A mixed incoherent feed-forward loop contributes to the regulation of bacterial photosynthesis genes.

Science.gov (United States)

Mank, Nils N; Berghoff, Bork A; Klug, Gabriele

2013-03-01

Living cells use a variety of regulatory network motifs for accurate gene expression in response to changes in their environment or during differentiation processes. In Rhodobacter sphaeroides, a complex regulatory network controls expression of photosynthesis genes to guarantee optimal energy supply on one hand and to avoid photooxidative stress on the other hand. Recently, we identified a mixed incoherent feed-forward loop comprising the transcription factor PrrA, the sRNA PcrZ and photosynthesis target genes as part of this regulatory network. This point-of-view provides a comparison to other described feed-forward loops and discusses the physiological relevance of PcrZ in more detail.

Statistical identification of the confidence limits of open loop transfer functions obtained by MAR analysis

International Nuclear Information System (INIS)

Antonopoulos-Domis, M.; Mourtzanos, K.

1996-01-01

Estimators of the confidence limits of open loop transfer functions via Multivariate Auto-Regressive (MAR) modelling are not available in the literature. The statistics of open loop transfer functions obtained by MAR modelling are investigated via numerical experiments. A system of known open loop transfer functions is simulated digitally and excited by random number series. The digital signals of the simulated system are then MAR modelled and the open loop transfer functions are estimated. Performing a large number of realizations, mean values and variances of the open loop transfer functions are estimated. It is found that if the record length N of each realization is long enough then the estimates of open loop transfer functions follow normal distribution. The variance of the open loop transfer functions is proportional to 1/N. For MAR processes the asymptotic covariance matrix of the estimate of open loop transfer functions was found in agreement with theoretical prediction. (author)

The visual corticostriatal loop through the tail of the caudate: Circuitry and function

Directory of Open Access Journals (Sweden)

Carol A Seger

2013-12-01

Full Text Available Although high level visual cortex projects to a specific region of the striatum, the tail of the caudate, and participates in corticostriatal loops, the function of this visual corticostriatal system is not well understood. This article first reviews what is known about the anatomy of the visual corticostriatal loop across mammals, including rodents, cats, monkeys, and humans. Like other corticostriatal systems, the visual corticostriatal system includes both closed loop components (recurrent projections that return to the originating cortical location and open loop components (projections that terminate in other neural regions. The article then reviews what previous empircal research has shown about the function of the tail of the caudate. The article finally addresses the possible functions of the closed and open loop connections of the visual loop in the context of theories and computational models of corticostriatal function.

Can we observe open loop transfer functions in a stochastic feedback system ?

International Nuclear Information System (INIS)

Kishida, Kuniharu; Suda, Nobuhide.

1991-01-01

There are two kinds of problems concerning open loop and closed loop transfer functions in a feedback system. One is a problem even in the deterministic case, and the other is in the stochastic case. In the deterministic case it is guaranteed under a necessary and sufficient condition that total sum of degrees of sub-transfer functions coincides to the degree of the total system. In the stochastic case a systematic understanding of a physical state model, a theoretical innovation model and a data-oriented innovation model is indispensable for determination of open loop transfer functions from time series data. Undesirable factors appear in determination of open loop transfer functions, since a transfer function matrix from input noises to output variables has a redundancy factor of diagonal matrix. (author)

First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin.

Science.gov (United States)

Yamashita, Takahiro; Tose, Koji; Shichida, Yoshinori

2008-01-01

G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.

Modulation of dynamic modes by interplay between positive and negative feedback loops in gene regulatory networks

Science.gov (United States)

Wang, Liu-Suo; Li, Ning-Xi; Chen, Jing-Jia; Zhang, Xiao-Peng; Liu, Feng; Wang, Wei

2018-04-01

A positive and a negative feedback loop can induce bistability and oscillation, respectively, in biological networks. Nevertheless, they are frequently interlinked to perform more elaborate functions in many gene regulatory networks. Coupled positive and negative feedback loops may exhibit either oscillation or bistability depending on the intensity of the stimulus in some particular networks. It is less understood how the transition between the two dynamic modes is modulated by the positive and negative feedback loops. We developed an abstract model of such systems, largely based on the core p53 pathway, to explore the mechanism for the transformation of dynamic behaviors. Our results show that enhancing the positive feedback may promote or suppress oscillations depending on the strength of both feedback loops. We found that the system oscillates with low amplitudes in response to a moderate stimulus and switches to the on state upon a strong stimulus. When the positive feedback is activated much later than the negative one in response to a strong stimulus, the system exhibits long-term oscillations before switching to the on state. We explain this intriguing phenomenon using quasistatic approximation. Moreover, early switching to the on state may occur when the system starts from a steady state in the absence of stimuli. The interplay between the positive and negative feedback plays a key role in the transitions between oscillation and bistability. Of note, our conclusions should be applicable only to some specific gene regulatory networks, especially the p53 network, in which both oscillation and bistability exist in response to a certain type of stimulus. Our work also underscores the significance of transient dynamics in determining cellular outcome.

The one-loop Green's functions of dimensionally reduced gauge theories

International Nuclear Information System (INIS)

Ketov, S.V.; Prager, Y.S.

1988-01-01

The dimensional regularization technique as well as that by dimensional reduction is applied to the calculation of the regularized one-loop Green's functions in dsub(o)-dimensional Yang-Mills theory with real massless scalars and spinors in arbitrary (real) representations of a gauge group G. As a particular example, the super-symmetrically regularized one-loop Green's functions of the N=4 supersymmetric Yang-Mills model are derived. (author). 17 refs

Four-loop beta function in the Wess-Zumino model

International Nuclear Information System (INIS)

Avdeev, L.V.; Gorishny, S.G.

1982-01-01

A method for calculating momentum integrals, proposed by Chetyrkin and Tkachov, is applied to the foUr-loop calculations of the ν-function in the Wess-Zumino model. The main advantage of the used method is the existence of a relatively simple calculational algorithm that allows one to write an effective computer program on the system of analytical evaluations SCHOONSCHIP. Any three-loop integral with one external momentum can be computed by this program. The four-loop calculation in the WZ model is one of the first and simplest applications of the program

Driver steering model for closed-loop steering function analysis

Science.gov (United States)

Bolia, Pratiksh; Weiskircher, Thomas; Müller, Steffen

2014-05-01

In this paper, a two level preview driver steering control model for the use in numerical vehicle dynamics simulation is introduced. The proposed model is composed of cascaded control loops: The outer loop is the path following layer based on potential field framework. The inner loop tries to capture the driver's physical behaviour. The proposed driver model allows easy implementation of different driving situations to simulate a wide range of different driver types, moods and vehicle types. The expediency of the proposed driver model is shown with the help of developed driver steering assist (DSA) function integrated with a conventional series production (Electric Power steering System with rack assist servo unit) system. With the help of the DSA assist function, the driver is prevented from over saturating the front tyre forces and loss of stability and controllability during cornering. The simulation results show different driver reactions caused by the change in the parameters or properties of the proposed driver model if the DSA assist function is activated. Thus, the proposed driver model is useful for the advanced driver steering and vehicle stability assist function evaluation in the early stage of vehicle dynamics handling and stability evaluation.

Identification of a basic helix-loop-helix-type transcription regulator gene in Aspergillus oryzae by systematically deleting large chromosomal segments.

Science.gov (United States)

Jin, Feng Jie; Takahashi, Tadashi; Machida, Masayuki; Koyama, Yasuji

2009-09-01

We previously developed two methods (loop-out and replacement-type recombination) for generating large-scale chromosomal deletions that can be applied to more effective chromosomal engineering in Aspergillus oryzae. In this study, the replacement-type method is used to systematically delete large chromosomal DNA segments to identify essential and nonessential regions in chromosome 7 (2.93 Mb), which is the smallest A. oryzae chromosome and contains a large number of nonsyntenic blocks. We constructed 12 mutants harboring deletions that spanned 16- to 150-kb segments of chromosome 7 and scored phenotypic changes in the resulting mutants. Among the deletion mutants, strains designated Delta5 and Delta7 displayed clear phenotypic changes involving growth and conidiation. In particular, the Delta5 mutant exhibited vigorous growth and conidiation, potentially beneficial characteristics for certain industrial applications. Further deletion analysis allowed identification of the AO090011000215 gene as the gene responsible for the Delta5 mutant phenotype. The AO090011000215 gene was predicted to encode a helix-loop-helix binding protein belonging to the bHLH family of transcription factors. These results illustrate the potential of the approach for identifying novel functional genes.

SQED two-loop beta function in the context of Implicit regularization

International Nuclear Information System (INIS)

Cherchiglia, Adriano Lana; Sampaio, Marcos; Nemes, Maria Carolina

2013-01-01

Full text: In this work we present the state-of-art for Implicit Regularization (IReg) in the context of supersymmetric theories. IReg is a four-dimensional regularization technique in momentum space which disentangles, in a consistent way at arbitrary order, the divergencies, regularization dependent and finite parts of any Feynman amplitude. Since it does not resort to modifications on the physical space-time dimensions of the underlying quantum field theoretical model, it can be consistently applied to supersymmetric theories. First we describe the technique and present previous results for supersymmetric models: the two-loop beta function for the Wess-Zumino model (both in the component and superfield formalism); the two-loop beta function for Super Yang-Mills (in the superfield formalism using the background field technique). After, we present our calculation of the two-loop beta function for massless and massive SQED using the superfield formalism with and without resorting to the background field technique. We find that only in the second case the two-loop divergence cancels out. We argue it is due to an anomalous Jacobian under the rescaling of the fields in the path-integral which is necessary for the application of the supersymmetric background field technique. We find, however, that in both cases the two-loop coefficients of beta function are non-null. Finally we briefly discuss the anomaly puzzle in the context of our technique. (author)

Heavy-quark QCD vacuum polarisation function. Analytical results at four loops

International Nuclear Information System (INIS)

Kniehl, B.A.; Kotikov, A.V.

2006-07-01

The first two moments of the heavy-quark vacuum polarisation function at four loops in quantum chromo-dynamics are found in fully analytical form by evaluating the missing massive four-loop tadpole master integrals. (orig.)

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters.

Science.gov (United States)

Chen, Liang; Chen, Jia-Yu; Zhang, Xuan; Gu, Ying; Xiao, Rui; Shao, Changwei; Tang, Peng; Qian, Hao; Luo, Daji; Li, Hairi; Zhou, Yu; Zhang, Dong-Er; Fu, Xiang-Dong

2017-11-16

R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase-H-based approach; this reveals predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. Transcription perturbation experiments further indicate that R-loop induction correlates to transcriptional pausing. Interestingly, we note that most mapped R-loops are each linked to a nearby free RNA end; by using a ribozyme to co-transcriptionally cleave nascent RNA, we demonstrate that such a free RNA end coupled with a G/C-skewed sequence is necessary and sufficient to induce R-loop. These findings provide a topological solution for RNA invasion into duplex DNA and suggest an order for R-loop initiation and elongation in an opposite direction to that previously proposed. Copyright © 2017 Elsevier Inc. All rights reserved.

A Nodal-independent and tissue-intrinsic mechanism controls heart-looping chirality

Science.gov (United States)

Noël, Emily S.; Verhoeven, Manon; Lagendijk, Anne Karine; Tessadori, Federico; Smith, Kelly; Choorapoikayil, Suma; den Hertog, Jeroen; Bakkers, Jeroen

2013-11-01

Breaking left-right symmetry in bilateria is a major event during embryo development that is required for asymmetric organ position, directional organ looping and lateralized organ function in the adult. Asymmetric expression of Nodal-related genes is hypothesized to be the driving force behind regulation of organ laterality. Here we identify a Nodal-independent mechanism that drives asymmetric heart looping in zebrafish embryos. In a unique mutant defective for the Nodal-related southpaw gene, preferential dextral looping in the heart is maintained, whereas gut and brain asymmetries are randomized. As genetic and pharmacological inhibition of Nodal signalling does not abolish heart asymmetry, a yet undiscovered mechanism controls heart chirality. This mechanism is tissue intrinsic, as explanted hearts maintain ex vivo retain chiral looping behaviour and require actin polymerization and myosin II activity. We find that Nodal signalling regulates actin gene expression, supporting a model in which Nodal signalling amplifies this tissue-intrinsic mechanism of heart looping.

Function of the activated protein C (APC) autolysis loop in activated FVIII inactivation.

Science.gov (United States)

Cramer, Thomas J; Gale, Andrew J

2011-06-01

Activated protein C (APC) binds to its substrates activated factor V (FVa) and activated factor VIII (FVIIIa) with a basic exosite that consists of loops 37, 60, 70 and the autolysis loop. These loops have a high density of basic residues, resulting in a positive charge on the surface of APC. Many of these residues are important in the interaction of APC with FVa and FVIIIa. The current study focused on the function of the autolysis loop in the interaction with FVIIIa. This loop was previously shown to interact with FVa, and it inhibits APC inactivation by plasma serpins. Charged residues of the autolysis loop were individually mutated to alanine and the activity of these mutants was assessed in functional FVIIIa inactivation assays. The autolysis loop was functionally important for FVIIIa inactivation. Mutation of R306, K311 and R314 each resulted in significantly reduced FVIIIa inactivation. The inactivating cleavages of FVIIIa at R336 and R562 were affected equally by the mutations. Protein S and FV stimulated cleavage at R562 more than cleavage at R336, independent of mutations in the autolysis loop. Together, these results confirmed that the autolysis loop plays a significant role as part of the basic exosite on APC in the interaction with FVIIIa. © 2011 Blackwell Publishing Ltd.

Reliability analysis and component functional allocations for the ESF multi-loop controller design

International Nuclear Information System (INIS)

Hur, Seop; Kim, D.H.; Choi, J.K.; Park, J.C.; Seong, S.H.; Lee, D.Y.

2006-01-01

This paper deals with the reliability analysis and component functional allocations to ensure the enhanced system reliability and availability. In the Engineered Safety Features, functionally dependent components are controlled by a multi-loop controller. The system reliability of the Engineered Safety Features-Component Control System, especially, the multi-loop controller which is changed comparing to the conventional controllers is an important factor for the Probability Safety Assessment in the nuclear field. To evaluate the multi-loop controller's failure rate of the k-out-of-m redundant system, the binomial process is used. In addition, the component functional allocation is performed to tolerate a single multi-loop controller failure without the loss of vital operation within the constraints of the piping and component configuration, and ensure that mechanically redundant components remain functional. (author)

The Y-located gonadoblastoma gene TSPY amplifies its own expression through a positive feedback loop in prostate cancer cells

Energy Technology Data Exchange (ETDEWEB)

Kido, Tatsuo; Lau, Yun-Fai Chris, E-mail: Chris.Lau@UCSF.edu

2014-03-28

Highlights: • Y-encoded proto-oncoprotein TSPY amplifies its expression level via a positive feedback loop. • TSPY binds to the chromatin/DNA at exon 1 of TSPY gene. • TSPY enhances the gene expression in a TSPY exon 1 sequence dependent manner. • The conserved SET/NAP-domain is essential for TSPY transactivation. • Insights on probable mechanisms on TSPY exacerbation on cancer development in men. - Abstract: The testis-specific protein Y-encoded (TSPY) is a repetitive gene located on the gonadoblastoma region of the Y chromosome, and has been considered to be the putative gene for this oncogenic locus on the male-only chromosome. It is expressed in spermatogonial cells and spermatocytes in normal human testis, but abundantly in gonadoblastoma, testicular germ cell tumors and a variety of somatic cancers, including melanoma, hepatocellular carcinoma and prostate cancer. Various studies suggest that TSPY accelerates cell proliferation and growth, and promotes tumorigenesis. In this report, we show that TSPY could bind directly to the chromatin/DNA at exon 1 of its own gene, and greatly enhance the transcriptional activities of the endogenous gene in the LNCaP prostate cancer cells. Domain mapping analyses of TSPY have localized the critical and sufficient domain to the SET/NAP-domain. These results suggest that TSPY could efficiently amplify its expression and oncogenic functions through a positive feedback loop, and contribute to the overall tumorigenic processes when it is expressed in various human cancers.

The four-loop six-gluon NMHV ratio function

Energy Technology Data Exchange (ETDEWEB)

Dixon, Lance J. [SLAC National Accelerator Lab., Stanford, CA (United States); California Inst. of Technology (CalTech), Pasadena, CA (United States); von Hippel, Matt [Perimeter Inst. for Theoretical Physics, Waterloo, ON (Canada); McLeod, Andrew J. [SLAC National Accelerator Lab., Stanford, CA (United States)

2016-01-11

We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N = 4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q^- differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We test the result against multi- Regge predictions at NNLL and N³LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We also study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. Furthermore, we provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.

The four-loop six-gluon NMHV ratio function

Energy Technology Data Exchange (ETDEWEB)

Dixon, Lance J. [SLAC National Accelerator Laboratory, Stanford University,Stanford, CA 94309 (United States); Walter Burke Institute for Theoretical Physics, California Institute of Technology,Pasadena, CA 91125 (United States); Hippel, Matt von [Perimeter Institute for Theoretical Physics,Waterloo, Ontario N2L 2Y5 (Canada); McLeod, Andrew J. [SLAC National Accelerator Laboratory, Stanford University,Stanford, CA 94309 (United States)

2016-01-11

We use the hexagon function bootstrap to compute the ratio function which characterizes the next-to-maximally-helicity-violating (NMHV) six-point amplitude in planar N=4 super-Yang-Mills theory at four loops. A powerful constraint comes from dual superconformal invariance, in the form of a Q̄ differential equation, which heavily constrains the first derivatives of the transcendental functions entering the ratio function. At four loops, it leaves only a 34-parameter space of functions. Constraints from the collinear limits, and from the multi-Regge limit at the leading-logarithmic (LL) and next-to-leading-logarithmic (NLL) order, suffice to fix these parameters and obtain a unique result. We test the result against multi-Regge predictions at NNLL and N{sup 3}LL, and against predictions from the operator product expansion involving one and two flux-tube excitations; all cross-checks are satisfied. We study the analytical and numerical behavior of the parity-even and parity-odd parts on various lines and surfaces traversing the three-dimensional space of cross ratios. As part of this program, we characterize all irreducible hexagon functions through weight eight in terms of their coproduct. We also provide representations of the ratio function in particular kinematic regions in terms of multiple polylogarithms.

LoopIng: a template-based tool for predicting the structure of protein loops.

KAUST Repository

Messih, Mario Abdel

2015-08-06

Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.

Off-Shell Green Functions: One-Loop with Growing Legs

International Nuclear Information System (INIS)

Bashir, A.; Concha-Sanchez, Y.; Delbourgo, R.; Tejeda-Yeomans, M. E.

2008-01-01

One loop calculations in gauge theories in arbitrary gauge and dimensions become exceedingly hard with growing number of external off-shell legs. Let alone higher point functions, such a calculation for even the three point one-loop vertices for quantum electrodynamics (QED) and quantum chromodynamics (QCD) has been made available only recently. In this article, we discuss how Ward-Fradkin-Green-Takahashi identities (WFGTI) may provide a helpful tool in these computations. After providing a glimpse of our suggestion for the case of the 3-point vertex, we present our preliminary findings towards our similar efforts for the 4-point function. We restrict ourselves to the example of scalar quantum electrodynamics (SQED)

Chromatin loops, gene positioning, and gene expression

NARCIS (Netherlands)

Holwerda, S.; de Laat, W.

2012-01-01

Technological developments and intense research over the last years have led to a better understanding of the 3D structure of the genome and its influence on genome function inside the cell nucleus. We will summarize topological studies performed on four model gene loci: the alpha- and beta-globin

The QED vacuum polarization function at four loops and the anomalous magnetic moment at five loops

International Nuclear Information System (INIS)

Baikov, P.

2013-07-01

The anomalous moment of the muon is one of the most fundamental observables. It has been measured experimentally with a very high precision and on theory side the contributions from perturbative QED have been calculated up to five-loop level by numerical methods. Contributions to the muon anomalous magnetic moment from certain diagram classes are also accessible by alternative methods. In this paper we present the evaluation of contributions to the QCD corrections due to insertions of the vacuum polarization function at five-loop level.

The QED vacuum polarization function at four loops and the anomalous magnetic moment at five loops

Energy Technology Data Exchange (ETDEWEB)

Baikov, P. [Moscow State Univ. (Russian Federation). D.V. Skobeltsyn Inst. of Nuclear Physics; Maier, A. [Technische Univ. Muenchen, Garching (Germany). Physics Dept. T31; Marquard, P. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany)

2013-07-15

The anomalous moment of the muon is one of the most fundamental observables. It has been measured experimentally with a very high precision and on theory side the contributions from perturbative QED have been calculated up to five-loop level by numerical methods. Contributions to the muon anomalous magnetic moment from certain diagram classes are also accessible by alternative methods. In this paper we present the evaluation of contributions to the QCD corrections due to insertions of the vacuum polarization function at five-loop level.

Scalar one-loop vertex integrals as meromorphic functions of space-time dimension d

International Nuclear Information System (INIS)

Bluemlein, Johannes; Phan, Khiem Hong; Vietnam National Univ., Ho Chi Minh City; Riemann, Tord; Silesia Univ., Chorzow

2017-11-01

Representations are derived for the basic scalar one-loop vertex Feynman integrals as meromorphic functions of the space-time dimension d in terms of (generalized) hypergeometric functions 2 F 1 and F 1 . Values at asymptotic or exceptional kinematic points as well as expansions around the singular points at d=4+2n, n non-negative integers, may be derived from the representations easily. The Feynman integrals studied here may be used as building blocks for the calculation of one-loop and higher-loop scalar and tensor amplitudes. From the recursion relation presented, higher n-point functions may be obtained in a straightforward manner.

Scalar one-loop vertex integrals as meromorphic functions of space-time dimension d

Energy Technology Data Exchange (ETDEWEB)

Bluemlein, Johannes [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Phan, Khiem Hong [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Vietnam National Univ., Ho Chi Minh City (Viet Nam). Univ. of Science; Riemann, Tord [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Silesia Univ., Chorzow (Poland). Inst. of Physics

2017-11-15

Representations are derived for the basic scalar one-loop vertex Feynman integrals as meromorphic functions of the space-time dimension d in terms of (generalized) hypergeometric functions {sub 2}F{sub 1} and F{sub 1}. Values at asymptotic or exceptional kinematic points as well as expansions around the singular points at d=4+2n, n non-negative integers, may be derived from the representations easily. The Feynman integrals studied here may be used as building blocks for the calculation of one-loop and higher-loop scalar and tensor amplitudes. From the recursion relation presented, higher n-point functions may be obtained in a straightforward manner.

Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

Directory of Open Access Journals (Sweden)

Wuyi Liu

2013-01-01

Full Text Available The previous survey identified 70 basic helix-loop-helix (bHLH proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation

Directory of Open Access Journals (Sweden)

Chauhan Virander S

2009-04-01

Full Text Available Abstract Background The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins. Method In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out. Results Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF1/2 helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified. Conclusion The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome. The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from

Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor.

Science.gov (United States)

Komatsu, Setsuko; Takasaki, Hironori

2009-07-01

Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.

Science.gov (United States)

Lareau, Caleb A; Aryee, Martin J; Berger, Bonnie

2018-02-15

The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state. Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html. aryee.martin@mgh.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Component Functional Allocations of the ESF Multi-loop Controller for the KNICS ESF-CCS Design

International Nuclear Information System (INIS)

Hur, Seop; Choi, Jong Kyun; Kim, Dong Hoon; Kim, Ho; Kim, Seong Tae

2006-01-01

The safety related components in nuclear power plants are traditionally controlled by single-loop controllers. Traditional single-loop controller systems utilize dedicated processors for each component but that components independence is compromised through a sharing of power supplies, auxiliary logic modules and auxiliary I/O cards. In the new design of the ESF-CCS, the multi-loop controllers with data networks are widely used. Since components are assigned to ESF-CCS functional groups in a manner consistent with their process relationship, the effects of the failures are predictable and manageable. Therefore, the key issues for the design of multi-loop controller is to allocate the components to the each multi-loop controller through plant and function analysis and grouping. This paper deals with an ESF component functional allocation which is performed through allocation criteria and a fault analysis

On strong-coupling correlation functions of circular Wilson loops and local operators

International Nuclear Information System (INIS)

Alday, Luis F; Tseytlin, Arkady A

2011-01-01

Motivated by the problem of understanding 3-point correlation functions of gauge-invariant operators in N=4 super Yang-Mills theory we consider correlators involving Wilson loops and a 'light' operator with fixed quantum numbers. At leading order in the strong-coupling expansion such correlators are given by the 'light' vertex operator evaluated on a semiclassical string world surface ending on the corresponding loops at the boundary of AdS 5 x S 5 . We study in detail the example of a correlator of two concentric circular Wilson loops and a dilaton vertex operator. The resulting expression is given by an integral of combinations of elliptic functions and can be computed analytically in some special limits. We also consider a generalization of the minimal surface ending on two circles to the case of non-zero angular momentum J in S 5 and discuss a special limit when one of the Wilson loops is effectively replaced by a 'heavy' operator with charge J. (paper)

Loop kinematics

International Nuclear Information System (INIS)

Migdal, A.A.

1982-01-01

Basic operators acting in the loop space are introduced. The topology of this space and properties of the Stokes type loop functionals are discussed. The parametrically invariant loop calculus developed here is used in the loop dynamics

Two-loop polygon Wilson loops in N = 4 SYM

International Nuclear Information System (INIS)

Anastasiou, C.; Brandhuber, A.; Heslop, P.; Spence, B.; Travaglini, G.; Khoze, V.V.

2009-01-01

We compute for the first time the two-loop corrections to arbitrary n-gon lightlike Wilson loops in N = 4 supersymmetric Yang-Mills theory, using efficient numerical methods. The calculation is motivated by the remarkable agreement between the finite part of planar six-point MHV amplitudes and hexagon Wilson loops which has been observed at two loops. At n = 6 we confirm that the ABDK/BDS ansatz must be corrected by adding a remainder function, which depends only on conformally invariant ratios of kinematic variables. We numerically compute remainder functions for n = 7,8 and verify dual conformal invariance. Furthermore, we study simple and multiple collinear limits of the Wilson loop remainder functions and demonstrate that they have precisely the form required by the collinear factorisation of the corresponding two-loop n-point amplitudes. The number of distinct diagram topologies contributing to the n-gon Wilson loops does not increase with n, and there is a fixed number of 'master integrals', which we have computed. Thus we have essentially computed general polygon Wilson loops, and if the correspondence with amplitudes continues to hold, all planar n-point two-loop MHV amplitudes in the N = 4 theory.

