibit an iris disease resembling exfoliation syndrome, a common cause of glaucoma in humans. Here, Lyst-mutant iris phenotypes were used in a search for genes that influence Lyst pathways. In a candidate gene-driven approach, albino Lyst-mutant mice homozygous for a mutation in Tyr, whose product is key to melanin synthesis within melanosomes, exhibited complete rescue of Lyst-mutant iris phenotypes. In a genetic background-driven approach using a DBA/2J strain of congenic mice, an interval containing Tyrp1 enhanced Lyst-dependent iris phenotypes. Thus, both experimental approaches implicated the melanosome, an organelle that is a potential source of oxidative stress, as contributing to the disease phenotype. Confirming an association with oxidative damage, Lyst mutation resulted in genetic context-sensitive changes in iris lipid hydroperoxide levels, being lowest in albino and highest in DBA/2J mice. Surprisingly, the DBA/2J genetic background also exposed a late-onset neurodegenerative phenotype involving cerebellar Purkinje-cell degeneration. These results identify an association between oxidative damage to lipid membranes and the severity of Lyst-mutant phenotypes, revealing a new mechanism that contributes to pathophysiology involving LYST.

  2. Phenotypic divergence in two lines of L-Fabp-/- mice reflects substrain differences and environmental modifiers.

    Science.gov (United States)

    Newberry, Elizabeth P; Kennedy, Susan; Xie, Yan; Luo, Jianyang; Jiang, Hui; Ory, Daniel S; Davidson, Nicholas O

    2015-10-15

    Phenotypic divergence in diet-induced obesity (DIO) and hepatic steatosis has been reported in two independently generated lines of L-Fabp(-/-) mice [New Jersey (NJ) L-Fabp(-/-) vs. Washington University (WU) L-Fabp(-/-) mice]. We performed side-by-side studies to examine differences between the lines and investigate the role of genetic background, intestinal microbiota, sex, and diet in the divergent phenotypes. Fasting-induced steatosis was attenuated in both L-Fabp(-/-) lines compared with C57BL/6J controls, with restoration of hepatic triglyceride levels following adenoviral L-Fabp rescue. Both lines were protected against DIO after high-saturated-fat diet feeding. Hepatic steatosis was attenuated in WU but not NJ L-Fabp(-/-) mice, although this difference between the lines disappeared upon antibiotic treatment and cohousing. In contrast, there was phenotypic divergence in L-Fabp(-/-) mice fed a high cocoa butter fat diet, with WU L-Fabp(-/-) mice, but not NJ L-Fabp(-/-) mice, showing protection against both DIO and hepatic steatosis, with some sex-dependent (female > male) differences. Dense mapping revealed no evidence of unintended targeting, duplications, or deletions surrounding the Fabp1 locus in either line and only minor differences in mRNA expression of genes located near the targeted allele. However, a C57BL/6 substrain screen showed that the NJ L-Fabp(-/-) line contains ∼40% C57BL/6N genomic DNA, despite reports that these mice were backcrossed six generations. Overall, these findings suggest that some of the phenotypic divergence between the two L-Fabp(-/-) lines may reflect unanticipated differences in genetic background, underscoring the importance of genetic background in phenotypic characterization.

  3. Constraining Modified Theories of Gravity with Gravitational-Wave Stochastic Backgrounds.

    Science.gov (United States)

    Maselli, Andrea; Marassi, Stefania; Ferrari, Valeria; Kokkotas, Kostas; Schneider, Raffaella

    2016-08-26

    The direct discovery of gravitational waves has finally opened a new observational window on our Universe, suggesting that the population of coalescing binary black holes is larger than previously expected. These sources produce an unresolved background of gravitational waves, potentially observable by ground-based interferometers. In this Letter we investigate how modified theories of gravity, modeled using the parametrized post-Einsteinian formalism, affect the expected signal, and analyze the detectability of the resulting stochastic background by current and future ground-based interferometers. We find the constraints that Advanced LIGO would be able to set on modified theories, showing that they may significantly improve the current bounds obtained from astrophysical observations of binary pulsars.

  4. Investigating the Synergistic Effects of Combined Modified Alginates on Macrophage Phenotype

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    Hannah C. Bygd

    2016-12-01

    Full Text Available Understanding macrophage responses to biomaterials is crucial to the success of implanted medical devices, tissue engineering scaffolds, and drug delivery vehicles. Cellular responses to materials may depend synergistically on multiple surface chemistries, due to the polyvalent nature of cell–ligand interactions. Previous work in our lab found that different surface functionalities of chemically modified alginate could sway macrophage phenotype toward either the pro-inflammatory or pro-angiogenic phenotype. Using these findings, this research aims to understand the relationship between combined material surface chemistries and macrophage phenotype. Tumor necrosis factor-α (TNF-α secretion, nitrite production, and arginase activity were measured and used to determine the ability of the materials to alter macrophage phenotype. Cooperative relationships between pairwise modifications of alginate were determined by calculating synergy values for the aforementioned molecules. Several materials appeared to improve M1 to M2 macrophage reprogramming capabilities, giving valuable insight into the complexity of surface chemistries needed for optimal incorporation and survival of implanted biomaterials.

  5. Can a strong magnetic background modify the nature of the chiral transition in QCD?

    OpenAIRE

    Fraga, Eduardo S.; Mizher, Ana Júlia

    2008-01-01

    The presence of a strong magnetic background can modify the nature and the dynamics of the chiral phase transition at finite temperature: for high enough magnetic fields, comparable to the ones expected to be created in noncentral high-energy heavy ion collisions at RHIC and the LHC, the original crossover is turned into a first-order transition. We illustrate this effect within the linear sigma model with quarks to one loop in the ${\\rm MS}$ scheme for $N_{f}=2$.

  6. Approaches for the identification of genetic modifiers of nutrient dependent phenotypes: Examples from folate

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    Amanda J. Macfarlane

    2014-07-01

    Full Text Available By combining the sciences of nutrition, bioinformatics, genomics, population genetics and epidemiology, nutrigenomics is improving our understanding of how diet and nutrient intake can interact with or modify gene expression and disease risk. In this review, we explore various approaches to examine gene-nutrient interactions and the modifying role of nutrient consumption, as they relate to nutrient status and disease risk in human populations. Two common approaches include the use of SNPs in candidate genes to identify their association with nutritional status or disease outcomes, or genome wide association studies to identify genetic polymorphisms associated with a given phenotype. Here, we examine the results of various gene-nutrient interaction studies, the association of genetic polymorphisms with disease expression and the identification of nutritional factors that modify gene-dependent disease phenotypes. We have focussed on specific examples from investigations of the interactions of folate and B-vitamin consumption and polymorphisms in the genes of B vitamin dependent enzymes and their association with disease risk, followed by an examination of the strengths and limitations of the methods employed. We also present suggestions for future studies, including an approach from an on-going large scale study, to examine the interaction of nutrient intake and genotypic variation and their impact on nutritional status.

  7. Phenotypic characterization of transgenic mice harboring Nf1+/- or Nf1-/- osteoclasts in otherwise Nf1+/+ background.

    Science.gov (United States)

    Alanne, Maria H; Siljamäki, Elina; Peltonen, Sirkku; Väänänen, Kalervo; Windle, Jolene J; Parada, Luis F; Määttä, Jorma A; Peltonen, Juha

    2012-06-01

    Skeletal abnormalities in neurofibromatosis type 1 syndrome (NF1) are observed in ∼50% of patients. Here, we describe the phenotype of Nf1(Ocl) mouse model with Nf1-deficient osteoclasts. Nf1Ocl mice with Nf1+/- or Nf1-/- osteoclasts in otherwise Nf1+/+ background were successfully generated by mating parental Nf1flox/flox and TRAP-Cre mice. Contrary to our original hypothesis, osteoporotic or fragile bone phenotype was not observed. The µCT analysis revealed that tibial bone marrow cavity, trabecular tissue volume, and the perimeter of cortical bone were smaller in Nf1 Ocl-/- mice compared to Nf1 Ocl+/+ control mice. Nf1 Ocl-/- mice also a displayed narrowed growth plate in the proximal tibia. In vitro analysis showed increased bone resorption capacity and cytoskeletal changes including irregular cell shape and abnormal actin ring formation in Nf1-/- osteoclasts. Surprisingly, the size of spleen in Nf1 Ocl-/- mice was two times larger than in controls and histomorphometric analysis showed splenic megakaryocytosis. In summary, Nf1Ocl mouse model presented with a mild but specific bone phenotype. This study shows that NF1-deficiency in osteoclasts may have a role in the development of NF1-related skeletal abnormalities, but Nf1-deficiency in osteoclasts in Nf1+/+ background is not sufficient to induce skeletal abnormalities analogous to those observed in patients with NF1.

  8. Mapping gravitational-wave backgrounds in modified theories of gravity using pulsar timing arrays

    CERN Document Server

    Gair, Jonathan R; Taylor, Stephen R

    2015-01-01

    We extend our previous work on applying CMB techniques to the mapping of gravitational-wave backgrounds to backgrounds which have non-GR polarisations. Our analysis and results are presented in the context of pulsar-timing array observations, but the overarching methods are general, and can be easily applied to LIGO or eLISA observations using appropriately modified response functions. Analytic expressions for the pulsar-timing response to gravitational waves with non-GR polarisation are given for each mode of a spin-weighted spherical-harmonic decomposition of the background, which permit the signal to be mapped across the sky to any desired resolution. We also derive the pulsar-timing overlap reduction functions for the various non-GR polarisations, finding analytic forms for anisotropic backgrounds with scalar-transverse ("breathing") and vector-longitudinal polarisations, and a semi-analytic form for scalar-longitudinal backgrounds. Our results indicate that pulsar-timing observations will be completely i...

  9. Can a strong magnetic background modify the nature of the chiral transition in QCD?

    CERN Document Server

    Fraga, Eduardo S

    2008-01-01

    The presence of a strong magnetic background can modify the nature and the dynamics of the chiral phase transition at finite temperature: for high enough magnetic fields, comparable to the ones expected to be created in noncentral high-energy heavy ion collisions at RHIC and the LHC, the original crossover is turned into a first-order transition. We illustrate this effect within the linear sigma model with quarks to one loop in the $\\overline{\\rm MS}$ scheme for $N_{f}=2$.

  10. Can a strong magnetic background modify the nature of the chiral transition in QCD?

    Energy Technology Data Exchange (ETDEWEB)

    Fraga, Eduardo S.; Mizher, Ana Julia [Instituto de Fisica, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, Rio de Janeiro, RJ 21941-972 (Brazil)

    2009-04-01

    The presence of a strong magnetic background can modify the nature and the dynamics of the chiral phase transition at finite temperature: for high enough magnetic fields, comparable to the ones expected to be created in noncentral high-energy heavy ion collisions at RHIC and the LHC, the original crossover is turned into a first-order transition. We illustrate this effect within the linear sigma model with quarks to one loop in the MS-bar scheme for N{sub f}=2.

  11. Cosmic Microwave Background Radiation Constraints on a Modified Chaplygin Gas Model

    Institute of Scientific and Technical Information of China (English)

    LIU Dao-Jun; LI Xin-Zhou

    2005-01-01

    @@ A modified Chaplygin gas model of unifying dark energy and dark matter with the exotic equation of state p = Bρ- A/ρα , which can also explain the recent expansion of the universe, is investigated by means of constraining the location of the peak of the cosmic microwave background radiation spectrum. We find that the result of CMBR measurements does not exclude the nonzero value of parameter B, but allows it in the range -0.35 (<~) B (<~) 0.025.

  12. Genetic backgrounds and modifier genes of NTD mouse models: An opportunity for greater understanding of the multifactorial etiology of neural tube defects.

    Science.gov (United States)

    Leduc, Renee Y M; Singh, Parmveer; McDermid, Heather E

    2016-10-21

    Neurulation, the early embryonic process of forming the presumptive brain and spinal cord, is highly complex and involves hundreds of genes in multiple genetic pathways. Mice have long served as a genetic model for studying human neurulation, and the resulting neural tube defects (NTDs) that arise when neurulation is disrupted. Because mice appear to show mostly single gene inheritance for NTDs and humans show multifactorial inheritance, mice sometimes have been characterized as a simpler model for the identification and study of NTD genes. But are they a simple model? When viewed on different genetic backgrounds, many genes show significant variation in the penetrance and expressivity of NTD phenotypes, suggesting the presence of modifier loci that interact with the target gene to affect the phenotypic expression. Looking at mutations on different genetic backgrounds provides us with an opportunity to explore these complex genetic interactions, which are likely to better emulate similar processes in human neurulation. Here, we review NTD genes known to show strain-specific phenotypic variation. We focus particularly on the gene Cecr2, which is studied using both a hypomorphic and a presumptive null mutation on two different backgrounds: one susceptible (BALB/c) and one resistant (FVB/N) to NTDs. This strain difference has led to a search for genetic modifiers within a region on murine chromosome 19. Understanding how genetic variants alter the phenotypic outcome in NTD mouse models will help to direct future studies in humans, particularly now that more genome wide sequencing approaches are being used. Birth Defects Research (Part A), 2016. © 2016 Wiley Periodicals, Inc.

  13. Arrhythmogenic Biophysical Phenotype for SCN5A Mutation S1787N Depends upon Splice Variant Background and Intracellular Acidosis.

    Directory of Open Access Journals (Sweden)

    Rou-Mu Hu

    Full Text Available SCN5A is a susceptibility gene for type 3 long QT syndrome, Brugada syndrome, and sudden infant death syndrome. INa dysfunction from mutated SCN5A can depend upon the splice variant background in which it is expressed and also upon environmental factors such as acidosis. S1787N was reported previously as a LQT3-associated mutation and has also been observed in 1 of 295 healthy white controls. Here, we determined the in vitro biophysical phenotype of SCN5A-S1787N in an effort to further assess its possible pathogenicity.We engineered S1787N in the two most common alternatively spliced SCN5A isoforms, the major isoform lacking a glutamine at position 1077 (Q1077del and the minor isoform containing Q1077, and expressed these two engineered constructs in HEK293 cells for electrophysiological study. Macroscopic voltage-gated INa was measured 24 hours after transfection with standard whole-cell patch clamp techniques. We applied intracellular solutions with pH7.4 or pH6.7. S1787N in the Q1077 background had WT-like INa including peak INa density, activation and inactivation parameters, and late INa amplitude in both pH 7.4 and pH 6.7. However, with S1787N in the Q1077del background, the percentages of INa late/peak were increased by 2.1 fold in pH 7.4 and by 2.9 fold in pH 6.7 when compared to WT.The LQT3-like biophysical phenotype for S1787N depends on both the SCN5A splice variant and on the intracellular pH. These findings provide further evidence that the splice variant and environmental factors affect the molecular phenotype of cardiac SCN5A-encoded sodium channel (Nav1.5, has implications for the clinical phenotype, and may provide insight into acidosis-induced arrhythmia mechanisms.

  14. A new mouse model for marfan syndrome presents phenotypic variability associated with the genetic background and overall levels of Fbn1 expression.

    Directory of Open Access Journals (Sweden)

    Bruno L Lima

    Full Text Available Marfan syndrome is an autosomal dominant disease of connective tissue caused by mutations in the fibrillin-1 encoding gene FBN1. Patients present cardiovascular, ocular and skeletal manifestations, and although being fully penetrant, MFS is characterized by a wide clinical variability both within and between families. Here we describe a new mouse model of MFS that recapitulates the clinical heterogeneity of the syndrome in humans. Heterozygotes for the mutant Fbn1 allele mgΔloxPneo, carrying the same internal deletion of exons 19-24 as the mgΔ mouse model, present defective microfibrillar deposition, emphysema, deterioration of aortic wall and kyphosis. However, the onset of a clinical phenotypes is earlier in the 129/Sv than in C57BL/6 background, indicating the existence of genetic modifiers of MFS between these two mouse strains. In addition, we characterized a wide clinical variability within the 129/Sv congenic heterozygotes, suggesting involvement of epigenetic factors in disease severity. Finally, we show a strong negative correlation between overall levels of Fbn1 expression and the severity of the phenotypes, corroborating the suggested protective role of normal fibrillin-1 in MFS pathogenesis, and supporting the development of therapies based on increasing Fbn1 expression.

  15. A model of functional brain connectivity and background noise as a biomarker for cognitive phenotypes: application to autism.

    Directory of Open Access Journals (Sweden)

    Luis García Domínguez

    Full Text Available We present an efficient approach to discriminate between typical and atypical brains from macroscopic neural dynamics recorded as magnetoencephalograms (MEG. Our approach is based on the fact that spontaneous brain activity can be accurately described with stochastic dynamics, as a multivariate Ornstein-Uhlenbeck process (mOUP. By fitting the data to a mOUP we obtain: 1 the functional connectivity matrix, corresponding to the drift operator, and 2 the traces of background stochastic activity (noise driving the brain. We applied this method to investigate functional connectivity and background noise in juvenile patients (n = 9 with Asperger's syndrome, a form of autism spectrum disorder (ASD, and compared them to age-matched juvenile control subjects (n = 10. Our analysis reveals significant alterations in both functional brain connectivity and background noise in ASD patients. The dominant connectivity change in ASD relative to control shows enhanced functional excitation from occipital to frontal areas along a parasagittal axis. Background noise in ASD patients is spatially correlated over wide areas, as opposed to control, where areas driven by correlated noise form smaller patches. An analysis of the spatial complexity reveals that it is significantly lower in ASD subjects. Although the detailed physiological mechanisms underlying these alterations cannot be determined from macroscopic brain recordings, we speculate that enhanced occipital-frontal excitation may result from changes in white matter density in ASD, as suggested in previous studies. We also venture that long-range spatial correlations in the background noise may result from less specificity (or more promiscuity of thalamo-cortical projections. All the calculations involved in our analysis are highly efficient and outperform other algorithms to discriminate typical and atypical brains with a comparable level of accuracy. Altogether our results demonstrate a promising potential of

  16. Identification of genetic modifiers of behavioral phenotypes in serotonin transporter knockout rats

    Directory of Open Access Journals (Sweden)

    Nijman Isaäc J

    2010-05-01

    Full Text Available Abstract Background Genetic variation in the regulatory region of the human serotonin transporter gene (SLC6A4 has been shown to affect brain functionality and personality. However, large heterogeneity in its biological effects is observed, which is at least partially due to genetic modifiers. To gain insight into serotonin transporter (SERT-specific genetic modifiers, we studied an intercross between the Wistar SERT-/- rat and the behaviorally and genetically divergent Brown Norway rat, and performed a QTL analysis. Results In a cohort of >150 intercross SERT-/- and control (SERT+/+ rats we characterized 12 traits that were previously associated with SERT deficiency, including activity, exploratory pattern, cocaine-induced locomotor activity, and abdominal and subcutaneous fat. Using 325 genetic markers, 10 SERT-/--specific quantitative trait loci (QTLs for parameters related to activity and exploratory pattern (Chr.1,9,11,14, and cocaine-induced anxiety and locomotor activity (Chr.5,8 were identified. No significant QTLs were found for fat parameters. Using in silico approaches we explored potential causal genes within modifier QTL regions and found interesting candidates, amongst others, the 5-HT1D receptor (Chr. 5, dopamine D2 receptor (Chr. 8, cannabinoid receptor 2 (Chr. 5, and genes involved in fetal development and plasticity (across chromosomes. Conclusions We anticipate that the SERT-/--specific QTLs may lead to the identification of new modulators of serotonergic signaling, which may be targets for pharmacogenetic and therapeutic approaches.

  17. Genetic heterogeneity, modifier genes, and quantitative phenotypes in psychiatric illness: searching for a framework.

    Science.gov (United States)

    Fanous, A H; Kendler, K S

    2005-01-01

    Schizophrenia has long been thought to be clinically heterogeneous. A range of studies suggests that this is due to genetic heterogeneity. Some clinical features, such as negative symptoms, are associated with a greater risk of illness in relatives. Affected sibling pairs are correlated for clinical and course features as well as subforms of illness, and twin studies suggest that this is due to genetic factors. This is further supported by findings that subjects from families linked to some chromosomal regions may differ clinically from those from unlinked families. Moreover, some genes may affect clinical features without altering susceptibility (ie are modifier genes). High-risk genotypes may have quantitative, rather than categorical effects, and may influence milder or subclinical phenotypes. Another recent finding is that nonpsychotic relatives may have personality features that resemble those of their affected relatives. These findings taken together suggest that there may be several classes of gene action in schizophrenia: some genes may influence susceptibility only, others may influence clinical features only, and still others may have a mixed effect. Furthermore, subsets of these classes may affect personality and other traits in nonpsychotic relatives. Understanding these classes of gene action may help guide the design of linkage and association studies that have increased power. We describe five classes of genes and their predictions of the outcomes of family, twin, and several types of linkage studies. We go on to explore how these predictions can in turn be used to aid in the design of linkage studies.

  18. Genetic background influences embryonic lethality and the occurrence of neural tube defects in Men1 null mice: relevance to genetic modifiers.

    Science.gov (United States)

    Lemos, Manuel C; Harding, Brian; Reed, Anita A C; Jeyabalan, Jeshmi; Walls, Gerard V; Bowl, Michael R; Sharpe, James; Wedden, Sarah; Moss, Julie E; Ross, Allyson; Davidson, Duncan; Thakker, Rajesh V

    2009-10-01

    Germline mutations of the multiple endocrine neoplasia type 1 (MEN1) gene cause parathyroid, pancreatic and pituitary tumours in man. MEN1 mutations also cause familial isolated primary hyperparathyroidism (FIHP) and the same MEN1 mutations, in different families, can cause either FIHP or MEN1. This suggests a role for genetic background and modifier genes in altering the expression of a mutation. We investigated the effects of genetic background on the phenotype of embryonic lethality that occurs in a mouse model for MEN1. Men1(+/-) mice were backcrossed to generate C57BL/6 and 129S6/SvEv incipient congenic strains, and used to obtain homozygous Men1(-/-) mice. No viable Men1(-/-) mice were obtained. The analysis of 411 live embryos obtained at 9.5-16.5 days post-coitum (dpc) revealed that significant deviations from the expected Mendelian 1:2:1 genotype ratio were first observed at 12.5 and 14.5 dpc in the 129S6/SvEv and C57BL/6 strains respectively (P<0.05). Moreover, live Men1(-/-) embryos were absent by 13.5 and 15.5 dpc in the 129S6/SvEv and C57BL/6 strains respectively thereby indicating an earlier lethality by 2 days in the 129S6/SvEv strain (P<0.01). Men1(-/-) embryos had macroscopic haemorrhages, and histology and optical projection tomography revealed them to have internal haemorrhages, myocardial hypotrophy, pericardial effusion, hepatic abnormalities and neural tube defects. The neural tube defects occurred exclusively in 129S6/SvEv embryos (21 vs 0%, P<0.01). Thus, our findings demonstrate the importance of genetic background in influencing the phenotypes of embryonic lethality and neural tube defects in Men1(-/-) mice, and implicate a role for genetic modifiers.

  19. Genetic background and phenotypic characterization over two farrowings of leg conformation defects in Landrace and Large White sows.

    Science.gov (United States)

    de Sevilla, X Fernàndez; Fàbrega, E; Tibau, J; Casellas, J

    2009-05-01

    A Bayesian threshold animal model was applied to evaluate the prevalence over 2 farrowings and genetic background of overall leg conformation score and the presence or absence of 6 specific leg defects (abnormal hoof growth, splay footed, plantigradism, straight pasterns, sickle-hocked legs, and the presence of swelling or injuries) in purebred Landrace and Large White sows. Data sets contained phenotypic records from 2,477 and 1,550 Landrace and Large White females, respectively, at the end of the growing period. Leg conformation data from first and second farrowings were available for 223 and 191 Landrace sows and 213 and 193 Large White sows, respectively. Overall leg conformation deteriorated with age, with statistically relevant differences between females at the end of the growing period, first farrowing (FF), and second farrowing (SF). In a similar way, the prevalence of the 6 specific leg defects increased between the end of the growing period and FF (with the exception of straight pasterns in the Landrace population). Differences between FF and second farrowing were statistically relevant for hoof growth (highest posterior density regions at 95% did not overlap), plantigradism, sickle-hocked legs, and overall leg conformation score in Landrace and for sickle-hocked leg and overall leg conformation score in Large White. The statistical relevance of the genetic background was tested through the Bayes factor (BF) between the model with the additive genetic component and the model with 0 heritability (nonheritable). Heritability (h(2)) was discarded (BF 100) of genetic background was obtained for overall leg conformation score in Landrace and Large White sows (h(2) = 0.27 and 0.38, respectively), hoof growth in both breeds (h(2) = 0.22 and 0.26, respectively), and plantigradism (h(2) = 0.34) and the presence of swelling or injuries in Landrace (h(2) = 0.27). Note that a BF > 100 implies that the model with infinitesimal genetic effects was more than 100 times

  20. Detection of KPC Carbapenemase in Pseudomonas aeruginosa Isolated From Clinical Samples Using Modified Hodge Test and Boronic Acid Phenotypic Methods and Their Comparison With the Polymerase Chain Reaction

    Science.gov (United States)

    Falahat, Saeed; Shojapour, Mana; Sadeghi, Abdorrahim

    2016-01-01

    Background Bacterial resistance to antibiotics has become a major source of concern for public health. Pseudomonas aeruginosa strains are important opportunistic pathogens. These bacteria have a high resistance to a wide range of existing antimicrobials and antibiotics. Objectives The present study was performed to evaluate the frequency of KPC in P. aeruginosa isolated from clinical samples of educational hospitals of Arak University of Medical Sciences, using the mentioned phenotypic and genotypic methods. Materials and Methods One hundred and eight non-duplicate clinical isolates of P. aeruginosa were collected from hospitals of Arak University of Medical Sciences, Arak, Iran. Antibacterial susceptibility was determined by the disk diffusion method. KPC production was confirmed by the Modified Hodge Test (MHT), which is a phenotypic test, and combined-disk test with boronic acid and the Polymerase Chain Reaction (PCR). Results In the present study, 13 isolates (12%) of P. aeruginosa were positive for KPC, using PCR. Comparison of the two phenotypic methods used in this study showed that boronic acid is more sensitive than MHT in identification of KPC-producing strains (84.6% vs. 77%). Conclusions Utilization of reliable methods for identifying carbapenemase-producing strains and determining their antibiotic resistance pattern could have a very important role in treatment of infections caused by these strains. A substantial amount of P. aeruginosa isolated from clinical samples of hospitals in Arak (Iran) produce KPC carbapenemase. Due to their low specificity, MHT and boronic acid phenotypic methods could not completely identify KPC-producing P. aeruginosa. However, the sensitivity of boronic acid phenotypic method in detection of KPC was higher than MHT.

  1. Genetic modifiers of sickle cell anemia in the BABY HUG cohort: influence on laboratory and clinical phenotypes.

    Science.gov (United States)

    Sheehan, Vivien A; Luo, Zhaoyu; Flanagan, Jonathan M; Howard, Thad A; Thompson, Bruce W; Wang, Winfred C; Kutlar, Abdullah; Ware, Russell E

    2013-07-01

    The recently completed BABY HUG trial investigated the safety and efficacy of hydroxyurea in infants with sickle cell anemia (SCA). To investigate the effects of known genetic modifiers, genomic DNA on 190 randomized subjects were analyzed for alpha thalassemia, beta-globin haplotype, polymorphisms affecting endogenous fetal hemoglobin (HbF) levels (XmnI, BCL11A, and HBS1L-MYB), UGT1A1 promoter polymorphisms, and the common G6PD A(-) mutation. At study entry, infants with alpha thalassemia trait had significantly lower mean corpuscular volume, total bilirubin, and absolute reticulocyte count. Beta-globin haplotypes associated with milder disease had significantly higher hemoglobin and %HbF. BCL11A and XmnI polymorphisms had significant effects on baseline HbF, while UGT1A1 promoter polymorphisms significantly influenced baseline serum bilirubin. At study exit, subjects randomized to placebo still exhibited laboratory effects of alpha thalassemia and other modifiers, while those assigned hydroxyurea had treatment effects that exceeded most genetic influences. The pain phenotype was influenced by HbF modifiers in both treatment groups. These data document that genetic polymorphisms do modify laboratory and clinical phenotypes even in very young patients with SCA. The hydroxyurea effects are more potent, however, indicating that treatment criteria should not be limited to certain genetic subsets, and supporting the use of hydroxyurea for all young patients with SCA.

  2. Asthma phenotypes modify the impact of environmetnal factors on lung function

    Science.gov (United States)

    Previous studies have examined the role of childhood asthma phenotypes based on clinical history on asthma severity and symptom aggravation by environmental risk factors. The current study focuses on the associations between lung function in childhood and environmental factors an...

  3. The effect of chemically modified alginates on macrophage phenotype and biomolecule transport.

    Science.gov (United States)

    Bygd, Hannah C; Bratlie, Kaitlin M

    2016-07-01

    Macrophage (MΦ) reprogramming has received significant attention in applications such as cancer therapeutics and tissue engineering where the host immune response to biomaterials is crucial in determining the success or failure of an implanted device. Polymeric systems can potentially be used to redirect infiltrating M1 MΦs toward a proangiogenic phenotype. This work exploits the concept of MΦ reprogramming in the engineering of materials for improving the longevity of tissue engineering scaffolds. We have investigated the effect of 13 different chemical modifications of alginate on MΦ phenotype. Markers of the M1 response-tumor necrosis factor-α (TNF-α) and inducible nitric oxide synthase-and the M2 response-arginase-were measured and used to determine the ability of the materials to alter MΦ phenotype. It was found that some modifications were able to reduce the pro-inflammatory response of M1 MΦs, others appeared to amplify the M2 phenotype, and the results for two materials suggested they were able to reprogram a MΦ population from M1 to M2. These findings were supplemented by studies done to examine the permselectivity of the materials. Diffusion of TNF-α was completely prevented through some of these materials, while up to 84% was found to diffuse through others. The diffusion of insulin through the materials was statistically consistent. These results suggest that the modification of these materials might alter mass transport in beneficial ways. The ability to control polarization of MΦ phenotypes with immunoprotective materials has the potential to augment the success of tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1707-1719, 2016.

  4. Approaches for the Identification of Genetic Modifiers of Nutrient Dependent Phenotypes: Examples from Folate

    OpenAIRE

    MacFarlane, Amanda J.; Ian eZinck

    2014-01-01

    By combining the sciences of nutrition, bioinformatics, genomics, population genetics, and epidemiology, nutrigenomics is improving our understanding of how diet and nutrient intake can interact with or modify gene expression and disease risk. In this review, we explore various approaches to examine gene–nutrient interactions and the modifying role of nutrient consumption, as they relate to nutrient status and disease risk in human populations. Two common approaches include the use of SNPs in...

  5. ATXN2 is a modifier of phenotype in ALS patients of Sardinian ancestry

    Science.gov (United States)

    Borghero, Giuseppe; Pugliatti, Maura; Marrosu, Francesco; Marrosu, Maria Giovanna; Murru, Maria Rita; Floris, Gianluca; Cannas, Antonino; Parish, Leslie D.; Cau, Tea B.; Loi, Daniela; Ticca, Anna; Traccis, Sebastiano; Manera, Umberto; Canosa, Antonio; Moglia, Cristina; Calvo, Andrea; Barberis, Marco; Brunetti, Maura; Renton, Alan E.; Nalls, Mike A.; Traynor, Bryan J.; Restagno, Gabriella; Chiò, Adriano

    2016-01-01

    Intermediate-length CAG expansions (encoding 27–33 glutamines, polyQ) of the Ataxin2 (ATXN2) gene represent a risk factor for amyotrophic lateral sclerosis (ALS). Recently, it has been proposed that ≥31 CAG expansions may influence ALS phenotype. We assessed whether ATXN2 intermediate-length polyQ expansions influence ALS phenotype in a series of 375 patients of Sardinian ancestry. Controls were 247 neurologically healthy subjects, resident in the study area, age- and gender-matched to cases. The frequency of ≥31 polyQ ATNX2 repeats was significantly more common in ALS cases (4 patients vs. no control, p = 0.0001). All patients with ≥31 polyQ repeats had a spinal onset versus 73.3% of patients with <31 polyQ repeats. Patients with an increased number of polyQ repeats have a shorter survival than those with <31 repeats (1.2 vs. 4.2 years, p = 0.035). In this large series of ALS patients of Sardinian ancestry, we have found that ≥31 polyQ repeats of the ATXN2 gene influenced patients' phenotype, being associated to a spinal onset and a significantly shorter survival. PMID:26208502

  6. The therapeutic potential of skeletal muscle plasticity in Duchenne muscular dystrophy: phenotypic modifiers as pharmacologic targets.

    Science.gov (United States)

    Ljubicic, Vladimir; Burt, Matthew; Jasmin, Bernard J

    2014-02-01

    Duchenne muscular dystrophy (DMD) is a life-limiting, neuromuscular disorder that causes progressive, severe muscle wasting in boys and young men. Although there is no cure, scientists and clinicians can leverage the fact that slower, more oxidative skeletal muscle fibers possess an enhanced degree of resistance to the dystrophic pathology relative to their faster, more glycolytic counterparts, and can thus use this knowledge when investigating novel therapeutic avenues. Several factors have been identified as powerful regulators of muscle plasticity. Some proteins, such as calcineurin, peroxisome proliferator-activated receptor (PPAR) γ coactivator 1α (PGC-1α), PPARβ/δ, and AMP-activated protein kinase (AMPK), when chronically stimulated in animal models, remodel skeletal muscle toward the slow, oxidative myogenic program, whereas others, such as receptor-interacting protein 140 (RIP140) and E2F transcription factor 1 (E2F1), repress this phenotype. Recent studies demonstrating that pharmacologic and physiological activation of targets that shift dystrophic muscle toward the slow, oxidative myogenic program provide appreciable molecular and functional benefits. This review surveys the rationale behind, and evidence for, the study of skeletal muscle plasticity in preclinical models of DMD and highlights the potential therapeutic opportunities in advancing a strategy focused on remodeling skeletal muscle in patients with DMD toward the slow, oxidative phenotype.

  7. Consistent and reproducible positioning in longitudinal imaging for phenotyping genetically modified swine

    Science.gov (United States)

    Hammond, Emily; Dilger, Samantha K. N.; Stoyles, Nicholas; Judisch, Alexandra; Morgan, John; Sieren, Jessica C.

    2015-03-01

    Recent growth of genetic disease models in swine has presented the opportunity to advance translation of developed imaging protocols, while characterizing the genotype to phenotype relationship. Repeated imaging with multiple clinical modalities provides non-invasive detection, diagnosis, and monitoring of disease to accomplish these goals; however, longitudinal scanning requires repeatable and reproducible positioning of the animals. A modular positioning unit was designed to provide a fixed, stable base for the anesthetized animal through transit and imaging. Post ventilation and sedation, animals were placed supine in the unit and monitored for consistent vitals. Comprehensive imaging was performed with a computed tomography (CT) chest-abdomen-pelvis scan at each screening time point. Longitudinal images were rigidly registered, accounting for rotation, translation, and anisotropic scaling, and the skeleton was isolated using a basic thresholding algorithm. Assessment of alignment was quantified via eleven pairs of corresponding points on the skeleton with the first time point as the reference. Results were obtained with five animals over five screening time points. The developed unit aided in skeletal alignment within an average of 13.13 +/- 6.7 mm for all five subjects providing a strong foundation for developing qualitative and quantitative methods of disease tracking.

  8. SCN4A mutation as modifying factor of myotonic dystrophy type 2 phenotype.

    Science.gov (United States)

    Bugiardini, E; Rivolta, I; Binda, A; Soriano Caminero, A; Cirillo, F; Cinti, A; Giovannoni, R; Botta, A; Cardani, R; Wicklund, M P; Meola, G

    2015-04-01

    In myotonic dystrophy type 2 (DM2), an association has been reported between early and severe myotonia and recessive chloride channel (CLCN1) mutations. No DM2 cases have been described with sodium channel gene (SCN4A) mutations. The aim is to describe a DM2 patient with severe and early onset myotonia and co-occurrence of a novel missense mutation in SNC4A. A 26-year-old patient complaining of hand cramps and difficulty relaxing her hands after activity was evaluated at our department. Neurophysiology and genetic analysis for DM1, DM2, CLCN1 and SCN4A mutations were performed. Genetic testing was positive for DM2 (2650 CCTG repeat) and for a variant c.215C>T (p.Pro72Leu) in the SCN4A gene. The variation affects the cytoplasmic N terminus domain of Nav1.4, where mutations have never been reported. The biophysical properties of the mutant Nav1.4 channels were evaluated by whole-cell voltage-clamp analysis of heterologously expressed mutant channel in tsA201 cells. Electrophysiological studies of the P72L variant showed a hyperpolarizing shift (-5 mV) of the voltage dependence of activation that may increase cell excitability. This case suggests that SCN4A mutations may enhance the myotonic phenotype of DM2 patients and should be screened for atypical cases with severe myotonia.

  9. Can galaxy clusters, type Ia supernovae and cosmic microwave background ruled out a class of modified gravity theories?

    CERN Document Server

    Holanda, R F L

    2016-01-01

    In this paper we study cosmological signatures of modified gravity theories that can be written as a coupling between a extra scalar field and the electromagnetic part of the usual Lagrangian for the matter fields. In these frameworks all the electromagnetic sector of the theory is affected and variations of fundamental constants, of the cosmic distance duality relation and of the evolution law of the cosmic microwave background radiation (CMB) are expected and are related each other. In order to search these variations we perform jointly analyses with angular diameter distances of galaxy clusters, luminosity distances of type Ia supernovae and $T_{CMB}(z)$ measurements. We obtain tight constraints with no indication of violation of the standard framework.

  10. Staphylococcal phenotypes induced by naturally occurring and synthetic membrane-interactive polyphenolic β-lactam resistance modifiers.

    Directory of Open Access Journals (Sweden)

    Lucia Palacios

    Full Text Available Galloyl catechins, in particular (--epicatechin gallate (ECg, have the capacity to abrogate β-lactam resistance in methicillin-resistant strains of Staphylococcus aureus (MRSA; they also prevent biofilm formation, reduce the secretion of a large proportion of the exoproteome and induce profound changes to cell morphology. Current evidence suggests that these reversible phenotypic traits result from their intercalation into the bacterial cytoplasmic membrane. We have endeavoured to potentiate the capacity of ECg to modify the MRSA phenotype by stepwise removal of hydroxyl groups from the B-ring pharmacophore and the A:C fused ring system of the naturally occurring molecule. ECg binds rapidly to the membrane, inducing up-regulation of genes responsible for protection against cell wall stress and maintenance of membrane integrity and function. Studies with artificial membranes modelled on the lipid composition of the staphylococcal bilayer indicated that ECg adopts a position deep within the lipid palisade, eliciting major alterations in the thermotropic behaviour of the bilayer. The non-galloylated homolog (--epicatechin enhanced ECg-mediated effects by facilitating entry of ECg molecules into the membrane. ECg analogs with unnatural B-ring hydroxylation patterns induced higher levels of gene expression and more profound changes to MRSA membrane fluidity than ECg but adopted a more superficial location within the bilayer. ECg possessed a high affinity for the positively charged staphylococcal membrane and induced changes to the biophysical properties of the bilayer that are likely to account for its capacity to disperse the cell wall biosynthetic machinery responsible for β-lactam resistance. The ability to enhance these properties by chemical modification of ECg raises the possibility that more potent analogs could be developed for clinical evaluation.

  11. F12-46C/T polymorphism as modifier of the clinical phenotype of hereditary angioedema.

    Science.gov (United States)

    Speletas, M; Szilágyi, Á; Csuka, D; Koutsostathis, N; Psarros, F; Moldovan, D; Magerl, M; Kompoti, M; Varga, L; Maurer, M; Farkas, H; Germenis, A E

    2015-12-01

    The factors influencing the heterogeneous clinical manifestation of hereditary angioedema due to C1-INH deficiency (C1-INH-HAE) represent one of the oldest unsolved problems of the disease. Considering that factor XII (FXII) levels may affect bradykinin production, we investigated the contribution of the functional promoter polymorphism F12-46C/T in disease phenotype. We studied 258 C1-INH-HAE patients from 113 European families, and we explored possible associations of F12-46C/T with clinical features and the SERPING1 mutational status. Given that our cohort consisted of related subjects, we implemented generalized estimating equations (GEEs), an extension of the generalized linear model accounting for the within-subject correlation. F12-46C/T carriers exhibited a significantly delayed disease onset (P < 0.001) and did not need long-term treatment (P = 0.02). In a GEE linear regression model, the presence of F12-46C/T was significantly associated with a 7-year delay in disease onset (P < 0.0001) regardless of SERPING1 mutational status. It is concluded that F12-46C/T carriage acts as an independent modifier of C1-INH-HAE severity.

  12. New Exact Solutions and Evolution of Solitons in Background Waves for (2+1)-Dimensional Modified Dispersive Water-Wave System

    Institute of Scientific and Technical Information of China (English)

    MA Song-Hua; JIANG Yong-Qing; FANG Jian-Ping

    2008-01-01

    With the help of the conditional similarity reduction method, some new exact solutions of the (2+1)-dimensional modified dispersive water-wave system (MDWW) are obtained. Based on the derived solution, we investigate the evolution of solitons in the background waves.

  13. Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.

    Science.gov (United States)

    Simčič, Mojca; Smetko, Anamarija; Sölkner, Johann; Seichter, Doris; Gorjanc, Gregor; Kompan, Dragomir; Medugorac, Ivica

    2015-01-01

    The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had

  14. Humans, Fish, and Whales: How Right Whales Modify Calling Behavior in Response to Shifting Background Noise Conditions.

    Science.gov (United States)

    Parks, Susan E; Groch, Karina; Flores, Paulo; Sousa-Lima, Renata; Urazghildiiev, Ildar R

    2016-01-01

    This study investigates the role of behavioral plasticity in the variation of sound production of southern right whales (Eubalaena australis) in response to changes in the ambient background noise conditions. Data were collected from southern right whales in Brazilian waters in October and November 2011. The goal of this study was to quantify differences in right whale vocalizations recorded in low background noise as a control, fish chorus noise, and vessel noise. Variation in call parameters were detected among the three background noise conditions and have implications for future studies of noise effects on whale sound production.

  15. Genetic screening of LCA in Belgium: predominance of CEP290 and identification of potential modifier alleles in AHI1 of CEP290-related phenotypes.

    Science.gov (United States)

    Coppieters, Frauke; Casteels, Ingele; Meire, Françoise; De Jaegere, Sarah; Hooghe, Sally; van Regemorter, Nicole; Van Esch, Hilde; Matuleviciene, Ausra; Nunes, Luis; Meersschaut, Valérie; Walraedt, Sophie; Standaert, Lieve; Coucke, Paul; Hoeben, Heidi; Kroes, Hester Y; Vande Walle, Johan; de Ravel, Thomy; Leroy, Bart P; De Baere, Elfride

    2010-10-01

    Leber Congenital Amaurosis (LCA), the most severe inherited retinal dystrophy, is genetically heterogeneous, with 14 genes accounting for 70% of patients. Here, 91 LCA probands underwent LCA chip analysis and subsequent sequencing of 6 genes (CEP290, CRB1, RPE65, GUCY2D, AIPL1and CRX), revealing mutations in 69% of the cohort, with major involvement of CEP290 (30%). In addition, 11 patients with early-onset retinal dystrophy (EORD) and 13 patients with Senior-Loken syndrome (SLS), LCA-Joubert syndrome (LCA-JS) or cerebello-oculo-renal syndrome (CORS) were included. Exhaustive re-inspection of the overall phenotypes in our LCA cohort revealed novel insights mainly regarding the CEP290-related phenotype. The AHI1 gene was screened as a candidate modifier gene in three patients with the same CEP290 genotype but different neurological involvement. Interestingly, a heterozygous novel AHI1 mutation, p.Asn811Lys, was found in the most severely affected patient. Moreover, AHI1 screening in five other patients with CEP290-related disease and neurological involvement revealed a second novel missense variant, p.His758Pro, in one LCA patient with mild mental retardation and autism. These two AHI1 mutations might thus represent neurological modifiers of CEP290-related disease.

  16. Biochemical evidence for a mitochondrial genetic modifier in the phenotypic manifestation of Leber's hereditary optic neuropathy-associated mitochondrial DNA mutation.

    Science.gov (United States)

    Jiang, Pingping; Liang, Min; Zhang, Chaofan; Zhao, Xiaoxu; He, Qiufen; Cui, Limei; Liu, Xiaoling; Sun, Yan-Hong; Fu, Qun; Ji, Yanchun; Bai, Yidong; Huang, Taosheng; Guan, Min-Xin

    2016-08-15

    Leber's hereditary optic neuropathy (LHON) is the most common mitochondrial disease. Mitochondrial modifiers are proposed to modify the phenotypic expression of primary LHON-associated mitochondrial DNA (mtDNA) mutations. In this study, we demonstrated that the LHON susceptibility allele (m.14502T > C, p. 58I > V) in the ND6 gene modulated the phenotypic expression of primary LHON-associated m.11778G > A mutation. Twenty-two Han Chinese pedigrees carrying m.14502T > C and m.11778G > A mutations exhibited significantly higher penetrance of optic neuropathy than those carrying only m.11778G > A mutation. We performed functional assays using the cybrid cell models, generated by fusing mtDNA-less ρ(o) cells with enucleated cells from LHON patients carrying both m.11778G > A and m.14502T > C mutations, only m.14502T > C or m.11778G > A mutation and a control belonging to the same mtDNA haplogroup. These cybrids cell lines bearing m.14502T > C mutation exhibited mild effects on mitochondrial functions compared with those carrying only m.11778G > A mutation. However, more severe mitochondrial dysfunctions were observed in cell lines bearing both m.14502T > C and m.11778G > A mutations than those carrying only m.11778G > A or m.14502T > C mutation. In particular, the m.14502T > C mutation altered assemble of complex I, thereby aggravating the respiratory phenotypes associated with m.11778G > A mutation, resulted in a more defective complex I. Furthermore, more reductions in the levels of mitochondrial ATP and increasing production of reactive oxygen species were also observed in mutant cells bearing both m.14502T > C and m.11778G > A mutation than those carrying only 11778G > A mutation. Our findings provided new insights into the pathophysiology of LHON that were manifested by interaction between primary and secondary mtDNA mutations.

  17. BODE-index, modified BODE-index and ADO-score in chronic obstructive pulmonary disease: relationship with COPD phenotypes and CT lung density changes.

    Science.gov (United States)

    Camiciottoli, Gianna; Bigazzi, Francesca; Bartolucci, Maurizio; Cestelli, Lucia; Paoletti, Matteo; Diciotti, Stefano; Cavigli, Edoardo; Magni, Chiara; Buonasera, Luigi; Mascalchi, Mario; Pistolesi, Massimo

    2012-06-01

    COPD is a heterogeneous disorder whose assessment is going to be increasingly multidimensional. Grading systems such as BODE (Body-Mass Index, Obstruction, Dyspnea, Exercise), mBODE (BODE modified in grading of walked distance), ADO (Age, Dyspnea, Obstruction) are proposed to assess COPD severity and outcome. Computed tomography (CT) is deemed to reflect COPD lung pathologic changes. We studied the relationship of multidimensional grading systems (MGS) with clinically determined COPD phenotypes and CT lung density. Seventy-two patients underwent clinical and chest x-ray evaluation, pulmonary function tests (PFT), 6-minute walking test (6MWT) to derive: predominant COPD clinical phenotype, BODE, mBODE, ADO. Inspiratory and expiratory CT was performed to calculate mean lung attenuation (MLA), relative area with density below-950 HU at inspiration (RAI(-950)), and below -910 HU at expiration (RAE(-910)). MGS, PFT, and CT data were compared between bronchial versus emphysematous COPD phenotype. MGS were correlated with CT data. The prediction of CT density by means of MGS was investigated by direct and stepwise multivariate regression. MGS did not differ in clinically determined COPD phenotypes. BODE was more closely related and better predicted CT findings than mBODE and ADO; the better predictive model was obtained for CT expiratory data; stepwise regression models of CT data did not include 6MWT distance; the dyspnea score MRC was included only to predict RA-950 and RA-910 which quantify emphysema extent. BODE reflect COPD severity better than other MGS, but not its clinical heterogeneity. 6MWT does not significantly increase BODE predictivity of CT lung density changes.

  18. Manufacture of gene-modified human T-cells with a memory stem/central memory phenotype

    NARCIS (Netherlands)

    Gomez-Eerland, Raquel; Nuijen, Bastiaan; Heemskerk, Bianca; van Rooij, Nienke; van den Berg, Joost H; Beijnen, Jos H; Uckert, Wolfgang; Kvistborg, Pia; Schumacher, Ton N; Haanen, John B A G; Jorritsma, Annelies

    2014-01-01

    Advances in genetic engineering have made it possible to generate human T-cell products that carry desired functionalities, such as the ability to recognize cancer cells. The currently used strategies for the generation of gene-modified T-cell products lead to highly differentiated cells within the

  19. Mutations in a guanylate cyclase GCY-35/GCY-36 modify Bardet-Biedl syndrome-associated phenotypes in Caenorhabditis elegans.

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    Calvin A Mok

    2011-10-01

    Full Text Available Ciliopathies are pleiotropic and genetically heterogeneous disorders caused by defective development and function of the primary cilium. Bardet-Biedl syndrome (BBS proteins localize to the base of cilia and undergo intraflagellar transport, and the loss of their functions leads to a multisystemic ciliopathy. Here we report the identification of mutations in guanylate cyclases (GCYs as modifiers of Caenorhabditis elegans bbs endophenotypes. The loss of GCY-35 or GCY-36 results in suppression of the small body size, developmental delay, and exploration defects exhibited by multiple bbs mutants. Moreover, an effector of cGMP signalling, a cGMP-dependent protein kinase, EGL-4, also modifies bbs mutant defects. We propose that a misregulation of cGMP signalling, which underlies developmental and some behavioural defects of C. elegans bbs mutants, may also contribute to some BBS features in other organisms.

  20. Mitochondrial genetic background modifies the relationship between traffic-related air pollution exposure and systemic biomarkers of inflammation.

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    Sharine Wittkopp

    Full Text Available BACKGROUND: Mitochondria are the main source of reactive oxygen species (ROS. Human mitochondrial haplogroups are linked to differences in ROS production and oxidative-stress induced inflammation that may influence disease pathogenesis, including coronary artery disease (CAD. We previously showed that traffic-related air pollutants were associated with biomarkers of systemic inflammation in a cohort panel of subjects with CAD in the Los Angeles air basin. OBJECTIVE: We tested whether air pollutant exposure-associated inflammation was stronger in mitochondrial haplogroup H than U (high versus low ROS production in this panel (38 subjects and 417 observations. METHODS: Inflammation biomarkers were measured weekly in each subject (≤ 12 weeks, including interleukin-6 (IL-6, tumor necrosis factor-α (TNF-α, C-reactive protein, interleukin-6 soluble receptor and tumor necrosis factor-soluble receptor II. We determined haplogroup by restriction fragment length polymorphism analysis. Air pollutants included nitrogen oxides (NOx, carbon monoxide (CO, organic carbon, elemental and black carbon (EC, BC; and particulate matter mass, three size fractions (<0.25 µm, 0.25-2.5 µm, and 2.5-10 µm in aerodynamic diameter. Particulate matter extracts were analyzed for organic compounds, including polycyclic aromatic hydrocarbons (PAH, and in vitro oxidative potential of aqueous extracts. Associations between exposures and biomarkers, stratified by haplogroup, were analyzed by mixed-effects models. RESULTS: IL-6 and TNF-α were associated with traffic-related air pollutants (BC, CO, NOx and PAH, and with mass and oxidative potential of quasi-ultrafine particles <0.25 µm. These associations were stronger for haplogroup H than haplogroup U. CONCLUSIONS: Results suggest that mitochondrial haplogroup U is a novel protective factor for air pollution-related systemic inflammation in this small group of subjects.

  1. Genetic knock-down of HDAC3 does not modify disease-related phenotypes in a mouse model of Huntington's disease.

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    Lara Moumné

    Full Text Available Huntington's disease (HD is an autosomal dominant progressive neurodegenerative disorder caused by an expansion of a CAG/polyglutamine repeat for which there are no disease modifying treatments. In recent years, transcriptional dysregulation has emerged as a pathogenic process that appears early in disease progression and has been recapitulated across multiple HD models. Altered histone acetylation has been proposed to underlie this transcriptional dysregulation and histone deacetylase (HDAC inhibitors, such as suberoylanilide hydroxamic acid (SAHA, have been shown to improve polyglutamine-dependent phenotypes in numerous HD models. However potent pan-HDAC inhibitors such as SAHA display toxic side-effects. To better understand the mechanism underlying this potential therapeutic benefit and to dissociate the beneficial and toxic effects of SAHA, we set out to identify the specific HDAC(s involved in this process. For this purpose, we are exploring the effect of the genetic reduction of specific HDACs on HD-related phenotypes in the R6/2 mouse model of HD. The study presented here focuses on HDAC3, which, as a class I HDAC, is one of the preferred targets of SAHA and is directly involved in histone deacetylation. To evaluate a potential benefit of Hdac3 genetic reduction in R6/2, we generated a mouse carrying a critical deletion in the Hdac3 gene. We confirmed that the complete knock-out of Hdac3 is embryonic lethal. To test the effects of HDAC3 inhibition, we used Hdac3(+/- heterozygotes to reduce nuclear HDAC3 levels in R6/2 mice. We found that Hdac3 knock-down does not ameliorate physiological or behavioural phenotypes and has no effect on molecular changes including dysregulated transcripts. We conclude that HDAC3 should not be considered as the major mediator of the beneficial effect induced by SAHA and other HDAC inhibitors in HD.

  2. Modified CLSI extended-spectrum β-lactamase (ESBL) confirmatory test for phenotypic detection of ESBLs among Enterobacteriaceae producing various β-lactamases.

    Science.gov (United States)

    Poulou, Aggeliki; Grivakou, Evgenia; Vrioni, Georgia; Koumaki, Vassiliki; Pittaras, Theodoros; Pournaras, Spyros; Tsakris, Athanassios

    2014-05-01

    The worldwide dissemination of Enterobacteriaceae producing AmpC β-lactamases and carbapenemases makes difficult the phenotypic detection of extended-spectrum β-lactamases (ESBLs), as they may be masked by these additional enzymes. A modification of the CLSI ESBL confirmatory test was developed and evaluated in a comparative study for its ability to successfully detect ESBLs among Enterobacteriaceae producing various carbapenemases (Klebsiella pneumoniae carbapenemase [KPC], VIM, NDM, and OXA-48) and plasmidic or derepressed AmpCs. The modified CLSI ESBL confirmatory test was performed with cefotaxime and ceftazidime disks with and without clavulanate, on which both boronic acid (BA) and EDTA were dispensed. A total of 162 genotypically confirmed ESBL-positive Enterobacteriaceae isolates (83 carbapenemase/ESBL producers, 25 AmpC/ESBL producers, and 54 ESBL-only producers) were examined. For comparison, 139 genotypically confirmed ESBL-negative Enterobacteriaceae isolates (94 of them possessed carbapenemases and 20 possessed AmpCs) were also tested. The standard CLSI ESBL confirmatory test was positive for 106 of the 162 ESBL producers (sensitivity, 65.4%) and showed false-positive results for 4 of the 139 non-ESBL producers (specificity, 97.1%). The modified CLSI ESBL confirmatory test detected 158 of 162 ESBL producers (sensitivity, 97.5%) and showed no false-positive results for non-ESBL producers (specificity, 100%). The findings of the study demonstrate that the modified CLSI ESBL confirmatory test using antibiotic disks containing both BA and EDTA accurately detects ESBLs in Enterobacteriaceae regardless of the coexistence of additional β-lactam resistance mechanisms.

  3. Levels of alpha-toxin correlate with distinct phenotypic response profiles of blood mononuclear cells and with agr background of community-associated Staphylococcus aureus isolates.

    Science.gov (United States)

    Mairpady Shambat, Srikanth; Haggar, Axana; Vandenesch, Francois; Lina, Gerard; van Wamel, Willem J B; Arakere, Gayathri; Svensson, Mattias; Norrby-Teglund, Anna

    2014-01-01

    Epidemiological studies of Staphylococcus aureus have shown a relation between certain clones and the presence of specific virulence genes, but how this translates into virulence-associated functional responses is not fully elucidated. Here we addressed this issue by analyses of community-acquired S. aureus strains characterized with respect to antibiotic resistance, ST types, agr types, and virulence gene profiles. Supernatants containing exotoxins were prepared from overnight bacterial cultures, and tested in proliferation assays using human peripheral blood mononuclear cells (PBMC). The strains displayed stable phenotypic response profiles, defined by either a proliferative or cytotoxic response. Although, virtually all strains elicited superantigen-mediated proliferative responses, the strains with a cytotoxic profile induced proliferation only in cultures with the most diluted supernatants. This indicated that the superantigen-response was masked by a cytotoxic effect which was also confirmed by flow cytometry analysis. The cytotoxic supernatants contained significantly higher levels of α-toxin than did the proliferative supernatants. Addition of α-toxin to supernatants characterized as proliferative switched the response into cytotoxic profiles. In contrast, no effect of Panton Valentine Leukocidin, δ-toxin or phenol soluble modulin α-3 was noted in the proliferative assay. Furthermore, a significant association between agr type and phenotypic profile was found, where agrII and agrIII strains had predominantly a proliferative profile whereas agrI and IV strains had a predominantly cytotoxic profile. The differential response profiles associated with specific S. aureus strains with varying toxin production could possibly have an impact on disease manifestations, and as such may reflect specific pathotypes.

  4. Genetic Modifiers of Sickle Cell Disease: A Genotype-Phenotype Relationship Study in a Cohort of 82 Children on Mayotte Island.

    Science.gov (United States)

    Muszlak, Mathias; Pissard, Serge; Badens, Catherine; Chamouine, Abdourahim; Maillard, Olivier; Thuret, Isabelle

    2015-01-01

    Sickle cell disease presents a great clinical variability that remains largely misunderstood. New disease protective genetic modifiers acting mainly through an increased Hb F level have recently been described. We studied relations between clinical and hematological phenotypes and known sickle cell disease genetic modifiers in patients from Mayotte Island, a remote French territory located in the Indian Ocean. Eighty-two children with sickle cell disease were enrolled; their median age was 5.9 years (range 1-18). Clinical and hematological features of sickle cell disease were retrospectively collected. Genetic studies included determination of β-globin genotypes [Hb SS, Hb S-β(0)-thalassemia (Hb S-β(0)-thal), Hb S-β(+)-thal], β(S)-globin locus haplotype, α-thalassemia (α-thal), and single nucleotide polymorphisms (SNPs) located in quantitative trait loci for Hb F expression (XmnI polymorphism, BCL11A rs4671393 and rs11886868, intergenic region of HBS1L-MYB rs28384513, rs4895441 and rs9399137). Univariate and multivariate analyses were conducted. Twenty-eight percent of the patients had Hb S-β-thal (eight different mutations in 21 patients), 55.0% had the -α(3.7) (rightward) deletion and 88.0% of the homozygous Hb SS patients were carrying a homozygous Bantu haplotype. In the multivariate model, the prognosis role of the SNP BCL11A rs4671393 was confirmed in the studied population showing a significant association with an elevated Hb F level and with a low hospitalization rate. The -α(3.7) deletion, XmnI polymorphism and intergenic region HBS1L-MYB SNPs were not significantly linked to any clinical criteria of severity. This report, the first to describe the main features of children with sickle cell disease on Mayotte Island, highlights the protective effect of the BCL11A polymorphism in this population.

  5. Identification and mapping stripe rust resistance gene YrLM168a using extreme individuals and recessive phenotype class in a complicate genetic background.

    Science.gov (United States)

    Feng, Junyan; Chen, Guoyue; Wei, Yuming; Liu, Yaxi; Jiang, Qiantao; Li, Wei; Pu, Zhien; Lan, Xiujin; Dai, Shoufen; Zhang, Min; Zheng, Youliang

    2015-12-01

    The identification and characterization of resistance genes effective against stripe rust of wheat is beneficial for modern wheat breeding programs. Molecular markers to such genes facilitate their deployment. The variety Milan has resistance that is effective against the predominant stripe rust races in the Sichuan region. Two resistant and two susceptible F8 lines from a cross between Milan and the susceptible variety Chuannong 16 were used to investigate inheritance of the Milan resistance. Three F2 populations were developed from crosses between the resistant lines and their susceptible sibling lines (LM168a × LM168c, LM168c × LM168a, LM168b × LM168d) and used for genetic analysis and molecular mapping of the genes for resistance. The stripe rust resistance in LM168a and LM168b was conferred by a single dominant gene, temporarily designated as YrLM168a. Forty-five extreme susceptible plants from the F2 families of LM168d × LM168b were genotyped with 836 simple sequence repeat (SSR) markers to map YrLM168a. YrLM168a was mapped in chromosome 6BL. The nearest flanking markers Xwmc756 and Xbarc146 were 4.6 and 4.6 cM away from the gene at both sides, respectively. The amplification results of twenty extreme resistant (IT 0) and susceptible (IT 4) F2 plants of LM168c × LM168a and LM168a × LM168c with marker Xwmc756 further validated the mapping results. The study suggested that extreme individuals and recessive phenotype class can be successfully used for mapping genes, which should be efficient and reliable. In addition, the flanking markers near YrLM168a should be helpful in marker-assisted breeding.

  6. Randomly detected genetically modified (GM maize (Zea mays L. near a transport route revealed a fragile 45S rDNA phenotype.

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    Nomar Espinosa Waminal

    Full Text Available Monitoring of genetically modified (GM crops has been emphasized to prevent their potential effects on the environment and human health. Monitoring of the inadvertent dispersal of transgenic maize in several fields and transport routes in Korea was carried out by qualitative multiplex PCR, and molecular analyses were conducted to identify the events of the collected GM maize. Cytogenetic investigations through fluorescence in situ hybridization (FISH of the GM maize were performed to check for possible changes in the 45S rDNA cluster because this cluster was reported to be sensitive to replication and transcription stress. Three GM maize kernels were collected from a transport route near Incheon port, Korea, and each was found to contain NK603, stacked MON863 x NK603, and stacked NK603 x MON810 inserts, respectively. Cytogenetic analysis of the GM maize containing the stacked NK603 x MON810 insert revealed two normal compact 5S rDNA signals, but the 45S rDNA showed a fragile phenotype, demonstrating a "beads-on-a-string" fragmentation pattern, which seems to be a consequence of genetic modification. Implications of the 45S rDNA cluster fragility in GM maize are also discussed.

  7. Fat and carbohydrate intake over three generations modify growth, metabolism and cardiovascular phenotype in female mice in an age-related manner.

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    Samuel P Hoile

    Full Text Available Environmental challenges such as a high fat diet during pregnancy can induce changes in offspring growth, metabolism and cardiovascular function. However, challenges that are sustained over several generations can induce progressive compensatory metabolic adjustments in young adults. It is not known if such effects persist during ageing. We investigated whether diets with different fat and carbohydrate contents over three generations modifies markers of ageing. Female C57BL/6 F0 mice were fed diets containing 5% or 21% fat (w/w throughout pregnancy and lactation. Female offspring were fed the same diet as their dams until the F3 generation. In each generation, body weight, 24-hour food intake were recorded weekly, and plasma metabolites were measured by colorimetric assays, blood pressure by tail cuff plethysmography and vasoconstriction by myography on postnatal day 90 or 456. There was little effect of diet or generation on phenotypic markers in day 90 adults. There was a significant increase in whole body, liver and heart weight with ageing (d456 in the F3 21% fat group compared to the F1 and F3 5% groups. Fasting plasma glucose concentration was significantly increased with ageing in the 5% group in the F3 generation and in the 21% group in both generations. There was a significant effect of diet and generation on ex-vivo vasoconstriction in ageing females. Differences in dietary fat may induce metabolic compensation in young adults that persist over three generations. However, such compensatory effects decline during ageing.

  8. The Protective Effect of Minocycline in a Paraquat-Induced Parkinson's Disease Model in Drosophila is Modified in Altered Genetic Backgrounds

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    Arati A. Inamdar

    2012-01-01

    Full Text Available Epidemiological studies link the herbicide paraquat to increased incidence of Parkinson's disease (PD. We previously reported that Drosophila exposed to paraquat recapitulate PD symptoms, including region-specific degeneration of dopaminergic neurons. Minocycline, a tetracycline derivative, exerts ameliorative effects in neurodegenerative disease models, including Drosophila. We investigated whether our environmental toxin-based PD model could contribute to an understanding of cellular and genetic mechanisms of minocycline action and whether we could assess potential interference with these drug effects in altered genetic backgrounds. Cofeeding of minocycline with paraquat prolonged survival, rescued mobility defects, blocked generation of reactive oxygen species, and extended dopaminergic neuron survival, as has been reported previously for a genetic model of PD in Drosophila. We then extended this study to identify potential interactions of minocycline with genes regulating dopamine homeostasis that might modify protection against paraquat and found that deficits in GTP cyclohydrolase adversely affect minocycline rescue. We further performed genetic studies to identify signaling pathways that are necessary for minocycline protection against paraquat toxicity and found that mutations in the Drosophila genes that encode c-Jun N-terminal kinase (JNK and Akt/Protein kinase B block minocycline rescue.

  9. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen.

    Science.gov (United States)

    Adissu, Hibret A; Estabel, Jeanne; Sunter, David; Tuck, Elizabeth; Hooks, Yvette; Carragher, Damian M; Clarke, Kay; Karp, Natasha A; Newbigging, Susan; Jones, Nora; Morikawa, Lily; White, Jacqueline K; McKerlie, Colin

    2014-05-01

    The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.

  10. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen

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    Hibret A. Adissu

    2014-05-01

    Full Text Available The Mouse Genetics Project (MGP at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30 or without (n=20 clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3% in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14% presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.

  11. LQTS-associated mutation A257G in α1-syntrophin interacts with the intragenic variant P74L to modify its biophysical phenotype

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    Michael J. Ackerman

    2011-08-01

    Full Text Available The SNTA1-encoded α1-syntrophin (SNTA1 missense mutation, p.A257G, causes long QT syndrome (LQTS by pathogenic accentuation of Nav1.5’s sodium current (INa. Subsequently, we found p.A257G in combination with the SNTA1 polymorphism, p.P74L in 4 victims of sudden infant death syndrome (SIDS as well as in 3 adult controls. We hypothesized that p.P74L-SNTA1 could functionally modify the pathogenic phenotype of p.A257G-SNTA1, thus explaining its occurrence in non-LQTS populations. The SNTA1 variants p.P74L, p.A257G, and the combination variant p.P74L/p.A257G were engineered using PCR-based overlapextension and were co-expressed heterologously with SCN5A in HEK293 cells. INa was recorded using the whole-cell method. Compared to wild-type (WT, the significant increase in peak INa and window current found with p.A257G was reversed by the intragenic variant p.P74L (p.P74L/p.A257G. These results report for the first time the intragenic rescue of an LQT-associated SNTA1 mutation when found in combination with the SNTA1 polymorphism p.P74L, suggesting an ever-increasing picture of complexity in terms of genetic risk stratification for arrhythmia.

  12. IGF2 promotes growth of adrenocortical carcinoma cells, but its overexpression does not modify phenotypic and molecular features of adrenocortical carcinoma.

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    Marine Guillaud-Bataille

    Full Text Available Insulin-like growth factor 2 (IGF2 overexpression is an important molecular marker of adrenocortical carcinoma (ACC, which is a rare but devastating endocrine cancer. It is not clear whether IGF2 overexpression modifies the biology and growth of this cancer, thus more studies are required before IGF2 can be considered as a major therapeutic target. We compared the phenotypical, clinical, biological, and molecular characteristics of ACC with or without the overexpression of IGF2, to address these issues. We also carried out a similar analysis in an ACC cell line (H295R in which IGF2 expression was knocked down with si- or shRNA. We found no significant differences in the clinical, biological and molecular (transcriptomic traits between IGF2-high and IGF2-low ACC. The absence of IGF2 overexpression had little influence on the activation of tyrosine kinase pathways both in tumors and in H295 cells that express low levels of IGF2. In IGF2-low tumors, other growth factors (FGF9, PDGFA are more expressed than in IGF2-high tumors, suggesting that they play a compensatory role in tumor progression. In addition, IGF2 knock-down in H295R cells substantially impaired growth (>50% inhibition, blocked cells in G1 phase, and promoted apoptosis (>2-fold. Finally, analysis of the 11p15 locus showed a paternal uniparental disomy in both IGF2-high and IGF2-low tumors, but low IGF2 expression could be explained in most IGF2-low ACC by an additional epigenetic modification at the 11p15 locus. Altogether, these observations confirm the active role of IGF2 in adrenocortical tumor growth, but also suggest that other growth promoting pathways may be involved in a subset of ACC with low IGF2 expression, which creates opportunities for the use of other targeted therapies.

  13. Estimating rice yield related traits and quantitative trait loci analysis under different nitrogen treatments using a simple tower-based field phenotyping system with modified single-lens reflex cameras

    Science.gov (United States)

    Naito, Hiroki; Ogawa, Satoshi; Valencia, Milton Orlando; Mohri, Hiroki; Urano, Yutaka; Hosoi, Fumiki; Shimizu, Yo; Chavez, Alba Lucia; Ishitani, Manabu; Selvaraj, Michael Gomez; Omasa, Kenji

    2017-03-01

    Application of field based high-throughput phenotyping (FB-HTP) methods for monitoring plant performance in real field conditions has a high potential to accelerate the breeding process. In this paper, we discuss the use of a simple tower based remote sensing platform using modified single-lens reflex cameras for phenotyping yield traits in rice under different nitrogen (N) treatments over three years. This tower based phenotyping platform has the advantages of simplicity, ease and stability in terms of introduction, maintenance and continual operation under field conditions. Out of six phenological stages of rice analyzed, the flowering stage was the most useful in the estimation of yield performance under field conditions. We found a high correlation between several vegetation indices (simple ratio (SR), normalized difference vegetation index (NDVI), transformed vegetation index (TVI), corrected transformed vegetation index (CTVI), soil-adjusted vegetation index (SAVI) and modified soil-adjusted vegetation index (MSAVI)) and multiple yield traits (panicle number, grain weight and shoot biomass) across a three trials. Among all of the indices studied, SR exhibited the best performance in regards to the estimation of grain weight (R2 = 0.80). Under our tower-based field phenotyping system (TBFPS), we identified quantitative trait loci (QTL) for yield related traits using a mapping population of chromosome segment substitution lines (CSSLs) and a single nucleotide polymorphism data set. Our findings suggest the TBFPS can be useful for the estimation of yield performance during early crop development. This can be a major opportunity for rice breeders whom desire high throughput phenotypic selection for yield performance traits.

  14. Real-time detection of cofactor availability in genetically modified living Saccharomyces cerevisiae cells - Simultaneous probing of different geno- and phenotypes

    DEFF Research Database (Denmark)

    Kostesha, Natalie; Heiskanen, Arto; Spegel, C.;

    2009-01-01

    This work describes a mediated amperometric method for simultaneous real-time probing of the NAD(P)H availability in two different phenotypes, fermentative and respiratory, of the phosphoglucose isomerase deletion mutant strain of S. cerevisiae. EBY44 [ENY.WA-1A pgi1-1D::URA3], and its parental s...

  15. Modified CLSI Extended-Spectrum β-Lactamase (ESBL) Confirmatory Test for Phenotypic Detection of ESBLs among Enterobacteriaceae Producing Various β-Lactamases

    OpenAIRE

    2014-01-01

    The worldwide dissemination of Enterobacteriaceae producing AmpC β-lactamases and carbapenemases makes difficult the phenotypic detection of extended-spectrum β-lactamases (ESBLs), as they may be masked by these additional enzymes. A modification of the CLSI ESBL confirmatory test was developed and evaluated in a comparative study for its ability to successfully detect ESBLs among Enterobacteriaceae producing various carbapenemases (Klebsiella pneumoniae carbapenemase [KPC], VIM, NDM, and OXA...

  16. The human adult cardiomyocyte phenotype

    NARCIS (Netherlands)

    Bird, SD; Doevendans, PA; van Rooijen, MA; de la Riviere, AB; Hassink, RJ; Passier, R; Mummery, CL

    2003-01-01

    Aim: Determination of the phenotype of adult human atrial and ventricular myocytes based on gene expression and morphology. Methods: Atrial and ventricular cardiomyocytes were obtained from patients undergoing cardiac surgery using a modified isolation procedure. Myocytes were isolated and cultured

  17. The impact of metabolic syndrome and CRP on vascular phenotype in type 2 diabetes mellitus

    NARCIS (Netherlands)

    Alizadeh Dehnavi, R.; Beishuizen, E.D.; Ree, M.A. van de; Le Cessie, S.; Huisman, M.V.; Kluft, C.; Princen, H.M.G.; Tamsma, J.T.

    2008-01-01

    Background: The burden of cardiovascular disease in diabetes mellitus type 2 (DM2) patients is variable. We hypothesize that metabolic syndrome (MS) and low-grade systemic inflammation modify the extent of atherosclerosis in DM2. Methods: Vascular phenotype was determined using the following endothe

  18. The exome sequencing identified the mutation in YARS2 encoding the mitochondrial tyrosyl-tRNA synthetase as a nuclear modifier for the phenotypic manifestation of Leber's hereditary optic neuropathy-associated mitochondrial DNA mutation.

    Science.gov (United States)

    Jiang, Pingping; Jin, Xiaofen; Peng, Yanyan; Wang, Meng; Liu, Hao; Liu, Xiaoling; Zhang, Zengjun; Ji, Yanchun; Zhang, Juanjuan; Liang, Min; Zhao, Fuxin; Sun, Yan-Hong; Zhang, Minglian; Zhou, Xiangtian; Chen, Ye; Mo, Jun Qin; Huang, Taosheng; Qu, Jia; Guan, Min-Xin

    2016-02-01

    Leber's hereditary optic neuropathy (LHON) is the most common mitochondrial disorder. Nuclear modifier genes are proposed to modify the phenotypic expression of LHON-associated mitochondrial DNA (mtDNA) mutations. By using an exome sequencing approach, we identified a LHON susceptibility allele (c.572G>T, p.191Gly>Val) in YARS2 gene encoding mitochondrial tyrosyl-tRNA synthetase, which interacts with m.11778G>A mutation to cause visual failure. We performed functional assays by using lymphoblastoid cell lines derived from members of Chinese families (asymptomatic individuals carrying m.11778G>A mutation, or both m.11778G>A and heterozygous p.191Gly>Val mutations and symptomatic subjects harboring m.11778G>A and homozygous p.191Gly>Val mutations) and controls lacking these mutations. The 191Gly>Val mutation reduced the YARS2 protein level in the mutant cells. The aminoacylated efficiency and steady-state level of tRNA(Tyr) were markedly decreased in the cell lines derived from patients both carrying homozygous YARS2 p.191Gly>Val and m.11778G>A mutations. The failure in tRNA(Tyr) metabolism impaired mitochondrial translation, especially for polypeptides with high content of tyrosine codon such as ND4, ND5, ND6 and COX2 in cells lines carrying homozygous YARS2 p.191Gly>Val and m.11778G>A mutations. The YARS2 p.191Gly>Val mutation worsened the respiratory phenotypes associated with m.11778G>A mutation, especially reducing activities of complexes I and IV. The respiratory deficiency altered the efficiency of mitochondrial ATP synthesis and increased the production of reactive oxygen species. Thus, mutated YARS2 aggravates mitochondrial dysfunctions associated with the m.11778G>A mutation, exceeding the threshold for the expression of blindness phenotype. Our findings provided new insights into the pathophysiology of LHON that were manifested by interaction between mtDNA mutation and mutated nuclear-modifier YARS2.

  19. Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration.

    Science.gov (United States)

    Dauwe, Rebecca; Morreel, Kris; Goeminne, Geert; Gielen, Birgit; Rohde, Antje; Van Beeumen, Jos; Ralph, John; Boudet, Alain-Michel; Kopka, Joachim; Rochange, Soizic F; Halpin, Claire; Messens, Eric; Boerjan, Wout

    2007-10-01

    Lignin is an important component of secondarily thickened cell walls. Cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) are two key enzymes that catalyse the penultimate and last steps in the biosynthesis of the monolignols. Downregulation of CCR in tobacco (Nicotiana tabacum) has been shown to reduce lignin content, whereas lignin in tobacco downregulated for CAD incorporates more aldehydes. We show that altering the expression of either or both genes in tobacco has far-reaching consequences on the transcriptome and metabolome. cDNA-amplified fragment length polymorphism-based transcript profiling, combined with HPLC and GC-MS-based metabolite profiling, revealed differential transcripts and metabolites within monolignol biosynthesis, as well as a substantial network of interactions between monolignol and other metabolic pathways. In general, in all transgenic lines, the phenylpropanoid biosynthetic pathway was downregulated, whereas starch mobilization was upregulated. CCR-downregulated lines were characterized by changes at the level of detoxification and carbohydrate metabolism, whereas the molecular phenotype of CAD-downregulated tobacco was enriched in transcript of light- and cell-wall-related genes. In addition, the transcript and metabolite data suggested photo-oxidative stress and increased photorespiration, mainly in the CCR-downregulated lines. These predicted effects on the photosynthetic apparatus were subsequently confirmed physiologically by fluorescence and gas-exchange measurements. Our data provide a molecular picture of a plant's response to altered monolignol biosynthesis.

  20. Hereditary hemochromatosis type 1 phenotype modifiers in Italian patients. The controversial role of variants in HAMP, BMP2, FTL and SLC40A1 genes.

    Science.gov (United States)

    Radio, Francesca Clementina; Majore, Silvia; Aurizi, Caterina; Sorge, Fiammetta; Biolcati, Gianfranco; Bernabini, Sara; Giotti, Irene; Torricelli, Francesca; Giannarelli, Diana; De Bernardo, Carmelilia; Grammatico, Paola

    2015-06-01

    Hereditary hemochromatosis (HH) is a heterogeneous disorder of iron metabolism. The most common form of the disease is Classic or type 1 HH, mainly caused by a biallelic missense p.Cys282Tyr (c.845G>A) mutation in the HFE gene. However, the penetrance of p.Cys282Tyr/p.Cys282Tyr genotype is incomplete in terms of both biochemical and clinical expressivity. Lack of penetrance is thought to be caused by several genetic and environmental factors. Recently, a lot of evidences on HH genetic modifiers were produced, often without conclusive results. We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene, rs2230267 in FTL gene, rs1439816 in SLC40A1 gene, rs41295942 in TFR2 gene and rs2111833 in TMPRSS6 gene) with uncertain function in order to further evaluate their role in an independent cohort of 109 HH type 1 patients. Our results make it likely the role of rs10421768, rs235756, rs2230267 and rs1439816 polymorphisms, respectively in HAMP, BMP2, FTL and SLC40A1 genes in HH expressivity. In addition, previous and our findings support a hypothetical multifactorial model of HH, characterized by a principal gene (HFE in HH type 1) and minor genetic and environmental factors that still have to be fully elucidated.

  1. Background Material

    DEFF Research Database (Denmark)

    Zandersen, Marianne; Hyytiäinen, Kari; Saraiva, Sofia;

    2016-01-01

    This document serves as a background material to the BONUS Pilot Scenario Workshop, which aims to develop harmonised regional storylines of socio-ecological futures in the Baltic Sea region in a collaborative effort together with other BONUS projects and stakeholders....

  2. Modifier factors influencing the phenotypic manifestation of the deafness-associated mitochondrial DNA mutations%修饰因子对线粒体DNA突变致聋的影响

    Institute of Scientific and Technical Information of China (English)

    杨爱芬; 郑静; 吕建新; 管敏鑫

    2011-01-01

    Mutations in the mitochondrial DNA have been found to be one of the most important causes of sensorineural hearing loss. In particular, these mutations often occur in the mitochondrial 12S rRNA and tRNA genes. Of these, the homoplasmic A1555G and C1494T mutations in the 12S rRNA have been associated with both aminoglycoside induced and nonsyndromic hearing impairment in many families worldwide. Children carrying the A1555G or C1494T mutation are susceptible to the exposure of ototoxic drugs, thereby inducing or worsening hearing loss. Individuals harboring A1555G or C1494T mutation can also develop hearing loss even in the absence of aminoglycoside exposure. However, matrilineal relatives of intra-families or inter-families carrying the A1555G or C1494T mutation exhibit a wide range of severity,age-at-onset, and audiometric configuration of hearing impairment. These indicate that the A1555G or C1494T mutation is a primary factor underlying the development of deafness but insufficient to produce the clinical phenotype. Thus, other modifier factors, such as aminoglycoside (s), mitochondrial DNA haplotype(s) or nuclear modifier gene(s), play a role in the phenotypic expression of the deafness-associated mitochondrial 12S rRNA A1555G or C1494T mutation. In this review, we summarize the modifier factors for the phenotypic expression of deafness-associated 12S rRNA A1555G and C1494T mutations and propose the molecular pathogenetic mechanism of maternally inherited deafness.%线粒体DNA突变是引起感音神经性耳聋的重要原因之一,这些突变主要位于线粒体12SrRNA和tRNA基因上.其中12S rRNA基因上的同质性A1555G和C1494T突变与氨基糖甙类抗生素造成的耳聋相关.携带这两个突变的个体对耳毒性药物高度敏感,导致临床上常见的"一针致聋"现象.但携带A1555G或C1494T突变的个体在没用药的情况下也能产生非综合征型耳聋,而且同一家系内和不同家系间的母系成员在听力损失

  3. Genetic modification of glaucoma associated phenotypes between AKXD-28/Ty and DBA/2J mice

    Directory of Open Access Journals (Sweden)

    Zabaleta Adriana

    2001-01-01

    Full Text Available Abstract Background Glaucoma is a common disease but its molecular etiology is poorly understood. It involves retinal ganglion cell death and optic nerve damage that is often associated with elevated intraocular pressure. Identifying genes that modify glaucoma associated phenotypes is likely to provide insights to mechanisms of glaucoma. We previously reported glaucoma in DBA/2J mice caused by recessive alleles at two loci, isa and ipd, that cause iris stromal atrophy and iris pigment dispersion, respectively. A approach for identifying modifier genes is to study the effects of specific mutations in different mouse strains. When the phenotypic effect of a mutation is modified upon its introduction into a new strain, crosses between the parental strains can be used to identify modifier genes. The purpose of this study was to determine if the effects of the DBA/2J derived isa and ipd loci are modified in strain AKXD-28/Ty. Results AKXD-28/Ty mice develop glaucoma characterized by intraocular pressure elevation, retinal ganglion loss, and optic nerve excavation. In AKXD-28/Ty, isa causes an iris stromal atrophy phenotype as in DBA/2J. However, the iris pigment dispersion phenotype associated with ipd in DBA/2J does not occur in AKXD-28/Ty. Additionally, a greater severity and speed of retinal and optic nerve damage following intraocular pressure elevation in AKXD-28/Ty compared to DBA/2J mice suggests that AKXD-28/Ty is more susceptible to pressure-induced cell death. Conclusions The consequences of the ipd and isa mutations are modified in the AKXD-28/Ty background. These strains provide a resource for the identification of modifier genes that modulate pigment dispersion and susceptibility to pressure-induced cell death.

  4. Genetic modifier loci of mouse Mfrp(rd6) identified by quantitative trait locus analysis.

    Science.gov (United States)

    Won, Jungyeon; Charette, Jeremy R; Philip, Vivek M; Stearns, Timothy M; Zhang, Weidong; Naggert, Jürgen K; Krebs, Mark P; Nishina, Patsy M

    2014-01-01

    The identification of genes that modify pathological ocular phenotypes in mouse models may improve our understanding of disease mechanisms and lead to new treatment strategies. Here, we identify modifier loci affecting photoreceptor cell loss in homozygous Mfrp(rd6) mice, which exhibit a slowly progressive photoreceptor degeneration. A cohort of 63 F2 homozygous Mfrp(rd6) mice from a (B6.C3Ga-Mfrp(rd6)/J × CAST/EiJ) F1 intercross exhibited a variable number of cell bodies in the retinal outer nuclear layer at 20 weeks of age. Mice were genotyped with a panel of single nucleotide polymorphism markers, and genotypes were correlated with phenotype by quantitative trait locus (QTL) analysis to map modifier loci. A genome-wide scan revealed a statistically significant, protective candidate locus on CAST/EiJ Chromosome 1 and suggestive modifier loci on Chromosomes 6 and 11. Multiple regression analysis of a three-QTL model indicated that the modifier loci on Chromosomes 1 and 6 together account for 26% of the observed phenotypic variation, while the modifier locus on Chromosome 11 explains only an additional 4%. Our findings indicate that the severity of the Mfrp(rd6) retinal degenerative phenotype in mice depends on the strain genetic background and that a significant modifier locus on CAST/EiJ Chromosome 1 protects against Mfrp(rd6)-associated photoreceptor loss.

  5. Chromosomal phenotypes and submicroscopic abnormalities

    Directory of Open Access Journals (Sweden)

    Devriendt Koen

    2004-01-01

    Full Text Available Abstract The finding, during the last decade, that several common, clinically delineated syndromes are caused by submicroscopic deletions or, more rarely, by duplications, has provided a powerful tool in the annotation of the human genome. Since most microdeletion/microduplication syndromes are defined by a common deleted/duplicated region, abnormal dosage of genes located within these regions can explain the phenotypic similarities among individuals with a specific syndrome. As such, they provide a unique resource towards the genetic dissection of complex phenotypes such as congenital heart defects, mental and growth retardation and abnormal behaviour. In addition, the study of phenotypic differences in individuals with the same microdeletion syndrome may also become a treasury for the identification of modifying factors for complex phenotypes. The molecular analysis of these chromosomal anomalies has led to a growing understanding of their mechanisms of origin. Novel tools to uncover additional submicroscopic chromosomal anomalies at a higher resolution and higher speed, as well as the novel tools at hand for deciphering the modifying factors and epistatic interactors, are 'on the doorstep' and will, besides their obvious diagnostic role, play a pivotal role in the genetic dissection of complex phenotypes.

  6. Phenotypic screens targeting neurodegenerative diseases.

    Science.gov (United States)

    Zhang, Minhua; Luo, Guangrui; Zhou, Yanjiao; Wang, Shaohui; Zhong, Zhong

    2014-01-01

    Neurodegenerative diseases affect millions of people worldwide, and the incidences increase as the population ages. Disease-modifying therapy that prevents or slows disease progression is still lacking, making neurodegenerative diseases an area of high unmet medical need. Target-based drug discovery for disease-modifying agents has been ongoing for many years, without much success due to incomplete understanding of the molecular mechanisms underlying neurodegeneration. Phenotypic screening, starting with a disease-relevant phenotype to screen for compounds that change the outcome of biological pathways rather than activities at certain specific targets, offers an alternative approach to find small molecules or targets that modulate the key characteristics of neurodegeneration. Phenotypic screens that focus on amelioration of disease-specific toxins, protection of neurons from degeneration, or promotion of neuroregeneration could be potential fertile grounds for discovering therapeutic agents for neurodegenerative diseases. In this review, we will summarize the progress of compound screening using these phenotypic-based strategies for this area, with a highlight on unique considerations for disease models, assays, and screening methodologies. We will further provide our perspectives on how best to use phenotypic screening to develop drug leads for neurodegenerative diseases.

  7. Improvement on controllable fabrication of streptavidin-modified three-layer core-shell Fe3O4@SiO2@Au magnetic nanocomposites with low fluorescence background.

    Science.gov (United States)

    Jiang, Hongrong; Zeng, Xin; Xi, Zhijiang; Liu, Ming; Li, Chuanyan; Li, Zhiyang; Jin, Lian; Wang, Zhifei; Deng, Yan; He, Nongyue

    2013-04-01

    In present study, we put forward an approach to prepare three-layer core-shell Fe3O4@SiO2@Au magnetic nanocomposites via the combination of self-assembling, seed-mediated growing and multi-step chemical reduction. The Fe3O4@SiO2@Au magnetic nanocomposites were analyzed and characterized by transmission electron microscope (TEM), scanning electronic microscope (SEM), energy dispersive spectrometer analysis (EDS), Fourier transform infrared spectroscopy (FT-IR), vibrating sample magnetometer (VSM), and ultraviolet and visible spectrophotometer (UV-Vis). TEM and SEM characterizations showed that the FeO4@SiO2@Au nanocomposites were obtained successfully with three-layer structures, especially a layer of thin, smooth and continuous gold shell. The average diameter of Fe3O4@SiO2@Au nanocomposites was about 600 nm and an excellent dispersity was observed for the as-prepared nanoparticles. EDS characterizations demonstrated that the nanocomposites contained three elements of the precursors, Fe, Si, and Au. Furthermore, FT-IR showed that the silica and gold shell were coated successfully. UV-Vis and VSM characterizations showed that the Fe3O4@SiO2@Au nanocomposites exhibited good optical and magnetic property, and the saturation magnetization was 25.76 emu/g. In conclusion, the Fe3O4@SiO2@Au magnetic nanocomposites with three-layer core-shell structures were prepared. Furthermore, Fe3O4@SiO2@Au magnetic nanocomposites were modified with streptavidin (SA) successfully, and it was validated that they performed low fluorescence background, suggesting that they should have good applications especially in bioassay based on fluorescence detection through bonding the biotinylated fluorescent probes.

  8. Superoxide dismutase phenotypes in duodenal ulcers: A genetic marker?

    Directory of Open Access Journals (Sweden)

    Sulekha S

    2006-01-01

    Full Text Available Background:Cu-Zn superoxide dismutases are antioxidative defensive enzymes that catalyze the reduction of superoxide anions to hydrogen peroxide. Aim:The study focuses on the association of electromorph of superoxide dismutase with duodenal ulcers, which result due to an imbalance between aggressive and defensive factors. Materials and Methods:Endoscopically confirmed 210 duodenal ulcer patients and 185 healthy individuals for comparative analysis were considered for the present study. Phenotyping of superoxide dismutase was carried out by subjecting the RBC membranes to polyacrylamide gel electrophoresis, using appropriate staining protocols. Results:Statistical analysis of SOD phenotypes revealed a significant increase of SOD AFNx012 allele and Superoxide dismutases (SOD 2-2 phenotype in duodenal ulcer group. Among these individuals, a predominance of Helicobacter pylori infection was observed. The increased preponderance of homozygotes can be explained on the basis of reduced and altered enzyme activity, which may lead to disturbance in homeostasis of antioxidant/oxidant culminating in high lipid peroxidative gastric mucosal tissue damage and ulceration. No variation in the distribution of SOD phenotypes with respect to Helicobacter pylori indicates the role of Mn-SOD rather than Cu-Zn SOD in the Helicobacter pylori infected cases as reported earlier. Conclusions:Superoxide dismutase as a genetic marker / gene modifier, encoding for an antioxidant enzyme in maintaining tissue homeostasis of the gastric mucosa is discussed.

  9. Capturing phenotypic heterogeneity in MPS I: results of an international consensus procedure

    Directory of Open Access Journals (Sweden)

    de Ru Minke H

    2012-04-01

    Full Text Available Abstract Background Mucopolysaccharidosis type I (MPS I is traditionally divided into three phenotypes: the severe Hurler (MPS I-H phenotype, the intermediate Hurler-Scheie (MPS I-H/S phenotype and the attenuated Scheie (MPS I-S phenotype. However, there are no clear criteria for delineating the different phenotypes. Because decisions about optimal treatment (enzyme replacement therapy or hematopoietic stem cell transplantation need to be made quickly and depend on the presumed phenotype, an assessment of phenotypic severity should be performed soon after diagnosis. Therefore, a numerical severity scale for classifying different MPS I phenotypes at diagnosis based on clinical signs and symptoms was developed. Methods A consensus procedure based on a combined modified Delphi method and a nominal group technique was undertaken. It consisted of two written rounds and a face-to-face meeting. Sixteen MPS I experts participated in the process. The main goal was to identify the most important indicators of phenotypic severity and include these in a numerical severity scale. The correlation between the median subjective expert MPS I rating and the scores derived from this severity scale was used as an indicator of validity. Results Full consensus was reached on six key clinical items for assessing severity: age of onset of signs and symptoms, developmental delay, joint stiffness/arthropathy/contractures, kyphosis, cardiomyopathy and large head/frontal bossing. Due to the remarkably large variability in the expert MPS I assessments, however, a reliable numerical scale could not be constructed. Because of this variability, such a scale would always result in patients whose calculated severity score differed unacceptably from the median expert severity score, which was considered to be the 'gold standard'. Conclusions Although consensus was reached on the six key items for assessing phenotypic severity in MPS I, expert opinion on phenotypic severity at

  10. Microglia phenotype diversity

    NARCIS (Netherlands)

    Olah, M.; Biber, K.; Vinet, J.; Boddeke, H. W. G. M.

    2011-01-01

    Microglia, the tissue macrophages of the brain, have under healthy conditions a resting phenotype that is characterized by a ramified morphology. With their fine processes microglia are continuously scanning their environment. Upon any homeostatic disturbance microglia rapidly change their phenotype

  11. Color change, phenotypic plasticity, and camouflage

    Directory of Open Access Journals (Sweden)

    Martin eStevens

    2016-05-01

    Full Text Available The ability to change appearance over a range of timescales is widespread in nature, existing in many invertebrate and vertebrate groups. This can include color change occurring in seconds, minutes, and hours, to longer term changes associated with phenotypic plasticity and development. A major function is for camouflage against predators because color change and plasticity enables animals to match their surroundings and potentially reduce the risk of predation. Recently, we published findings (Stevens et al. 2014a showing how shore crabs can change their appearance and better match the background to predator vision in the short term. This, coupled with a number of past studies, emphasizes the potential that animals have to modify their appearance for camouflage. However, the majority of studies on camouflage and color plasticity have focused on a small number of species capable of unusually rapid changes. There are many broad questions that remain about the nature, mechanisms, evolution, and adaptive value of color change and plasticity for concealment. Here, I discuss past work and outline six questions relating to color change and plasticity, as well as major avenues for future work.

  12. Large phenotype jumps in biomolecular evolution

    CERN Document Server

    Bardou, F

    2003-01-01

    By defining the phenotype of a biopolymer by its active three-dimensional shape, and its genotype by its primary sequence, we propose a model that predicts and characterizes the statistical distribution of a population of biopolymers with a specific phenotype, that originated from a given genotypic sequence by a single mutational event. Depending on the ratio g0 that characterizes the spread of potential energies of the mutated population with respect to temperature, three different statistical regimes have been identified. We suggest that biopolymers found in nature are in a critical regime with g0 in the range 1-6, corresponding to a broad, but not too broad, phenotypic distribution resembling a truncated Levy flight. Thus the biopolymer phenotype can be considerably modified in just a few mutations.

  13. Single cell dynamic phenotyping

    OpenAIRE

    Katherin Patsch; Chi-Li Chiu; Mark Engeln; Agus, David B.; Parag Mallick; Shannon M. Mumenthaler; Daniel Ruderman

    2016-01-01

    Live cell imaging has improved our ability to measure phenotypic heterogeneity. However, bottlenecks in imaging and image processing often make it difficult to differentiate interesting biological behavior from technical artifact. Thus there is a need for new methods that improve data quality without sacrificing throughput. Here we present a 3-step workflow to improve dynamic phenotype measurements of heterogeneous cell populations. We provide guidelines for image acquisition, phenotype track...

  14. Background independence in a background dependent renormalization group

    CERN Document Server

    Labus, Peter; Slade, Zoë H

    2016-01-01

    Within the derivative expansion of conformally reduced gravity, the modified split Ward identities are shown to be compatible with the flow equations if and only if either the anomalous dimension vanishes or the cutoff profile is chosen to be power law. No solutions exist if the Ward identities are incompatible. In the compatible case, a clear reason is found for why Ward identities can still forbid the existence of fixed points; however, for any cutoff profile, a background independent (and parametrisation independent) flow equation is uncovered. Finally, expanding in vertices, the combined equations are shown generically to become either over-constrained or highly redundant beyond the six-point level.

  15. Mitochondrial haplogroup M9a specific variant ND1 T3394C may have a modifying role in the phenotypic expression of the LHON-associated ND4 G11778A mutation.

    Science.gov (United States)

    Zhang, Minglian; Zhou, Xiangtian; Li, Chengwu; Zhao, Fuxin; Zhang, Juanjuan; Yuan, Meixia; Sun, Yan-Hong; Wang, Jingzheng; Tong, Yi; Liang, Min; Yang, Li; Cai, Wanshi; Wang, Lifei; Qu, Jia; Guan, Min-Xin

    2010-01-01

    We report here the clinical, genetic and molecular characterization of four Han Chinese families with Leber's hereditary optic neuropathy (LHON). The penetrances of optic neuropathy in these Chinese pedigrees were 38%, 38%, 44% and 56%. This observation is in contrast with the previously identified 14 Chinese families with very low penetrance of LHON. The age-at-onset for visual impairment in matrilineal relatives in these Chinese families varied from 18 to 30years. Furthermore, the ratios between affected male and female matrilineal relatives in these families were 3:0, 3:0, 3:1 and 2:3, respectively. Molecular analysis of mitochondrial genomes identified the known ND4 G11778A mutation and distinct sets of variants belonging to the Asian haplogroups M9a. Of these, the ND1 T3394C mutation caused the substitution of a highly conserved histidine for tyrosine (Y30H) at amino acid position 30. This mutation was associated with LHON in other families with low penetrance of optic neuropathy and other clinical abnormalities. The presence of both G11778A and T3394C mutations appears to contribute to higher penetrance of optic neuropathy in these four Chinese families than other Chinese families carrying only the G11778A mutation. Therefore, the mitochondrial haplogroup M9a specific variant T3394C may modulate the phenotypic manifestation of LHON-associated G11778A mutation in these Chinese pedigrees.

  16. Metabolomic phenotyping of a cloned pig model

    Directory of Open Access Journals (Sweden)

    Callesen Henrik

    2011-08-01

    Full Text Available Abstract Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5 was for the first time elucidated by nuclear magnetic resonance (NMR-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6 by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals.

  17. Phenotypic covariance at species’ borders

    Science.gov (United States)

    2013-01-01

    Background Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species’ borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Results Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Conclusions Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species’ borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future. PMID:23714580

  18. Background sources at PEP

    Energy Technology Data Exchange (ETDEWEB)

    Lynch, H.; Schwitters, R.F.; Toner, W.T.

    1988-01-01

    Important sources of background for PEP experiments are studied. Background particles originate from high-energy electrons and positrons which have been lost from stable orbits, ..gamma..-rays emitted by the primary beams through bremsstrahlung in the residual gas, and synchrotron radiation x-rays. The effect of these processes on the beam lifetime are calculated and estimates of background rates at the interaction region are given. Recommendations for the PEP design, aimed at minimizing background are presented. 7 figs., 4 tabs.

  19. Para Bombay phenotype--a case report.

    Science.gov (United States)

    Mathai, J; Sulochana, P V; Sathyabhama, S

    1997-10-01

    Bombay phenotype is peculiar in that red cells are not agglutinated by antisera A, B or H; while serum contains anti A, B and H. Existence of modifying genes at independent loci with variable expression of ABO genes is postulated. We report here a case of partial suppression where antigens could be detected by elution tests and unlike classical Bombay type, normal amount of appropriate blood group substances were present in saliva. This case of para Bombay phenotype was detected as a result of discrepancy in cell and serum group ng. This highlights the importance of both forward and reverse grouping in ABO testing.

  20. Phenotype definition in epilepsy.

    Science.gov (United States)

    Winawer, Melodie R

    2006-05-01

    Phenotype definition consists of the use of epidemiologic, biological, molecular, or computational methods to systematically select features of a disorder that might result from distinct genetic influences. By carefully defining the target phenotype, or dividing the sample by phenotypic characteristics, we can hope to narrow the range of genes that influence risk for the trait in the study population, thereby increasing the likelihood of finding them. In this article, fundamental issues that arise in phenotyping in epilepsy and other disorders are reviewed, and factors complicating genotype-phenotype correlation are discussed. Methods of data collection, analysis, and interpretation are addressed, focusing on epidemiologic studies. With this foundation in place, the epilepsy subtypes and clinical features that appear to have a genetic basis are described, and the epidemiologic studies that have provided evidence for the heritability of these phenotypic characteristics, supporting their use in future genetic investigations, are reviewed. Finally, several molecular approaches to phenotype definition are discussed, in which the molecular defect, rather than the clinical phenotype, is used as a starting point.

  1. Building Background Knowledge

    Science.gov (United States)

    Neuman, Susan B.; Kaefer, Tanya; Pinkham, Ashley

    2014-01-01

    This article make a case for the importance of background knowledge in children's comprehension. It suggests that differences in background knowledge may account for differences in understanding text for low- and middle-income children. It then describes strategies for building background knowledge in the age of common core standards.

  2. Phenotypic shift in Pseudomonas aeruginosa populations from cystic fibrosis lungs after 2-week antipseudomonal treatment

    DEFF Research Database (Denmark)

    Fernández-Barat, Laia; Ciofu, Oana; Kragh, Kasper N

    2017-01-01

    BACKGROUND: The influence of suppressive therapy on the different P. aeruginosa phenotypes harbored in the lungs of cystic fibrosis (CF) patients remains unclear. Our aim was to investigate the phenotypic changes (mucoidy, hypermutability, antibiotic resistance, transcriptomic profiles and biofil...

  3. The Diffuse Supernova Neutrino Background

    CERN Document Server

    Beacom, John F

    2010-01-01

    The Diffuse Supernova Neutrino Background (DSNB) is the weak glow of MeV neutrinos and antineutrinos from distant core-collapse supernovae. The DSNB has not been detected yet, but the Super-Kamiokande (SK) 2003 upper limit on the electron antineutrino flux is close to predictions, now quite precise, based on astrophysical data. If SK is modified with dissolved gadolinium to reduce detector backgrounds and increase the energy range for analysis, then it should detect the DSNB at a rate of a few events per year, providing a new probe of supernova neutrino emission and the cosmic core-collapse rate. If the DSNB is not detected, then new physics will be required. Neutrino astronomy, while uniquely powerful, has proven extremely difficult -- only the Sun and the nearby Supernova 1987A have been detected to date -- so the promise of detecting new sources soon is exciting indeed.

  4. Characteristics of phenotypes of elderly patients with asthma

    OpenAIRE

    Hiroyuki Sano; Takashi Iwanaga; Osamu Nishiyama; Akiko Sano; Yuji Higashimoto; Katsuyuki Tomita; Yuji Tohda

    2016-01-01

    Background: The characteristics of phenotypes of elderly patients with asthma are unknown. The aim of this study was to classify these phenotypes using lung function tests and images from high-resolution computed tomography (HRCT), and to identify associations between clinical characteristics and phenotypes. Methods: A cross-sectional study was conducted in 165 elderly patients (>65 years of age) who underwent a multidimensional assessment of clinical and functional status and comorbidity....

  5. Congenital Cataract in Gpr161vl/vl Mice Is Modified by Proximal Chromosome 15

    Science.gov (United States)

    Li, Bo I.; Ababon, Myka R.; Matteson, Paul G.; Lin, Yong; Nanda, Vikas; Millonig, James H.

    2017-01-01

    The morphology and severity of human congenital cataract varies even among individuals with the same mutation, suggesting that genetic background modifies phenotypic penetrance. The spontaneous mouse mutant, vacuolated lens (vl), arose on the C3H/HeSnJ background. The mutation disrupts secondary lens fiber development by E16.5, leading to full penetrance of congenital cataract. The vl locus was mapped to a frameshift deletion in the orphan G protein-coupled receptor, Gpr161, which is expressed in differentiating lens fiber cells. When Gpr161vl/vl C3H mice are crossed to MOLF/EiJ mice an unexpected rescue of cataract is observed, suggesting that MOLF modifiers affect cataract penetrance. Subsequent QTL analysis mapped three modifiers (Modvl3-5: Modifier of vl) and in this study we characterized Modvl4 (Chr15; LOD = 4.4). A Modvl4MOLF congenic was generated and is sufficient to rescue congenital cataract and the lens fiber defect at E16.5. Additional phenotypic analysis on three subcongenic lines narrowed down the interval from 55 to 15Mb. In total only 18 protein-coding genes and 2 micro-RNAs are in this region. Fifteen of the 20 genes show detectable expression in the E16.5 eye. Subsequent expression studies in Gpr161vl/vl and subcongenic E16.5 eyes, bioinformatics analysis of C3H/MOLF polymorphisms, and the biological relevancy of the genes in the interval identified three genes (Cdh6, Ank and Trio) that likely contribute to the rescue of the lens phenotype. These studies demonstrate that modification of the Gpr161vl/vl cataract phenotype is likely due to genetic variants in at least one of three closely linked candidate genes on proximal Chr15. PMID:28135291

  6. Modified cyanobacteria

    Science.gov (United States)

    Vermaas, Willem F J.

    2014-06-17

    Disclosed is a modified photoautotrophic bacterium comprising genes of interest that are modified in terms of their expression and/or coding region sequence, wherein modification of the genes of interest increases production of a desired product in the bacterium relative to the amount of the desired product production in a photoautotrophic bacterium that is not modified with respect to the genes of interest.

  7. Expression of Drosophila mushroom body mutations in alternative genetic backgrounds: a case study of the mushroom body miniature gene (mbm).

    Science.gov (United States)

    de Belle, J S; Heisenberg, M

    1996-01-01

    Mutations in 12 genes regulating Drosophila melanogaster mushroom body (MB) development were each studied in two genetic backgrounds. In all cases, brain structure was qualitatively or quantitatively different after replacement of the "original" genetic background with that of the Canton Special wild-type strain. The mushroom body miniature gene (mbm) was investigated in detail. mbm supports the maintenance of MB Kenyon cell fibers in third instar larvae and their regrowth during metamorphosis. Adult mbm1 mutant females are lacking many or most Kenyon cell fibers and are impaired in MB-mediated associative odor learning. We show here that structural defects in mbm1 are apparent only in combination with an X-linked, dosage-dependent modifier (or modifiers). In the Canton Special genetic background, the mbm1 anatomical phenotype is suppressed, and MBs develop to a normal size. However, the olfactory learning phenotype is not fully restored, suggesting that submicroscopic defects persist in the MBs. Mutant mbm1 flies with full-sized MBs have normal retention but show a specific acquisition deficit that cannot be attributed to reductions in odor avoidance, shock reactivity, or locomotor behavior. We propose that polymorphic gene interactions (in addition to ontogenetic factors) determine MB size and, concomitantly, the ability to recognize and learn odors. Images Fig. 1 Fig. 2 Fig. 3 PMID:8790424

  8. Expression of Drosophila mushroom body mutations in alternative genetic backgrounds: a case study of the mushroom body miniature gene (mbm).

    Science.gov (United States)

    de Belle, J S; Heisenberg, M

    1996-09-03

    Mutations in 12 genes regulating Drosophila melanogaster mushroom body (MB) development were each studied in two genetic backgrounds. In all cases, brain structure was qualitatively or quantitatively different after replacement of the "original" genetic background with that of the Canton Special wild-type strain. The mushroom body miniature gene (mbm) was investigated in detail. mbm supports the maintenance of MB Kenyon cell fibers in third instar larvae and their regrowth during metamorphosis. Adult mbm1 mutant females are lacking many or most Kenyon cell fibers and are impaired in MB-mediated associative odor learning. We show here that structural defects in mbm1 are apparent only in combination with an X-linked, dosage-dependent modifier (or modifiers). In the Canton Special genetic background, the mbm1 anatomical phenotype is suppressed, and MBs develop to a normal size. However, the olfactory learning phenotype is not fully restored, suggesting that submicroscopic defects persist in the MBs. Mutant mbm1 flies with full-sized MBs have normal retention but show a specific acquisition deficit that cannot be attributed to reductions in odor avoidance, shock reactivity, or locomotor behavior. We propose that polymorphic gene interactions (in addition to ontogenetic factors) determine MB size and, concomitantly, the ability to recognize and learn odors.

  9. High-throughput discovery of novel developmental phenotypes.

    Science.gov (United States)

    Dickinson, Mary E; Flenniken, Ann M; Ji, Xiao; Teboul, Lydia; Wong, Michael D; White, Jacqueline K; Meehan, Terrence F; Weninger, Wolfgang J; Westerberg, Henrik; Adissu, Hibret; Baker, Candice N; Bower, Lynette; Brown, James M; Caddle, L Brianna; Chiani, Francesco; Clary, Dave; Cleak, James; Daly, Mark J; Denegre, James M; Doe, Brendan; Dolan, Mary E; Edie, Sarah M; Fuchs, Helmut; Gailus-Durner, Valerie; Galli, Antonella; Gambadoro, Alessia; Gallegos, Juan; Guo, Shiying; Horner, Neil R; Hsu, Chih-Wei; Johnson, Sara J; Kalaga, Sowmya; Keith, Lance C; Lanoue, Louise; Lawson, Thomas N; Lek, Monkol; Mark, Manuel; Marschall, Susan; Mason, Jeremy; McElwee, Melissa L; Newbigging, Susan; Nutter, Lauryl M J; Peterson, Kevin A; Ramirez-Solis, Ramiro; Rowland, Douglas J; Ryder, Edward; Samocha, Kaitlin E; Seavitt, John R; Selloum, Mohammed; Szoke-Kovacs, Zsombor; Tamura, Masaru; Trainor, Amanda G; Tudose, Ilinca; Wakana, Shigeharu; Warren, Jonathan; Wendling, Olivia; West, David B; Wong, Leeyean; Yoshiki, Atsushi; MacArthur, Daniel G; Tocchini-Valentini, Glauco P; Gao, Xiang; Flicek, Paul; Bradley, Allan; Skarnes, William C; Justice, Monica J; Parkinson, Helen E; Moore, Mark; Wells, Sara; Braun, Robert E; Svenson, Karen L; de Angelis, Martin Hrabe; Herault, Yann; Mohun, Tim; Mallon, Ann-Marie; Henkelman, R Mark; Brown, Steve D M; Adams, David J; Lloyd, K C Kent; McKerlie, Colin; Beaudet, Arthur L; Bućan, Maja; Murray, Stephen A

    2016-09-22

    Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.

  10. Phenotypical variation within 22 families with Pompe disease

    NARCIS (Netherlands)

    S.C.A. Wens (Stephan); C.M. Van Gelder (Carin); M.E. Kruijshaar (Michelle); J.M. de Vries (Juna); N.A.M.E. van der Beek (Nadine); A.J.J. Reuser (Arnold); P.A. van Doorn (Pieter); A.T. van der Ploeg (Ans); E. Brusse (Esther)

    2013-01-01

    textabstractBackground: Pompe disease has a broad clinical spectrum, in which the phenotype is partially explained by the genotype. The aim of this study was to describe phenotypical variation among siblings with non-classic Pompe disease. We hypothesized that siblings and families with the same gen

  11. 改良亚胺培南-EDTA纸片增效试验检测铜绿假单胞菌产金属酶表型%The phenotypic detection of metallo-beta-lactamase-producing Pseudomonas aeruginosa by modified imipenem-EDTA disk potentiation test

    Institute of Scientific and Technical Information of China (English)

    严育忠; 范惠清; 郑文龙; 杨焕章; 陆燕春; 石毅

    2014-01-01

    目的:评估改良亚胺培南-乙二胺四乙酸(EDTA)纸片增效试验在检测铜绿假单胞菌(PA)产金属酶表型中的应用价值。方法收集95株耐碳青霉烯类药物PA,采用琼脂稀释法测定所有菌株对亚胺培南和美罗培南的最低抑菌浓度(MIC)值,聚合酶链反应(PCR)和DNA测序鉴定金属酶基因型,亚胺培南-EDTA纸片增效试验常规法和改良法检测金属酶表型。结果95株耐碳青霉烯类药物PA对亚胺培南和美罗培南的耐药率分别为100.0%和71.6%;常规法敏感性、特异性、阳性预测值和阴性预测值分别是100.0%、96.6%、72.7%和100.0%,而改良法均为100.0%。结论改良亚胺培南-EDTA纸片增效试验可能是一种检测PA产金属酶表型的有效方法。%Objective To evaluate the modified imipenem-ethylene diamine tetraacetic acid (EDTA ) disk potentiation test for the phenotypic detection of metallo-beta-lactamase-producing Pseudomonas aeruginosa (PA ). Methods A total of 95 carbapenem-resistant PA were collected.The minimum inhibition concentrations(MIC)of imipenem and meropenem were determined by agar dilution method.Polymerase chain reaction (PCR ) and DNA sequencing were used for the identification of metallo-beta-lactamase genotypes.The phenotypic detection of metallo-beta-lactamase was done by conventional and modified imipenem-EDTA disk potentiation test.Results The resistance rates of imipenem and meropenem were 1 00.0%and 71 .6%among these 95 carbapenem-resistant PA.The sensitivity, specificity,positive predictive value and negative predictive value of conventional test were 1 00.0%,96.6%,72.7%and 1 00.0%,respectively.Those of modified test were all 1 00.0%.Conclusions The modified imipenem-EDTA disk potentiation test could be an effective method for the phenotypic detection of metallo-beta-lactamase-producing PA.

  12. Phenotypic evolution from genetic polymorphisms in a radial network architecture

    Directory of Open Access Journals (Sweden)

    Siegel Paul B

    2007-11-01

    Full Text Available Abstract Background The genetic architecture of a quantitative trait influences the phenotypic response to natural or artificial selection. One of the main objectives of genetic mapping studies is to identify the genetic factors underlying complex traits and understand how they contribute to phenotypic expression. Presently, we are good at identifying and locating individual loci with large effects, but there is a void in describing more complex genetic architectures. Although large networks of connected genes have been reported, there is an almost complete lack of information on how polymorphisms in these networks contribute to phenotypic variation and change. To date, most of our understanding comes from theoretical, model-based studies, and it remains difficult to assess how realistic their conclusions are as they lack empirical support. Results A previous study provided evidence that nearly half of the difference in eight-week body weight between two divergently selected lines of chickens was a result of four loci organized in a 'radial' network (one central locus interacting with three 'radial' loci that, in turn, only interacted with the central locus. Here, we study the relationship between phenotypic change and genetic polymorphism in this empirically detected network. We use a model-free approach to study, through individual-based simulations, the dynamic properties of this polymorphic and epistatic genetic architecture. The study provides new insights to how epistasis can modify the selection response, buffer and reveal effects of major loci leading to a progressive release of genetic variation. We also illustrate the difficulty of predicting genetic architecture from observed selection response, and discuss mechanisms that might lead to misleading conclusions on underlying genetic architectures from quantitative trait locus (QTL experiments in selected populations. Conclusion Considering both molecular (QTL and phenotypic (selection

  13. Differential Impact of Lactose/Lactase Phenotype on Colonic Microflora

    Directory of Open Access Journals (Sweden)

    Andrew Szilagyi

    2010-01-01

    Full Text Available BACKGROUND: The ability to digest lactose divides the world’s population into two phenotypes that may be risk variability markers for several diseases. Prebiotic effects likely favour lactose maldigesters who experience lactose spilling into their colon.

  14. Aging Phenotypes of Common Marmosets (Callithrix jacchus

    Directory of Open Access Journals (Sweden)

    Corinna N. Ross

    2012-01-01

    Full Text Available Characterizing the phenotypic changes associated with aging in a short-lived primate is necessary in order to develop better translational models for human health, aging, and disease research. A population of conventionally housed marmoset monkeys was assessed to determine if phenotypes of body composition, hematology, and morphometrical measures were associated with age or risk of death. We found that the cause of mortality in older marmosets was more likely to be due to cardiac and chronic kidney disease than in younger marmosets. Older marmosets have decreased fat mass, morphometric measures, and serum albumin. Older marmosets are more likely to show a modified posture while at rest and this modified posture was significantly associated with an increased risk of imminent death. These assessments provide an initial definition of aged health in marmosets and a base for future translational aging research with this species.

  15. Phenotypic Approaches to Drought in Cassava: Review

    Directory of Open Access Journals (Sweden)

    Emmanuel eOkogbenin

    2013-05-01

    Full Text Available Cassava is an important crop in Africa, Asia, Latin America and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12 - 18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance

  16. Phenotypic approaches to drought in cassava: review.

    Science.gov (United States)

    Okogbenin, Emmanuel; Setter, Tim L; Ferguson, Morag; Mutegi, Rose; Ceballos, Hernan; Olasanmi, Bunmi; Fregene, Martin

    2013-01-01

    Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12-18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding.

  17. Supersymmetric heterotic string backgrounds

    NARCIS (Netherlands)

    Gran, U.; Papadopoulos, G.; Roest, D.; Cvetič, M.

    2007-01-01

    We present the main features of the solution of the gravitino and dilatino Killing spinor equations derived in hep-th/0510176 and hep-th/0703143 which have led to the classification of geometric types of all type I backgrounds. We then apply these results to the supersymmetric backgrounds of the het

  18. The Cosmic Microwave Background

    OpenAIRE

    Silk, Joseph

    2002-01-01

    This set of lectures provides an overview of the basic theory and phenomenology of the cosmic microwave background. Topics include a brief historical review; the physics of temperature and polarization fluctuations; acoustic oscillations of the primordial plasma; the space of inflationary cosmological models; current and potential constraints on these models from the microwave background; and constraints on inflation.

  19. The Athena Background

    Science.gov (United States)

    Piro, Luigi; Lotti, Simone; Macculi, Claudio; Molendi, Silvano; Eraerds, Tanja; Laurent, Philippe

    2015-09-01

    Estimating, reducing and controlling the residual particle background is fundamental for achieving the objectives of several science topics of Athena, in particular those connected with background dominated observations of faint and/or diffuse sources. This requires assessing the particle environment in L2, propagating the various particle components throughout the mirror, spacecraft, and instruments via proper modelling and simulations of various physical processes, implementing design and h/w measures at instrument and mission level to reduce the un-rejected background and identifying proper calibration methods to control the background variations. Likewise, an adequate knowledge of the XRB, made of components that may vary spatially or temporally, is required as well. Here we will review the present status of the background knowledge, and summarize the activities on-going within Athena at various levels.

  20. Cosmogenic Backgrounds to 0{\

    CERN Document Server

    :,; Auty, D J; Barbeau, P S; Beck, D; Belov, V; Breidenbach, M; Brunner, T; Burenkov, A; Cao, G F; Chambers, C; Cleveland, B; Coon, M; Craycraft, A; Daniels, T; Danilov, M; Daugherty, S J; Davis, J; Delaquis, S; Der Mesrobian-Kabakian, A; DeVoe, R; Didberidze, T; Dilling, J; Dolgolenko, A; Dolinski, M J; Dunford, M; Fairbank, W; Farine, J; Feldmeier, W; Feyzbakhsh, S; Fierlinger, P; Fudenberg, D; Gornea, R; Graham, K; Gratta, G; Hall, C; Herrin, S; Hughes, M; Jewell, M J; Johnson, A; Johnson, T N; Johnston, S; Karelin, A; Kaufman, L J; Killick, R; Koffas, T; Kravitz, S; Krücken, R; Kuchenkov, A; Kumar, K S; Leonard, D S; Licciardi, C; Lin, Y H; Ling, J; MacLellan, R; Marino, M G; Mong, B; Moore, D; Njoya, O; Nelson, R; Odian, A; Ostrovskiy, I; Piepke, A; Pocar, A; Prescott, C Y; Retière, F; Rowson, P C; Russell, J J; Schubert, A; Sinclair, D; Smith, E; Stekhanov, V; Tarka, M; Tolba, T; Tsang, R; Twelker, K; Vuilleumier, J -L; Waite, A; Walton, J; Walton, T; Weber, M; Wen, L J; Wichoski, U; Wood, J; Yang, L; Yen, Y -R; Zeldovich, O Ya

    2015-01-01

    As neutrinoless double-beta decay experiments become more sensitive and intrinsic radioactivity in detector materials is reduced, previously minor contributions to the background must be understood and eliminated. With this in mind, cosmogenic backgrounds have been studied with the EXO-200 experiment. Using the EXO-200 TPC, the muon flux (through a flat horizontal surface) underground at the Waste Isolation Pilot Plant (WIPP) has been measured to be {\\Phi} = 4.07 $\\pm$ 0.14 (sys) $\\pm$ 0.03 (stat) $\\times$ $10^{-7}$cm$^{-2}$ s$^{-1}$, with a vertical intensity of $I_{v}$ = 2.97$^{+0.14}_{-0.13}$ (sys) $\\pm$ 0.02 (stat) $\\times$ $10^{-7}$cm$^{-2}$ s$^{-1}$ sr$^{-1}$. Simulations of muon-induced backgrounds identified several potential cosmogenic radionuclides, though only 137Xe is a significant background for the 136Xe 0{\

  1. Zambia Country Background Report

    DEFF Research Database (Denmark)

    Hampwaye, Godfrey; Jeppesen, Søren; Kragelund, Peter

    This paper provides background data and general information for the Zambia studies focusing on local food processing sub­‐sector; and the local suppliers to the mines as part of the SAFIC project (Successful African Firms and Institutional Change).......This paper provides background data and general information for the Zambia studies focusing on local food processing sub­‐sector; and the local suppliers to the mines as part of the SAFIC project (Successful African Firms and Institutional Change)....