Analytic continuation of massless two-loop four-point functions

International Nuclear Information System (INIS)

Gehrmann, T.; Remiddi, E.

2002-01-01

We describe the analytic continuation of two-loop four-point functions with one off-shell external leg and internal massless propagators from the Euclidean region of space-like 1→3 decay to Minkowskian regions relevant to all 1→3 and 2→2 reactions with one space-like or time-like off-shell external leg. Our results can be used to derive two-loop master integrals and unrenormalized matrix elements for hadronic vector-boson-plus-jet production and deep inelastic two-plus-one-jet production, from results previously obtained for three-jet production in electron-positron annihilation. (author)

Twist operator correlation functions in O(n) loop models

International Nuclear Information System (INIS)

Simmons, Jacob J H; Cardy, John

2009-01-01

Using conformal field theoretic methods we calculate correlation functions of geometric observables in the loop representation of the O(n) model at the critical point. We focus on correlation functions containing twist operators, combining these with anchored loops, boundaries with SLE processes and with double SLE processes. We focus further upon n = 0, representing self-avoiding loops, which corresponds to a logarithmic conformal field theory (LCFT) with c = 0. In this limit the twist operator plays the role of a 0-weight indicator operator, which we verify by comparison with known examples. Using the additional conditions imposed by the twist operator null states, we derive a new explicit result for the probabilities that an SLE 8/3 winds in various ways about two points in the upper half-plane, e.g. that the SLE passes to the left of both points. The collection of c = 0 logarithmic CFT operators that we use deriving the winding probabilities is novel, highlighting a potential incompatibility caused by the presence of two distinct logarithmic partners to the stress tensor within the theory. We argue that both partners do appear in the theory, one in the bulk and one on the boundary and that the incompatibility is resolved by restrictive bulk-boundary fusion rules

A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

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Karen A. Hudson

2015-01-01

Full Text Available The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281 of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

SATB1 packages densely-looped, transciptionally-active chromatinfor coordinated expression of cytokine genes

Energy Technology Data Exchange (ETDEWEB)

Cai, Shutao; Lee, Charles C.; Kohwi-Shigematsu, Terumi

2006-05-23

SATB1 is an important regulator of nuclear architecture that anchors specialized DNA sequences onto its cage-like network and recruits chromatin remodeling/modifying factors to control gene transcription. We studied the role of SATB1 in regulating the coordinated expression of Il5, Il4, and Il13 from the 200kb cytokine gene cluster region of mouse chromosome 11 during T-helper 2 (Th2)-cell activation. We show that upon cell activation, SATB1 is rapidly induced to form a unique transcriptionally-active chromatin structure that includes the cytokine gene region. Chromatin is folded into numerous small loops all anchored by SATB1, is histone H3 acetylated at lysine 9/14, and associated with Th2-specific factors, GATA3, STAT6, c-Maf, the chromatin-remodeling enzyme Brg-1, and RNA polymerase II across the 200kb region. Before activation, the chromatin displays some of these features, such as association with GATA3 and STAT6, but these were insufficient for cytokine gene expression. Using RNA interference (RNAi), we show that upon cell activation, SATB1 is not only required for chromatin folding into dense loops, but also for c-Maf induction and subsequently for Il4, Il5, and Il13 transcription. Our results show that SATB1 is an important determinant for chromatin architecture that constitutes a novel higher-order, transcriptionally-active chromatin structure upon Th2-cell activation.

Loop Transfer Matrix and Loop Quantum Mechanics

International Nuclear Information System (INIS)

Savvidy, George K.

2000-01-01

The gonihedric model of random surfaces on a 3d Euclidean lattice has equivalent representation in terms of transfer matrix K(Q i ,Q f ), which describes the propagation of loops Q. We extend the previous construction of the loop transfer matrix to the case of nonzero self-intersection coupling constant κ. We introduce the loop generalization of Fourier transformation which allows to diagonalize transfer matrices, that depend on symmetric difference of loops only and express all eigenvalues of 3d loop transfer matrix through the correlation functions of the corresponding 2d statistical system. The loop Fourier transformation allows to carry out the analogy with quantum mechanics of point particles, to introduce conjugate loop momentum P and to define loop quantum mechanics. We also consider transfer matrix on 4d lattice which describes propagation of memebranes. This transfer matrix can also be diagonalized by using the generalized Fourier transformation, and all its eigenvalues are equal to the correlation functions of the corresponding 3d statistical system. In particular the free energy of the 4d membrane system is equal to the free energy of 3d gonihedric system of loops and is equal to the free energy of 2d Ising model. (author)

Four-loop non-singlet splitting functions in the planar limit and beyond

Energy Technology Data Exchange (ETDEWEB)

Moch, S. [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Ruijl, B. [Nikhef, Amsterdam (Netherlands). Theory Group; Leiden Univ. (Netherlands). Leiden Centre of Data Science; Ueda, T.; Vermaseren, J.A.M. [Nikhef, Amsterdam (Netherlands). Theory Group; Vogt, A. [Liverpool Univ. (United Kingdom). Dept. of Mathematical Sciences

2017-08-15

We present the next-to-next-to-next-to-leading order (N{sup 3}LO) contributions to the non-singlet splitting functions for both parton distribution and fragmentation functions in perturbative QCD. The exact expressions are derived for the terms contributing in the limit of a large number of colours. For the remaining contributions, approximations are provided that are sufficient for all collider-physics applications. From their threshold limits we derive analytical and high-accuracy numerical results, respectively, for all contributions to the four-loop cusp anomalous dimension for quarks, including the terms proportional to quartic Casimir operators. We briefly illustrate the numerical size of the four-loop corrections, and the remarkable renormalization-scale stability of the N{sup 3}LO results, for the evolution of the non-singlet parton distribution and the fragmentation functions. Our results appear to provide a first point of contact of four-loop QCD calculations and the so-called wrapping corrections to anomalous dimensions in N=4 super Yang-Mills theory.

One-loop correlation functions in the model of noncritical fermionic strings

International Nuclear Information System (INIS)

Belokurov, V.V.; Iofa, M.Z.

1996-01-01

In the model of noncritical fermionic strings, the David-Distler-Kawai ansatz is used to study one-loop n-point (n≤4) correlation functions for the vertex operators of massless bosonic states. The action functional of the model is the sum of super-Liouville action functional for the conformal mode and the action functional of d scalar supermultiplets. It is assumed that the total cosmological term is equal to zero. The amplitudes are calculated as the residues at the pole of the correlation function that corresponds to the conservation of Liouville momentum in the form Σβi=Q(1-h), where Q=√(9-d)/2 and h is the genus of the work sheet. In the one-loop approximation, the amplitudes can be obtained in the modular-invariant form, provided that the coefficients appearing in the sum over spin structures depend on moduli. In this case, the modular measure is defined up to a modular-invariant factor. This arbitrariness can be used to represent one-point correlation functions in the same functional form as for strings of critical dimension

The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization.

Directory of Open Access Journals (Sweden)

Qian Yan

Full Text Available Basic/helix-loop-helix (bHLH proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum, a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062 showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus.

Gene2Function: An Integrated Online Resource for Gene Function Discovery

Directory of Open Access Journals (Sweden)

Yanhui Hu

2017-08-01

Full Text Available One of the most powerful ways to develop hypotheses regarding the biological functions of conserved genes in a given species, such as humans, is to first look at what is known about their function in another species. Model organism databases and other resources are rich with functional information but difficult to mine. Gene2Function addresses a broad need by integrating information about conserved genes in a single online resource.

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

Directory of Open Access Journals (Sweden)

Hahnbeom Park

Full Text Available Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

Three-loop SM beta-functions for matrix Yukawa couplings

Directory of Open Access Journals (Sweden)

A.V. Bednyakov

2014-10-01

Full Text Available We present the extension of our previous results for three-loop Yukawa coupling beta-functions to the case of complex Yukawa matrices describing the flavour structure of the SM. The calculation is carried out in the context of unbroken phase of the SM with the help of the MINCER program in a general linear gauge and cross-checked by means of MATAD/BAMBA codes. In addition, ambiguities in Yukawa matrix beta-functions are studied.

The three-loop splitting functions Pqg(2) and Pgg(2 ,NF)

Science.gov (United States)

Ablinger, J.; Behring, A.; Blümlein, J.; De Freitas, A.; von Manteuffel, A.; Schneider, C.

2017-09-01

We calculate the unpolarized twist-2 three-loop splitting functions Pqg(2) (x) and Pgg(2 ,NF) (x) and the associated anomalous dimensions using massive three-loop operator matrix elements. While we calculate Pgg(2 ,NF) (x) directly, Pqg(2) (x) is computed from 1200 even moments, without any structural prejudice, using a hierarchy of recurrences obtained for the corresponding operator matrix element. The largest recurrence to be solved is of order 12 and degree 191. We confirm results in the foregoing literature.

Two-loop QED corrections to the Altarelli-Parisi splitting functions

Energy Technology Data Exchange (ETDEWEB)

Florian, Daniel de [International Center for Advanced Studies (ICAS), UNSAM,Campus Miguelete, 25 de Mayo y Francia (1650) Buenos Aires (Argentina); Sborlini, Germán F.R.; Rodrigo, Germán [Instituto de Física Corpuscular, Universitat de València,Consejo Superior de Investigaciones Científicas,Parc Científic, E-46980 Paterna, Valencia (Spain)

2016-10-11

We compute the two-loop QED corrections to the Altarelli-Parisi (AP) splitting functions by using a deconstructive algorithmic Abelianization of the well-known NLO QCD corrections. We present explicit results for the full set of splitting kernels in a basis that includes the leptonic distribution functions that, starting from this order in the QED coupling, couple to the partonic densities. Finally, we perform a phenomenological analysis of the impact of these corrections in the splitting functions.

The three-loop splitting functions Pqg(2 and Pgg(2,NF

Directory of Open Access Journals (Sweden)

J. Ablinger

2017-09-01

Full Text Available We calculate the unpolarized twist-2 three-loop splitting functions Pqg(2(x and Pgg(2,NF(x and the associated anomalous dimensions using massive three-loop operator matrix elements. While we calculate Pgg(2,NF(x directly, Pqg(2(x is computed from 1200 even moments, without any structural prejudice, using a hierarchy of recurrences obtained for the corresponding operator matrix element. The largest recurrence to be solved is of order 12 and degree 191. We confirm results in the foregoing literature.

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

Energy Technology Data Exchange (ETDEWEB)

Xu, M.; Wu, W.-M.; Wu, L.; He, Z.; Van Nostrand, J.D.; Deng, Y.; Luo, J.; Carley, J.; Ginder-Vogel, M.; Gentry, T.J.; Gu, B.; Watson, D.; Jardine, P.M.; Marsh, T.L.; Tiedje, J.M.; Hazen, T.C.; Criddle, C.S.; Zhou, J.

2010-02-15

A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 {micro}gl{sup -1}) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.

Two-point boundary correlation functions of dense loop models

Directory of Open Access Journals (Sweden)

Alexi Morin-Duchesne, Jesper Lykke Jacobsen

2018-06-01

Full Text Available We investigate six types of two-point boundary correlation functions in the dense loop model. These are defined as ratios $Z/Z^0$ of partition functions on the $m\\times n$ square lattice, with the boundary condition for $Z$ depending on two points $x$ and $y$. We consider: the insertion of an isolated defect (a and a pair of defects (b in a Dirichlet boundary condition, the transition (c between Dirichlet and Neumann boundary conditions, and the connectivity of clusters (d, loops (e and boundary segments (f in a Neumann boundary condition. For the model of critical dense polymers, corresponding to a vanishing loop weight ($\\beta = 0$, we find determinant and pfaffian expressions for these correlators. We extract the conformal weights of the underlying conformal fields and find $\\Delta = -\\frac18$, $0$, $-\\frac3{32}$, $\\frac38$, $1$, $\\tfrac \\theta \\pi (1+\\tfrac{2\\theta}\\pi$, where $\\theta$ encodes the weight of one class of loops for the correlator of type f. These results are obtained by analysing the asymptotics of the exact expressions, and by using the Cardy-Peschel formula in the case where $x$ and $y$ are set to the corners. For type b, we find a $\\log|x-y|$ dependence from the asymptotics, and a $\\ln (\\ln n$ term in the corner free energy. This is consistent with the interpretation of the boundary condition of type b as the insertion of a logarithmic field belonging to a rank two Jordan cell. For the other values of $\\beta = 2 \\cos \\lambda$, we use the hypothesis of conformal invariance to predict the conformal weights and find $\\Delta = \\Delta_{1,2}$, $\\Delta_{1,3}$, $\\Delta_{0,\\frac12}$, $\\Delta_{1,0}$, $\\Delta_{1,-1}$ and $\\Delta_{\\frac{2\\theta}\\lambda+1,\\frac{2\\theta}\\lambda+1}$, extending the results of critical dense polymers. With the results for type f, we reproduce a Coulomb gas prediction for the valence bond entanglement entropy of Jacobsen and Saleur.

Loop averages and partition functions in U(N) gauge theory on two-dimensional manifolds

International Nuclear Information System (INIS)

Rusokov, B.Y.

1990-01-01

Loop averages and partition functions in the U(N) gauge theory are calculated for loops without intersections on arbitrary two-dimensional manifolds including non-orientable one. The physical quantities are directly expressed through geometrical characteristics of a manifold (areas enclosed by loops and the genus) and gauge group parameters (Casimir eigenvalues and dimensions of the irreducible representations). It is shown that, from the physical quantities' point of view, non-orientability of the manifold is equivalent to its non-compactness

Loop mediated isothermal amplification: An innovative gene amplification technique for animal diseases

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Pravas Ranjan Sahoo

2016-05-01

Full Text Available India being a developing country mainly depends on livestock sector for its economy. However, nowadays, there is emergence and reemergence of more transboundary animal diseases. The existing diagnostic techniques are not so quick and with less specificity. To reduce the economy loss, there should be a development of rapid, reliable, robust diagnostic technique, which can work with high degree of sensitivity and specificity. Loop mediated isothermal amplification assay is a rapid gene amplification technique that amplifies nucleic acid under an isothermal condition with a set of designed primers spanning eight distinct sequences of the target. This assay can be used as an emerging powerful, innovative gene amplification diagnostic tool against various pathogens of livestock diseases. This review is to highlight the basic concept and methodology of this assay in livestock disease.

Loop mediated isothermal amplification: An innovative gene amplification technique for animal diseases.

Science.gov (United States)

Sahoo, Pravas Ranjan; Sethy, Kamadev; Mohapatra, Swagat; Panda, Debasis

2016-05-01

India being a developing country mainly depends on livestock sector for its economy. However, nowadays, there is emergence and reemergence of more transboundary animal diseases. The existing diagnostic techniques are not so quick and with less specificity. To reduce the economy loss, there should be a development of rapid, reliable, robust diagnostic technique, which can work with high degree of sensitivity and specificity. Loop mediated isothermal amplification assay is a rapid gene amplification technique that amplifies nucleic acid under an isothermal condition with a set of designed primers spanning eight distinct sequences of the target. This assay can be used as an emerging powerful, innovative gene amplification diagnostic tool against various pathogens of livestock diseases. This review is to highlight the basic concept and methodology of this assay in livestock disease.

Supersymmetric localization for BPS black hole entropy: 1-loop partition function from vector multiplets

International Nuclear Information System (INIS)

Gupta, Rajesh Kumar; Ito, Yuto; Jeon, Imtak

2015-01-01

We use the techniques of supersymmetric localization to compute the BPS black hole entropy in N=2 supergravity. We focus on the n_v+1 vector multiplets on the black hole near horizon background which is AdS_2× S"2 space. We find the localizing saddle point of the vector multiplets by solving the localization equations, and compute the exact one-loop partition function on the saddle point. Furthermore, we propose the appropriate functional integration measure. Through this measure, the one-loop determinant is written in terms of the radius of the physical metric, which depends on the localizing saddle point value of the vector multiplets. The result for the one-loop determinant is consistent with the logarithmic corrections to the BPS black hole entropy from vector multiplets.

A Nodal-independent and tissue-intrinsic mechanism controls heart-looping chirality

NARCIS (Netherlands)

Noel, E.S.; Verhoeven, M.; Lagendijk, A.K.; Tessadori, F.; Smith, K.; Choorapoikayil, S.; den Hertog, J.; Bakkers, J.

2013-01-01

Breaking left-right symmetry in bilateria is a major event during embryo development that is required for asymmetric organ position, directional organ looping and lateralized organ function in the adult. Asymmetric expression of Nodal-related genes is hypothesized to be the driving force behind

The Euclidean three-point function in loop and perturbative gravity

International Nuclear Information System (INIS)

Rovelli, Carlo; Zhang Mingyi

2011-01-01

We compute the leading order of the three-point function in loop quantum gravity, using the vertex expansion of the Euclidean version of the new spin foam dynamics, in the region of γ < 1. We find results consistent with Regge calculus in the limit γ → 0, j → ∞. We also compute the tree-level three-point function of perturbative quantum general relativity in position space and discuss the possibility of directly comparing the two results.

1-loop partition function in AdS{sub 3}/CFT{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Chen, Bin [Department of Physics and State Key Laboratory of Nuclear Physics and Technology,Peking University,5 Yiheyuan Rd, Beijing 100871 (China); Collaborative Innovation Center of Quantum Matter,5 Yiheyuan Rd, Beijing 100871 (China); Center for High Energy Physics, Peking University,5 Yiheyuan Rd, Beijing 100871 (China); Wu, Jie-qiang [Department of Physics and State Key Laboratory of Nuclear Physics and Technology,Peking University,5 Yiheyuan Rd, Beijing 100871 (China)

2015-12-16

The 1-loop partition function of the handlebody solutions in the AdS{sub 3} gravity have been derived some years ago using the heat kernel techniques and the method of images. In the semiclassical limit, such partition function should correspond to the order O(c{sup 0}) part in the partition function of dual conformal field theory(CFT) on the boundary Riemann surface. The higher genus partition function could be computed by the multi-point functions in the Riemann sphere via sewing prescription. In the large central charge limit, the CFT is effectively free in the sense that to the leading order of c the multi-point function is further simplified to be a summation over the products of two-point functions of single-particle states. Correspondingly in the bulk, the graviton is freely propagating without interaction. Furthermore the product of the two-point functions may define the links, each of which is in one-to-one correspondence with the conjugacy class of the Schottky group of the Riemann surface. Moreover, the value of a link is determined by the multiplier of the element in the conjugacy class. This allows us to reproduce exactly the gravitational 1-loop partition function. The proof can be generalized to the higher spin gravity and its dual CFT.

The four-loop remainder function and multi-Regge behavior at NNLLA in planar N=4 super-Yang-Mills theory

Energy Technology Data Exchange (ETDEWEB)

Dixon, Lance J. [SLAC National Accelerator Laboratory,Stanford University, Stanford, CA 94309 (United States); Drummond, James M. [CERN,Geneva 23 (Switzerland); School of Physics and Astronomy, University of Southampton,Highfield, Southampton, SO17 1BJ (United Kingdom); LAPTH, CNRS et Université de Savoie,F-74941 Annecy-le-Vieux Cedex (France); Duhr, Claude [Institute for Particle Physics Phenomenology, University of Durham,Durham, DH1 3LE (United Kingdom); Pennington, Jeffrey [SLAC National Accelerator Laboratory,Stanford University, Stanford, CA 94309 (United States)

2014-06-19

We present the four-loop remainder function for six-gluon scattering with maximal helicity violation in planar N=4 super-Yang-Mills theory, as an analytic function of three dual-conformal cross ratios. The function is constructed entirely from its analytic properties, without ever inspecting any multi-loop integrand. We employ the same approach used at three loops, writing an ansatz in terms of hexagon functions, and fixing coefficients in the ansatz using the multi-Regge limit and the operator product expansion in the near-collinear limit. We express the result in terms of multiple polylogarithms, and in terms of the coproduct for the associated Hopf algebra. From the remainder function, we extract the BFKL eigenvalue at next-to-next-to-leading logarithmic accuracy (NNLLA), and the impact factor at N{sup 3}LLA. We plot the remainder function along various lines and on one surface, studying ratios of successive loop orders. As seen previously through three loops, these ratios are surprisingly constant over large regions in the space of cross ratios, and they are not far from the value expected at asymptotically large orders of perturbation theory.

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

Science.gov (United States)

Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

2010-01-01

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

Appell functions and the scalar one-loop three-point integrals in Feynman diagrams

Energy Technology Data Exchange (ETDEWEB)

Cabral-Rosetti, L G [Departamento de Posgrado, Centro Interdisciplinario de Investigacion y Docencia en Educacion Tecnica (CIIDET), Av. Universidad 282 Pte., Col. Centro, A. Postal 752, C.P. 76000, Santiago de Queretaro, Qro. (Mexico); Sanchis-Lozano, M A [Departamento de Fisica Teorica and IFIC, Centro Mixto Universidad de Valencia-CSIC, 46100 Burjassot, Valencia (Spain)

2006-05-15

The scalar three-point function appearing in one-loop Feynman diagrams is compactly expressed in terms of a generalized hypergeometric function of two variables. Use is made of the connection between such Appell function and dilogarithms coming from a previous investigation. Special cases are obtained for particular values of internal masses and external momenta.

Causal transfer function analysis to describe closed loop interactions between cardiovascular and cardiorespiratory variability signals.

Science.gov (United States)

Faes, L; Porta, A; Cucino, R; Cerutti, S; Antolini, R; Nollo, G

2004-06-01

Although the concept of transfer function is intrinsically related to an input-output relationship, the traditional and widely used estimation method merges both feedback and feedforward interactions between the two analyzed signals. This limitation may endanger the reliability of transfer function analysis in biological systems characterized by closed loop interactions. In this study, a method for estimating the transfer function between closed loop interacting signals was proposed and validated in the field of cardiovascular and cardiorespiratory variability. The two analyzed signals x and y were described by a bivariate autoregressive model, and the causal transfer function from x to y was estimated after imposing causality by setting to zero the model coefficients representative of the reverse effects from y to x. The method was tested in simulations reproducing linear open and closed loop interactions, showing a better adherence of the causal transfer function to the theoretical curves with respect to the traditional approach in presence of non-negligible reverse effects. It was then applied in ten healthy young subjects to characterize the transfer functions from respiration to heart period (RR interval) and to systolic arterial pressure (SAP), and from SAP to RR interval. In the first two cases, the causal and non-causal transfer function estimates were comparable, indicating that respiration, acting as exogenous signal, sets an open loop relationship upon SAP and RR interval. On the contrary, causal and traditional transfer functions from SAP to RR were significantly different, suggesting the presence of a considerable influence on the opposite causal direction. Thus, the proposed causal approach seems to be appropriate for the estimation of parameters, like the gain and the phase lag from SAP to RR interval, which have a large clinical and physiological relevance.

Phylogenetic Analysis, Lineage-Specific Expansion and Functional Divergence of seed dormancy 4-Like Genes in Plants.

Directory of Open Access Journals (Sweden)

Saminathan Subburaj

Full Text Available The rice gene seed dormancy 4 (OsSdr4 functions in seed dormancy and is a major factor associated with pre-harvest sprouting (PHS. Although previous studies of this protein family were reported for rice and other species, knowledge of the evolution of genes homologous to OsSdr4 in plants remains inadequate. Fifty four Sdr4-like (hereafter designated Sdr4L genes were identified in nine plant lineages including 36 species. Phylogenetic analysis placed these genes in eight subfamilies (I-VIII. Genes from the same lineage clustered together, supported by analysis of conserved motifs and exon-intron patterns. Segmental duplications were present in both dicot and monocot clusters, while tandemly duplicated genes occurred only in monocot clusters indicating that both tandem and segmental duplications contributed to expansion of the grass I and II subfamilies. Estimation of the approximate ages of the duplication events indicated that ancestral Sdr4 genes evolved from a common angiosperm ancestor, about 160 million years ago (MYA. Moreover, diversification of Sdr4L genes in mono and dicot plants was mainly associated with genome-wide duplication and speciation events. Functional divergence was observed in all subfamily pairs, except IV/VIIIa. Further analysis indicated that functional constraints between subfamily pairs I/II, I/VIIIb, II/VI, II/VIIIb, II/IV, and VI/VIIIb were statistically significant. Site and branch-site model analyses of positive selection suggested that these genes were under strong adaptive selection pressure. Critical amino acids detected for both functional divergence and positive selection were mostly located in the loops, pointing to functional importance of these regions in this protein family. In addition, differential expression studies by transcriptome atlas of 11 Sdr4L genes showed that the duplicated genes may have undergone divergence in expression between plant species. Our findings showed that Sdr4L genes are

Three-point functions in N=4 SYM: the hexagon proposal at three loops

Energy Technology Data Exchange (ETDEWEB)

Eden, Burkhard [Institut für Mathematik & Institut für Physik, Humboldt-Universität zu Berlin,Zum großen Windkanal 6, D-12489 Berlin (Germany); Sfondrini, Alessandro [Institut für Theoretische Physik, ETH Zürich,Wolfgang-Pauli-Str. 27, CH-8093 Zürich (Switzerland)

2016-02-24

Basso, Komatsu and Vieira recently proposed an all-loop framework for the computation of three-point functions of single-trace operators of N=4 super-Yang-Mills, the “hexagon program”. This proposal results in several remarkable predictions, including the three-point function of two protected operators with an unprotected one in the SU(2) and SL(2) sectors. Such predictions consist of an “asymptotic” part — similar in spirit to the asymptotic Bethe Ansatz of Beisert and Staudacher for two-point functions — as well as additional finite-size “wrapping” Lüscher-like corrections. The focus of this paper is on such wrapping corrections, which we compute at three-loops in the SL(2) sector. The resulting structure constants perfectly match the ones obtained in the literature from four-point correlators of protected operators.

Concentration and length dependence of DNA looping in transcriptional regulation.

Directory of Open Access Journals (Sweden)

Lin Han

2009-05-01

Full Text Available In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage, to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping.

Single amino acid insertions in extracellular loop 2 of Bombyx mori ABCC2 disrupt its receptor function for Bacillus thuringiensis Cry1Ab and Cry1Ac but not Cry1Aa toxins.