  2. Social-Cognition and the Broad Autism Phenotype: Identifying Genetically Meaningful Phenotypes

    Science.gov (United States)

    Losh, Molly; Piven, Joseph

    2007-01-01

    Background: Strong evidence from twin and family studies suggests that the genetic liability to autism may be expressed through personality and language characteristics qualitatively similar, but more subtly expressed than those defining the full syndrome. This study examined behavioral features of this "broad autism phenotype" (BAP) in relation…

  3. Neutrino refraction by the cosmic neutrino background

    CERN Document Server

    Diaz, J S

    2015-01-01

    We have determined the dispersion relation of a neutrino test particle propagating in the cosmic neutrino background. Describing the relic neutrinos and antineutrinos from the hot big bang as a dense medium, a matter potential or refractive index is obtained. The vacuum neutrino mixing angles are unchanged, but the energy of each mass state is modified. Using a matrix in the space of neutrino species, the induced potential is decomposed into a part which produces signatures in beta-decay experiments and another part which modifies neutrino oscillations. The low temperature of the relic neutrinos makes a direct detection extremely challenging. From a different point of view, the identified refractive effects of the cosmic neutrino background constitute an ultralow background for future experimental studies of nonvanishing Lorentz violation in the neutrino sector.

  4. Exploring String Theory Backgrounds

    CERN Document Server

    Williams, B P

    2004-01-01

    This thesis examines phenomenological and theoretical questions by exploring string theoretic backgrounds. Part I focuses on cosmology. First we propose that the induced metric along a brane moving through a curved bulk may be interpreted as the cosmology of the brane universe, providing a resolution to the apparent cosmological singularity on the brane. We then look at various decay channels of the certain meta-stable de Sitter vacua and show that there exist NS5-brane meditated decays which are much faster than decays to decompactification. Part II discusses a new class of nongeometric vacua in string theory. These backgrounds may be described locally as T2 fibrations. By enlarging the monodromy group of the fiber to include perturbative stringy duality symmetries we are able to explicitly construct nongeometric backgrounds.

  5. Cosmic Tachyon Background Radiation

    CERN Document Server

    Tomaschitz, R

    1999-01-01

    The equilibrium statistical mechanics of a background radiation of superluminal particles is investigated, based on a vectorial wave equation for tachyons of the Proca type. The partition function, the spectral energy density, and the various thermodynamic variables of an ideal Bose gas of tachyons in an open Robertson-Walker cosmology are derived. The negative mass square in the wave equation changes the frequency scaling in the Rayleigh-Jeans law, and there are also significant changes in the low temperature regime as compared to the microwave background, in particular in the caloric and thermal equations of state.

  6. COPD: Definition and Phenotypes

    DEFF Research Database (Denmark)

    Vestbo, J.

    2014-01-01

    particles or gases. Exacerbations and comorbidities contribute to the overall severity in individual patients. The evolution of this definition and the diagnostic criteria currently in use are discussed. COPD is increasingly divided in subgroups or phenotypes based on specific features and association...

  7. Mixed phenotype acute leukemia

    Institute of Scientific and Technical Information of China (English)

    Ye Zixing; Wang Shujie

    2014-01-01

    Objective To highlight the current understanding of mixed phenotype acute leukemia (MPAL).Data sources We collected the relevant articles in PubMed (from 1985 to present),using the terms "mixed phenotype acute leukemia","hybrid acute leukemia","biphenotypic acute leukemia",and "mixed lineage leukemia".We also collected the relevant studies in WanFang Data base (from 2000 to present),using the terms "mixed phenotype acute leukemia" and "hybrid acute leukemia".Study selection We included all relevant studies concerning mixed phenotype acute leukemia in English and Chinese version,with no limitation of research design.The duplicated articles are excluded.Results MPAL is a rare subgroup of acute leukemia which expresses the myeloid and lymphoid markers simultaneously.The clinical manifestations of MPAL are similar to other acute leukemias.The World Health Organization classification and the European Group for Immunological classification of Leukaemias 1998 cdteria are most widely used.MPAL does not have a standard therapy regimen.Its treatment depends mostly on the patient's unique immunophenotypic and cytogenetic features,and also the experience of individual physician.The lack of effective treatment contributes to an undesirable prognosis.Conclusion Our understanding about MPAL is still limited.The diagnostic criteria have not been unified.The treatment of MPAL remains to be investigated.The prognostic factor is largely unclear yet.A better diagnostic cdteria and targeted therapeutics will improve the therapy effect and a subsequently better prognosis.

  8. The DFNA10 phenotype.

    NARCIS (Netherlands)

    Leenheer, E. de; Huygen, P.L.M.; Wayne, S.; Smith, R.J.H.; Cremers, C.W.R.J.

    2001-01-01

    We present a detailed analysis of the DFNA10 phenotype based on data from 25 hearing-impaired persons coming from a large American pedigree segregating for deafness at the DFNA10 locus (chromosome 6q22.3-23.2). Cross-sectional analysis of air conduction threshold-on-age data from all available last-

  9. Mox: a novel modifier of the tomato Xa locus.

    Science.gov (United States)

    Peterson, P W; Yoder, J I

    1995-01-01

    We have isolated a novel mutation that caused variegated leaf color in a tomato plant which had multiple maize Ac transposable elements and the tomato Xa allele. Xa is a previously characterized semi-dominant mutation that causes tomato leaves to be bright yellow when heterozygous (Xa/xa+). The mutation responsible for the new phenotype was named Mox (Modifier of Xa). The Mox mutation modified the Xa/xa+ yellow leaf phenotype in two ways: it compensated for the Xa allele resulting in a plant with a wildtype green color, and it caused somatic variegation which appeared as white and yellow sectors on the green background. Somatic variegation was visible only if the plant contained both the Mox and Xa loci. Genetic studies indicated that the Mox locus was linked in repulsion to Xa and that the Mox locus was genetically transmitted at a reduced frequency through the male gamete. Molecular characterization of the Ac elements in lines segregating for Mox identified an Ac insertion that appeared to cosegregate with Mox variegation. We propose a model in which the Mox mutation consists of a duplication of the xa+ allele and subsequent Ac-induced breakage of the duplicated region causes variegation.

  10. Backgrounded but not peripheral

    DEFF Research Database (Denmark)

    Hovmark, Henrik

    2013-01-01

    -cultural construction of identity, and, as a matter of fact, that their role might be quite important. I argue that the DDAs are backgrounded but not peripheral, i.e. marginal or insignificant. And I introduce the notion of “contextualization cue” in this argument (Levinson, 2003a, Gumperz, 1992)....

  11. China: Background Notes Series.

    Science.gov (United States)

    Reams, Joanne Reppert

    Concise background information on the People's Republic of China is provided. The publication begins with a profile of the country, outlining the people, geography, economy, and membership in international organizations. The bulk of the document then discusses in more detail China's people, geography, history, government, education, economy, and…

  12. Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes

    Science.gov (United States)

    Arbogast, Thomas; Ouagazzal, Abdel-Mouttalib; Chevalier, Claire; Kopanitsa, Maksym; Afinowi, Nurudeen; Migliavacca, Eugenia; Cowling, Belinda S.; Birling, Marie-Christine; Champy, Marie-France; Reymond, Alexandre; Herault, Yann

    2016-01-01

    The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+) or a duplication (Dup/+) of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice. PMID:26872257

  13. Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes.

    Science.gov (United States)

    Arbogast, Thomas; Ouagazzal, Abdel-Mouttalib; Chevalier, Claire; Kopanitsa, Maksym; Afinowi, Nurudeen; Migliavacca, Eugenia; Cowling, Belinda S; Birling, Marie-Christine; Champy, Marie-France; Reymond, Alexandre; Herault, Yann

    2016-02-01

    The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+) or a duplication (Dup/+) of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice.

  14. Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes.

    Directory of Open Access Journals (Sweden)

    Thomas Arbogast

    2016-02-01

    Full Text Available The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+ or a duplication (Dup/+ of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice.

  15. Chiral transition in a strong magnetic background

    CERN Document Server

    Fraga, Eduardo S

    2008-01-01

    The presence of a strong magnetic background can modify the nature and the dynamics of the chiral phase transition at finite temperature. We compute the modified effective potential in the linear sigma model with quarks to one loop in the $\\bar{MS}$ scheme for $N_{f}=2$. For fields $eB\\sim 5 m_{\\pi}^{2}$ and larger a crossover is turned into a weak first-order transition. We discuss possible implications for non-central heavy ion collisions at RHIC and LHC, and for the primordial QCD transition.

  16. Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2016-01-01

    BACKGROUND The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. METHODS The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. RESULTS Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. CONCLUSIONS Starting with a system’s relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy. PMID:26998346

  17. Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

    Directory of Open Access Journals (Sweden)

    Yook Karen

    2011-01-01

    Full Text Available Abstract Background Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form. Results We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO. The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor. Conclusions We provide a phenotype ontology (WPO that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and

  18. The Cosmic Microwave Background

    Directory of Open Access Journals (Sweden)

    Jones Aled

    1998-01-01

    Full Text Available We present a brief review of current theory and observations of the cosmic microwave background (CMB. New predictions for cosmological defect theories and an overview of the inflationary theory are discussed. Recent results from various observations of the anisotropies of the microwave background are described and a summary of the proposed experiments is presented. A new analysis technique based on Bayesian statistics that can be used to reconstruct the underlying sky fluctuations is summarised. Current CMB data is used to set some preliminary constraints on the values of fundamental cosmological parameters $Omega$ and $H_circ$ using the maximum likelihood technique. In addition, secondary anisotropies due to the Sunyaev-Zel'dovich effect are described.

  19. The extragalactic IR background

    CERN Document Server

    De Zotti, G; Mazzei, P; Toffolatti, L; Danese, L; De Zotti, G; Franceschini, A; Mazzei, P; Toffolatti, L; Danese, L

    1994-01-01

    Current limits on the intensity of the extragalactic infrared background are consistent with the expected contribution from evolving galaxies. Depending on the behaviour of the star formation rate and of the initial mass function, we can expect that dust extinction during early evolutionary phases ranges from moderate to strong. An example of the latter case may be the ultraluminous galaxy IRAS F10214 + 4724. The remarkable lack of high redshift galaxies in faint optically selected samples may be indirect evidence that strong extinction is common during early phases. Testable implications of different scenarios are discussed; ISO can play a key role in this context. Estimates of possible contributions of galaxies to the background under different assumptions are presented. The COBE/FIRAS limits on deviations from a blackbody spectrum at sub-mm wavelengths already set important constraints on the evolution of the far-IR emission of galaxies and on the density of obscured (``Type 2'') AGNs. A major progress in ...

  20. Identification of five novel modifier loci of Apc(Min) harbored in the BXH14 recombinant inbred strain.

    Science.gov (United States)

    Nnadi, Stephanie C; Watson, Rayneisha; Innocent, Julie; Gonye, Gregory E; Buchberg, Arthur M; Siracusa, Linda D

    2012-08-01

    Every year thousands of people in the USA are diagnosed with small intestine and colorectal cancers (CRC). Although environmental factors affect disease etiology, uncovering underlying genetic factors is imperative for risk assessment and developing preventative therapies. Familial adenomatous polyposis is a heritable genetic disorder in which individuals carry germ-line mutations in the adenomatous polyposis coli (APC) gene that predisposes them to CRC. The Apc ( Min ) mouse model carries a point mutation in the Apc gene and develops polyps along the intestinal tract. Inbred strain background influences polyp phenotypes in Apc ( Min ) mice. Several Modifier of Min (Mom) loci that alter tumor phenotypes associated with the Apc ( Min ) mutation have been identified to date. We screened BXH recombinant inbred (RI) strains by crossing BXH RI females with C57BL/6J (B6) Apc ( Min ) males and quantitating tumor phenotypes in backcross progeny. We found that the BXH14 RI strain harbors five modifier loci that decrease polyp multiplicity. Furthermore, we show that resistance is determined by varying combinations of these modifier loci. Gene interaction network analysis shows that there are multiple networks with proven gene-gene interactions, which contain genes from all five modifier loci. We discuss the implications of this result for studies that define susceptibility loci, namely that multiple networks may be acting concurrently to alter tumor phenotypes. Thus, the significance of this work resides not only with the modifier loci we identified but also with the combinations of loci needed to get maximal protection against polyposis and the impact of this finding on human disease studies.

  1. Penetrance of craniofacial anomalies in mouse models of Smith-Magenis syndrome is modified by genomic sequence surrounding Rai1: not all null alleles are alike.

    Science.gov (United States)

    Yan, Jiong; Bi, Weimin; Lupski, James R

    2007-03-01

    Craniofacial abnormality is one of the major clinical manifestations of Smith-Magenis syndrome (SMS). Previous analyses in a mixed genetic background of several SMS mouse models--including Df(11)17/+ and Df(11)17-1/+, which have 2-Mb and 590-kb deletions, respectively, and Rai1(-/+)--revealed that the penetrance of the craniofacial phenotype appears to be influenced by deletion size and genetic background. We generated an additional strain with a 1-Mb deletion intermediate in size between the two described above. Remarkably, the penetrance of its craniofacial anomalies in the mixed background was between those of Df(11)17 and Df(11)17-1. We further analyzed the deletion mutations and the Rai1(-/+) allele in a pure C57BL/6 background, to control for nonlinked modifier loci. The penetrance of the craniofacial anomalies was markedly increased for all the strains in comparison with the mixed background. Mice with Df(11)17 and Df(11)17-1 deletions had a similar penetrance, suggesting that penetrance may be less influenced by deletion size, whereas that of Rai1(-/+) mice was significantly lower than that of the deletion strains. We hypothesize that potential trans-regulatory sequence(s) or gene(s) that reside within the 590-kb genomic interval surrounding Rai1 are the major modifying genetic element(s) affecting the craniofacial penetrance. Moreover, we confirmed the influence of genetic background and different deletion sizes on the phenotype. The complicated control of the penetrance for one phenotype in SMS mouse models provides tools to elucidate molecular mechanisms for penetrance and clearly shows that a null allele caused by chromosomal deletion can have different phenotypic consequences than one caused by gene inactivation.

  2. Relationship between endophenotype and phenotype in ADHD

    Directory of Open Access Journals (Sweden)

    Buitelaar Jan K

    2008-01-01

    Full Text Available Abstract Background It has been hypothesized that genetic and environmental factors relate to psychiatric disorders through the effect of intermediating, vulnerability traits called endophenotypes. The study had a threefold aim: to examine the predictive validity of an endophenotypic construct for the ADHD diagnosis, to test whether the magnitude of group differences at the endophenotypic and phenotypic level is comparable, and to investigate whether four factors (gender, age, IQ, rater bias have an effect (moderation or mediation on the relation between endophenotype and phenotype. Methods Ten neurocognitive tasks were administered to 143 children with ADHD, 68 non-affected siblings, and 120 control children (first-borns and 132 children with ADHD, 78 non-affected siblings, and 113 controls (second-borns (5 – 19 years. The task measures have been investigated previously for their endophenotypic viability and were combined to one component which was labeled 'the endophenotypic construct': one measure representative of endophenotypic functioning across several domains of functioning. Results The endophenotypic construct classified children with moderate accuracy (about 50% for each of the three groups. Non-affected children differed as much from controls at the endophenotypic as at the phenotypic level, but affected children displayed a more severe phenotype than endophenotype. Although a potentially moderating effect (age and several mediating effects (gender, age, IQ were found affecting the relation between endophenotypic construct and phenotype, none of the effects studied could account for the finding that affected children had a more severe phenotype than endophenotype. Conclusion Endophenotypic functioning is moderately predictive of the ADHD diagnosis, though findings suggest substantial overlap exists between endophenotypic functioning in the groups of affected children, non-affected siblings, and controls. Results suggest other

  3. Family Background and Entrepreneurship

    DEFF Research Database (Denmark)

    Lindquist, Matthew J.; Sol, Joeri; Van Praag, Mirjam

    Vast amounts of money are currently being spent on policies aimed at promoting entrepreneurship. The success of such policies, however, rests in part on the assumption that individuals are not ‘born entrepreneurs’. In this paper, we assess the importance of family background and neighborhood...... treatment within families by gender and birth order does little to further increase our estimates of the importance of family-wide factors. We then go on to show that neighborhood effects, sibling peer effects, and parental income and education explain very little of these correlations. Parental...

  4. Ultraviolet Background Radiation (Preprint)

    Science.gov (United States)

    1991-03-01

    importance is that the sky may be truly outstandingly black in the far ultraviolet, offering a "dark site " that is unprecedented in astronomy...Estimated spectral energy distribution of the night-sky background near the zenith at an excellent ground-based site on a moonless night and in a...1977. Ap. J. Suppl. 33:451 31. Henry, R. C. 1981. Ap. J. Lett. 244: L69 32. Henry, R. C. 1981. 16th Rencontre de Moriond, ed. J. Tran Thanh Van, p

  5. Malaysia; Background Paper

    OpenAIRE

    International Monetary Fund

    1996-01-01

    This Background Paper on Malaysia examines developments and trends in the labor market since the mid-1980s. The paper describes the changes in the employment structure and the labor force. It reviews wages and productivity trends and their effects on unit labor cost. The paper highlights that Malaysia’s rapid growth, sustained since 1987, has had a major impact on the labor market. The paper outlines the major policy measures to address the labor constraints. It also analyzes Malaysia’s r...

  6. Hypertriglyceridemic Waist Phenotype in Adolescents Aged 15 to 18 Years

    OpenAIRE

    Caridad Hernández Gutiérrez; Elodia Rivas Alpízar; Teresita Rodríguez Izaguirre; Alain Francisco Morejón Giraldoni

    2015-01-01

    Background: presence of the hypertriglyceridemic waist phenotype is a predictor of cardiometabolic deterioration, increased type 2 diabetes mellitus and coronary heart disease. Objective: to determine the hypertriglyceridemic waist phenotype in adolescents aged 15 to 18 years from the Area III of Cienfuegos. Method: a case series study was conducted in a universe of 198 adolescents aged 15 to 18 years who attended a consultation created for this study at the Octavio de la Concepción y de la P...

  7. Fine Mapping of a Dravet Syndrome Modifier Locus on Mouse Chromosome 5 and Candidate Gene Analysis by RNA-Seq

    Science.gov (United States)

    Hawkins, Nicole A.; Zachwieja, Nicole J.; Miller, Alison R.; Anderson, Lyndsey L.; Kearney, Jennifer A.

    2016-01-01

    A substantial number of mutations have been identified in voltage-gated sodium channel genes that result in various forms of human epilepsy. SCN1A mutations result in a spectrum of severity ranging from mild febrile seizures to Dravet syndrome, an infant-onset epileptic encephalopathy. Dravet syndrome patients experience multiple seizures types that are often refractory to treatment, developmental delays, and elevated risk for SUDEP. The same sodium channel mutation can produce epilepsy phenotypes of varying clinical severity. This suggests that other factors, including genetic, modify the primary mutation and change disease severity. Mouse models provide a useful tool in studying the genetic basis of epilepsy. The mouse strain background can alter phenotype severity, supporting a contribution of genetic modifiers in epilepsy. The Scn1a+/- mouse model has a strain-dependent epilepsy phenotype. Scn1a+/- mice on the 129S6/SvEvTac (129) strain have a normal phenotype and lifespan, while [129xC57BL/6J]F1-Scn1a+/- mice experience spontaneous seizures, hyperthermia-induced seizures and high rates of premature death. We hypothesize the phenotypic differences are due to strain-specific genetic modifiers that influence expressivity of the Scn1a+/- phenotype. Low resolution mapping of Scn1a+/- identified several Dravet syndrome modifier (Dsm) loci responsible for the strain-dependent difference in survival. One locus of interest, Dsm1 located on chromosome 5, was fine mapped to a 9 Mb region using interval specific congenics. RNA-Seq was then utilized to identify candidate modifier genes within this narrowed region. Three genes with significant total gene expression differences between 129S6/SvEvTac and [129xC57BL/6J]F1 were identified, including the GABAA receptor subunit, Gabra2. Further analysis of Gabra2 demonstrated allele-specific expression. Pharmological manipulation by clobazam, a common anticonvulsant with preferential affinity for the GABRA2 receptor, revealed

  8. Fine Mapping of a Dravet Syndrome Modifier Locus on Mouse Chromosome 5 and Candidate Gene Analysis by RNA-Seq.

    Directory of Open Access Journals (Sweden)

    Nicole A Hawkins

    2016-10-01

    Full Text Available A substantial number of mutations have been identified in voltage-gated sodium channel genes that result in various forms of human epilepsy. SCN1A mutations result in a spectrum of severity ranging from mild febrile seizures to Dravet syndrome, an infant-onset epileptic encephalopathy. Dravet syndrome patients experience multiple seizures types that are often refractory to treatment, developmental delays, and elevated risk for SUDEP. The same sodium channel mutation can produce epilepsy phenotypes of varying clinical severity. This suggests that other factors, including genetic, modify the primary mutation and change disease severity. Mouse models provide a useful tool in studying the genetic basis of epilepsy. The mouse strain background can alter phenotype severity, supporting a contribution of genetic modifiers in epilepsy. The Scn1a+/- mouse model has a strain-dependent epilepsy phenotype. Scn1a+/- mice on the 129S6/SvEvTac (129 strain have a normal phenotype and lifespan, while [129xC57BL/6J]F1-Scn1a+/- mice experience spontaneous seizures, hyperthermia-induced seizures and high rates of premature death. We hypothesize the phenotypic differences are due to strain-specific genetic modifiers that influence expressivity of the Scn1a+/- phenotype. Low resolution mapping of Scn1a+/- identified several Dravet syndrome modifier (Dsm loci responsible for the strain-dependent difference in survival. One locus of interest, Dsm1 located on chromosome 5, was fine mapped to a 9 Mb region using interval specific congenics. RNA-Seq was then utilized to identify candidate modifier genes within this narrowed region. Three genes with significant total gene expression differences between 129S6/SvEvTac and [129xC57BL/6J]F1 were identified, including the GABAA receptor subunit, Gabra2. Further analysis of Gabra2 demonstrated allele-specific expression. Pharmological manipulation by clobazam, a common anticonvulsant with preferential affinity for the GABRA2

  9. Strain background influences neurotoxicity and behavioral abnormalities in mice expressing the tetracycline transactivator.

    Science.gov (United States)

    Han, Harry J; Allen, Carolyn C; Buchovecky, Christie M; Yetman, Michael J; Born, Heather A; Marin, Miguel A; Rodgers, Shaefali P; Song, Bryan J; Lu, Hui-Chen; Justice, Monica J; Probst, Frank J; Jankowsky, Joanna L

    2012-08-01

    The tet-off system has been widely used to create transgenic models of neurological disorders including Alzheimer's, Parkinson's, Huntington's, and prion disease. The utility of this system lies in the assumption that the tetracycline transactivator (TTA) acts as an inert control element and does not contribute to phenotypes under study. Here we report that neuronal expression of TTA can affect hippocampal cytoarchitecture and behavior in a strain-dependent manner. While studying neurodegeneration in two tet-off Alzheimer's disease models, we unexpectedly discovered neuronal loss within the dentate gyrus of single transgenic TTA controls. Granule neurons appeared most sensitive to TTA exposure during postnatal development, and doxycycline treatment during this period was neuroprotective. TTA-induced degeneration could be rescued by moving the transgene onto a congenic C57BL/6J background and recurred on reintroduction of either CBA or C3H/He backgrounds. Quantitative trait analysis of B6C3 F2 TTA mice identified a region on Chromosome 14 that contains a major modifier of the neurodegenerative phenotype. Although B6 mice were resistant to degeneration, they were not ideal for cognitive testing. F1 offspring of TTA C57BL/6J and 129X1/SvJ, FVB/NJ, or DBA/1J showed improved spatial learning, but TTA expression caused subtle differences in contextual fear conditioning on two of these backgrounds, indicating that strain and genotype can interact independently under different behavioral settings. All model systems have limitations that should be recognized and mitigated where possible; our findings stress the importance of mapping the effects caused by TTA alone when working with tet-off models.

  10. Cosmic microwave background theory.

    Science.gov (United States)

    Bond, J R

    1998-01-01

    A long-standing goal of theorists has been to constrain cosmological parameters that define the structure formation theory from cosmic microwave background (CMB) anisotropy experiments and large-scale structure (LSS) observations. The status and future promise of this enterprise is described. Current band-powers in -space are consistent with a DeltaT flat in frequency and broadly follow inflation-based expectations. That the levels are approximately (10(-5))2 provides strong support for the gravitational instability theory, while the Far Infrared Absolute Spectrophotometer (FIRAS) constraints on energy injection rule out cosmic explosions as a dominant source of LSS. Band-powers at 100 suggest that the universe could not have re-ionized too early. To get the LSS of Cosmic Background Explorer (COBE)-normalized fluctuations right provides encouraging support that the initial fluctuation spectrum was not far off the scale invariant form that inflation models prefer: e.g., for tilted Lambda cold dark matter sequences of fixed 13-Gyr age (with the Hubble constant H0 marginalized), ns = 1.17 +/- 0.3 for Differential Microwave Radiometer (DMR) only; 1.15 +/- 0.08 for DMR plus the SK95 experiment; 1.00 +/- 0.04 for DMR plus all smaller angle experiments; 1.00 +/- 0.05 when LSS constraints are included as well. The CMB alone currently gives weak constraints on Lambda and moderate constraints on Omegatot, but theoretical forecasts of future long duration balloon and satellite experiments are shown which predict percent-level accuracy among a large fraction of the 10+ parameters characterizing the cosmic structure formation theory, at least if it is an inflation variant.

  11. Ultraviolet Background Radiation

    Science.gov (United States)

    Henry, R. C.; Murthy, J.

    1993-12-01

    The UVX experiment was carried on the Space Shuttle Columbia between 1986 January 12 and 19 (STS-61C). Several ultraviolet spectrometers were used to obtain measurements of the diffuse ultraviolet background at 8 locations in the sky. We have reanalysed the UVX measurements of the surface brightness of the diffuse ultraviolet background above b = 40 using the dust-scattering model of Onaka & Kodaira (1991), which explicitly takes into account the variation of the source function with galactic longitude. The range of allowed values of interstellar grain albedoJa, and scattering asymmetry parameter g, is considerably expanded over those of a previous analysis. The new chi square probability contours come close to, but do not include, the values of a and g found for the interstellar grains by Witt et al. (1992) using the Ultraviolet Imaging Telescope (UIT) on the Astro mission. If we hypothesize in additon to the dust-scattered light an extragalactic component, of 300 1 100 photons cm-2 s-1 sr-1 A-1, attenuated by a cosecant b law, the new reduction of the UVX data gives complete consistency with the Witt et al. determination of the optical parameters of the grains in the ultraviolet. This work was supported by United States Air Force Contract F19628-93-K-0004, and by National Aeronautics and Space Administration grant NASA NAG5-619. We are grateful for the encouragement of Dr. Stephan Price, and we thank Dr. L. Danly for information. Onaka, T., & Kodaira, K. 1991, ApJ, 379, 532 Witt, A. N., Petersohn, J. K., Bohlin, R. C., O'Connell, R. W., Roberts, M. S., Smith, A. M., & Stecher, T. P. 1992, ApJ, 395, L5

  12. Modified Ureterosigmoidostomy

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective To introduce an operation procedure and evaluate the coutinence diversion results of the modified ureterosigmoidostomy after radical cystectomy. Methods Fourteen cases of bladder cancer or prostate carcinoma were operated on with modified Sigma pouch from Feb, 1998 to Dec, 1999. A longitudinal incision about 25 cm on the sigmoid uall was done to form a low pressure pouch. The vertex of the new pouch was fixed to sacrum. Both ends of ureters were anastomosed side to side and to form a big nipple and inserted into the top of pouch for 2 to 3 centimeters. Results It took about sixty five minutes to create a new low pressure pouch after radical cystectomy. Early complication of was found in two cases postoperatively, and cured with temporary colonostomy. Hydronephrosis and hypokalemia in one patient were cured by percutaneous anterograde ureter dilatation with balloon and oral replacement of potassium salt. All patients displayed urinary continence. No symptomatic renal infection or hypercholoraemic acidosis occurred. Conclusion Modified ureterosigmoidostomy is a safe procedure of urinary diversion and provides a big volume, low intravesical pressure pouch. The patients are free from the troublesome urine-bag, intermittert catheterization , and upper urinary tracts are protected effectively. The quality of life is satisfied.

  13. Low background infrared (LBIR) facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Low background infrared (LBIR) facility was originally designed to calibrate user supplied blackbody sources and to characterize low-background IR detectors and...

  14. Cosmic Microwave Background Mapping

    Science.gov (United States)

    Verkhodanov, O. V.; Doroshkevich, A. G.

    2012-03-01

    The last decade of research in cosmology was connected with the ambitious experiments including space and ground base observations. Among the most impressive results of these investigations are the measurements of the cosmic microwave background (CMB) radiation like WMAP* and Planck. Exactly from the CMB studies, we have started the epoch of the precision cosmology when generally the values of cosmological parameters have been known and present research is devoted to improvement of the precision. These achievements are connected with both the creation of the new facilities in millimeter and submillimeter astronomy (e.g., satellites, receivers, antennas, computers) and development of the methods for the CMB data analysis. Actually, the process of data analysis contains several technical stages including 1. Registration of time-ordered data (TOD) 2. Pixelization of the CMB data - map preparation 3. Component separation 4. Map statistics analysis 5. Map - spherical harmonics transformation 6. C(l)-spectrum calculation and spectrum statistics analysis 7. Cosmological parameters estimation Starting from the cosmic background explorer (COBE) experiment using the so-called Quadrilateralized Sky Cube Projection (see [1-3]), the problem of the whole sky CMB pixelization has attracted great interest and many such schemes were developed. Let us note however that accurate pixelization of the CMB data on the sphere is very important but not the final step of analysis. Usually, the next step implies the determination of the coefficients of the spherical harmonic decomposition of the CMB signal for both anisotropy and polarization. This means that some of the pixelization schemes provide a very accurate map but are inconvenient for further decomposition. This also means that the choice of suitable pixelization schemes depends upon the general goals of the investigation. In this review, we consider several of the most popular sky map pixelization schemes and link them with the

  15. Background and introduction

    DEFF Research Database (Denmark)

    2012-01-01

    Purpose: To explain the purpose and background of this book and introduce the three basic perspectives behind the research presented as well as the structure and editing process of the book. Methodology: The editors shared and discussed individual contributions to this chapter, based on their own...... behind the scenes of the making of this book and connects contributions from three different fields - FM, CREM, and B2B marketing - to shed more light on the concept of added value of FM. It serves as an introduction to the research presented in the other chapters in this book....... expertise, the involvement in the process leading to this the book including a number of workshops, and a literature review of the development of their disciplinary fields: Facilities Management (FM), Corporate Real Estate Management (CREM) and Business to Business (B2B) Marketing. Findings: The difference...... in scope between FM and CREM is that CREM has its focus on real estate as physical and economical assets utilized by an organisation, while FM has a wider service focus. The difference in scope between FM and CREM on one side and B2B marketing on the other is that FM and CREM are related to organisations...

  16. Haploinsufficient Bmp4 ocular phenotypes include anterior segment dysgenesis with elevated intraocular pressure

    Directory of Open Access Journals (Sweden)

    Nusinowitz Steven

    2001-11-01

    Full Text Available Abstract Background Glaucoma is a blinding disease usually associated with high intraocular pressure (IOP. In some families, abnormal anterior segment development contributes to glaucoma. The genes causing anterior segment dysgenesis and glaucoma in most of these families are not identified and the affected developmental processes are poorly understood. Bone morphogenetic proteins (BMPs participate in various developmental processes. We tested the importance of Bmp4 gene dosage for ocular development and developmental glaucoma. Results Bmp4+/- mice have anterior segment abnormalities including malformed, absent or blocked trabecular meshwork and Schlemm's canal drainage structures. Mice with severe drainage structure abnormalities, over 80% or more of their angle's extent, have elevated IOP. The penetrance and severity of abnormalities is strongly influenced by genetic background, being most severe on the C57BL/6J background and absent on some other backgrounds. On the C57BL/6J background there is also persistence of the hyaloid vasculature, diminished numbers of inner retinal cells, and absence of the optic nerve. Conclusions We demonstrate that heterozygous deficiency of BMP4 results in anterior segment dysgenesis and elevated IOP. The abnormalities are similar to those in human patients with developmental glaucoma. Thus, BMP4 is a strong candidate to contribute to Axenfeld-Rieger anomaly and other developmental conditions associated with human glaucoma. BMP4 also participates in posterior segment development and wild-type levels are usually critical for optic nerve development on the C57BL/6J background. Bmp4+/- mice are useful for studying various components of ocular development, and may allow identification of strain specific modifiers affecting a variety of ocular phenotypes.

  17. Evaluation of phenotypic tests for the detection of AmpC beta-lactamase in clinical isolates of Escherichia coli

    Directory of Open Access Journals (Sweden)

    Deepika Handa

    2013-01-01

    Full Text Available Background: AmpC beta lactamases are cephalosporinases that confer resistance to a wide range of beta lactam drugs thereby causing serious therapeautic problem. As there are no CLSI guidelines for detection of AmpC mediated resistance in Gram negative clinical isolates and it may pose a problem due to misleading results, especially so in phenotypic tests. Although cefoxitin resistance is used as a screening test, it does not reliably indicate AmpC production. Materials and Methods: We planned a study to determine the occurrence of AmpC beta lactamase in hospital and community, clinical isolates of Escherichia coli and simultaneously evaluate different phenotypic methods for detection of AmpC beta lactamases. Results: It was observed that 82.76% isolates were ESBL positive and 59% were cefoxitin screen positive. Using phenotypic confirmatory tests the occurrence of Amp C beta lactamases was found to be 40% and 39% by inhibitor based method using boronic acid (IBM and modified three dimensional test (M3D respectively. Conclusion: Both the test showed concordant result. Co-production was observed in 84.62% isolates Screening of ESBL and Amp C can be done in routine clinical microbiology laboratory using aztreonam and IBM respectively as it is a simple, rapid and technically less demanding procedure which can be used in all clinical laboratories.

  18. MPHASYS: a mouse phenotype analysis system

    Directory of Open Access Journals (Sweden)

    Mian I

    2007-06-01

    Full Text Available Abstract Background Systematic, high-throughput studies of mouse phenotypes have been hampered by the inability to analyze individual animal data from a multitude of sources in an integrated manner. Studies generally make comparisons at the level of genotype or treatment thereby excluding associations that may be subtle or involve compound phenotypes. Additionally, the lack of integrated, standardized ontologies and methodologies for data exchange has inhibited scientific collaboration and discovery. Results Here we introduce a Mouse Phenotype Analysis System (MPHASYS, a platform for integrating data generated by studies of mouse models of human biology and disease such as aging and cancer. This computational platform is designed to provide a standardized methodology for working with animal data; a framework for data entry, analysis and sharing; and ontologies and methodologies for ensuring accurate data capture. We describe the tools that currently comprise MPHASYS, primarily ones related to mouse pathology, and outline its use in a study of individual animal-specific patterns of multiple pathology in mice harboring a specific germline mutation in the DNA repair and transcription-specific gene Xpd. Conclusion MPHASYS is a system for analyzing multiple data types from individual animals. It provides a framework for developing data analysis applications, and tools for collecting and distributing high-quality data. The software is platform independent and freely available under an open-source license 1.

  19. The Broad Autism Phenotype Questionnaire

    Science.gov (United States)

    Hurley, Robert S. E.; Losh, Molly; Parlier, Morgan; Reznick, J. Steven; Piven, Joseph

    2007-01-01

    The broad autism phenotype (BAP) is a set of personality and language characteristics that reflect the phenotypic expression of the genetic liability to autism, in non-autistic relatives of autistic individuals. These characteristics are milder but qualitatively similar to the defining features of autism. A new instrument designed to measure the…

  20. Plant Phenotype Characterization System

    Energy Technology Data Exchange (ETDEWEB)

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  1. Plants having modified response to ethylene

    Science.gov (United States)

    Meyerowitz, E.M.; Chang, C.; Bleecker, A.B.

    1997-11-18

    The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype. 31 figs.

  2. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

  3. Global phenotypic characterization of bacteria.

    Science.gov (United States)

    Bochner, Barry R

    2009-01-01

    The measure of the quality of a systems biology model is how well it can reproduce and predict the behaviors of a biological system such as a microbial cell. In recent years, these models have been built up in layers, and each layer has been growing in sophistication and accuracy in parallel with a global data set to challenge and validate the models in predicting the content or activities of genes (genomics), proteins (proteomics), metabolites (metabolomics), and ultimately cell phenotypes (phenomics). This review focuses on the latter, the phenotypes of microbial cells. The development of Phenotype MicroArrays, which attempt to give a global view of cellular phenotypes, is described. In addition to their use in fleshing out and validating systems biology models, there are many other uses of this global phenotyping technology in basic and applied microbiology research, which are also described.

  4. Coulomb field in a constant electromagnetic background

    CERN Document Server

    Adorno, T C; Shabad, A E

    2016-01-01

    Nonlinear Maxwell equations are written up to the third-power deviations from a constant-field background, valid within any local nonlinear electrodynamics including QED with Euler-Heisenberg effective Lagrangian. Linear electric response to imposed static finite-sized charge is found in the vacuum filled by an arbitrary combination of constant and homogeneous electric and magnetic fields. The modified Coulomb field, corrections to the total charge and to the charge density are given in terms of derivatives of the effective Lagrangian with respect to the field invariants.

  5. Discordant phenotype in siblings with X-linked agammaglobulinemia

    Energy Technology Data Exchange (ETDEWEB)

    Bykowsky, M.J.; Veksler, K.S.; Sullivan, K.E. [Children`s Hospital, Philadelphia, PA (United States)] [and others

    1996-03-01

    X-linked agammaglobulinemia (XLA) is a congenital humoral immunodeficiency caused by a defect in a B-cell-specific signaling molecule, Btk. There has been little concordance of phenotype with genotype in this disorder, and defects in Btk cause immunodeficiencies that range from mild impairment to complete inability to produce antibodies. The factors modifying the phenotype of XLA are not understood. The current study is the first description of two male siblings with identical T{sup 134}{yields}C mutations in the translation initiation ATG of Btk who have different clinical phenotypes as well as different laboratory phenotypes. The proband lacks immunoglobulins and B cells and has recurrent infections, while the elder, affected brother has normal levels of IgG and IgM and very few infections. Both have undetectable levels of Btk kinase activity in circulating mononuclear cells. Complete sequencing of Btk gene transcripts in both brothers revealed no additional mutations to account for the discordant phenotypes. This description provides unequivocal evidence that the phenotype of XLA is influenced by factors additional to the Btk gene. 39 refs., 3 figs., 3 tabs.

  6. Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens

    Directory of Open Access Journals (Sweden)

    Sun Youxian

    2008-06-01

    Full Text Available Abstract Background The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologists. Such qualitative analysis is particularly effective in detecting subtle, but important, deviations in phenotypes. However, while the rapid and continuing development of automated microscope-based technologies now facilitates the acquisition of trillions of cells in thousands of diverse experimental conditions, such as in the context of RNA interference (RNAi or small-molecule screens, the massive size of these datasets precludes human analysis. Thus, the development of automated methods which aim to identify novel and biological relevant phenotypes online is one of the major challenges in high-throughput image-based screening. Ideally, phenotype discovery methods should be designed to utilize prior/existing information and tackle three challenging tasks, i.e. restoring pre-defined biological meaningful phenotypes, differentiating novel phenotypes from known ones and clarifying novel phenotypes from each other. Arbitrarily extracted information causes biased analysis, while combining the complete existing datasets with each new image is intractable in high-throughput screens. Results Here we present the design and implementation of a novel and robust online phenotype discovery method with broad applicability that can be used in diverse experimental contexts, especially high-throughput RNAi screens. This method features phenotype modelling and iterative cluster merging using improved gap statistics. A Gaussian Mixture Model (GMM is employed to estimate the distribution of each existing phenotype, and then used as reference distribution in gap statistics. This method is broadly applicable to a number of different types of

  7. JEM-X background models

    DEFF Research Database (Denmark)

    Huovelin, J.; Maisala, S.; Schultz, J.

    2003-01-01

    Background and determination of its components for the JEM-X X-ray telescope on INTEGRAL are discussed. A part of the first background observations by JEM-X are analysed and results are compared to predictions. The observations are based on extensive imaging of background near the Crab Nebula...

  8. A developmental, longitudinal investigation of autism phenotypic profiles in fragile X syndrome

    OpenAIRE

    Lee, Michelle; Martin, Gary E; Berry-Kravis, Elizabeth; Losh, Molly

    2016-01-01

    Background Targeting overlapping behavioral phenotypes in neurogenetic disorders can help elucidate gene-behavior relationships. Fragile X syndrome (FXS) and autism spectrum disorder (ASD) have been studied as a model for this approach, and important areas of phenotypic overlap and divergence have been documented. However, few studies have examined how the manifestation of ASD-related phenotypes in FXS may change over development, a question which has important implications for conceptualizin...

  9. Societal aspects of genetically modified foods

    DEFF Research Database (Denmark)

    Frewer, L.J.; Lassen, J.; Kettlitz, B.

    2004-01-01

    This paper aims to examine some of the reasons behind public controversy associated with the introduction of genetically modified foods in Europe the 1990s. The historical background to the controversy is provided to give context. The issue of public acceptance of genetically modified foods...... efficaciously into risk analysis processes, specifically with respect to the biosciences and to technology implementation in general....

  10. Computable visually observed phenotype ontological framework for plants

    Directory of Open Access Journals (Sweden)

    Schaeffer Mary

    2011-06-01

    Full Text Available Abstract Background The ability to search for and precisely compare similar phenotypic appearances within and across species has vast potential in plant science and genetic research. The difficulty in doing so lies in the fact that many visual phenotypic data, especially visually observed phenotypes that often times cannot be directly measured quantitatively, are in the form of text annotations, and these descriptions are plagued by semantic ambiguity, heterogeneity, and low granularity. Though several bio-ontologies have been developed to standardize phenotypic (and genotypic information and permit comparisons across species, these semantic issues persist and prevent precise analysis and retrieval of information. A framework suitable for the modeling and analysis of precise computable representations of such phenotypic appearances is needed. Results We have developed a new framework called the Computable Visually Observed Phenotype Ontological Framework for plants. This work provides a novel quantitative view of descriptions of plant phenotypes that leverages existing bio-ontologies and utilizes a computational approach to capture and represent domain knowledge in a machine-interpretable form. This is accomplished by means of a robust and accurate semantic mapping module that automatically maps high-level semantics to low-level measurements computed from phenotype imagery. The framework was applied to two different plant species with semantic rules mined and an ontology constructed. Rule quality was evaluated and showed high quality rules for most semantics. This framework also facilitates automatic annotation of phenotype images and can be adopted by different plant communities to aid in their research. Conclusions The Computable Visually Observed Phenotype Ontological Framework for plants has been developed for more efficient and accurate management of visually observed phenotypes, which play a significant role in plant genomics research. The

  11. Alpha Background Rejection in Bolometer Detectors

    Science.gov (United States)

    Deporzio, Nicholas

    2016-03-01

    This study presents the modification of bolometer detectors used in particle searches to veto or otherwise reject alpha radiation background and the statistical advantages of doing so. Several techniques are presented in detail - plastic film scintillator vetoes, metallic film ionization vetoes, and scintillating bolometer vetoes. Plastic scintillator films are cooled to bolometer temperatures and bombarded with 1.4MeV to 6.0MeV alpha particles representative of documented detector background. Photomultipliers detect this scintillation light and produce a veto signal. Layered metallic films of a primary metal, dielectric, and secondary metal, such as gold-polyethylene-gold films, are cooled to milli-kelvin temperatures and biased to produce a current signal veto when incident 1.4MeV to 6.0MeV alpha particles ionize conduction paths through the film. Modified Zinc Molybdate Bolometers are used to produce scintillation light when stimulated by alpha background. Calibration of veto signal to background energy is presented. Results are used to quantify the statistical impact of such modifications on bolometer searches.

  12. Supergravity backgrounds and symmetry superalgebras

    CERN Document Server

    Ertem, Ümit

    2016-01-01

    We consider the bosonic sectors of supergravity theories in ten and eleven dimensions which correspond to the low energy limits of string theories and M-theory. The solutions of supergravity field equations are known as supergravity backgrounds and the number of preserved supersymmetries in those backgrounds are determined by Killing spinors. We provide some examples of supergravity backgrounds which preserve different fractions of supersymmetry. An important invariant for the characterization of supergravity backgrounds is their Killing superalgebras which are constructed out of Killing vectors and Killing spinors of the background. After constructing Killing superalgebras of some special supergravity backgrounds, we discuss about the possibilities of the extensions of these superalgebras to include the higher degree hidden symmetries of the background.

  13. Phenotypic plasticity, costs of phenotypes, and costs of plasticity

    DEFF Research Database (Denmark)

    Callahan, Hilary S; Maughan, Heather; Steiner, Uli

    2008-01-01

    Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns...... of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both...... types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic...

  14. Extreme phenotypic variation in Cetraria aculeata (lichenized Ascomycota): adaptation or incidental modification?

    Science.gov (United States)

    Pérez-Ortega, Sergio; Fernández-Mendoza, Fernando; Raggio, José; Vivas, Mercedes; Ascaso, Carmen; Sancho, Leopoldo G.; Printzen, Christian; de los Ríos, Asunción

    2012-01-01

    Background and Aims Phenotypic variability is a successful strategy in lichens for colonizing different habitats. Vagrancy has been reported as a specific adaptation for lichens living in steppe habitats around the world. Among the facultatively vagrant species, the cosmopolitan Cetraria aculeata apparently forms extremely modified vagrant thalli in steppe habitats of Central Spain. The aim of this study was to investigate whether these changes are phenotypic plasticity (a single genotype producing different phenotypes), by characterizing the anatomical and ultrastructural changes observed in vagrant morphs, and measuring differences in ecophysiological performance. Methods Specimens of vagrant and attached populations of C. aculeata were collected on the steppes of Central Spain. The fungal internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GPD) and the large sub-unit of the mitochondrial ribosomal DNA (mtLSUm), and the algal ITS and actin were studied within a population genetics framework. Semi-thin and ultrathin sections were analysed by means of optical, scanning electron and transmission electron microscopy. Gas exchange and chlorophyll fluorescence were used to compare the physiological performance of both morphs. Key Results and Conclusions Vagrant and attached morphs share multilocus haplotypes which may indicate that they belong to the same species in spite of their completely different anatomy. However, differentiation tests suggested that vagrant specimens do not represent a random sub-set of the surrounding population. The morphological differences were related to anatomical and ultrastructural differences. Large intercalary growth rates of thalli after the loss of the basal–apical thallus polarity may be the cause of the increased growth shown by vagrant specimens. The anatomical and morphological changes lead to greater duration of ecophysiological activity in vagrant specimens. Although the anatomical and physiological

  15. Perinatal risk factors for wheezing phenotypes in the first 8 years of life

    NARCIS (Netherlands)

    Caudri, D.; Savenije, O. E. M.; Smit, H. A.; Postma, D. S.; Koppelman, G. H.; Wijga, A. H.; Kerkhof, M.; Gehring, U.; Hoekstra, M. O.; Brunekreef, B.; de Jongste, J. C.

    2013-01-01

    Background A novel data-driven approach was used to identify wheezing phenotypes in pre-schoolchildren aged 0-8 years, in the Prevention and Incidence of Asthma and Mite Allergy (PIAMA) birth cohort. Five phenotypes were identified: never/infrequent wheeze, transient early wheeze, intermediate onset

  16. Phenotype and genotype in 101 males with X-linked creatine transporter deficiency

    NARCIS (Netherlands)

    Kamp, J.M. van de; Betsalel, O.T.; Mercimek-Mahmutoglu, S.; Abulhoul, L.; Grunewald, S.; Anselm, I.; Azzouz, H.; Bratkovic, D.; Brouwer, A.; Hamel, B.C.J.; Kleefstra, T.; Yntema, H.G.; Campistol, J.; Vilaseca, M.A.; Cheillan, D.; D'Hooghe, M.; Diogo, L.; Garcia, P.; Valongo, C.; Fonseca, M.; Frints, S.; Wilcken, B.; Haar, S. van der; Meijers-Heijboer, H.E.; Hofstede, F.; Johnson, D.; Kant, S.G.; Lion-Francois, L.; Pitelet, G.; Longo, N.; Maat-Kievit, J.A.; Monteiro, J.P.; Munnich, A.; Muntau, A.C.; Nassogne, M.C.; Osaka, H.; Ounap, K.; Pinard, J.M.; Quijano-Roy, S.; Poggenburg, I.; Poplawski, N.; Abdul-Rahman, O.; Ribes, A.; Arias Vasquez, A.; Yaplito-Lee, J.; Schulze, A.; Schwartz, C.E.; Schwenger, S.; Soares, G.; Sznajer, Y.; Valayannopoulos, V.; Esch, H. van; Waltz, S.; Wamelink, M.M.; Pouwels, P.J.; Errami, A.; Knaap, M.S. van der; Jakobs, C.; Mancini, G.M.; Salomons, G.S.

    2013-01-01

    BACKGROUND: Creatine transporter deficiency is a monogenic cause of X-linked intellectual disability. Since its first description in 2001 several case reports have been published but an overview of phenotype, genotype and phenotype-genotype correlation has been lacking. METHODS: We performed a retro

  17. Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods

    NARCIS (Netherlands)

    Bayjanov, J.; Starrenburg, M.J.; Sijde, M.R. van der; Siezen, R.J.; Hijum, S.A.F.T. van

    2013-01-01

    BACKGROUND: Lactococcus lactis is used in dairy food fermentation and for the efficient production of industrially relevant enzymes. The genome content and different phenotypes have been determined for multiple L. lactis strains in order to understand intra-species genotype and phenotype diversity a

  18. Integration of multi-omics data for prediction of phenotypic traits using random forest

    NARCIS (Netherlands)

    Acharjee, Animesh; Kloosterman, Bjorn; Visser, Richard G.F.; Maliepaard, Chris

    2016-01-01

    Background: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data from a diploid segregating mapping population

  19. Primary sclerosing cholangitis is associated with a distinct phenotype of inflammatory bowel disease

    NARCIS (Netherlands)

    Boonstra, K.; Erpecum, K.J. van; Nieuwkerk, K.M. van; Drenth, J.P.H.; Poen, A.C.; Witteman, B.J.; Tuynman, H.A.; Beuers, U.; Ponsioen, C.Y.

    2012-01-01

    BACKGROUND: Primary sclerosing cholangitis (PSC) is strongly associated with inflammatory bowel disease (IBD). The aim of this study was to assess the IBD phenotype associated with PSC in a large well-phenotyped population-based PSC cohort using endoscopic and histopathologic criteria. METHODS: PSC

  20. Pathogenic mutations in GLI2 cause a specific phenotype that is distinct from holoprosencephaly

    NARCIS (Netherlands)

    Bear, Kelly A.; Solomon, Benjamin D.; Antonini, Sonir; Arnhold, Ivo J. P.; Franca, Marcela M.; Gerkes, Erica H.; Grange, Dorothy K.; Hadley, Donald W.; Jaaskelainen, Jarmo; Paulo, Sabrina S.; Rump, Patrick; Stratakis, Constantine A.; Thompson, Elizabeth M.; Willis, Mary; Winder, Thomas L.; Jorge, Alexander A. L.; Roessler, Erich; Muenke, Maximilian

    2014-01-01

    Background Mutations in GLI2 have been associated with holoprosencephaly (HPE), a neuroanatomic anomaly resulting from incomplete cleavage of the developing forebrain, and an HPE-like phenotype involving pituitary anomalies and polydactyly. Objective To characterise the genotypic and phenotypic find

  1. Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes

    Directory of Open Access Journals (Sweden)

    Wolfinger Russell D

    2007-02-01

    Full Text Available Abstract Background Commonly employed clustering methods for analysis of gene expression data do not directly incorporate phenotypic data about the samples. Furthermore, clustering of samples with known phenotypes is typically performed in an informal fashion. The inability of clustering algorithms to incorporate biological data in the grouping process can limit proper interpretation of the data and its underlying biology. Results We present a more formal approach, the modk-prototypes algorithm, for clustering biological samples based on simultaneously considering microarray gene expression data and classes of known phenotypic variables such as clinical chemistry evaluations and histopathologic observations. The strategy involves constructing an objective function with the sum of the squared Euclidean distances for numeric microarray and clinical chemistry data and simple matching for histopathology categorical values in order to measure dissimilarity of the samples. Separate weighting terms are used for microarray, clinical chemistry and histopathology measurements to control the influence of each data domain on the clustering of the samples. The dynamic validity index for numeric data was modified with a category utility measure for determining the number of clusters in the data sets. A cluster's prototype, formed from the mean of the values for numeric features and the mode of the categorical values of all the samples in the group, is representative of the phenotype of the cluster members. The approach is shown to work well with a simulated mixed data set and two real data examples containing numeric and categorical data types. One from a heart disease study and another from acetaminophen (an analgesic exposure in rat liver that causes centrilobular necrosis. Conclusion The modk-prototypes algorithm partitioned the simulated data into clusters with samples in their respective class group and the heart disease samples into two groups (sick and

  2. Invasion strategies in clonal aquatic plants: Are phenotypic differences caused by phenotypic plasticity or local adaptation?

    DEFF Research Database (Denmark)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit

    2010-01-01

    populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis...... and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained by local nutrient conditions. All together this strongly suggests that invasive clonal aquatic plants adapt to a wide......Background and Aims: The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important...

  3. The acute stress response of red porgy, Pagrus pagrus, kept on a red or white background

    NARCIS (Netherlands)

    Salm, A.L. van der; Pavlidis, M.; Flik, G.; Wendelaar Bonga, S.E.

    2005-01-01

    The skin colour of red porgy, Pagrus pagrus, can be modified by exposure to different background colours. Red and white background colours brighten the dark skin colour that develops under common culture conditions in red porgy. To assess whether skin colour is also modified by aquaculture related h

  4. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

    KAUST Repository

    Hoehndorf, Robert

    2016-11-14

    Background The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text. Results We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities. Conclusions The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established

  5. Phenotypic Plasticity Promotes Balanced Polymorphism in Periodic Environments by a Genomic Storage Effect.

    Science.gov (United States)

    Gulisija, Davorka; Kim, Yuseob; Plotkin, Joshua B

    2016-04-01

    Phenotypic plasticity is known to evolve in perturbed habitats, where it alleviates the deleterious effects of selection. But the effects of plasticity on levels of genetic polymorphism, an important precursor to adaptation in temporally varying environments, are unclear. Here we develop a haploid, two-locus population-genetic model to describe the interplay between a plasticity modifier locus and a target locus subject to periodically varying selection. We find that the interplay between these two loci can produce a "genomic storage effect" that promotes balanced polymorphism over a large range of parameters, in the absence of all other conditions known to maintain genetic variation. The genomic storage effect arises as recombination allows alleles at the two loci to escape more harmful genetic backgrounds and associate in haplotypes that persist until environmental conditions change. Using both Monte Carlo simulations and analytical approximations we quantify the strength of the genomic storage effect across a range of selection pressures, recombination rates, plasticity modifier effect sizes, and environmental periods.

  6. Finding our way through phenotypes.

    Directory of Open Access Journals (Sweden)

    Andrew R Deans

    2015-01-01

    Full Text Available Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

  7. Finding our way through phenotypes.

    Science.gov (United States)

    Deans, Andrew R; Lewis, Suzanna E; Huala, Eva; Anzaldo, Salvatore S; Ashburner, Michael; Balhoff, James P; Blackburn, David C; Blake, Judith A; Burleigh, J Gordon; Chanet, Bruno; Cooper, Laurel D; Courtot, Mélanie; Csösz, Sándor; Cui, Hong; Dahdul, Wasila; Das, Sandip; Dececchi, T Alexander; Dettai, Agnes; Diogo, Rui; Druzinsky, Robert E; Dumontier, Michel; Franz, Nico M; Friedrich, Frank; Gkoutos, George V; Haendel, Melissa; Harmon, Luke J; Hayamizu, Terry F; He, Yongqun; Hines, Heather M; Ibrahim, Nizar; Jackson, Laura M; Jaiswal, Pankaj; James-Zorn, Christina; Köhler, Sebastian; Lecointre, Guillaume; Lapp, Hilmar; Lawrence, Carolyn J; Le Novère, Nicolas; Lundberg, John G; Macklin, James; Mast, Austin R; Midford, Peter E; Mikó, István; Mungall, Christopher J; Oellrich, Anika; Osumi-Sutherland, David; Parkinson, Helen; Ramírez, Martín J; Richter, Stefan; Robinson, Peter N; Ruttenberg, Alan; Schulz, Katja S; Segerdell, Erik; Seltmann, Katja C; Sharkey, Michael J; Smith, Aaron D; Smith, Barry; Specht, Chelsea D; Squires, R Burke; Thacker, Robert W; Thessen, Anne; Fernandez-Triana, Jose; Vihinen, Mauno; Vize, Peter D; Vogt, Lars; Wall, Christine E; Walls, Ramona L; Westerfeld, Monte; Wharton, Robert A; Wirkner, Christian S; Woolley, James B; Yoder, Matthew J; Zorn, Aaron M; Mabee, Paula

    2015-01-01

    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

  8. Epigenetics in heart failure phenotypes

    Directory of Open Access Journals (Sweden)

    Alexander Berezin

    2016-12-01

    Full Text Available Chronic heart failure (HF is a leading clinical and public problem posing a higher risk of morbidity and mortality in different populations. HF appears to be in both phenotypic forms: HF with reduced left ventricular ejection fraction (HFrEF and HF with preserved left ventricular ejection fraction (HFpEF. Although both HF phenotypes can be distinguished through clinical features, co-morbidity status, prediction score, and treatment, the clinical outcomes in patients with HFrEF and HFpEF are similar. In this context, investigation of various molecular and cellular mechanisms leading to the development and progression of both HF phenotypes is very important. There is emerging evidence that epigenetic regulation may have a clue in the pathogenesis of HF. This review represents current available evidence regarding the implication of epigenetic modifications in the development of different HF phenotypes and perspectives of epigenetic-based therapies of HF.

  9. Latent cluster analysis of ALS phenotypes identifies prognostically differing groups.

    Directory of Open Access Journals (Sweden)

    Jeban Ganesalingam

    Full Text Available BACKGROUND: Amyotrophic lateral sclerosis (ALS is a degenerative disease predominantly affecting motor neurons and manifesting as several different phenotypes. Whether these phenotypes correspond to different underlying disease processes is unknown. We used latent cluster analysis to identify groupings of clinical variables in an objective and unbiased way to improve phenotyping for clinical and research purposes. METHODS: Latent class cluster analysis was applied to a large database consisting of 1467 records of people with ALS, using discrete variables which can be readily determined at the first clinic appointment. The model was tested for clinical relevance by survival analysis of the phenotypic groupings using the Kaplan-Meier method. RESULTS: The best model generated five distinct phenotypic classes that strongly predicted survival (p<0.0001. Eight variables were used for the latent class analysis, but a good estimate of the classification could be obtained using just two variables: site of first symptoms (bulbar or limb and time from symptom onset to diagnosis (p<0.00001. CONCLUSION: The five phenotypic classes identified using latent cluster analysis can predict prognosis. They could be used to stratify patients recruited into clinical trials and generating more homogeneous disease groups for genetic, proteomic and risk factor research.

  10. Distribution profile of paraoxonase phenotypes among the Gujaratis

    Directory of Open Access Journals (Sweden)

    Patel A

    2007-01-01

    Full Text Available Background: Paraoxonase (PON1 can hydrolyze organophosphate pesticides (OP and has a key role in the susceptibility of human in OP toxicity. The human-enzyme shows polymorphism and variations in the distribution profile of its phenotypes among different ethnic groups have been observed. Aims: To see the distribution pattern of total PON1 activity in 45 healthy attendants of poisoning cases; 121 healthy unrelated farm-labours and 59 normal subjects of trauma. Materials and Methods: The PON1 activities from serum/plasma samples of these healthy normal individuals were estimated with/without addition of 1M NaCl in order to determine salt-stimulated and basal activity. The PON 1 phenotypes were determined on the basis of percent activation of enzyme activity. Results: Tri-modal distribution of basal PON1 activity was observed among all these individuals. 52.0% of the individuals belonged to Phenotype A, 46.6% to phenotype AB while 1.4% to Phenotype B with gene frequency of allele-A and allele-B being 0.753 and 0.247 respectively in excellent agreement with Hardy-Weinberg equilibrium. Conclusion: Maximum number of individuals belonged to phenotype-A (low PON1 activity showing potential vulnerability towards Op-poisoning.

  11. Evaluating diabetes and hypertension disease causality using mouse phenotypes

    Directory of Open Access Journals (Sweden)

    Han Jing-Dong J

    2010-07-01

    Full Text Available Abstract Background Genome-wide association studies (GWAS have found hundreds of single nucleotide polymorphisms (SNPs associated with common diseases. However, it is largely unknown what genes linked with the SNPs actually implicate disease causality. A definitive proof for disease causality can be demonstration of disease-like phenotypes through genetic perturbation of the genes or alleles, which is obviously a daunting task for complex diseases where only mammalian models can be used. Results Here we tapped the rich resource of mouse phenotype data and developed a method to quantify the probability that a gene perturbation causes the phenotypes of a disease. Using type II diabetes (T2D and hypertension (HT as study cases, we found that the genes, when perturbed, having high probability to cause T2D and HT phenotypes tend to be hubs in the interactome networks and are enriched for signaling pathways regulating metabolism but not metabolic pathways, even though the genes in these metabolic pathways are often the most significantly changed in expression levels in these diseases. Conclusions Compared to human genetic disease-based predictions, our mouse phenotype based predictors greatly increased the coverage while keeping a similarly high specificity. The disease phenotype probabilities given by our approach can be used to evaluate the likelihood of disease causality of disease-associated genes and genes surrounding disease-associated SNPs.

  12. Wilsonian flows and background fields

    CERN Document Server

    Litim, Daniel F; Litim, Daniel F.; Pawlowski, Jan M.

    2002-01-01

    We study exact renormalisation group flows for background field dependent regularisations. It is shown that proper-time flows are approximations to exact background field flows for a specific class of regulators. We clarify the role of the implicit scale dependence introduced by the background field. Its impact on the flow is evaluated numerically for scalar theories at criticality for different approximations and regularisations. Implications for gauge theories are discussed.

  13. Spice: discovery of phenotype-determining component interplays

    Directory of Open Access Journals (Sweden)

    Chen Zhengzhang

    2012-05-01

    Full Text Available Abstract Background A latent behavior of a biological cell is complex. Deriving the underlying simplicity, or the fundamental rules governing this behavior has been the Holy Grail of systems biology. Data-driven prediction of the system components and their component interplays that are responsible for the target system’s phenotype is a key and challenging step in this endeavor. Results The proposed approach, which we call System Phenotype-related Interplaying Components Enumerator (Spice, iteratively enumerates statistically significant system components that are hypothesized (1 to play an important role in defining the specificity of the target system’s phenotype(s; (2 to exhibit a functionally coherent behavior, namely, act in a coordinated manner to perform the phenotype-specific function; and (3 to improve the predictive skill of the system’s phenotype(s when used collectively in the ensemble of predictive models. Spice can be applied to both instance-based data and network-based data. When validated, Spice effectively identified system components related to three target phenotypes: biohydrogen production, motility, and cancer. Manual results curation agreed with the known phenotype-related system components reported in literature. Additionally, using the identified system components as discriminatory features improved the prediction accuracy by 10% on the phenotype-classification task when compared to a number of state-of-the-art methods applied to eight benchmark microarray data sets. Conclusion We formulate a problem—enumeration of phenotype-determining system component interplays—and propose an effective methodology (Spice to address this problem. Spice improved identification of cancer-related groups of genes from various microarray data sets and detected groups of genes associated with microbial biohydrogen production and motility, many of which were reported in literature. Spice also improved the predictive skill of the

  14. The digital revolution in phenotyping

    Science.gov (United States)

    Oellrich, Anika; Collier, Nigel; Groza, Tudor; Rebholz-Schuhmann, Dietrich; Shah, Nigam; Bodenreider, Olivier; Boland, Mary Regina; Georgiev, Ivo; Liu, Hongfang; Livingston, Kevin; Luna, Augustin; Mallon, Ann-Marie; Manda, Prashanti; Robinson, Peter N.; Rustici, Gabriella; Simon, Michelle; Wang, Liqin; Winnenburg, Rainer; Dumontier, Michel

    2016-01-01

    Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, defined as observable characteristics of organisms, can be seen as one of the bridges that lead to a translation of experimental findings into clinical applications and thereby support ‘bench to bedside’ efforts. However, to build this translational bridge, a common and universal understanding of phenotypes is required that goes beyond domain-specific definitions. To achieve this ambitious goal, a digital revolution is ongoing that enables the encoding of data in computer-readable formats and the data storage in specialized repositories, ready for integration, enabling translational research. While phenome research is an ongoing endeavor, the true potential hidden in the currently available data still needs to be unlocked, offering exciting opportunities for the forthcoming years. Here, we provide insights into the state-of-the-art in digital phenotyping, by means of representing, acquiring and analyzing phenotype data. In addition, we provide visions of this field for future research work that could enable better applications of phenotype data. PMID:26420780

  15. Background subtraction theory and practice

    CERN Document Server

    Elgammal, Ahmed

    2014-01-01

    Background subtraction is a widely used concept for detection of moving objects in videos. In the last two decades there has been a lot of development in designing algorithms for background subtraction, as well as wide use of these algorithms in various important applications, such as visual surveillance, sports video analysis, motion capture, etc. Various statistical approaches have been proposed to model scene backgrounds. The concept of background subtraction also has been extended to detect objects from videos captured from moving cameras. This book reviews the concept and practice of back

  16. Comprehensive genotyping and clinical characterisation reveal 27 novel NKX2-1 mutations and expand the phenotypic spectrum

    Science.gov (United States)

    Thorwarth, Anne; Schnittert-Hübener, Sarah; Schrumpf, Pamela; Müller, Ines; Jyrch, Sabine; Dame, Christof; Biebermann, Heike; Kleinau, Gunnar; Katchanov, Juri; Schuelke, Markus; Ebert, Grit; Steininger, Anne; Bönnemann, Carsten; Brockmann, Knut; Christen, Hans-Jürgen; Crock, Patricia; deZegher, Francis; Griese, Matthias; Hewitt, Jacqueline; Ivarsson, Sten; Hübner, Christoph; Kapelari, Klaus; Plecko, Barbara; Rating, Dietz; Stoeva, Iva; Ropers, Hans-Hilger; Grüters, Annette; Ullmann, Reinhard; Krude, Heiko

    2017-01-01

    Background NKX2-1 encodes a transcription factor with large impact on the development of brain, lung and thyroid. Germline mutations of NKX2-1 can lead to dysfunction and malformations of these organs. Starting from the largest coherent collection of patients with a suspected phenotype to date, we systematically evaluated frequency, quality and spectrum of phenotypic consequences of NKX2-1 mutations. Methods After identifying mutations by Sanger sequencing and array CGH, we comprehensively reanalysed the phenotype of affected patients and their relatives. We employed electrophoretic mobility shift assay (EMSA) to detect alterations of NKX2-1 DNA binding. Gene expression was monitored by means of in situ hybridisation and compared with the expression level of MBIP, a candidate gene presumably involved in the disorders and closely located in close genomic proximity to NKX2-1. Results Within 101 index patients, we detected 17 point mutations and 10 deletions. Neurological symptoms were the most consistent finding (100%), followed by lung affection (78%) and thyroidal dysfunction (75%). Novel symptoms associated with NKX2-1 mutations comprise abnormal height, bouts of fever and cardiac septum defects. In contrast to previous reports, our data suggest that missense mutations in the homeodomain of NKX2-1 not necessarily modify its DNA binding capacity and that this specific type of mutations may be associated with mild pulmonary phenotypes such as asthma. Two deletions did not include NKX2-1, but MBIP, whose expression spatially and temporarily coincides with NKX2-1 in early murine development. Conclusions The high incidence of NKX2-1 mutations strongly recommends the routine screen for mutations in patients with corresponding symptoms. However, this analysis should not be confined to the exonic sequence alone, but should take advantage of affordable NGS technology to expand the target to adjacent regulatory sequences and the NKX2-1 interactome in order to maximise the

  17. Klinefelter syndrome (KS): genetics, clinical phenotype and hypogonadism.

    Science.gov (United States)

    Bonomi, M; Rochira, V; Pasquali, D; Balercia, G; Jannini, E A; Ferlin, A

    2017-02-01

    Klinefelter Syndrome (KS) is characterized by an extreme heterogeneity in its clinical and genetic presentation. The relationship between clinical phenotype and genetic background has been partially disclosed; nevertheless, physicians are aware that several aspects concerning this issue are far to be fully understood. By improving our knowledge on the role of some genetic aspects as well as on the KS, patients' interindividual differences in terms of health status will result in a better management of this chromosomal disease. The aim of this review is to provide an update on both genetic and clinical phenotype and their interrelationships.

  18. The background scale Ward identity in quantum gravity

    CERN Document Server

    Percacci, Roberto

    2016-01-01

    We show that with suitable choices of parametrization, gauge fixing and cutoff, the anomalous variation of the effective action under global rescalings of the background metric is identical to the derivative with respect to the cutoff, i.e. to the beta functional, as defined by the exact RG equation. The Ward identity and the RG equation can be combined, resulting in a modified flow equation that is manifestly invariant under global background rescalings.

  19. Snowshoe hares display limited phenotypic plasticity to mismatch in seasonal camouflage

    Science.gov (United States)

    Zimova, Marketa; Mills, L. Scott; Lukacs, Paul M.; Mitchell, Michael S.

    2014-01-01

    As duration of snow cover decreases owing to climate change, species undergoing seasonal colour moults can become colour mismatched with their background. The immediate adaptive solution to this mismatch is phenotypic plasticity, either in phenology of seasonal colour moults or in behaviours that reduce mismatch or its consequences. We observed nearly 200 snowshoe hares across a wide range of snow conditions and two study sites in Montana, USA, and found minimal plasticity in response to mismatch between coat colour and background. We found that moult phenology varied between study sites, likely due to differences in photoperiod and climate, but was largely fixed within study sites with only minimal plasticity to snow conditions during the spring white-to-brown moult. We also found no evidence that hares modify their behaviour in response to colour mismatch. Hiding and fleeing behaviours and resting spot preference of hares were more affected by variables related to season, site and concealment by vegetation, than by colour mismatch. We conclude that plasticity in moult phenology and behaviours in snowshoe hares is insufficient for adaptation to camouflage mismatch, suggesting that any future adaptation to climate change will require natural selection on moult phenology or behaviour.

  20. Backgrounds and characteristics of arsonists

    NARCIS (Netherlands)

    Labree, W.; Nijman, H.L.I.; Marle, H.J.C. van; Rassin, E.

    2010-01-01

    The aim of this study was to gain more insight in the backgrounds and characteristics of arsonists. For this, the psychiatric, psychological, personal, and criminal backgrounds of all arsonists (n = 25), sentenced to forced treatment in the maximum security forensic hospital “De Kijvelanden”, were c

  1. Measurement of natural background neutron

    CERN Document Server

    Li Jain, Ping; Tang Jin Hua; Tang, E S; Xie Yan Fong

    1982-01-01

    A high sensitive neutron monitor is described. It has an approximate counting rate of 20 cpm for natural background neutrons. The pulse amplitude resolution, sensitivity and direction dependence of the monitor were determined. This monitor has been used for natural background measurement in Beijing area. The yearly average dose is given and compared with the results of KEK and CERN.

  2. Phenotypic and genetic characterization of a novel phenotype in pigs characterized by juvenile hairlessness and age dependent emphysema

    DEFF Research Database (Denmark)

    Bruun, Camilla S.; Jørgensen, Claus B.; Bay, Lene

    2008-01-01

    Background: A pig phenotype characterized by juvenile hairlessness, thin skin and age dependent lung emphysema has been discovered in a Danish pig herd. The trait shows autosomal co-dominant inheritance with all three genotypes distinguishable. Since the phenotype shows resemblance to the integrin...... of musculi arrectores pili, and at puberty or later localized areas of emphysema are seen in the lungs. Comparative mapping predicted that the porcine ITGB6 and ITGAV orthologs map to SSC15. In an experimentall family (n=113), showing segregation of the trait, the candidate region was confirmed by linkage...

  3. Epigenetic reversion of breast carcinoma phenotype is accompaniedby DNA sequestration

    Energy Technology Data Exchange (ETDEWEB)

    Sandal, Tone; Valyi-Nagy, Klara; Spencer, Virginia A.; Folberg,Robert; Bissell, Mina J.; Maniotis, Andrew J.

    2006-07-19

    The importance of microenvironment and context in regulation of tissue-specific genes is finally well established. DNA exposure to, or sequestration from, nucleases can be used to detect differences in higher order chromatin structure in intact cells without disturbing cellular or tissue architecture. To investigate the relationship between chromatin organization and tumor phenotype, we utilized an established 3-D assay where normal and malignant human breast cells can be easily distinguished by the morphology of the structures they make (acinus-like vs tumor-like, respectively). We show that these phenotypes can be distinguished also by sensitivity to AluI digestion where the malignant cells are resistant to digestion relative to non-malignant cells. Reversion of the T4-2 breast cancer cells by either cAMP analogs, or a phospatidylinositol 3-kinase (P13K) inhibitor not only reverted the phenotype, but also the chromatin sensitivity to AluI. By using different cAMP-analogs, we show that the cAMP-induced phenotypic reversion, polarization, and shift in DNA organization act through a cAMP-dependent-protein-kinase A-coupled signaling pathway. Importantly, inhibitory antibody to fibronectin also reverted the malignant phenotype, polarized the acini, and changed chromatin sequestration. These experiments show not only that modifying the tumor microenvironment can alter the organization of tumor cells but also that architecture of the tissues and the global chromatin organization are coupled and yet highly plastic.

  4. The phenotypic plasticity of developmental modules

    Directory of Open Access Journals (Sweden)

    Aabha I. Sharma

    2016-08-01

    Full Text Available Abstract Background Organisms develop and evolve in a modular fashion, but how individual modules interact with the environment remains poorly understood. Phenotypically plastic traits are often under selection, and studies are needed to address how traits respond to the environment in a modular fashion. In this study, tissue-specific plasticity of melanic spots was examined in the large milkweed bug, Oncopeltus fasciatus. Results Although the size of the abdominal melanic bands varied according to rearing temperatures, wing melanic bands were more robust. To explore the regulation of abdominal pigmentation plasticity, candidate genes involved in abdominal melanic spot patterning and biosynthesis of melanin were analyzed. While the knockdown of dopa decarboxylase (Ddc led to lighter pigmentation in both the wings and the abdomen, the shape of the melanic elements remained unaffected. Although the knockdown of Abdominal-B (Abd-B partially phenocopied the low-temperature phenotype, the abdominal bands were still sensitive to temperature shifts. These observations suggest that regulators downstream of Abd-B but upstream of DDC are responsible for the temperature response of the abdomen. Ablation of wings led to the regeneration of a smaller wing with reduced melanic bands that were shifted proximally. In addition, the knockdown of the Wnt signaling nuclear effector genes, armadillo 1 and armadillo 2, altered both the melanic bands and the wing shape. Thus, the pleiotropic effects of Wnt signaling may constrain the amount of plasticity in wing melanic bands. Conclusions We propose that when traits are regulated by distinct pre-patterning mechanisms, they can respond to the environment in a modular fashion, whereas when the environment impacts developmental regulators that are shared between different modules, phenotypic plasticity can manifest as a developmentally integrated system.

  5. Boc modifies the holoprosencephaly spectrum of Cdo mutant mice

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2011-05-01

    Holoprosencephaly (HPE is caused by a failure to form the midline of the forebrain and/or midface. It is one of the most common human birth defects, but clinical expression is extremely variable. HPE is associated with mutations in the sonic hedgehog (SHH pathway. Mice lacking the Shh pathway regulator Cdo (also called Cdon display HPE with strain-dependent penetrance and expressivity, implicating silent modifier genes as one cause of the variability. However, the identities of potential HPE modifiers of this type are unknown. We report here that whereas mice lacking the Cdo paralog Boc do not have HPE, Cdo;Boc double mutants on a largely Cdo-resistant genetic background have lobar HPE with strong craniofacial anomalies and defects in Shh target gene expression in the developing forebrain. Boc is therefore a silent HPE modifier gene in mice. Furthermore, Cdo and Boc have specific, selective roles in Shh signaling in mammals, because Cdo;Boc double-mutant mice do not display the most severe HPE phenotype seen in Shh-null mice, nor do they have major defects in digit patterning or development of vertebrae, which are also Shh-dependent processes. This is in contrast to reported observations in Drosophila, where genetic removal of the Cdo and Boc orthologs Ihog and Boi results in a complete loss of response to the hedgehog ligand. Therefore, there is evolutionary divergence between mammals and insects in the requirement of the hedgehog pathway for Cdo/Ihog family members, with mammalian development involving additional factors and/or distinct mechanisms at this level of pathway regulation.

  6. Phenotypic features and phylogenetic background of extraintestinal hemolytic Escherichia coli responsible of mortality in puppies.

    Science.gov (United States)

    Turchetto, Sara; Ustulin, Martina; Citterio, Carlo Vittorio; Zanardello, Claudia; Vascellari, Marta; Vio, Denis; Conedera, Gabriella; Milone, Nicola Maria Ferro; Cocchi, Monia

    2015-08-31

    A 10-day-old litter of five puppies of Bracco Italiano dog breed showed weakness and diarrhea and, 2 days later, four of them died. At the same time, the bitch showed high hyperthermia (40 °C) and endometritis. The necropsy of a puppy revealed a severe lobar pneumonia accompanied with a bilateral nephrosis. No gross lesions were detected in other organs. Histopathology of the lung revealed severe multifocal fibrino-suppurative necrotizing bronchiolar-alveolitis associated with rod-shaped bacterial aggregates and diffuse interstitial lymphocytic infiltration. The kidney showed severe multifocal necrosis of the tubular epithelium and diffuse severe congestion of the parenchyma. A pure culture of hemolytic Escherichia coli carrying the Cnf-1 gene was identified, from both the puppy organs and bitch's milk. Moreover, phylo-typing assigned them to the phylogroup B2. Two weeks later, fecal samples from the bitch and the survived puppy were collected for a second microbiological analysis, identifying two hemolytic E. coli strains, Cnf positive and Cdt negative and Cnf and Cdt negative, respectively. Some E. coli pathogenic strains may cause enteric or extraintestinal disease. In dogs and cats, strains of extraintestinal pathogenic E. coli (ExPEC) produce specific virulent factors such as hemolysis and cytotoxin necrotizing factors (Cnf). In this episode, we hypothesize that the bitch's milk could be the main source of ExPEC infection causing high puppies mortality. The role of the bitch as a carrier could not be excluded: stressful conditions, such as pregnancy and delivery, would change the host-pathogen dynamics possibly increasing the release of the infectious burden.

  7. Berkeley Low Background Counting Facility

    Data.gov (United States)

    Federal Laboratory Consortium — Sensitive low background assay detectors and sample analysis are available for non-destructive direct gamma-ray assay of samples. Neutron activation analysis is also...

  8. Backgrounds in AFP Detector Estimation

    CERN Document Server

    Huang, Yicong

    2016-01-01

    The ATLAS Forward Proton (AFP) detectors aim to measure protons that are scattered in the ATLAS interaction point under very small angles ($90-160 \\mu rad$). The diffractive protons detected by the AFP may be accompanied by beam halo. This report presents an estimation of the beam halo backgrounds in the AFP using low pile-up data, and position distributions of the backgrounds in the AFP.

  9. Similarity-based search of model organism, disease and drug effect phenotypes

    KAUST Repository

    Hoehndorf, Robert

    2015-02-19

    Background: Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, novel pathways, gene functions, druggable therapeutic targets, and determination of pathogenicity. Results: We have developed PhenomeNET 2, a system that enables similarity-based searches over a large repository of phenotypes in real-time. It can be used to identify strains of model organisms that are phenotypically similar to human patients, diseases that are phenotypically similar to model organism phenotypes, or drug effect profiles that are similar to the phenotypes observed in a patient or model organism. PhenomeNET 2 is available at http://aber-owl.net/phenomenet. Conclusions: Phenotype-similarity searches can provide a powerful tool for the discovery and investigation of molecular mechanisms underlying an observed phenotypic manifestation. PhenomeNET 2 facilitates user-defined similarity searches and allows researchers to analyze their data within a large repository of human, mouse and rat phenotypes.

  10. Natural variation of model mutant phenotypes in Ciona intestinalis.

    Directory of Open Access Journals (Sweden)

    Paolo Sordino

    Full Text Available BACKGROUND: The study of ascidians (Chordata, Tunicata has made a considerable contribution to our understanding of the origin and evolution of basal chordates. To provide further information to support forward genetics in Ciona intestinalis, we used a combination of natural variation and neutral population genetics as an approach for the systematic identification of new mutations. In addition to the significance of developmental variation for phenotype-driven studies, this approach can encompass important implications in evolutionary and population biology. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report a preliminary survey for naturally occurring mutations in three geographically interconnected populations of C. intestinalis. The influence of historical, geographical and environmental factors on the distribution of abnormal phenotypes was assessed by means of 12 microsatellites. We identified 37 possible mutant loci with stereotyped defects in embryonic development that segregate in a way typical of recessive alleles. Local populations were found to differ in genetic organization and frequency distribution of phenotypic classes. CONCLUSIONS/SIGNIFICANCE: Natural genetic polymorphism of C. intestinalis constitutes a valuable source of phenotypes for studying embryonic development in ascidians. Correlating genetic structure and the occurrence of abnormal phenotypes is a crucial focus for understanding the selective forces that shape natural finite populations, and may provide insights of great importance into the evolutionary mechanisms that generate animal diversity.

  11. Putative modifier genes in mevalonate kinase deficiency.

    Science.gov (United States)

    Marcuzzi, Annalisa; Vozzi, Diego; Girardelli, Martina; Tricarico, Paola Maura; Knowles, Alessandra; Crovella, Sergio; Vuch, Josef; Tommasini, Alberto; Piscianz, Elisa; Bianco, Anna Monica

    2016-04-01

    Mevalonate kinase deficiency (MKD) is an autosomal recessive auto‑inflammatory disease, caused by impairment of the mevalonate pathway. Although the molecular mechanism remains to be elucidated, there is clinical evidence suggesting that other regulatory genes may be involved in determining the phenotype. The identification of novel target genes may explain non‑homogeneous genotype‑phenotype correlations, and provide evidence in support of the hypothesis that novel regulatory genes predispose or amplify deregulation of the mevalonate pathway in this orphan disease. In the present study, DNA samples were obtained from five patients with MKD, which were then analyzed using whole exome sequencing. A missense variation in the PEX11γ gene was observed in homozygosis in P2, possibly correlating with visual blurring. The UNG rare gene variant was detected in homozygosis in P5, without correlating with a specific clinical phenotype. A number of other variants were found in the five analyzed DNA samples from the MKD patients, however no correlation with the phenotype was established. The results of the presents study suggested that further analysis, using next generation sequencing approaches, is required on a larger sample size of patients with MKD, who share the same MVK mutations and exhibit 'extreme' clinical phenotypes. As MVK mutations may be associated with MKD, the identification of specific modifier genes may assist in providing an earlier diagnosis.

  12. Phenotypic spectrum of GABRA1

    DEFF Research Database (Denmark)

    Johannesen, Katrine; Marini, Carla; Pfeffer, Siona

    2016-01-01

    OBJECTIVE: To delineate phenotypic heterogeneity, we describe the clinical features of a cohort of patients with GABRA1 gene mutations. METHODS: Patients with GABRA1 mutations were ascertained through an international collaboration. Clinical, EEG, and genetic data were collected. Functional analy...

  13. Forensic DNA phenotyping : Regulatory issues

    NARCIS (Netherlands)

    Koops, E.J.; Schellekens, M.H.M.

    2008-01-01

    Forensic DNA phenotyping is an interesting new investigation method: crime-scene DNA is analyzed to compose a description of the unknown suspect, including external and behavioral features, geographic origin and perhaps surname. This method is allowed in some countries but prohibited in a few others

  14. Leaf segmentation in plant phenotyping

    NARCIS (Netherlands)

    Scharr, Hanno; Minervini, Massimo; French, Andrew P.; Klukas, Christian; Kramer, David M.; Liu, Xiaoming; Luengo, Imanol; Pape, Jean Michel; Polder, Gerrit; Vukadinovic, Danijela; Yin, Xi; Tsaftaris, Sotirios A.

    2016-01-01

    Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. Although leaves do share appearance and shape cha

  15. Background Independent String Field Theory

    CERN Document Server

    Bars, Itzhak

    2014-01-01

    We develop a new background independent Moyal star formalism in bosonic open string field theory. The new star product is formulated in a half-phase-space, and because phase space is independent of any background fields, the interactions are background independent. In this basis there is a large amount of symmetry, including a supersymmetry OSp(d|2) that acts on matter and ghost degrees of freedom, and simplifies computations. The BRST operator that defines the quadratic kinetic term of string field theory may be regarded as the solution of the equation of motion A*A=0 of a purely cubic background independent string field theory. We find an infinite number of non-perturbative solutions to this equation, and are able to associate them to the BRST operator of conformal field theories on the worldsheet. Thus, the background emerges from a spontaneous-type breaking of a purely cubic highly symmetric theory. The form of the BRST field breaks the symmetry in a tractable way such that the symmetry continues to be us...

  16. The Cosmic Infrared Background Experiment

    CERN Document Server

    Bock, J; Cooray, A R; Kawada, M; Keating, B; Lange, A; Lee, D H; Matsumoto, T; Matsuura, S; Pak, S; Renbarger, T; Sullivan, I; Tsumura, K; Wada, T; Watabe, T; Bock, James; Battle, John; Cooray, Asantha; Kawada, Mitsunobu; Keating, Brian; Lange, Andrew; Lee, Dae-Hea; Matsumoto, Toshio; Matsuura, Shuji; Pak, Soojong; Renbarger, Tom; Sullivan, Ian; Tsumura, Kohji; Wada, Takehiko; Watabe, Toyoki

    2006-01-01

    We are developing a rocket-borne instrument (the Cosmic Infrared Background ExpeRiment, or CIBER) to search for signatures of primordial galaxy formation in the cosmic near-infrared extra-galactic background. CIBER consists of a wide-field two-color camera, a low-resolution absolute spectrometer, and a high-resolution narrow-band imaging spectrometer. The cameras will search for spatial fluctuations in the background on angular scales from 7 arcseconds to 2 degrees over a range of angular scales poorly covered by previous experiments. CIBER will determine if the fluctuations reported by the IRTS arise from first-light galaxies or have a local origin. In a short rocket flight CIBER has sensitivity to probe fluctuations 100 times fainter than IRTS/DIRBE. By jointly observing regions of the sky studied by Spitzer and ASTRO-F, CIBER will build a multi-color view of the near-infrared background, accurately assessing the contribution of local (z = 1-3) galaxies to the observed background fluctuations, allowing a de...

  17. Neutron background estimates in GESA

    Directory of Open Access Journals (Sweden)

    Fernandes A.C.

    2014-01-01

    Full Text Available The SIMPLE project looks for nuclear recoil events generated by rare dark matter scattering interactions. Nuclear recoils are also produced by more prevalent cosmogenic neutron interactions. While the rock overburden shields against (μ,n neutrons to below 10−8 cm−2 s−1, it itself contributes via radio-impurities. Additional shielding of these is similar, both suppressing and contributing neutrons. We report on the Monte Carlo (MCNP estimation of the on-detector neutron backgrounds for the SIMPLE experiment located in the GESA facility of the Laboratoire Souterrain à Bas Bruit, and its use in defining additional shielding for measurements which have led to a reduction in the extrinsic neutron background to ∼ 5 × 10−3 evts/kgd. The calculated event rate induced by the neutron background is ∼ 0,3 evts/kgd, with a dominant contribution from the detector container.

  18. Background simulations and shielding calculations

    Science.gov (United States)

    Kudryavtsev, Vitaly A.

    2011-04-01

    Key improvements in the sensitivity of the underground particle astrophysics experiments can only be achieved if the radiation causing background events in detectors is well understood and proper measures are taken to suppress it. The background radiation arising from radioactivity and cosmic-ray muons is discussed here together with the methods of its suppression. Different shielding designs are considered to attenuate gamma-rays and neutrons coming from radioactivity in rock and lab walls. Purity of materials used in detector construction is analysed and the background event rates due to the presence of radioactive isotopes in detector components are discussed. Event rates in detectors caused by muon-induced neutrons with and without active veto systems are presented leading to the requirements for the depth of an underground laboratory and the efficiency of the veto system.

  19. Saethre-Chotzen syndrome: notable intrafamilial phenotypic variability in a large family with Q28X TWIST mutation.

    Science.gov (United States)

    Dollfus, Hélène; Biswas, Partha; Kumaramanickavel, Govindsamy; Stoetzel, Corinne; Quillet, Renaud; Biswas, Jyotirmay; Lajeunie, Elisabeth; Renier, Dominique; Perrin-Schmitt, Fabienne

    2002-05-01

    Saethre-Chotzen syndrome is an autosomal dominant disease characterized by craniosynostosis, ptosis, and limb and external ear abnormalities. Variable expressivity is a well-known phenomenon in this disorder. A large Indian family has been recently identified as carrying a nonsense TWIST mutation (Q28 X) in 17 members, of whom 16 were examined in detail. Only 4 (25%) of the patients showed patent craniostenosis, namely, oxycephaly. The penetrance of craniosynostosis in this family is lower than previously reported in the literature. Fifteen patients (93%) had moderate to severe ptosis. Minor limb and external ear abnormalities were present in most patients. Eyelid features were the hallmark of the disease for 12 members of the family, suggesting that mutations in TWIST may lead to a phenotype with mainly palpebral features and no craniostenosis. The clinical analysis of this large family clearly illustrates the significant variable expressivity, probably related to haploinsufficiency because of the TWIST mutation. This phenotypic variability remains unclear but could be the result of modifier genes and/or genetic background effect, as noticed previously in the transgenic twist-null heterozygous mice.

  20. Children of ethnic minority backgrounds

    DEFF Research Database (Denmark)

    Johansen, Stine Liv

    2010-01-01

    media products and toys just as they will have knowledge of different media texts, play genres, rhymes etc. This has consequences for their ability to access social settings, for instance in play. New research in this field will focus on how children themselves make sense of this balancing of cultures......Children of ethnic minority background balance their everyday life between a cultural background rooted in their ethnic origin and a daily life in day care, schools and with peers that is founded in a majority culture. This means, among other things, that they often will have access to different...

  1. Generative electronic background music system

    Energy Technology Data Exchange (ETDEWEB)

    Mazurowski, Lukasz [Faculty of Computer Science, West Pomeranian University of Technology in Szczecin, Zolnierska Street 49, Szczecin, PL (Poland)

    2015-03-10

    In this short paper-extended abstract the new approach to generation of electronic background music has been presented. The Generative Electronic Background Music System (GEBMS) has been located between other related approaches within the musical algorithm positioning framework proposed by Woller et al. The music composition process is performed by a number of mini-models parameterized by further described properties. The mini-models generate fragments of musical patterns used in output composition. Musical pattern and output generation are controlled by container for the mini-models - a host-model. General mechanism has been presented including the example of the synthesized output compositions.

  2. Exotic branes and nongeometric backgrounds.

    Science.gov (United States)

    de Boer, Jan; Shigemori, Masaki

    2010-06-25

    When string or M theory is compactified to lower dimensions, the U-duality symmetry predicts so-called exotic branes whose higher-dimensional origin cannot be explained by the standard string or M-theory branes. We argue that exotic branes can be understood in higher dimensions as nongeometric backgrounds or U folds, and that they are important for the physics of systems which originally contain no exotic charges, since the supertube effect generically produces such exotic charges. We discuss the implications of exotic backgrounds for black hole microstate (non-)geometries.

  3. Transgene x environment interactions in genetically modified wheat.

    Directory of Open Access Journals (Sweden)

    Simon L Zeller

    Full Text Available BACKGROUND: The introduction of transgenes into plants may cause unintended phenotypic effects which could have an impact on the plant itself and the environment. Little is published in the scientific literature about the interrelation of environmental factors and possible unintended effects in genetically modified (GM plants. METHODS AND FINDINGS: We studied transgenic bread wheat Triticum aestivum lines expressing the wheat Pm3b gene against the fungus powdery mildew Blumeria graminis f.sp. tritici. Four independent offspring pairs, each consisting of a GM line and its corresponding non-GM control line, were grown under different soil nutrient conditions and with and without fungicide treatment in the glasshouse. Furthermore, we performed a field experiment with a similar design to validate our glasshouse results. The transgene increased the resistance to powdery mildew in all environments. However, GM plants reacted sensitive to fungicide spraying in the glasshouse. Without fungicide treatment, in the glasshouse GM lines had increased vegetative biomass and seed number and a twofold yield compared with control lines. In the field these results were reversed. Fertilization generally increased GM/control differences in the glasshouse but not in the field. Two of four GM lines showed up to 56% yield reduction and a 40-fold increase of infection with ergot disease Claviceps purpurea compared with their control lines in the field experiment; one GM line was very similar to its control. CONCLUSIONS: Our results demonstrate that, depending on the insertion event, a particular transgene can have large effects on the entire phenotype of a plant and that these effects can sometimes be reversed when plants are moved from the glasshouse to the field. However, it remains unclear which mechanisms underlie these effects and how they may affect concepts in molecular plant breeding and plant evolutionary ecology.

  4. The genotype-phenotype correlation in Pompe disease.

    Science.gov (United States)

    Kroos, Marian; Hoogeveen-Westerveld, Marianne; van der Ploeg, Ans; Reuser, Arnold J J

    2012-02-15

    Pompe disease is an autosomal recessive lysosomal glycogen storage disorder that is caused by acid α-glucosidase (GAA) deficiency and is due to pathogenic sequence variations in the corresponding GAA gene. The correlation between genotypes and phenotypes is strict, in that patients with the most severe phenotype, classic infantile Pompe disease, have two pathogenic mutations, one in each GAA allele, that prevent the formation of GAA or totally obliterates its function. All patients with less progressive phenotypes have at least one sequence variation that allows normal or low level synthesis of GAA leading to the formation of analytically measurable, low level GAA activity in most cases. There is an overall trend of finding higher GAA enzyme levels in patients with onset of symptoms in adulthood when compared to patients who show clinical manifestations in early childhood, aged 0-5 years, with a rapidly progressive course, but who lack the severe characteristics of classic infantile Pompe disease. However, several cases have been reported of adult-onset disease with very low GAA activity, which in all those cases corresponds with the GAA genotype. The clinical diversity observed within a large group of patients with functionally the same GAA genotype and the same c.-32-13C > T haplotype demonstrates that modifying factors can have a substantial effect on the clinical course of Pompe disease, disturbing the GAA genotype-phenotype correlation. The present day challenge is to identify these factors and explore them as therapeutic targets.

  5. Teaching about Natural Background Radiation

    Science.gov (United States)

    Al-Azmi, Darwish; Karunakara, N.; Mustapha, Amidu O.

    2013-01-01

    Ambient gamma dose rates in air were measured at different locations (indoors and outdoors) to demonstrate the ubiquitous nature of natural background radiation in the environment and to show that levels vary from one location to another, depending on the underlying geology. The effect of a lead shield on a gamma radiation field was also…

  6. Low Background Micromegas in CAST

    CERN Document Server

    Garza, J G; Aznar, F.; Calvet, D.; Castel, J.F.; Christensen, F.E.; Dafni, T.; Davenport, M.; Decker, T.; Ferrer-Ribas, E.; Galán, J.; García, J.A.; Giomataris, I.; Hill, R.M.; Iguaz, F.J.; Irastorza, I.G.; Jakobsen, A.C.; Jourde, D.; Mirallas, H.; Ortega, I.; Papaevangelou, T.; Pivovaroff, M.J.; Ruz, J.; Tomás, A.; Vafeiadis, T.; Vogel, J.K.

    2015-01-01

    Solar axions could be converted into x-rays inside the strong magnetic field of an axion helioscope, triggering the detection of this elusive particle. Low background x-ray detectors are an essential component for the sensitivity of these searches. We report on the latest developments of the Micromegas detectors for the CERN Axion Solar Telescope (CAST), including technological pathfinder activities for the future International Axion Observatory (IAXO). The use of low background techniques and the application of discrimination algorithms based on the high granularity of the readout have led to background levels below 10$^{-6}$ counts/keV/cm$^2$/s, more than a factor 100 lower than the first generation of Micromegas detectors. The best levels achieved at the Canfranc Underground Laboratory (LSC) are as low as 10$^{-7}$ counts/keV/cm$^2$/s, showing good prospects for the application of this technology in IAXO. The current background model, based on underground and surface measurements, is presented, as well as ...

  7. Low Background Micromegas in CAST

    DEFF Research Database (Denmark)

    Garza, J G; Aune, S.; Aznar, F.

    2014-01-01

    Solar axions could be converted into x-rays inside the strong magnetic field of an axion helioscope, triggering the detection of this elusive particle. Low background x-ray detectors are an essential component for the sensitivity of these searches. We report on the latest developments of the Micr...

  8. Educational Choice. A Background Paper.

    Science.gov (United States)

    Quality Education for Minorities Network, Washington, DC.

    This paper addresses school choice, one proposal to address parental involvement concerns, focusing on historical background, definitions, rationale for advocating choice, implementation strategies, and implications for minorities and low-income families. In the past, transfer payment programs such as tuition tax credits and vouchers were…

  9. The Cosmic Infrared Background Experiment

    Science.gov (United States)

    Bock, James; Battle, J.; Cooray, A.; Hristov, V.; Kawada, M.; Keating, B.; Lee, D.; Matsumoto, T.; Matsuura, S.; Nam, U.; Renbarger, T.; Sullivan, I.; Tsumura, K.; Wada, T.; Zemcov, M.

    2009-01-01

    We are developing the Cosmic Infrared Background ExpeRiment (CIBER) to search for signatures of first-light galaxy emission in the extragalactic background. The first generation of stars produce characteristic signatures in the near-infrared extragalactic background, including a redshifted Ly-cutoff feature and a characteristic fluctuation power spectrum, that may be detectable with a specialized instrument. CIBER consists of two wide-field cameras to measure the fluctuation power spectrum, and a low-resolution and a narrow-band spectrometer to measure the absolute background. The cameras will search for fluctuations on angular scales from 7 arcseconds to 2 degrees, where the first-light galaxy spatial power spectrum peaks. The cameras have the necessary combination of sensitivity, wide field of view, spatial resolution, and multiple bands to make a definitive measurement. CIBER will determine if the fluctuations reported by Spitzer arise from first-light galaxies. The cameras observe in a single wide field of view, eliminating systematic errors associated with mosaicing. Two bands are chosen to maximize the first-light signal contrast, at 1.6 um near the expected spectral maximum, and at 1.0 um; the combination is a powerful discriminant against fluctuations arising from local sources. We will observe regions of the sky surveyed by Spitzer and Akari. The low-resolution spectrometer will search for the redshifted Lyman cutoff feature in the 0.7 - 1.8 um spectral region. The narrow-band spectrometer will measure the absolute Zodiacal brightness using the scattered 854.2 nm Ca II Fraunhofer line. The spectrometers will test if reports of a diffuse extragalactic background in the 1 - 2 um band continues into the optical, or is caused by an under estimation of the Zodiacal foreground. We report performance of the assembled and tested instrument as we prepare for a first sounding rocket flight in early 2009. CIBER is funded by the NASA/APRA sub-orbital program.

  10. The molecular basis of beta-thalassemia intermedia in southern China: genotypic heterogeneity and phenotypic diversity

    Directory of Open Access Journals (Sweden)

    Sun Manna

    2010-02-01

    Full Text Available Abstract Background The clinical syndrome of thalassemia intermedia (TI results from the β-globin genotypes in combination with factors to produce fetal haemoglobin (HbF and/or co-inheritance of α-thalassemia. However, very little is currently known of the molecular basis of Chinese TI patients. Methods We systematically analyzed and characterized β-globin genotypes, α-thalassemia determinants, and known primary genetic modifiers linked to the production of HbF and the aggravation of α/β imbalance in 117 Chinese TI patients. Genotype-phenotype correlations were analyzed based on retrospective clinical observations. Results A total of 117 TI patients were divided into two major groups, namely heterozygous β-thalassemia (n = 20 in which 14 were characterized as having a mild TI with the Hb levels of 68-95 g/L except for five co-inherited αααanti-3.7 triplication and one carried a dominant mutation; and β-thalassemia homozygotes or compound heterozygotes for β-thalassemia and other β-globin defects in which the β+-thalassemia mutation was the most common (49/97, hemoglobin E (HbE variants was second (27/97, and deletional hereditary persistence of fetal hemoglobin (HPFH or δβ-thalassemia was third (11/97. Two novel mutations, Term CD+32(A→C and Cap+39(C→T, have been detected. Conclusions Chinese TI patients showed considerable heterogeneity, both phenotypically and genotypically. The clinical outcomes of our TI patients were mostly explained by the genotypes linked to the β- and α-globin gene cluster. However, for a group of 14 patients (13 β0/βN and 1 β+/βN with known heterozygous mutations of β-thalassemia and three with homozygous β-thalassemia (β0/β0, the existence of other causative genetic determinants is remaining to be molecularly defined.

  11. Distinct genetic regions modify specific muscle groups in muscular dystrophy

    OpenAIRE

    2010-01-01

    Phenotypic expression in the muscular dystrophies is variable, even with the identical mutation, providing strong evidence that genetic modifiers influence outcome. To identify genetic modifier loci, we used quantitative trait locus mapping in two differentially affected mouse strains with muscular dystrophy. Using the Sgcg model of limb girdle muscular dystrophy that lacks the dystrophin-associated protein γ-sarcoglycan, we evaluated chromosomal regions that segregated with two distinct quan...

  12. Deciphering the Galaxy Guppy phenotype

    Directory of Open Access Journals (Sweden)

    Philip Shaddock

    2011-01-01

    Full Text Available Animal breeding hobbyists have been useful to science because they identify and isolate colorcoat mutations that geneticists can in turn use in their studies of the development and differentiation ofcolor cells. This paper discusses a very interesting color mutant, the Japanese Galaxy, tracing its creationfrom back to a self-educated genetics hobbyist, Hoskiki Tsutsui. The paper discusses a constituent genepreviously studied by Dr. Violet Phang, the snakeskin gene (the linked body and fin genes Ssb and Sst.And it discusses a gene previously unknown to science, the Schimmelpfennig Platinum gene (Sc.Through crossing experiments, the author determines that the combination of these two genes producesan intermediate phenotype, the Medusa. Incorporating the Grass (Gr, another gene unknown to sciencegene into the Medusa through a crossover produces the Galaxy phenotype. Microscope studies of thesnakeskin pattern in Galaxies and snakeskins reveals some parallels with similar studies made of theZebrafish Danio.

  13. Phenotypic deconstruction of gene circuitry.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2013-06-01

    It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

  14. Statistical models for trisomic phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Lamb, N.E.; Sherman, S.L.; Feingold, E. [Emory Univ., Atlanta, GA (United States)

    1996-01-01

    Certain genetic disorders are rare in the general population but more common in individuals with specific trisomies, which suggests that the genes involved in the etiology of these disorders may be located on the trisomic chromosome. As with all aneuploid syndromes, however, a considerable degree of variation exists within each phenotype so that any given trait is present only among a subset of the trisomic population. We have previously presented a simple gene-dosage model to explain this phenotypic variation and developed a strategy to map genes for such traits. The mapping strategy does not depend on the simple model but works in theory under any model that predicts that affected individuals have an increased likelihood of disomic homozygosity at the trait locus. This paper explores the robustness of our mapping method by investigating what kinds of models give an expected increase in disomic homozygosity. We describe a number of basic statistical models for trisomic phenotypes. Some of these are logical extensions of standard models for disomic phenotypes, and some are more specific to trisomy. Where possible, we discuss genetic mechanisms applicable to each model. We investigate which models and which parameter values give an expected increase in disomic homozygosity in individuals with the trait. Finally, we determine the sample sizes required to identify the increased disomic homozygosity under each model. Most of the models we explore yield detectable increases in disomic homozygosity for some reasonable range of parameter values, usually corresponding to smaller trait frequencies. It therefore appears that our mapping method should be effective for a wide variety of moderately infrequent traits, even though the exact mode of inheritance is unlikely to be known. 21 refs., 8 figs., 1 tab.

  15. Phenotyping jasmonate regulation of senescence.

    Science.gov (United States)

    Seltmann, Martin A; Berger, Susanne

    2013-01-01

    Osmotic stress induces several senescence-like processes in leaves, such as specific changes in gene expression and yellowing. These processes are dependent on the accumulation of jasmonates and on intact jasmonate signaling. This chapter describes the treatment of Arabidopsis thaliana leaves with sorbitol as an osmotic stress agent and the determination of the elicited phenotypes encompassing chlorophyll loss, degradation of plastidial membrane lipids, and induction of genes regulated by senescence and jasmonate.

  16. Wine Expertise Predicts Taste Phenotype.

    Science.gov (United States)

    Hayes, John E; Pickering, Gary J

    2012-03-01

    Taste phenotypes have long been studied in relation to alcohol intake, dependence, and family history, with contradictory findings. However, on balance - with appropriate caveats about populations tested, outcomes measured and psychophysical methods used - an association between variation in taste responsiveness and some alcohol behaviors is supported. Recent work suggests super-tasting (operationalized via propylthiouracil (PROP) bitterness) not only associates with heightened response but also with more acute discrimination between stimuli. Here, we explore relationships between food and beverage adventurousness and taste phenotype. A convenience sample of wine drinkers (n=330) were recruited in Ontario and phenotyped for PROP bitterness via filter paper disk. They also filled out a short questionnaire regarding willingness to try new foods, alcoholic beverages and wines as well as level of wine involvement, which was used to classify them as a wine expert (n=110) or wine consumer (n=220). In univariate logisitic models, food adventurousness predicted trying new wines and beverages but not expertise. Likewise, wine expertise predicted willingness to try new wines and beverages but not foods. In separate multivariate logistic models, willingness to try new wines and beverages was predicted by expertise and food adventurousness but not PROP. However, mean PROP bitterness was higher among wine experts than wine consumers, and the conditional distribution functions differed between experts and consumers. In contrast, PROP means and distributions did not differ with food adventurousness. These data suggest individuals may self-select for specific professions based on sensory ability (i.e., an active gene-environment correlation) but phenotype does not explain willingness to try new stimuli.

  17. Adaptive evolution of molecular phenotypes

    Science.gov (United States)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-09-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.

  18. Genotype-Phenotype Correlation of SMN1 and NAIP Deletions in Korean Patients with Spinal Muscular Atrophy

    Science.gov (United States)

    Ahn, Eun-Ji; Yum, Mi-Sun; Kim, Eun-Hee; Yoo, Han-Wook; Lee, Beom Hee; Kim, Gu-Hwan

    2017-01-01

    Background and Purpose Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease characterized by progressive muscle weakness and atrophy. Most SMA patients have a homozygous deletion in survival of motor neuron 1 (SMN1) gene, and neuronal apoptosis inhibitory protein (NAIP) gene is considered a phenotype modifier. We investigated the genotype-phenotype correlation of SMN1 and NAIP deletions in Korean SMA patients. Methods Thirty-three patients (12 males and 21 females) treated at the Asan Medical Center between 1999 and 2013 were analyzed retrospectively. The polymerase chain reaction (PCR), restriction-fragment-length polymorphism analysis, and multiplex PCR were used to detect deletions in SMN1 (exons 7 and 8) and NAIP (exons 4 and 5). We reviewed clinical presentations and outcomes and categorized the patients into three clinical types. NAIP deletion-driven differences between the two genotypes were analyzed. Results Deletion analysis identified homozygous deletions of SMN1 exons 7 and 8 in 30 patients (90.9%). Among these, compared with patients without an NAIP deletion, those with an NAIP deletion showed a significantly lower age at symptom onset (1.9±1.7 months vs. 18.4±20.4 months, mean±SD; p=0.007), more frequent type 1 phenotype (6/6 vs. 8/24, p=0.005), and worse outcomes, with early death or a requirement for ventilator support (4/4 vs. 2/12, p=0.008). Conclusions Homozygous deletion in SMN1 and a concurrent NAIP deletion were associated with an early onset, severe hypotonia, and worse outcome in SMA patients. Deletion analysis of NAIP and SMN1 can help to accurately predict prognostic outcomes in SMA. PMID:27730768

  19. Phenotypic plasticity with instantaneous but delayed switches

    NARCIS (Netherlands)

    Utz, Margarete; Jeschke, Jonathan M.; Loeschcke, Volker; Gabriel, Wilfried

    2014-01-01

    Phenotypic plasticity is a widespread phenomenon, allowing organisms to better adapt to changing environments. Most empirical and theoretical studies are restricted to irreversible plasticity where the expression of a specific phenotype is mostly determined during development. However, reversible pl

  20. Atypical disease phenotypes in pediatric ulcerative colitis

    DEFF Research Database (Denmark)

    Levine, Arie; de Bie, Charlotte I; Turner, Dan

    2013-01-01

    Definitive diagnosis of pediatric ulcerative colitis (UC) may be particularly challenging since isolated colitis with overlapping features is common in pediatric Crohn's disease (CD), while atypical phenotypes of UC are not uncommon. The Paris classification allows more accurate phenotyping...

  1. Phenotypic and Genetic Associations between Reading Comprehension, Decoding Skills, and ADHD Dimensions: Evidence from Two Population-Based Studies

    Science.gov (United States)

    Plourde, Vickie; Boivin, Michel; Forget-Dubois, Nadine; Brendgen, Mara; Vitaro, Frank; Marino, Cecilia; Tremblay, Richard T.; Dionne, Ginette

    2015-01-01

    Background: The phenotypic and genetic associations between decoding skills and ADHD dimensions have been documented but less is known about the association with reading comprehension. The aim of the study is to document the phenotypic and genetic associations between reading comprehension and ADHD dimensions of inattention and…

  2. Simulation of PEP-II Accelerator Backgrounds Using TURTLE

    CERN Document Server

    Barlow, Roger J; Kozanecki, Witold; Majewski, Stephanie; Roudeau, Patrick; Stocchi, Achille

    2005-01-01

    We present studies of accelerator-induced backgrounds in the BaBar detector at the SLAC B-Factory, carried out using a modified version ofthe DECAY TURTLE simulation package. Lost-particle backgrounds in PEP-II are dominated by a combination of beam-gas bremstrahlung, beam-gas Coulomb scattering, radiative-Bhabha events and beam-beam blow-up. The radiation damage and detector occupancy caused by the associated electromagnetic shower debris can limit the usable luminosity. In order to understand and mitigate such backgrounds, we have performed a full programme of beam-gas and luminosity-background simulations, that include the effects of the detector solenoidal field, detailed modelling of limiting apertures in both collider rings, and optimization of the betatron collimation scheme in the presence of large transverse tails.

  3. An Adaptive Background Subtraction Method Based on Kernel Density Estimation

    Directory of Open Access Journals (Sweden)

    Mignon Park

    2012-09-01

    Full Text Available In this paper, a pixel-based background modeling method, which uses nonparametric kernel density estimation, is proposed. To reduce the burden of image storage, we modify the original KDE method by using the first frame to initialize it and update it subsequently at every frame by controlling the learning rate according to the situations. We apply an adaptive threshold method based on image changes to effectively subtract the dynamic backgrounds. The devised scheme allows the proposed method to automatically adapt to various environments and effectively extract the foreground. The method presented here exhibits good performance and is suitable for dynamic background environments. The algorithm is tested on various video sequences and compared with other state-of-the-art background subtraction methods so as to verify its performance.

  4. Locating a modifier gene of Ovum mutant through crosses between DDK and C57BL/6J inbred strains in mice

    Indian Academy of Sciences (India)

    JING TAN; GEN DI SONG; JIA SHENG SONG; SHI HAO REN; CHUN LI LI; ZHEN YU ZHENG; WEI DONG ZHAO

    2016-06-01

    A striking infertile phenotype has been discovered in the DDK strain of mouse. The DDK females are usually infertile when crossed with males of other inbred strains, whereas DDK males exhibit normal fertility in reciprocal crosses. This phenomenon is caused by mutation in the ovum (Om) locus on chromosome 11 and known as the DDK syndrome. Previously, some research groups reported that the embryonic mortality deviated from the semilethal rate in backcrosses between heterozygous (Om/+) females and males of other strains. This embryonic mortality exhibited an aggravated trend with increasing background genes of other strains. These results indicated that some modifier genes of Om were present in other strains. In the present study, a population of N 2(Om/+) females from the backcrosses between C57BL/6J (B6) and F1(B6♀×DDK♂) was used to map potential modifier genes of Om. Quantitative trait locus showed that a major locus, namely Amom1 (aggravate modifier gene of Om 1), was located at the middle part of chromosome 9 in mice. The Amom1 could increase the expressivity of Om gene, thereby aggravating embryonic lethality when heterozygous (Om/+)females mated with males of B6 strain. Further, the 1.5 LOD-drop analysis indicated that the confidence interval was between 37.54 and 44.46 cM,∼6.92 cM. Amom1 is the first modifier gene of Om in the B6 background.

  5. The small ubiquitin-like modifier (SUMO) is required for gonadal and uterine-vulval morphogenesis in Caenorhabditis elegans.

    Science.gov (United States)

    Broday, Limor; Kolotuev, Irina; Didier, Christine; Bhoumik, Anindita; Gupta, Bhagwati P; Sternberg, Paul W; Podbilewicz, Benjamin; Ronai, Ze'ev

    2004-10-01

    The small ubiquitin-like modifier (SUMO) modification alters the subcellular distribution and function of its substrates. Here we show the major role of SUMO during the development of the Caenorhabditis elegans reproductive system. smo-1 deletion mutants develop into sterile adults with abnormal somatic gonad, germ line, and vulva. SMO-1::GFP reporter is highly expressed in the somatic reproductive system. smo-1 animals lack a vulval-uterine connection as a result of impaired ventral uterine pi-cell differentiation and anchor cell fusion. Mutations in the LIN-11 LIM domain transcription factor lead to a uterine phenotype that resembles the smo-1 phenotype. LIN-11 is sumoylated, and its sumoylation is required for its activity during uterine morphogenesis. Expression of a SUMO-modified LIN-11 in the smo-1 background partially rescued pi-cell differentiation and retained LIN-11 in nuclear bodies. Thus, our results identify the reproductive system as the major SUMO target during postembryonic development and highlight LIN-11 as a physiological substrate whose sumoylation is associated with the formation of a functional vulval-uterine connection.

  6. Lamina propria macrophage phenotypes in relation to Escherichia coli in Crohn’s disease

    OpenAIRE

    Elliott, Timothy R.; Rayment, Neil B.; Barry N Hudspith; Hands, Rebecca E; Taylor, Kirstin; Parkes, Gareth C; Prescott, Natalie J.; Petrovska, Liljana; Hermon-Taylor, John; Brostoff, Jonathan; Boussioutas, Alex; Mathew, Christopher G.; Bustin, Stephen A.; Sanderson, Jeremy D.

    2015-01-01

    Background Abnormal handling of E. coli by lamina propria (LP) macrophages may contribute to Crohn’s disease (CD) pathogenesis. We aimed to determine LP macrophage phenotypes in CD, ulcerative colitis (UC) and healthy controls (HC), and in CD, to compare macrophage phenotypes according to E. coli carriage. Methods Mucosal biopsies were taken from 35 patients with CD, 9 with UC and 18 HCs. Laser capture microdissection was used to isolate E. coli-laden and unladen LP macrophages from ileal or ...

  7. Phenotypic and molecular insights into CASK-related disorders in males

    OpenAIRE

    Moog, U.; T Bierhals; Brand, K.; Bautsch, J.; Biskup, S.; Brune, T.; J. Denecke; Die-Smulders, C E M de; Evers, C.; Hempel, M.; Henneke, M; Yntema, H.G.; Menten, B.; Pietz, J.; Pfundt, R.P.

    2015-01-01

    Background Heterozygous loss-of-function mutations in the X-linked CASK gene cause progressive microcephaly with pontine and cerebellar hypoplasia (MICPCH) and severe intellectual disability (ID) in females. Different CASK mutations have also been reported in males. The associated phenotypes range from nonsyndromic ID to Ohtahara syndrome with cerebellar hypoplasia. However, the phenotypic spectrum in males has not been systematically evaluated to date. Methods We identified a CASK alteration...

  8. Microenvironment-Dependent Phenotypic Changes in a SCID Mouse Model for Malignant Mesothelioma

    OpenAIRE

    Darai-Ramqvist, Eva; Nilsonne, Gustav; Flores-Staino, Carmen; Hjerpe, Anders; Dobra, Katalin

    2013-01-01

    Background and Aims: Malignant mesothelioma is an aggressive, therapy-resistant tumor. Mesothelioma cells may assume an epithelioid or a sarcomatoid phenotype, and presence of sarcomatoid cells predicts poor prognosis. In this study, we investigated differentiation of mesothelioma cells in a xenograft model, where mesothelioma cells of both phenotypes were induced to form tumors in severe combined immunodeficiency mice. Methods: Xenografts were established and thoroughly characterized usin...

  9. Microenvironment-dependent phenotypic changes in a SCID mouse model for malignant mesothelioma

    OpenAIRE

    Eva eDarai-Ramqvist; Gustav eNilsonne; Carmen eFlores-Staino; Anders eHjerpe; Katalin eDobra

    2013-01-01

    Background and Aims: Malignant mesothelioma is an aggressive, therapy-resistant tumor. Mesothelioma cells may assume an epithelioid or a sarcomatoid phenotype, and presence of sarcomatoid cells predicts poor prognosis. In this study, we investigated differentiation of mesothelioma cells in a xenograft model, where mesothelioma cells of both phenotypes were induced to form tumors in SCID mice. Methods: Xenografts were established and thoroughly characterized using a comprehensive immunohistoch...

  10. Using text mining techniques to extract phenotypic information from the PhenoCHF corpus

    OpenAIRE

    Alnazzawi, Noha; Thompson, Paul; Batista-Navarro, Riza; Ananiadou, Sophia

    2015-01-01

    Background Phenotypic information locked away in unstructured narrative text presents significant barriers to information accessibility, both for clinical practitioners and for computerised applications used for clinical research purposes. Text mining (TM) techniques have previously been applied successfully to extract different types of information from text in the biomedical domain. They have the potential to be extended to allow the extraction of information relating to phenotypes from fre...

  11. Neutrinos and electrons in background matter: a new approach

    CERN Document Server

    Studenikin, A

    2006-01-01

    We present a rather powerful method in investigations of different phenomena that can appear when neutrinos and electrons are moving in the background matter. This method is based on the use of the modified Dirac equations for the particles wave functions, in which the correspondent effective potentials that account for the matter influence on particles are included. The developed approach establishes a basis for investigation of different phenomena which can arise when neutrinos and electrons move in dense media, including those peculiar for astrophysical and cosmological environments. The approach developed is similar to the Furry representation of quantum electrodynamics, widely used for description of particles interactions in the presence of external electromagnetic fields, and it works when a macroscopic amount of the background particles are confined within the scale of a neutrino or electron de Broglie wave lengths. We consider the modified Dirac equations for neutrinos (of both Dirac and Majorana typ...

  12. Phenotype diversity in type 1 Gaucher disease: discovering the genetic basis of Gaucher disease/hematologic malignancy phenotype by individual genome analysis.