Science.gov (United States)

Tanaka, Shiho; Miyamoto, Kazuhisa; Noda, Hiroaki; Endo, Haruka; Kikuta, Shingo; Sato, Ryoichi

2016-04-01

In a previous report, seven Cry1Ab-resistant strains were identified in the silkworm, Bombyx mori; these strains were shown to have a tyrosine insertion at position 234 in extracellular loop 2 of the ABC transporter C2 (BmABCC2). This insertion was confirmed to destroy the receptor function of BmABCC2 and confer the strains resistance against Cry1Ab and Cry1Ac. However, these strains were susceptible to Cry1Aa. In this report, we examined the mechanisms of the loss of receptor function of the transporter by expressing mutations in Sf9 cells. After replacement of one or two of the five amino acid residues in loop 2 of the susceptible BmABCC2 gene [BmABCC2_S] with alanine, cells still showed susceptibility, retaining the receptor function. Five mutants with single amino acid insertions at position 234 in BmABCC2 were also generated, resulting in loop 2 having six amino acids, which corresponds to replacing the tyrosine insertion in the resistant BmABCC2 gene [BmABCC2_R(+(234)Y)] with another amino acid. All five mutants exhibited loss of function against Cry1Ab and Cry1Ac. These results suggest that the amino acid sequence in loop 2 is less important than the loop size (five vs. six amino acids) or loop structure for Cry1Ab and Cry1Ac activity. Several domain-swapped mutant toxins were then generated among Cry1Aa, Cry1Ab, and Cry1Ac, which are composed of three domains. Swapped mutants containing domain II of Cry1Ab or Cry1Ac did not kill Sf9 cells expressing BmABCC2_R(+(234)Y), suggesting that domain II of the Cry toxin is related to the interaction with the receptor function of BmABCC2. This also suggests that different reactions against Bt-toxins in some B. mori strains, that is, Cry1Ab resistance or Cry1Aa susceptibility, are attributable to structural differences in domain II of Cry1A toxins. Copyright © 2016. Published by Elsevier Inc.

Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing.

Science.gov (United States)

Zhao, Yingwen; Fu, Guangyuan; Wang, Jun; Guo, Maozu; Yu, Guoxian

2018-02-23

Gene Ontology (GO) uses structured vocabularies (or terms) to describe the molecular functions, biological roles, and cellular locations of gene products in a hierarchical ontology. GO annotations associate genes with GO terms and indicate the given gene products carrying out the biological functions described by the relevant terms. However, predicting correct GO annotations for genes from a massive set of GO terms as defined by GO is a difficult challenge. To combat with this challenge, we introduce a Gene Ontology Hierarchy Preserving Hashing (HPHash) based semantic method for gene function prediction. HPHash firstly measures the taxonomic similarity between GO terms. It then uses a hierarchy preserving hashing technique to keep the hierarchical order between GO terms, and to optimize a series of hashing functions to encode massive GO terms via compact binary codes. After that, HPHash utilizes these hashing functions to project the gene-term association matrix into a low-dimensional one and performs semantic similarity based gene function prediction in the low-dimensional space. Experimental results on three model species (Homo sapiens, Mus musculus and Rattus norvegicus) for interspecies gene function prediction show that HPHash performs better than other related approaches and it is robust to the number of hash functions. In addition, we also take HPHash as a plugin for BLAST based gene function prediction. From the experimental results, HPHash again significantly improves the prediction performance. The codes of HPHash are available at: http://mlda.swu.edu.cn/codes.php?name=HPHash. Copyright © 2018 Elsevier Inc. All rights reserved.

Loop diuretics, renal function and clinical outcome in patients with heart failure and reduced ejection fraction

NARCIS (Netherlands)

Damman, Kevin; Kjekshus, John; Wikstrand, John; Cleland, John G. F.; Komajda, Michel; Wedel, Hans; Waagstein, Finn; McMurray, John J. V.

AimWe aimed to study the relationships of loop diuretic dose with renal function and clinical outcomes in patients with chronic heart failure (HF). Methods and resultsLoop diuretic dose at baseline was recorded in patients included in the Controlled Rosuvastatin Multinational Trial in Heart Failure

The free-energy cost of interaction between DNA loops.

Science.gov (United States)

Huang, Lifang; Liu, Peijiang; Yuan, Zhanjiang; Zhou, Tianshou; Yu, Jianshe

2017-10-03

From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.

The one loop calculation of the strong coupling β function in the Toy Model

International Nuclear Information System (INIS)

Bai Zhiming; Jiang Yuanfang

1991-01-01

The background field quantization is used to calculate the one-loop β function in the Toy Model which has the strong coupling and the SU(3) symmetry. The function obtained is consistent with the Appalquist-Carrazone theorem in the low energy condition

Mutations in the catalytic loop HRD motif alter the activity and function of Drosophila Src64.

Directory of Open Access Journals (Sweden)

Taylor C Strong

Full Text Available The catalytic loop HRD motif is found in most protein kinases and these amino acids are predicted to perform functions in catalysis, transition to, and stabilization of the active conformation of the kinase domain. We have identified mutations in a Drosophila src gene, src64, that alter the three HRD amino acids. We have analyzed the mutants for both biochemical activity and biological function during development. Mutation of the aspartate to asparagine eliminates biological function in cytoskeletal processes and severely reduces fertility, supporting the amino acid's critical role in enzymatic activity. The arginine to cysteine mutation has little to no effect on kinase activity or cytoskeletal reorganization, suggesting that the HRD arginine may not be critical for coordinating phosphotyrosine in the active conformation. The histidine to leucine mutant retains some kinase activity and biological function, suggesting that this amino acid may have a biochemical function in the active kinase that is independent of its side chain hydrogen bonding interactions in the active site. We also describe the phenotypic effects of other mutations in the SH2 and tyrosine kinase domains of src64, and we compare them to the phenotypic effects of the src64 null allele.

Regularization independent analysis of the origin of two loop contributions to N=1 Super Yang-Mills beta function

Energy Technology Data Exchange (ETDEWEB)

Fargnoli, H.G.; Sampaio, Marcos; Nemes, M.C. [Federal University of Minas Gerais, ICEx, Physics Department, P.O. Box 702, Belo Horizonte, MG (Brazil); Hiller, B. [Coimbra University, Faculty of Science and Technology, Physics Department, Center of Computational Physics, Coimbra (Portugal); Baeta Scarpelli, A.P. [Setor Tecnico-Cientifico, Departamento de Policia Federal, Lapa, Sao Paulo (Brazil)

2011-05-15

We present both an ultraviolet and an infrared regularization independent analysis in a symmetry preserving framework for the N=1 Super Yang-Mills beta function to two loop order. We show explicitly that off-shell infrared divergences as well as the overall two loop ultraviolet divergence cancel out, whilst the beta function receives contributions of infrared modes. (orig.)

Regularization independent analysis of the origin of two loop contributions to N=1 Super Yang-Mills beta function

International Nuclear Information System (INIS)

Fargnoli, H.G.; Sampaio, Marcos; Nemes, M.C.; Hiller, B.; Baeta Scarpelli, A.P.

2011-01-01

We present both an ultraviolet and an infrared regularization independent analysis in a symmetry preserving framework for the N=1 Super Yang-Mills beta function to two loop order. We show explicitly that off-shell infrared divergences as well as the overall two loop ultraviolet divergence cancel out, whilst the beta function receives contributions of infrared modes. (orig.)

Towards the five-loop beta function for a general gauge group

International Nuclear Information System (INIS)

Luthe, Thomas; Schroeder, York

2016-06-01

We present analytical results for the N"4_f and N"3_f terms of the five-loop beta function, for a general gauge group. While the former term agrees with results available from large-N_f studies, the latter is new and extends the value known for SU(3) from an independent calculation.

Epigenetic modifications and chromatin loop organization explain the different expression profiles of the Tbrg4, WAP and Ramp3 genes

International Nuclear Information System (INIS)

Montazer-Torbati, Mohammad Bagher; Hue-Beauvais, Cathy; Droineau, Stephanie; Ballester, Maria; Coant, Nicolas; Aujean, Etienne; Petitbarat, Marie; Rijnkels, Monique; Devinoy, Eve

2008-01-01

Whey Acidic Protein (WAP) gene expression is specific to the mammary gland and regulated by lactogenic hormones to peak during lactation. It differs markedly from the more constitutive expression of the two flanking genes, Ramp3 and Tbrg4. Our results show that the tight regulation of WAP gene expression parallels variations in the chromatin structure and DNA methylation profile throughout the Ramp3-WAP-Tbrg4 locus. Three Matrix Attachment Regions (MAR) have been predicted in this locus. Two of them are located between regions exhibiting open and closed chromatin structures in the liver. The third, located around the transcription start site of the Tbrg4 gene, interacts with topoisomerase II in HC11 mouse mammary cells, and in these cells anchors the chromatin loop to the nuclear matrix. Furthermore, if lactogenic hormones are present in these cells, the chromatin loop surrounding the WAP gene is more tightly attached to the nuclear structure, as observed after a high salt treatment of the nuclei and the formation of nuclear halos. Taken together, our results point to a combination of several epigenetic events that may explain the differential expression pattern of the WAP locus in relation to tissue and developmental stages

Towards three-loop QCD corrections to the time-like splitting functions

International Nuclear Information System (INIS)

Gituliar, O.; Moch, S.

2015-05-01

We report on the status of a direct computation of the time-like splitting functions at next-to-next-to-leading order in QCD. Time-like splitting functions govern the collinear kinematics of inclusive hadron production and the evolution of the parton fragmentation distributions. Current knowledge about them at three loops has been inferred by means of crossing symmetry from their related space-like counterparts, which has left certain parts of the off-diagonal quark-gluon splitting function undetermined. This motivates an independent calculation from first principles. We review the tools and methods which are applied to attack the problem.

Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development.

Directory of Open Access Journals (Sweden)

Chao Gao

Full Text Available The basic/helix-loop-helix (bHLH proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as Arabidopsis, rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts, Arachis duranensis (AA and Arachis ipaensis (BB, respectively. Phylogenetic analysis indicated that these bHLHs could be classified into 19 subfamilies. Distribution mapping results showed that peanut bHLH genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120 bHLH gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184 bHLH genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61 bHLH genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.

An ATR-dependent function for the Ddx19 RNA helicase in nuclear R-loop metabolism.

Science.gov (United States)

Hodroj, Dana; Recolin, Bénédicte; Serhal, Kamar; Martinez, Susan; Tsanov, Nikolay; Abou Merhi, Raghida; Maiorano, Domenico

2017-05-02

Coordination between transcription and replication is crucial in the maintenance of genome integrity. Disturbance of these processes leads to accumulation of aberrant DNA:RNA hybrids (R-loops) that, if unresolved, generate DNA damage and genomic instability. Here we report a novel, unexpected role for the nucleopore-associated mRNA export factor Ddx19 in removing nuclear R-loops formed upon replication stress or DNA damage. We show, in live cells, that Ddx19 transiently relocalizes from the nucleopore to the nucleus upon DNA damage, in an ATR/Chk1-dependent manner, and that Ddx19 nuclear relocalization is required to clear R-loops. Ddx19 depletion induces R-loop accumulation, proliferation-dependent DNA damage and defects in replication fork progression. Further, we show that Ddx19 resolves R-loops in vitro via its helicase activity. Furthermore, mutation of a residue phosphorylated by Chk1 in Ddx19 disrupts its interaction with Nup214 and allows its nuclear relocalization. Finally, we show that Ddx19 operates in resolving R-loops independently of the RNA helicase senataxin. Altogether these observations put forward a novel, ATR-dependent function for Ddx19 in R-loop metabolism to preserve genome integrity in mammalian cells. © 2017 The Authors.

The functional significance of the autolysis loop in protein C and activated protein C.

Science.gov (United States)

Yang, Likui; Manithody, Chandrashekhara; Rezaie, Alireza R

2005-07-01

The autolysis loop of activated protein C (APC) is five residues longer than the autolysis loop of other vitamin K-dependent coagulation proteases. To investigate the role of this loop in the zymogenic and anticoagulant properties of the molecule, a protein C mutant was constructed in which the autolysis loop of the protein was replaced with the corresponding loop of factor X. The protein C mutant was activated by thrombin with approximately 5-fold higher rate in the presence of Ca2+. Both kinetics and direct binding studies revealed that the Ca2+ affinity of the mutant has been impaired approximately 3-fold. The result of a factor Va degradation assay revealed that the anticoagulant function of the mutant has been improved 4-5-fold in the absence but not in the presence of protein S. The improvement was due to a better recognition of both the P1-Arg506 and P1-Arg306 cleavage sites by the mutant protease. However, the plasma half-life of the mutant was markedly shortened due to faster inactivation by plasma serpins. These results suggest that the autolysis loop of protein C is critical for the Ca(2+)-dependence of activation by thrombin. Moreover, a longer autolysis loop in APC is not optimal for interaction with factor Va in the absence of protein S, but it contributes to the lack of serpin reactivity and longer half-life of the protease in plasma.

Four loop wave function renormalization in the non-abelian Thirring model

International Nuclear Information System (INIS)

Ali, D.B.; Gracey, J.A.

2001-01-01

We compute the anomalous dimension of the fermion field with N f flavours in the fundamental representation of a general Lie colour group in the non-abelian Thirring model at four loops. The implications on the renormalization of the two point Green's function through the loss of multiplicative renormalizability of the model in dimensional regularization due to the appearance of evanescent four fermi operators are considered at length. We observe the appearance of one new colour group Casimir, d F abcd d F abcd , in the final four loop result and discuss its consequences for the relation of the Knizhnik-Zamolodchikov critical exponents in the Wess-Zumino-Witten-Novikov model to the non-abelian Thirring model. Renormalization scheme changes are also considered to ensure that the underlying Fierz symmetry broken by dimensional regularization is restored

Genes2FANs: connecting genes through functional association networks

Science.gov (United States)

2012-01-01

Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in

Stability, structure, and evolution of cool loops

International Nuclear Information System (INIS)

Cally, P.S.; Robb, T.D.

1991-01-01

The criteria for the existence and stability of cool loops are reexamined. It is found that the stability of the loops strongly depends on the form of the heating and radiative loss functions and that if the Ly-alpha peak which appears in most calculations of the radiative loss function is real, cool loops are almost certainly unstable. Removing the hydrogen contribution from the recent loss function Q(T) by Cook et al. (1989) does not produce the much-used result, Q proportional to T-cubed, which is so favorable to cool loop stability. Even using the probably unrealistically favorable loss function Q1 of Cook et al. with the hydrogen contribution removed, the maximum temperature attainable in stable cool loops is a factor of 2-3 too small to account for the excess emission observed in lower transition region lines. Dynamical simulations of cool loop instabilities reveal that the final state of such a model is the hot loop equilibrium. 26 refs

Comments on correlation functions of large spin operators and null polygonal Wilson loops

Energy Technology Data Exchange (ETDEWEB)

Cardona, Carlos A., E-mail: cargicar@iafe.uba.ar [Instituto de Astronomia y Fisica del Espacio (CONICET-UBA), C.C. 67 - Suc. 28, 1428 Buenos Aires (Argentina); Physics Department, University of Buenos Aires, CONICET, Ciudad Universitaria, 1428 Buenos Aires (Argentina)

2013-02-11

We discuss the relation between correlation functions of twist-two large spin operators and expectation values of Wilson loops along light-like trajectories. After presenting some heuristic field theoretical arguments suggesting this relation, we compute the divergent part of the correlator in the limit of large 't Hooft coupling and large spins, using a semi-classical world-sheet which asymptotically looks like a GKP rotating string. We show this diverges as expected from the expectation value of a null Wilson loop, namely, as (ln{mu}{sup -2}){sup 2}, {mu} being a cut-off of the theory.

Comments on correlation functions of large spin operators and null polygonal Wilson loops

International Nuclear Information System (INIS)

Cardona, Carlos A.

2013-01-01

We discuss the relation between correlation functions of twist-two large spin operators and expectation values of Wilson loops along light-like trajectories. After presenting some heuristic field theoretical arguments suggesting this relation, we compute the divergent part of the correlator in the limit of large 't Hooft coupling and large spins, using a semi-classical world-sheet which asymptotically looks like a GKP rotating string. We show this diverges as expected from the expectation value of a null Wilson loop, namely, as (lnμ −2 ) 2 , μ being a cut-off of the theory.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

Science.gov (United States)

He, Zhili; Zhang, Ping; Wu, Linwei; Rocha, Andrea M; Tu, Qichao; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D; Wu, Liyou; Yang, Yunfeng; Elias, Dwayne A; Watson, David B; Adams, Michael W W; Fields, Matthew W; Alm, Eric J; Hazen, Terry C; Adams, Paul D; Arkin, Adam P; Zhou, Jizhong

2018-02-20

Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly ( P contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as

Mediator and Cohesin Connect Gene Expression and Chromatin Architecture

Science.gov (United States)

Kagey, Michael H.; Newman, Jamie J.; Bilodeau, Steve; Zhan, Ye; Orlando, David A.; van Berkum, Nynke L.; Ebmeier, Christopher C.; Goossens, Jesse; Rahl, Peter B.; Levine, Stuart S.; Taatjes, Dylan J.; Dekker, Job; Young, Richard A.

2010-01-01

Summary Transcription factors control cell specific gene expression programs through interactions with diverse coactivators and the transcription apparatus. Gene activation may involve DNA loop formation between enhancer-bound transcription factors and the transcription apparatus at the core promoter, but this process is not well understood. We report here that Mediator and Cohesin physically and functionally connect the enhancers and core promoters of active genes in embryonic stem cells. Mediator, a transcriptional coactivator, forms a complex with Cohesin, which can form rings that connect two DNA segments. The Cohesin loading factor Nipbl is associated with Mediator/Cohesin complexes, providing a means to load Cohesin at promoters. DNA looping is observed between the enhancers and promoters occupied by Mediator and Cohesin. Mediator and Cohesin occupy different promoters in different cells, thus generating cell-type specific DNA loops linked to the gene expression program of each cell. PMID:20720539

LOOP CALCULUS AND BELIEF PROPAGATION FOR Q-ARY ALPHABET: LOOP TOWER

Energy Technology Data Exchange (ETDEWEB)

CHERTKOV, MICHAEL [Los Alamos National Laboratory; CHERNYAK, VLADIMIR [Los Alamos National Laboratory

2007-01-10

Loop calculus introduced in [1], [2] constitutes a new theoretical tool that explicitly expresses symbol Maximum-A-Posteriori (MAP) solution of a general statistical inference problem via a solution of the Belief Propagation (BP) equations. This finding brought a new significance to the BP concept, which in the past was thought of as just a loop-free approximation. In this paper they continue a discussion of the Loop Calculus, partitioning the results into three Sections. In Section 1 they introduce a new formulation of the Loop Calculus in terms of a set of transformations (gauges) that keeping the partition function of the problem invariant. The full expression contains two terms referred to as the 'ground state' and 'excited states' contributions. The BP equations are interpreted as a special (BP) gauge fixing condition that emerges as a special orthogonality constraint between the ground state and excited states, which also selects loop contributions as the only surviving ones among the excited states. In Section 2 they demonstrate how the invariant interpretation of the Loop Calculus, introduced in Section 1, allows a natural extension to the case of a general q-ary alphabet, this is achieved via a loop tower sequential construction. The ground level in the tower is exactly equivalent to assigning one color (out of q available) to the 'ground state' and considering all 'excited' states colored in the remaining (q-1) colors, according to the loop calculus rule. Sequentially, the second level in the tower corresponds to selecting a loop from the previous step, colored in (q-1) colors, and repeating the same ground vs excited states splitting procedure into one and (q-2) colors respectively. The construction proceeds till the full (q-1)-levels deep loop tower (and the corresponding contributions to the partition function) are established. In Section 3 they discuss an ultimate relation between the loop calculus and the Bethe

A type of loop algebra and the associated loop algebras

International Nuclear Information System (INIS)

Tam Honwah; Zhang Yufeng

2008-01-01

A higher-dimensional twisted loop algebra is constructed. As its application, a new Lax pair is presented, whose compatibility gives rise to a Liouville integrable hierarchy of evolution equations by making use of Tu scheme. One of the reduction cases of the hierarchy is an analogous of the well-known AKNS system. Next, the twisted loop algebra, furthermore, is extended to another higher dimensional loop algebra, from which a hierarchy of evolution equations with 11-potential component functions is obtained, whose reduction is just standard AKNS system. Especially, we prove that an arbitrary linear combination of the four Hamiltonian operators directly obtained from the recurrence relations is still a Hamiltonian operator. Therefore, the hierarchy with 11-potential functions possesses 4-Hamiltonian structures. Finally, an integrable coupling of the hierarchy is worked out

Bootstrapping the Three-Loop Hexagon

Energy Technology Data Exchange (ETDEWEB)

Dixon, Lance J.; /CERN /SLAC; Drummond, James M.; /CERN /Annecy, LAPTH; Henn, Johannes M.; /Humboldt U., Berlin /Santa Barbara, KITP

2011-11-08

We consider the hexagonal Wilson loop dual to the six-point MHV amplitude in planar N = 4 super Yang-Mills theory. We apply constraints from the operator product expansion in the near-collinear limit to the symbol of the remainder function at three loops. Using these constraints, and assuming a natural ansatz for the symbol's entries, we determine the symbol up to just two undetermined constants. In the multi-Regge limit, both constants drop out from the symbol, enabling us to make a non-trivial confirmation of the BFKL prediction for the leading-log approximation. This result provides a strong consistency check of both our ansatz for the symbol and the duality between Wilson loops and MHV amplitudes. Furthermore, we predict the form of the full three-loop remainder function in the multi-Regge limit, beyond the leading-log approximation, up to a few constants representing terms not detected by the symbol. Our results confirm an all-loop prediction for the real part of the remainder function in multi-Regge 3 {yields} 3 scattering. In the multi-Regge limit, our result for the remainder function can be expressed entirely in terms of classical polylogarithms. For generic six-point kinematics other functions are required.

The one-loop partition function of N=4 super-Yang-Mills theory on RxS3

International Nuclear Information System (INIS)

Spradlin, Marcus; Volovich, Anastasia

2005-01-01

We study weakly coupled SU(N)N=4 super-Yang-Mills theory on RxS 3 at infinite N, which has interesting thermodynamics, including a Hagedorn transition, even at zero Yang-Mills coupling. We calculate the exact one-loop partition function below the Hagedorn temperature. Our calculation employs the representation of the one-loop dilatation operator as a spin chain Hamiltonian acting on neighboring sites and a generalization of Polya's counting of necklaces (gauge-invariant operators) to include necklaces with a 'pendant' (an operator which acts on neighboring beads). We find that the one-loop correction to the Hagedorn temperature is δlnT H =+λ/8π 2

FunGene: the functional gene pipeline and repository.

Science.gov (United States)

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

FunGene: the Functional Gene Pipeline and Repository

Directory of Open Access Journals (Sweden)

Jordan A. Fish

2013-10-01

Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

Reactor loops at Chalk River

International Nuclear Information System (INIS)

Sochaski, R.O.

1962-07-01

This report describes broadly the nine in-reactor loops, and their components, located in and around the NRX and NRU reactors at Chalk River. First an introduction and general description is given of the loops and their function, supplemented with a table outlining some loop specifications and nine simplified flow sheets, one for each individual loop. The report then proceeds to classify each loop into two categories, the 'main loop circuit' and the 'auxiliary circuit', and descriptions are given of each circuit's components in turn. These components, in part, are comprised of the main loop pumps, the test section, loop heaters, loop coolers, delayed-neutron monitors, surge tank, Dowtherm coolers, loop piping. Here again photographs, drawings and tables are included to provide a clearer understanding of the descriptive literature and to include, in tables, some specifications of the more important components in each loop. (author)

Functional analysis of the stem-loop structures at the 5' end of the Aichi virus genome

International Nuclear Information System (INIS)

Nagashima, Shigeo; Sasaki, Jun; Taniguchi, Koki

2003-01-01

Aichi virus is a member of the family Picornaviridae. Computer-assisted secondary structure prediction suggested the formation of three stem-loop structures (SL-A, SL-B, and SL-C from the 5' end) within the 5'-end 120 nucleotides of the genome. We have already shown that the most 5'-end stem-loop, SL-A, is critical for viral RNA replication. Here, using an infectious cDNA clone and a replicon harboring a luciferase gene, we revealed that formation of SL-B and SL-C on the positive strand is essential for viral RNA replication. In addition, the specific nucleotide sequence of the loop segment of SL-B was also shown to be critical for viral RNA replication. Mutations of the upper and lower stems of SL-C that do not disrupt the base-pairings hardly affected RNA replication, but decreased the yields of viable viruses significantly compared with for the wild-type. This suggests that SL-C plays a role at some step besides RNA replication during virus infection

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes.

Science.gov (United States)

Osato, Naoki

2018-01-19

Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes. Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5-60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes. Human putative transcriptional target genes showed significant functional enrichments. Functional

Two-point functions in (loop) quantum cosmology

Energy Technology Data Exchange (ETDEWEB)

Calcagni, Gianluca; Oriti, Daniele [Max-Planck-Institute for Gravitational Physics (Albert Einstein Institute), Am Muehlenberg 1, D-14476 Golm (Germany); Gielen, Steffen [Max-Planck-Institute for Gravitational Physics (Albert Einstein Institute), Am Muehlenberg 1, D-14476 Golm (Germany); DAMTP, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA (United Kingdom)

2011-07-01

We discuss the path-integral formulation of quantum cosmology with a massless scalar field as a sum-over-histories of volume transitions, with particular but non-exclusive reference to loop quantum cosmology (LQC). Exploiting the analogy with the relativistic particle, we give a complete overview of the possible two-point functions, pointing out the choices involved in their definitions, deriving their vertex expansions and the composition laws they satisfy. We clarify the origin and relations of different quantities previously defined in the literature, in particular the tie between definitions using a group averaging procedure and those in a deparametrized framework. Finally, we draw some conclusions about the physics of a single quantum universe (where there exist superselection rules on positive- and negative-frequency sectors and different choices of inner product are physically equivalent) and multiverse field theories where the role of these sectors and the inner product are reinterpreted.