    Science.gov (United States)

    Lo, Sarah M; Choi, Murim; Liu, Jun; Jain, Dhanpat; Boot, Rolf G; Kallemeijn, Wouter W; Aerts, Johannes M F G; Pashankar, Farzana; Kupfer, Gary M; Mane, Shrikant; Lifton, Richard P; Mistry, Pramod K

    2012-05-17

    Gaucher disease (GD), an inherited macrophage glycosphingolipidosis, manifests with an extraordinary variety of phenotypes that show imperfect correlation with mutations in the GBA gene. In addition to the classic manifestations, patients suffer from increased susceptibility to hematologic and nonhematologic malignancies. The mechanism(s) underlying malignancy in GD is not known, but is postulated to be secondary to macrophage dysfunction and immune dysregulation arising from lysosomal accumulation of glucocerebroside. However, there is weak correlation between GD/cancer phenotype and the systemic burden of glucocerebroside-laden macrophages. Therefore, we hypothesized that genetic modifier(s) may underlie the GD/cancer phenotype. In the present study, the genetic basis of GD/T-cell acute lymphoblastic lymphoma in 2 affected siblings was deciphered through genomic analysis. GBA gene sequencing revealed homozygosity for a novel mutation, D137N. Whole-exome capture and massively parallel sequencing combined with homozygosity mapping identified a homozygous novel mutation in the MSH6 gene that leads to constitutional mismatch repair deficiency syndrome and increased cancer risk. Enzyme studies demonstrated that the D137N mutation in GBA is a pathogenic mutation, and immunohistochemistry confirmed the absence of the MSH6 protein. Therefore, precise phenotype annotation followed by individual genome analysis has the potential to identify genetic modifiers of GD, facilitate personalized management, and provide novel insights into disease pathophysiology.

  13. Background-independent quantization and the uncertainty principle

    Energy Technology Data Exchange (ETDEWEB)

    Hossain, Golam Mortuza; Husain, Viqar; Seahra, Sanjeev S, E-mail: ghossain@unb.c, E-mail: vhusain@unb.c, E-mail: sseahra@unb.c [Department of Mathematics and Statistics, University of New Brunswick, Fredericton, NB E3B 5A3 (Canada)

    2010-08-21

    It is shown that polymer quantization leads to a modified uncertainty principle similar to that motivated by string theory and non-commutative geometry. When applied to quantum field theory on general background spacetimes, corrections to the uncertainty principle acquire a metric dependence. For Friedmann-Robertson-Walker cosmology this translates to a scale factor dependence which gives a large effect in the early Universe.

  14. Family Background and Educational Choices

    DEFF Research Database (Denmark)

    McIntosh, James; D. Munk, Martin

    We examine the participation in secondary and tertiary education of five cohorts of Danish males and females who were aged twenty starting in 1982 and ending in 2002. We find that the large expansion of secondary education in this period was characterized by a phenomenal increase in gymnasium...... enrollments, especially for females. Not only did the educational opportunities for individuals with disadvantaged backgrounds improve absolutely, but their relative position also improved. A similarly dramatic increase in attendance at university for the period 1985-2005 was found for these cohorts when...

  15. Particle propagation in cosmological backgrounds

    CERN Document Server

    Arteaga, Daniel

    2007-01-01

    We study the quantum propagation of particles in cosmological backgrounds, by considering a doublet of massive scalar fields propagating in an expanding universe, possibly filled with radiation. We focus on the dissipative effects related to the expansion rate. At first order, we recover the expected result that the decay rate is determined by the local temperature. Beyond linear order, the decay rate has an additional contribution governed by the expansion parameter. This latter contribution is present even for stable particles in the vacuum. Finally, we analyze the long time behaviour of the propagator and briefly discuss applications to the trans-Planckian question.

  16. Knowledge-based analysis of phenotypes

    KAUST Repository

    Hoendorf, Robert

    2016-01-27

    Phenotypes are the observable characteristics of an organism, and they are widely recorded in biology and medicine. To facilitate data integration, ontologies that formally describe phenotypes are being developed in several domains. I will describe a formal framework to describe phenotypes. A formalized theory of phenotypes is not only useful for domain analysis, but can also be applied to assist in the diagnosis of rare genetic diseases, and I will show how our results on the ontology of phenotypes is now applied in biomedical research.

  17. Pain relief with lidocaine 5% patch in localized peripheral neuropathic pain in relation to pain phenotype

    DEFF Research Database (Denmark)

    Demant, Dyveke T; Lund, Karen; Finnerup, Nanna B

    2015-01-01

    irritable nociceptor phenotype as defined by hypersensitivity and preserved small fibre function determined by quantitative sensory testing. Forty-six patients with neuropathic pain due to nerve injury or postherpetic neuralgia were randomised. The modified intention-to-treat population comprised 15...

  18. Analysis of Pena Shokeir phenotype.

    Science.gov (United States)

    Hall, J G

    1986-09-01

    At this point in time, we recognize that "Pena Shokeir" is not a diagnosis or a specific syndrome but rather a description of a phenotype produced by fetal akinesia or decreased in utero movement. In its "full blown" form, it is characterized by polyhydramnios, intrauterine growth retardation, pulmonary hypoplasia, craniofacial and limb anomalies, congenital contractures, short umbilical cord, and lethality. From the cases thus far reported, we would anticipate that the phenotype is present in a very heterogeneous group of disorders--heterogeneous both with regard to the specific anomalies present and with regard to the causes (which must include many environmental agents and multiple genetic forms). One challenge for the future is to better describe and delineate specific entities. In the meantime, we would do well to use the terms "Pena Shokeir phenotype" or "fetal akinesia/hypokinesia sequence," which do not imply a single entity. There are many practical aspects of recognizing this phenotype. The presence of any one of the cardinal signs of the fetal akinesia/hypokinesia sequence should alert the physician to look for the other associated anomalies, since specific treatment may be indicated, and catch-up or compensatory growth may occur, if given a chance. The ability to provide prenatal diagnosis and perhaps prenatal treatment in the future may allow us to alter dramatically the natural history of some cases. In others, we need to establish when treatment is possible and when it gives no benefit. Perhaps the most important insight gained from the study of the fetal akinesia sequence is the reaffirmation of the concept that function is an integral part of normal development. Specific structures do not develop in isolation but are part of a carefully timed and integrated system. The "use" of a structure in utero is necessary for its continuing and normal development. The old adage "use it or lose it" seems to apply just as appropriately to prenatal normal

  19. Phenotypic MicroRNA Microarrays

    OpenAIRE

    2013-01-01

    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the bio...

  20. Phenotype of normal hairline maturation.

    Science.gov (United States)

    Rassman, William R; Pak, Jae P; Kim, Jino

    2013-08-01

    Hairlines change shape with age, starting at birth. A good head of hair is frequently present some time after ages 3 to 5 years. The look of childhood has its corresponding hairline, and, as the child grows and develops into adulthood, facial morphology migrate changes from a childlike look to a more mature look. This article discusses the dynamics of hairline evolution and the phenotypic variations of the front and side hairlines in men and women. A modeling system is introduced that provides a common language to define the various anatomic points of the full range of hairlines.

  1. The Human Phenotype Ontology in 2017

    Science.gov (United States)

    Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin; McMurry, Julie; Aymé, Ségolène; Baynam, Gareth; Bello, Susan M.; Boerkoel, Cornelius F.; Boycott, Kym M.; Brudno, Michael; Buske, Orion J.; Chinnery, Patrick F.; Cipriani, Valentina; Connell, Laureen E.; Dawkins, Hugh J.S.; DeMare, Laura E.; Devereau, Andrew D.; de Vries, Bert B.A.; Firth, Helen V.; Freson, Kathleen; Greene, Daniel; Hamosh, Ada; Helbig, Ingo; Hum, Courtney; Jähn, Johanna A.; James, Roger; Krause, Roland; F. Laulederkind, Stanley J.; Lochmüller, Hanns; Lyon, Gholson J.; Ogishima, Soichi; Olry, Annie; Ouwehand, Willem H.; Pontikos, Nikolas; Rath, Ana; Schaefer, Franz; Scott, Richard H.; Segal, Michael; Sergouniotis, Panagiotis I.; Sever, Richard; Smith, Cynthia L.; Straub, Volker; Thompson, Rachel; Turner, Catherine; Turro, Ernest; Veltman, Marijcke W.M.; Vulliamy, Tom; Yu, Jing; von Ziegenweidt, Julie; Zankl, Andreas; Züchner, Stephan; Zemojtel, Tomasz; Jacobsen, Julius O.B.; Groza, Tudor; Smedley, Damian; Mungall, Christopher J.; Haendel, Melissa; Robinson, Peter N.

    2017-01-01

    Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology. PMID:27899602

  2. Equilibrium thermodynamics in modified gravitational theories

    CERN Document Server

    Bamba, Kazuharu; Tsujikawa, Shinji

    2009-01-01

    We show that it is possible to obtain a picture of equilibrium thermodynamics on the apparent horizon in the expanding cosmological background for a wide class of modified gravity theories with the Lagrangian density $f(R, \\phi, X)$, where $R$ is the Ricci scalar and $X=-(\

  3. Asthma trajectories in early childhood: identifying modifiable factors.

    Directory of Open Access Journals (Sweden)

    Lidia Panico

    Full Text Available BACKGROUND: There are conflicting views as to whether childhood wheezing represents several discreet entities or a single but variable disease. Classification has centered on phenotypes often derived using subjective criteria, small samples, and/or with little data for young children. This is particularly problematic as asthmatic features appear to be entrenched by age 6/7. In this paper we aim to: identify longitudinal trajectories of wheeze and other atopic symptoms in early childhood; characterize the resulting trajectories by the socio-economic background of children; and identify potentially modifiable processes in infancy correlated with these trajectories. DATA AND METHODS: The Millennium Cohort Study is a large, representative birth cohort of British children born in 2000-2002. Our analytical sample includes 11,632 children with data on key variables (wheeze in the last year; ever hay-fever and/or eczema reported by the main carers at age 3, 5 and 7 using a validated tool, the International Study of Asthma and Allergies in Childhood module. We employ longitudinal Latent Class Analysis, a clustering methodology which identifies classes underlying the observed population heterogeneity. RESULTS: Our model distinguished four latent trajectories: a trajectory with both low levels of wheeze and other atopic symptoms (54% of the sample; a trajectory with low levels of wheeze but high prevalence of other atopic symptoms (29%; a trajectory with high prevalence of both wheeze and other atopic symptoms (9%; and a trajectory with high levels of wheeze but low levels of other atopic symptoms (8%. These groups differed in terms of socio-economic markers and potential intervenable factors, including household damp and breastfeeding initiation. CONCLUSION: Using data-driven techniques, we derived four trajectories of asthmatic symptoms in early childhood in a large, population based sample. These groups differ in terms of their socio-economic profiles

  4. String Thermodynamics in D-Brane Backgrounds

    CERN Document Server

    Abel, S A; Kogan, I I; Rabinovici, Eliezer

    1999-01-01

    We discuss the thermal properties of string gases propagating in various D-brane backgrounds in the weak-coupling limit, and at temperatures close to the Hagedorn temperature. We determine, in the canonical ensemble, whether the Hagedorn temperature is limiting or non-limiting. This depends on the dimensionality of the D-brane, and the size of the compact dimensions. We find that in many cases the non-limiting behaviour manifest in the canonical ensemble is modified to a limiting behaviour in the microcanonical ensemble and show that, when there are different systems in thermal contact, the energy flows into open strings on the `limiting' D-branes of largest dimensionality. Such energy densities may eventually exceed the D-brane intrinsic tension. We discuss possible implications of this for the survival of Dp-branes with large values of p in an early cosmological Hagedorn regime. We also discuss the general phase diagram of the interacting theory, as implied by the holographic and black-hole/string correspon...

  5. The superhealing MRL background improves muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Heydemann Ahlke

    2012-12-01

    Full Text Available Abstract Background Mice from the MRL or “superhealing” strain have enhanced repair after acute injury to the skin, cornea, and heart. We now tested an admixture of the MRL genome and found that it altered the course of muscle pathology and cardiac function in a chronic disease model of skeletal and cardiac muscle. Mice lacking γ-sarcoglycan (Sgcg, a dystrophin-associated protein, develop muscular dystrophy and cardiomyopathy similar to their human counterparts with limb girdle muscular dystrophy. With disruption of the dystrophin complex, the muscle plasma membrane becomes leaky and muscles develop increased fibrosis. Methods MRL/MpJ mice were bred with Sgcg mice, and cardiac function was measured. Muscles were assessed for fibrosis and membrane leak using measurements of hydroxyproline and Evans blue dye. Quantitative trait locus mapping was conducted using single nucleotide polymorphisms distinct between the two parental strains. Results Introduction of the MRL genome reduced fibrosis but did not alter membrane leak in skeletal muscle of the Sgcg model. The MRL genome was also associated with improved cardiac function with reversal of depressed fractional shortening and the left ventricular ejection fraction. We conducted a genome-wide analysis of genetic modifiers and found that a region on chromosome 2 was associated with cardiac, diaphragm muscle and abdominal muscle fibrosis. Conclusions These data are consistent with a model where the MRL genome acts in a dominant manner to suppress fibrosis in this chronic disease setting of heart and muscle disease.

  6. Modelling neuroinflammatory phenotypes in vivo

    Directory of Open Access Journals (Sweden)

    Wyss-Coray Tony

    2004-07-01

    Full Text Available Abstract Inflammation of the central nervous system is an important but poorly understood part of neurological disease. After acute brain injury or infection there is a complex inflammatory response that involves activation of microglia and astrocytes and increased production of cytokines, chemokines, acute phase proteins, and complement factors. Antibodies and T lymphocytes may be involved in the response as well. In neurodegenerative disease, where injury is more subtle but consistent, the inflammatory response is continuous. The purpose of this prolonged response is unclear, but it is likely that some of its components are beneficial and others are harmful. Animal models of neurological disease can be used to dissect the specific role of individual mediators of the inflammatory response and assess their potential benefit. To illustrate this approach, we discuss how mutant mice expressing different levels of the cytokine transforming growth factor β-1 (TGF-β1, a major modulator of inflammation, produce important neuroinflammatory phenotypes. We then demonstrate how crosses of TGF-β1 mutant mice with mouse models of Alzheimer's disease (AD produced important new information on the role of inflammation in AD and on the expression of different neuropathological phenotypes that characterize this disease.

  7. Phenotypic plasticity in bacterial plasmids.

    Science.gov (United States)

    Turner, Paul E

    2004-01-01

    Plasmid pB15 was previously shown to evolve increased horizontal (infectious) transfer at the expense of reduced vertical (intergenerational) transfer and vice versa, a key trade-off assumed in theories of parasite virulence. Whereas the models predict that susceptible host abundance should determine which mode of transfer is selectively favored, host density failed to mediate the trade-off in pB15. One possibility is that the plasmid's transfer deviates from the assumption that horizontal spread (conjugation) occurs in direct proportion to cell density. I tested this hypothesis using Escherichia coli/pB15 associations in laboratory serial culture. Contrary to most models of plasmid transfer kinetics, my data show that pB15 invades static (nonshaking) bacterial cultures only at intermediate densities. The results can be explained by phenotypic plasticity in traits governing plasmid transfer. As cells become more numerous, the plasmid's conjugative transfer unexpectedly declines, while the trade-off between transmission routes causes vertical transfer to increase. Thus, at intermediate densities the plasmid's horizontal transfer can offset selection against plasmid-bearing cells, but at high densities pB15 conjugates so poorly that it cannot invade. I discuss adaptive vs. nonadaptive causes for the phenotypic plasticity, as well as potential mechanisms that may lead to complex transfer dynamics of plasmids in liquid environments. PMID:15166133

  8. Egg phenotype differentiation in sympatric cuckoo Cuculus canorus gentes.

    Science.gov (United States)

    Antonov, Anton; Stokke, B G; Vikan, J R; Fossøy, F; Ranke, P S; Røskaft, E; Moksnes, A; Møller, A P; Shykoff, J A

    2010-06-01

    The brood parasitic common cuckoo Cuculus canorus consists of gentes, which typically parasitize only a single host species whose eggs they often mimic. Where multiple cuckoo gentes co-exist in sympatry, we may expect variable but generally poorer mimicry because of host switches or inter-gens gene flow via males if these also contribute to egg phenotypes. Here, we investigated egg trait differentiation and mimicry in three cuckoo gentes parasitizing great reed warblers Acrocephalus arundinaceus, marsh warblers Acrocephalus palustris and corn buntings Miliaria calandra breeding in close sympatry in partially overlapping habitat types. The three cuckoo gentes showed a remarkable degree of mimicry to their three host species in some but not all egg features, including egg size, a hitherto largely ignored feature of egg mimicry. Egg phenotype matching for both background and spot colours as well as for egg size has been maintained in close sympatry despite the possibility for gene flow.

  9. Cystatin C is Associated With Plaque Phenotype and Plaque Burden

    Directory of Open Access Journals (Sweden)

    Yufeng Wen

    2016-03-01

    Full Text Available Background/Aims: The relationship between carotid artery plaque burden, phenotype and serum cystatin C at normal and impaired renal function is still unclear. Methods: Demographic characteristics, carotid ultrasonography and other relevant information of 1,477 patients were collected. The association of carotid artery plaque burden, plaque phenotype with serum cystatin C was evaluated by strategy analysis based on renal function. Results: Serum cystatin C (OR=2.05, 95% CI: 1.83-2.29, POR=1.60, 95%CI: 1.43-1.78, POR=1.21, 95%CI: 1.10-1.32, P Conclusion: In normal renal function, serum cystatin C may confer stability of plaques. In mildly impaired renal function, serum cystatin C is a risk predictor of plaques. In normal renal function circumstances, serum cystatin C may benefit to the stability of plaques. In mild impaired renal function circumstances, serum cystatin C are a risk predictors of plaques.

  10. Intra-family phenotypic heterogeneity of 16p11.2 deletion carriers in a three-generation Chinese family.

    Science.gov (United States)

    Shen, Yiping; Chen, Xiaoli; Wang, Liwen; Guo, Jin; Shen, Jianliang; An, Yu; Zhu, Haitao; Zhu, Yanli; Xin, Ruolei; Bao, Yihua; Gusella, James F; Zhang, Ting; Wu, Bai-Lin

    2011-03-01

    The 16p11.2 deletion is a recurrent genomic event and a significant risk factor for autism spectrum disorders (ASD). This genomic disorder also exhibits extensive phenotypic variability and diverse clinical phenotypes. The full extent of phenotypic heterogeneity associated with the 16p11.2 deletion disorder and the factors that modify the clinical phenotypes are currently unknown. Multiplex families with deletion offer unique opportunities for exploring the degree of heterogeneity and implicating modifiers. Here we reported the clinical and genomic characteristics of three 16p11.2 deletion carriers in a Chinese family. The father carries a de novo 16p11.2 deletion, and it was transmitted to the proband and sib. The proband presented with ASD, intellectual disability, learning difficulty, congenital malformations such as atrial septal defect, scoliosis. His dysmorphic features included myopia and strabismus, flat and broad nasal bridge, etc. While the father shared same neurodevelopmental problems as the proband, the younger brother did not show many of the proband's phenotypes. The possible unmasked mutation of TBX6 and MVP gene in this deleted region and the differential distribution of other genomic CNVs were explored to explain the phenotypic heterogeneity in these carriers. This report demonstrated the different developmental trajectory and discordant phenotypes among family members with the same 16p11.2 deletion, thus further illustrated the phenotypic complexity and heterogeneity of the 16p11.2 deletion.

  11. Background reionization history from omniscopes

    CERN Document Server

    Clesse, Sebastien; Ringeval, Christophe; Tashiro, Hiroyuki; Tytgat, Michel

    2012-01-01

    The measurements of the 21 cm brightness temperature fluctuations from the neutral hydrogen at the epoch of reionization (EoR) should inaugurate the next generation of cosmological observables. In this respect, many works have concentrated on the disambiguation of the cosmological signals from the dominant reionization foregrounds. However, even after perfect foregrounds removal, our ignorance on the background reionization history can significantly affect the cosmological parameter estimation. In particular, the interdependence between the hydrogen ionized fraction, the baryon density and the optical depth to the redshift of observation induce non-trivial degeneracies between the cosmological parameters that have not been considered so far. Using a simple, but consistent, reionization model, we revisit their expected constraints for a futuristic giant 21 cm omniscope by using for the first time Monte-Carlo-Markov-Chains (MCMC) methods on multi-redshift full sky simulated data. Our results agree well with the...

  12. Background illumination and automated perimetry.

    Science.gov (United States)

    Klewin, K M; Radius, R L

    1986-03-01

    Visual field function in the right and left eyes of 31 normal volunteers was evaluated with an automated projection perimeter (OCTOPUS). Serial visual field evaluations were repeated in these same eyes with neutral filters of increasing optical density. We compared the results of threshold determinations with the different neutral filters in place before the examined eye. Significant reduction in threshold sensitivity at several test spots throughout the central 30 degrees visual field was seen with neutral density filters of 0.5 log units or greater. The low level of background illumination of the OCTOPUS perimeter (4.0 apostilbs) may allow relatively minor reduction in light transmission by the ocular media to produce significant changes in the recorded level of threshold sensitivity during visual field evaluation.

  13. Polarization of Cosmic Microwave Background

    CERN Document Server

    Buzzelli, Alessandro; de Gasperis, Giancarlo; Vittorio, Nicola

    2016-01-01

    In this work we present an extension of the ROMA map-making code for data analysis of Cosmic Microwave Background polarization, with particular attention given to the inflationary polarization B-modes. The new algorithm takes into account a possible cross-correlated noise component among the different detectors of a CMB experiment. We tested the code on the observational data of the BOOMERanG (2003) experiment and we show that we are provided with a better estimate of the power spectra, in particular the error bars of the BB spectrum are smaller up to 20% for low multipoles. We point out the general validity of the new method. A possible future application is the LSPE balloon experiment, devoted to the observation of polarization at large angular scales.

  14. Very mild disease phenotype of congenic CftrTgH(neoimHgu cystic fibrosis mice

    Directory of Open Access Journals (Sweden)

    Leonhard-Marek Sabine

    2008-04-01

    Full Text Available Abstract Background A major boost to cystic fibrosis disease research was given by the generation of various mouse models using gene targeting in embryonal stem cells. Moreover, the introduction of the same mutation on different inbred strains generating congenic strains facilitated the search for modifier genes. From the original CftrTgH(neoimHgu mouse model with a divergent genetic background (129/Sv, C57BL/6, HsdOla:MF1 two inbred mutant mouse strains CF/1-CftrTgH(neoimHgu and CF/3-CftrTgH(neoimHgu had been generated using strict brother × sister mating. CF/1-CftrTgH(neoimHgu and CF/3-CftrTgH(neoimHgu mice were fertile and showed normal growth and lifespan. In this work the CftrTgH(neoimHgu insertional mutation was backcrossed from CF/3-CftrTgH(neoimHgu onto the inbred backgrounds C57BL/6J and DBA/2J generating congenic animals in order to clarify the differential impact of the Cftr mutation and the genetic background on the disease phenotype of the cystic fibrosis mutant mice. Clinical and electrophysiological features of the two congenic strains were compared with those of CF/1-CftrTgH(neoimHgu and CF/3-CftrTgH(neoimHgu and wild type controls. Results Under the standardized housing conditions of the animal facility, the four mouse strains CF/1-CftrTgH(neoimHgu, CF/3-CftrTgH(neoimHgu, D2.129P2(CF/3-CftrTgH(neoimHgu and B6.129P2(CF/3-CftrTgH(neoimHgu exhibited normal life expectancy. Growth of congenic cystic fibrosis mice was comparable with that of wild type controls. All mice but D2.129P2(CF/3-CftrTgH(neoimHgu females were fertile. Short circuit current measurements revealed characteristic response profiles of the HsdOla:MF1, DBA/2J and C57BL/6J backgrounds in nose, ileum and colon. All cystic fibrosis mouse lines showed the disease-typical hyperresponsiveness to amiloride in the respiratory epithelium. The mean chloride secretory responses to carbachol or forskolin were 15–100% of those of the cognate wild type control animals

  15. Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Chandra H McAllister

    Full Text Available Alanine aminotransferase (AlaAT, E.C. 2.6.1.2, is a pyridoxal-5'-phosphate-dependent (PLP enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1 knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s previously observed.

  16. Frequency of the cancer-resistant phenotype in SR/CR mice and the effect of litter seriation

    DEFF Research Database (Denmark)

    Koch, Janne; Boschian, Anna; Hau, Jann;

    2008-01-01

    . The frequency of the SR/CR phenotype in the present study was 30% for the BALB/c strain and 22% for the C57BL/6 strain in the first litters, but the overall frequency was 8% for both strains. A frequency of about 30% was reported in the original US colony. A litter seriation effect on the frequency of the SR....../CR phenotype was recorded. The phenotype frequency in the first-born litters was similar to that recorded in the founder colony in the US. There was no significant difference in the frequency of the SR/CR phenotype between the two genders, but the overall frequency of the SR/CR phenotype was significantly...... higher in litters from SR/CR mice on a BALB/c background compared to litters from SR/CR mice on a C57BL/6 background....

  17. Phenotypic plasticity: molecular mechanisms and adaptive significance.

    Science.gov (United States)

    Kelly, Scott A; Panhuis, Tami M; Stoehr, Andrew M

    2012-04-01

    Phenotypic plasticity can be broadly defined as the ability of one genotype to produce more than one phenotype when exposed to different environments, as the modification of developmental events by the environment, or as the ability of an individual organism to alter its phenotype in response to changes in environmental conditions. Not surprisingly, the study of phenotypic plasticity is innately interdisciplinary and encompasses aspects of behavior, development, ecology, evolution, genetics, genomics, and multiple physiological systems at various levels of biological organization. From an ecological and evolutionary perspective, phenotypic plasticity may be a powerful means of adaptation and dramatic examples of phenotypic plasticity include predator avoidance, insect wing polymorphisms, the timing of metamorphosis in amphibians, osmoregulation in fishes, and alternative reproductive tactics in male vertebrates. From a human health perspective, documented examples of plasticity most commonly include the results of exercise, training, and/or dieting on human morphology and physiology. Regardless of the discipline, phenotypic plasticity has increasingly become the target of a plethora of investigations with the methodological approaches utilized ranging from the molecular to whole organsimal. In this article, we provide a brief historical outlook on phenotypic plasticity; examine its potential adaptive significance; emphasize recent molecular approaches that provide novel insight into underlying mechanisms, and highlight examples in fishes and insects. Finally, we highlight examples of phenotypic plasticity from a human health perspective and underscore the use of mouse models as a powerful tool in understanding the genetic architecture of phenotypic plasticity.

  18. Phenotype microarray profiling of the antibacterial activity of red cabbage

    Directory of Open Access Journals (Sweden)

    Hafidh RR

    2012-06-01

    Full Text Available Background: Functional food can be a potent source of wide array of biocomonents with antimicrobial activity. We investigated the antibacterial activity of red cabbage (RC extract on Gram negative and positive ATCC strains. Most intersting, we, for the first time, explored and analysed the complete phenotypic profile of RC-treated bacteria using Omnilog Phenotype Microarray. Results: This study revealed that the phenotype microarray (PM screen was a valuable tool in the search for compounds and their antibacterial mechanisms that can inhibit bacterial growth by affecting certain metabolic pathways. It was shown that RC exerted remarkable antibacterial effect on S. aureus and E. coli bacteria, and PM showed a wide range phenotypic profile of the exerted RC antibacterial activity. RC targeted the peptide, carbon, nutriontional assembly, and sulfur metbolic pathways altogether. The peptidoglycan synthesis pathway was inferred to be targeted by RC extract at a metabolic point different from other available cell wall-targeting drugs; these could be hot targets for the discovery of new therapy for many problematic microbes.Conclusions: Taken together, the phenotype microarray for functional food and medicinal plants can be a very useful tool for profiling their antimicrobial activity. Moreover, extracts of functional food can exert antibacterial activity by hitting a wide range of metabolic pathways, at the same time leading to very difficult condition for bacteria to rapidly develop resistance. Therefore, using functional foods or medicinal plants as such, or as extracts, can be superior on mono-targeting antibiotics if the optimal concentrations and conditions of these functional foods were sought.

  19. Cosmological Hints of Modified Gravity ?

    CERN Document Server

    Di Valentino, Eleonora; Silk, Joseph

    2016-01-01

    The recent measurements of Cosmic Microwave Background temperature and polarization anisotropies made by the Planck satellite have provided impressive confirmation of the $\\Lambda$CDM cosmological model. However interesting hints of slight deviations from $\\Lambda$CDM have been found, including a $95 \\%$ c.l. preference for a "modified gravity" structure formation scenario. In this paper we confirm the preference for a modified gravity scenario from Planck 2015 data, find that modified gravity solves the so-called $A_{lens}$ anomaly in the CMB angular spectrum, and constrains the amplitude of matter density fluctuations to $\\sigma_8=0.815_{-0.048}^{+0.032}$, in better agreement with weak lensing constraints. Moreover, we find a lower value for the reionization optical depth of $\\tau=0.059\\pm0.020$ (to be compared with the value of $\\tau= 0.079 \\pm 0.017$ obtained in the standard scenario), more consistent with recent optical and UV data. We check the stability of this result by considering possible degeneraci...

  20. The local potential approximation in the background field formalism

    CERN Document Server

    Bridle, I Hamzaan; Morris, Tim R

    2013-01-01

    Working within the familiar local potential approximation, and concentrating on the example of a single scalar field in three dimensions, we show that the commonly used approximation method of identifying the total and background fields, leads to pathologies in the resulting fixed point structure and the associated spaces of eigenoperators. We then show how a consistent treatment of the background field through the corresponding modified shift Ward identity, can cure these pathologies, restoring universality of physical quantities with respect to the choice of dependence on the background field, even within the local potential approximation. Along the way we point out similarities to what has been previously found in the f(R) approximation in asymptotic safety for gravity.

  1. DBA/2J genetic background exacerbates spontaneous lethal seizures but lessens amyloid deposition in a mouse model of Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Harriet M Jackson

    Full Text Available Alzheimer's disease (AD is a leading cause of dementia in the elderly and is characterized by amyloid plaques, neurofibrillary tangles (NFTs and neuronal dysfunction. Early onset AD (EOAD is commonly caused by mutations in amyloid precursor protein (APP or genes involved in the processing of APP including the presenilins (e.g. PSEN1 or PSEN2. In general, mouse models relevant to EOAD recapitulate amyloidosis, show only limited amounts of NFTs and neuronal cell dysfunction and low but significant levels of seizure susceptibility. To investigate the effect of genetic background on these phenotypes, we generated APPswe and PSEN1de9 transgenic mice on the seizure prone inbred strain background, DBA/2J. Previous studies show that the DBA/2J genetic background modifies plaque deposition in the presence of mutant APP but the impact of PSEN1de9 has not been tested. Our study shows that DBA/2J.APPswePSEN1de9 mice are significantly more prone to premature lethality, likely to due to lethal seizures, compared to B6.APPswePSEN1de9 mice-70% of DBA/2J.APPswePSEN1de9 mice die between 2-3 months of age. Of the DBA/2J.APPswePSEN1de9 mice that survived to 6 months of age, plaque deposition was greatly reduced compared to age-matched B6.APPswePSEN1de9 mice. The reduction in plaque deposition appears to be independent of microglia numbers, reactive astrocytosis and complement C5 activity.

  2. Phenotypic Plasticity and Species Coexistence.

    Science.gov (United States)

    Turcotte, Martin M; Levine, Jonathan M

    2016-10-01

    Ecologists are increasingly interested in predicting how intraspecific variation and changing trait values impact species interactions and community composition. For many traits, much of this variation is caused by phenotypic plasticity, and thus the impact of plasticity on species coexistence deserves robust quantification. Partly due to a lack of sound theoretical expectations, empirical studies make contradictory claims regarding plasticity effects on coexistence. Our critical review of this literature, framed in modern coexistence theory, reveals that plasticity affects species interactions in ways that could impact stabilizing niche differences and competitive asymmetries. However, almost no study integrates these measures to quantify the net effect of plasticity on species coexistence. To address this challenge, we outline novel empirical approaches grounded in modern theory.

  3. Phenotypic checkpoints regulate neuronal development.

    Science.gov (United States)

    Ben-Ari, Yehezkel; Spitzer, Nicholas C

    2010-11-01

    Nervous system development proceeds by sequential gene expression mediated by cascades of transcription factors in parallel with sequences of patterned network activity driven by receptors and ion channels. These sequences are cell type- and developmental stage-dependent and modulated by paracrine actions of substances released by neurons and glia. How and to what extent these sequences interact to enable neuronal network development is not understood. Recent evidence demonstrates that CNS development requires intermediate stages of differentiation providing functional feedback that influences gene expression. We suggest that embryonic neuronal functions constitute a series of phenotypic checkpoint signatures; neurons failing to express these functions are delayed or developmentally arrested. Such checkpoints are likely to be a general feature of neuronal development and constitute presymptomatic signatures of neurological disorders when they go awry.

  4. Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution.

    Science.gov (United States)

    Chandler, Christopher H; Chari, Sudarshan; Dworkin, Ian

    2013-06-01

    The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. However, it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but are instead due to interactions of the focal allele with other genes and the environment. Although an experimentally rigorous approach focused on individual mutations and isogenic control strains has facilitated amazing progress within genetics and related fields, a glimpse back suggests that a vast complexity has been omitted from our current understanding of allelic effects. Armed with traditional genetic analyses and the foundational knowledge they have provided, we argue that the time and tools are ripe to return to the underexplored aspects of gene function and embrace the context-dependent nature of genetic effects. We assert that a broad understanding of genetic effects and the evolutionary dynamics of alleles requires identifying how mutational outcomes depend upon the 'wild type' genetic background. Furthermore, we discuss how best to exploit genetic background effects to broaden genetic research programs.

  5. Evolution of phenotypic plasticity in colonizing species.

    Science.gov (United States)

    Lande, Russell

    2015-05-01

    I elaborate an hypothesis to explain inconsistent empirical findings comparing phenotypic plasticity in colonizing populations or species with plasticity from their native or ancestral range. Quantitative genetic theory on the evolution of plasticity reveals that colonization of a novel environment can cause a transient increase in plasticity: a rapid initial increase in plasticity accelerates evolution of a new optimal phenotype, followed by slow genetic assimilation of the new phenotype and reduction of plasticity. An association of colonization with increased plasticity depends on the difference in the optimal phenotype between ancestral and colonized environments, the difference in mean, variance and predictability of the environment, the cost of plasticity, and the time elapsed since colonization. The relative importance of these parameters depends on whether a phenotypic character develops by one-shot plasticity to a constant adult phenotype or by labile plasticity involving continuous and reversible development throughout adult life.

  6. Neurobiological background of negative symptoms.

    Science.gov (United States)

    Galderisi, Silvana; Merlotti, Eleonora; Mucci, Armida

    2015-10-01

    Studies investigating neurobiological bases of negative symptoms of schizophrenia failed to provide consistent findings, possibly due to the heterogeneity of this psychopathological construct. We tried to review the findings published to date investigating neurobiological abnormalities after reducing the heterogeneity of the negative symptoms construct. The literature in electronic databases as well as citations and major articles are reviewed with respect to the phenomenology, pathology, genetics and neurobiology of schizophrenia. We searched PubMed with the keywords "negative symptoms," "deficit schizophrenia," "persistent negative symptoms," "neurotransmissions," "neuroimaging" and "genetic." Additional articles were identified by manually checking the reference lists of the relevant publications. Publications in English were considered, and unpublished studies, conference abstracts and poster presentations were not included. Structural and functional imaging studies addressed the issue of neurobiological background of negative symptoms from several perspectives (considering them as a unitary construct, focusing on primary and/or persistent negative symptoms and, more recently, clustering them into factors), but produced discrepant findings. The examined studies provided evidence suggesting that even primary and persistent negative symptoms include different psychopathological constructs, probably reflecting the dysfunction of different neurobiological substrates. Furthermore, they suggest that complex alterations in multiple neurotransmitter systems and genetic variants might influence the expression of negative symptoms in schizophrenia. On the whole, the reviewed findings, representing the distillation of a large body of disparate data, suggest that further deconstruction of negative symptomatology into more elementary components is needed to gain insight into underlying neurobiological mechanisms.

  7. On Modified Bar recursion

    DEFF Research Database (Denmark)

    Oliva, Paulo Borges

    2002-01-01

    Modified bar recursion is a variant of Spector's bar recursion which can be used to give a realizability interpretation of the classical axiom of dependent choice. This realizability allows for the extraction of witnesses from proofs of forall-exists-formulas in classical analysis. In this talk I...... shall report on results regarding the relationship between modified and Spector's bar recursion. I shall also show that a seemingly weak form of modified bar recursion is as strong as "full" modified bar recursion in higher types....

  8. POLYCAPROLACTAM MODIFIED BY POLYPHENYLQUINOXALINE

    Institute of Scientific and Technical Information of China (English)

    YANG Guisheng; LU Fengcai

    1990-01-01

    Three polycaprolactam samples modified by 0.05- 0.50% polyphenylquinoxaline (PPQ) by weight were prepared. Their structure and mechanical properties were characterized by FT-IR, SEM, density, tensile,impact,DTA and visco-elastic method. PPQ induced the formation of "crystal grains" distributed evenly over nylon spherulites in modified samples, which were observed for the first time, and strengthened modified samples. Modified nylons had higher crystallinities, higher Tg ,more nearly perfect spherulites than MC nylon itself, and showed typical reinforcing effect on mechanical properties.

  9. Cluster analysis of obesity and asthma phenotypes.

    Directory of Open Access Journals (Sweden)

    E Rand Sutherland

    Full Text Available BACKGROUND: Asthma is a heterogeneous disease with variability among patients in characteristics such as lung function, symptoms and control, body weight, markers of inflammation, and responsiveness to glucocorticoids (GC. Cluster analysis of well-characterized cohorts can advance understanding of disease subgroups in asthma and point to unsuspected disease mechanisms. We utilized an hypothesis-free cluster analytical approach to define the contribution of obesity and related variables to asthma phenotype. METHODOLOGY AND PRINCIPAL FINDINGS: In a cohort of clinical trial participants (n = 250, minimum-variance hierarchical clustering was used to identify clinical and inflammatory biomarkers important in determining disease cluster membership in mild and moderate persistent asthmatics. In a subset of participants, GC sensitivity was assessed via expression of GC receptor alpha (GCRα and induction of MAP kinase phosphatase-1 (MKP-1 expression by dexamethasone. Four asthma clusters were identified, with body mass index (BMI, kg/m(2 and severity of asthma symptoms (AEQ score the most significant determinants of cluster membership (F = 57.1, p<0.0001 and F = 44.8, p<0.0001, respectively. Two clusters were composed of predominantly obese individuals; these two obese asthma clusters differed from one another with regard to age of asthma onset, measures of asthma symptoms (AEQ and control (ACQ, exhaled nitric oxide concentration (F(ENO and airway hyperresponsiveness (methacholine PC(20 but were similar with regard to measures of lung function (FEV(1 (% and FEV(1/FVC, airway eosinophilia, IgE, leptin, adiponectin and C-reactive protein (hsCRP. Members of obese clusters demonstrated evidence of reduced expression of GCRα, a finding which was correlated with a reduced induction of MKP-1 expression by dexamethasone CONCLUSIONS AND SIGNIFICANCE: Obesity is an important determinant of asthma phenotype in adults. There is heterogeneity in

  10. Marital assortment and phenotypic convergence: longitudinal evidence.

    Science.gov (United States)

    Caspi, A; Herbener, E S

    1993-01-01

    This study provides a direct test of whether the observed similarity of spouses is due to initial assortment rather than to convergence of phenotypes. With data from three well-known longitudinal studies, phenotypic convergence is examined using both variable- and person-centered analyses. The longitudinal evidence does not support the hypothesis that couples increasingly resemble each other with time. Spouse correlations most likely reflect initial assortment at marriage and not the convergence of phenotypes.

  11. Phenotypic plasticity's impacts on diversification and speciation.

    Science.gov (United States)

    Pfennig, David W; Wund, Matthew A; Snell-Rood, Emilie C; Cruickshank, Tami; Schlichting, Carl D; Moczek, Armin P

    2010-08-01

    Phenotypic plasticity (the ability of a single genotype to produce multiple phenotypes in response to variation in the environment) is commonplace. Yet its evolutionary significance remains controversial, especially in regard to whether and how it impacts diversification and speciation. Here, we review recent theory on how plasticity promotes: (i) the origin of novel phenotypes, (ii) divergence among populations and species, (iii) the formation of new species and (iv) adaptive radiation. We also discuss the latest empirical support for each of these evolutionary pathways to diversification and identify potentially profitable areas for future research. Generally, phenotypic plasticity can play a largely underappreciated role in driving diversification and speciation.

  12. Immunogenetic phenotypes in inflammatory bowel disease

    Institute of Scientific and Technical Information of China (English)

    Marla C Dubinsky; Kent Taylor; Stephan R Targan; Jerome I Rotter

    2006-01-01

    The currently accepted etiopathogenic hypothesis suggests that the chronic intestinal inflammation and related systemic manifestations characteristic of inflammatory bowel disease (IBD) are due to an overly aggressive or pathologic immune response to resident luminal bacterial constituents. Predisposing factors are genetic dysregulation of mucosal immune responses and/or barrier function, with onset triggered by environmental stimuli. These factors and their interactions may also be important determinants of disease phenotype and disease progression. The emergence of immunogenetic phenotypes lends support to the proposed hypothesis that susceptibility genes regulate distinct immune processes, driven by luminal antigens, expressed as specific immune phenotypes which in turn influence clinical phenotypes in IBD patient

  13. Phenotypic screening: the future of antibody discovery.

    Science.gov (United States)

    Gonzalez-Munoz, Andrea L; Minter, Ralph R; Rust, Steven J

    2016-01-01

    Most antibody therapeutics have been isolated from high throughput target-based screening. However, as the number of validated targets diminishes and the target space becomes increasingly competitive, alternative strategies, such as phenotypic screening, are gaining momentum. Here, we review successful phenotypic screens, including those used to isolate antibodies against cancer and infectious agents. We also consider exciting advances in the expression and phenotypic screening of antibody repertoires in single cell autocrine systems. As technologies continue to develop, we believe that antibody phenotypic screening will increase further in popularity and has the potential to provide the next generation of therapeutic antibodies.

  14. Cosmic Microwave Background Data Analysis

    Science.gov (United States)

    Paykari, Paniez; Starck, Jean-Luc Starck

    2012-03-01

    About 400,000 years after the Big Bang the temperature of the Universe fell to about a few thousand degrees. As a result, the previously free electrons and protons combined and the Universe became neutral. This released a radiation which we now observe as the cosmic microwave background (CMB). The tiny fluctuations* in the temperature and polarization of the CMB carry a wealth of cosmological information. These so-called temperature anisotropies were predicted as the imprints of the initial density perturbations which gave rise to the present large-scale structures such as galaxies and clusters of galaxies. This relation between the present-day Universe and its initial conditions has made the CMB radiation one of the most preferred tools to understand the history of the Universe. The CMB radiation was discovered by radio astronomers Arno Penzias and Robert Wilson in 1965 [72] and earned them the 1978 Nobel Prize. This discovery was in support of the Big Bang theory and ruled out the only other available theory at that time - the steady-state theory. The crucial observations of the CMB radiation were made by the Far-Infrared Absolute Spectrophotometer (FIRAS) instrument on the Cosmic Background Explorer (COBE) satellite [86]- orbited in 1989-1996. COBE made the most accurate measurements of the CMB frequency spectrum and confirmed it as being a black-body to within experimental limits. This made the CMB spectrum the most precisely measured black-body spectrum in nature. The CMB has a thermal black-body spectrum at a temperature of 2.725 K: the spectrum peaks in the microwave range frequency of 160.2 GHz, corresponding to a 1.9mmwavelength. The results of COBE inspired a series of ground- and balloon-based experiments, which measured CMB anisotropies on smaller scales over the next decade. During the 1990s, the first acoustic peak of the CMB power spectrum (see Figure 5.1) was measured with increasing sensitivity and by 2000 the BOOMERanG experiment [26] reported

  15. A Turner syndrome neurocognitive phenotype maps to Xp22.3

    Directory of Open Access Journals (Sweden)

    Elder Frederick F

    2007-05-01

    Full Text Available Abstract Background Turner syndrome (TS is associated with a neurocognitive phenotype that includes selective nonverbal deficits, e.g., impaired visual-spatial abilities. We previously reported evidence that this phenotype results from haploinsufficiency of one or more genes on distal Xp. This inference was based on genotype/phenotype comparisons of individual girls and women with partial Xp deletions, with the neurocognitive phenotype considered a dichotomous trait. We sought to confirm our findings in a large cohort (n = 47 of adult women with partial deletions of Xp or Xq, enriched for subjects with distal Xp deletions. Methods Subjects were recruited from North American genetics and endocrinology clinics. Phenotype assessment included measures of stature, ovarian function, and detailed neurocognitive testing. The neurocognitive phenotype was measured as a quantitative trait, the Turner Syndrome Cognitive Summary (TSCS score, derived from discriminant function analysis. Genetic analysis included karyotyping, X inactivation studies, fluorescent in situ hybridization, microsatellite marker genotyping, and array comparative genomic hybridization. Results We report statistical evidence that deletion of Xp22.3, an interval containing 31 annotated genes, is sufficient to cause the neurocognitive phenotype described by the TSCS score. Two other cardinal TS features, ovarian failure and short stature, as well as X chromosome inactivation pattern and subject's age, were unrelated to the TSCS score. Conclusion Detailed mapping suggests that haploinsufficiency of one or more genes in Xp22.3, the distal 8.3 megabases (Mb of the X chromosome, is responsible for a TS neurocognitive phenotype. This interval includes the 2.6 Mb Xp-Yp pseudoautosomal region (PAR1. Haploinsufficiency of the short stature gene SHOX in PAR1 probably does not cause this TS neurocognitive phenotype. Two genes proximal to PAR1 within the 8.3 Mb critical region, STS and NLGN4X, are

  16. Desiderata for computable representations of electronic health records-driven phenotype algorithms

    Science.gov (United States)

    Mo, Huan; Thompson, William K; Rasmussen, Luke V; Pacheco, Jennifer A; Jiang, Guoqian; Kiefer, Richard; Zhu, Qian; Xu, Jie; Montague, Enid; Carrell, David S; Lingren, Todd; Mentch, Frank D; Ni, Yizhao; Wehbe, Firas H; Peissig, Peggy L; Tromp, Gerard; Larson, Eric B; Chute, Christopher G; Pathak, Jyotishman; Speltz, Peter; Kho, Abel N; Jarvik, Gail P; Bejan, Cosmin A; Williams, Marc S; Borthwick, Kenneth; Kitchner, Terrie E; Roden, Dan M; Harris, Paul A

    2015-01-01

    Background Electronic health records (EHRs) are increasingly used for clinical and translational research through the creation of phenotype algorithms. Currently, phenotype algorithms are most commonly represented as noncomputable descriptive documents and knowledge artifacts that detail the protocols for querying diagnoses, symptoms, procedures, medications, and/or text-driven medical concepts, and are primarily meant for human comprehension. We present desiderata for developing a computable phenotype representation model (PheRM). Methods A team of clinicians and informaticians reviewed common features for multisite phenotype algorithms published in PheKB.org and existing phenotype representation platforms. We also evaluated well-known diagnostic criteria and clinical decision-making guidelines to encompass a broader category of algorithms. Results We propose 10 desired characteristics for a flexible, computable PheRM: (1) structure clinical data into queryable forms; (2) recommend use of a common data model, but also support customization for the variability and availability of EHR data among sites; (3) support both human-readable and computable representations of phenotype algorithms; (4) implement set operations and relational algebra for modeling phenotype algorithms; (5) represent phenotype criteria with structured rules; (6) support defining temporal relations between events; (7) use standardized terminologies and ontologies, and facilitate reuse of value sets; (8) define representations for text searching and natural language processing; (9) provide interfaces for external software algorithms; and (10) maintain backward compatibility. Conclusion A computable PheRM is needed for true phenotype portability and reliability across different EHR products and healthcare systems. These desiderata are a guide to inform the establishment and evolution of EHR phenotype algorithm authoring platforms and languages. PMID:26342218

  17. Phenotypic resistance of resistant strains of HIV type-1 subtype B in China

    Institute of Scientific and Technical Information of China (English)

    LI Jue; WANG Zhe; WU Hao; LI Jing-yun; LU Jun-feng; DONG Hua-huang; BAO Zuo-yi; LIU Si-yang; LI Han-ping; ZHUANG Dao-min; LIU Yong-jian; LI Hong

    2006-01-01

    Background This study was aim to explore the characteristics of phenotypic resistance of resistant strains of HIV type-1 (HIV-1) subtype B and to compare the concordance between the phenotypic resistance and genotypic resistance. Methods The genotypic resistance assay for the HIV-1 clinical isolates was performed. One isolate without resistance mutation was chosen as a drug-sensitive reference strain and seven subtype B isolates with resistance mutations were phenotypically tested. Fifty percent inhibitory concentrations (IC50) between resistant and sensitive viruses were compared. The resistance extent was determined by the folds of the increased IC50. The concordance between the phenotypic resistance and genotypic resistance was also analyzed.Results IC50 of resistant isolates were 0.0006-0.1300 μmol/L for zidovudine (AZT), 0.0016-0.0390 μmol/L for lamivudine (3TC), 0.0104-0.4234 μmol/L for nevirapine (NVP), and 0.0163-0.1142 μmol/L for indinavir (IDV), respectively. Genotypic and phenotypic resistance assays indicated that the resistant strains were intermediately and highly resistant to nucleotide analog reverse transcriptase inhibitors and non-nucleotide analog reverse transcriptase inhibitors. The phenotypic assay was consistent with the genotypic assay. For measuring the potential resistance, the genotypic assay was more sensitive than the phenotypic. In evaluating the resistance to protease inhibitors, these two assays were discrepant.Conclusions Both the phenotypic and genotypic assays indicate that the resistant viruses exist in HIV-infected patients in China who have received treatment. Phenotypic and genotypic assays have high concordance, and the genotypic assay could replace the phenotypic assay to predict the HIV-1 resistance.

  18. Phenotypic and genotypic data integration and exploration through a web-service architecture

    Science.gov (United States)

    Nuzzo, Angelo; Riva, Alberto; Bellazzi, Riccardo

    2009-01-01

    Background Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in particular studies aimed at the analysis of complex traits, which require the definition of multifaceted phenotypes and the integration genotypic information to discover the most prevalent diseases, is a paradigmatic goal of Biomedical Informatics. This paper describes the use of Information Technology methods and tools to develop a system for the management, inspection and integration of phenotypic and genotypic data. Results We present the design and architecture of the Phenotype Miner, a software system able to flexibly manage phenotypic information, and its extended functionalities to retrieve genotype information from external repositories and to relate it to phenotypic data. For this purpose we developed a module to allow customized data upload by the user and a SOAP-based communications layer to retrieve data from existing biomedical knowledge management tools. In this paper we also demonstrate the system functionality by an example application of the system in which we analyze two related genomic datasets. Conclusion In this paper we show how a comprehensive, integrated and automated workbench for genotype and phenotype integration can facilitate and improve the hypothesis generation process underlying modern genetic studies. PMID:19828081

  19. "Dynamic range" of inferred phenotypic HIV drug resistance values in clinical practice.

    Directory of Open Access Journals (Sweden)

    Luke C Swenson

    Full Text Available BACKGROUND: 'Virtual' or inferred phenotypes (vPhenotypes are commonly used to assess resistance to antiretroviral agents in patients failing therapy. In this study, we provide a clinical context for understanding vPhenotype values. METHODS: All HIV-infected persons enrolled in the British Columbia Drug Treatment Program with a baseline plasma viral load (pVL and follow-up genotypic resistance and pVL results were included up to October 29, 2008 (N = 5,277. Change from baseline pVL was determined as a function of Virco vPhenotype, and the "dynamic range" (defined here by the 10th and 90th percentiles for fold-change in IC₅₀ amongst all patients was estimated from the distribution of vPhenotye fold-changes across the cohort. RESULTS: The distribution of vPhenotypes from a large cohort of HIV patients who have failed therapy are presented for all available antiretroviral agents. A maximum change in IC₅₀ of at least 13-fold was observed for all drugs. The dideoxy drugs, tenofovir and most PIs exhibited small "dynamic ranges" with values of 99% of samples. In contrast, zidovudine, lamivudine, emtricitabine and the non-nucleoside reverse transcriptase inihibitors (excluding etravirine had large dynamic ranges. CONCLUSION: We describe the populational distribution of vPhenotypes such that vPhenotype results can be interpreted relative to other patients in a drug-specific manner.

  20. Computer-Assisted Transgenesis of Caenorhabditis elegans for Deep Phenotyping.

    Science.gov (United States)

    Gilleland, Cody L; Falls, Adam T; Noraky, James; Heiman, Maxwell G; Yanik, Mehmet F

    2015-09-01

    A major goal in the study of human diseases is to assign functions to genes or genetic variants. The model organism Caenorhabditis elegans provides a powerful tool because homologs of many human genes are identifiable, and large collections of genetic vectors and mutant strains are available. However, the delivery of such vector libraries into mutant strains remains a long-standing experimental bottleneck for phenotypic analysis. Here, we present a computer-assisted microinjection platform to streamline the production of transgenic C. elegans with multiple vectors for deep phenotyping. Briefly, animals are immobilized in a temperature-sensitive hydrogel using a standard multiwell platform. Microinjections are then performed under control of an automated microscope using precision robotics driven by customized computer vision algorithms. We demonstrate utility by phenotyping the morphology of 12 neuronal classes in six mutant backgrounds using combinations of neuron-type-specific fluorescent reporters. This technology can industrialize the assignment of in vivo gene function by enabling large-scale transgenic engineering.

  1. Ethnic differences in the phenotypic expression of polycystic ovary syndrome.

    Science.gov (United States)

    Zhao, Yue; Qiao, Jie

    2013-08-01

    Polycystic ovary syndrome (PCOS) is the most common endocrine problem affecting women of reproductive age and is investigated from many regions of the world. Some reports have indicated ethnic difference in its manifestation. This review addressed the evidences for ethnic variation in the expression of PCOS phenotypes and explored the potential ethnic-specific diagnosis of this syndrome. To determine ethnic variation, community prevalence and clinical and metabolic problems, including hyperandrogenism, oligomenorrhoea/amenorrhoea, polycystic ovaries, obesity, insulin resistance and the metabolic syndrome, had been compared from differing backgrounds and populations. Moreover, a link between ethnicity and variation in the metabolic phenotype of PCOS had also been identified. East Asian women with PCOS have a lower BMI and a milder hyperandrogenic phenotype, but with the highest prevalence of metabolic syndrome. South Asians in particular have a high prevalence of insulin resistance and metabolic syndrome, and are at risk for type 2 diabetes, with central obesity more than BMI reflecting their metabolic risk. African American and Hispanic women are more obese and more prone to metabolic problems. Besides, there is a higher prevalence of hirsutism among women of Middle Eastern and Mediterranean origin. Ethnically appropriate guidelines are needed for identifying anthropometric thresholds for better screening and diagnosis in high-risk ethnic groups.

  2. HDACs and the senescent phenotype of WI-38 cells

    Directory of Open Access Journals (Sweden)

    Noonan Emily J

    2005-10-01

    Full Text Available Abstract Background Normal cells possess a limited proliferative life span after which they enter a state of irreversible growth arrest. This process, known as replicative senescence, is accompanied by changes in gene expression that give rise to a variety of senescence-associated phenotypes. It has been suggested that these gene expression changes result in part from alterations in the histone acetylation machinery. Here we examine the influence of HDAC inhibitors on the expression of senescent markers in pre- and post-senescent WI-38 cells. Results Pre- and post-senescent WI-38 cells were treated with the HDAC inhibitors butyrate or trichostatin A (TSA. Following HDAC inhibitor treatment, pre-senescent cells increased p21WAF1 and β-galactosidase expression, assumed a flattened senescence-associated morphology, and maintained a lower level of proteasome activity. These alterations also occurred during normal replicative senescence of WI-38 cells, but were not accentuated further by HDAC inhibitors. We also found that HDAC1 levels decline during normal replicative senescence. Conclusion Our findings indicate that HDACs impact numerous phenotypic changes associated with cellular senescence. Reduced HDAC1 expression levels in senescent cells may be an important event in mediating the transition to a senescent phenotype.

  3. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

    NARCIS (Netherlands)

    Kohler, S.; Doelken, S.C.; Mungall, C.J.; Bauer, S.; Firth, H.V.; Bailleul-Forestier, I.; Black, G.C.M.; Brown, D.L.; Brudno, M.; Campbell, J.; FitzPatrick, D.R.; Eppig, J.T.; Jackson, A.P.; Freson, K.; Girdea, M.; Helbig, I.; Hurst, J.A.; Jahn, J.; Jackson, L.G.; Kelly, A.M.; Ledbetter, D.H.; Mansour, S.; Martin, C.L.; Moss, C.; Mumford, A.; Ouwehand, W.H.; Park, S.M.; Riggs, E.R.; Scott, R.H.; Sisodiya, S.; Vooren, S. van der; Wapner, R.J.; Wilkie, A.O.; Wright, C.F.; Silfhout, A.T. van; Leeuw, N. de; Vries, B. de; Washingthon, N.L.; Smith, C.L.; Westerfield, M.; Schofield, P.; Ruef, B.J.; Gkoutos, G.V.; Haendel, M.; Smedley, D.; Lewis, S.E.; Robinson, P.N.

    2014-01-01

    The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have d

  4. Regulatory mechanisms link phenotypic plasticity to evolvability

    NARCIS (Netherlands)

    van Gestel, Jordi; Weissing, Franz J

    2016-01-01

    Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticit

  5. Emerging semantics to link phenotype and environment

    Directory of Open Access Journals (Sweden)

    Anne E. Thessen

    2015-12-01

    Full Text Available Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1 use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2 two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3 two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE and the Biological Collections Ontology (BCO; these provide a starting point for the development of a data model linking phenotypes and environments.

  6. The Cognitive Phenotype of Spina Bifida Meningomyelocele

    Science.gov (United States)

    Dennis, Maureen; Barnes, Marcia A.

    2010-01-01

    A cognitive phenotype is a product of both assets and deficits that specifies what individuals with spina bifida meningomyelocele (SBM) can and cannot do and why they can or cannot do it. In this article, we review the cognitive phenotype of SBM and describe the processing assets and deficits that cut within and across content domains, sensory…

  7. The Neuroanatomy of the Autistic Phenotype

    Science.gov (United States)

    Fahim, Cherine; Meguid, Nagwa A.; Nashaat, Neveen H.; Yoon, Uicheul; Mancini-Marie, Adham; Evans, Alan C.

    2012-01-01

    The autism phenotype is associated with an excess of brain volume due in part to decreased pruning during development. Here we aimed at assessing brain volume early in development to further elucidate previous findings in autism and determine whether this pattern is restricted to idiopathic autism or shared within the autistic phenotype (fragile X…

  8. Background and introduction: Chapter 1

    Science.gov (United States)

    Shafroth, Patrick B.

    2010-01-01

    The Salt Cedar and Russian Olive Control Demonstration Act of 2006 (Public Law 109-320; hereafter the Act) directs the Department of the Interior to submit a report to Congress1 that includes an assessment of several issues surrounding these two nonnative trees, now dominant components of the vegetation along many rivers in the Western United States. Specifically, the Act calls for “…an assessment of the extent of salt cedar and Russian olive infestation on public and private land in the western United States,” which shall“A) consider existing research on methods to control salt cedar and Russian olive trees; B) consider the feasibility of reducing water consumption by salt cedar and Russian olive trees; C) consider methods of and challenges associated with the revegetation or restoration of infested land; and D) estimate the costs of destruction of salt cedar and Russian olive trees, related biomass removal, and revegetation or restoration and maintenance of the infested land.”Finally, the Act calls for discussion of“(i) long-term management and funding strategies…that could be implemented by Federal, State, tribal, and private land managers and owners to address the infestation by salt cedar and Russian olive; (ii) any deficiencies in the assessment or areas for additional study; and (iii) any field demonstrations that would be useful in the effort to control salt cedar and Russian olive.”The primary intent of this report is to provide the science assessment called for under the Act. A secondary purpose is to provide a common background for applicants for prospective demonstration projects, should funds be appropriated for this second phase of the Act. In addition to relying on the direction provided under Section C of the Act, the authors of this report also drew upon the detailed list of considerations presented in Section E of the Act to guide development of more expansive discussions of topics relevant to saltcedar and Russian olive control

  9. Bronchiectasis: Phenotyping a Complex Disease.

    Science.gov (United States)

    Chalmers, James D

    2017-03-15

    Bronchiectasis is a long-neglected disease currently experiencing a surge in interest. It is a highly complex condition with numerous aetiologies, co-morbidities and a heterogeneous disease presentation and clinical course. The past few years have seen major advances in our understanding of the disease, primarily through large real-life cohort studies. The main outcomes of interest in bronchiectasis are symptoms, exacerbations, treatment response, disease progression and death. We are now more able to identify clearly the radiological, clinical, microbiological and inflammatory contributors to these outcomes. Over the past couple of years, multidimensional scoring systems such as the Bronchiectasis Severity Index have been introduced to predict disease severity and mortality. Although there are currently no licensed therapies for bronchiectasis, an increasing number of clinical trials are planned or ongoing. While this emerging evidence is awaited, bronchiectasis guidelines will continue to be informed largely by real-life evidence from observational studies and patient registries. Key developments in the bronchiectasis field include the establishment of international disease registries and characterisation of disease phenotypes using cluster analysis and biological data.