Two-point functions in (loop) quantum cosmology

Energy Technology Data Exchange (ETDEWEB)

Calcagni, Gianluca; Gielen, Steffen; Oriti, Daniele, E-mail: calcagni@aei.mpg.de, E-mail: gielen@aei.mpg.de, E-mail: doriti@aei.mpg.de [Max Planck Institute for Gravitational Physics (Albert Einstein Institute), Am Muehlenberg 1, D-14476 Golm (Germany)

2011-06-21

The path-integral formulation of quantum cosmology with a massless scalar field as a sum-over-histories of volume transitions is discussed, with particular but non-exclusive reference to loop quantum cosmology. Exploiting the analogy with the relativistic particle, we give a complete overview of the possible two-point functions, pointing out the choices involved in their definitions, deriving their vertex expansions and the composition laws they satisfy. We clarify the origin and relations of different quantities previously defined in the literature, in particular the tie between definitions using a group averaging procedure and those in a deparametrized framework. Finally, we draw some conclusions about the physics of a single quantum universe (where there exist superselection rules on positive- and negative-frequency sectors and different choices of inner product are physically equivalent) and multiverse field theories where the role of these sectors and the inner product are reinterpreted.

Two-point functions in (loop) quantum cosmology

International Nuclear Information System (INIS)

Calcagni, Gianluca; Gielen, Steffen; Oriti, Daniele

2011-01-01

The path-integral formulation of quantum cosmology with a massless scalar field as a sum-over-histories of volume transitions is discussed, with particular but non-exclusive reference to loop quantum cosmology. Exploiting the analogy with the relativistic particle, we give a complete overview of the possible two-point functions, pointing out the choices involved in their definitions, deriving their vertex expansions and the composition laws they satisfy. We clarify the origin and relations of different quantities previously defined in the literature, in particular the tie between definitions using a group averaging procedure and those in a deparametrized framework. Finally, we draw some conclusions about the physics of a single quantum universe (where there exist superselection rules on positive- and negative-frequency sectors and different choices of inner product are physically equivalent) and multiverse field theories where the role of these sectors and the inner product are reinterpreted.

Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense.

Science.gov (United States)

Arya, Preeti; Acharya, Vishal

2018-02-01

STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

Science.gov (United States)

Zhang, Ping; Wu, Linwei; Rocha, Andrea M.; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D.; Wu, Liyou; Watson, David B.; Adams, Michael W. W.; Alm, Eric J.; Adams, Paul D.; Arkin, Adam P.

2018-01-01

ABSTRACT Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. PMID:29463661

Effects of two-loop contributions in the pseudofermion functional renormalization group method for quantum spin systems

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Rück, Marlon; Reuther, Johannes

2018-04-01

We implement an extension of the pseudofermion functional renormalization group method for quantum spin systems that takes into account two-loop diagrammatic contributions. An efficient numerical treatment of the additional terms is achieved within a nested graph construction which recombines different one-loop interaction channels. In order to be fully self-consistent with respect to self-energy corrections, we also include certain three-loop terms of Katanin type. We first apply this formalism to the antiferromagnetic J1-J2 Heisenberg model on the square lattice and benchmark our results against the previous one-loop plus Katanin approach. Even though the renormalization group (RG) equations undergo significant modifications when including the two-loop terms, the magnetic phase diagram, comprising Néel ordered and collinear ordered phases separated by a magnetically disordered regime, remains remarkably unchanged. Only the boundary position between the disordered and the collinear phases is found to be moderately affected by two-loop terms. On the other hand, critical RG scales, which we associate with critical temperatures Tc, are reduced by a factor of ˜2 indicating that the two-loop diagrams play a significant role in enforcing the Mermin-Wagner theorem. Improved estimates for critical temperatures are also obtained for the Heisenberg ferromagnet on the three-dimensional simple cubic lattice where errors in Tc are reduced by ˜34 % . These findings have important implications for the quantum phase diagrams calculated within the previous one-loop plus Katanin approach which turn out to be already well converged.

Optical and electrochemical detection of a verotoxigenic E. coli gene using DNAzyme-labeled stem-loops

Directory of Open Access Journals (Sweden)

Gloria Longinotti

2017-12-01

Full Text Available The activity of a peroxidase-mimicking DNAzyme was optimized to be used as a catalytic label in a stem-loop genosensor construction for quantifying the gene sequence Shiga-like toxin I of verotoxigenic E. coli. Experimental conditions such as pH, buffer composition, potassium ion concentration, and hemin-to-oligonucleotides ratio, were analyzed to maximize optical and electrochemical responses using microvolumes. Different stem-loop constructions were evaluated to obtain the optimum response against the target concentration. Linear ranges of 0.05-0.5 µM and limits of detection of 174 nM and 144 nM were estimated for the optical and electrochemical measurements, respectively. Selectivity was proved by assaying other verotoxigenic, enterotoxigenic and enteroinvasive sequences. The results show that, if a combination of small-volume electrochemical cells and low-cost untreated screen-printed electrodes with a relatively high geometric area is used, electrochemical measurements present similar sensitivity and limits of detection to the more usual optical ones, allowing the development of low-cost electrochemical biosensors based on the use of soluble DNAzymes as labels.

Retroviruses Hijack Chromatin Loops to Drive Oncogene Expression and Highlight the Chromatin Architecture around Proto-Oncogenic Loci

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Pattison, Jillian M.; Wright, Jason B.; Cole, Michael D.

2015-01-01

The majority of the genome consists of intergenic and non-coding DNA sequences shown to play a major role in different gene regulatory networks. However, the specific potency of these distal elements as well as how these regions exert function across large genomic distances remains unclear. To address these unresolved issues, we closely examined the chromatin architecture around proto-oncogenic loci in the mouse and human genomes to demonstrate a functional role for chromatin looping in distal gene regulation. Using cell culture models, we show that tumorigenic retroviral integration sites within the mouse genome occur near existing large chromatin loops and that this chromatin architecture is maintained within the human genome as well. Significantly, as mutagenesis screens are not feasible in humans, we demonstrate a way to leverage existing screens in mice to identify disease relevant human enhancers and expose novel disease mechanisms. For instance, we characterize the epigenetic landscape upstream of the human Cyclin D1 locus to find multiple distal interactions that contribute to the complex cis-regulation of this cell cycle gene. Furthermore, we characterize a novel distal interaction upstream of the Cyclin D1 gene which provides mechanistic evidence for the abundant overexpression of Cyclin D1 occurring in multiple myeloma cells harboring a pathogenic translocation event. Through use of mapped retroviral integrations and translocation breakpoints, our studies highlight the importance of chromatin looping in oncogene expression, elucidate the epigenetic mechanisms crucial for distal cis-regulation, and in one particular instance, explain how a translocation event drives tumorigenesis through upregulation of a proto-oncogene. PMID:25799187

Gas Test Loop Functional and Technical Requirements

International Nuclear Information System (INIS)

Glen R. Longhurst; Soli T. Khericha; James L. Jones

2004-01-01

This document defines the technical and functional requirements for a gas test loop (GTL) to be constructed for the purpose of providing a high intensity fast-flux irradiation environment for developers of advanced concept nuclear reactors. This capability is needed to meet fuels and materials testing requirements of the designers of Generation IV (GEN IV) reactors and other programs within the purview of the Advanced Fuel Cycle Initiative (AFCI). Space nuclear power development programs may also benefit by the services the GTL will offer. The overall GTL technical objective is to provide developers with the means for investigating and qualifying fuels and materials needed for advanced reactor concepts. The testing environment includes a fast-flux neutron spectrum of sufficient intensity to perform accelerated irradiation testing. Appropriate irradiation temperature, gaseous environment, test volume, diagnostics, and access and handling features are also needed. This document serves to identify those requirements as well as generic requirements applicable to any system of this kind

Gas Test Loop Functional and Technical Requirements

Energy Technology Data Exchange (ETDEWEB)

Glen R. Longhurst; Soli T. Khericha; James L. Jones

2004-09-01

This document defines the technical and functional requirements for a gas test loop (GTL) to be constructed for the purpose of providing a high intensity fast-flux irradiation environment for developers of advanced concept nuclear reactors. This capability is needed to meet fuels and materials testing requirements of the designers of Generation IV (GEN IV) reactors and other programs within the purview of the Advanced Fuel Cycle Initiative (AFCI). Space nuclear power development programs may also benefit by the services the GTL will offer. The overall GTL technical objective is to provide developers with the means for investigating and qualifying fuels and materials needed for advanced reactor concepts. The testing environment includes a fast-flux neutron spectrum of sufficient intensity to perform accelerated irradiation testing. Appropriate irradiation temperature, gaseous environment, test volume, diagnostics, and access and handling features are also needed. This document serves to identify those requirements as well as generic requirements applicable to any system of this kind.

Function analysis of unknown genes

DEFF Research Database (Denmark)

Rogowska-Wrzesinska, A.

2002-01-01

  This thesis entitled "Function analysis of unknown genes" presents the use of proteome analysis for the characterisation of yeast (Saccharomyces cerevisiae) genes and their products (proteins especially those of unknown function). This study illustrates that proteome analysis can be used...... to describe different aspects of molecular biology of the cell, to study changes that occur in the cell due to overexpression or deletion of a gene and to identify various protein modifications. The biological questions and the results of the described studies show the diversity of the information that can...... genes and proteins. It reports the first global proteome database collecting 36 yeast single gene deletion mutants and selecting over 650 differences between analysed mutants and the wild type strain. The obtained results show that two-dimensional gel electrophoresis and mass spectrometry based proteome...

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

Directory of Open Access Journals (Sweden)

Zhili He

2018-02-01

Full Text Available Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN, representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5 increased significantly (P < 0.05 as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.

One-loop beta functions for the orientable non-commutative Gross Neveu model TH1"-->

Science.gov (United States)

Lakhoua, A.; Vignes-Tourneret, F.; Wallet, J.-C.

2007-11-01

We compute at the one-loop order the β-functions for a renormalisable non-commutative analog of the Gross Neveu model defined on the Moyal plane. The calculation is performed within the so called x-space formalism. We find that this non-commutative field theory exhibits asymptotic freedom for any number of colors. The β-function for the non-commutative counterpart of the Thirring model is found to be non vanishing.

In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory.

Science.gov (United States)

Watson, L Ashley; Tsai, Li-Huei

2017-04-01

Different aspects of learning, memory, and cognition are regulated by epigenetic mechanisms such as covalent DNA modifications and histone post-translational modifications. More recently, the modulation of chromatin architecture and nuclear organization is emerging as a key factor in dynamic transcriptional regulation of the post-mitotic neuron. For instance, neuronal activity induces relocalization of gene loci to 'transcription factories', and specific enhancer-promoter looping contacts allow for precise transcriptional regulation. Moreover, neuronal activity-dependent DNA double-strand break formation in the promoter of immediate early genes appears to overcome topological constraints on transcription. Together, these findings point to a critical role for genome topology in integrating dynamic environmental signals to define precise spatiotemporal gene expression programs supporting cognitive processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

The functional landscape of mouse gene expression

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Zhang Wen

2004-12-01

Full Text Available Abstract Background Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related but distinct strategy of correlating gene co-expression as a means to predict gene function. Results We generated microarray expression data for nearly 40,000 known and predicted mRNAs in 55 mouse tissues, using custom-built oligonucleotide arrays. We show that quantitative transcriptional co-expression is a powerful predictor of gene function. Hundreds of functional categories, as defined by Gene Ontology 'Biological Processes', are associated with characteristic expression patterns across all tissues, including categories that bear no overt relationship to the tissue of origin. In contrast, simple tissue-specific restriction of expression is a poor predictor of which genes are in which functional categories. As an example, the highly conserved mouse gene PWP1 is widely expressed across different tissues but is co-expressed with many RNA-processing genes; we show that the uncharacterized yeast homolog of PWP1 is required for rRNA biogenesis. Conclusions We conclude that 'functional genomics' strategies based on quantitative transcriptional co-expression will be as fruitful in mammals as they have been in simpler organisms, and that transcriptional control of mammalian physiology is more modular than is generally appreciated. Our data and analyses provide a public resource for mammalian functional genomics.

HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it.

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Khrustalev, Vladislav Victorovich

2009-01-01

Guanine is the most mutable nucleotide in HIV genes because of frequently occurring G to A transitions, which are caused by cytosine deamination in viral DNA minus strands catalyzed by APOBEC enzymes. Distribution of guanine between three codon positions should influence the probability for G to A mutation to be nonsynonymous (to occur in first or second codon position). We discovered that nucleotide sequences of env genes coding for third variable regions (V3 loops) of gp120 from HIV1 and HIV2 have different kinds of guanine usage biases. In the HIV1 reference strain and 100 additionally analyzed HIV1 strains the guanine usage bias in V3 loop coding regions (2G>1G>3G) should lead to elevated nonsynonymous G to A transitions occurrence rates. In the HIV2 reference strain and 100 other HIV2 strains guanine usage bias in V3 loop coding regions (3G>2G>1G) should protect V3 loops from hypermutability. According to the HIV1 and HIV2 V3 alignment, insertion of the sequence enriched with 2G (21 codons in length) occurred during the evolution of HIV1 predecessor, while insertion of the different sequence enriched with 3G (19 codons in length) occurred during the evolution of HIV2 predecessor. The higher is the level of 3G in the V3 coding region, the lower should be the immune escaping mutation occurrence rates. This hypothesis was tested in this study by comparing the guanine usage in V3 loop coding regions from HIV1 fast and slow progressors. All calculations have been performed by our algorithms "VVK In length", "VVK Dinucleotides" and "VVK Consensus" (www.barkovsky.hotmail.ru).

LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

Science.gov (United States)

Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

2017-10-01

Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

Large-nf contributions to the four-loop splitting functions in QCD

Directory of Open Access Journals (Sweden)

J. Davies

2017-02-01

Full Text Available We have computed the fourth-order nf2 contributions to all three non-singlet quark–quark splitting functions and their four nf3 flavour-singlet counterparts for the evolution of the parton distributions of hadrons in perturbative QCD with nf effectively massless quark flavours. The analytic form of these functions is presented in both Mellin N-space and momentum-fraction x-space; the large-x and small-x limits are discussed. Our results agree with all available predictions derived from lower-order information. The large-x limit of the quark–quark cases provides the complete nf2 part of the four-loop cusp anomalous dimension which agrees with two recent partial computations.

New insights into the structural and functional involvement of the gate loop in AcrB export activity.

Science.gov (United States)

Ababou, Abdessamad

2018-02-01

AcrB is a major multidrug exporter in Escherichia coli and other Gram-negative bacteria. Its gate loop, located between the proximal and the distal pockets, have been reported to play important role in the export of many antibiotics. This loop location, rigidity and interactions with substrates have led recent reports to suggest that AcrB export mechanism operates in a sequential manner. First the substrate binds the proximal pocket in the access monomer, then it moves to bind the distal pocket in the binding monomer and subsequently it is extruded in the extrusion monomer. Recently, we have demonstrated that the gate loop is not required for the binding of Erythromycin but the integrity of this loop is important for an efficient export of this substrate. However, here we show that the antibiotic susceptibilities of the same AcrB gate loop mutants for Doxorubicin were unaffected, suggesting that this loop is not required for its export, and we demonstrate that this substrate may use principally the tunnel-1, located between transmembranes 8 and 9, more often than previously reported. To further explain our findings, here we address the gate loop mutations effects on AcrB solution energetics (fold, stability, molecular dynamics) and on the in vivo efflux of Erythromycin and Doxorubicin. Finally, we discuss the efflux and the discrepancy between the structural and the functional experiments for Erythromycin in these gate loop mutants. Copyright © 2017 Elsevier B.V. All rights reserved.

A calculation of the three-loop helicity-dependent splitting functions in QCD

International Nuclear Information System (INIS)

Vogt, A.

2014-05-01

We have calculated the complete matrix of three-loop helicity-difference ('polarized') splitting functions ΔP ik (2) (x), i,k=q,g, in massless perturbative QCD. In this note we briefly discuss some properties of the polarized splitting functions and our non-standard determination of the hitherto missing lower-row quantities ΔP gq (2) and ΔP gg (2) . The resulting next-to-next-to-leading order (NNLO) corrections to the evolution of polarized parton distributions are illustrated and found to be small even at rather large values of the strong coupling constant α s .

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

Science.gov (United States)

Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

2012-01-01

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

One-loop quantum gravitational corrections to the scalar two-point function at fixed geodesic distance

Science.gov (United States)

Fröb, Markus B.

2018-02-01

We study a proposal for gauge-invariant correlation functions in perturbative quantum gravity, which are obtained by fixing the geodesic distance between points in the fluctuating geometry. These correlation functions are non-local and strongly divergent, and we show how to renormalise them by performing a ‘wave function renormalisation’ of the geodesic embedding coordinates. The result is finite and gauge-independent, but displays unusual features such as double logarithms at one-loop order.

Sigma models and renormalization of string loops

International Nuclear Information System (INIS)

Tseytlin, A.A.

1989-05-01

An extension of the ''σ-model β-functions - string equations of motion'' correspondence to the string loop level is discussed. Special emphasis is made on how the renormalization group acts in string loops and, in particular, on the renormalizability property of the generating functional Z-circumflex for string amplitudes (related to the σ model partition function integrated over moduli). Renormalization of Z-circumflex at one and two loop order is analyzed in some detail. We also discuss an approach to renormalization based on operators of insertion of topological fixtures. (author). 70 refs

Gene coexpression network analysis as a source of functional annotation for rice genes.

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Kevin L Childs

Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

A new measure for functional similarity of gene products based on Gene Ontology

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Lengauer Thomas

2006-06-01

Full Text Available Abstract Background Gene Ontology (GO is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. Results We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; simRel and funSim. One measure (simRel is applied in the comparison of the biological processes found in different groups of organisms. The other measure (funSim is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. Conclusion The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families.

A Role for the Cytoskeleton in Heart Looping

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Kersti K. Linask

2007-01-01

Full Text Available Over the past 10 years, key genes involved in specification of left-right laterality pathways in the embryo have been defined. The read-out for misexpression of laterality genes is usually the direction of heart looping. The question of how dextral looping direction occurred mechanistically and how the heart tube bends remains unknown. It is becoming clear from our experiments and those of others that left-right differences in cell proliferation in the second heart field (anterior heart field drives the dextral direction. Evidence is accumulating that the cytoskeleton is at the center of laterality, and the bending and rotational forces associated with heart looping. If laterality pathways are modulated upstream, the cytoskeleton, including nonmuscle myosin II (NMHC-II, is altered downstream within the cardiomyocytes, leading to looping abnormalities. The cytoskeleton is associated with important mechanosensing and signaling pathways in cell biology and development. The initiation of blood flow during the looping period and the inherent stresses associated with increasing volumes of blood flowing into the heart may help to potentiate the process. In recent years, the steps involved in this central and complex process of heart development that is the basis of numerous congenital heart defects are being unraveled.

Gene analogue finder: a GRID solution for finding functionally analogous gene products

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Licciulli Flavio

2007-09-01

Full Text Available Abstract Background To date more than 2,1 million gene products from more than 100000 different species have been described specifying their function, the processes they are involved in and their cellular localization using a very well defined and structured vocabulary, the gene ontology (GO. Such vast, well defined knowledge opens the possibility of compare gene products at the level of functionality, finding gene products which have a similar function or are involved in similar biological processes without relying on the conventional sequence similarity approach. Comparisons within such a large space of knowledge are highly data and computing intensive. For this reason this project was based upon the use of the computational GRID, a technology offering large computing and storage resources. Results We have developed a tool, GENe AnaloGue FINdEr (ENGINE that parallelizes the search process and distributes the calculation and data over the computational GRID, splitting the process into many sub-processes and joining the calculation and the data on the same machine and therefore completing the whole search in about 3 days instead of occupying one single machine for more than 5 CPU years. The results of the functional comparison contain potential functional analogues for more than 79000 gene products from the most important species. 46% of the analyzed gene products are well enough described for such an analysis to individuate functional analogues, such as well-known members of the same gene family, or gene products with similar functions which would never have been associated by standard methods. Conclusion ENGINE has produced a list of potential functionally analogous relations between gene products within and between species using, in place of the sequence, the gene description of the GO, thus demonstrating the potential of the GO. However, the current limiting factor is the quality of the associations of many gene products from non

Gene Overexpression Resources in Cereals for Functional Genomics and Discovery of Useful Genes

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Kiyomi Abe

2016-09-01

Full Text Available Identification and elucidation of functions of plant genes is valuable for both basic and applied research. In addition to natural variation in model plants, numerous loss-of-function resources have been produced by mutagenesis with chemicals, irradiation, or insertions of transposable elements or T-DNA. However, we may be unable to observe loss-of-function phenotypes for genes with functionally redundant homologs, and for those essential for growth and development. To offset such disadvantages, gain-of-function transgenic resources have been exploited. Activation-tagged lines have been generated using obligatory overexpression of endogenous genes by random insertion of an enhancer. Recent progress in DNA sequencing technology and bioinformatics has enabled the preparation of genomewide collections of full-length cDNAs (fl-cDNAs in some model species. Using the fl-cDNA clones, a novel gain-of-function strategy, Fl-cDNA OvereXpressor gene (FOX-hunting system, has been developed. A mutant phenotype in a FOX line can be directly attributed to the overexpressed fl-cDNA. Investigating a large population of FOX lines could reveal important genes conferring favorable phenotypes for crop breeding. Alternatively, a unique loss-of-function approach Chimeric REpressor gene Silencing Technology (CRES-T has been developed. In CRES-T, overexpression of a chimeric repressor, composed of the coding sequence of a transcription factor (TF and short peptide designated as the repression domain, could interfere with the action of endogenous TF in plants. Although plant TFs usually consist of gene families, CRES-T is effective, in principle, even for the TFs with functional redundancy. In this review, we focus on the current status of the gene-overexpression strategies and resources for identifying and elucidating novel functions of cereal genes. We discuss the potential of these research tools for identifying useful genes and phenotypes for application in crop

Sugarcane genes related to mitochondrial function

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Fonseca Ghislaine V.

2001-01-01

Full Text Available Mitochondria function as metabolic powerhouses by generating energy through oxidative phosphorylation and have become the focus of renewed interest due to progress in understanding the subtleties of their biogenesis and the discovery of the important roles which these organelles play in senescence, cell death and the assembly of iron-sulfur (Fe/S centers. Using proteins from the yeast Saccharomyces cerevisiae, Homo sapiens and Arabidopsis thaliana we searched the sugarcane expressed sequence tag (SUCEST database for the presence of expressed sequence tags (ESTs with similarity to nuclear genes related to mitochondrial functions. Starting with 869 protein sequences, we searched for sugarcane EST counterparts to these proteins using the basic local alignment search tool TBLASTN similarity searching program run against 260,781 sugarcane ESTs contained in 81,223 clusters. We were able to recover 367 clusters likely to represent sugarcane orthologues of the corresponding genes from S. cerevisiae, H. sapiens and A. thaliana with E-value <= 10-10. Gene products belonging to all functional categories related to mitochondrial functions were found and this allowed us to produce an overview of the nuclear genes required for sugarcane mitochondrial biogenesis and function as well as providing a starting point for detailed analysis of sugarcane gene structure and physiology.

Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns

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Wan Hongjian

2012-09-01

Full Text Available Abstract Background Pepper (Capsicum annuum L. is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site (NBS-leucine-rich repeat (LRR gene family is the largest class of known disease resistance genes (R genes effective against such pathogens. Therefore, the isolation and identification of such R gene homologues from pepper will provide a critical foundation for improving disease resistance breeding programs. Results A total of 78 R gene analogues (CaRGAs were identified in pepper by degenerate PCR amplification and database mining. Phylogenetic tree analysis of the deduced amino acid sequences for 51 of these CaRGAs with typically conserved motifs ( P-loop, kinase-2 and GLPL along with some known R genes from Arabidopsis and tomato grouped these CaRGAs into the non-Toll interleukin-1 receptor (TIR-NBS-LRR (CaRGAs I to IV and TIR-NBS-LRR (CaRGAs V to VII subfamilies. The presence of consensus motifs (i.e. P-loop, kinase-2 and hydrophobic domain is typical of the non-TIR- and TIR-NBS-LRR gene subfamilies. This finding further supports the view that both subfamilies are widely distributed in dicot species. Functional divergence analysis provided strong statistical evidence of altered selective constraints during protein evolution between the two subfamilies. Thirteen critical amino acid sites involved in this divergence were also identified using DIVERGE version 2 software. Analyses of non-synonymous and synonymous substitutions per site showed that purifying selection can play a critical role in the evolutionary processes of non-TIR- and TIR-NBS-LRR RGAs in pepper. In addition, four specificity-determining positions were predicted to be responsible for functional specificity. qRT-PCR analysis showed that both salicylic and abscisic acids induce the expression of CaRGA genes, suggesting that they may primarily be involved in

Loop Replacement Enhances the Ancestral Antibacterial Function of a Bifunctional Scorpion Toxin

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Shangfei Zhang

2018-06-01

Full Text Available On the basis of the evolutionary relationship between scorpion toxins targeting K+ channels (KTxs and antibacterial defensins (Zhu S., Peigneur S., Gao B., Umetsu Y., Ohki S., Tytgat J. Experimental conversion of a defensin into a neurotoxin: Implications for origin of toxic function. Mol. Biol. Evol. 2014, 31, 546–559, we performed protein engineering experiments to modify a bifunctional KTx (i.e., weak inhibitory activities on both K+ channels and bacteria via substituting its carboxyl loop with the structurally equivalent loop of contemporary defensins. As expected, the engineered peptide (named MeuTXKα3-KFGGI remarkably improved the antibacterial activity, particularly on some Gram-positive bacteria, including several antibiotic-resistant opportunistic pathogens. Compared with the unmodified toxin, its antibacterial spectrum also enlarged. Our work provides a new method to enhance the antibacterial activity of bifunctional scorpion venom peptides, which might be useful in engineering other proteins with an ancestral activity.

Fermions and loops on graphs: I. Loop calculus for determinants

International Nuclear Information System (INIS)

Chernyak, Vladimir Y; Chertkov, Michael

2008-01-01

This paper is the first in a series devoted to evaluation of the partition function in statistical models on graphs with loops in terms of the Berezin/fermion integrals. The paper focuses on a representation of the determinant of a square matrix in terms of a finite series, where each term corresponds to a loop on the graph. The representation is based on a fermion version of the loop calculus, previously introduced by the authors for graphical models with finite alphabets. Our construction contains two levels. First, we represent the determinant in terms of an integral over anti-commuting Grassmann variables, with some reparametrization/gauge freedom hidden in the formulation. Second, we show that a special choice of the gauge, called the BP (Bethe–Peierls or belief propagation) gauge, yields the desired loop representation. The set of gauge fixing BP conditions is equivalent to the Gaussian BP equations, discussed in the past as efficient (linear scaling) heuristics for estimating the covariance of a sparse positive matrix

Independence of protein kinase C-delta activity from activation loop phosphorylation: structural basis and altered functions in cells.