  10. Measurement Equivalence of the Autism Symptom Phenotype in Children and Youth

    Science.gov (United States)

    Duku, Eric; Szatmari, Peter; Vaillancourt, Tracy; Georgiades, Stelios; Thompson, Ann; Liu, Xiao-Qing; Paterson, Andrew D.; Bennett, Terry

    2013-01-01

    Background: The Autism Diagnostic Interview-Revised (ADI-R) is a gold standard assessment of Autism Spectrum Disorder (ASD) symptoms and behaviours. A key underlying assumption of studies using the ADI-R is that it measures the same phenotypic constructs across different populations (i.e. males/females, younger/older, verbal/nonverbal). The…

  11. Phenotypic and molecular insights into CASK-related disorders in males

    NARCIS (Netherlands)

    Moog, U.; Bierhals, T.; Brand, K.; Bautsch, J.; Biskup, S.; Brune, T.; Denecke, J.; Die-Smulders, C.E.M. de; Evers, C.; Hempel, M.; Henneke, M.; Yntema, H.G.; Menten, B.; Pietz, J.; Pfundt, R.P.; Schmidtke, J.; Steinemann, D.; Stumpel, C.T.; Maldergem, L. Van; Kutsche, K.

    2015-01-01

    BACKGROUND: Heterozygous loss-of-function mutations in the X-linked CASK gene cause progressive microcephaly with pontine and cerebellar hypoplasia (MICPCH) and severe intellectual disability (ID) in females. Different CASK mutations have also been reported in males. The associated phenotypes range

  12. Adaptive developmental plasticity: Compartmentalized responses to environmental cues and corresponding internal signals provide phenotypic flexibility

    NARCIS (Netherlands)

    Mateus, A.R.A.; Marques-Pita, M.; Oostra, V.; Lafuente, E.; Brakefield, P.M.; Zwaan, B.J.; Beldade, P.

    2014-01-01

    Background The environmental regulation of development can result in the production of distinct phenotypes from the same genotype and provide the means for organisms to cope with environmental heterogeneity. The effect of the environment on developmental outcomes is typically mediated by hormonal si

  13. The phenotypic spectrum of organic acidurias and urea cycle disorders. Part 2

    DEFF Research Database (Denmark)

    Kölker, Stefan; Valayannopoulos, Vassili; Burlina, Alberto B;

    2015-01-01

    BACKGROUND: The disease course and long-term outcome of patients with organic acidurias (OAD) and urea cycle disorders (UCD) are incompletely understood. AIMS: To evaluate the complex clinical phenotype of OAD and UCD patients at different ages. RESULTS: Acquired microcephaly and movement disorde...

  14. Is Sensory Over-Responsivity Distinguishable from Childhood Behavior Problems? A Phenotypic and Genetic Analysis

    Science.gov (United States)

    Van Hulle, Carol A.; Schmidt, Nicole L.; Goldsmith, H. Hill

    2012-01-01

    Background: Although impaired sensory processing accompanies various clinical conditions, the question of its status as an independent disorder remains open. Our goal was to delineate the comorbidity (or lack thereof) between childhood psychopathology and sensory over-responsivity (SOR) in middle childhood using phenotypic and behavior-genetic…

  15. Early phenotypic differences between Parkinson's disease patients with and without freezing of gait

    NARCIS (Netherlands)

    Hall, J. M.; Shine, J. M.; Walton, C. C.; Gilat, M.; Kamsma, Y. P. T.; Naismith, S. L.; Lewis, S. J. G.

    2014-01-01

    Background: Previous studies have associated freezing of gait in Parkinson's disease with the presence of specific phenotypic features such as mood disturbances, REM sleep behavior disorder and selective cognitive impairments. However, it is not clear whether these features are present in the earlie

  16. Oncogenic driver genes and the inflammatory microenvironment dictate liver tumor phenotype

    DEFF Research Database (Denmark)

    Matter, Matthias S; Marquardt, Jens U; Andersen, Jesper B

    2016-01-01

    The majority of hepatocellular carcinoma (HCC) develops in the background of chronic liver inflammation caused by viral hepatitis and alcoholic or non-alcoholic steatohepatitis. However, the impact of different types of chronic inflammatory microenvironments on the phenotypes of tumors generated...

  17. Genotypes and phenotypes for apolipoprotein E and Alzheimer disease in the Honolulu-Asia aging study

    NARCIS (Netherlands)

    J.W.P.F. Kardaun (Jan); L. White (Lon); H.E. Resnick; H. Petrovitch; S.M. Marcovina; A.M. Saunders (Ann); D.J. Foley (Dan); R.J. Havlik

    2000-01-01

    textabstractBACKGROUND: The utility of apolipoprotein E (ApoE) type as an indicator of genetic susceptibility to Alzheimer disease (AD) depends on the reliability of typing. Although ApoE protein isoform phenotyping is generally assumed equivalent to genotyping from DNA

  18. HDL does not influence the polarization of human monocytes toward an alternative phenotype

    NARCIS (Netherlands)

    Colin, Sophie; Fanchon, Melanie; Belloy, Loic; Bochem, Andrea E.; Copin, Corinne; Derudas, Bruno; Stroes, Erik S. G.; Hovingh, G. Kees; Kuivenhoven, Jan A.; Dallinga-Thie, Geesje M.; Staels, Bart; Chinetti-Gbaguidi, Giulia

    2014-01-01

    BACKGROUND: Macrophages are crucial cells in the pathogenesis of atherosclerosis. Macrophages are plastic cells which can switch from a classical pro-inflammatory M1 to an alternative anti-inflammatory M2 macrophage phenotype, depending on the environmental stimuli. Because high-density lipoprotein

  19. Dietary patterns and the insulin resistance phenotype among non-diabetic adults

    Science.gov (United States)

    Background: Information on the relation between dietary patterns derived by cluster analysis and insulin resistance is scarce. Objective: To compare insulin resistance phenotypes, including waist circumference, body mass index, fasting and 2-hour post-challenge insulin, insulin sensitivity index (I...

  20. The Behavioural Phenotype of Smith-Magenis Syndrome: Evidence for a Gene-Environment Interaction

    Science.gov (United States)

    Taylor, L.; Oliver, C.

    2008-01-01

    Background: Behaviour problems and a preference for adult contact are reported to be prominent in the phenotype of Smith-Magenis syndrome. In this study we examined the relationship between social interactions and self-injurious and aggressive/disruptive behaviour in Smith-Magenis syndrome to explore potential operant reinforcement of problem…

  1. A study comparing chemical peeling using modified jessner′s solution and 15% trichloroacetic acid versus 15% trichloroacetic acid in the treatment of melasma

    Directory of Open Access Journals (Sweden)

    Safoury Omar

    2009-01-01

    Full Text Available Background: Melasma is a symmetric progressive hyperpigmentation of the facial skin that occurs in all races but has a predilection for darker skin phenotypes. Depigmenting agents, laser and chemical peeling as classic Jessner′s solution, modified Jessner′s solution and trichloroacetic acid have been used alone and in combination in the treatment of melasma. Objectives: The aim of the study was to compare the therapeutic effect of combined 15% Trichloroacetic acid (TCA and modified Jessner′s solution with 15% TCA on melasma. Materials and Methods: Twenty married females with melasma (epidermal type, with a mean age of 38.25 years, were included in this study. All were of skin type III or IV. Fifteen percent TCA was applied to the whole face, with the exception of the left malar area to which combined TCA 15% and modified Jessner′s solution was applied. Results: Our results revealed statistically highly significant difference between MASI Score (Melasma Area and Severity Index between the right malar area and the left malar area. Conclusion: Modified Jessner′s solution proved to be useful as an adjuvant treatment with TCA in the treatment of melasma, improving the results and minimizing postinflammatory hyperpigmentation.

  2. A STUDY COMPARING CHEMICAL PEELING USING MODIFIED JESSNER'S SOLUTION AND 15%TRICHLOROACETIC ACID VERSUS 15% TRICHLOROACETIC ACID IN THE TREATMENT OF MELASMA

    Science.gov (United States)

    Safoury, Omar Soliman; Zaki, Nagla Mohamed; El Nabarawy, Eman Ahmad; Farag, Eman Abas

    2009-01-01

    Background: Melasma is a symmetric progressive hyperpigmentation of the facial skin that occurs in all races but has a predilection for darker skin phenotypes. Depigmenting agents, laser and chemical peeling as classic Jessner's solution, modified Jessner's solution and trichloroacetic acid have been used alone and in combination in the treatment of melasma. Objectives: The aim of the study was to compare the therapeutic effect of combined 15% Trichloroacetic acid (TCA) and modified Jessner's solution with 15% TCA on melasma. Materials and Methods: Twenty married females with melasma (epidermal type), with a mean age of 38.25 years, were included in this study. All were of skin type III or IV. Fifteen percent TCA was applied to the whole face, with the exception of the left malar area to which combined TCA 15% and modified Jessner's solution was applied. Results: Our results revealed statistically highly significant difference between MASI Score (Melasma Area and Severity Index) between the right malar area and the left malar area. Conclusion: Modified Jessner's solution proved to be useful as an adjuvant treatment with TCA in the treatment of melasma, improving the results and minimizing postinflammatory hyperpigmentation. PMID:20049268

  3. The other side of phenotypic plasticity: a developmental system that generates an invariant phenotype despite environmental variation.

    Science.gov (United States)

    Braendle, Christian; Felix, Marie-Anne

    2009-10-01

    Understanding how the environment impacts development is of central interest in developmental and evolutionary biology. On the one hand, we would like to understand how the environment induces phenotypic changes (the study of phenotypic plasticity). On the other hand, we may ask how a development system maintains a stable and precise phenotypic output despite the presence of environmental variation. We study such developmental robustness to environmental variation using vulval cell fate patterning in the nematode Caenorhabditis elegans as a study system. Here we review both mechanistic and evolutionary aspects of these studies, focusing on recently obtained experimental results. First, we present evidence indicating that vulval formation is under stabilizing selection. Second, we discuss quantitative data on the precision and variability in the output of the vulval developmental system in different environments and different genetic backgrounds. Third, we illustrate how environmental and genetic variation modulate the cellular and molecular processes underlying the formation of the vulva. Fourth, we discuss the evolutionary significance of environmental sensitivity of this developmental system.

  4. The other side of phenotypic plasticity: a developmental system that generates an invariant phenotype despite environmental variation

    Indian Academy of Sciences (India)

    Christian Braendle; Marie-Anne Félix

    2009-10-01

    Understanding how the environment impacts development is of central interest in developmental and evolutionary biology. On the one hand, we would like to understand how the environment induces phenotypic changes (the study of phenotypic plasticity). On the other hand, we may ask how a development system maintains a stable and precise phenotypic output despite the presence of environmental variation. We study such developmental robustness to environmental variation using vulval cell fate patterning in the nematode Caenorhabditis elegans as a study system. Here we review both mechanistic and evolutionary aspects of these studies, focusing on recently obtained experimental results. First, we present evidence indicating that vulval formation is under stabilizing selection. Second, we discusss quantitative data on the precision and variability in the output of the vulval developmental system in different environments and different genetic backgrounds. Third, we illustrate how environmental and genetic variation modulate the cellular and molecular processes underlying the formation of the vulva. Fourth, we discuss the evolutionary significance of environmental sensitivity of this developmental system.

  5. Fried frailty phenotype assessment components as applied to geriatric inpatients

    Directory of Open Access Journals (Sweden)

    Bieniek J

    2016-04-01

    Full Text Available Joanna Bieniek, Krzysztof Wilczynski, Jan Szewieczek Department of Geriatrics, School of Health Sciences in Katowice, Medical University of Silesia, Katowice, Poland Background: Management of geriatric patients would be simplified if a universally accepted definition of frailty for clinical use was defined. Among definitions of frailty, Fried frailty phenotype criteria constitute a common reference frame for many geriatric studies. However, this reference frame has been tested primarily in elderly patients presenting with relatively good health status. Objective: The aim of this article was to assess the usefulness and limitations of Fried frailty phenotype criteria in geriatric inpatients, characterized by comorbidity and functional impairments, and to estimate the frailty phenotype prevalence in this group. Patients and methods: Five hundred consecutive patients of the university hospital subacute geriatric ward, aged 79.0±8.4 years (67% women and 33% men, participated in this cross-sectional study. Comprehensive geriatric assessment and Fried frailty phenotype component evaluation were performed in all patients. Results: Multimorbidity (6.0±2.8 diseases characterized our study group, with a wide range of clinical conditions and functional states (Barthel Index of Activities of Daily Living 72.2±28.2 and Mini-Mental State Examination 23.6±7.1 scores. All five Fried frailty components were assessed in 65% of patients (95% confidence interval [CI] =60.8–69.2 (diagnostic group. One or more components were not feasible to be assessed in 35% of the remaining patients (nondiagnostic group because of lack of past patient’s body mass control and/or cognitive or physical impairment. Patients from the nondiagnostic group, as compared to patients from the diagnostic group, presented with more advanced age, higher prevalence of dementia, lower prevalence of hypertension, lower systolic and diastolic blood pressure, body mass index, Mini

  6. Modifying toxicokinetics with antidotes.

    Science.gov (United States)

    Baud, F J; Borron, S W; Bismuth, C

    1995-12-01

    Five approaches may be described through which antidotes can modify toxicokinetics: (1) Decreased bioavailability of the toxins; (2) Cellular redistribution of the toxin in the organism; (3) Promotion of elimination in an unchanged form; (4) Slowing of metabolic activation pathways; (5) Acceleration of metabolic deactivation pathways. However, the ability to modify toxicokinetics with a new treatment, while demonstrating an understanding of the mechanism of action, must never be construed to be, in and of itself, the goal of therapy. The ultimate evaluation of an antidote modifying toxicokinetics is strictly clinical.

  7. Detection of mutually exclusive mosaicism in a girl with genotype-phenotype discrepancies.

    Science.gov (United States)

    Luo, Minjie; Mulchandani, Surabhi; Dubbs, Holly A; Swarr, Daniel; Pyle, Louise; Zackai, Elaine H; Spinner, Nancy B; Conlin, Laura K

    2015-12-01

    Discordance between clinical phenotype and genotype has multiple causes, including mosaicism. Phenotypes can be modified due to tissue distribution, or the presence of multiple abnormal cell lines with different genomic contributions. We have studied a 20-month-old female whose main phenotypes were failure to thrive, developmental delay, and patchy skin pigmentation. Initial chromosome and SNP microarray analysis of her blood revealed a non-mosaic ∼24 Mb duplication of 15q25.1q26.3 resulting from the unbalanced translocation of terminal 15q to the short arm of chromosome 15. The most common feature associated with distal trisomy 15q is prenatal and postnatal overgrowth, which was not consistent with this patient's phenotype. The phenotypic discordance, in combination with the patchy skin pigmentation, suggested the presence of mosaicism. Further analysis of skin biopsies from both hyper- and hypopigmented regions confirmed the presence of an additional cell line with the short arm of chromosome X deleted and replaced by the entire long arm of chromosome 15. The Xp deletion, consistent with a variant Turner Syndrome diagnosis, better explained the patient's phenotype. Parental studies revealed that the alterations in both cell lines were de novo and the duplicated distal 15q and the deleted Xp were from different parental origins, suggesting a mitotic event. The possible mechanism for the occurrence of two mutually exclusive structural rearrangements with both involving the long arm of chromosome 15 is discussed.

  8. Invasive ecosystem engineer selects for different phenotypes of an associated native species.

    Science.gov (United States)

    Wright, Jeffrey T; Gribben, Paul E; Byers, James E; Monro, Keyne

    2012-06-01

    Invasive habitat-forming ecosystem engineers modify the abiotic environment and thus represent a major perturbation to many ecosystems. Because native species often persist in these invaded habitats but have no shared history with the ecosystem engineer, the engineer may impose novel selective pressure on native species. In this study, we used a phenotypic selection framework to determine whether an invasive habitat-forming ecosystem engineer (the seaweed Caulerpa taxifolia) selects for different phenotypes of a common co-occurring native species (the bivalve Anadara trapezia). Compared to unvegetated habitat, Caulerpa habitat has lower water flow, lower dissolved oxygen, and sediments are more silty and anoxic. We determined the performance consequences of variation in key functional traits that may be affected by these abiotic changes (shell morphology, gill mass, and palp mass) for Anadara transplanted into Caulerpa and unvegetated habitat. Both linear and nonlinear performance gradients in Anadara differed between habitats, and these gradients were stronger in Caulerpa compared to unvegetated sediment. Moreover, in Caulerpa alternate phenotypes performed well, and these phenotypes were different from the dominant phenotype in unvegetated sediment. By demonstrating that phenotype-performance gradients differ between habitats, we have highlighted a role for Caulerpa as an agent of selection on native species.

  9. Rethinking phenotypic plasticity and its consequences for individuals, populations and species.

    Science.gov (United States)

    Forsman, A

    2015-10-01

    Much research has been devoted to identify the conditions under which selection favours flexible individuals or genotypes that are able to modify their growth, development and behaviour in response to environmental cues, to unravel the mechanisms of plasticity and to explore its influence on patterns of diversity among individuals, populations and species. The consequences of developmental plasticity and phenotypic flexibility for the performance and ecological success of populations and species have attracted a comparatively limited but currently growing interest. Here, I re-emphasize that an increased understanding of the roles of plasticity in these contexts requires a 'whole organism' (rather than 'single trait') approach, taking into consideration that organisms are integrated complex phenotypes. I further argue that plasticity and genetic polymorphism should be analysed and discussed within a common framework. I summarize predictions from theory on how phenotypic variation stemming from developmental plasticity and phenotypic flexibility may affect different aspects of population-level performance. I argue that it is important to distinguish between effects associated with greater interindividual phenotypic variation resulting from plasticity, and effects mediated by variation among individuals in the capacity to express plasticity and flexibility as such. Finally, I claim that rigorous testing of predictions requires methods that allow for quantifying and comparing whole organism plasticity, as well as the ability to experimentally manipulate the level of and capacity for developmental plasticity and phenotypic flexibility independent of genetic variation.

  10. Multi-dimensional discovery of biomarker and phenotype complexes

    Directory of Open Access Journals (Sweden)

    Huang Kun

    2010-10-01

    Full Text Available Abstract Background Given the rapid growth of translational research and personalized healthcare paradigms, the ability to relate and reason upon networks of bio-molecular and phenotypic variables at various levels of granularity in order to diagnose, stage and plan treatments for disease states is highly desirable. Numerous techniques exist that can be used to develop networks of co-expressed or otherwise related genes and clinical features. Such techniques can also be used to create formalized knowledge collections based upon the information incumbent to ontologies and domain literature. However, reports of integrative approaches that bridge such networks to create systems-level models of disease or wellness are notably lacking in the contemporary literature. Results In response to the preceding gap in knowledge and practice, we report upon a prototypical series of experiments that utilize multi-modal approaches to network induction. These experiments are intended to elicit meaningful and significant biomarker-phenotype complexes spanning multiple levels of granularity. This work has been performed in the experimental context of a large-scale clinical and basic science data repository maintained by the National Cancer Institute (NCI funded Chronic Lymphocytic Leukemia Research Consortium. Conclusions Our results indicate that it is computationally tractable to link orthogonal networks of genes, clinical features, and conceptual knowledge to create multi-dimensional models of interrelated biomarkers and phenotypes. Further, our results indicate that such systems-level models contain interrelated bio-molecular and clinical markers capable of supporting hypothesis discovery and testing. Based on such findings, we propose a conceptual model intended to inform the cross-linkage of the results of such methods. This model has as its aim the identification of novel and knowledge-anchored biomarker-phenotype complexes.

  11. Thermodynamics in Modified Gravity Theories

    CERN Document Server

    Bamba, Kazuharu; Tsujikawa, Shinji

    2011-01-01

    We demonstrate that there does exist an equilibrium description of thermodynamics on the apparent horizon in the expanding cosmological background for a wide class of modified gravity theories with the Lagrangian density $f(R, \\phi, X)$, where $R$ is the Ricci scalar and $X$ is the kinetic energy of a scalar field $\\phi$. This comes from a suitable definition of an energy momentum tensor of the "dark" component obeying the local energy conservation law in the Jordan frame. It is shown that the equilibrium description in terms of the horizon entropy $S$ is convenient because it takes into account the contribution of the horizon entropy $\\hat{S}$ in non-equilibrium thermodynamics as well as an entropy production term.

  12. Minimal parameterizations for modified gravity

    CERN Document Server

    Scott, Ali Narimani Douglas

    2013-01-01

    The increasing precision of cosmological data provides us with an opportunity to test general relativity (GR) on the largest accessible scales. Parameterizing modified gravity models facilitates the systematic testing of the predictions of GR, and gives a framework for detecting possible deviations from it. Several different parameterizations have already been suggested, some linked to classifications of theories, and others more empirically motivated. Here we describe a particular new approach which casts modifications to gravity through two free functions of time and scale, which are directly linked to the field equations, but also easy to confront with observational data. We compare our approach with other existing methods of parameterizing modied gravity, specifically the parameterized post-Friedmann approach and the older method using the parameter set $\\{\\mu,\\gamma\\}$. We explain the connection between our parameters and the physics that is most important for generating cosmic microwave background aniso...

  13. The "Goldilocks Effect" in Cystic Fibrosis: identification of a lung phenotype in the cftr knockout and heterozygous mouse

    OpenAIRE

    Bates Jason HT; Lundblad Lennart KA; Craig Cohen J; Levitzky Michael; Larson Janet E

    2004-01-01

    Abstract Background Cystic Fibrosis is a pleiotropic disease in humans with primary morbidity and mortality associated with a lung disease phenotype. However, knockout in the mouse of cftr, the gene whose mutant alleles are responsible for cystic fibrosis, has previously failed to produce a readily, quantifiable lung phenotype. Results Using measurements of pulmonary mechanics, a definitive lung phenotype was demonstrated in the cftr-/- mouse. Lungs showed decreased compliance and increased a...

  14. Investigation of a background suppression transimpedance amplifier for photovoltaic detectors

    Science.gov (United States)

    Metzger, Ferdinand J., Jr.

    1992-12-01

    The current generation of transimpedance amplifier based detector systems are limited by opamp saturation when operating at a high gain or in the presence of a large background signal. To eliminate saturation, an amplifier that is frequency dependent is developed. Additionally, the noise sources in the conventional transimpedance amplifier and photovoltaic detector are quantified for comparison to any modified circuit. Initial results indicate that the frequency dependent detector system is a viable system, however, further development is required. Further research of this technology is expected to support future infrared and long range detection applications.

  15. Kinetics of spontaneous baryogenesis in non-stationary background

    CERN Document Server

    Arbuzova, Elena; Novikov, Victor

    2016-01-01

    Generation of the cosmological baryon asymmetry in frameworks of spontaneous baryogenesis is studied in detail. It is shown that the relation between baryonic chemical potential and the time derivative of the (pseudo)Goldstone field essentially depends upon the representation chosen for the fermionic fields with non-zero baryonic number (quarks). Kinetic equation is modified and numerically solved in equilibrium for the case of time dependent external background or finite integration time to be applicable to the case when energy conservation law is formally violated.

  16. Kinetics of spontaneous baryogenesis in non-stationary background

    Directory of Open Access Journals (Sweden)

    Arbuzova Elena

    2016-01-01

    Full Text Available Generation of the cosmological baryon asymmetry in frameworks of spontaneous baryogenesis is studied in detail. It is shown that the relation between baryonic chemical potential and the time derivative of the (pseudoGoldstone field essentially depends upon the representation chosen for the fermionic fields with non-zero baryonic number (quarks. Kinetic equation is modified and numerically solved in equilibrium for the case of time dependent external background or finite integration time to be applicable to the case when energy conservation law is formally violated.

  17. Multipurpose background for standardization in medical photography.

    Science.gov (United States)

    Hallock, G G

    1985-08-01

    A dual photography background system consisting of a quadrilled format on one side and a plain background on the other is described. It is mobile and efficient as a space- and time-saving device for medical photography.

  18. [National Elk Refuge background and operating statement

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This document is a background on National Elk Refuge in Wyoming. Part I is solely background information concerning the physical characteristics, habitat, major...

  19. Efficient α, β-motif finder for identification of phenotype-related functional modules

    Directory of Open Access Journals (Sweden)

    Schmidt Matthew C

    2011-11-01

    Full Text Available Abstract Background Microbial communities in their natural environments exhibit phenotypes that can directly cause particular diseases, convert biomass or wastewater to energy, or degrade various environmental contaminants. Understanding how these communities realize specific phenotypic traits (e.g., carbon fixation, hydrogen production is critical for addressing health, bioremediation, or bioenergy problems. Results In this paper, we describe a graph-theoretical method for in silico prediction of the cellular subsystems that are related to the expression of a target phenotype. The proposed (α, β-motif finder approach allows for identification of these phenotype-related subsystems that, in addition to metabolic subsystems, could include their regulators, sensors, transporters, and even uncharacterized proteins. By comparing dozens of genome-scale networks of functionally associated proteins, our method efficiently identifies those statistically significant functional modules that are in at least α networks of phenotype-expressing organisms but appear in no more than β networks of organisms that do not exhibit the target phenotype. It has been shown via various experiments that the enumerated modules are indeed related to phenotype-expression when tested with different target phenotypes like hydrogen production, motility, aerobic respiration, and acid-tolerance. Conclusion Thus, we have proposed a methodology that can identify potential statistically significant phenotype-related functional modules. The functional module is modeled as an (α, β-clique, where α and β are two criteria introduced in this work. We also propose a novel network model, called the two-typed, divided network. The new network model and the criteria make the problem tractable even while very large networks are being compared. The code can be downloaded from http://www.freescience.org/cs/ABClique/

  20. POLYCAPROLACTAM MODIFIED BY POLYBENZIMIDAZOLE

    Institute of Scientific and Technical Information of China (English)

    YANG Guisheng; LU Fengcai

    1990-01-01

    Three polycaprolactam samples modified by 0.05 - 0.50% polybenzimidazole (PBI) by weight were prepared. Their structure and mechanical properties were characterized by means of FT- IR, SEM, DTA,density tensile,impact and viscoelastic method. PBI delayed the superimposed polymerization-crystallization process of the activated anionic polymerization of caprolactam. The monomer casting (MC) nylons modified by PBI had lower crystallinities,lower Tg and more nearly perfect spherulites than MCnylon itself, and showed a typical toughening effect.

  1. Phenotyping: targeting genotype's rich cousin for diagnosis.

    Science.gov (United States)

    Baynam, Gareth; Walters, Mark; Claes, Peter; Kung, Stefanie; LeSouef, Peter; Dawkins, Hugh; Bellgard, Matthew; Girdea, Marta; Brudno, Michael; Robinson, Peter; Zankl, Andreas; Groza, Tudor; Gillett, David; Goldblatt, Jack

    2015-04-01

    There are many current and evolving tools to assist clinicians in their daily work of phenotyping. In medicine, the term 'phenotype' is usually taken to mean some deviation from normal morphology, physiology and behaviour. It is ascertained via history, examination and investigations, and a primary aim is diagnosis. Therefore, doctors are, by necessity, expert 'phenotypers'. There is an inherent and partially realised power in phenotypic information that when harnessed can improve patient care. Furthermore, phenotyping developments are increasingly important in an era of rapid advances in genomic technology. Fortunately, there is an expanding network of phenotyping tools that are poised for clinical translation. These tools will preferentially be implemented to mirror clinical workflows and to integrate with advances in genomic and information-sharing technologies. This will synergise with and augment the clinical acumen of medical practitioners. We outline key enablers of the ascertainment, integration and interrogation of clinical phenotype by using genetic diseases, particularly rare ones, as a theme. Successes from the test bed or rare diseases will support approaches to common disease.

  2. Evolution of molecular phenotypes under stabilizing selection

    Science.gov (United States)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes.

  3. 16 CFR 1101.1 - General background.

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false General background. 1101.1 Section 1101.1 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS INFORMATION DISCLOSURE UNDER SECTION 6(b) OF THE CONSUMER PRODUCT SAFETY ACT Background § 1101.1 General background. (a) Basic purpose. This rule sets...

  4. Backgrounds in Boundary String Field Theory

    CERN Document Server

    Baumgartl, M

    2009-01-01

    We study the role of closed string backgrounds in boundary string field theory. Background independence requires the introduction of dual boundary fields, which are reminiscent of the doubled field formalism. We find a correspondence between closed string backgrounds and collective excitations of open strings described by vertex operators involving dual fields. Renormalization group flow, solutions and stability are discussed in an example.

  5. Annexin A6 modifies muscular dystrophy by mediating sarcolemmal repair.

    Science.gov (United States)

    Swaggart, Kayleigh A; Demonbreun, Alexis R; Vo, Andy H; Swanson, Kaitlin E; Kim, Ellis Y; Fahrenbach, John P; Holley-Cuthrell, Jenan; Eskin, Ascia; Chen, Zugen; Squire, Kevin; Heydemann, Ahlke; Palmer, Abraham A; Nelson, Stanley F; McNally, Elizabeth M

    2014-04-22

    Many monogenic disorders, including the muscular dystrophies, display phenotypic variability despite the same disease-causing mutation. To identify genetic modifiers of muscular dystrophy and its associated cardiomyopathy, we used quantitative trait locus mapping and whole genome sequencing in a mouse model. This approach uncovered a modifier locus on chromosome 11 associated with sarcolemmal membrane damage and heart mass. Whole genome and RNA sequencing identified Anxa6, encoding annexin A6, as a modifier gene. A synonymous variant in exon 11 creates a cryptic splice donor, resulting in a truncated annexin A6 protein called ANXA6N32. Live cell imaging showed that annexin A6 orchestrates a repair zone and cap at the site of membrane disruption. In contrast, ANXA6N32 dramatically disrupted the annexin A6-rich cap and the associated repair zone, permitting membrane leak. Anxa6 is a modifier of muscular dystrophy and membrane repair after injury.

  6. Background Electromagnetic Fields and NRQED Matching: Scalar Case

    CERN Document Server

    Lee, Jong-Wan

    2013-01-01

    The low-energy structure of hadrons can be described systematically using effective field theory, and the parameters of the effective theory can be determined from lattice QCD computations. Recent work, however, points to inconsistencies between the background field method in lattice QCD and effective field theory matching conditions. We show that the background field problem necessitates inclusion of operators related by equations of motion. In the presence of time-dependent electromagnetic fields, for example, such operators modify Green's functions, thereby complicating the isolation of hadronic parameters which enter on-shell scattering amplitudes. The particularly simple case of a scalar hadron coupled to uniform electromagnetic fields is investigated in detail. At the level of the relativistic effective theory, operators related by equations of motion are demonstrated to be innocuous. The same result does not hold in the non-relativistic effective theory, and inconsistencies in matching are resolved by ...

  7. Recursive least squares background prediction of univariate syndromic surveillance data

    Directory of Open Access Journals (Sweden)

    Burkom Howard

    2009-01-01

    Full Text Available Abstract Background Surveillance of univariate syndromic data as a means of potential indicator of developing public health conditions has been used extensively. This paper aims to improve the performance of detecting outbreaks by using a background forecasting algorithm based on the adaptive recursive least squares method combined with a novel treatment of the Day of the Week effect. Methods Previous work by the first author has suggested that univariate recursive least squares analysis of syndromic data can be used to characterize the background upon which a prediction and detection component of a biosurvellance system may be built. An adaptive implementation is used to deal with data non-stationarity. In this paper we develop and implement the RLS method for background estimation of univariate data. The distinctly dissimilar distribution of data for different days of the week, however, can affect filter implementations adversely, and so a novel procedure based on linear transformations of the sorted values of the daily counts is introduced. Seven-days ahead daily predicted counts are used as background estimates. A signal injection procedure is used to examine the integrated algorithm's ability to detect synthetic anomalies in real syndromic time series. We compare the method to a baseline CDC forecasting algorithm known as the W2 method. Results We present detection results in the form of Receiver Operating Characteristic curve values for four different injected signal to noise ratios using 16 sets of syndromic data. We find improvements in the false alarm probabilities when compared to the baseline W2 background forecasts. Conclusion The current paper introduces a prediction approach for city-level biosurveillance data streams such as time series of outpatient clinic visits and sales of over-the-counter remedies. This approach uses RLS filters modified by a correction for the weekly patterns often seen in these data series, and a threshold

  8. Genetics of human sleep behavioral phenotypes.

    Science.gov (United States)

    Hsu, Pei-Ken; Ptáček, Louis J; Fu, Ying-Hui

    2015-01-01

    Quality sleep is critical for daily functions of human beings and thus the timing and duration of sleep are tightly controlled. However, rare genetic variants affecting sleep regulatory mechanisms can result in sleep phenotypes of extremely deviated sleep/wake onset time or duration. Using genetic analyses in families with multiple members expressing particular sleep phenotypes, these sleep-associated genetic variants can be identified. Deciphering the nature of these genetic variants using animal models or biochemical methods helps further our understanding of sleep processes. In this chapter, we describe the methods for studying genetics of human sleep behavioral phenotypes.

  9. Modifying Factors of Cystic Fibrosis Disease: Residual Chloride Secrefion, Genefic Background and Epigenetics

    NARCIS (Netherlands)

    I. Bronsveld (Inez)

    2000-01-01

    textabstractCystic fibrosis (CF) is an autosomal recessive disease caused by genetic lesions in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This CFTR gene was cloned in 1989,1-3 and located to the long arm of chromosome 7 (7q3L2). lt encodes the CFTR protein that functions a

  10. Neurobehavioral phenotype of Klinefelter syndrome.

    Science.gov (United States)

    Geschwind, D H; Boone, K B; Miller, B L; Swerdloff, R S

    2000-01-01

    ; Geschwind et al., 1998]. Furthermore, the interaction of genetic factors and hormonal influences in the cognitive phenotypes described remains an unexplored area for future investigation. MRDD Research Reviews 2000;6:117-124.

  11. Metabolic phenotype of bladder cancer.

    Science.gov (United States)

    Massari, Francesco; Ciccarese, Chiara; Santoni, Matteo; Iacovelli, Roberto; Mazzucchelli, Roberta; Piva, Francesco; Scarpelli, Marina; Berardi, Rossana; Tortora, Giampaolo; Lopez-Beltran, Antonio; Cheng, Liang; Montironi, Rodolfo

    2016-04-01

    serine hydroxymethyltransferase-2 (SHMT2), resulting in an increased glycine and purine ring of nucleotides synthesis, thus supporting cells proliferation. A deep understanding of the metabolic phenotype of bladder cancer will provide novel opportunities for targeted therapeutic strategies.

  12. The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data.

    Science.gov (United States)

    Smith, Cynthia L; Eppig, Janan T

    2012-10-01

    The Mammalian Phenotype Ontology (MP) is a structured vocabulary for describing mammalian phenotypes and serves as a critical tool for efficient annotation and comprehensive retrieval of phenotype data. Importantly, the ontology contains broad and specific terms, facilitating annotation of data from initial observations or screens and detailed data from subsequent experimental research. Using the ontology structure, data are retrieved inclusively, i.e., data annotated to chosen terms and to terms subordinate in the hierarchy. Thus, searching for "abnormal craniofacial morphology" also returns annotations to "megacephaly" and "microcephaly," more specific terms in the hierarchy path. The development and refinement of the MP is ongoing, with new terms and modifications to its organization undergoing continuous assessment as users and expert reviewers propose expansions and revisions. A wealth of phenotype data on mouse mutations and variants annotated to the MP already exists in the Mouse Genome Informatics database. These data, along with data curated to the MP by many mouse mutagenesis programs and mouse repositories, provide a platform for comparative analyses and correlative discoveries. The MP provides a standard underpinning to mouse phenotype descriptions for existing and future experimental and large-scale phenotyping projects. In this review we describe the MP as it presently exists, its application to phenotype annotations, the relationship of the MP to other ontologies, and the integration of the MP within large-scale phenotyping projects. Finally we discuss future application of the MP in providing standard descriptors of the phenotype pipeline test results from the International Mouse Phenotype Consortium projects.

  13. The multi-systemic nature of diabetes mellitus: Genotype or phenotype?

    Directory of Open Access Journals (Sweden)

    Graham Wilfred Ewing

    2010-01-01

    Full Text Available Background: This article discusses factors which materially influence the diagnosis, prevention and treatment of diabetes mellitus but which may be overlooked by the prevailing biomedical paradigm. That cognition can be mathematically linked to the function of the autonomic nervous system and physiological systems casts new light upon the mechanisms responsible for homeostasis and origins of disease. In particular, it highlights the limitations of the reductionist biomedical approach which considers mainly the biochemistry of single pathologies rather than considering the neural mechanisms which regulate the function of physiological systems, and inherent visceral organs; and which are subsequently manifest as biochemistries of varying degrees of complexity and severity. As a consequence, histopathological tests are fraught with inherent limitations and many categories of drugs are significantly ineffective. Aims: Such limitations may be explained if disease (in particular diabetes mellitus has multiple origins, is multi-systemic in nature and, depending upon the characteristics of each pathology, is influenced by genotype and/or phenotype. Results:This article highlights the influence of factors which are not yet considered re. the aetiology of diabetes mellitus e.g. the influence of light and sensory input upon the stability of the autonomic nervous system; the influence of raised plasma viscosity upon rates of reaction; the influence of viruses and/or of modified live viruses given in vaccinations; systemic instability, in particular the adverse influence of drinks and lack of exercise upon the body′s prevailing pH and its subsequent influence upon levels of magnesium and other essential trace elements. Conclusions: This application of the top-down systems biology approach may provide a plausible and inclusive explanation for the nature and occurrence of diabetes mellitus.

  14. The multi-systemic nature of diabetes mellitus: Genotype or phenotype?

    Directory of Open Access Journals (Sweden)

    Graham Wilfred Ewing

    2010-10-01

    Full Text Available Background: This article discusses factors which materially influence the diagnosis, prevention and treatment of diabetes mellitus but which may be overlooked by the prevailing biomedical paradigm. That cognition can be mathematically linked to the function of the autonomic nervous system and physiological systems casts new light upon the mechanisms responsible for homeostasis and origins of disease. In particular, it highlights the limitations of the reductionist biomedical approach which considers mainly the biochemistry of single pathologies rather than considering the neural mechanisms which regulate the function of physiological systems, and inherent visceral organs; and which are subsequently manifest as biochemistries of varying degrees of complexity and severity. As a consequence, histopathological tests are fraught with inherent limitations and many categories of drugs are significantly ineffective. Aims: Such limitations may be explained if disease (in particular diabetes mellitus has multiple origins, is multi-systemic in nature and, depending upon the characteristics of each pathology, is influenced by genotype and/or phenotype. Results: This article highlights the influence of factors which are not yet considered re. the aetiology of diabetes mellitus e.g. the influence of light and sensory input upon the stability of the autonomic nervous system; the influence of raised plasma viscosity upon rates of reaction; the influence of viruses and/or of modified live viruses given in vaccinations; systemic instability, in particular the adverse influence of drinks and lack of exercise upon the body’s prevailing pH and its subsequent influence upon levels of magnesium and other essential trace elements. Conclusions: This application of the top-down systems biology approach may provide a plausible and inclusive explanation for the nature and occurrence of diabetes mellitus.

  15. Highly efficient transduction of human plasmacytoid dendritic cells without phenotypic and functional maturation

    Directory of Open Access Journals (Sweden)

    Plumas Joel

    2009-01-01

    Full Text Available Abstract Background Gene modified dendritic cells (DC are able to modulate DC functions and induce therapeutic immunity or tolerance in an antigen-specific manner. Among the different DC subsets, plasmacytoid DC (pDC are well known for their ability to recognize and respond to a variety of viruses by secreting high levels of type I interferon. Methods We analyzed here, the transduction efficiency of a pDC cell line, GEN2.2, and of pDC derived from CD34+ progenitors, using lentiviral vectors (LV pseudotyped with different envelope glycoproteins such as the vesicular stomatitis virus envelope (VSVG, the gibbon ape leukaemia virus envelope (GaLV or the feline endogenous virus envelope (RD114. At the same time, we evaluated transgene expression (E-GFP reporter gene under the control of different promoters. Results We found that efficient gene transfer into pDC can be achieved with VSVG-pseudotyped lentiviral vectors (LV under the control of phoshoglycerate kinase (PGK and elongation factor-1 (EF1α promoters (28% to 90% of E-GFP+ cells, respectively in the absence of phenotypic and functional maturation. Surprisingly, promoters (desmin or synthetic C5–12 described as muscle-specific and which drive gene expression in single strand AAV vectors in gene therapy protocols were very highly active in pDC using VSVG-LV. Conclusion Taken together, our results indicate that LV vectors can serve to design pDC-based vaccines in humans, and they are also useful in vitro to evaluate the immunogenicity of the vector preparations, and the specificity and safety of given promoters used in gene therapy protocols.

  16. The proton pump inhibitor lansoprazole improves the skeletal phenotype in dystrophin deficient mdx mice.

    Directory of Open Access Journals (Sweden)

    Arpana Sali

    Full Text Available BACKGROUND: In Duchenne muscular dystrophy (DMD, loss of the membrane stabilizing protein dystrophin results in myofiber damage. Microinjury to dystrophic myofibers also causes secondary imbalances in sarcolemmic ion permeability and resting membrane potential, which modifies excitation-contraction coupling and increases proinflammatory/apoptotic signaling cascades. Although glucocorticoids remain the standard of care for the treatment of DMD, there is a need to investigate the efficacy of other pharmacological agents targeting the involvement of imbalances in ion flux on dystrophic pathology. METHODOLOGY/PRINCIPAL FINDINGS: We designed a preclinical trial to investigate the effects of lansoprazole (LANZO administration, a proton pump inhibitor, on the dystrophic muscle phenotype in dystrophin deficient (mdx mice. Eight to ten week-old female mice were assigned to one of four treatment groups (n = 12 per group: (1 vehicle control; (2 5 mg/kg/day LANZO; (3 5 mg/kg/day prednisolone; and (4 combined treatment of 5 mg/kg/day prednisolone (PRED and 5 mg/kg/day LANZO. Treatment was administered orally 5 d/wk for 3 months. At the end of the study, behavioral (Digiscan and functional outcomes (grip strength and Rotarod were assessed prior to sacrifice. After sacrifice, body, tissue and organ masses, muscle histology, in vitro muscle force, and creatine kinase levels were measured. Mice in the combined treatment groups displayed significant reductions in the number of degenerating muscle fibers and number of inflammatory foci per muscle field relative to vehicle control. Additionally, mice in the combined treatment group displayed less of a decline in normalized forelimb and hindlimb grip strength and declines in in vitro EDL force after repeated eccentric contractions. CONCLUSIONS/SIGNIFICANCE: Together our findings suggest that combined treatment of LANZO and prednisolone attenuates some components of dystrophic pathology in mdx mice. Our findings

  17. Phenotyping animal models of diabetic neuropathy

    DEFF Research Database (Denmark)

    Biessels, G J; Bril, V; Calcutt, N A

    2014-01-01

    NIDDK, JDRF, and the Diabetic Neuropathy Study Group of EASD sponsored a meeting to explore the current status of animal models of diabetic peripheral neuropathy. The goal of the workshop was to develop a set of consensus criteria for the phenotyping of rodent models of diabetic neuropathy...... with a discussion on the merits and limitations of a unified approach to phenotyping rodent models of diabetic neuropathy and a consensus formed on the definition of the minimum criteria required for establishing the presence of the disease. A neuropathy phenotype in rodents was defined as the presence....... The discussion was divided into five areas: (1) status of commonly used rodent models of diabetes, (2) nerve structure, (3) electrophysiological assessments of nerve function, (4) behavioral assessments of nerve function, and (5) the role of biomarkers in disease phenotyping. Participants discussed the current...

  18. PhenoBlocks: Phenotype Comparison Visualizations.

    Science.gov (United States)

    Glueck, Michael; Hamilton, Peter; Chevalier, Fanny; Breslav, Simon; Khan, Azam; Wigdor, Daniel; Brudno, Michael

    2016-01-01

    The differential diagnosis of hereditary disorders is a challenging task for clinicians due to the heterogeneity of phenotypes that can be observed in patients. Existing clinical tools are often text-based and do not emphasize consistency, completeness, or granularity of phenotype reporting. This can impede clinical diagnosis and limit their utility to genetics researchers. Herein, we present PhenoBlocks, a novel visual analytics tool that supports the comparison of phenotypes between patients, or between a patient and the hallmark features of a disorder. An informal evaluation of PhenoBlocks with expert clinicians suggested that the visualization effectively guides the process of differential diagnosis and could reinforce the importance of complete, granular phenotypic reporting.

  19. Counsel the genotype, treat the phenotype

    NARCIS (Netherlands)

    van der Zwaag, Paul A.; van Tintelen, J. Peter

    2011-01-01

    This editorial refers to 'Novel correlations between the genotype and the phenotype of hypertrophic and dilated cardiomyopathy: results from the German Competence Network Heart Failure' by S. Waldmuller et al., published in this issue on pages 1185-1192.

  20. Mining skeletal phenotype descriptions from scientific literature.

    Directory of Open Access Journals (Sweden)

    Tudor Groza

    Full Text Available Phenotype descriptions are important for our understanding of genetics, as they enable the computation and analysis of a varied range of issues related to the genetic and developmental bases of correlated characters. The literature contains a wealth of such phenotype descriptions, usually reported as free-text entries, similar to typical clinical summaries. In this paper, we focus on creating and making available an annotated corpus of skeletal phenotype descriptions. In addition, we present and evaluate a hybrid Machine Learning approach for mining phenotype descriptions from free text. Our hybrid approach uses an ensemble of four classifiers and experiments with several aggregation techniques. The best scoring technique achieves an F-1 score of 71.52%, which is close to the state-of-the-art in other domains, where training data exists in abundance. Finally, we discuss the influence of the features chosen for the model on the overall performance of the method.

  1. Phenotypic Plasticity and Selection: Nonexclusive Mechanisms of Adaptation.

    Science.gov (United States)

    Grenier, S; Barre, P; Litrico, I

    2016-01-01

    Selection and plasticity are two mechanisms that allow the adaptation of a population to a changing environment. Interaction between these nonexclusive mechanisms must be considered if we are to understand population survival. This review discusses the ways in which plasticity and selection can interact, based on a review of the literature on selection and phenotypic plasticity in the evolution of populations. The link between selection and phenotypic plasticity is analysed at the level of the individual. Plasticity can affect an individual's response to selection and so may modify the end result of genetic diversity evolution at population level. Genetic diversity increases the ability of populations or communities to adapt to new environmental conditions. Adaptive plasticity increases individual fitness. However this effect must be viewed from the perspective of the costs of plasticity, although these are not easy to estimate. It is becoming necessary to engage in new experimental research to demonstrate the combined effects of selection and plasticity for adaptation and their consequences on the evolution of genetic diversity.

  2. Genetic variations strongly influence phenotypic outcome in the mouse retina.

    Directory of Open Access Journals (Sweden)

    Austin S Jelcick

    Full Text Available Variation in genetic background can significantly influence the phenotypic outcome of both disease and non-disease associated traits. Additionally, differences in temporal and strain specific gene expression can also contribute to phenotypes in the mammalian retina. This is the first report of microarray based cross-strain analysis of gene expression in the retina investigating genetic background effects. Microarray analyses were performed on retinas from the following mouse strains: C57BL6/J, AKR/J, CAST/EiJ, and NOD.NON-H2(-nb1 at embryonic day 18.5 (E18.5 and postnatal day 30.5 (P30.5. Over 3000 differentially expressed genes were identified between strains and developmental stages. Differential gene expression was confirmed by qRT-PCR, Western blot, and immunohistochemistry. Three major gene networks were identified that function to regulate retinal or photoreceptor development, visual perception, cellular transport, and signal transduction. Many of the genes in these networks are implicated in retinal diseases such as bradyopsia, night-blindness, and cone-rod dystrophy. Our analysis revealed strain specific variations in cone photoreceptor cell patterning and retinal function. This study highlights the substantial impact of genetic background on both development and function of the retina and the level of gene expression differences tolerated for normal retinal function. These strain specific genetic variations may also be present in other tissues. In addition, this study will provide valuable insight for the development of more accurate models for human retinal diseases.

  3. Modified blank ammunition injuries.

    Science.gov (United States)

    Ogunc, Gokhan I; Ozer, M Tahir; Coskun, Kagan; Uzar, Ali Ihsan

    2009-12-15

    Blank firing weapons are designed only for discharging blank ammunition cartridges. Because they are cost-effective, are easily accessible and can be modified to live firearms plus their unclear legal situation in Turkish Law makes them very popular in Turkey. 2004 through 2008, a total of 1115 modified blank weapons were seized in Turkey. Blank firing weapons are easily modified by owners, making them suitable for discharging live firearm ammunition or modified blank ammunitions. Two common methods are used for modification of blank weapons. After the modification, these weapons can discharge the live ammunition. However, due to compositional durability problems with these types of weapons; the main trend is to use the modified blank ammunitions rather than live firearm ammunition fired from modified blank firing weapons. In this study, two types of modified blank weapons and two types of modified blank cartridges were tested on three different target models. Each of the models' shooting side was coated with 1.3+/-2 mm thickness chrome tanned cowhide as a skin simulant. The first model was only coated with skin simulant. The second model was coated with skin simulant and 100% cotton police shirt. The third model was coated with skin simulant and jean denim. After the literature evaluation four high risky anatomic locations (the neck area; the eyes; the thorax area and inguinal area) were pointed out for the steel and lead projectiles are discharged from the modified blank weapons especially in close range (0-50 cm). The target models were designed for these anatomic locations. For the target models six Transparent Ballistic Candle blocks (TCB) were prepared and divided into two test groups. The first group tests were performed with lead projectiles and second group with steel projectile. The shortest penetration depth (lead projectile: 4.358 cm; steel projectile 8.032 cm) was recorded in the skin simulant and jean denim coated block for both groups. In both groups

  4. Phenotypic impact of genomic structural variation

    DEFF Research Database (Denmark)

    Weischenfeldt, Joachim; Symmons, Orsolya; Spitz, François;

    2013-01-01

    Genomic structural variants have long been implicated in phenotypic diversity and human disease, but dissecting the mechanisms by which they exert their functional impact has proven elusive. Recently however, developments in high-throughput DNA sequencing and chromosomal engineering technology have...... facilitated the analysis of structural variants in human populations and model systems in unprecedented detail. In this Review, we describe how structural variants can affect molecular and cellular processes, leading to complex organismal phenotypes, including human disease. We further present advances...

  5. Searching for the phenotypes of schizophrenia.

    Science.gov (United States)

    Cromwell, R L; Elkins, I J; McCarthy, M E; O'Neil, T S

    1994-01-01

    Use of clinical diagnosis as the phenotype for genetic study is discussed, and criteria for appropriate alternative phenotypes are presented. Then, recent research on four alternatives is discussed: (a) resistance to interference from an associative prime, (b) reaction time crossover, (c) creativity, and (d) socioeconomic achievement. It is concluded that resistance to interference from an associative prime and reaction time crossover at 3-sec. preparatory interval level are the most promising of these candidates.

  6. Phenotyping of robustness and milk quality

    OpenAIRE

    Berry, D. P.; McParland, S.; Bastin, Catherine; Wall, E.; Gengler, Nicolas; Soyeurt, Hélène

    2013-01-01

    A phenotype describes the outcome of the interacting development between the genotype of an individual and its specific environment throughout life. Animal breeding currently exploits large data sets of phenotypic and pedigree information to estimate the genetic merit of animals. Here we describe rapid, low-cost phenomic tools for dairy cattle. We give particular emphasis to infrared spectroscopy of milk because the necessary spectral data are already routinely available on milk samples from ...

  7. Computer vision and machine learning for robust phenotyping in genome-wide studies

    Science.gov (United States)

    Zhang, Jiaoping; Naik, Hsiang Sing; Assefa, Teshale; Sarkar, Soumik; Reddy, R. V. Chowda; Singh, Arti; Ganapathysubramanian, Baskar; Singh, Asheesh K.

    2017-01-01

    Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems. PMID:28272456

  8. Computer vision and machine learning for robust phenotyping in genome-wide studies.

    Science.gov (United States)

    Zhang, Jiaoping; Naik, Hsiang Sing; Assefa, Teshale; Sarkar, Soumik; Reddy, R V Chowda; Singh, Arti; Ganapathysubramanian, Baskar; Singh, Asheesh K

    2017-03-08

    Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems.

  9. Partial complementarity of the mimetic yellow bar phenotype in Heliconius butterflies.

    Directory of Open Access Journals (Sweden)

    Luana S Maroja

    Full Text Available Heliconius butterflies are an excellent system for understanding the genetic basis of phenotypic change. Here we document surprising diversity in the genetic control of a common phenotype. Two disjunct H. erato populations have each recruited the Cr and/or Sd loci that control similar yellow hindwing patterns, but the alleles involved partially complement one another indicating either multiple origins for the patterning alleles or developmental drift in genetic control of similar patterns. We show that in these H. erato populations cr and sd are epistatically interacting and that the parental origin of alleles can explain phenotypes of backcross individuals. In contrast, mimetic H. melpomene populations with identical phenotypes (H. m. rosina and H. m. amaryllis do not show genetic complementation (F(1s and F(2s are phenotypically identical to parentals. Finally, we report hybrid female inviability in H. m. melpomene × H. m. rosina crosses (previously only female infertility had been reported and presence of standing genetic variation for alternative color alleles at the Yb locus in true breeding H. melpomene melpomene populations (expressed when in a different genomic background that could be an important source of variation for the evolution of novel phenotypes or a result of developmental drift. Although recent work has emphasized the simple genetic control of wing pattern in Heliconius, we show there is underlying complexity in the allelic variation and epistatic interactions between major patterning loci.

  10. Cluster analysis in severe emphysema subjects using phenotype and genotype data: an exploratory investigation

    Directory of Open Access Journals (Sweden)

    Martinez Fernando J

    2010-03-01

    Full Text Available Abstract Background Numerous studies have demonstrated associations between genetic markers and COPD, but results have been inconsistent. One reason may be heterogeneity in disease definition. Unsupervised learning approaches may assist in understanding disease heterogeneity. Methods We selected 31 phenotypic variables and 12 SNPs from five candidate genes in 308 subjects in the National Emphysema Treatment Trial (NETT Genetics Ancillary Study cohort. We used factor analysis to select a subset of phenotypic variables, and then used cluster analysis to identify subtypes of severe emphysema. We examined the phenotypic and genotypic characteristics of each cluster. Results We identified six factors accounting for 75% of the shared variability among our initial phenotypic variables. We selected four phenotypic variables from these factors for cluster analysis: 1 post-bronchodilator FEV1 percent predicted, 2 percent bronchodilator responsiveness, and quantitative CT measurements of 3 apical emphysema and 4 airway wall thickness. K-means cluster analysis revealed four clusters, though separation between clusters was modest: 1 emphysema predominant, 2 bronchodilator responsive, with higher FEV1; 3 discordant, with a lower FEV1 despite less severe emphysema and lower airway wall thickness, and 4 airway predominant. Of the genotypes examined, membership in cluster 1 (emphysema-predominant was associated with TGFB1 SNP rs1800470. Conclusions Cluster analysis may identify meaningful disease subtypes and/or groups of related phenotypic variables even in a highly selected group of severe emphysema subjects, and may be useful for genetic association studies.

  11. Phenotypic consequences of aneuploidy in Arabidopsis thaliana.

    Science.gov (United States)

    Henry, Isabelle M; Dilkes, Brian P; Miller, Eric S; Burkart-Waco, Diana; Comai, Luca

    2010-12-01

    Aneuploid cells are characterized by incomplete chromosome sets. The resulting imbalance in gene dosage has phenotypic consequences that are specific to each karyotype. Even in the case of Down syndrome, the most viable and studied form of human aneuploidy, the mechanisms underlying the connected phenotypes remain mostly unclear. Because of their tolerance to aneuploidy, plants provide a powerful system for a genome-wide investigation of aneuploid syndromes, an approach that is not feasible in animal systems. Indeed, in many plant species, populations of aneuploid individuals can be easily obtained from triploid individuals. We phenotyped a population of Arabidopsis thaliana aneuploid individuals containing 25 different karyotypes. Even in this highly heterogeneous population, we demonstrate that certain traits are strongly associated with the dosage of specific chromosome types and that chromosomal effects can be additive. Further, we identified subtle developmental phenotypes expressed in the diploid progeny of aneuploid parent(s) but not in euploid controls from diploid lineages. These results indicate long-term phenotypic consequences of aneuploidy that can persist after chromosomal balance has been restored. We verified the diploid nature of these individuals by whole-genome sequencing and discuss the possibility that trans-generational phenotypic effects stem from epigenetic modifications passed from aneuploid parents to their diploid progeny.

  12. The Genetics of Phenotypic Plasticity. XIV. Coevolution.

    Science.gov (United States)

    Scheiner, Samuel M; Gomulkiewicz, Richard; Holt, Robert D

    2015-05-01

    Plastic changes in organisms' phenotypes can result from either abiotic or biotic effectors. Biotic effectors create the potential for a coevolutionary dynamic. Through the use of individual-based simulations, we examined the coevolutionary dynamic of two species that are phenotypically plastic. We explored two modes of biotic and abiotic interactions: ecological interactions that determine the form of natural selection and developmental interactions that determine phenotypes. Overall, coevolution had a larger effect on the evolution of phenotypic plasticity than plasticity had on the outcome of coevolution. Effects on the evolution of plasticity were greater when the fitness-maximizing coevolutionary outcomes were antagonistic between the species pair (predator-prey interactions) than when those outcomes were augmenting (competitive or mutualistic). Overall, evolution in the context of biotic interactions reduced selection for plasticity even when trait development was responding to just the abiotic environment. Thus, the evolution of phenotypic plasticity must always be interpreted in the full context of a species' ecology. Our results show how the merging of two theory domains--coevolution and phenotypic plasticity--can deepen our understanding of both and point to new empirical research.

  13. Increased entropy of signal transduction in the cancer metastasis phenotype

    Directory of Open Access Journals (Sweden)

    Teschendorff Andrew E

    2010-07-01

    Full Text Available Abstract Background The statistical study of biological networks has led to important novel biological insights, such as the presence of hubs and hierarchical modularity. There is also a growing interest in studying the statistical properties of networks in the context of cancer genomics. However, relatively little is known as to what network features differ between the cancer and normal cell physiologies, or between different cancer cell phenotypes. Results Based on the observation that frequent genomic alterations underlie a more aggressive cancer phenotype, we asked if such an effect could be detectable as an increase in the randomness of local gene expression patterns. Using a breast cancer gene expression data set and a model network of protein interactions we derive constrained weighted networks defined by a stochastic information flux matrix reflecting expression correlations between interacting proteins. Based on this stochastic matrix we propose and compute an entropy measure that quantifies the degree of randomness in the local pattern of information flux around single genes. By comparing the local entropies in the non-metastatic versus metastatic breast cancer networks, we here show that breast cancers that metastasize are characterised by a small yet significant increase in the degree of randomness of local expression patterns. We validate this result in three additional breast cancer expression data sets and demonstrate that local entropy better characterises the metastatic phenotype than other non-entropy based measures. We show that increases in entropy can be used to identify genes and signalling pathways implicated in breast cancer metastasis and provide examples of de-novo discoveries of gene modules with known roles in apoptosis, immune-mediated tumour suppression, cell-cycle and tumour invasion. Importantly, we also identify a novel gene module within the insulin growth factor signalling pathway, alteration of which may

  14. Infrared-modified Universe

    CERN Document Server

    Piazza, Federico

    2012-01-01

    We consider a Hubble expansion law modified in the infra-red by distance-dependent terms, and attempt to enforce homogeneity upon it. As a warm-up, we re-derive the basic kinematics of a Friedman Robertson Walker universe without using standard general relativistic tools: we describe the expansion with a `Hubble velocity field' rather than with a four dimensional metric. Then we extend this analysis to the modified Hubble expansion and impose a transformation for velocities that makes it identical for all comoving observers, and therefore homogeneous. We derive the modified equation for light ray trajectories and other geometrical properties that are incompatible with the general relativistic description. We speculate that this extended framework could help addressing cosmological problems which are normally explained with accelerating expansions.

  15. Differences in phenotype and disease course in adult and paediatric inflammatory bowel disease

    DEFF Research Database (Denmark)

    Jakobsen, Christian; Bartek, Jiri; Wewer, Anne Vibeke;

    2011-01-01

    Background Few studies have compared phenotype and disease course in children and adults with inflammatory bowel disease (IBD). Aim To compare phenotype, treatment and disease course in children (IBD. Methods Two population-based cohorts comprising paediatric...... or disease course. Cumulative 5-year surgery rates for paediatric and adult patients were 5% and 9% for UC (N.S.) and 18% and 21% for CD (N.S.), respectively. Conclusions Paediatric UC patients had more extensive disease, were more often treated with systemic steroids and AZA, had a higher frequency...

  16. Pathobiology of aging mice and GEM: background strains and experimental design.

    Science.gov (United States)

    Brayton, C F; Treuting, P M; Ward, J M

    2012-01-01

    The use of induced and spontaneous mutant mice and genetically engineered mice (and combinations thereof) to study cancers and other aging phenotypes to advance improved functional human life spans will involve studies of aging mice. Genetic background contributes to pathology phenotypes and to causes of death as well as to longevity. Increased recognition of expected phenotypes, experimental variables that influence phenotypes and research outcomes, and experimental design options and rationales can maximize the utility of genetically engineered mice (GEM) models to translational research on aging. This review aims to provide resources to enhance the design and practice of chronic and longevity studies involving GEM. C57BL6, 129, and FVB/N strains are emphasized because of their widespread use in the generation of knockout, transgenic, and conditional mutant GEM. Resources are included also for pathology of other inbred strain families, including A, AKR, BALB/c, C3H, C57L, C58, CBA, DBA, GR, NOD.scid, SAMP, and SJL/J, and non-inbred mice, including 4WC, AB6F1, Ames dwarf, B6, 129, B6C3F1, BALB/c,129, Het3, nude, SENCAR, and several Swiss stocks. Experimental strategies for long-term cross-sectional and longitudinal studies to assess causes of or contributors to death, disease burden, spectrum of pathology phenotypes, longevity, and functional healthy life spans (health spans) are compared and discussed.

  17. Tip-modified Propellers

    DEFF Research Database (Denmark)

    Andersen, Poul

    1999-01-01

    The paper deals with tip-modified propellers and the methods which, over a period of two decades, have been applied to develop such propellers. The development is driven by the urge to increase the efficiency of propellers and can be seen as analogous to fitting end plates and winglets to aircraft...... wings. The literature on four different designs is reviewed: the end-plate propeller; the two-sided, shifted end-plate propeller; the tip-fin propeller; and the bladelet propeller. The conclusion is that it is indeed possible to design tip-modified propellers that, relative to an optimum conventional...

  18. Extragalactic Background Light: Measurements and Applications

    CERN Document Server

    Cooray, Asantha

    2016-01-01

    This review covers the measurements related to the extragalactic background light (EBL) intensity from gamma-rays to radio in the electromagnetic spectrum over 20 decades in the wavelength. The cosmic microwave background (CMB) remains the best measured spectrum with an accuracy better than 1%. The measurements related to the cosmic optical background (COB), centered at 1 microns, are impacted by the large zodiacal light associated with interplanetary dust in the inner Solar system. The best measurements of COB come from an indirect technique involving Gamma-ray spectra of bright blazars with an absorption feature resulting from pair-production off of COB photons. The cosmic infrared background (CIB) peaking at around 100 microns established an energetically important background with an intensity comparable to the optical background. This discovery paved the path for large aperture far-infrared and sub-millimeter observations resulting in the discovery of dusty, starbursting galaxies. Their role in galaxy for...

  19. Compressive Background Modeling for Foreground Extraction

    Directory of Open Access Journals (Sweden)

    Yong Wang

    2015-01-01

    Full Text Available Robust and efficient foreground extraction is a crucial topic in many computer vision applications. In this paper, we propose an accurate and computationally efficient background subtraction method. The key idea is to reduce the data dimensionality of image frame based on compressive sensing and in the meanwhile apply sparse representation to build the current background by a set of preceding background images. According to greedy iterative optimization, the background image and background subtracted image can be recovered by using a few compressive measurements. The proposed method is validated through multiple challenging video sequences. Experimental results demonstrate the fact that the performance of our approach is comparable to those of existing classical background subtraction techniques.

  20. Cognitive abilities, sociocultural background and academic achievement

    OpenAIRE

    Diniz, António; Pocinho, Margarida Maria Ferreira Diogo Dias; Almeida,Leandro Silva

    2011-01-01

    The infl uence of students’ sociocultural background on academic achievement is a well established fact. Research also points out that sociocultural background is related to students’ cognitive abilities and these have an effect on their academic achievement. However, the mediator role of cognitive abilities on the relationship between sociocultural background and academic achievement is less well known. A structural equation model that represents these relationships was tested in a sample...

  1. On Cultural Background Knowledge in English Reading

    Institute of Scientific and Technical Information of China (English)

    苏琴; 郭成

    2009-01-01

    Reading comprehension is undoubtedly one of the most important abilities for English learners. This paper firstly makes a brief introduction to the reading theory and cultural background knowledge. Then using schema theory and typical examples, the paper demons~ates the role of cultural background knowledge in reading comprehension. The application of cultural background knowledge inreading practice is proposed as the keys to the improvement of reading comprehension ability.

  2. Gauge theories with non-trivial backgrounds

    CERN Document Server

    Binosi, Daniele

    2014-01-01

    We review our most recent results in formulating gauge theories in the presence of a background field on the basis of symmetry arguments only. In particular we show how one can gain full control over the dependence on the background field of the effective action, and how the so-called background field method emerges naturally from the requirement of invariance under the BRST and antiBRST symmetries.

  3. Genotypic and Phenotypic Analysis of Fasciola Isolates

    Directory of Open Access Journals (Sweden)

    SN Mosavinasab

    2009-07-01

    Full Text Available "nBackground: To identify the fasciolid species by morphometric and molecular methods in Zanjan, north­west of Iran. "nMethods: Adult Fasciola worms (n=584 were obtained from cattle and sheep in Zanjan slaughterhouse in 2007. Living flukes were washed, then worms' images were taken by 3CCD camera and finally apical zone of each worm was obtained. Morphometric values such as body length, body width, body area, body pe­rimeter and the distance between ventral sucker and posterior end of body were obtained using Auto­CAD image analysis software. Total gDNA was extracted from individual flukes by modified phenol-chloroform method. PCR amplification of ITS2 fragment was performed the isolated DNA samples and the amplicons were consequently subjected to RFLP assay and nucleotide sequencing to distinguish be­tween fasciolid species. "nResults: Mean of morphometric values in flukes from sheep was greater than those of cattle. Accordingly, the identified species included 31% F. hepatica-like, 7% F. gigantica-like and 62% intermediate forms. How­ever, ITS2 fragment of 535 amplified specimens, showed no variation at the species-specific nucleo­tide sites 230, 340 and 341. The amplified fragment composed of partial 5.8S sequence (62bp, the com­plete ITS2 sequence (361bp and partial 28S sequence (34bp. The nucleotide contents of ITS2 region were 69 A, 116 T, 81 C and 95 G and the average G+C content was approximately 49%. Comparing of ITS2 sequences with the BLAST GenBank database, also confirmed that all specimens were F. hepatica. "nConclusion: A simple and rapid PCR-RFLP assay can be used for distinguishing between these species.

  4. Detection of fruit by the Cerrado's marmoset (Callithrix penicillata): modeling color signals for different background scenarios and ambient light intensities.

    Science.gov (United States)

    Perini, Eduardo Sosti; Pessoa, Valdir Filgueiras; Pessoa, Daniel Marques de Almeida

    2009-04-01

    Among placental mammals, only primates have trichromatic color vision, however this is not a uniform condition. Under different genetic status, Old World monkeys have routine trichromacy, while New World monkeys show a visual polymorphism, characterized by obligatory male dichromacy. The ecological role of this genetic difference still remains unclear, but some studies show that dichromats and trichromats appear to have different abilities in detecting colored targets against a background of leaves. The Cerrado's marmoset (Callithrix penicillata) is known to forage in brightly illuminated (savanna-like vegetation) and dimly illuminated (forests) environments, exploiting a high amount of dark fruits. Hence, it seems to be a good model for studying the differential advantages enjoyed by each color vision phenotype under natural conditions. Our aim was to verify how the different phenotypes of Cerrado's marmoset detect components of their diet, evaluating the existence of differential phenotype advantages. Under two different light conditions, visual signals of naturally consumed fruits were modeled against different backgrounds scenarios. Even though dichromats and trichromats appear to be equally suited for tasks involving fruit detection, phenotype differential advantages are observed in this marmoset. In many conditions trichromats are predicted to perform better than dichromats, but under low ambient light dichromats manage to outperform trichromats in some scenarios. Phenotypes that carry widely spaced and longer M/L pigments enjoy the most advantage. These differential performances of trichromatic phenotypes, together with overdominance selection, seem to explain the maintenance of the tri-allelic system found in callitrichids.

  5. Biotechnology: Two Decades of Experimentation with Genetically Modified Foods

    Directory of Open Access Journals (Sweden)

    Marjan Ajami

    2016-10-01

    Full Text Available Background and Objective: Over the recent years, genetically modified food in varieties of corn, soybeans, canola and cotton have been introduced to the global market. This study reviews the health and nutritional value of genetically modified foods in the past two decades.Results and Conclusions: Contrary to the present biotechnological claims, transgenic products did not prove to be so flawless, and actually failed to maintain social satisfaction. Genetically modified foods could not gain an increase in the yield potential. Planting natural products and genetically modified products in parallel lines will absolutely result in genetic infection from the side of genetically modified foods. One of the major anxieties of the anti- genetically modified foods activism is the claim that genetically modified crops would alter the consumable parts of the plant quality and safety. Genetically modified foods have shown to have inadequate efficiency and potential adverse effects in both fields of health and biodiversity. This review has presented studies of genetically modified foods performances in the past two decades, and concludes that the wide application and the over generalization of genetically modified foods are not fundamentally recommended.Conflict of interest: Authors declare that there is no conflict of interest.

  6. Modeling Lost-Particle Accelerator Backgrounds in PEP-II Using LPTURTLE

    CERN Document Server

    Fieguth, Theodore; Kozanecki, Witold

    2005-01-01

    Background studies during the design, construction, commissioning, operation and improvement of BaBar and PEP-II have been greatly influenced by results from a program referred to as LPTURTLE (Lost Particle TURTLE a modified version of Decay TURTLE) which was originally conceived for the purpose of studying gas background for SLC. This venerable program is still in use today. We describe its use, capabilities and improvements and refer to current results now being applied to BaBar.

  7. iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum.

    Science.gov (United States)

    Dönitz, Jürgen; Schmitt-Engel, Christian; Grossmann, Daniela; Gerischer, Lizzy; Tech, Maike; Schoppmeier, Michael; Klingler, Martin; Bucher, Gregor

    2015-01-01

    The iBeetle-Base (http://ibeetle-base.uni-goettingen.de) makes available annotations of RNAi phenotypes, which were gathered in a large scale RNAi screen in the red flour beetle Tribolium castaneum (iBeetle screen). In addition, it provides access to sequence information and links for all Tribolium castaneum genes. The iBeetle-Base contains the annotations of phenotypes of several thousands of genes knocked down during embryonic and metamorphic epidermis and muscle development in addition to phenotypes linked to oogenesis and stink gland biology. The phenotypes are described according to the EQM (entity, quality, modifier) system using controlled vocabularies and the Tribolium morphological ontology (TrOn). Furthermore, images linked to the respective annotations are provided. The data are searchable either for specific phenotypes using a complex 'search for morphological defects' or a 'quick search' for gene names and IDs. The red flour beetle Tribolium castaneum has become an important model system for insect functional genetics and is a representative of the most species rich taxon, the Coleoptera, which comprise several devastating pests. It is used for studying insect typical development, the evolution of development and for research on metabolism and pest control. Besides Drosophila, Tribolium is the first insect model organism where large scale unbiased screens have been performed.

  8. The evolution of phenotypic plasticity: genealogy of a debate in genetics.

    Science.gov (United States)

    Nicoglou, Antonine

    2015-04-01

    The paper describes the context and the origin of a particular debate that concerns the evolution of phenotypic plasticity. In 1965, British biologist A. D. Bradshaw proposed a widely cited model intended to explain the evolution of norms of reaction, based on his studies of plant populations. Bradshaw's model went beyond the notion of the "adaptive norm of reaction" discussed before him by Dobzhansky and Schmalhausen by suggesting that "plasticity"--the ability of a phenotype to be modified by the environment--should be genetically determined. To prove Bradshaw's hypothesis, it became necessary for some authors to identify the pressures exerted by natural selection on phenotypic plasticity in particular traits, and thus to model its evolution. In this paper, I contrast two different views, based on quantitative genetic models, proposed in the mid-1980s: Russell Lande and Sara Via's conception of phenotypic plasticity, which assumes that the evolution of plasticity is linked to the evolution of the plastic trait itself, and Samuel Scheiner and Richard Lyman's view, which assumes that the evolution of plasticity is independent from the evolution of the trait. I show how the origin of this specific debate, and different assumptions about the evolution of phenotypic plasticity, depended on Bradshaw's definition of plasticity and the context of quantitative genetics.

  9. Hanford Site background: Part 1, Soil background for nonradioactive analytes. Revision 1, Volume 2

    Energy Technology Data Exchange (ETDEWEB)

    1993-04-01

    Volume two contains the following appendices: Description of soil sampling sites; sampling narrative; raw data soil background; background data analysis; sitewide background soil sampling plan; and use of soil background data for the detection of contamination at waste management unit on the Hanford Site.

  10. Pharmacogenetics of antipsychotic-induced movement disorders as a resource for better understanding Parkinson's disease modifier genes.

    Science.gov (United States)

    Greenbaum, Lior; Lerer, Bernard

    2015-01-01

    Antipsychotic-induced movement disorders are major side effects of antipsychotic drugs among schizophrenia patients, and include antipsychotic-induced parkinsonism (AIP) and tardive dyskinesia (TD). Substantial pharmacogenetic work has been done in this field, and several susceptibility variants have been suggested. In this paper, the genetics of antipsychotic-induced movement disorders is considered in a broader context. We hypothesize that genetic variants that are risk factors for AIP and TD may provide insights into the pathophysiology of motor symptoms in Parkinson's disease (PD). Since loss of dopaminergic stimulation (albeit pharmacological in AIP and degenerative in PD) is shared by the two clinical entities, genes associated with susceptibility to AIP may be modifier genes that influence clinical expression of PD motor sub-phenotypes, such as age at onset, disease severity, or rate of progression. This is due to their possible functional influence on compensatory mechanisms for striatal dopamine loss. Better compensatory potential might be beneficial at the early and later stages of the PD course. AIP vulnerability variants could also be related to latent impairment in the nigrostriatal pathway, affecting its functionality, and leading to subclinical dopaminergic deficits in the striatum. Susceptibility of PD patients to early development of l-DOPA induced dyskinesia (LID) is an additional relevant sub-phenotype. LID might share a common genetic background with TD, with which it shares clinical features. Genetic risk variants may predispose to both phenotypes, exerting a pleiotropic effect. According to this hypothesis, elucidating the genetics of antipsychotic-induced movement disorders may advance our understanding of multiple aspects of PD and it clinical course, rendering this a potentially rewarding field of study.

  11. Pharmacogenetics of antipsychotic-induced movement disorders as a resource for better understanding Parkinson's disease modifier genes

    Directory of Open Access Journals (Sweden)

    Lior eGreenbaum

    2015-02-01

    Full Text Available Antipsychotic-induced movement disorders are major side effects of antipsychotic drugs among schizophrenia patients, and include antipsychotic-induced parkinsonism (AIP and tardive dyskinesia (TD. Substantial pharmacogenetic work has been done in this field, and several susceptibility variants have been suggested. In this paper, the genetics of antipsychotic-induced movement disorders is considered in a broader context. We hypothesize that genetic variants that are risk factors for AIP and TD may provide insights into the pathophysiology of Parkinson's disease (PD. Since loss of dopaminergic stimulation (albeit pharmacological in AIP and degenerative in PD is shared by the two clinical entities, genes associated with susceptibility to AIP may be modifier genes that influence clinical expression of PD sub-phenotypes, such as age at onset, disease severity or rate of progression. This is due to their possible functional influence on compensatory mechanisms for striatal dopamine loss. Better compensatory potential might be beneficial at the early and later stages of the PD course. AIP vulnerability variants may also be related to latent impairment in the nigrostriatal pathway, affecting its functionality, and leading to subclinical dopaminergic deficits in the striatum. Susceptibility of PD patients to early development of L-dopa induced dyskinesia (LID, is an additional relevant sub-phenotype. LID may share a common genetic background with TD, with which it shares clinical features. Genetic risk variants may predispose to both phenotypes, exerting a pleiotropic effect. According to this hypothesis, elucidating the genetics of antipsychotic-induced movement disorders may advance our understanding of multiple aspects of PD and it clinical course, rendering this a potentially rewarding field of study.

  12. Lack of association of TIM3 polymorphisms and allergic phenotypes

    Directory of Open Access Journals (Sweden)

    Laprise Catherine

    2009-06-01

    Full Text Available Abstract Background T-cell immunoglobulin mucin-3 (TIM3 is a TH1-specific type 1 membrane protein that regulates TH1 proliferation and the development of immunological tolerance. TIM3 and its genetic variants have been suggested to play a role in regulating allergic diseases. Polymorphisms in the TIM3 promoter region have been reported to be associated with allergic phenotypes in several populations. The aims of this study were to examine whether genetic variation in the promoter region of TIM3 influenced transcription of the gene and risk for allergic phenotypes. Methods We performed 5' rapid amplification of cDNA ends and reverse transcription-polymerase chain reaction. We screened for polymorphisms in the promoter region. Deletion analysis was used to localize the promoter region of TIM3. Genotyping was performed by TaqMan assays in three asthma/allergy population samples. Results We found two regions with promoter activity in TIM3. One region was from -214 bp to +58 bp and the other from -1.6 kb to -914 bp relative to the transcription start site. None of the single nucleotide polymorphisms (SNPs or haplotypes affected the transcriptional activity in reporter gene assays. No association between the SNPs and any phenotype was observed in the study cohorts. Conclusion Our findings indicate that SNPs and haplotypes in the TIM3 promoter region do not have a functional effect in vitro and are not associated with allergic diseases. These data suggest that polymorphisms in the TIM3 promoter region are unlikely to play an important role in susceptibility to allergic diseases.

  13. Phenotypic insights into ADCY5‐associated disease

    Science.gov (United States)

    Chang, Florence C.F.; Westenberger, Ana; Dale, Russell C.; Smith, Martin; Pall, Hardev S.; Perez‐Dueñas, Belen; Grattan‐Smith, Padraic; Ouvrier, Robert A.; Mahant, Neil; Hanna, Bernadette C.; Hunter, Matthew; Lawson, John A.; Max, Christoph; Sachdev, Rani; Meyer, Esther; Crimmins, Dennis; Pryor, Donald; Morris, John G.L.; Münchau, Alex; Grozeva, Detelina; Carss, Keren J.; Raymond, Lucy; Kurian, Manju A.; Klein, Christine

    2016-01-01

    ABSTRACT Background Adenylyl cyclase 5 (ADCY5) mutations is associated with heterogenous syndromes: familial dyskinesia and facial myokymia; paroxysmal chorea and dystonia; autosomal‐dominant chorea and dystonia; and benign hereditary chorea. We provide detailed clinical data on 7 patients from six new kindreds with mutations in the ADCY5 gene, in order to expand and define the phenotypic spectrum of ADCY5 mutations. Methods In 5 of the 7 patients, followed over a period of 9 to 32 years, ADCY5 was sequenced by Sanger sequencing. The other 2 unrelated patients participated in studies for undiagnosed pediatric hyperkinetic movement disorders and underwent whole‐exome sequencing. Results Five patients had the previously reported p.R418W ADCY5 mutation; we also identified two novel mutations at p.R418G and p.R418Q. All patients presented with motor milestone delay, infantile‐onset action‐induced generalized choreoathetosis, dystonia, or myoclonus, with episodic exacerbations during drowsiness being a characteristic feature. Axial hypotonia, impaired upward saccades, and intellectual disability were variable features. The p.R418G and p.R418Q mutation patients had a milder phenotype. Six of seven patients had mild functional gain with clonazepam or clobazam. One patient had bilateral globus pallidal DBS at the age of 33 with marked reduction in dyskinesia, which resulted in mild functional improvement. Conclusion We further delineate the clinical features of ADCY5 gene mutations and illustrate its wide phenotypic expression. We describe mild improvement after treatment with clonazepam, clobazam, and bilateral pallidal DBS. ADCY5‐associated dyskinesia may be under‐recognized, and its diagnosis has important prognostic, genetic, and therapeutic implications. © 2016 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society PMID:27061943

  14. The Temperature of the Cosmic Microwave Background

    CERN Document Server

    Fixsen, D J

    2009-01-01

    The FIRAS data are independently recalibrated using the WMAP data to obtain a CMB temperature of 2.7260 +/- 0.0013. Measurements of the temperature of the cosmic microwave background are reviewed. The determination from the measurements from the literature is cosmic microwave background temperature of 2.72548 +/- 0.00057 K.

  15. 45 CFR 650.16 - Background rights.

    Science.gov (United States)

    2010-10-01

    ... of the Bayh-Dole Act (35 U.S.C. 202(f)) as implemented by 37 CFR 401.12). ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Background rights. 650.16 Section 650.16 Public... Background rights. The Foundation will acquire rights to a research performer's pre-existing technology...

  16. Multiple Scatters in Single Site Gamma Backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Brodsky, J. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-09-16

    nEXO aims to reduce its gamma backgrounds by taking advantage of the fact that a large number of gammas that would otherwise be backgrounds will undergo multiple compton scattering in the TPC and produce spatially distinct signals. These multi-sited (MS) events can be excluded from the 0νββ search.

  17. Delineating the GRIN1 phenotypic spectrum

    Science.gov (United States)

    Geider, Kirsten; Helbig, Katherine L.; Heyne, Henrike O.; Schütz, Hannah; Hentschel, Julia; Courage, Carolina; Depienne, Christel; Nava, Caroline; Heron, Delphine; Møller, Rikke S.; Hjalgrim, Helle; Lal, Dennis; Neubauer, Bernd A.; Nürnberg, Peter; Thiele, Holger; Kurlemann, Gerhard; Arnold, Georgianne L.; Bhambhani, Vikas; Bartholdi, Deborah; Pedurupillay, Christeen Ramane J.; Misceo, Doriana; Frengen, Eirik; Strømme, Petter; Dlugos, Dennis J.; Doherty, Emily S.; Bijlsma, Emilia K.; Ruivenkamp, Claudia A.; Hoffer, Mariette J.V.; Goldstein, Amy; Rajan, Deepa S.; Narayanan, Vinodh; Ramsey, Keri; Belnap, Newell; Schrauwen, Isabelle; Richholt, Ryan; Koeleman, Bobby P.C.; Sá, Joaquim; Mendonça, Carla; de Kovel, Carolien G.F.; Weckhuysen, Sarah; Hardies, Katia; De Jonghe, Peter; De Meirleir, Linda; Milh, Mathieu; Badens, Catherine; Lebrun, Marine; Busa, Tiffany; Francannet, Christine; Piton, Amélie; Riesch, Erik; Biskup, Saskia; Vogt, Heinrich; Dorn, Thomas; Helbig, Ingo; Michaud, Jacques L.; Laube, Bodo; Syrbe, Steffen

    2016-01-01

    Objective: To determine the phenotypic spectrum caused by mutations in GRIN1 encoding the NMDA receptor subunit GluN1 and to investigate their underlying functional pathophysiology. Methods: We collected molecular and clinical data from several diagnostic and research cohorts. Functional consequences of GRIN1 mutations were investigated in Xenopus laevis oocytes. Results: We identified heterozygous de novo GRIN1 mutations in 14 individuals and reviewed the phenotypes of all 9 previously reported patients. These 23 individuals presented with a distinct phenotype of profound developmental delay, severe intellectual disability with absent speech, muscular hypotonia, hyperkinetic movement disorder, oculogyric crises, cortical blindness, generalized cerebral atrophy, and epilepsy. Mutations cluster within transmembrane segments and result in loss of channel function of varying severity with a dominant-negative effect. In addition, we describe 2 homozygous GRIN1 mutations (1 missense, 1 truncation), each segregating with severe neurodevelopmental phenotypes in consanguineous families. Conclusions: De novo GRIN1 mutations are associated with severe intellectual disability with cortical visual impairment as well as oculomotor and movement disorders being discriminating phenotypic features. Loss of NMDA receptor function appears to be the underlying disease mechanism. The identification of both heterozygous and homozygous mutations blurs the borders of dominant and recessive inheritance of GRIN1-associated disorders. PMID:27164704

  18. Association of alkaline phosphatase phenotypes with arthritides

    Directory of Open Access Journals (Sweden)

    Padmini A

    2004-01-01

    Full Text Available Arthritides, a symmetrical polyarticular disease of the bone are a heterogenous group of disorders in which hereditary and environmental factors in combination with an altered immune response appear to play a causative and pathogenic role in its occurrence. Alkaline phosphatase (ALP is an enzyme found in all tissues, with particularly high concentrations of ALP observed in the liver, bile ducts, placenta, and bone.Alkaline phosphatase is an orthophosphoric monoester phosphohydrolase catalyzing the hydrolysis of organic esters at alkaline pH, indicating that alkaline phosphatase is involved in fundamental biological processes.1 The present study envisages on identifying the specific electromorphic association of alkaline phosphatase with arthritides. Phenotyping of serum samples was carried out by PAGE (Polyacrylamide gel electrophoresis following Davies (19642 protocol on 41 juvenile arthritis, 150 rheumatoid arthritis and 100 osteo arthritis apart from, 25 normal children and 100 adult healthy subjects. Phenotyping of alkaline phosphatase revealed an increase in preponderance of p+ and p++ phenotypes in juvenile, rheumatoid and osteo arthritic patients. However a significant association of these phenotypes was observed only with rheumatoid arthritis condition (c2:17.46. Similarly, a significant increase of p+ phenotypes in female rheumatoid arthritis patients was observed (c2:14.973, suggesting that the decrease in p° (tissue non specific synthesis/secretion of alkaline phosphatase could be associated with decreased mineralization and ossification process in arthritis condition.

  19. Can Bohmian Mechanics Be Made Background Independent?

    CERN Document Server

    Vassallo, Antonio

    2015-01-01

    The paper presents an inquiry into the question regarding the compatibility of Bohmian mechanics, intended as a non-local theory of moving point-like particles, with background independence. This issue is worth being investigated because, if the Bohmian framework has to be of some help in developing new physics, it has to be compatible with the most well-established traits of modern physics, background independence being one of such traits. The paper highlights the fact that the notion of background independence in the context of spacetime physics is slippery and interpretation-laden. It is then suggested that the best-matching framework developed by Julian Barbour might provide a robust enough meaning of background independence. The structure of Bohmian dynamics is evaluated against this framework, reaching some intermediate results that speak in favor of the fact that Bohmian mechanics can be made background independent.

  20. Genetic and Molecular Characterization of Drosophia Brakeless: A Novel Modifier of Merlin Phenotypes

    Science.gov (United States)

    2005-07-01

    Neuroscience, 5: 746-750. Kissil J. L., K. C. Johnson, M. S. Eckman , T. Jacks (2002) Merlin Phosphorylation by p21- activated Kinase 2 and Effects of...fixation conditions. ACKNOWLEDGMENTS Thanks to Dr. Amy Adamson, Dr Paul Steimle, Andrea Durst, Q.C. Po- Figure 3. Effect of permeabilization on enhanced

  1. Phenotypic and functional markers for 1alpha,25-dihydroxyvitamin D(3)-modified regulatory dendritic cells

    DEFF Research Database (Denmark)

    Pedersen, A W; Holmstrøm, K; Jensen, S S;

    2009-01-01

    The clinical use of dendritic cells (DCs) to induce antigen-specific immune tolerance has been hampered by the lack of a widely acknowledged method for generating human regulatory DCs but even more so by the non-existence of reliable markers. Thus, we set out to find reliable markers that can...... CD14 and reduced CD1a on the cell surface. These VD3-treated DCs exert a long-lasting inefficient T cell stimulation and induce T cell hyporesponsiveness with regulatory potential. Importantly, such VD3-treated DCs were readily distinguishable from untreated DCs by low levels of interleukin-23...

  2. New modification of modified bentall procedure (A single centre experience)

    OpenAIRE

    Hussain, Ghulam; Ahmad, Naseem; Ahmad, Sohail; Baig, Mirza Ahmad Raza; Zaheer, Sara; Furkan, Aamir

    2015-01-01

    Background and Objectives: Modified Bentall procedure has become a gold standard in the treatment of combined aortic root and aortic valve diseases. Bleeding is an important predictor of morbidity and mortality after the Bentall operation. Our objective was to evaluate the early outcomes of Modified Button-Bentall procedure with cuff technique for aortic root replacement surgery regarding hemostasis. Methods: A total number of 32 patients who underwent elective Bentall operation from January ...

  3. Background sounds contribute to spectrotemporal plasticity in primary auditory cortex.

    Science.gov (United States)

    Moucha, Raluca; Pandya, Pritesh K; Engineer, Navzer D; Rathbun, Daniel L; Kilgard, Michael P

    2005-05-01

    The mammalian auditory system evolved to extract meaningful information from complex acoustic environments. Spectrotemporal selectivity of auditory neurons provides a potential mechanism to represent natural sounds. Experience-dependent plasticity mechanisms can remodel the spectrotemporal selectivity of neurons in primary auditory cortex (A1). Electrical stimulation of the cholinergic nucleus basalis (NB) enables plasticity in A1 that parallels natural learning and is specific to acoustic features associated with NB activity. In this study, we used NB stimulation to explore how cortical networks reorganize after experience with frequency-modulated (FM) sweeps, and how background stimuli contribute to spectrotemporal plasticity in rat auditory cortex. Pairing an 8-4 kHz FM sweep with NB stimulation 300 times per day for 20 days decreased tone thresholds, frequency selectivity, and response latency of A1 neurons in the region of the tonotopic map activated by the sound. In an attempt to modify neuronal response properties across all of A1 the same NB activation was paired in a second group of rats with five downward FM sweeps, each spanning a different octave. No changes in FM selectivity or receptive field (RF) structure were observed when the neural activation was distributed across the cortical surface. However, the addition of unpaired background sweeps of different rates or direction was sufficient to alter RF characteristics across the tonotopic map in a third group of rats. These results extend earlier observations that cortical neurons can develop stimulus specific plasticity and indicate that background conditions can strongly influence cortical plasticity.

  4. Chiral asymmetry in propagation of soliton defects in crystalline backgrounds

    CERN Document Server

    Arancibia, Adrian

    2015-01-01

    By applying Darboux-Crum transformations to the Lax pair formulation of the Korteweg-de Vries (KdV) equation, we construct new sets of multi-soliton solutions to it as well as to the modified Korteweg-de Vries (mKdV) equation. The obtained solutions exhibit a chiral asymmetry in propagation of different types defects in crystalline backgrounds. We show that the KdV solitons of pulse and compression modulation types, which support bound states in semi-infinite and finite forbidden bands in the spectrum of the perturbed quantum one-gap Lame system, propagate in opposite directions with respect to the asymptotically periodic background. A similar but more complicated picture also appears for the multi-kink-antikink mKdV solitons that propagate with a privileged direction over topologically trivial or topologically nontrivial crystalline background in dependence on position of energy levels of the trapped bound states in spectral gaps of the associated Dirac system. Exotic N=4 nonlinear supersymmetric structure i...

  5. SOME STRANGE FINDINGS: NON - INTERPRETABLE PATTERNS IN MODIFIED HODGE TEST

    Directory of Open Access Journals (Sweden)

    Jayashree

    2013-10-01

    Full Text Available ABSTRACT: Many clinically relevant species of Gram - negative bacilli are often resistant to β - lactam antibiotics even to c arbapenems. According to CLS I guideline 2013, Carbapenemase producers are screened by zone size <21mm to Meropenem or Etrapenem and phenotypically confirmed by Modified Hodge test. The test of Hodge et al was modified by substituting Escherichia coli for penicillin - susceptible Staphy lococcus aureus ATCC 25923, and 10 - μg Imipenem disk for a 10 - U Penicillin disk. While looking for the Carbapenemase producing strains, some astonishing, unexplainable facts were revealed in this study. Meropenem - resistant test strains were screened (zone d iameter in Modified Kirby - Bauer technique<21mm & for phenotypic confirmation of Carbapenemase production, modified Hodge test was performed. Thereafter the test strains were examined for production of Metallo β Lactamase using Imipenem (10μg disk and com bination of Imipenem and EDTA, followed by test for Bacteriocin production. Two Acinetobacter and one Pseudomonas aeruginosa strains were found to produce a Star like outward distortion. They did not produce Metallo β lactamase. Moreover, screening test fo r bacteriocin production was also found to be negative. The strains resistant to Carbapenem antibiotics but nonproducers of metallo β lactamase and/or Bacteriocins, have left behind a head twister for us

  6. PENGARUH BACKGROUND MAHASISWA TERHADAP KINERJA AKADEMIK

    Directory of Open Access Journals (Sweden)

    Trianasari Angkawijaya

    2014-09-01

    Full Text Available Abstract: The Effect of Students’ Background on Academic Performance. This study examines the effect of background variables on the academic performance of accounting students in a private university in Surabaya. The background variables under study included previous academic performance, prior knowledge on accounting, sex, motivation, preparedness, and expectations. The results show that previous academic performance, motivation, and expectations have positive and significant effects on the students’ overall academic performance in accounting, while preparedness affects only the students’ performance in management accounting. In contrast, prior knowledge on accounting and sex do not give significant impacts to the students’ overall academic performance.These findings indicate the importance of previous aca­demic performance as well as motivation and expectations as background variables in current academic performance. Keywords: students’ background, academic performance, accounting Abstrak: Pengaruh Background Mahasiswa terhadap Kinerja Akademik. Penelitian ini mengkaji pengaruh variabel background terhadap kinerja akademik mahasiswa akuntansi di Universitas Surabaya. Lima variabel background utama dipergunakan, yaitu kinerja akademik sebelumnya, pengetahuan akun­tansi sebelumnya, jenis kelamin, motivasi, kesiapan, dan ekspektasi. Hipotesis diuji menggunakan model regresi linier berganda OLS dan Robust Standar Error. Hasil penelitian memerlihatkan bahwa kinerja akademik sebelumnya, motivasi, dan ekspektasi memiliki pengaruh positif signifikan terhadap kinerja akademik keseluruhan, sementara kesiapan memberikan pengaruh positif hanya pada kinerja akademik akuntansi manajemen. Sebaliknya, pengetahuan akuntansi sebelumnya dan jenis kelamin tidak memberi­kan pengaruh signifikan terhadap kinerja akademik keseluruhan. Temuan ini mengindikasikan bahwa kinerja akademik sebelumnya beserta motivasi dan ekspektasi adalah variabel background

  7. The overshoot and phenotypic equilibrium in characterizing cancer dynamics of reversible phenotypic plasticity.

    Science.gov (United States)

    Chen, Xiufang; Wang, Yue; Feng, Tianquan; Yi, Ming; Zhang, Xingan; Zhou, Da

    2016-02-07

    The paradigm of phenotypic plasticity indicates reversible relations of different cancer cell phenotypes, which extends the cellular hierarchy proposed by the classical cancer stem cell (CSC) theory. Since it is still questionable if the phenotypic plasticity is a crucial improvement to the hierarchical model or just a minor extension to it, it is worthwhile to explore the dynamic behavior characterizing the reversible phenotypic plasticity. In this study we compare the hierarchical model and the reversible model in predicting the cell-state dynamics observed in biological experiments. Our results show that the hierarchical model shows significant disadvantages over the reversible model in describing both long-term stability (phenotypic equilibrium) and short-term transient dynamics (overshoot) in cancer cell populations. In a very specific case in which the total growth of population due to each cell type is identical, the hierarchical model predicts neither phenotypic equilibrium nor overshoot, whereas the reversible model succeeds in predicting both of them. Even though the performance of the hierarchical model can be improved by relaxing the specific assumption, its prediction to the phenotypic equilibrium strongly depends on a precondition that may be unrealistic in biological experiments. Moreover, it still does not show as rich dynamics as the reversible model in capturing the overshoots of both CSCs and non-CSCs. By comparison, it is more likely for the reversible model to correctly predict the stability of the phenotypic mixture and various types of overshoot behavior.

  8. A New Method to Infer Causal Phenotype Networks Using QTL and Phenotypic Information

    NARCIS (Netherlands)

    Wang, H.; Eeuwijk, van F.

    2014-01-01

    In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at

  9. Familial adenomatous polyposis patients without an identified APC germline mutation have a severe phenotype

    DEFF Research Database (Denmark)

    Bisgaard, M L; Ripa, R; Knudsen, Anne Louise;

    2004-01-01

    BACKGROUND: Development of more than 100 colorectal adenomas is diagnostic of the dominantly inherited autosomal disease familial adenomatous polyposis (FAP). Germline mutations can be identified in the adenomatous polyposis coli (APC) gene in approximately 80% of patients. The APC protein...... comprises several regions and domains for interaction with other proteins, and specific clinical manifestations are associated with the mutation assignment to one of these regions or domains. AIMS: The phenotype in patients without an identified causative APC mutation was compared with the phenotype...... in patients with a known APC mutation and with the phenotypes characteristic of patients with mutations in specific APC regions and domains. PATIENTS: Data on 121 FAP probands and 149 call up patients from 70 different families were extracted from the Danish Polyposis register. METHODS: Differences in 16...

  10. Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype

    Directory of Open Access Journals (Sweden)

    Ignatova Zoya

    2007-09-01

    Full Text Available Abstract Background A finite state machine manipulating information-carrying DNA strands can be used to perform autonomous molecular-scale computations at the cellular level. Results We propose a new finite state machine able to detect and correct aberrant molecular phenotype given by mutated genetic transcripts. The aberrant mutations trigger a cascade reaction: specific molecular markers as input are released and induce a spontaneous self-assembly of a wild type protein or peptide, while the mutational disease phenotype is silenced. We experimentally demostrated in in vitro translation system that a viable protein can be autonomously assembled. Conclusion Our work demostrates the basic principles of computational genes and particularly, their potential to detect mutations, and as a response thereafter administer an output that suppresses the aberrant disease phenotype and/or restores the lost physiological function.

  11. Bone phenotypes of P2 receptor knockout mice

    DEFF Research Database (Denmark)

    Orriss, Isabel; Syberg, Susanne; Wang, Ning;

    2011-01-01

    The action of extracellular nucleotides is mediated by ionotropic P2X receptors and G-protein coupled P2Y receptors. The human genome contains 7 P2X and 8 P2Y receptor genes. Knockout mice strains are available for most of them. As their phenotypic analysis is progressing, bone abnormalities have...... been observed in an impressive number of these mice: distinct abnormalities in P2X7-/- mice, depending on the gene targeting construct and the genetic background, decreased bone mass in P2Y1-/- mice, increased bone mass in P2Y2-/- mice, decreased bone resorption in P2Y6-/- mice, decreased bone...... formation and bone resorption in P2Y13-/- mice. These findings demonstrate the unexpected importance of extracellular nucleotide signalling in the regulation of bone metabolism via multiple P2 receptors and distinct mechanisms involving both osteoblasts and osteoclasts....

  12. Influences of tumor stroma on the malignant phenotype

    DEFF Research Database (Denmark)

    Nielsen, Jørgen Dau; Moeslund, Mette; Wandall, Hans H;

    2008-01-01

    influence cell proliferation and invasion of oral carcinoma cell lines. METHOD: Oral cancer cells were cultured in an organotypic culture system on different collagen concentrations, and invasion was measured. Furthermore, the presence of cancer associated proteins such as glycosylated oncofetal fibronectin...... and laminin 5 was investigated. RESULTS: We found that expression of glycosylated oncofetal fibronectin was increased in the invasive phenotype of oral carcinoma cell lines. Furthermore we demonstrated that certain concentrations of collagen in the connective tissue equivalent, appears to stimulate......BACKGROUND: The microenvironment makes a significant contribution to the progression of oral carcinomas. Many different stromal events, such as vascularization, fibroblast activation, myofibroblast differentiation, and the presence of specific stromal proteins, such as proteolytic enzymes...

  13. Frailty phenotypes in the elderly based on cluster analysis

    DEFF Research Database (Denmark)

    Dato, Serena; Montesanto, Alberto; Lagani, Vincenzo

    2012-01-01

    genetic background on the frailty status is still questioned. We investigated the applicability of a cluster analysis approach based on specific geriatric parameters, previously set up and validated in a southern Italian population, to two large longitudinal Danish samples. In both cohorts, we identified...... groups of subjects homogeneous for their frailty status and characterized by different survival patterns. A subsequent survival analysis availing of Accelerated Failure Time models allowed us to formulate an operative index able to correlate classification variables with survival probability. From...... these models, we quantified the differential effect of various parameters on survival, and we estimated the heritability of the frailty phenotype by exploiting the twin pairs in our sample. These data suggest the presence of a genetic influence on the frailty variability and indicate that cluster analysis can...

  14. GABA(A)-benzodiazepine receptor complex sensitivity in 5-HT(1A) receptor knockout mice on a 129/Sv background.

    NARCIS (Netherlands)

    Pattij, T.; Groenink, L.; Oosting, R.S.; Gugten, J. van der; Maes, R.A.A.; Olivier, B.

    2002-01-01

    Previous studies in 5-HT(1A) receptor knockout (1AKO) mice on a mixed Swiss Websterx129/Sv (SWx129/Sv) and a pure 129/Sv genetic background suggest a differential gamma-aminobutyric acid (GABA(A))-benzodiazepine receptor complex sensitivity in both strains, independent from the anxious phenotype. To

  15. Regulatory mechanisms link phenotypic plasticity to evolvability.

    Science.gov (United States)

    van Gestel, Jordi; Weissing, Franz J

    2016-04-18

    Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticity tend to adopt a phenomenological reaction norm (RN) approach, which neglects the mechanisms underlying plasticity. Focusing on a concrete question - the optimal timing of bacterial sporulation - we here also consider a mechanistic approach, the evolution of a gene regulatory network (GRN) underlying plasticity. Using individual-based simulations, we compare the RN and GRN approach and find a number of striking differences. Most importantly, the GRN model results in a much higher diversity of responsive strategies than the RN model. We show that each of the evolved strategies is pre-adapted to a unique set of unseen environmental conditions. The regulatory mechanisms that control plasticity therefore critically link phenotypic plasticity to the adaptive potential of biological populations.

  16. Phenotypic and genetic consequences of protein damage.

    Directory of Open Access Journals (Sweden)

    Anita Krisko

    Full Text Available Although the genome contains all the information necessary for maintenance and perpetuation of life, it is the proteome that repairs, duplicates and expresses the genome and actually performs most cellular functions. Here we reveal strong phenotypes of physiological oxidative proteome damage at the functional and genomic levels. Genome-wide mutations rates and biosynthetic capacity were monitored in real time, in single Escherichia coli cells with identical levels of reactive oxygen species and oxidative DNA damage, but with different levels of irreversible oxidative proteome damage (carbonylation. Increased protein carbonylation correlates with a mutator phenotype, whereas reducing it below wild type level produces an anti-mutator phenotype identifying proteome damage as the leading cause of spontaneous mutations. Proteome oxidation elevates also UV-light induced mutagenesis and impairs cellular biosynthesis. In conclusion, protein damage reduces the efficacy and precision of vital cellular processes resulting in high mutation rates and functional degeneracy akin to cellular aging.

  17. Neurocognitive Phenotypes in Severe Childhood Psychiatric Disorders.

    Science.gov (United States)

    Kavanaugh, Brian C; Dupont-Frechette, Jennifer A; Tellock, Perrin P; Maher, Isolde D; Haisley, Lauren D; Holler, Karen A

    2016-10-01

    This study investigated the presence of potential neurocognitive phenotypes within a severe childhood psychiatric sample. A medical chart review was conducted for 106 children who received a neuropsychological evaluation during children's psychiatric inpatient program hospitalization. A hierarchical cluster analysis was conducted to identify distinct clinical clusters based on neurocognitive measures. Cluster analysis identified four distinct clusters, subsequently labeled neurocognitive phenotypes: "intact cognition" (27%), "global dysfunction" (20%), "organization/planning" (21%), and "inhibition-memory" (32%). Significant differences were identified in history of legal involvement and antipsychotic medications at hospital admission. Differences between none-minimal and moderate-high neurocognitive dysfunction were identified in age, amount of diagnoses and antipsychotic medications at admission, and hospital length of stay. Current findings provide preliminary evidence of underlying neurocognitive phenotypes within severe childhood psychiatric disorders. Findings highlight the importance of neuropsychological evaluation in the treatment of childhood psychiatric disorders.

  18. Genetic background specific hypoxia resistance in rat is correlated with balanced activation of a cross-chromosomal genetic network centering on physiological homeostasis

    Directory of Open Access Journals (Sweden)

    Lei eMao

    2012-10-01

    Full Text Available Genetic background of an individual can drastically influence an organism’s response upon environmental stress and pathological stimulus. Previous studies in inbred rats showed that compared to Brown Norway (BN, Dahl salt-sensitive (SS rat exerts strong hypoxia susceptibility. However, despite extensive narrow-down approaches via the chromosome substitution methodology, this genome-based physiological predisposition could not be traced back to distinct quantitative trait loci. Upon the completion and public data availability of PhysGen SS-BN consomic rat platform, I employed systems biology approach attempting to further our understanding of the molecular basis of genetic background effect in light of hypoxia response. I analyzed the physiological screening data of 22 consomic rat strains under normoxia and two-weeks of hypoxia, and cross-compared them to the parental strains. The analyses showed that SS-9BN and SS-18BN represent the most hypoxia resistant CS strains with phenotype similar to BN, whereas SS-6BN and SS-YBN segregated to the direction of SS. A meta-analysis on the transcriptomic profiles of these consomic rat strains under hypoxia treatment showed that although polymorphisms on the substituted BN chromosomes could be directly involved in hypoxia resistance, this seems to be embedded in a more complex trans-chromosomal genetic regulatory network. Via information theory based modeling approach, this hypoxia-relevant core genetic network was reverse-engineered. Network analyses showed that the protective effects of BN chromosome 9 and 18 were reflected by a balanced activation of this core network centering on physiological homeostasis. Presumably, it is the system robustness constituted on such differential network activation that acts as hypoxia response modifier. Understanding of the intrinsic link between the individual genetic background and the network robustness will set a basis in the current scientific efforts toward

  19. Genetic Background Specific Hypoxia Resistance in Rat is Correlated with Balanced Activation of a Cross-Chromosomal Genetic Network Centering on Physiological Homeostasis.

    Science.gov (United States)

    Mao, Lei

    2012-01-01

    Genetic background of an individual can drastically influence an organism's response upon environmental stress and pathological stimulus. Previous studies in inbred rats showed that compared to Brown Norway (BN), Dahl salt-sensitive (SS) rat exerts strong hypoxia susceptibility. However, despite extensive narrow-down approaches via the chromosome substitution methodology, this genome-based physiological predisposition could not be traced back to distinct quantitative trait loci. Upon the completion and public data availability of PhysGen SS-BN consomic (CS) rat platform, I employed systems biology approach attempting to further our understanding of the molecular basis of genetic background effect in light of hypoxia response. I analyzed the physiological screening data of 22 CS rat strains under normoxia and 2-weeks of hypoxia, and cross-compared them to the parental strains. The analyses showed that SS-9(BN) and SS-18(BN) represent the most hypoxia-resistant CS strains with phenotype similar to BN, whereas SS-6(BN) and SS-Y(BN) segregated to the direction of SS. A meta-analysis on the transcriptomic profiles of these CS rat strains under hypoxia treatment showed that although polymorphisms on the substituted BN chromosomes could be directly involved in hypoxia resistance, this seems to be embedded in a more complex trans-chromosomal genetic regulatory network. Via information theory based modeling approach, this hypoxia relevant core genetic network was reverse engineered. Network analyses showed that the protective effects of BN chromosome 9 and 18 were reflected by a balanced activation of this core network centering on physiological homeostasis. Presumably, it is the system robustness constituted on such differential network activation that acts as hypoxia response modifier. Understanding of the intrinsic link between the individual genetic background and the network robustness will set a basis in the current scientific efforts toward personalized medicine.

  20. The Phenotype of Spontaneous Preterm Birth: Application of a Clinical Phenotyping Tool

    Science.gov (United States)

    Manuck, Tracy A.; Esplin, M. Sean; Biggio, Joseph; Bukowski, Radek; Parry, Samuel; Zhang, Heping; Varner, Michael W.; Andrews, William; Saade, George; Sadovsky, Yoel; Reddy, Uma M.; Ilekis, John

    2015-01-01

    Objective Spontaneous preterm birth (SPTB) is a complex condition that is likely a final common pathway with multiple possible etiologies. We hypothesized that a comprehensive classification system could appropriately group women with similar STPB etiologies, and provide an explanation, at least in part, for the disparities in SPTB associated with race and gestational age at delivery. Study Design Planned analysis of a multicenter, prospective study of singleton SPTB. Women with SPTB < 34 weeks were included. We defined 9 potential SPTB phenotypes based on clinical data, including infection/inflammation, maternal stress, decidual hemorrhage, uterine distention, cervical insufficiency, placental dysfunction, premature rupture of the membranes, maternal comorbidities, and familial factors. Each woman was evaluated for each phenotype. Delivery gestational age was compared between those with and without each phenotype. Phenotype profiles were also compared between women with very early (20.0–27.9 weeks) SPTB vs. those with early SPTB (28.0–34.0 weeks), and between African-American and Caucasian women. Statistical analysis was by t-test and chi-square as appropriate. Results The phenotyping tool was applied to 1025 women with SPTB who delivered at a mean 30.0 (+/− 3.2) weeks gestation. Of these, 800 (78%) had ≥2 phenotypes. Only 43 (4.2%) had no phenotypes. The 281 women with early SPTB were more likely to have infection/inflammation, decidual hemorrhage, and cervical insufficiency phenotypes (all p≤0.001). African-American women had more maternal stress and cervical insufficiency but less decidual hemorrhage and placental dysfunction compared to Caucasian women (all p<0.05). Gestational age at delivery decreased as the number of phenotypes present increased. Conclusions Precise SPTB phenotyping classifies women with SPTB and identifies specific differences between very early and early SPTB and between African-Americans and Caucasians. PMID:25687564

  1. Genetically modified bacteriophages.

    Science.gov (United States)

    Sagona, Antonia P; Grigonyte, Aurelija M; MacDonald, Paul R; Jaramillo, Alfonso

    2016-04-18

    Phages or bacteriophages, viruses that infect and replicate inside bacteria, are the most abundant microorganisms on earth. The realization that antibiotic resistance poses a substantial risk to the world's health and global economy is revitalizing phage therapy as a potential solution. The increasing ease by which phage genomes can be modified, owing to the influx of new technologies, has led to an expansion of their natural capabilities, and a reduced dependence on phage isolation from environmental sources. This review will discuss the way synthetic biology has accelerated the construction of genetically modified phages and will describe the wide range of their applications. It will further provide insight into the societal and economic benefits that derive from the use of recombinant phages in various sectors, from health to biodetection, biocontrol and the food industry.

  2. Modified Newton's rings: II

    CERN Document Server

    Chaitanya, T Sai; Krishna, V Sai; Anandh, B Shankar; Umesh, K S

    2010-01-01

    In an earlier work (Shankar kumar Jha, A Vyas, O S K S Sastri, Rajkumar Jain & K S Umesh, 'Determination of wavelength of laser light using Modified Newton's rings setup', Physics Education, vol. 22, no.3, 195-202(2005)) reported by our group, a version of Newton's rings experiment called Modified Newton's rings was proposed. The present work is an extension of this work. Here, a general formula for wavelength has been derived, applicable for a plane of observation at any distance. A relation between the focal length and the radius curvature is also derived for a plano-convex lens which is essentially used as a concave mirror. Tracker, a video analysis software, freely downloadable from the net, is employed to analyze the fringes captured using a CCD camera. Two beams which give rise to interference fringes in conventional Newton's rings and in the present setup are clearly distinguished.

  3. [Seldinger modified technique].

    Science.gov (United States)

    Ramos Cuenca, Francisco; Linares Escudero, Joaquín; Romo García, Raquel; Cubo Amaya, Manuel; Climent Villanueva, Magdalena; Santos Sarria, Remedios

    2008-12-01

    The authors describe the procedure to insert central blood vessel catheters through peripheral blood vessel catheters using the Seldinger modified technique since critically ill patients service at the Carlos Haya Regional University Hospital in Malaga cares for a high number of patients who need to have canalized a central blood vessel catheter to maximize the treatment they receive. In many cases it is not possible to insert a DRUM type central blood vessel catheter due to an insufficient blood vessel caliber and then the nursing team at this hospital opts to carry out a procedure to canalize a central blood vessel using the Seldinger modified technique. This report was presented at the III National Social-Sanitary Nursing Congress.

  4. Modified Faraday cup

    Science.gov (United States)

    Elmer, John W.; Teruya, Alan T.; O'Brien, Dennis W.

    1996-01-01

    A tomographic technique for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees form 0.degree. to 360.degree. and the waveforms are recorded by a digitizing storage oscilloscope. Two-din-tensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment.

  5. NIC: a robust background extraction algorithm for foreground detection in dynamic scenes

    NARCIS (Netherlands)

    Huynh-The, Thien; Banos, Oresti; Lee, Sungyoung; Kang, Byeong Ho; Kim, Eun-Soo; Le-Tien, Thuong

    2016-01-01

    This paper presents a robust foreground detection method capable of adapting to different motion speeds in scenes. A key contribution of this paper is the background estimation using a proposed novel algorithm, neighbor-based intensity correction (NIC), that identifies and modifies the motion pixels

  6. RNA-modifying enzymes.

    Science.gov (United States)

    Ferré-D'Amaré, Adrian R

    2003-02-01

    A bewildering number of post-transcriptional modifications are introduced into cellular RNAs by enzymes that are often conserved among archaea, bacteria and eukaryotes. The modifications range from those with well-understood functions, such as tRNA aminoacylation, to widespread but more mysterious ones, such as pseudouridylation. Recent structure determinations have included two types of RNA nucleobase modifying enzyme: pseudouridine synthases and tRNA guanine transglycosylases.

  7. Gravity with background fields and diffeomorphism breaking

    CERN Document Server

    Bluhm, Robert

    2016-01-01

    Effective gravitational field theories with background fields break local Lorentz symmetry and diffeomorphism invariance. Examples include Chern-Simons gravity, massive gravity, and the Standard-Model Extension (SME). The physical properties and behavior of these theories depend greatly on whether the spacetime symmetry breaking is explicit or spontaneous. With explicit breaking, the background fields are fixed and nondynamical, and the resulting theories are fundamentally different from Einstein's General Relativity (GR). However, when the symmetry breaking is spontaneous, the background fields are dynamical in origin, and many of the usual features of Einstein's GR still apply.

  8. Do instantons like a colorful background?

    Energy Technology Data Exchange (ETDEWEB)

    Gies, H.; Pawlowski, J.M.; Wetterich, C. [Heidelberg Univ. (Germany). Inst. fuer Theoretische Physik; Jaeckel, J. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2006-08-15

    We investigate chiral symmetry breaking and color symmetry breaking in QCD. The effective potential of the corresponding scalar condensates is discussed in the presence of non-perturbative contributions from the semiclassical one-instanton sector. We concentrate on a color singlet scalar background which can describe chiral condensation, as well as a color cotet scalar background which can generate mass for the gluons. Whereas a non-vanishing singlet chiral field is favored by the instantons, we have found no indication for a preference of color octet backgrounds. (orig.)

  9. ARCADE Detection of an Extragalactic Radio Background

    Science.gov (United States)

    Kogut, Alan J.

    2009-01-01

    Sometimes when we look for one thing we stumble on something else. The Absolute Radiometer for Cosmology, Astrophysics, and Diffuse Emission (ARCADE) was designed to measure the blackbody spectrum of the cosmic microwave background to search for spectral distortions related to the epoch of reionization. Instead, the July 2006 flight found evidence for an extragalactic radio background with amplitude six times brighter than the expected contribution from faint radio sources. The author discusses the ARCADE instrument and the evidence for an extragalactic radio background.

  10. The astrophysical gravitational wave stochastic background

    Institute of Scientific and Technical Information of China (English)

    Tania Regimbau

    2011-01-01

    A stochastic background of gravitational waves with astrophysical origins may have resulted from the superposition of a large number of unresolved sources since the beginning of stellar activity.Its detection would put very strong constraints on the physical properties of compact objects, the initial mass function and star formarion history.On the other hand, it could be a ‘noise' that would mask the stochastic background of its cosmological origin.We review the main astrophysical processes which are able to produce a stochastic background and discuss how they may differ from the primordial contribution in terms of statistical properties.Current detection methods are also presented.

  11. Gravitational wave background from rotating neutron stars

    Science.gov (United States)

    Rosado, Pablo A.

    2012-11-01

    The background of gravitational waves produced by the ensemble of rotating neutron stars (which includes pulsars, magnetars, and gravitars) is investigated. A formula for Ω(f) (a function that is commonly used to quantify the background, and is directly related to its energy density) is derived, without making the usual assumption that each radiating system evolves on a short time scale compared to the Hubble time; the time evolution of the systems since their formation until the present day is properly taken into account. Moreover, the formula allows one to distinguish the different parts of the background: the unresolvable (which forms a stochastic background or confusion noise, since the waveforms composing it cannot be either individually observed or subtracted out of the data of a detector) and the resolvable. Several estimations of the background are obtained, for different assumptions on the parameters that characterize neutron stars and their population. In particular, different initial spin period distributions lead to very different results. For one of the models, with slow initial spins, the detection of the background by present or planned detectors can be rejected. However, other models do predict the detection of the background, that would be unresolvable, by the future ground-based gravitational wave detector ET. A robust upper limit for the background of rotating neutron stars is obtained; it does not exceed the detection threshold of two cross-correlated Advanced LIGO interferometers. If gravitars exist and constitute more than a few percent of the neutron star population, then they produce an unresolvable background that could be detected by ET. Under the most reasonable assumptions on the parameters characterizing a neutron star, the background is too faint to be detected. Previous papers have suggested neutron star models in which large magnetic fields (like the ones that characterize magnetars) induce big deformations in the star, which

  12. Exploiting background knowledge in automated discovery

    Energy Technology Data Exchange (ETDEWEB)

    Aronis, J.M.; Buchanan, B.G. [Univ. of Pittsburgh, PA (United States); Provost, F.J. [NYNEX Science and Technology, White Plains, NY (United States)

    1996-12-31

    Prior work in automated scientific discovery has been successful in finding patterns in data, given that a reasonably small set of mostly relevant features is specified. The work described in this paper places data in the context of large bodies of background knowledge. Specifically, data items are connected to multiple databases of background knowledge represented as inheritance networks. The system has made a practical impact on botanical toxicology research, which required linking examples of cases of plant exposures to databases of botanical, geographical, and climate background knowledge.