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Liu, Yin; Belkina, Natalya V; Graham, Caroline; Shaw, Stephen

2006-04-28

Activation loop phosphorylation plays critical regulatory roles for many kinases. Unlike other protein kinase Cs (PKC), PKC-delta does not require phosphorylation of its activation loop (Thr-507) for in vitro activity. We investigated the structural basis for this unusual capacity and its relevance to PKC-delta function in intact cells. Mutational analysis demonstrated that activity without Thr-507 phosphorylation depends on 20 residues N-terminal to the kinase domain and a pair of phenylalanines (Phe-500/Phe-527) unique to PKC-delta in/near the activation loop. Molecular modeling demonstrated that these elements stabilize the activation loop by forming a hydrophobic chain of interactions from the C-lobe to activation loop to N-terminal (helical) extension. In cells PKC-delta mediates both apoptosis and transcription regulation. We found that the T507A mutant of the PKC-delta kinase domain resembled the corresponding wild type in mediating apoptosis in transfected HEK293T cells. But the T507A mutant was completely defective in AP-1 and NF-kappaB reporter assays. A novel assay in which the kinase domain of PKC-delta and its substrate (a fusion protein of PKC substrate peptide with green fluorescent protein) were co-targeted to lipid rafts revealed a major substrate-selective defect of the T507A mutant in phosphorylating the substrate in cells. In vitro analysis showed strong product inhibition on the T507A mutant with particular substrates whose characteristics suggest it contributes to the substrate selective defect of the PKC-delta T507A mutant in cells. Thus, activation loop phosphorylation of PKC-delta may regulate its function in cells in a novel way.

Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

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Di, Chao; Xu, Wenying; Su, Zhen; Yuan, Joshua S

2010-10-07

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out

A True Open-Loop Synchronization Technique

DEFF Research Database (Denmark)

Golestan, Saeed; Vidal, Ana; Yepes, Alejandro G.

2016-01-01

Synchronization techniques can be broadly classified into two major categories: Closed-loop and open-loop methods. The open-loop synchronization (OLS) techniques, contrary to the closed-loop ones, are unconditionally stable and benefit from a fast dynamic response. Their performance, however, tends...... is to develop a true OLS (and therefore, unconditionally stable) technique without any need for the calculation of sine and cosine functions. The effectiveness of the proposed synchronization technique is confirmed through the simulation and experimental results....

The Adler D-function for N = 1 SQCD regularized by higher covariant derivatives in the three-loop approximation

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Kataev, A. L.; Kazantsev, A. E.; Stepanyantz, K. V.

2018-01-01

We calculate the Adler D-function for N = 1 SQCD in the three-loop approximation using the higher covariant derivative regularization and the NSVZ-like subtraction scheme. The recently formulated all-order relation between the Adler function and the anomalous dimension of the matter superfields defined in terms of the bare coupling constant is first considered and generalized to the case of an arbitrary representation for the chiral matter superfields. The correctness of this all-order relation is explicitly verified at the three-loop level. The special renormalization scheme in which this all-order relation remains valid for the D-function and the anomalous dimension defined in terms of the renormalized coupling constant is constructed in the case of using the higher derivative regularization. The analytic expression for the Adler function for N = 1 SQCD is found in this scheme to the order O (αs2). The problem of scheme-dependence of the D-function and the NSVZ-like equation is briefly discussed.

The Adler D-function for N=1 SQCD regularized by higher covariant derivatives in the three-loop approximation

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A.L. Kataev

2018-01-01

Full Text Available We calculate the Adler D-function for N=1 SQCD in the three-loop approximation using the higher covariant derivative regularization and the NSVZ-like subtraction scheme. The recently formulated all-order relation between the Adler function and the anomalous dimension of the matter superfields defined in terms of the bare coupling constant is first considered and generalized to the case of an arbitrary representation for the chiral matter superfields. The correctness of this all-order relation is explicitly verified at the three-loop level. The special renormalization scheme in which this all-order relation remains valid for the D-function and the anomalous dimension defined in terms of the renormalized coupling constant is constructed in the case of using the higher derivative regularization. The analytic expression for the Adler function for N=1 SQCD is found in this scheme to the order O(αs2. The problem of scheme-dependence of the D-function and the NSVZ-like equation is briefly discussed.

Zero value for the three-loop β function in N=4 supersymmetric Yang-Mills theory

International Nuclear Information System (INIS)

Grisaru, M.; Rocek, M.; Siegel, W.

1980-01-01

This Letter describes a calculation using superfield techniques, showing that the β function is zero to three loops in N=4 supersymmetric Yang-Mills theory. This result gives further indication that the theory is likely to be finite and conformally invariant order by order in perturbation theory

Combining many interaction networks to predict gene function and analyze gene lists.

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Mostafavi, Sara; Morris, Quaid

2012-05-01

In this article, we review how interaction networks can be used alone or in combination in an automated fashion to provide insight into gene and protein function. We describe the concept of a "gene-recommender system" that can be applied to any large collection of interaction networks to make predictions about gene or protein function based on a query list of proteins that share a function of interest. We discuss these systems in general and focus on one specific system, GeneMANIA, that has unique features and uses different algorithms from the majority of other systems. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA.

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Saraiya, Ashesh A; Lamichhane, Tek N; Chow, Christine S; SantaLucia, John; Cunningham, Philip R

2008-02-22

The 970 loop (helix 31) of Escherichia coli 16S ribosomal RNA contains two modified nucleotides, m(2)G966 and m(5)C967. Positions A964, A969, and C970 are conserved among the Bacteria, Archaea, and Eukarya. The nucleotides present at positions 965, 966, 967, 968, and 971, however, are only conserved and unique within each domain. All organisms contain a modified nucleoside at position 966, but the type of the modification is domain specific. Biochemical and structure studies have placed this loop near the P site and have shown it to be involved in the decoding process and in binding the antibiotic tetracycline. To identify the functional components of this ribosomal RNA hairpin, the eight nucleotides of the 970 loop of helix 31 were subjected to saturation mutagenesis and 107 unique functional mutants were isolated and analyzed. Nonrandom nucleotide distributions were observed at each mutated position among the functional isolates. Nucleotide identity at positions 966 and 969 significantly affects ribosome function. Ribosomes with single mutations of m(2)G966 or m(5)C967 produce more protein in vivo than do wild-type ribosomes. Overexpression of initiation factor 3 specifically restored wild-type levels of protein synthesis to the 966 and 967 mutants, suggesting that modification of these residues is important for initiation factor 3 binding and for the proper initiation of protein synthesis.

Five-loop Konishi in N=4 SYM

International Nuclear Information System (INIS)

Eden, Burkhard; Heslop, Paul; Korchemsky, Gregory P.; Smirnov, Vladimir A.; Sokatchev, Emery

2012-01-01

We present a new method for computing the Konishi anomalous dimension in N=4 SYM at weak coupling. It does not rely on the conventional Feynman diagram technique and is not restricted to the planar limit. It is based on the OPE analysis of the four-point correlation function of stress-tensor multiplets, which has been recently constructed up to six loops. The Konishi operator gives the leading contribution to the singlet SU(4) channel of this OPE. Its anomalous dimension is the coefficient of the leading single logarithmic singularity of the logarithm of the correlation function in the double short-distance limit, in which the operator positions coincide pairwise. We regularize the logarithm of the correlation function in this singular limit by a version of dimensional regularization. At any loop level, the resulting singularity is a simple pole whose residue is determined by a finite two-point integral with one loop less. This drastically simplifies the five-loop calculation of the Konishi anomalous dimension by reducing it to a set of known four-loop two-point integrals and two unknown integrals which we evaluate analytically. We obtain an analytic result at five loops in the planar limit and observe perfect agreement with the prediction based on integrability in AdS/CFT.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

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Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

2011-06-20

One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

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Martin Juliette

2011-06-01

Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

Coupling between feedback loops in autoregulatory networks affects bistability range, open-loop gain and switching times

International Nuclear Information System (INIS)

Tiwari, Abhinav; Igoshin, Oleg A

2012-01-01

Biochemical regulatory networks governing diverse cellular processes such as stress-response, differentiation and cell cycle often contain coupled feedback loops. We aim at understanding how features of feedback architecture, such as the number of loops, the sign of the loops and the type of their coupling, affect network dynamical performance. Specifically, we investigate how bistability range, maximum open-loop gain and switching times of a network with transcriptional positive feedback are affected by additive or multiplicative coupling with another positive- or negative-feedback loop. We show that a network's bistability range is positively correlated with its maximum open-loop gain and that both quantities depend on the sign of the feedback loops and the type of feedback coupling. Moreover, we find that the addition of positive feedback could decrease the bistability range if we control the basal level in the signal-response curves of the two systems. Furthermore, the addition of negative feedback has the capacity to increase the bistability range if its dissociation constant is much lower than that of the positive feedback. We also find that the addition of a positive feedback to a bistable network increases the robustness of its bistability range, whereas the addition of a negative feedback decreases it. Finally, we show that the switching time for a transition from a high to a low steady state increases with the effective fold change in gene regulation. In summary, we show that the effect of coupled feedback loops on the bistability range and switching times depends on the underlying mechanistic details. (paper)

Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

Science.gov (United States)

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Closed-loop control of spinal cord stimulation to restore hand function after paralysis

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Jonas B Zimmermann

2014-05-01

Full Text Available As yet, no cure exists for upper-limb paralysis resulting from the damage to motor pathways after spinal cord injury or stroke. Recently, neural activity from the motor cortex of paralyzed individuals has been used to control the movements of a robot arm but restoring function to patients’ actual limbs remains a considerable challenge. Previously we have shown that electrical stimulation of the cervical spinal cord in anesthetized monkeys can elicit functional upper-limb movements like reaching and grasping. Here we show that stimulation can be controlled using cortical activity in awake animals to bypass disruption of the corticospinal system, restoring their ability to perform a simple upper-limb task. Monkeys were trained to grasp and pull a spring-loaded handle. After temporary paralysis of the hand was induced by reversible inactivation of primary motor cortex using muscimol, grasp-related single-unit activity from the ventral premotor cortex was converted into stimulation patterns delivered in real-time to the cervical spinal grey matter. During periods of closed-loop stimulation, task-modulated electromyogram, movement amplitude and task success rate were improved relative to interleaved control periods without stimulation. In some sessions, single motor unit activity from weakly active muscles was also used successfully to control stimulation. These results are the first use of a neural prosthesis to improve the hand function of primates after motor cortex disruption, and demonstrate the potential for closed-loop cortical control of spinal cord stimulation to reanimate paralyzed limbs.

Assessing gene function in the ruminant placenta.

Science.gov (United States)

Anthony, R V; Cantlon, J D; Gates, K C; Purcell, S H; Clay, C M

2010-01-01

The placenta provides the means for nutrient transfer from the mother to the fetus, waste transfer from the fetus to the mother, protection of the fetus from the maternal immune system, and is an active endocrine organ. While many placental functions have been defined and investigated, assessing the function of specific genes expressed by the placenta has been problematic, since classical ablation-replacement methods are not feasible with the placenta. The pregnant sheep has been a long-standing animal model for assessing in vivo physiology during pregnancy, since surgical placement of indwelling catheters into both maternal and fetal vasculature has allowed the assessment of placental nutrient transfer and utilization, as well as placental hormone secretion, under unanesthetized-unstressed steady state sampling conditions. However, in ruminants the lack of well-characterized trophoblast cell lines and the inefficiency of creating transgenic pregnancies in ruminants have inhibited our ability to assess specific gene function. Recently, sheep and cattle primary trophoblast cell lines have been reported, and may further our ability to investigate trophoblast function and transcriptional regulation of genes expressed by the placenta. Furthermore, viral infection of the trophoectoderm layer of hatched blastocysts, as a means for placenta-specific transgenesis, holds considerable potential to assess gene function in the ruminant placenta. This approach has been used successfully to "knockdown" gene expression in the developing sheep conceptus, and has the potential for gain-of-function experiments as well. While this technology is still being developed, it may provide an efficient approach to assess specific gene function in the ruminant placenta.

Quantum chromodynamics as dynamics of loops

International Nuclear Information System (INIS)

Makeenko, Yu.; Migdal, A.A.

1980-01-01

The problem of a possibility of reformulating quantum chromodynamics (QCD) in terms of colourless composite fields instead of coloured quarks and gluons is considered. The role of such fields is played by the gauge invariant loop functionals. The Shwinger equations of motion is derived in the loop space which completely describe dynamics of the loop fields. New manifestly gauge invariant diagram technique in the loop space is developed. These diagrams reproduce asymptotic freedom in the ultraviolet range and are consistent with the confinement law in the infrared range

Multi-loop PWR modeling and hardware-in-the-loop testing using ACSL

International Nuclear Information System (INIS)

Thomas, V.M.; Heibel, M.D.; Catullo, W.J.

1989-01-01

Westinghouse has developed an Advanced Digital Feedwater Control System (ADFCS) which is aimed at reducing feedwater related reactor trips through improved control performance for pressurized water reactor (PWR) power plants. To support control system setpoint studies and functional design efforts for the ADFCS, an ACSL based model of the nuclear steam supply system (NSSS) of a Westinghouse (PWR) was generated. Use of this plant model has been extended from system design to system testing through integration of the model into a Hardware-in-Loop test environment for the ADFCS. This integration includes appropriate interfacing between a Gould SEL 32/87 computer, upon which the plant model executes in real time, and the Westinghouse Distributed Processing family (WDPF) test hardware. A development program has been undertaken to expand the existing ACSL model to include capability to explicitly model multiple plant loops, steam generators, and corresponding feedwater systems. Furthermore, the program expands the ADFCS Hardware-in-Loop testing to include the multi-loop plant model. This paper provides an overview of the testing approach utilized for the ADFCS with focus on the role of Hardware-in-Loop testing. Background on the plant model, methodology and test environment is also provided. Finally, an overview is presented of the program to expand the model and associated Hardware-in-Loop test environment to handle multiple loops

Morphological and functional changes after benzalkonium chloride treatment of the small intestinal Thiry-Vella loop in rats.

Science.gov (United States)

Móricz, K; Gyetvai, B; Bárdos, G

1998-08-01

The aim of this work was to study the effects of benzalkonium chloride (BAC) treatment on the small intestine and its functioning in rats surgically prepared with Thiry-Vella intestinal loop. The loops were treated with either BAC, which ablated much of the myenteric plexus and extrinsic innervation, or with physiological saline (SAL). In vivo drinking experiments were performed to examine the effect on fluid intake and behavioral indices of distending the loop with a balloon. Spontaneous motility and its changes induced by acetylcholine (ACh) and histamine (His) were studied on isolated stripes in vitro. Finally, samples from the loops were examined histologically. Though reduction of the cell number was less than expected and no differences of the thickness of the muscular layer between the two groups was observed, BAC treatment altered the pattern of spontaneous activity and also the sensitivity to ACh and His in isolated stripes. In vivo distension of the SAL-treated loops reduced fluid intake and produced signs of aversivity; these effects were absent in the BAC-treated group. Our results show that despite the differences in the degree of ablation from those obtained by others, BAC treatment can be used to study the mechanisms underlying the effects of the enteral stimuli on the behavior.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

Directory of Open Access Journals (Sweden)

Marion Ouedraogo

Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

New Genes and Functional Innovation in Mammals.

Science.gov (United States)

Luis Villanueva-Cañas, José; Ruiz-Orera, Jorge; Agea, M Isabel; Gallo, Maria; Andreu, David; Albà, M Mar

2017-07-01

The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions, we have obtained a large collection of mammalian-specific gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mammalian species, obtaining ∼6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from noncoding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Wilson loop and some applications

International Nuclear Information System (INIS)

Bezerra, V.B.

1983-01-01

A simple relation between the classical Wilson loop and the angular deviation in the parallel shift is found. An example of potential which given field copies and which give the same classical Wilson loop for a given trajectory is exchibited. Afterwards, the asymptotic behaviour of the Wilson loop for the BPST instanton and meron is discussed. Using the dimensional regularization technique to calculate the second order term of Quantum Wilson loop, the influence of geometrical factors for the residue in the polo due to contact points, cusp and intersections, in function of the upsilon dimension of the space-time is investigated. Finally, the charge renormalization in Quantum Electrodynamics using Quantum Wilson loop is calculated. (L.C.) [pt

The Wilson loop and some applications

International Nuclear Information System (INIS)

Bezerra, V.B.

1983-04-01

A simple relation between the classical Wilson loop and the angular deviation in the parallel displacement is found. An example of potentials which give field copies and which suplly the same classical Wilson loop for a particular trajectory is exhibited. The asymptotic behaviour of the Wilson loop for the BPST instanton and the meron, is discussed. By using the dimensional regularization technique to calculate the second order term of the quantum Wilson loop, the influence of geometrical factors for the residue in the pole due to contact points, cuspides and intersections, in function of the space-time ν, is investigated. Charge renormalization in Quantum electrodynamics is finally calculated by using the quantum Wilson loop. (L.C.) [pt

CTCF Mediates the Cell-Type Specific Spatial Organization of the Kcnq5 Locus and the Local Gene Regulation

OpenAIRE

Ren, Licheng; Wang, Yang; Shi, Minglei; Wang, Xiaoning; Yang, Zhong; Zhao, Zhihu

2012-01-01

Chromatin loops play important roles in the dynamic spatial organization of genes in the nucleus. Growing evidence has revealed that the multivalent functional zinc finger protein CCCTC-binding factor (CTCF) is a master regulator of genome spatial organization, and mediates the ubiquitous chromatin loops within the genome. Using circular chromosome conformation capture (4C) methodology, we discovered that CTCF may be a master organizer in mediating the spatial organization of the kcnq5 gene l...

Investigating Gene Function in Cereal Rust Fungi by Plant-Mediated Virus-Induced Gene Silencing.

Science.gov (United States)

Panwar, Vinay; Bakkeren, Guus

2017-01-01

Cereal rust fungi are destructive pathogens, threatening grain production worldwide. Targeted breeding for resistance utilizing host resistance genes has been effective. However, breakdown of resistance occurs frequently and continued efforts are needed to understand how these fungi overcome resistance and to expand the range of available resistance genes. Whole genome sequencing, transcriptomic and proteomic studies followed by genome-wide computational and comparative analyses have identified large repertoire of genes in rust fungi among which are candidates predicted to code for pathogenicity and virulence factors. Some of these genes represent defence triggering avirulence effectors. However, functions of most genes still needs to be assessed to understand the biology of these obligate biotrophic pathogens. Since genetic manipulations such as gene deletion and genetic transformation are not yet feasible in rust fungi, performing functional gene studies is challenging. Recently, Host-induced gene silencing (HIGS) has emerged as a useful tool to characterize gene function in rust fungi while infecting and growing in host plants. We utilized Barley stripe mosaic virus-mediated virus induced gene silencing (BSMV-VIGS) to induce HIGS of candidate rust fungal genes in the wheat host to determine their role in plant-fungal interactions. Here, we describe the methods for using BSMV-VIGS in wheat for functional genomics study in cereal rust fungi.

Variational solution of the loop equation in QCD

International Nuclear Information System (INIS)

Agishtein, M.E.; Migdal, A.A.

1988-01-01

A new technique for the large N loop equation of QCD is worked out. The Wilson loop W(C) is approximated by a Gaussian functional. The parameters are fitted to the loop equation, after which the equation is statisfied up to 0.2%. The resulting Wilson loop corresponds to linearly rising Regge trajectories. The problem of tachyon is still present, but it could be cured by iteration of the loop equation starting from this variational solution. (orig.)

Variational solution of the loop equation in QCD

International Nuclear Information System (INIS)

Agishtein, M.E.; Migdal, A.A.

1988-01-01

A new technique for the large N loop equation of QCD is worked out. The Wilson loop W(C) is approximated by a Gaussian functional. The parameters are fitted to the loop equation, after which the equation is satisfied up to 0.2%. The resulting Wilson loop corresponds to linearly rising Regge trajectories. The problem of tachyon is still present, but it could be cured by iteration of the loop equation starting from this variational solution

Comments on the integrability of the loop-space chiral equations

International Nuclear Information System (INIS)

Gu, C.; Wang, L.L.C.

1980-01-01

A demonstration is given how the ordinary space chiral equations provide the existence conditions for the infinite number of conserved currents and how these currents are related to the so-called inverse-scattering equations, whose integrability is provided by the original chiral equations. Loop-space chiral equations are introduced. The integrability conditions of the non-local currents in two possible different situations are discussed. In the first case, the generating functions are functionals of the loop alone. The integrability conditions are not satisfied and higher order conserved non-local currents do not exist. In the second case, the generating functions are functionals of the loop as well as a parameter the integrability conditions at a restricted point of the parameter are satisfied, however there is an infinite fold of arbitrariness. It indicates that additional guiding principles are needed in addition to the original loop-space chiral equation in order to uniquely determine the infinite conserved non-local currents as functionals of the loop and the parameter

Baseline albumin is associated with worsening renal function in patients with acute decompensated heart failure receiving continuous infusion loop diuretics.

Science.gov (United States)

Clarke, Megan M; Dorsch, Michael P; Kim, Susie; Aaronson, Keith D; Koelling, Todd M; Bleske, Barry E

2013-06-01

To identify baseline predictors of worsening renal function (WRF) in an acute decompensated heart failure (ADHF) patient population receiving continuous infusion loop diuretics. Retrospective observational analysis. Academic tertiary medical center. A total of 177 patients with ADHF receiving continuous infusion loop diuretics from January 2006 through June 2009. The mean patient age was 61 years, 63% were male, ~45% were classified as New York Heart Association functional class III, and the median length of loop diuretic infusion was 4 days. Forty-eight patients (27%) developed WRF, and 34 patients (19%) died during hospitalization. Cox regression time-to-event analysis was used to determine the time to WRF based on different demographic and clinical variables. Baseline serum albumin 3 g/dl or less was the only significant predictor of WRF (hazard ratio [HR] 2.87, 95% confidence interval [CI] 1.60-5.16, p=0.0004), which remained significant despite adjustments for other covariates. Serum albumin 3 g/dl or less is a practical baseline characteristic associated with the development of WRF in patients with ADHF receiving continuous infusion loop diuretics. © 2013 Pharmacotherapy Publications, Inc.

Evolutionary relationship and structural characterization of the EPF/EPFL gene family.

Directory of Open Access Journals (Sweden)

Naoki Takata

Full Text Available EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Studying Functions of All Yeast Genes Simultaneously

Science.gov (United States)

Stolc, Viktor; Eason, Robert G.; Poumand, Nader; Herman, Zelek S.; Davis, Ronald W.; Anthony Kevin; Jejelowo, Olufisayo

2006-01-01

A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain.

Pomeron calculus in zero transverse dimensions: Summation of pomeron loops and generating functional for multiparticle production processes

International Nuclear Information System (INIS)

Levin, E.; Prygarin, A.

2008-01-01

In this paper we address two problems in pomeron calculus in zero transverse dimensions: the summation of the pomeron loops and the calculation of the processes of multiparticle generation. We introduce a new generating functional for these processes and obtain the evolution equation for it. We argue that in the kinematic range given by 1 2 ) S Y S ), we can reduce the pomeron calculus to the exchange of non-interacting pomerons with the renormalized amplitude of their interaction with the target. Therefore, the summation of the pomeron loops can be performed using the Mueller-Patel-Salam-Iancu approximation. (orig.)

The 3-loop pure singlet heavy flavor contributions to the structure function F2(x,Q2 and the anomalous dimension

Directory of Open Access Journals (Sweden)

J. Ablinger

2015-01-01

Full Text Available The pure singlet asymptotic heavy flavor corrections to 3-loop order for the deep-inelastic scattering structure function F2(x,Q2 and the corresponding transition matrix element AQq(3,PS in the variable flavor number scheme are computed. In Mellin-N space these inclusive quantities depend on generalized harmonic sums. We also recalculate the complete 3-loop pure singlet anomalous dimension for the first time. Numerical results for the Wilson coefficients, the operator matrix element and the contribution to the structure function F2(x,Q2 are presented.

The 3-loop pure singlet heavy flavor contributions to the structure function F2(x,Q2) and the anomalous dimension

International Nuclear Information System (INIS)

Ablinger, J.; Behring, A.; Blümlein, J.; De Freitas, A.; Manteuffel, A. von; Schneider, C.

2015-01-01

The pure singlet asymptotic heavy flavor corrections to 3-loop order for the deep-inelastic scattering structure function F 2 (x,Q 2 ) and the corresponding transition matrix element A Qq (3),PS in the variable flavor number scheme are computed. In Mellin-N space these inclusive quantities depend on generalized harmonic sums. We also recalculate the complete 3-loop pure singlet anomalous dimension for the first time. Numerical results for the Wilson coefficients, the operator matrix element and the contribution to the structure function F 2 (x,Q 2 ) are presented

Mitochondrial D-loop sequence of domesticated waterfowl in Central Java: goose and muscovy duck

Science.gov (United States)

Susanti, R.; Iswari, R. S.

2018-03-01

This study aims to determine the genetic characterization of domesticated waterfowl (goose and Muscovy duck) in Central Java based on a D-loop mtDNA gene. The D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method. Multiple alignments of D-loop gene obtained were 710 nucleotides at position 74 to 783 at the 5’ end (for goose) and 712 nucleotides at position 48 to 759 at the 5’ end (for Muscovy duck). The results of the polymorphism analysis on D-loop sequences of muscovy duck produced 3 haplotypes. In the D-loop gene of goose does not show polymorphism, with substitution at G117A. Phylogenetic trees reconstructions of goose and Muscovy duck, which was collected during this research compared with another species from Anser, Chairina and Anas was generated 2 forms of clusters. The first group consists of all kind of Muscovy duck together with Chairina moschata and Anas, while the second group consists of all geese and Anser cygnoides the other. The determination of Muscovy duck and geese identity can be distinguished from the genetic marker information. Based on the phylogenetic analysis, it can be concluded that the Muscovy duck is closely related to Chairina moschata, while geese is closely related to Anser cygnoides.

Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element.

Science.gov (United States)

Lim, Chun Shen; Brown, Chris M

2016-09-01

Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (~600 bases) composite cis-acting 'post-transcriptional regulatory element' (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are 2 conserved RNA cis-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose 2 covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel.