  13. Are cuckoos maximizing egg mimicry by selecting host individuals with better matching egg phenotypes?

    Directory of Open Access Journals (Sweden)

    Anton Antonov

    Full Text Available BACKGROUND: Avian brood parasites and their hosts are involved in complex offence-defense coevolutionary arms races. The most common pair of reciprocal adaptations in these systems is egg discrimination by hosts and egg mimicry by parasites. As mimicry improves, more advanced host adaptations evolve such as decreased intra- and increased interclutch variation in egg appearance to facilitate detection of parasitic eggs. As interclutch variation increases, parasites able to choose hosts matching best their own egg phenotype should be selected, but this requires that parasites know their own egg phenotype and select host nests correspondingly. METHODOLOGY/PRINCIPAL FINDINGS: We compared egg mimicry of common cuckoo Cuculus canorus eggs in naturally parasitized marsh warbler Acrocephalus palustris nests and their nearest unparasitized conspecific neighbors having similar laying dates and nest-site characteristics. Modeling of avian vision and image analyses revealed no evidence that cuckoos parasitize nests where their eggs better match the host eggs. Cuckoo eggs were as good mimics, in terms of background and spot color, background luminance, spotting pattern and egg size, of host eggs in the nests actually exploited as those in the neighboring unparasitized nests. CONCLUSIONS/SIGNIFICANCE: We reviewed the evidence for brood parasites selecting better-matching host egg phenotypes from several relevant studies and argue that such selection probably cannot exist in host-parasite systems where host interclutch variation is continuous and overall low or moderate. To date there is also no evidence that parasites prefer certain egg phenotypes in systems where it should be most advantageous, i.e., when both hosts and parasites lay polymorphic eggs. Hence, the existence of an ability to select host nests to maximize mimicry by brood parasites appears unlikely, but this possibility should be further explored in cuckoo-host systems where the host has evolved

  14. Genetically Modified Organisms

    Directory of Open Access Journals (Sweden)

    Claro Llaguno

    2001-06-01

    Full Text Available Recent reports have brought to public attention concerns about Bt corn and genetically modified organisms (GMO in general. The timing, it seems, is most appropriate considering two related developments early this year: the final approval of the Cartagena Protocol on Biosafety in Montreal on January 29, 2001, and the OECD Edinburgh Conference on GM food safety last February 28- March 1, 2001. The protocol makes clear that GMOs include all living modified organisms (LMO defined as "any living organism that possesses a novel combination of genetic material obtained through the use of modern biotechnology". This includes seeds, live fish, and other organisms intentionally obtained for release to the environment. It would seem that the common understanding about GMOs as referring to farm-to-table products is perforce expanded to embrace genetically modified farm animals and aquatic resources. Being a trade agreement, the Montreal accord primarily deals with the safety issues related to the transboundary movement of LMOs around the globe. The OECD conference on the other hand, called for an international body "to address all sides of the GM debate" in response to the public outcry, particularly in Western Europe, regarding the risks the new products pose to human health and the environment. Some points of contention, which remain unresolved, include issues such as whether countries should be allowed to develop their own GM food based on their needs, and whether a global moratorium on GMOs and mandatory labeling should be enforced worldwide.

  15. Cyclic-AMP metabolism in synaptic growth, strength and precision: Neural and behavioral phenotype-specific counterbalancing effects between dnc PDE and rut AC mutations

    OpenAIRE

    Ueda, Atsushi; Wu, Chun-Fang

    2012-01-01

    Two classic learning mutants in Drosophila, rutabaga (rut) and dunce (dnc), are defective in cAMP synthesis and degradation, respectively, exhibiting a variety of neuronal and behavioral defects. We ask how the opposing effects of these mutations on cAMP levels modify subsets of phenotypes, and whether any specific phenotypes could be ameliorated by biochemical counter balancing effects in dnc rut double mutants. Our study at larval neuromuscular junctions (NMJs) demonstrate that dnc mutation...

  16. Genetic Regulation of Phenotypic Plasticity and Canalisation in Yeast Growth

    OpenAIRE

    Yadav, Anupama; Dhole, Kaustubh; Sinha, Himanshu

    2016-01-01

    The ability of a genotype to show diverse phenotypes in different environments is called phenotypic plasticity. Phenotypic plasticity helps populations to evade extinctions in novel environments, facilitates adaptation and fuels evolution. However, most studies focus on understanding the genetic basis of phenotypic regulation in specific environments. As a result, while it’s evolutionary relevance is well established, genetic mechanisms regulating phenotypic plasticity and their overlap with ...

  17. Lubiprostone ameliorates the cystic fibrosis mouse intestinal phenotype

    Directory of Open Access Journals (Sweden)

    De Lisle Robert C

    2010-09-01

    Full Text Available Abstract Background Cystic fibrosis (CF is caused by mutations in the CFTR gene that impair the function of CFTR, a cAMP-regulated anion channel. In the small intestine loss of CFTR function creates a dehydrated, acidic luminal environment which is believed to cause an accumulation of mucus, a phenotype characteristic of CF. CF mice have small intestinal bacterial overgrowth, an altered innate immune response, and impaired intestinal transit. We investigated whether lubiprostone, which can activate the CLC2 Cl- channel, would improve the intestinal phenotype in CF mice. Methods Cftrtm1UNC (CF and wildtype (WT littermate mice on the C57BL/6J background were used. Lubiprostone (10 μg/kg-day was administered by gavage for two weeks. Mucus accumulation was estimated from crypt lumen widths in periodic acid-Schiff base, Alcian blue stained sections. Luminal bacterial load was measured by qPCR for the bacterial 16S gene. Gastric emptying and small intestinal transit in fasted mice were assessed using gavaged rhodamine dextran. Gene expression was evaluated by Affymetrix Mouse430 2.0 microarray and qRT-PCR. Results Crypt width in control CF mice was 700% that of WT mice (P P = 0.001. Lubiprostone increased bacterial load in WT mice to 490% of WT control levels (P = 0.008. Conversely, lubiprostone decreased bacterial overgrowth in CF mice by 60% (P = 0.005. Lubiprostone increased gastric emptying at 20 min postgavage in both WT (P P P = 0.024 but not in CF mice (P = 0.377. Among other innate immune markers, expression of mast cell genes was elevated 4-to 40-fold in the CF intestine as compared to WT, and lubiprostone treatment of CF mice decreased expression to WT control levels. Conclusions These results indicate that lubiprostone has some benefits for the CF intestinal phenotype, especially on bacterial overgrowth and the innate immune response. The unexpected observation of increased mucus accumulation in the crypts of lubiprostone-treated CF mice

  18. The Spin-2 Equation on Minkowski Background

    CERN Document Server

    Beyer, Florian; Frauendiener, Jörg; Whale, Ben

    2014-01-01

    The linearised general conformal field equations in their first and second order form are used to study the behaviour of the spin-2 zero-rest-mass equation on Minkowski background in the vicinity of space-like infinity.

  19. Activating Background Knowledge in Reading Comprehension Assessment.

    Science.gov (United States)

    Rowe, Deborah Wells; Rayford, Lawrence

    1987-01-01

    Indicates that a broad age range of students can use some purpose questions as cues to activate background knowledge. Suggest topic familiarity, amount of information presented, and the presence of genre clues as text features affecting schema activation. (NKA)

  20. Dyonic branes and linear dilaton background

    CERN Document Server

    Clément, G; Leygnac, C; Orlov, D; Clement, Gerard; Gal'tsov, Dmitri; Leygnac, Cedric; Orlov, Dmitri

    2006-01-01

    We study dyonic solutions to the gravity-dilaton-antisymmetric form equations with the goal of identifying new $p$-brane solutions on the fluxed linear dilaton background. Starting with the generic solutions constructed by reducing the system to decoupled Liouville equations for certain values of parameters, we identify the most general solution whose singularities are hidden behind a regular event horizon, and then explore the admissible asymptotic behaviors. In addition to known asymptotically flat dyonic branes, we find two classes of asymptotically non-flat solutions which can be interpreted as describing magnetically charged branes on the electrically charged linear dilaton background (and the $S$-dual configuration of electrically charged branes on the magnetically charged background), and uncharged black branes on the dyonically charged linear dilaton background. This interpretation is shown to be consistent with the first law of thermodynamics for the new solutions.

  1. Cognitive abilities, sociocultural background and academic achievement.

    Science.gov (United States)

    Diniz, António; Dias Pocinho, Margarida; Silva Almeida, Leandro

    2011-11-01

    The influence of students' sociocultural background on academic achievement is a well established fact. Research also points out that sociocultural background is related to students' cognitive abilities and these have an effect on their academic achievement. However, the mediator role of cognitive abilities on the relationship between sociocultural background and academic achievement is less well known. A structural equation model that represents these relationships was tested in a sample (N= 728) of Portuguese junior high school students. Multigroup analysis of the model showed the importance of the cognitive ability mediation effect between sociocultural background and academic achievement in the 7th and 9th grades, but not in the 8th grade. This difference may be the result of the academic transition experienced in the 7th and 9th grades in the Portuguese educational system, which requires parents' higher involvement in school.

  2. Background by neutron activation in GERDA

    Energy Technology Data Exchange (ETDEWEB)

    Meierhofer, Georg; Dietrich, Dennis; Freund, Kai; Grabmayr, Peter; Hegai, Alexander; Jochum, Josef; Knapp, Markus; Ritter, Florian [Kepler Center for Astro and Particle Physics, Universitaet Tuebingen (Germany); Canella, Lea [Institut fuer Radiochemie, Technische Universitaet Muenchen (Germany); Jolie, Jan [Institut fuer Kernphysik, Universitaet zu Koeln (Germany); Kudejova, Petra [FRM II, Technische Universitaet Muenchen (Germany)

    2010-07-01

    The observation of the neutrinoless double beta decay is a proof of the Majorana nature of the neutrino. The long half-life of this decay requires experiments of very low background rates in the region of interest at Q{sub {beta}}{sub {beta}}. Prompt {gamma}-rays after neutron capture on germanium and the {beta}-decay of {sup 77}Ge contribute to the background in experiments using {sup 76}Ge for the search of the neutrinoless double beta decay. The poorly known prompt {gamma}-ray spectra and the neutron capture cross sections for the (n,{gamma}) reactions of {sup 74}Ge and {sup 76}Ge were measured at the research reactor FRM II (Munich). The obtained data are needed in MC simulations for qualitative and quantitative background prediction in the Gerda experiment. The data and their implication on the background in Gerda are presented.

  3. Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain-Specific Terminological Resource.

    Science.gov (United States)

    Alnazzawi, Noha; Thompson, Paul; Ananiadou, Sophia

    2016-01-01

    Biomedical literature articles and narrative content from Electronic Health Records (EHRs) both constitute rich sources of disease-phenotype information. Phenotype concepts may be mentioned in text in multiple ways, using phrases with a variety of structures. This variability stems partly from the different backgrounds of the authors, but also from the different writing styles typically used in each text type. Since EHR narrative reports and literature articles contain different but complementary types of valuable information, combining details from each text type can help to uncover new disease-phenotype associations. However, the alternative ways in which the same concept may be mentioned in each source constitutes a barrier to the automatic integration of information. Accordingly, identification of the unique concepts represented by phrases in text can help to bridge the gap between text types. We describe our development of a novel method, PhenoNorm, which integrates a number of different similarity measures to allow automatic linking of phenotype concept mentions to known concepts in the UMLS Metathesaurus, a biomedical terminological resource. PhenoNorm was developed using the PhenoCHF corpus-a collection of literature articles and narratives in EHRs, annotated for phenotypic information relating to congestive heart failure (CHF). We evaluate the performance of PhenoNorm in linking CHF-related phenotype mentions to Metathesaurus concepts, using a newly enriched version of PhenoCHF, in which each phenotype mention has an expert-verified link to a concept in the UMLS Metathesaurus. We show that PhenoNorm outperforms a number of alternative methods applied to the same task. Furthermore, we demonstrate PhenoNorm's wider utility, by evaluating its ability to link mentions of various other types of medically-related information, occurring in texts covering wider subject areas, to concepts in different terminological resources. We show that PhenoNorm can maintain

  4. Phenotype Clustering of Breast Epithelial Cells in Confocal Imagesbased on Nuclear Protein Distribution Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Long, Fuhui; Peng, Hanchuan; Sudar, Damir; Levievre, Sophie A.; Knowles, David W.

    2006-09-05

    Background: The distribution of the chromatin-associatedproteins plays a key role in directing nuclear function. Previously, wedeveloped an image-based method to quantify the nuclear distributions ofproteins and showed that these distributions depended on the phenotype ofhuman mammary epithelial cells. Here we describe a method that creates ahierarchical tree of the given cell phenotypes and calculates thestatistical significance between them, based on the clustering analysisof nuclear protein distributions. Results: Nuclear distributions ofnuclear mitotic apparatus protein were previously obtained fornon-neoplastic S1 and malignant T4-2 human mammary epithelial cellscultured for up to 12 days. Cell phenotype was defined as S1 or T4-2 andthe number of days in cultured. A probabilistic ensemble approach wasused to define a set of consensus clusters from the results of multipletraditional cluster analysis techniques applied to the nucleardistribution data. Cluster histograms were constructed to show how cellsin any one phenotype were distributed across the consensus clusters.Grouping various phenotypes allowed us to build phenotype trees andcalculate the statistical difference between each group. The resultsshowed that non-neoplastic S1 cells could be distinguished from malignantT4-2 cells with 94.19 percent accuracy; that proliferating S1 cells couldbe distinguished from differentiated S1 cells with 92.86 percentaccuracy; and showed no significant difference between the variousphenotypes of T4-2 cells corresponding to increasing tumor sizes.Conclusion: This work presents a cluster analysis method that canidentify significant cell phenotypes, based on the nuclear distributionof specific proteins, with high accuracy.

  5. Multivariate models of mixed assortment: phenotypic assortment and social homogamy for education and fluid ability.

    Science.gov (United States)

    Reynolds, C A; Baker, L A; Pedersen, N L

    2000-11-01

    Phenotypic assortment is assumed to be the principal mechanism of spouse similarity in most biometrical studies. Other assortment mechanisms, such as social homogamy, may be plausible. Two models are presented that consider phenotypic assortment and social homogamy simultaneously (i.e., mixed assortment), where selective associations between social background factors (Model I) versus selective associations between total environments (Model II) distinguish the models. A series of illustrative analyses was undertaken for education and fluid ability available on a sample of 116 Swedish twin pairs and their spouses. On the basis of several fit criteria Model I was preferred over Model II. Both social homogamy and phenotypic assortment may contribute to spouse similarity for educational attainment and fluid ability. Furthermore, spouse similarity for fluid ability may arise indirectly from social homogamy and phenotypic assortment for educational attainment. Power analyses indicated greater observed power for Model I than Model II. Additional power analyses indicated that considerably more twin-spouse sets would be needed for Model II than Model I, to resolve social homogamy and phenotypic assortment. Effects of misspecification of mechanisms of spouse similarity are also briefly discussed.

  6. Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast

    Science.gov (United States)

    NIDELET, Thibault; MARTIN, Juliette; LEGRAND, Judith; DILLMANN, Christine; BOURGAIS, Aurélie; de VIENNE, Dominique; SHERLOCK, Gavin; SICARD, Delphine

    2015-01-01

    Different organisms have independently and recurrently evolved similar phenotypic traits at different points throughout history. This phenotypic convergence may be caused by genotypic convergence and constrained by historical contingency. To investigate how convergence may be driven by selection in a particular environment and constrained by history, we analyzed nine life-history traits and four metabolic traits during an experimental evolution of six yeast strains in four different environments. In each of the environments, the population converged towards a different life-history strategy. However, phenotypic convergence was partly associated with the selection of mutations in genes involved in the same pathway. In a fifth of our evolution experiments, mutations in the same gene, BMH1, were selected, in three out of the six ancestral genotypes. Two types of BMH1 mutation with opposite phenotypic effects on several traits were found. The evolution of most traits, as well as the occurrence of BMH1 mutations, was significantly influenced by the ancestral strain. However, this effect could not be easily predicted from ancestors’ phylogeny or past-selection. All together, our data demonstrate that phenotypic and its underlying genotypic convergence depends on a complex interplay between the evolutionary environment, pleiotropy and the ancestor genetic background but are not straightforwardly predicable. PMID:24164389

  7. An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data

    Directory of Open Access Journals (Sweden)

    Bozek Katarzyna

    2012-07-01

    Full Text Available Abstract Background Entry of human immunodeficiency virus type 1 (HIV-1 into the host cell involves interactions between the viral envelope glycoproteins (Env and the cellular receptor CD4 as well as a coreceptor molecule (most importantly CCR5 or CXCR4. Viral preference for a specific coreceptor (tropism is in particular determined by the third variable loop (V3 of the Env glycoprotein gp120. The approval and use of a coreceptor antagonist for antiretroviral therapy make detailed understanding of tropism and its accurate prediction from patient derived virus isolates essential. The aim of the present study is the development of an extended description of the HIV entry phenotype reflecting its co-dependence on several key determinants as the basis for a more accurate prediction of HIV-1 entry phenotype from genotypic data. Results Here, we established a new protocol of quantitation and computational analysis of the dependence of HIV entry efficiency on receptor and coreceptor cell surface levels as well as viral V3 loop sequence and the presence of two prototypic coreceptor antagonists in varying concentrations. Based on data collected at the single-cell level, we constructed regression models of the HIV-1 entry phenotype integrating the measured determinants. We developed a multivariate phenotype descriptor, termed phenotype vector, which facilitates a more detailed characterization of HIV entry phenotypes than currently used binary tropism classifications. For some of the tested virus variants, the multivariant phenotype vector revealed substantial divergences from existing tropism predictions. We also developed methods for computational prediction of the entry phenotypes based on the V3 sequence and performed an extrapolating calculation of the effectiveness of this computational procedure. Conclusions Our study of the HIV cell entry phenotype and the novel multivariate representation developed here contributes to a more detailed

  8. Standard Model Background of the Cosmological Collider

    CERN Document Server

    Chen, Xingang; Xianyu, Zhong-Zhi

    2016-01-01

    The inflationary universe can be viewed as a "Cosmological Collider" with energy of Hubble scale, producing very massive particles and recording their characteristic signals in primordial non-Gaussianities. To utilize this collider to explore any new physics at very high scales, it is a prerequisite to understand the background signals from the particle physics Standard Model. In this paper we describe the Standard Model background of the Cosmological Collider.

  9. CORSIKA modifications for faster background generation

    Science.gov (United States)

    Jero, Kyle

    2016-04-01

    CORSIKA is a simulation program for extensive air showers initiated by high energy cosmic particles. These air showers create the majority of the muons and neutrinos which neutrino that telescopes detect and are considered a background signature in searches for astrophysical neutrinos. This contribution will discuss changes to CORSIKA which allow for faster high energy background simulation. The theory, implementation, application, and performance of these modifications will be presented.

  10. CORSIKA modifications for faster background generation

    Directory of Open Access Journals (Sweden)

    Jero Kyle

    2016-01-01

    Full Text Available CORSIKA is a simulation program for extensive air showers initiated by high energy cosmic particles. These air showers create the majority of the muons and neutrinos which neutrino that telescopes detect and are considered a background signature in searches for astrophysical neutrinos. This contribution will discuss changes to CORSIKA which allow for faster high energy background simulation. The theory, implementation, application, and performance of these modifications will be presented.

  11. Mathematical Background of Public Key Cryptography

    DEFF Research Database (Denmark)

    Frey, Gerhard; Lange, Tanja

    2005-01-01

    The two main systems used for public key cryptography are RSA and protocols based on the discrete logarithm problem in some cyclic group. We focus on the latter problem and state cryptographic protocols and mathematical background material.......The two main systems used for public key cryptography are RSA and protocols based on the discrete logarithm problem in some cyclic group. We focus on the latter problem and state cryptographic protocols and mathematical background material....

  12. Military Retirement: Background and Recent Developments

    Science.gov (United States)

    2014-05-28

    Military Retirement: Background and Recent Developments David F. Burrelli Specialist in Military Manpower Policy Barbara Salazar Torreon...00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE Military Retirement: Background and Recent Developments 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...Recent Developments Congressional Research Service Summary The military retirement system is a noncontributory, defined benefit system that has

  13. A background free double beta decay experiment

    OpenAIRE

    Giomataris, Ioannis

    2010-01-01

    We present a new detection scheme for rejecting backgrounds in neutrino less double beta decay experiments. It relies on the detection of Cherenkov light emitted by electrons in the MeV region. The momentum threshold is tuned to reach a good discrimination between background and good events. We consider many detector concepts and a range of target materials. The most promising is a high-pressure 136Xe emitter for which the required energy threshold is easily adjusted. Combination of this conc...

  14. Supermembrane actions for Gaiotto-Maldacena backgrounds

    Science.gov (United States)

    Stefański, Bogdan

    2014-06-01

    We write down the supermembrane actions for M-theory backgrounds dual to general N=2 four-dimensional superconformal field theories. The actions are given to all orders in fermions and are in a particular κ-gauge. When an extra U(1) isometry is present, our actions reduce to κ-gauge fixed Green-Schwarz actions for the corresponding Type IIA backgrounds.

  15. Supermembrane actions for Gaiotto–Maldacena backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Stefański, Bogdan, E-mail: Bogdan.Stefanski.1@city.ac.uk

    2014-06-15

    We write down the supermembrane actions for M-theory backgrounds dual to general N=2 four-dimensional superconformal field theories. The actions are given to all orders in fermions and are in a particular κ-gauge. When an extra U(1) isometry is present, our actions reduce to κ-gauge fixed Green–Schwarz actions for the corresponding Type IIA backgrounds.

  16. Moving object detection using background subtraction

    CERN Document Server

    Shaikh, Soharab Hossain; Chaki, Nabendu

    2014-01-01

    This Springer Brief presents a comprehensive survey of the existing methodologies of background subtraction methods. It presents a framework for quantitative performance evaluation of different approaches and summarizes the public databases available for research purposes. This well-known methodology has applications in moving object detection from video captured with a stationery camera, separating foreground and background objects and object classification and recognition. The authors identify common challenges faced by researchers including gradual or sudden illumination change, dynamic bac

  17. Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

    DEFF Research Database (Denmark)

    Otero, José Manuel; Vongsangnak, Wanwipa; Asadollahi, Mohammadali;

    2010-01-01

    BACKGROUND: The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where s...... that provides clear and high-probability of success metabolic engineering targets. The genome sequence, annotation, and a SNP viewer of CEN.PK113-7D are deposited at http://www.sysbio.se/cenpk.......BACKGROUND: The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where...... selective pressure is applied to a partially genetically engineered strain to confer a desirable phenotype. The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering. RESULTS: In this work we...

  18. Non-collision backgrounds in ATLAS

    CERN Document Server

    Gibson, S M; The ATLAS collaboration

    2012-01-01

    The proton-proton collision events recorded by the ATLAS experiment are on top of a background that is due to both collision debris and non-collision components. The latter comprises of three types: beam-induced backgrounds, cosmic particles and detector noise. We present studies that focus on the first two of these. We give a detailed description of beam-related and cosmic backgrounds based on the full 2011 ATLAS data set, and present their rates throughout the whole data-taking period. Studies of correlations between tertiary proton halo and muon backgrounds, as well as, residual pressure and resulting beam-gas events seen in beam-condition monitors will be presented. Results of simulations based on the LHC geometry and its parameters will be presented. They help to better understand the features of beam-induced backgrounds in each ATLAS sub-detector. The studies of beam-induced backgrounds in ATLAS reveal their characteristics and serve as a basis for designing rejection tools that can be applied in physic...

  19. String pair production in non homogeneous backgrounds

    CERN Document Server

    Bolognesi, Stefano; Tallarita, Gianni

    2016-01-01

    We consider string pair production in non homogeneous electric backgrounds. We study several particular configurations which can be addressed with the Euclidean world-sheet instanton technique, the analogue of the world-line instanton for particles. In the first case the string is suspended between two D-branes in flat space-time, in the second case the string lives in AdS and terminates on one D-brane (this realizes the holographic Schwinger effect). In some regions of parameter space the result is well approximated by the known analytical formulas, either the particle pair production in non-homogeneous background or the string pair production in homogeneous background. In other cases we see effects which are intrinsically stringy and related to the non-homogeneity of the background. The pair production is enhanced already for particles in time dependent electric field backgrounds. The string nature enhances this even further. For spacial varying electrical background fields the string pair production is les...

  20. A new method to infer causal phenotype networks using QTL and phenotypic information.

    Directory of Open Access Journals (Sweden)

    Huange Wang

    Full Text Available In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request.

  1. Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

    Directory of Open Access Journals (Sweden)

    Wasila M Dahdul

    Full Text Available BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org. We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology in combination with terms from a quality ontology (Phenotype and Trait Ontology. Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to

  2. The coupling of Poisson sigma models to topological backgrounds

    CERN Document Server

    Rosa, Dario

    2016-01-01

    We extend the coupling to the topological backgrounds, recently worked out for the 2-dimensional BF-model, to the most general Poisson sigma models. The coupling involves the choice of a Casimir function on the target manifold and modifies the BRST transformations. This in turn induces a change in the BRST cohomology of the resulting theory. The observables of the coupled theory are analyzed and their geometrical intrepretation is given. We finally couple the theory to 2-dimensional topological gravity: this is the first step to study a topological string theory in propagation on a Poisson manifold. As an application, we show that the gauge-fixed vectorial supersymmetry of the Poisson sigma models has a natural explanation in terms of the theory coupled to topological gravity.

  3. The coupling of Poisson sigma models to topological backgrounds

    Science.gov (United States)

    Rosa, Dario

    2016-12-01

    We extend the coupling to the topological backgrounds, recently worked out for the 2-dimensional BF-model, to the most general Poisson sigma models. The coupling involves the choice of a Casimir function on the target manifold and modifies the BRST transformations. This in turn induces a change in the BRST cohomology of the resulting theory. The observables of the coupled theory are analyzed and their geometrical interpretation is given. We finally couple the theory to 2-dimensional topological gravity: this is the first step to study a topological string theory in propagation on a Poisson manifold. As an application, we show that the gauge-fixed vectorial supersymmetry of the Poisson sigma models has a natural explanation in terms of the theory coupled to topological gravity.

  4. Phenotyping for Abiotic Stress Tolerance in Maize

    Institute of Scientific and Technical Information of China (English)

    Benhilda Masuka; Jose Luis Araus; Biswanath Das; Kai Sonder; Jill E. Cairns

    2012-01-01

    The ability to quickly develop germplasm having tolerance to several complex polygenic inherited abiotic and biotic stresses combined is critical to the resilience of cropping systems in the face of climate change.Molecular breeding offers the tools to accelerate cereal breeding; however,suitable phenotyping protocols are essential to ensure that the much-anticipated benefits of molecular breeding can be realized.To facilitate the full potential of molecular tools,greater emphasis needs to be given to reducing the within-experimental site variability,application of stress and characterization of the environment and appropriate phenotyping tools.Yield is a function of many processes throughout the plant cycle,and thus integrative traits that encompass crop performance over time or organization level (i.e.canopy level) will provide a better alternative to instantaneous measurements which provide only a snapshot of a given plant process.Many new phenotyping tools based on remote sensing are now available including non-destructive measurements of growth-related parameters based on spectral reflectance and infrared thermometry to estimate plant water status.Here we describe key field phenotyping protocols for maize with emphasis on tolerance to drought and low nitrogen.

  5. Radiofrequency treatment alters cancer cell phenotype

    Science.gov (United States)

    Ware, Matthew J.; Tinger, Sophia; Colbert, Kevin L.; Corr, Stuart J.; Rees, Paul; Koshkina, Nadezhda; Curley, Steven; Summers, H. D.; Godin, Biana

    2015-07-01

    The importance of evaluating physical cues in cancer research is gradually being realized. Assessment of cancer cell physical appearance, or phenotype, may provide information on changes in cellular behavior, including migratory or communicative changes. These characteristics are intrinsically different between malignant and non-malignant cells and change in response to therapy or in the progression of the disease. Here, we report that pancreatic cancer cell phenotype was altered in response to a physical method for cancer therapy, a non-invasive radiofrequency (RF) treatment, which is currently being developed for human trials. We provide a battery of tests to explore these phenotype characteristics. Our data show that cell topography, morphology, motility, adhesion and division change as a result of the treatment. These may have consequences for tissue architecture, for diffusion of anti-cancer therapeutics and cancer cell susceptibility within the tumor. Clear phenotypical differences were observed between cancerous and normal cells in both their untreated states and in their response to RF therapy. We also report, for the first time, a transfer of microsized particles through tunneling nanotubes, which were produced by cancer cells in response to RF therapy. Additionally, we provide evidence that various sub-populations of cancer cells heterogeneously respond to RF treatment.

  6. Phenotype as Agent for Epigenetic Inheritance

    Directory of Open Access Journals (Sweden)

    John S. Torday

    2016-07-01

    Full Text Available The conventional understanding of phenotype is as a derivative of descent with modification through Darwinian random mutation and natural selection. Recent research has revealed Lamarckian inheritance as a major transgenerational mechanism for environmental action on genomes whose extent is determined, in significant part, by germ line cells during meiosis and subsequent stages of embryological development. In consequence, the role of phenotype can productively be reconsidered. The possibility that phenotype is directed towards the effective acquisition of epigenetic marks in consistent reciprocation with the environment during the life cycle of an organism is explored. It is proposed that phenotype is an active agent in niche construction for the active acquisition of epigenetic marks as a dominant evolutionary mechanism rather than a consequence of Darwinian selection towards reproductive success. The reproductive phase of the life cycle can then be appraised as a robust framework in which epigenetic inheritance is entrained to affect growth and development in continued reciprocal responsiveness to environmental stresses. Furthermore, as first principles of physiology determine the limits of epigenetic inheritance, a coherent justification can thereby be provided for the obligate return of all multicellular eukaryotes to the unicellular state.

  7. KSHV Induction of Angiogenic and Lymphangiogenic Phenotypes

    Directory of Open Access Journals (Sweden)

    Terri A. DiMiao

    2012-03-01

    Full Text Available Kaposi’s Sarcoma is a highly vascularized tumor supporting large amounts of neo-angiogenesis. The major cell type in KS tumors is the spindle cell, a cell that expresses markers of lymphatic endothelium. KSHV, the etiologic agent of KS, is found in the spindle cells of all KS tumors. Considering the extreme extent of angiogenesis in KS tumors at all stages it has been proposed that KSHV directly induces angiogenesis in a paracrine fashion. In accordance with this theory, KSHV infection of endothelial cells in culture induces a number of host pathways involved in activation of angiogenesis and a number of KSHV genes themselves can induce pathways involved in angiogenesis. Because spindle cells are phenotypically endothelial in nature, activation through the induction of angiogenic and/or lymphangiogenic phenotypes by the virus may also be directly involved in spindle cell growth and tumor induction. Accordingly, KSHV infection of endothelial cells induces cell autonomous angiogenic phenotypes to activate host cells. KSHV infection can also reprogram blood endothelial cells to lymphatic endothelium. However, KSHV induces some blood endothelial specific genes upon infection of lymphatic endothelial cells creating a phenotypic intermediate between blood and lymphatic endothelium. Induction of pathways involved in angiogenesis and lymphangiogenesis are likely to be critical for tumor cell growth and spread. Thus, induction of both cell autonomous and non-autonomous changes in angiogenic and lymphangiogenic pathways by KSHV likely plays a key role in the formation of KS tumors.

  8. Phenotype Presentation of Hypophosphatemic Rickets in Adults

    DEFF Research Database (Denmark)

    Beck-Nielsen, Signe S; Brusgaard, Klaus; Rasmussen, Lars M

    2010-01-01

    Hypophosphatemic rickets (HR) is a group of rare disorders caused by excessive renal phosphate wasting. The purpose of this cross-sectional study of 38 HR patients was to characterize the phenotype of adult HR patients. Moreover, skeletal and endodontic severity scores were defined to assess poss...

  9. Cognitive Phenotype of Velocardiofacial Syndrome: A Review

    Science.gov (United States)

    Furniss, Frederick; Biswas, Asit B.; Gumber, Rohit; Singh, Niraj

    2011-01-01

    The behavioural phenotype of velocardiofacial syndrome (VCFS), one of the most common human multiple anomaly syndromes, includes developmental disabilities, frequently including intellectual disability (ID) and high risk of diagnosis of psychotic disorders including schizophrenia. VCFS may offer a model of the relationship between ID and risk of…

  10. Constraints on the evolution of phenotypic plasticity

    DEFF Research Database (Denmark)

    Murren, Courtney J; Auld, Josh R.; Callahan, Hilary S

    2015-01-01

    Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change. Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce an opti...

  11. Phenotypic variation in plants : Roles for epigenetics

    NARCIS (Netherlands)

    Lauss, K.

    2017-01-01

    Besides genetics, also epigenetics can play a role in shaping the characteristics of a plant (phenotype). Epigenetics refers to chemical modifications of DNA and proteins associated with the DNA that can influence gene activity (the ‘epigenome’) and can be passed on through cell divisions and follow

  12. Phenotype Information Retrieval for Existing GWAS Studies.

    Science.gov (United States)

    Alipanah, Neda; Lin, Ko-Wei; Venkatesh, Vinay; Farzaneh, Seena; Kim, Hyeon-Eui

    2013-01-01

    The database of Genotypes and Phenotypes (dbGaP) is archiving the results of different Genome Wide Association Studies (GWAS). dbGaP has a multitude of phenotype variables, but they are not harmonized across studies. We proposed a method to standardize phenotype variables by classifying similar variables based on semantic distances. We first extracted variables description, enriched them using domain knowledge, and computed the distances among them. We used clustering techniques to classify the most similar variables. We used domain experts to audit clusters, annotated the clusters with appropriate labels, and used re-clustering to build a semantically-driven Genotypes and Phenotypes (sdGaP) ontology using the UMLS semantic network and metathesaurus. The sdGaP ontology allowed us to expand user queries and retrieve information using a semantic metric called density measure (DM). We illustrated the potential improvement of information retrieval using the sdGaP ontology in one search scenario using the variables from the Cleveland Family Study.

  13. Delineating the GRIN1 phenotypic spectrum

    DEFF Research Database (Denmark)

    Lemke, Johannes R; Geider, Kirsten; Helbig, Katherine L

    2016-01-01

    impairment as well as oculomotor and movement disorders being discriminating phenotypic features. Loss of NMDA receptor function appears to be the underlying disease mechanism. The identification of both heterozygous and homozygous mutations blurs the borders of dominant and recessive inheritance of GRIN1...

  14. Colorectal Cancer "Methylator Phenotype": Fact or Artifact?

    Directory of Open Access Journals (Sweden)

    Charles Anacleto

    2005-04-01

    Full Text Available It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI. We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.

  15. Monocyte-Platelet Interaction Induces a Pro-Inflammatory Phenotype in Circulating Monocytes

    OpenAIRE

    2011-01-01

    BACKGROUND: Activated platelets exert a pro-inflammatory action that can be largely ascribed to their ability to interact with leukocytes and modulate their activity. We hypothesized that platelet activation and consequent formation of monocyte-platelet aggregates (MPA) induces a pro-inflammatory phenotype in circulating monocytes. METHODOLOGY/PRINCIPAL FINDINGS: CD62P(+) platelets and MPA were measured, and monocytes characterized, by whole blood flow cytometry in healthy subjects, before an...

  16. Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study

    DEFF Research Database (Denmark)

    Druley, Todd E; Wang, Lihua; Lin, Shiow J;

    2016-01-01

    BACKGROUND: The Long Life Family Study (LLFS) is an international study to identify the genetic components of various healthy aging phenotypes. We hypothesized that pedigree-specific rare variants at longevity-associated genes could have a similar functional impact on healthy phenotypes. METHODS...... that was significantly associated with three phenotypes (GSK3B with the Healthy Aging Index, NOTCH1 with diastolic blood pressure and TP53 with serum HDL). CONCLUSIONS: Sequencing analysis of family-based associations for age-related phenotypes can identify rare or novel variants.......: We performed custom hybridization capture sequencing to identify the functional variants in 464 candidate genes for longevity or the major diseases of aging in 615 pedigrees (4,953 individuals) from the LLFS, using a multiplexed, custom hybridization capture. Variants were analyzed individually...

  17. Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study

    DEFF Research Database (Denmark)

    Druley, Todd E; Wang, Lihua; Lin, Shiow J;

    2016-01-01

    BACKGROUND: The Long Life Family Study (LLFS) is an international study to identify the genetic components of various healthy aging phenotypes. We hypothesized that pedigree-specific rare variants at longevity-associated genes could have a similar functional impact on healthy phenotypes. METHODS......: We performed custom hybridization capture sequencing to identify the functional variants in 464 candidate genes for longevity or the major diseases of aging in 615 pedigrees (4,953 individuals) from the LLFS, using a multiplexed, custom hybridization capture. Variants were analyzed individually...... that was significantly associated with three phenotypes (GSK3B with the Healthy Aging Index, NOTCH1 with diastolic blood pressure and TP53 with serum HDL). CONCLUSIONS: Sequencing analysis of family-based associations for age-related phenotypes can identify rare or novel variants....

  18. Alcohol consumption, Lewis phenotypes, and risk of ischemic heart disease

    Energy Technology Data Exchange (ETDEWEB)

    Hein, H.O.; Suadicani, P.; Gyntelberg, F. (Rigshospitalet State Univ. Hospital, Copenhagen (Denmark). Epidemiological Research Unit); Sorenson, H. (Rigshospitalet State Univ. Hospital, Copenhagen (Denmark). Dept. of Chemical Immunology); Hein, H.O. (Univ. of Copenhagen (Denmark). Dept. of Internal Medicine)

    1993-02-13

    The authors have previously found an increased risk of ischemic heart disease (IHD) in men with the Lewis phenotype Le(a[minus]b[minus]) and suggested that the Lewis blood group has a close genetic relation with insulin resistance. The authors have investigated whether any conventional risk factors explain the increased risk in Le(a[minus]b[minus]) men. 3,383 men aged 53-75 years were examined in 1985-86, and morbidity and mortality during the next 4 years were recorded. At baseline, the authors excluded 343 men with a history of myocardial infarction, angina pectoris, intermittent claudication, or stroke. The potential risk factors examined were alcohol consumption, physical activity, tobacco smoking, serum cotinine, serum lipids, body-mass index, blood pressure, prevalence of hypertension and non-insulin-dependent diabetes mellitus, and social class. In 280 (9.6%) men with Le(a[minus]b[minus]), alcohol was the only risk factor significantly associated with risk of IHD. There was a significant inverse dose-effect relation between alcohol consumption and risk; trend tests, with adjustment for age, were significant for fatal IHD (p=0.02), all IHD (p=0.03), and all causes of death (p=0.02). In 2649 (90.4%) men with other phenotypes, there was a limited negative association with alcohol consumption. In Le(a[minus]b[minus]) men, a group genetically at high risk of IHD, alcohol consumption seems to be especially protective. The authors suggest that alcohol consumption may modify insulin resistance in Le(a[minus]b[minus]) men.

  19. Phenotypic plasticity and divergence in gene expression.

    Science.gov (United States)

    Healy, Timothy M; Schulte, Patricia M

    2015-07-01

    The extent to which phenotypic plasticity, or the ability of a single genotype to produce different phenotypes in different environments, impedes or promotes genetic divergence has been a matter of debate within evolutionary biology for many decades (see, for example, Ghalambor et al. ; Pfennig et al. ). Similarly, the role of evolution in shaping phenotypic plasticity remains poorly understood (Pigliucci ). In this issue of Molecular Ecology, Dayan et al. () provide empirical data relevant to these questions by assessing the extent of plasticity and divergence in the expression levels of 2272 genes in muscle tissue from killifish (genus Fundulus) exposed to different temperatures. F. heteroclitus (Fig. A) and F. grandis are minnows that inhabit estuarine marshes (Fig. B) along the coasts of the Atlantic Ocean and Gulf of Mexico in North America. These habitats undergo large variations in temperature both daily and seasonally, and these fish are known to demonstrate substantial phenotypic plasticity in response to temperature change (e.g. Fangue et al. ). Furthermore, the range of F. heteroclitus spans a large latitudinal gradient of temperatures, such that northern populations experience temperatures that are on average ~10°C colder than do southern populations (Schulte ). By comparing gene expression patterns between populations of these fish from different thermal habitats held in the laboratory at three different temperatures, Dayan et al. () address two important questions regarding the interacting effects of plasticity and evolution: (i) How does phenotypic plasticity affect adaptive divergence? and (ii) How does adaptive divergence affect plasticity?

  20. Phenotypic plasticity changes correlations of traits following experimental introductions of Trinidadian guppies (Poecilia reticulata).

    Science.gov (United States)

    Handelsman, Corey A; Ruell, Emily W; Torres-Dowdall, Julián; Ghalambor, Cameron K

    2014-11-01

    Colonization of novel environments can alter selective pressures and act as a catalyst for rapid evolution in nature. Theory and empirical studies suggest that the ability of a population to exhibit an adaptive evolutionary response to novel selection pressures should reflect the presence of sufficient additive genetic variance and covariance for individual and correlated traits. As correlated traits should not respond to selection independently, the structure of correlations of traits can bias or constrain adaptive evolution. Models of how multiple correlated traits respond to selection often assume spatial and temporal stability of trait-correlations within populations. Yet, trait-correlations can also be plastic in response to environmental variation. Phenotypic plasticity, the ability of a single genotype to produce different phenotypes across environments, is of particular interest because it can induce population-wide changes in the combination of traits exposed to selection and change the trajectory of evolutionary divergence. We tested the ability of phenotypic plasticity to modify trait-correlations by comparing phenotypic variance and covariance in the body-shapes of four experimental populations of Trinidadian guppies (Poecilia reticulata) to their ancestral population. We found that phenotypic plasticity produced both adaptive and novel aspects of body-shape, which was repeated in all four experimental populations. Further, phenotypic plasticity changed patterns of covariance among morphological characters. These findings suggest our ability to make inferences about patterns of divergence based on correlations of traits in extant populations may be limited if novel environments not only induce plasticity in multiple traits, but also change the correlations among the traits.

  1. Automated FingerPrint Background removal: FPB

    Directory of Open Access Journals (Sweden)

    Morgante Michele

    2009-04-01

    Full Text Available Abstract Background The construction of a whole-genome physical map has been an essential component of numerous genome projects initiated since the inception of the Human Genome Project. Its usefulness has been proved for whole-genome shotgun projects as a post-assembly validation and recently it has also been used in the assembly step to constrain on BACs positions. Fingerprinting is usually the method of choice for construction of physical maps. A clone fingerprint is composed of true peaks representing real fragments and background peaks, mainly composed of E. coli genomic DNA, partial digestions, star activity by-products, and machine background. High-throughput fingerprinting leads to the production of thousands of BAC clone fingerprints per day. That is why background peaks removal has become an important issue and needs to be automatized, especially in capillary electrophoresis based fingerprints. Results At the moment, the only tools available for such a task are GenoProfiler and its descendant FPMiner. The large variation in the quality of fingerprints that is usually present in large fingerprinting projects represents a major difficulty in the correct removal of background peaks that has only been partially addressed by the methods so far adopted that all require a long manual optimization of parameters. Thus, we implemented a new data-independent tool, FPB (FingerPrint Background removal, suitable for large scale projects as well as mapping of few clones. Conclusion FPB is freely available at http://www.appliedgenomics.org/tools.php. FPB was used to remove the background from all fingerprints of three grapevine physical map projects. The first project consists of about 50,000 fingerprints, the second one consists of about 70,000 fingerprints, and the third one consists of about 45,000 fingerprints. In all cases a successful assembly was built.

  2. The Modified Magnetohydrodynamical Equations

    Institute of Scientific and Technical Information of China (English)

    EvangelosChaliasos

    2003-01-01

    After finding the really self-consistent electromagnetic equations for a plasma, we proceed in a similar fashion to find how the magnetohydrodynamical equations have to be modified accordingly. Substantially this is done by replacing the "Lorentz" force equation by the correct (in our case) force equation. Formally we have to use the vector potential instead of the magnetic field intensity. The appearance of the formulae presented is the one of classical vector analysis. We thus find a set of eight equations in eight unknowns, as previously known concerning the traditional MHD equations.

  3. Modified Slash Lindley Distribution

    Directory of Open Access Journals (Sweden)

    Jimmy Reyes

    2017-01-01

    Full Text Available In this paper we introduce a new distribution, called the modified slash Lindley distribution, which can be seen as an extension of the Lindley distribution. We show that this new distribution provides more flexibility in terms of kurtosis and skewness than the Lindley distribution. We derive moments and some basic properties for the new distribution. Moment estimators and maximum likelihood estimators are calculated using numerical procedures. We carry out a simulation study for the maximum likelihood estimators. A fit of the proposed model indicates good performance when compared with other less flexible models.

  4. The Modified Magnetohydrodynamical Equations

    Institute of Scientific and Technical Information of China (English)

    Evangelos Chaliasos

    2003-01-01

    After finding the really self-consistent electromagnetic equations for a plasma, we proceed in a similarfashion to find how the magnetohydrodynamical equations have to be modified accordingly. Substantially this is doneby replacing the "Lorentz" force equation by the correct (in our case) force equation. Formally we have to use the vectorpotential instead of the magnetic field intensity. The appearance of the formulae presented is the one of classical vectoranalysis. We thus find a set of eight equations in eight unknowns, as previously known concerning the traditional MHDequations.

  5. Dynamical properties of background neural networks with uniform firing rate and background input

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Lei [Computational Intelligence Laboratory, School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054 (China); Yi Zhang [Computational Intelligence Laboratory, School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054 (China)]. E-mail: zhangyi@uestc.edu.cn

    2007-08-15

    In this paper, the dynamic properties of the background neural networks with the uniform firing rate and background input is investigated with a series of mathematical arguments including nondivergence, global attractivity and complete stability analysis. Moreover, it shows that shifting the background level affects the existence and stability of the equilibrium point. Depending on the increase or decrease in background input, the network can engender bifurcation and chaos. It may be have one or two different stable firing levels. That means the background neural network can exhibit not only monostability but also multistability.

  6. COBE Observations of the Cosmic Infrared Background

    CERN Document Server

    Wright, E L

    2004-01-01

    The Diffuse InfraRed Background Experiment on COBE measured the total infrared signal seen from space at a distance of 1 astronomical unit from the Sun. Using time variations as the Earth orbits the Sun, it is possible to remove most of the foreground signal produced by the interplanetary dust cloud [zodiacal light]. By correlating the DIRBE signal with the column density of atomic hydrogen measured using the 21 cm line, it is possible to remove most of the foreground signal produced by interstellar dust, although one must still be concerned by dust associated with H_2 (molecular gas) and H II (the warm ionized medium). DIRBE was not able to determine the CIRB in the 5-60 micron wavelength range, but did detect both a far infrared background and a near infrared background. The far infrared background has an integrated intensity of about 34 nW/m^2/sr, while the near infrared and optical extragalactic background has about 59 nW/m^2/sr. The Far InfraRed Absolute Spectrophotometer (FIRAS) on COBE has been used to...

  7. Holographic backgrounds from D-brane probes

    CERN Document Server

    Moskovic, Micha

    2014-01-01

    This thesis focuses on the derivation of holographic backgrounds from the field theory side, without using any supergravity equations of motion. Instead, we rely on the addition of probe D-branes to the stack of D-branes generating the background. From the field theory description of the probe branes, one can compute an effective action for the probes (in a suitable low-energy/near-horizon limit) by integrating out the background branes. Comparing this action with the generic probe D-brane action then allows to determine the holographic background dual to the considered field theory vacuum. In the first part, the required pre-requisites of field and string theory are recalled and this strategy to derive holographic backgrounds is explained in more detail on the basic case of D3-branes in flat space probed by a small number of D-instantons. The second part contains our original results, which have already appeared in arXiv:1301.3738, arXiv:1301.7062 and arXiv:1312.0621. We first derive the duals to three conti...

  8. Infrared Background and Missiles Signature Survey

    Directory of Open Access Journals (Sweden)

    D.V. Renuka

    2013-11-01

    Full Text Available The proliferation of the missile threats in the existing threat scenario for airborne platform is a serious point of consideration for any mission planning. Missile warning system is an electronic warfare support system which gives warning to the pilot when a missile is detected in the scenario. The airborne platform has to be installed with missile warning sensors to give a spherical coverage, so that the sensors can detect the IR intensity variation in the ground scenario. This IR intensity variation has to be further analysed to differentiate the raising missile intensity from the varying background clutter. In order to differentiate the threat from the background clutter, the system should have sufficient background data set for online comparison thereby having less false alarm rate. The efficiency and performance of any missile warning system is validated with respect to its probability of declaration against the false alarm rate. Hence, to realize an efficient functioning of missile warning system, building IR background data base and missile signature database are the primary task. This paper details the methodology to be adapted for the building of tactical missile IR signatures and background data.

  9. Infrared Background and Missiles Signature Survey

    Directory of Open Access Journals (Sweden)

    D.V. Renuka

    2013-12-01

    Full Text Available The proliferation of the missile threats in the existing threat scenario for airborne platform is a serious point of consideration for any mission planning. Missile warning system is an electronic warfare support system which gives warning to the pilot when a missile is detected in the scenario. The airborne platform has to be installed with missile warning sensors to give a spherical coverage, so that the sensors can detect the IR intensity variation in the ground scenario. This IR intensity variation has to be further analysed to differentiate the raising missile intensity from the varying background clutter. In order to differentiate the threat from the background clutter, the system should have sufficient background data set for online comparison thereby having less false alarm rate. The efficiency and performance of any missile warning system is validated with respect to its probability of declaration against the false alarm rate. Hence, to realize an efficient functioning of missile warning system, building IR background data base and missile signature database are the primary task. This paper details the methodology to be adapted for the building of tactical missile IR signatures and background data.Defence Science Journal, 2013, 63(6, pp.611-615, DOI:http://dx.doi.org/10.14429/dsj.63.5762

  10. On conformal higher spins in curved background

    Science.gov (United States)

    Grigoriev, M.; Tseytlin, A. A.

    2017-03-01

    We address the question of how to represent an interacting action for a tower of conformal higher spin fields in a form covariant with respect to a background metric. We use the background metric to define the star product which plays a central role in the definition of the corresponding gauge transformations. By analogy with the kinetic term in the 4-derivative Weyl gravity action expanded near an on-shell background one expects that the kinetic term in such an action should be gauge-invariant in a Bach-flat metric. We demonstrate this fact to first order in expansion in powers of the curvature of the background metric. This generalizes the result of arXiv:1404.7452 for spin 3 case to all conformal higher spins. We also comment on a possibility of extending this claim to terms quadratic in the curvature and discuss the appearance of background-dependent mixing terms in the quadratic part of the conformal higher spin action.

  11. On conformal higher spins in curved background

    CERN Document Server

    Grigoriev, M

    2016-01-01

    We address the question of how to represent an interacting action for the tower of conformal higher spin fields in a form covariant with respect to a background metric. We use a background metric to define a star product which plays a central role in the definition of the corresponding gauge transformations. By an analogy with the kinetic term in the 4-derivative Weyl gravity action expanded near an on-shell background one expects that the kinetic term in such an action should be gauge-invariant in a Bach-flat metric. We demonstrate this fact to first order in expansion in powers of the curvature of the background metric. This generalizes the result of arXiv:1404.7452 for spin 3 case to all conformal higher spins. We also comment on a possibility of extending this claim to terms quadratic in the curvature and discuss the appearance of background-dependent mixing terms in the quadratic part of the conformal higher spin action.

  12. Can one measure the Cosmic Neutrino Background?

    CERN Document Server

    Faessler, Amand; Kovalenko, Sergey; Simkovic, Fedor

    2016-01-01

    The Cosmic Microwave Background (CMB) yields information about our Universe at around 380 000 years after the Big Bang (BB). Due to the weak interaction of the neutrinos with matter the Cosmic Neutrino Background (CNB) should give information about a much earlier time of our Universe, around one second after the Big Bang. Probably the most promising method to `see' the Cosmic Neutrino Background is the capture of the electron neutrinos from the Background by Tritium, which then decays into 3He and an electron with the energy of the the Q-value = 18.562 keV plus the electron neutrino rest mass. The `KArlsruhe TRItium Neutrino' (KATRIN) experiment, which is in preparation, seems presently the most sensitive proposed method for measuring the electron antineutrino mass. At the same time KATRIN can also look by the reaction: electron neutrino (~1.95 Kelvin) + 3H --> 3He + e- (with the energy Q = 18.6 keV + electron neutrino mass). The capture of the Cosmic Background Neutrinos (CNB) should show in the electron spe...

  13. Factor analysis in the Genetics of Asthma International Network family study identifies five major quantitative asthma phenotypes

    NARCIS (Netherlands)

    Pillai, S. G.; Tang, Y.; van den Oord, E.; Klotsman, M.; Barnes, K.; Carlsen, K.; Gerritsen, J.; Lenney, W.; Silverman, M.; Sly, P.; Sundy, J.; Tsanakas, J.; von Berg, A.; Whyte, M.; Ortega, H. G.; Anderson, W. H.; Helms, P. J.

    2008-01-01

    Background Asthma is a clinically heterogeneous disease caused by a complex interaction between genetic susceptibility and diverse environmental factors. In common with other complex diseases the lack of a standardized scheme to evaluate the phenotypic variability poses challenges in identifying the

  14. Non-CLL-like monoclonal B-Cell lymphocytosis in the general population: Prevalence and phenotypic/genetic characteristics

    NARCIS (Netherlands)

    W.G. Nieto (Wendy); C. Teodosio (Cristina); A. López (Antonio); A. Rodríguez-Caballero (Arancha); A. Romero (Alfonso); P. Bárcena (Paloma); M.L. Gutierrez; A.W. Langerak (Ton); P. Fernandez-Navarro (Paulino); A. Orfao; J. Almeida (Julia); A.O.M.C.C.S. Santa Marta de Tormes; B.H.P.C.S. Garrido Sur; C.L.M.T.C.S. Ledesma; C.R.J.M.C.S. Alba de Tormes; C.L.R.C.S.F. Villalobos; D.V.P.J.C.S. Peñaranda; F.E.E.C.S. Pizarrales-Vidal; G.R.B.L.C.S. La Alberca; G.S.F.C.S. Periurbana Norte; G.M.J.C.S. Guijuelo; G.M.J.M.C.S. Vitigudino; J.R.M.J.C.S. Garrido Norte; J.C.T.B.C.S. Elena Ginel Diez; M.P.M.C.S. Fuentes de Oñoro; M.L.J.C.S. San Juan; M.D.M.P.C.S. Miguel Armijo; S.A.B.C.S. Aldeadavila de La Ribera; S.P.R.C.S. San Jose

    2010-01-01

    textabstractBackground: Monoclonal B-cell lymphocytosis (MBL) indicates <5 × 109peripheral blood (PB) clonal B-cells/L in healthy individuals. In most cases, MBL cells show similar phenotypic/genetic features to chronic lymphocytic leukemia cells - CLL-like MBL - but little is known about non-CLL-li

  15. Sensorimotor adaptation is influenced by background music.

    Science.gov (United States)

    Bock, Otmar

    2010-06-01

    It is well established that listening to music can modify subjects' cognitive performance. The present study evaluates whether this so-called Mozart Effect extends beyond cognitive tasks and includes sensorimotor adaptation. Three subject groups listened to musical pieces that in the author's judgment were serene, neutral, or sad, respectively. This judgment was confirmed by the subjects' introspective reports. While listening to music, subjects engaged in a pointing task that required them to adapt to rotated visual feedback. All three groups adapted successfully, but the speed and magnitude of adaptive improvement was more pronounced with serene music than with the other two music types. In contrast, aftereffects upon restoration of normal feedback were independent of music type. These findings support the existence of a "Mozart effect" for strategic movement control, but not for adaptive recalibration. Possibly, listening to music modifies neural activity in an intertwined cognitive-emotional network.

  16. Pythia Jet Finding Study with Trento Backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Joseph [United States Naval Academy, Annapolis, MD (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Soltz, Ron [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-06-22

    We present results applying the Pythia SlowJet Finder to Pythia generated QCD and QED hard processes in the presence of simulated heavy ion backgrounds. The hard process events are generated with Pythia version 8.219 for √sNN=200 GeV proton-proton collisions and the backgrounds are generated by the Reduced Thickness Event-by-event Nuclear Topology model TRENTo for Au-Au collisions with a nucleon-nucleon cross-section of 4.23 fm2. The TRENTo model is used to calculate the initial entropy and ellipticity from which the total charged particle multiplicity and elliptic ow are determined. We report results in the form of event displays, total pT distributions, and fragmentation distributions for SlowJet applied to Pythia events with and without the simulated heavy ion backgrounds.

  17. Background modeling for the GERDA experiment

    CERN Document Server

    Becerici-Schmidt, N

    2013-01-01

    The neutrinoless double beta (0nubb) decay experiment GERDA at the LNGS of INFN has started physics data taking in November 2011. This paper presents an analysis aimed at understanding and modeling the observed background energy spectrum, which plays an essential role in searches for a rare signal like 0nubb decay. A very promising preliminary model has been obtained, with the systematic uncertainties still under study. Important information can be deduced from the model such as the expected background and its decomposition in the signal region. According to the model the main background contributions around Qbb come from Bi-214, Th-228, K-42, Co-60 and alpha emitting isotopes in the Ra-226 decay chain, with a fraction depending on the assumed source positions.

  18. Background Model for the Majorana Demonstrator

    CERN Document Server

    Cuesta, C; Aguayo, E; Avignone, F T; Barabash, A S; Bertrand, F E; Boswell, M; Brudanin, V; Busch, M; Byram, D; Caldwell, A S; Chan, Y-D; Christofferson, C D; Combs, D C; Cuesta, C; Detwiler, J A; Doe, P J; Efremenko, Yu; Egorov, V; Ejiri, H; Elliott, S R; Fast, J E; Finnerty, P; Fraenkle, F M; Galindo-Uribarri, A; Giovanetti, G K; Goett, J; Green, M P; Gruszko, J; Guiseppe, V E; Gusev, K; Hallin, A L; Hazama, R; Hegai, A; Henning, R; Hoppe, E W; Howard, S; Howe, M A; Keeter, K J; Kidd, M F; Kochetov, O; Konovalov, S I; Kouzes, R T; LaFerriere, B D; Leon, J; Leviner, L E; Loach, J C; MacMullin, J; MacMullin, S; Martin, R D; Meijer, S; Mertens, S; Nomachi, M; Orrell, J L; O'Shaughnessy, C; Overman, N R; Phillips, D G; Poon, A W P; Pushkin, K; Radford, D C; Rager, J; Rielage, K; Robertson, R G H; Romero-Romero, E; Ronquest, M C; Schubert, A G; Shanks, B; Shima, T; Shirchenko, M; Snavely, K J; Snyder, N; Suriano, A M; Thompson, J; Timkin, V; Tornow, W; Trimble, J E; Varner, R L; Vasilyev, S; Vetter, K; Vorren, K; White, B R; Wilkerson, J F; Wiseman, C; Xu, W; Yakushev, E; Young, A R; Yu, C H; Yumatov, V

    2014-01-01

    The Majorana Collaboration is constructing a system containing 40 kg of HPGe detectors to demonstrate the feasibility and potential of a future tonne-scale experiment capable of probing the neutrino mass scale in the inverted-hierarchy region. To realize this, a major goal of the Majorana Demonstrator is to demonstrate a path forward to achieving a background rate at or below 1 cnt/(ROI-t-y) in the 4 keV region of interest around the Q-value at 2039 keV. This goal is pursued through a combination of a significant reduction of radioactive impurities in construction materials with analytical methods for background rejection, for example using powerful pulse shape analysis techniques profiting from the p-type point contact HPGe detectors technology. The effectiveness of these methods is assessed using simulations of the different background components whose purity levels are constrained from radioassay measurements.

  19. Cross correlations of the cosmic infrared background

    CERN Document Server

    Zhang, P

    2003-01-01

    Cosmic infrared background (CIB) is a sensitive measure of the structure formation of the universe, especially the star formation history. But this background is overwhelmed by foregrounds. The cross correlation of CIB with galaxies is able to eliminate such foregrounds, minimize and localize several backgrounds which could bias the study of the star formation history. The cross correlation study of CIB has three advantages. (1) Combining the galaxy photometric redshift information, it directly measures the structure formation history. (2) The sky area used for CIB analysis is no long limited to the relatively clean sky. The utilization of CIB full sky data minimizes the sample variance. (3) The CIB measurement is no longer limited to several narrow frequency windows. This allows the measurement of CIB based on integrated intensity, whose theoretical prediction is based on energy conservation, thus is fairly model independent and robust. The cross correlation can be measured with 10% accuracy (statistical and...

  20. Tidal Forces in Naked Singularity Backgrounds

    CERN Document Server

    Goel, Akash; Roy, Pratim; Sarkar, Tapobrata

    2015-01-01

    The end stage of a gravitational collapse process can generically result in a black hole or a naked singularity. Here we undertake a comparative analysis of the nature of tidal forces in these backgrounds. The effect of such forces is generically exemplified by the Roche limit, which predicts the distance within which a celestial object disintegrates due to the tidal effects of a second more massive object. In this paper, using Fermi normal coordinates, we numerically compute the Roche limit for a class of non-rotating naked singularity backgrounds, and compare them with known results for Schwarzschild black holes. Our analysis indicates that there might be substantially large deviations in the magnitudes of tidal forces in naked singularity backgrounds, compared to the black hole cases. If observationally established, these can prove to be an effective indicator of the nature of the singularity at a galactic centre.