Behavior of a solar collector loop during stagnation

DEFF Research Database (Denmark)

Chen, Ziqian; Dragsted, Janne; Furbo, Simon

2015-01-01

A mathematical model simulating the emptying behavior of a pressurized solar collector loop with solar collectors with a good emptying behavior is developed and validated with measured data. The calculated results are in good agreement with the measured results. The developed simulation model...... is therefore suitable to determine the behavior of a solar collector loop during stagnation. A volume ratio R, which is the ratio of the volume of the vapour in the upper pipes of the solar collector loop during stagnation and the fluid content of solar collectors, is introduced to determine the mass...... of the collector fluid pushed into the expansion vessel during stagnation, Min. A correlation function for the mass Min and the volume ratio R for solar collector loops is obtained. The function can be used to determine a suitable size of expansion vessels for solar collector loops....

A Circadian Clock Gene, Cry, Affects Heart Morphogenesis and Function in Drosophila as Revealed by Optical Coherence Microscopy.

Directory of Open Access Journals (Sweden)

Aneesh Alex

Full Text Available Circadian rhythms are endogenous, entrainable oscillations of physical, mental and behavioural processes in response to local environmental cues such as daylight, which are present in the living beings, including humans. Circadian rhythms have been related to cardiovascular function and pathology. However, the role that circadian clock genes play in heart development and function in a whole animal in vivo are poorly understood. The Drosophila cryptochrome (dCry is a circadian clock gene that encodes a major component of the circadian clock negative feedback loop. Compared to the embryonic stage, the relative expression levels of dCry showed a significant increase (>100-fold in Drosophila during the pupa and adult stages. In this study, we utilized an ultrahigh resolution optical coherence microscopy (OCM system to perform non-invasive and longitudinal analysis of functional and morphological changes in the Drosophila heart throughout its post-embryonic lifecycle for the first time. The Drosophila heart exhibited major morphological and functional alterations during its development. Notably, heart rate (HR and cardiac activity period (CAP of Drosophila showed significant variations during the pupa stage, when heart remodeling took place. From the M-mode (2D + time OCM images, cardiac structural and functional parameters of Drosophila at different developmental stages were quantitatively determined. In order to study the functional role of dCry on Drosophila heart development, we silenced dCry by RNAi in the Drosophila heart and mesoderm, and quantitatively measured heart morphology and function in those flies throughout its development. Silencing of dCry resulted in slower HR, reduced CAP, smaller heart chamber size, pupal lethality and disrupted posterior segmentation that was related to increased expression of a posterior compartment protein, wingless. Collectively, our studies provided novel evidence that the circadian clock gene, dCry, plays

A Circadian Clock Gene, Cry, Affects Heart Morphogenesis and Function in Drosophila as Revealed by Optical Coherence Microscopy

Science.gov (United States)

Zeng, Xianxu; Tate, Rebecca E.; McKee, Mary L.; Capen, Diane E.; Zhang, Zhan; Tanzi, Rudolph E.; Zhou, Chao

2015-01-01

Circadian rhythms are endogenous, entrainable oscillations of physical, mental and behavioural processes in response to local environmental cues such as daylight, which are present in the living beings, including humans. Circadian rhythms have been related to cardiovascular function and pathology. However, the role that circadian clock genes play in heart development and function in a whole animal in vivo are poorly understood. The Drosophila cryptochrome (dCry) is a circadian clock gene that encodes a major component of the circadian clock negative feedback loop. Compared to the embryonic stage, the relative expression levels of dCry showed a significant increase (>100-fold) in Drosophila during the pupa and adult stages. In this study, we utilized an ultrahigh resolution optical coherence microscopy (OCM) system to perform non-invasive and longitudinal analysis of functional and morphological changes in the Drosophila heart throughout its post-embryonic lifecycle for the first time. The Drosophila heart exhibited major morphological and functional alterations during its development. Notably, heart rate (HR) and cardiac activity period (CAP) of Drosophila showed significant variations during the pupa stage, when heart remodeling took place. From the M-mode (2D + time) OCM images, cardiac structural and functional parameters of Drosophila at different developmental stages were quantitatively determined. In order to study the functional role of dCry on Drosophila heart development, we silenced dCry by RNAi in the Drosophila heart and mesoderm, and quantitatively measured heart morphology and function in those flies throughout its development. Silencing of dCry resulted in slower HR, reduced CAP, smaller heart chamber size, pupal lethality and disrupted posterior segmentation that was related to increased expression of a posterior compartment protein, wingless. Collectively, our studies provided novel evidence that the circadian clock gene, dCry, plays an essential

Two- and three-loop amplitudes in covariant loop calculus

International Nuclear Information System (INIS)

Roland, K.

1988-04-01

We study 2- and 3-loop vacuum-amplitudes for the closed bosonic string. We compare two sets of expressions for the corresponding density on moduli space: One, based on the covariant Reggeon loop calculus (where modular invariance is not manifest). The other, based on analytic geometry. We want to prove identity between the two sets of expressions. Quite apart from demonstrating modular invariance of the Reggeon results, this would in itself be a remarkable mathematical feature. Identity is established to 'high' order in some moduli and exactly in others. The expansions reveal an essentially number-theoretical structure. Agreement is found only by exploiting the connection between the 4 Jacobi θ-functions and number theory. (orig.)

Two- and three-loop amplitudes in covariant loop calculus

International Nuclear Information System (INIS)

Roland, K.

1989-01-01

We study two- and three-loop vacuum amplitudes for the closed bosonic string. We compare two sets of expressions for the corresponding density on moduli space. One is based on the covariant reggeon loop calculus (where modular invariance is not manifest). The other is based on analytic geometry. We want to prove identity between the two sets of expressions. Quite apart from demonstrating modular invariance of the reggeon results, this would in itself be a remarkable mathematical feature. Identity is established to ''high'' order in some moduli and exactly in others. The expansions reveal an essentially number-theoretic structure. Agreement is found only by exploiting the connection between the four Jacobi θ-functions and number theory. (orig.)

Loop-quantum-gravity vertex amplitude.

Science.gov (United States)

Engle, Jonathan; Pereira, Roberto; Rovelli, Carlo

2007-10-19

Spin foam models are hoped to provide the dynamics of loop-quantum gravity. However, the most popular of these, the Barrett-Crane model, does not have the good boundary state space and there are indications that it fails to yield good low-energy n-point functions. We present an alternative dynamics that can be derived as a quantization of a Regge discretization of Euclidean general relativity, where second class constraints are imposed weakly. Its state space matches the SO(3) loop gravity one and it yields an SO(4)-covariant vertex amplitude for Euclidean loop gravity.

Protein Loop Structure Prediction Using Conformational Space Annealing.

Science.gov (United States)

Heo, Seungryong; Lee, Juyong; Joo, Keehyoung; Shin, Hang-Cheol; Lee, Jooyoung

2017-05-22

We have developed a protein loop structure prediction method by combining a new energy function, which we call E PLM (energy for protein loop modeling), with the conformational space annealing (CSA) global optimization algorithm. The energy function includes stereochemistry, dynamic fragment assembly, distance-scaled finite ideal gas reference (DFIRE), and generalized orientation- and distance-dependent terms. For the conformational search of loop structures, we used the CSA algorithm, which has been quite successful in dealing with various hard global optimization problems. We assessed the performance of E PLM with two widely used loop-decoy sets, Jacobson and RAPPER, and compared the results against the DFIRE potential. The accuracy of model selection from a pool of loop decoys as well as de novo loop modeling starting from randomly generated structures was examined separately. For the selection of a nativelike structure from a decoy set, E PLM was more accurate than DFIRE in the case of the Jacobson set and had similar accuracy in the case of the RAPPER set. In terms of sampling more nativelike loop structures, E PLM outperformed E DFIRE for both decoy sets. This new approach equipped with E PLM and CSA can serve as the state-of-the-art de novo loop modeling method.

[Fanconi anemia: genes and function(s) revisited].

Science.gov (United States)

Papadopoulo, Dora; Moustacchi, Ethel

2005-01-01

Fanconi anemia (FA), a rare inherited disorder, exhibits a complex phenotype including progressive bone marrow failure, congenital malformations and increased risk of cancers, mainly acute myeloid leukaemia. At the cellular level, FA is characterized by hypersensitivity to DNA cross-linking agents and by high frequencies of induced chromosomal aberrations, a property used for diagnosis. FA results from mutations in one of the eleven FANC (FANCA to FANCJ) genes. Nine of them have been identified. In addition, FANCD1 gene has been shown to be identical to BRCA2, one of the two breast cancer susceptibility genes. Seven of the FANC proteins form a complex, which exists in four different forms depending of its subcellular localisation. Four FANC proteins (D1(BRCA2), D2, I and J) are not associated to the complex. The presence of the nuclear form of the FA core complex is necessary for the mono-ubiquitinylation of FANCD2 protein, a modification required for its re-localization to nuclear foci, likely to be sites of DNA repair. A clue towards understanding the molecular function of the FANC genes comes from the recently identified connection of FANC to the BRCA1, ATM, NBS1 and ATR genes. Two of the FANC proteins (A and D2) directly interact with BRCA1, which in turn interacts with the MRE11/RAD50/NBS1 complex, which is one of the key components in the mechanisms involved in the cellular response to DNA double strand breaks (DSB). Moreover, ATM, a protein kinase that plays a central role in the network of DSB signalling, phosphorylates in vitro and in vivo FANCD2 in response to ionising radiations. Moreover, the NBS1 protein and the monoubiquitinated form of FANCD2 seem to act together in response to DNA crosslinking agents. Taken together with the previously reported impaired DSB and DNA interstrand crosslinks repair in FA cells, the connection of FANC genes to the ATM, ATR, NBS1 and BRCA1 links the FANC genes function to the finely orchestrated network involved in the

The pea branching RMS2 gene encodes the PsAFB4/5 auxin receptor and is involved in an auxin-strigolactone regulation loop.

Science.gov (United States)

Ligerot, Yasmine; de Saint Germain, Alexandre; Waldie, Tanya; Troadec, Christelle; Citerne, Sylvie; Kadakia, Nikita; Pillot, Jean-Paul; Prigge, Michael; Aubert, Grégoire; Bendahmane, Abdelhafid; Leyser, Ottoline; Estelle, Mark; Debellé, Frédéric; Rameau, Catherine

2017-12-01

Strigolactones (SLs) are well known for their role in repressing shoot branching. In pea, increased transcript levels of SL biosynthesis genes are observed in stems of highly branched SL deficient (ramosus1 (rms1) and rms5) and SL response (rms3 and rms4) mutants indicative of negative feedback control. In contrast, the highly branched rms2 mutant has reduced transcript levels of SL biosynthesis genes. Grafting studies and hormone quantification led to a model where RMS2 mediates a shoot-to-root feedback signal that regulates both SL biosynthesis gene transcript levels and xylem sap levels of cytokinin exported from roots. Here we cloned RMS2 using synteny with Medicago truncatula and demonstrated that it encodes a putative auxin receptor of the AFB4/5 clade. Phenotypes similar to rms2 were found in Arabidopsis afb4/5 mutants, including increased shoot branching, low expression of SL biosynthesis genes and high auxin levels in stems. Moreover, afb4/5 and rms2 display a specific resistance to the herbicide picloram. Yeast-two-hybrid experiments supported the hypothesis that the RMS2 protein functions as an auxin receptor. SL root feeding using hydroponics repressed auxin levels in stems and down-regulated transcript levels of auxin biosynthesis genes within one hour. This auxin down-regulation was also observed in plants treated with the polar auxin transport inhibitor NPA. Together these data suggest a homeostatic feedback loop in which auxin up-regulates SL synthesis in an RMS2-dependent manner and SL down-regulates auxin synthesis in an RMS3 and RMS4-dependent manner.

SUSY non-Abelian gauge models: exact beta function from one loop of perturbation theory

International Nuclear Information System (INIS)

Shifman, M.A.; Vajnshtejn, A.I.; Zakharov, V.I.

1985-01-01

The method for calculating the exact β function (to all orders in the coupling constant) proposed earlier in supersymmetric electrodynamics is extended. The starting point is the observation that the low-energy effective action is exhausted by one loop provided that the theory is regularized supersymmetrically both in the ultraviolet and infrared domains in four dimensions. The Pouli-Villars method of the ultraviolet regularization is used. Two methods for the infrared regularization are considered. The first one - quantization in a box with a finite volume L 3 - is universally applicable to anygauge theory. The second method is based on the effective Higgs mechanism for mass generation and requires the presence of certain matter superfields in the lagrangian. Within this method the necessary condition is the existence of flat directions, so called valeys, along which the vacuum energy vanishes. The theory is quantized near epsilon non-vanishing value of the scalar field from the bottom of the valley. After calculating the one-loop effective action one and the same exact expression is obtained for the β function within the both approaches, and it also coincides with our earlier result extracted from instanton calculus. A few remarks on the problem of anomalies in SUSY gauge theories are presented

Wilson loops to 20th order numerical stochastic perturbation theory

Energy Technology Data Exchange (ETDEWEB)

Horsley, R. [Edinburgh Univ. (United Kingdom). School of Physics; Hotzel, G.; Perlt, H.; Schiller, A. [Leipzig Univ. (Germany). Inst. fuer Theoretische Physik; Ilgenfritz, E.M. [Humboldt-Universitaet, Berlin (Germany). Inst. fuer Physik; Joint Institute for Nuclear Research, VBLHEP, Dubna (Russian Federation); Millo, R.; Rakow, P.E.L. [Liverpool Univ. (Germany). Theoretical Physics Div.; Nakamura, Y. [RIKEN Advanced Institute for Computational Science, Kobe, Hyogo (Japan); Schierholz, G. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2012-05-15

We calculate Wilson loops of various sizes up to 20 loops in SU(3) pure lattice gauge theory at different lattice sizes for Wilson gauge action using the technique of numerical stochastic perturbation theory. This allows us to investigate the perturbative series for various Wilson loops at high loop orders. We observe differences in the behavior of those series as function of the loop order. Up to n=20 we do not find evidence for the factorial growth of the expansion coefficients often assumed to characterize an asymptotic series. Based on the actually observed behavior we sum the series in a model parametrized by hypergeometric functions. Alternatively we estimate the total series in boosted perturbation theory using information from the first 14 loops. We introduce generalized ratios of Wilson loops of different sizes. Together with the corresponding Wilson loops from standard Monte Carlo measurements they enable us to assess their non-perturbative parts.

Pemakaian Crown Loop dan Band Loop di Rahang Bawah Anak Usia Enam Tahun (Laporan Kasus

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Rivi Isabela

2015-11-01

Full Text Available The function of space maintainer is to preserve arch length following the premature loss of a primary teeth. Early loss of primary tooth may compromise the eruption of succedaneous teeth if there is a reduction in the arch length. The Band and Crown Loop are used to maintain the loss of primary molar. The report describe a 6 year old girl who has premature loss of second left mandibular primary molar and first right mandibular primary molar treated using crown and band loop space maintainer. The patient still has mastication function from other posterior primary teeth.

R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome.

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Sarkar, Koustav; Han, Seong-Su; Wen, Kuo-Kuang; Ochs, Hans D; Dupré, Loïc; Seidman, Michael M; Vyas, Yatin M

2017-12-15

Wiskott-Aldrich syndrome (WAS), X-linked thrombocytopenia (XLT), and X-linked neutropenia, which are caused by WAS mutations affecting Wiskott-Aldrich syndrome protein (WASp) expression or activity, manifest in immunodeficiency, autoimmunity, genomic instability, and lymphoid and other cancers. WASp supports filamentous actin formation in the cytoplasm and gene transcription in the nucleus. Although the genetic basis for XLT/WAS has been clarified, the relationships between mutant forms of WASp and the diverse features of these disorders remain ill-defined. We sought to define how dysfunctional gene transcription is causally linked to the degree of T H cell deficiency and genomic instability in the XLT/WAS clinical spectrum. In human T H 1- or T H 2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double-strand breaks (DSBs) were monitored in multiple samples from patients with XLT and WAS and in normal T cells depleted of WASp. WASp deficiency provokes increased R-loops and R-loop-mediated DSBs in T H 1 cells relative to T H 2 cells. Mechanistically, chromatin occupancy of serine 2-unphosphorylated RNA polymerase II is increased, and that of topoisomerase 1, an R-loop preventing factor, is decreased at R-loop-enriched regions of IFNG and TBX21 (T H 1 genes) in T H 1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (T H 2 gene). Significantly, increased cellular load of R-loops and DSBs, which are normalized on RNaseH1-mediated suppression of ectopic R-loops, inversely correlates with disease severity scores. Transcriptional R-loop imbalance is a novel molecular defect causative in T H 1 immunodeficiency and genomic instability in patients with WAS. The study proposes that cellular R-loop load could be used as a potential biomarker for monitoring symptom severity and prognostic outcome in the XLT-WAS clinical spectrum

miRNA-mediated functional changes through co-regulating function related genes.

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Jie He

Full Text Available BACKGROUND: MicroRNAs play important roles in various biological processes involving fairly complex mechanism. Analysis of genome-wide miRNA microarray demonstrate that a single miRNA can regulate hundreds of genes, but the regulative extent on most individual genes is surprisingly mild so that it is difficult to understand how a miRNA provokes detectable functional changes with such mild regulation. RESULTS: To explore the internal mechanism of miRNA-mediated regulation, we re-analyzed the data collected from genome-wide miRNA microarray with bioinformatics assay, and found that the transfection of miR-181b and miR-34a in Hela and HCT-116 tumor cells regulated large numbers of genes, among which, the genes related to cell growth and cell death demonstrated high Enrichment scores, suggesting that these miRNAs may be important in cell growth and cell death. MiR-181b induced changes in protein expression of most genes that were seemingly related to enhancing cell growth and decreasing cell death, while miR-34a mediated contrary changes of gene expression. Cell growth assays further confirmed this finding. In further study on miR-20b-mediated osteogenesis in hMSCs, miR-20b was found to enhance osteogenesis by activating BMPs/Runx2 signaling pathway in several stages by co-repressing of PPARγ, Bambi and Crim1. CONCLUSIONS: With its multi-target characteristics, miR-181b, miR-34a and miR-20b provoked detectable functional changes by co-regulating functionally-related gene groups or several genes in the same signaling pathway, and thus mild regulation from individual miRNA targeting genes could have contributed to an additive effect. This might also be one of the modes of miRNA-mediated gene regulation.

fabp4 is central to eight obesity associated genes: a functional gene network-based polymorphic study.

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Bag, Susmita; Ramaiah, Sudha; Anbarasu, Anand

2015-01-07

Network study on genes and proteins offers functional basics of the complexity of gene and protein, and its interacting partners. The gene fatty acid-binding protein 4 (fabp4) is found to be highly expressed in adipose tissue, and is one of the most abundant proteins in mature adipocytes. Our investigations on functional modules of fabp4 provide useful information on the functional genes interacting with fabp4, their biochemical properties and their regulatory functions. The present study shows that there are eight set of candidate genes: acp1, ext2, insr, lipe, ostf1, sncg, usp15, and vim that are strongly and functionally linked up with fabp4. Gene ontological analysis of network modules of fabp4 provides an explicit idea on the functional aspect of fabp4 and its interacting nodes. The hierarchal mapping on gene ontology indicates gene specific processes and functions as well as their compartmentalization in tissues. The fabp4 along with its interacting genes are involved in lipid metabolic activity and are integrated in multi-cellular processes of tissues and organs. They also have important protein/enzyme binding activity. Our study elucidated disease-associated nsSNP prediction for fabp4 and it is interesting to note that there are four rsID׳s (rs1051231, rs3204631, rs140925685 and rs141169989) with disease allelic variation (T104P, T126P, G27D and G90V respectively). On the whole, our gene network analysis presents a clear insight about the interactions and functions associated with fabp4 gene network. Copyright © 2014 Elsevier Ltd. All rights reserved.

Functional characterization of antibodies against Neisseria gonorrhoeae opacity protein loops.

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Jessica G Cole

2009-12-01

Full Text Available The development of a gonorrhea vaccine is challenged by the lack of correlates of protection. The antigenically variable neisserial opacity (Opa proteins are expressed during infection and have a semivariable (SV and highly conserved (4L loop that could be targeted in a vaccine. Here we compared antibodies to linear (Ab(linear and cyclic (Ab(cyclic peptides that correspond to the SV and 4L loops and selected hypervariable (HV(2 loops for surface-binding and protective activity in vitro and in vivo.Ab(SV cyclic bound a greater number of different Opa variants than Ab(SV linear, including variants that differed by seven amino acids. Antibodies to the 4L peptide did not bind Opa-expressing bacteria. Ab(SV (cyclic and Ab(HV2 (cyclic, but not Ab(SV (linear or Ab(HV2 linear agglutinated homologous Opa variants, and Ab(HV2BD (cyclic but not Ab(HV2BD (linear blocked the association of OpaB variants with human endocervical cells. Only Ab(HV2BD (linear were bactericidal against the serum resistant parent strain. Consistent with host restrictions in the complement cascade, the bactericidal activity of Ab(HV2BD (linear was increased 8-fold when rabbit complement was used. None of the antibodies was protective when administered vaginally to mice. Antibody duration in the vagina was short-lived, however, with <50% of the antibodies recovered 3 hrs post-administration.We conclude that an SV loop-specific cyclic peptide can be used to induce antibodies that recognize a broad spectrum of antigenically distinct Opa variants and have agglutination abilities. HV(2 loop-specific cyclic peptides elicited antibodies with agglutination and adherence blocking abilities. The use of human complement when testing the bactericidal activity of vaccine-induced antibodies against serum resistant gonococci is also important.

Elucidating gene function and function evolution through comparison of co-expression networks in plants

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Marek eMutwil

2014-08-01

Full Text Available The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species, Frontiers in Plant Science 2:23. In this paper we applied cross-species analysis to co-expression networks of genes involved in cellulose biosynthesis. We show that the co-expression networks from different species are highly similar, indicating that whole biological pathways are conserved across species. This finding has two important implications. First, the analysis can transfer gene function annotation from well-studied plants, such as Arabidopsis, to other, uncharacterized plant species. As the analysis finds genes that have similar sequence and similar expression pattern across different organisms, functionally equivalent genes can be identified. Second, since co-expression analyses are often noisy, a comparative analysis should have higher performance, as parts of co-expression networks that are conserved are more likely to be functionally relevant. In this Focused Review, we outline the comparative analysis done in the original paper and comment on the recent advances and approaches that allow comparative analyses of co-function networks. We hypothesize that, in comparison to simple co-expression analysis, comparative analysis would yield more accurate gene function predictions. Finally, by combining comparative analysis with genomic information of green plants, we propose a possible composition of cellulose biosynthesis machinery during earlier stages of plant evolution.

Inferring gene expression dynamics via functional regression analysis

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Leng Xiaoyan

2008-01-01

Full Text Available Abstract Background Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene expression associated with different developmental stages to each other to study patterns of long-term developmental gene regulation. We use tools from functional data analysis to study dynamic changes by relating temporal gene expression profiles of different developmental stages to each other. Results We demonstrate that functional regression methodology can pinpoint relationships that exist between temporary gene expression profiles for different life cycle phases and incorporates dimension reduction as needed for these high-dimensional data. By applying these tools, gene expression profiles for pupa and adult phases are found to be strongly related to the profiles of the same genes obtained during the embryo phase. Moreover, one can distinguish between gene groups that exhibit relationships with positive and others with negative associations between later life and embryonal expression profiles. Specifically, we find a positive relationship in expression for muscle development related genes, and a negative relationship for strictly maternal genes for Drosophila, using temporal gene expression profiles. Conclusion Our findings point to specific reactivation patterns of gene expression during the Drosophila life cycle which differ in characteristic ways between various gene groups. Functional regression emerges as a useful tool for relating gene expression patterns from different developmental stages, and avoids the problems with large numbers of parameters and multiple testing that affect alternative approaches.

One loop integration with hypergeometric series by using recursion relations

International Nuclear Information System (INIS)

Watanabe, Norihisa; Kaneko, Toshiaki

2014-01-01

General one-loop integrals with arbitrary mass and kinematical parameters in d-dimensional space-time are studied. By using Bernstein theorem, a recursion relation is obtained which connects (n + 1)-point to n-point functions. In solving this recursion relation, we have shown that one-loop integrals are expressed by a newly defined hypergeometric function, which is a special case of Aomoto-Gelfand hypergeometric functions. We have also obtained coefficients of power series expansion around 4-dimensional space-time for two-, three- and four-point functions. The numerical results are compared with ''LoopTools'' for the case of two- and three-point functions as examples

On the loop-loop scattering amplitudes in Abelian and non-Abelian gauge theories

International Nuclear Information System (INIS)

Meggiolaro, Enrico

2005-01-01

The high-energy elastic scattering amplitude of two colour-singlet qq-bar pairs is governed by the correlation function of two Wilson loops, which follow the classical straight lines for quark (antiquark) trajectories. This quantity is expected to be free of IR divergences, differently from what happens for the parton-parton elastic scattering amplitude, described, in the high-energy limit, by the expectation value of two Wilson lines. We shall explicitly test this IR finiteness by a direct non-perturbative computation of the loop-loop scattering amplitudes in the (pedagogic, but surely physically interesting) case of quenched QED. The results obtained for the Abelian case will be generalized to the case of a non-Abelian gauge theory with Nc colours, but stopping to the order O(g4) in perturbation theory. In connection with the above-mentioned IR finiteness, we shall also discuss some analytic properties of the loop-loop scattering amplitudes in both Abelian and non-Abelian gauge theories, when going from Minkowskian to Euclidean theory, which can be relevant to the still unsolved problem of the s-dependence of hadron-hadron total cross-sections

A Platform for Closing the Open Data Feedback Loop Based on Web2.0 Functionality

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Charalampos Alexopoulos

2014-11-01

Full Text Available One essential element of open data ecosystems concerns their development through feedback loops, discussions and dynamic supplier and user interactions. These user-centric features communicate the users’ needs to the open data community as well to the public sector bodies responsible for data publication. Addressing these needs by the corresponding public sector bodies or even by utilising the power of the community as ENGAGE supports will actually accelerate innovation. However, these elements appear barely to be part of existing open data practices. We conducted a survey which showed that most professional open data users did not know at least one open data infrastructure that enabled five specific types of discussion and feedback mechanisms. The survey showed that much can still be done to improve feedback and discussion on open data infrastructures. In this paper we discuss an open data platform which has started to contribute to filling this gap and present a usage scenario explaining the sequence of the underlined functionality. The discussed ENGAGE open data infrastructure combines functionalities to close the feedback loop and to return information to public authorities for better open data use and publication as well as establishing communication channels between stakeholders. This may effectively lead to the stimulation and facilitation of value generation from open data, as such functionality position the user at the centre of the open data publication process.

Dispersion relations in loop calculations

International Nuclear Information System (INIS)

Kniehl, B.A.

1996-01-01

These lecture notes give a pedagogical introduction to the use of dispersion relations in loop calculations. We first derive dispersion relations which allow us to recover the real part of a physical amplitude from the knowledge of its absorptive part along the branch cut. In perturbative calculations, the latter may be constructed by means of Cutkosky's rule, which is briefly discussed. For illustration, we apply this procedure at one loop to the photon vacuum-polarization function induced by leptons as well as to the γf anti-f vertex form factor generated by the exchange of a massive vector boson between the two fermion legs. We also show how the hadronic contribution to the photon vacuum polarization may be extracted from the total cross section of hadron production in e + e - annihilation measured as a function of energy. Finally, we outline the application of dispersive techniques at the two-loop level, considering as an example the bosonic decay width of a high-mass Higgs boson. (author)

Non-functional genes repaired at the RNA level.

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Burger, Gertraud

2016-01-01

Genomes and genes continuously evolve. Gene sequences undergo substitutions, deletions or nucleotide insertions; mobile genetic elements invade genomes and interleave in genes; chromosomes break, even within genes, and pieces reseal in reshuffled order. To maintain functional gene products and assure an organism's survival, two principal strategies are used - either repair of the gene itself or of its product. I will introduce common types of gene aberrations and how gene function is restored secondarily, and then focus on systematically fragmented genes found in a poorly studied protist group, the diplonemids. Expression of their broken genes involves restitching of pieces at the RNA-level, and substantial RNA editing, to compensate for point mutations. I will conclude with thoughts on how such a grotesquely unorthodox system may have evolved, and why this group of organisms persists and thrives since tens of millions of years. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

A Culture-Behavior-Brain Loop Model of Human Development.

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Han, Shihui; Ma, Yina

2015-11-01

Increasing evidence suggests that cultural influences on brain activity are associated with multiple cognitive and affective processes. These findings prompt an integrative framework to account for dynamic interactions between culture, behavior, and the brain. We put forward a culture-behavior-brain (CBB) loop model of human development that proposes that culture shapes the brain by contextualizing behavior, and the brain fits and modifies culture via behavioral influences. Genes provide a fundamental basis for, and interact with, the CBB loop at both individual and population levels. The CBB loop model advances our understanding of the dynamic relationships between culture, behavior, and the brain, which are crucial for human phylogeny and ontogeny. Future brain changes due to cultural influences are discussed based on the CBB loop model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conformational sampling in template-free protein loop structure modeling: an overview.

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Li, Yaohang

2013-01-01

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

CONFORMATIONAL SAMPLING IN TEMPLATE-FREE PROTEIN LOOP STRUCTURE MODELING: AN OVERVIEW

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Yaohang Li

2013-02-01

Full Text Available Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized.

Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis.

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Liu, Ake; Wang, Yong; Zhang, Debao; Wang, Xuhua; Song, Huifang; Dang, Chunwang; Yao, Qin; Chen, Keping

2013-08-01

Helix-loop-helix (bHLH) proteins play essential regulatory roles in a variety of biological processes. These highly conserved proteins form a large transcription factor superfamily, and are commonly identified in large numbers within animal, plant, and fungal genomes. The bHLH domain has been well studied in many animal species, but has not yet been characterized in non-avian reptiles. In this study, we identified 102 putative bHLH genes in the genome of the green anole lizard, Anolis carolinensis. Based on phylogenetic analysis, these genes were classified into 43 families, with 43, 24, 16, 3, 10, and 3 members assigned into groups A, B, C, D, E, and F, respectively, and 3 members categorized as "orphans". Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with highly conserved patterns observed for introns and additional domains. Results from phylogenetic analysis of the H/E(spl) family suggest that genome and tandem gene duplications have contributed to this family's expansion. Our classification and evolutionary analysis has provided insights into the evolutionary diversification of animal bHLH genes, and should aid future studies on bHLH protein regulation of key growth and developmental processes.

A genome-wide gene function prediction resource for Drosophila melanogaster.

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Han Yan

2010-08-01

Full Text Available Predicting gene functions by integrating large-scale biological data remains a challenge for systems biology. Here we present a resource for Drosophila melanogaster gene function predictions. We trained function-specific classifiers to optimize the influence of different biological datasets for each functional category. Our model predicted GO terms and KEGG pathway memberships for Drosophila melanogaster genes with high accuracy, as affirmed by cross-validation, supporting literature evidence, and large-scale RNAi screens. The resulting resource of prioritized associations between Drosophila genes and their potential functions offers a guide for experimental investigations.

Constructing QCD one-loop amplitudes

International Nuclear Information System (INIS)

Forde, D

2008-01-01

In the context of constructing one-loop amplitudes using a unitarity bootstrap approach we discuss a general systematic procedure for obtaining the coefficients of the scalar bubble and triangle integral functions of one-loop amplitudes. Coefficients are extracted after examining the behavior of the cut integrand as the unconstrained parameters of a specifically chosen parameterization of the cut loop momentum approach infinity. Measurements of new physics at the forthcoming experimental program at CERN's Large Hadron Collider (LHC) will require a precise understanding of processes at next-to-leading order (NLO). This places increased demands for the computation of new one-loop amplitudes. This in turn has spurred recent developments towards improved calculational techniques. Direct calculations using Feynman diagrams are in general inefficient. Developments of more efficient techniques have usually centered around unitarity techniques [1], where tree amplitudes are effectively 'glued' together to form loops. The most straightforward application of this method, in which the cut loop momentum is in D = 4, allows for the computation of 'cut-constructible' terms only, i.e. (poly)logarithmic containing terms and any related constants. QCD amplitudes contain, in addition to such terms, rational pieces which cannot be derived using such cuts. These 'missing' rational parts can be extracted using cut loop momenta in D = 4-2 (var e psilon). The greater difficulty of such calculations has restricted the application of this approach, although recent developments [3, 4] have provided new promise for this technique. Recently the application of on-shell recursion relations [5] to obtaining the 'missing' rational parts of one-loop processes [6] has provided an alternative very promising solution to this problem. In combination with unitarity methods an 'on-shell bootstrap' approach provides an efficient technique for computing complete one-loop QCD amplitudes [7]. Additionally

Construction of functional linkage gene networks by data integration.

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Linghu, Bolan; Franzosa, Eric A; Xia, Yu

2013-01-01

Networks of functional associations between genes have recently been successfully used for gene function and disease-related research. A typical approach for constructing such functional linkage gene networks (FLNs) is based on the integration of diverse high-throughput functional genomics datasets. Data integration is a nontrivial task due to the heterogeneous nature of the different data sources and their variable accuracy and completeness. The presence of correlations between data sources also adds another layer of complexity to the integration process. In this chapter we discuss an approach for constructing a human FLN from data integration and a subsequent application of the FLN to novel disease gene discovery. Similar approaches can be applied to nonhuman species and other discovery tasks.

One loop beta functions and fixed points in higher derivative sigma models

International Nuclear Information System (INIS)

Percacci, Roberto; Zanusso, Omar

2010-01-01

We calculate the one loop beta functions of nonlinear sigma models in four dimensions containing general two- and four-derivative terms. In the O(N) model there are four such terms and nontrivial fixed points exist for all N≥4. In the chiral SU(N) models there are in general six couplings, but only five for N=3 and four for N=2; we find fixed points only for N=2, 3. In the approximation considered, the four-derivative couplings are asymptotically free but the coupling in the two-derivative term has a nonzero limit. These results support the hypothesis that certain sigma models may be asymptotically safe.

When natural selection gives gene function the cold shoulder.

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Cutter, Asher D; Jovelin, Richard

2015-11-01

It is tempting to invoke organismal selection as perpetually optimizing the function of any given gene. However, natural selection can drive genic functional change without improvement of biochemical activity, even to the extinction of gene activity. Detrimental mutations can creep in owing to linkage with other selectively favored loci. Selection can promote functional degradation, irrespective of genetic drift, when adaptation occurs by loss of gene function. Even stabilizing selection on a trait can lead to divergence of the underlying molecular constituents. Selfish genetic elements can also proliferate independent of any functional benefits to the host genome. Here we review the logic and evidence for these diverse processes acting in genome evolution. This collection of distinct evolutionary phenomena - while operating through easily understandable mechanisms - all contribute to the seemingly counterintuitive notion that maintenance or improvement of a gene's biochemical function sometimes do not determine its evolutionary fate. © 2015 WILEY Periodicals, Inc.

Gauge theory loop operators and Liouville theory

International Nuclear Information System (INIS)

Drukker, Nadav; Teschner, Joerg

2009-10-01

We propose a correspondence between loop operators in a family of four dimensional N=2 gauge theories on S 4 - including Wilson, 't Hooft and dyonic operators - and Liouville theory loop operators on a Riemann surface. This extends the beautiful relation between the partition function of these N=2 gauge theories and Liouville correlators found by Alday, Gaiotto and Tachikawa. We show that the computation of these Liouville correlators with the insertion of a Liouville loop operator reproduces Pestun's formula capturing the expectation value of a Wilson loop operator in the corresponding gauge theory. We prove that our definition of Liouville loop operators is invariant under modular transformations, which given our correspondence, implies the conjectured action of S-duality on the gauge theory loop operators. Our computations in Liouville theory make an explicit prediction for the exact expectation value of 't Hooft and dyonic loop operators in these N=2 gauge theories. The Liouville loop operators are also found to admit a simple geometric interpretation within quantum Teichmueller theory as the quantum operators representing the length of geodesics. We study the algebra of Liouville loop operators and show that it gives evidence for our proposal as well as providing definite predictions for the operator product expansion of loop operators in gauge theory. (orig.)

One-loop calculations with massive particles

International Nuclear Information System (INIS)

Oldenborgh, G.J. van.

1990-01-01

In this thesis some techniques for performing one-loop calculations with massive particles are presented. Numerical techniques are presented necessary for evaluating one-loop integrals which occur in one-loop calculations of photon-photon scattering. The algorithms have been coded in FORTRAN (to evaluate the scalar integrals) and the algebraic language FORM (to reduce the tensor integrals to scalar integrals). Applications are made in the theory of the strong interaction, QCD, i.e. in handling one-loop integrals with massive particles, in order to regulate the infinities by mass parameters encountered in this theory. However this simplifies the computation considerably, the description of the proton structure functions have to be renormalized in order to obtain physical results. This renormalization is different from the published results for the gluon and thus has to be redone. The first physics results that have been obtained with these new methods are presented. These concern heavy quark production in semi-leptonic interactions, for instance neutrino charm production and top production at the electron-proton (ep) collider HERA and the proposed LEP/LHC combination. Total and differential cross-sections for one-loop corrections to top production at the HERA and proposed LEP/HLC ep colliders are given and structure functions for charmed quark production are compared with previously published results. (author). 58 refs.; 18 figs.; 5 tabs

Reveal genes functionally associated with ACADS by a network study.

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Chen, Yulong; Su, Zhiguang

2015-09-15

Establishing a systematic network is aimed at finding essential human gene-gene/gene-disease pathway by means of network inter-connecting patterns and functional annotation analysis. In the present study, we have analyzed functional gene interactions of short-chain acyl-coenzyme A dehydrogenase gene (ACADS). ACADS plays a vital role in free fatty acid β-oxidation and regulates energy homeostasis. Modules of highly inter-connected genes in disease-specific ACADS network are derived by integrating gene function and protein interaction data. Among the 8 genes in ACADS web retrieved from both STRING and GeneMANIA, ACADS is effectively conjoined with 4 genes including HAHDA, HADHB, ECHS1 and ACAT1. The functional analysis is done via ontological briefing and candidate disease identification. We observed that the highly efficient-interlinked genes connected with ACADS are HAHDA, HADHB, ECHS1 and ACAT1. Interestingly, the ontological aspect of genes in the ACADS network reveals that ACADS, HAHDA and HADHB play equally vital roles in fatty acid metabolism. The gene ACAT1 together with ACADS indulges in ketone metabolism. Our computational gene web analysis also predicts potential candidate disease recognition, thus indicating the involvement of ACADS, HAHDA, HADHB, ECHS1 and ACAT1 not only with lipid metabolism but also with infant death syndrome, skeletal myopathy, acute hepatic encephalopathy, Reye-like syndrome, episodic ketosis, and metabolic acidosis. The current study presents a comprehensible layout of ACADS network, its functional strategies and candidate disease approach associated with ACADS network. Copyright © 2015 Elsevier B.V. All rights reserved.

Natively unstructured loops differ from other loops.

Directory of Open Access Journals (Sweden)

Avner Schlessinger

2007-07-01

Full Text Available Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%-70% of all worm proteins observed to have more than seven protein-protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested

Loop-mediated isothermal amplification (LAMP) as an alternative to PCR: A rapid on-site detection of gene doping.

Science.gov (United States)

Salamin, Olivier; Kuuranne, Tiia; Saugy, Martial; Leuenberger, Nicolas

2017-11-01

Innovation in medical research has been diverted at multiple occasions to enhance human performance. The predicted great progress in gene therapy has raised some concerns regarding its misuse in the world of sports (gene doping) for several years now. Even though there is no evidence that gene doping has ever been used in sports, the continuous improvement of gene therapy techniques increases the likelihood of abuse. Therefore, since 2004, efforts have been invested by the anti-doping community and WADA for the development of detection methods. Several nested PCR and qPCR-based strategies exploiting the absence of introns in the transgenic DNA have been proposed for the long-term detection of transgene in blood. Despite their great sensitivity, those protocols are hampered by limitations of the techniques that can be cumbersome and costly. The purpose of this perspective is to describe a new approach based on loop-mediated isothermal amplification (LAMP) for the detection of gene doping. This protocol enables a rapid and simple method to amplify nucleic acids with a high sensitivity and specificity and with a simple visual detection of the results. LAMP is already being used in clinical application for the detection of viruses or mutations. Therefore, this technique has the potential to be further developed for the detection of foreign genetic material in elite athletes. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Effects of subtherapeutic concentrations of antimicrobials on gene acquisition events in Yersinia, Proteus, Shigella, and Salmonella recipient organisms in isolated ligated intestinal loops of swine.

Science.gov (United States)

Brewer, Matt T; Xiong, Nalee; Anderson, Kristi L; Carlson, Steve A

2013-08-01

To assess antimicrobial resistance and transfer of virulence genes facilitated by subtherapeutic concentrations of antimicrobials in swine intestines. 20 anesthetized pigs experimentally inoculated with donor and recipient bacteria. 4 recipient pathogenic bacteria (Salmonella enterica serotype Typhimurium, Yersinia enterocolitica, Shigella flexneri, or Proteus mirabilis) were incubated with donor bacteria in the presence of subinhibitory concentrations of 1 of 16 antimicrobials in isolated ligated intestinal loops in swine. Donor Escherichia coli contained transferrable antimicrobial resistance or virulence genes. After coincubations, intestinal contents were removed and assessed for pathogens that acquired new antimicrobial resistance or virulence genes following exposure to the subtherapeutic concentrations of antimicrobials. 3 antimicrobials (apramycin, lincomycin, and neomycin) enhanced transfer of an antimicrobial resistance plasmid from commensal E coli organisms to Yersinia and Proteus organisms, whereas 7 antimicrobials (florfenicol, hygromycin, penicillin G, roxarsone, sulfamethazine, tetracycline, and tylosin) exacerbated transfer of an integron (Salmonella genomic island 1) from Salmonella organisms to Yersinia organisms. Sulfamethazine induced the transfer of Salmonella pathogenicity island 1 from pathogenic to nonpathogenic Salmonella organisms. Six antimicrobials (bacitracin, carbadox, erythromycin, sulfathiazole, tiamulin, and virginiamycin) did not mediate any transfer events. Sulfamethazine was the only antimicrobial implicated in 2 types of transfer events. 10 of 16 antimicrobials at subinhibitory or subtherapeutic concentrations augmented specific antimicrobial resistance or transfer of virulence genes into pathogenic bacteria in isolated intestinal loops in swine. Use of subtherapeutic antimicrobials in animal feed may be associated with unwanted collateral effects.

Using riboswitches to regulate gene expression and define gene function in mycobacteria.

Science.gov (United States)

Van Vlack, Erik R; Seeliger, Jessica C

2015-01-01

Mycobacteria include both environmental species and many pathogenic species such as Mycobacterium tuberculosis, an intracellular pathogen that is the causative agent of tuberculosis in humans. Inducible gene expression is a powerful tool for examining gene function and essentiality, both in in vitro culture and in host cell infections. The theophylline-inducible artificial riboswitch has recently emerged as an alternative to protein repressor-based systems. The riboswitch is translationally regulated and is combined with a mycobacterial promoter that provides transcriptional control. We here provide methods used by our laboratory to characterize the riboswitch response to theophylline in reporter strains, recombinant organisms containing riboswitch-regulated endogenous genes, and in host cell infections. These protocols should facilitate the application of both existing and novel artificial riboswitches to the exploration of gene function in mycobacteria. © 2015 Elsevier Inc. All rights reserved.

Mathematical Modeling of Loop Heat Pipes

Science.gov (United States)

Kaya, Tarik; Ku, Jentung; Hoang, Triem T.; Cheung, Mark L.

1998-01-01

The primary focus of this study is to model steady-state performance of a Loop Heat Pipe (LHP). The mathematical model is based on the steady-state energy balance equations at each component of the LHP. The heat exchange between each LHP component and the surrounding is taken into account. Both convection and radiation environments are modeled. The loop operating temperature is calculated as a function of the applied power at a given loop condition. Experimental validation of the model is attempted by using two different LHP designs. The mathematical model is tested at different sink temperatures and at different elevations of the loop. Tbc comparison of the calculations and experimental results showed very good agreement (within 3%). This method proved to be a useful tool in studying steady-state LHP performance characteristics.

Loop quantum cosmology and singularities.

Science.gov (United States)

Struyve, Ward

2017-08-15

Loop quantum gravity is believed to eliminate singularities such as the big bang and big crunch singularity. This belief is based on studies of so-called loop quantum cosmology which concerns symmetry-reduced models of quantum gravity. In this paper, the problem of singularities is analysed in the context of the Bohmian formulation of loop quantum cosmology. In this formulation there is an actual metric in addition to the wave function, which evolves stochastically (rather than deterministically as the case of the particle evolution in non-relativistic Bohmian mechanics). Thus a singularity occurs whenever this actual metric is singular. It is shown that in the loop quantum cosmology for a homogeneous and isotropic Friedmann-Lemaître-Robertson-Walker space-time with arbitrary constant spatial curvature and cosmological constant, coupled to a massless homogeneous scalar field, a big bang or big crunch singularity is never obtained. This should be contrasted with the fact that in the Bohmian formulation of the Wheeler-DeWitt theory singularities may exist.

The three-loop splitting functions P{sup (2)}{sub qg} and P{sup (2,N{sub F})}{sub gg}

Energy Technology Data Exchange (ETDEWEB)

Ablinger, J.; Schneider, C. [Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation (RISC); Behring, A. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); RWTH Aachen Univ. (Germany). Inst. fuer Theoretische Teilchenphysik und Kosmologie; Bluemlein, J.; Freitas, A. de [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Von Manteuffel, A. [Michigan State Univ., East Lansing, MI (United States). Dept. of Physics and Astronomy

2017-04-15

We calculate the unpolarized twist-2 three-loop splitting functions P{sup (2)}{sub qg}(x) and P{sup (2,N{sub F})}{sub gg}(x) and the associated anomalous dimensions using massive three-loop operator matrix elements. While we calculate P{sup (2,N{sub F})}{sub gg}(x) directly, P{sup (2)}{sub qg}(x) is computed from 1200 even moments, without any structural prejudice, using a hierarchy of recurrences obtained for the corresponding operator matrix element. The largest recurrence to be solved is of order 12 and degree 191. We confirm results in the foregoing literature.

Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

KAUST Repository

Maadooliat, Mehdi

2015-10-21

This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

KAUST Repository

Maadooliat, Mehdi; Zhou, Lan; Najibi, Seyed Morteza; Gao, Xin; Huang, Jianhua Z.

2015-01-01

This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast.

Science.gov (United States)

Hartono, Stella R; Malapert, Amélie; Legros, Pénélope; Bernard, Pascal; Chédin, Frédéric; Vanoosthuyse, Vincent

2018-02-02

R-loops, which result from the formation of stable DNA:RNA hybrids, can both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loops in fission yeast, we used the S9.6 antibody-based DRIPc-seq method to sequence the RNA strand of R-loops and obtain strand-specific R-loop maps at near nucleotide resolution. Surprisingly, preliminary DRIPc-seq experiments identified mostly RNase H-resistant but exosome-sensitive RNAs that mapped to both DNA strands and resembled RNA:RNA hybrids (dsRNAs), suggesting that dsRNAs form widely in fission yeast. We confirmed in vitro that S9.6 can immuno-precipitate dsRNAs and provide evidence that dsRNAs can interfere with its binding to R-loops. dsRNA elimination by RNase III treatment prior to DRIPc-seq allowed the genome-wide and strand-specific identification of genuine R-loops that responded in vivo to RNase H levels and displayed classical features associated with R-loop formation. We also found that most transcripts whose levels were altered by in vivo manipulation of RNase H levels did not form detectable R-loops, suggesting that prolonged manipulation of R-loop levels could indirectly alter the transcriptome. We discuss the implications of our work in the design of experimental strategies to probe R-loop functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks.

Science.gov (United States)

Mai, Hans-Jörg; Pateyron, Stéphanie; Bauer, Petra

2016-10-03

FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes. 448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes. We could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons.

Gauge theory loop operators and Liouville theory

Energy Technology Data Exchange (ETDEWEB)

Drukker, Nadav [Humboldt Univ. Berlin (Germany). Inst. fuer Physik; Gomis, Jaume; Okuda, Takuda [Perimeter Inst. for Theoretical Physics, Waterloo, ON (Canada); Teschner, Joerg [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2009-10-15

We propose a correspondence between loop operators in a family of four dimensional N=2 gauge theories on S{sup 4} - including Wilson, 't Hooft and dyonic operators - and Liouville theory loop operators on a Riemann surface. This extends the beautiful relation between the partition function of these N=2 gauge theories and Liouville correlators found by Alday, Gaiotto and Tachikawa. We show that the computation of these Liouville correlators with the insertion of a Liouville loop operator reproduces Pestun's formula capturing the expectation value of a Wilson loop operator in the corresponding gauge theory. We prove that our definition of Liouville loop operators is invariant under modular transformations, which given our correspondence, implies the conjectured action of S-duality on the gauge theory loop operators. Our computations in Liouville theory make an explicit prediction for the exact expectation value of 't Hooft and dyonic loop operators in these N=2 gauge theories. The Liouville loop operators are also found to admit a simple geometric interpretation within quantum Teichmueller theory as the quantum operators representing the length of geodesics. We study the algebra of Liouville loop operators and show that it gives evidence for our proposal as well as providing definite predictions for the operator product expansion of loop operators in gauge theory. (orig.)

Conformal boundary loop models

International Nuclear Information System (INIS)

Jacobsen, Jesper Lykke; Saleur, Hubert

2008-01-01

We study a model of densely packed self-avoiding loops on the annulus, related to the Temperley-Lieb algebra with an extra idempotent boundary generator. Four different weights are given to the loops, depending on their homotopy class and whether they touch the outer rim of the annulus. When the weight of a contractible bulk loop x≡q+q -1 element of (-2,2], this model is conformally invariant for any real weight of the remaining three parameters. We classify the conformal boundary conditions and give exact expressions for the corresponding boundary scaling dimensions. The amplitudes with which the sectors with any prescribed number and types of non-contractible loops appear in the full partition function Z are computed rigorously. Based on this, we write a number of identities involving Z which hold true for any finite size. When the weight of a contractible boundary loop y takes certain discrete values, y r ≡([r+1] q )/([r] q ) with r integer, other identities involving the standard characters K r,s of the Virasoro algebra are established. The connection with Dirichlet and Neumann boundary conditions in the O(n) model is discussed in detail, and new scaling dimensions are derived. When q is a root of unity and y=y r , exact connections with the A m type RSOS model are made. These involve precise relations between the spectra of the loop and RSOS model transfer matrices, valid in finite size. Finally, the results where y=y r are related to the theory of Temperley-Lieb cabling

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Directory of Open Access Journals (Sweden)

Baseler Michael W

2007-11-01

Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

Evolutionary Relationship and Structural Characterization of the EPF/EPFL Gene Family

OpenAIRE

Takata, Naoki; Yokota, Kiyonobu; Ohki, Shinya; Mori, Masashi; Taniguchi, Toru; Kurita, Manabu

2013-01-01

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that...

Closed-loop, pilot/vehicle analysis of the approach and landing task

Science.gov (United States)

Anderson, M. R.; Schmidt, D. K.

1986-01-01

In the case of approach and landing, it is universally accepted that the pilot uses more than one vehicle response, or output, to close his control loops. Therefore, to model this task, a multi-loop analysis technique is required. The analysis problem has been in obtaining reasonable analytic estimates of the describing functions representing the pilot's loop compensation. Once these pilot describing functions are obtained, appropriate performance and workload metrics must then be developed for the landing task. The optimal control approach provides a powerful technique for obtaining the necessary describing functions, once the appropriate task objective is defined in terms of a quadratic objective function. An approach is presented through the use of a simple, reasonable objective function and model-based metrics to evaluate loop performance and pilot workload. The results of an analysis of the LAHOS (Landing and Approach of Higher Order Systems) study performed by R.E. Smith is also presented.

F4 symmetric ϕ3 theory at four loops

Science.gov (United States)

Gracey, J. A.

2017-03-01

The renormalization group functions for six dimensional scalar ϕ3 theory with an F4 symmetry are provided at four loops in the modified minimal subtraction (MS ¯ ) scheme. Aside from the anomalous dimension of ϕ and the β -function this includes the mass operator and a ϕ2-type operator. The anomalous dimension of the latter is computed explicitly at four loops for the 26 and 324 representations of F4. The ɛ expansion of all the related critical exponents are determined to O (ɛ4). For instance the value for Δϕ agrees with recent conformal bootstrap estimates in 5 and 5.95 dimensions. The renormalization group functions are also provided at four loops for the group E6.

Autoregulation of transcription of the hupA gene in Escherichia coli: evidence for steric hindrance of the functional promoter domains induced by HU.

Science.gov (United States)

Kohno, K; Yasuzawa, K; Hirose, M; Kano, Y; Goshima, N; Tanaka, H; Imamoto, F

1994-06-01

The molecular mechanism of autoregulation of expression of the hupA gene in Escherichia coli was examined. The promoter of the gene contains a palindromic sequence with the potential to form a cruciform DNA structure in which the -35 sequence lies at the base of the stem and the -10 sequence forms a single-stranded loop. An artificial promoter lacking the palindrome, which was constructed by replacing a 10 nucleotide repeat for the predicted cruciform arm by a sequence in the opposite orientation, was not subject to HU-repression. DNA relaxation induced by deleting HU proteins and/or inhibiting DNA gyrase in cells results in increased expression from the hupA promoter. We propose that initiation of transcription of the hupA gene is negatively regulated by steric hindrance of the functional promoter domains for formation of the cruciform configuration, which is facilitated at least in part by negative supercoiling of the hupA promoter DNA region. The promoter region of the hupB gene also contains a palindromic sequence that can assume a cruciform configuration. Negative regulation of this gene by HU proteins may occur by a mechanism similar to that operating for the hupA gene.

Closed-loop conductance scanning tunneling spectroscopy: demonstrating the equivalence to the open-loop alternative.

Science.gov (United States)

Hellenthal, Chris; Sotthewes, Kai; Siekman, Martin H; Kooij, E Stefan; Zandvliet, Harold J W

2015-01-01

We demonstrate the validity of using closed-loop z(V) conductance scanning tunneling spectroscopy (STS) measurements for the determination of the effective tunneling barrier by comparing them to more conventional open-loop I(z) measurements. Through the development of a numerical model, the individual contributions to the effective tunneling barrier present in these experiments, such as the work function and the presence of an image charge, are determined quantitatively. This opens up the possibility of determining tunneling barriers of both vacuum and molecular systems in an alternative and more detailed manner.

FMFT. Fully massive four-loop tadpoles

Energy Technology Data Exchange (ETDEWEB)

Pikelner, Andrey [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik

2017-07-15

We present FMFT - a package written in FORM that evaluates four-loop fully massive tadpole Feynman diagrams. It is a successor of the MATAD package that has been successfully used to calculate many renormalization group functions at three-loop order in a wide range of quantum field theories especially in the Standard Model. We describe an internal structure of the package and provide some examples of its usage.

FMFT: fully massive four-loop tadpoles

Science.gov (United States)

Pikelner, Andrey

2018-03-01

We present FMFT - a package written in FORM that evaluates four-loop fully massive tadpole Feynman diagrams. It is a successor of the MATAD package that has been successfully used to calculate many renormalization group functions at three-loop order in a wide range of quantum field theories especially in the Standard Model. We describe an internal structure of the package and provide some examples of its usage.

Gene function in early mouse embryonic stem cell differentiation

Directory of Open Access Journals (Sweden)

Campbell Pearl A

2007-03-01

Full Text Available Abstract Background Little is known about the genes that drive embryonic stem cell differentiation. However, such knowledge is necessary if we are to exploit the therapeutic potential of stem cells. To uncover the genetic determinants of mouse embryonic stem cell (mESC differentiation, we have generated and analyzed 11-point time-series of DNA microarray data for three biologically equivalent but genetically distinct mESC lines (R1, J1, and V6.5 undergoing undirected differentiation into embryoid bodies (EBs over a period of two weeks. Results We identified the initial 12 hour period as reflecting the early stages of mESC differentiation and studied probe sets showing consistent changes of gene expression in that period. Gene function analysis indicated significant up-regulation of genes related to regulation of transcription and mRNA splicing, and down-regulation of genes related to intracellular signaling. Phylogenetic analysis indicated that the genes showing the largest expression changes were more likely to have originated in metazoans. The probe sets with the most consistent gene changes in the three cell lines represented 24 down-regulated and 12 up-regulated genes, all with closely related human homologues. Whereas some of these genes are known to be involved in embryonic developmental processes (e.g. Klf4, Otx2, Smn1, Socs3, Tagln, Tdgf1, our analysis points to others (such as transcription factor Phf21a, extracellular matrix related Lama1 and Cyr61, or endoplasmic reticulum related Sc4mol and Scd2 that have not been previously related to mESC function. The majority of identified functions were related to transcriptional regulation, intracellular signaling, and cytoskeleton. Genes involved in other cellular functions important in ESC differentiation such as chromatin remodeling and transmembrane receptors were not observed in this set. Conclusion Our analysis profiles for the first time gene expression at a very early stage of m

The 3-loop pure singlet heavy flavor contributions to the structure function F{sub 2}(x,Q{sup 2}) and the anomalous dimension

Energy Technology Data Exchange (ETDEWEB)

Ablinger, J. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria); Behring, A.; Blümlein, J.; De Freitas, A. [Deutsches Elektronen-Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany); Manteuffel, A. von [PRISMA Cluster of Excellence, Institute of Physics, J. Gutenberg University, D-55099 Mainz (Germany); Schneider, C. [Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Altenbergerstraße 69, A-4040 Linz (Austria)

2015-01-15

The pure singlet asymptotic heavy flavor corrections to 3-loop order for the deep-inelastic scattering structure function F{sub 2}(x,Q{sup 2}) and the corresponding transition matrix element A{sub Qq}{sup (3),PS} in the variable flavor number scheme are computed. In Mellin-N space these inclusive quantities depend on generalized harmonic sums. We also recalculate the complete 3-loop pure singlet anomalous dimension for the first time. Numerical results for the Wilson coefficients, the operator matrix element and the contribution to the structure function F{sub 2}(x,Q{sup 2}) are presented.

The running coupling from the QCD Schrödinger functional a one-loop analysis

CERN Document Server

Sint, S; Sint, Stefan; Sommer, Rainer

1996-01-01

Starting from the Schr\\"odinger functional, we give a non-perturbative definition of the running coupling constant in QCD. The spatial boundary conditions for the quark fields are chosen such that the massless Dirac operator in the classical background field has a large smallest eigenvalue. At one-loop order of perturbation theory, we determine the matching coefficient to the \\MSbar-scheme and discuss the quark mass effects in the \\beta-function. To this order, we also compute the Symanzik improvement coefficient necessary to remove the \\Oa lattice artefacts originating from the boundaries. For reasonable lattice resolutions and the standard Wilson action, lattice artefacts are found to be only weakly dependent on the lattice spacing a, while they vanish quickly with the improved action of Sheikholeslami and Wohlert.

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

Energy Technology Data Exchange (ETDEWEB)

Wang, Jing; Ma, Zihao; Carr, Steven A.; Mertins, Philipp; Zhang, Hui; Zhang, Zhen; Chan, Daniel W.; Ellis, Matthew J. C.; Townsend, R. Reid; Smith, Richard D.; McDermott, Jason E.; Chen, Xian; Paulovich, Amanda G.; Boja, Emily S.; Mesri, Mehdi; Kinsinger, Christopher R.; Rodriguez, Henry; Rodland, Karin D.; Liebler, Daniel C.; Zhang, Bing

2016-11-11

Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies

Human Intellectual Disability Genes Form Conserved Functional Modules in Drosophila

Science.gov (United States)

Oortveld, Merel A. W.; Keerthikumar, Shivakumar; Oti, Martin; Nijhof, Bonnie; Fernandes, Ana Clara; Kochinke, Korinna; Castells-Nobau, Anna; van Engelen, Eva; Ellenkamp, Thijs; Eshuis, Lilian; Galy, Anne; van Bokhoven, Hans; Habermann, Bianca; Brunner, Han G.; Zweier, Christiane; Verstreken, Patrik; Huynen, Martijn A.; Schenck, Annette

2013-01-01

Intellectual Disability (ID) disorders, defined by an IQ below 70, are genetically and phenotypically highly heterogeneous. Identification of common molecular pathways underlying these disorders is crucial for understanding the molecular basis of cognition and for the development of therapeutic intervention strategies. To systematically establish their functional connectivity, we used transgenic RNAi to target 270 ID gene orthologs in the Drosophila eye. Assessment of neuronal function in behavioral and electrophysiological assays and multiparametric morphological analysis identified phenotypes associated with knockdown of 180 ID gene orthologs. Most of these genotype-phenotype associations were novel. For example, we uncovered 16 genes that are required for basal neurotransmission and have not previously been implicated in this process in any system or organism. ID gene orthologs with morphological eye phenotypes, in contrast to genes without phenotypes, are relatively highly expressed in the human nervous system and are enriched for neuronal functions, suggesting that eye phenotyping can distinguish different classes of ID genes. Indeed, grouping genes by Drosophila phenotype uncovered 26 connected functional modules. Novel links between ID genes successfully predicted that MYCN, PIGV and UPF3B regulate synapse development. Drosophila phenotype groups show, in addition to ID, significant phenotypic similarity also in humans, indicating that functional modules are conserved. The combined data indicate that ID disorders, despite their extreme genetic diversity, are caused by disruption of a limited number of highly connected functional modules. PMID:24204314

Methodology for the inference of gene function from phenotype data.

Science.gov (United States)

Ascensao, Joao A; Dolan, Mary E; Hill, David P; Blake, Judith A

2014-12-12

Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies. The ability to infer data associated with one ontology to data associated with another ontology would prove useful in expanding information content and scope. We here focus on relating two ontologies: the Gene Ontology (GO), which encodes canonical gene function, and the Mammalian Phenotype Ontology (MP), which describes non-canonical phenotypes, using statistical methods to suggest GO functional annotations from existing MP phenotype annotations. This work is in contrast to previous studies that have focused on inferring gene function from phenotype primarily through lexical or semantic similarity measures. We have designed and tested a set of algorithms that represents a novel methodology to define rules for predicting gene function by examining the emergent structure and relationships between the gene functions and phenotypes rather than inspecting the terms semantically. The algorithms inspect relationships among multiple phenotype terms to deduce if there are cases where they all arise from a single gene function. We apply this methodology to data about genes in the laboratory mouse that are formally represented in the Mouse Genome Informatics (MGI) resource. From the data, 7444 rule instances were generated from five generalized rules, resulting in 4818 unique GO functional predictions for 1796 genes. We show that our method is capable of inferring high-quality functional annotations from curated phenotype data. As well as creating inferred annotations, our method has the potential to allow for the elucidation of unforeseen, biologically significant associations between gene function and

Polyploidization altered gene functions in cotton (Gossypium spp.).

Science.gov (United States)

Xu, Zhanyou; Yu, John Z; Cho, Jaemin; Yu, Jing; Kohel, Russell J; Percy, Richard G

2010-12-16

Cotton (Gossypium spp.) is an important crop plant that is widely grown to produce both natural textile fibers and cottonseed oil. Cotton fibers, the economically more important product of the cotton plant, are seed trichomes derived from individual cells of the epidermal layer of the seed coat. It has been known for a long time that large numbers of genes determine the development of cotton fiber, and more recently it has been determined that these genes are distributed across At and Dt subgenomes of tetraploid AD cottons. In the present study, the organization and evolution of the fiber development genes were investigated through the construction of an integrated genetic and physical map of fiber development genes whose functions have been verified and confirmed. A total of 535 cotton fiber development genes, including 103 fiber transcription factors, 259 fiber development genes, and 173 SSR-contained fiber ESTs, were analyzed at the subgenome level. A total of 499 fiber related contigs were selected and assembled. Together these contigs covered about 151 Mb in physical length, or about 6.7% of the tetraploid cotton genome. Among the 499 contigs, 397 were anchored onto individual chromosomes. Results from our studies on the distribution patterns of the fiber development genes and transcription factors between the At and Dt subgenomes showed that more transcription factors were from Dt subgenome than At, whereas more fiber development genes were from At subgenome than Dt. Combining our mapping results with previous reports that more fiber QTLs were mapped in Dt subgenome than At subgenome, the results suggested a new functional hypothesis for tetraploid cotton. After the merging of the two diploid Gossypium genomes, the At subgenome has provided most of the genes for fiber development, because it continues to function similar to its fiber producing diploid A genome ancestor. On the other hand, the Dt subgenome, with its non-fiber producing D genome ancestor

Penguin loops with confined quark propagators

International Nuclear Information System (INIS)

Eeg, J.O.

1984-12-01

The ΔS = 1 penguin diagram is calculated by representing the internal quark lines in the loop by bag model wave functions. Because of the involved GIM-mecanism, only the lowest internal quark modes are kept in the loop. The result depends cruically on the values of the strong coupling constant and the quark energy of the bag model wave functions. With reasonable values of parameters, contributions corresponding to effective penguin coeffisient values of approximately two to five times the standard pertubative ones, have been found. Thus the theoretical value for the ratio between ΔI = 1/2 and ΔI = 3/2 amplitudes seems to be improved

FUNCTIONAL SPECIALIZATION OF DUPLICATED FLAVONOID BIOSYNTHESIS GENES IN WHEAT

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Khlestkina E.

2012-08-01

Full Text Available Gene duplication followed by subfunctionalization and neofunctionalization is of a great evolutionary importance. In plant genomes, duplicated genes may result from either polyploidization (homoeologous genes or segmental chromosome duplications (paralogous genes. In allohexaploid wheat Triticum aestivum L. (2n=6x=42, genome BBAADD, both homoeologous and paralogous copies were found for the regulatory gene Myc encoding MYC-like transcriptional factor in the biosynthesis of flavonoid pigments, anthocyanins, and for the structural gene F3h encoding one of the key enzymes of flavonoid biosynthesis, flavanone 3-hydroxylase. From the 5 copies (3 homoeologous and 2 paralogous of the Myc gene found in T. aestivum, only one plays a regulatory role in anthocyanin biosynthesis, interacting complementary with another transcriptional factor (MYB-like to confer purple pigmentation of grain pericarp in wheat. The role and functionality of the other 4 copies of the Myc gene remain unknown. From the 4 functional copies of the F3h gene in T. aestivum, three homoeologues have similar function. They are expressed in wheat organs colored with anthocyanins or in the endosperm, participating there in biosynthesis of uncolored flavonoid substances. The fourth copy (the B-genomic paralogue is transcribed neither in wheat organs colored with anthocyanins nor in seeds, however, it’s expression has been noticed in roots of aluminium-stressed plants, where the three homoeologous copies are not active. Functional diversification of the duplicated flavonoid biosynthesis genes in wheat may be a reason for maintenance of the duplicated copies and preventing them from pseudogenization.The study was supported by RFBR (11-04-92707. We also thank Ms. Galina Generalova for technical assistance.

Defining functional distances over Gene Ontology

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del Pozo Angela

2008-01-01

Full Text Available Abstract Background A fundamental problem when trying to define the functional relationships between proteins is the difficulty in quantifying functional similarities, even when well-structured ontologies exist regarding the activity of proteins (i.e. 'gene ontology' -GO-. However, functional metrics can overcome the problems in the comparing and evaluating functional assignments and predictions. As a reference of proximity, previous approaches to compare GO terms considered linkage in terms of ontology weighted by a probability distribution that balances the non-uniform 'richness' of different parts of the Direct Acyclic Graph. Here, we have followed a different approach to quantify functional similarities between GO terms. Results We propose a new method to derive 'functional distances' between GO terms that is based on the simultaneous occurrence of terms in the same set of Interpro entries, instead of relying on the structure of the GO. The coincidence of GO terms reveals natural biological links between the GO functions and defines a distance model Df which fulfils the properties of a Metric Space. The distances obtained in this way can be represented as a hierarchical 'Functional Tree'. Conclusion The method proposed provides a new definition of distance that enables the similarity between GO terms to be quantified. Additionally, the 'Functional Tree' defines groups with biological meaning enhancing its utility for protein function comparison and prediction. Finally, this approach could be for function-based protein searches in databases, and for analysing the gene clusters produced by DNA array experiments.

Novel loop-like solitons for the generalized Vakhnenko equation

International Nuclear Information System (INIS)

Zhang Min; Ma Yu-Lan; Li Bang-Qing

2013-01-01

A non-traveling wave solution of a generalized Vakhnenko equation arising from the high-frequent wave motion in a relaxing medium is derived via the extended Riccati mapping method. The solution includes an arbitrary function of an independent variable. Based on the solution, two hyperbolic functions are chosen to construct new solitons. Novel single-loop-like and double-loop-like solitons are found for the equation

Tissue-specific functional networks for prioritizing phenotype and disease genes.

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Yuanfang Guan

Full Text Available Integrated analyses of functional genomics data have enormous potential for identifying phenotype-associated genes. Tissue-specificity is an important aspect of many genetic diseases, reflecting the potentially different roles of proteins and pathways in diverse cell lineages. Accounting for tissue specificity in global integration of functional genomics data is challenging, as "functionality" and "functional relationships" are often not resolved for specific tissue types. We address this challenge by generating tissue-specific functional networks, which can effectively represent the diversity of protein function for more accurate identification of phenotype-associated genes in the laboratory mouse. Specifically, we created 107 tissue-specific functional relationship networks through integration of genomic data utilizing knowledge of tissue-specific gene expression patterns. Cross-network comparison revealed significantly changed genes enriched for functions related to specific tissue development. We then utilized these tissue-specific networks to predict genes associated with different phenotypes. Our results demonstrate that prediction performance is significantly improved through using the tissue-specific networks as compared to the global functional network. We used a testis-specific functional relationship network to predict genes associated with male fertility and spermatogenesis phenotypes, and experimentally confirmed one top prediction, Mbyl1. We then focused on a less-common genetic disease, ataxia, and identified candidates uniquely predicted by the cerebellum network, which are supported by both literature and experimental evidence. Our systems-level, tissue-specific scheme advances over traditional global integration and analyses and establishes a prototype to address the tissue-specific effects of genetic perturbations, diseases and drugs.

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations.

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Sahra Uygun

2016-12-01

Full Text Available Gene co-expression has been widely used to hypothesize gene function through guilt-by association. However, it is not clear to what degree co-expression is informative, whether it can be applied to genes involved in different biological processes, and how the type of dataset impacts inferences about gene functions. Here our goal is to assess the utility and limitations of using co-expression as a criterion to recover functional associations between genes. By determining the percentage of gene pairs in a metabolic pathway with significant expression correlation, we found that many genes in the same pathway do not have similar transcript profiles and the choice of dataset, annotation quality, gene function, expression similarity measure, and clustering approach significantly impacts the ability to recover functional associations between genes using Arabidopsis thaliana as an example. Some datasets are more informative in capturing coordinated expression profiles and larger data sets are not always better. In addition, to recover the maximum number of known pathways and identify candidate genes with similar functions, it is important to explore rather exhaustively multiple dataset combinations, similarity measures, clustering algorithms and parameters. Finally, we validated the biological relevance of co-expression cluster memberships with an independent phenomics dataset and found that genes that consistently cluster with leucine degradation genes tend to have similar leucine levels in mutants. This study provides a framework for obtaining gene functional associations by maximizing the information that can be obtained from gene expression datasets.

Two-loop SL(2) form factors and maximal transcendentality

International Nuclear Information System (INIS)

Loebbert, Florian; Sieg, Christoph; Wilhelm, Matthias; Yang, Gang

2016-01-01

Form factors of composite operators in the SL(2) sector of N=4 SYM theory are studied up to two loops via the on-shell unitarity method. The non-compactness of this subsector implies the novel feature and technical challenge of an unlimited number of loop momenta in the integrand’s numerator. At one loop, we derive the full minimal form factor to all orders in the dimensional regularisation parameter. At two loops, we construct the complete integrand for composite operators with an arbitrary number of covariant derivatives, and we obtain the remainder functions as well as the dilatation operator for composite operators with up to three covariant derivatives. The remainder functions reveal curious patterns suggesting a hidden maximal uniform transcendentality for the full form factor. Finally, we speculate about an extension of these patterns to QCD.

Two-loop SL(2) form factors and maximal transcendentality

Energy Technology Data Exchange (ETDEWEB)

Loebbert, Florian [Institut für Physik, Humboldt-Universität zu Berlin,Zum Großen Windkanal 6, 12489 Berlin (Germany); Sieg, Christoph [Institut für Physik, Humboldt-Universität zu Berlin,Zum Großen Windkanal 6, 12489 Berlin (Germany); Institut für Mathematik, Humboldt-Universität zu Berlin,Zum Großen Windkanal 6, 12489 Berlin (Germany); Wilhelm, Matthias [Institut für Physik, Humboldt-Universität zu Berlin,Zum Großen Windkanal 6, 12489 Berlin (Germany); Institut für Mathematik, Humboldt-Universität zu Berlin,Zum Großen Windkanal 6, 12489 Berlin (Germany); Niels Bohr Institute, Copenhagen University,Blegdamsvej 17, 2100 Copenhagen Ø (Denmark); Yang, Gang [CAS Key Laboratory of Theoretical Physics,Institute of Theoretical Physics, Chinese Academy of Sciences,Beijing 100190 (China); Institut für Physik, Humboldt-Universität zu Berlin,Zum Großen Windkanal 6, 12489 Berlin (Germany)

2016-12-19

Form factors of composite operators in the SL(2) sector of N=4 SYM theory are studied up to two loops via the on-shell unitarity method. The non-compactness of this subsector implies the novel feature and technical challenge of an unlimited number of loop momenta in the integrand’s numerator. At one loop, we derive the full minimal form factor to all orders in the dimensional regularisation parameter. At two loops, we construct the complete integrand for composite operators with an arbitrary number of covariant derivatives, and we obtain the remainder functions as well as the dilatation operator for composite operators with up to three covariant derivatives. The remainder functions reveal curious patterns suggesting a hidden maximal uniform transcendentality for the full form factor. Finally, we speculate about an extension of these patterns to QCD.

Pdlim7 is required for maintenance of the mesenchymal/epidermal Fgf signaling feedback loop during zebrafish pectoral fin development

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Klosowiak Julian

2010-10-01

Full Text Available Abstract Background Vertebrate limb development involves a reciprocal feedback loop between limb mesenchyme and the overlying apical ectodermal ridge (AER. Several gene pathways participate in this feedback loop, including Fgf signaling. In the forelimb lateral plate mesenchyme, Tbx5 activates Fgf10 expression, which in turn initiates and maintains the mesenchyme/AER Fgf signaling loop. Recent findings have revealed that Tbx5 transcriptional activity is regulated by dynamic nucleocytoplasmic shuttling and interaction with Pdlim7, a PDZ-LIM protein family member, along actin filaments. This Tbx5 regulation is critical in heart formation, but the coexpression of both proteins in other developing tissues suggests a broader functional role. Results Knock-down of Pdlim7 function leads to decreased pectoral fin cell proliferation resulting in a severely stunted fin phenotype. While early gene induction and patterning in the presumptive fin field appear normal, the pectoral fin precursor cells display compaction and migration defects between 18 and 24 hours post-fertilization (hpf. During fin growth fgf24 is sequentially expressed in the mesenchyme and then in the apical ectodermal ridge (AER. However, in pdlim7 antisense morpholino-treated embryos this switch of expression is prevented and fgf24 remains ectopically active in the mesenchymal cells. Along with the lack of fgf24 in the AER, other critical factors including fgf8 are reduced, suggesting signaling problems to the underlying mesenchyme. As a consequence of perturbed AER function in the absence of Pdlim7, pathway components in the fin mesenchyme are misregulated or absent, indicating a breakdown of the Fgf signaling feedback loop, which is ultimately responsible for the loss of fin outgrowth. Conclusion This work provides the first evidence for the involvement of Pdlim7 in pectoral fin development. Proper fin outgrowth requires fgf24 downregulation in the fin mesenchyme with subsequent

Hardware-in-the-loop simulation for the virtual application of control functions for a coordination of the interaction between a gasoline engine and the 14V-power electrical system; Hardware-in-the-Loop-Simulation fuer die virtuelle Applikation von Steuerungsfunktionen zur Motor-Energiebordnetz-Koordination

Energy Technology Data Exchange (ETDEWEB)

Schiele, Thomas

2010-07-01

The development of advanced engine management systems increasingly is supported by model-based development tools. Thereby the hardware-in-the-loop simulation is one of these tools. The author of the contribution under consideration reports on an extension of the capabilities of the hardware-in-the-loop simulation from the classic functional testing and safety tests up to the model-based application. Using the control functions for the coordination of the interaction between a gasoline engine and the 14V-power electrical system as an example, the practical application of hardware-in-the-loop systems is presented. Here, the author reviews on the state of technology for the real-time modeling of internal combustion engines and wiring systems.

Effect of vacancy loops on swelling of metals under irradiation

International Nuclear Information System (INIS)

Golubov, S.I.

1981-01-01

Subsequent analysis of vacancy loops formation in metals under irradiation is carried out and effect of vacancy loops on vacancy porosity is studied. Expression for quasistationary function of vacancy loops distribution according to sizes taking into consideration two mechanisms of their initiation-cascade and fluctuational ones - is obtained. It is shown that rate of vacancy absorption and interstitials by vacancy loops in quasiequilibrium state is similar and depends only on summary length of loops, for its calculations the self-coordinated procedure is formulated. For the rate of metal swelling under irradiation obtained is the expression taking into consideration the presence of vacancy loops [ru

Towards precise classification of cancers based on robust gene functional expression profiles

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Zhu Jing

2005-03-01

Full Text Available Abstract Background Development of robust and efficient methods for analyzing and interpreting high dimension gene expression profiles continues to be a focus in computational biology. The accumulated experiment evidence supports the assumption that genes express and perform their functions in modular fashions in cells. Therefore, there is an open space for development of the timely and relevant computational algorithms that use robust functional expression profiles towards precise classification of complex human diseases at the modular level. Results Inspired by the insight that genes act as a module to carry out a highly integrated cellular function, we thus define a low dimension functional expression profile for data reduction. After annotating each individual gene to functional categories defined in a proper gene function classification system such as Gene Ontology applied in this study, we identify those functional categories enriched with differentially expressed genes. For each functional category or functional module, we compute a summary measure (s for the raw expression values of the annotated genes to capture the overall activity level of the module. In this way, we can treat the gene expressions within a functional module as an integrative data point to replace the multiple values of individual genes. We compare the classification performance of decision trees based on functional expression profiles with the conventional gene expression profiles using four publicly available datasets, which indicates that precise classification of tumour types and improved interpretation can be achieved with the reduced functional expression profiles. Conclusion This modular approach is demonstrated to be a powerful alternative approach to analyzing high dimension microarray data and is robust to high measurement noise and intrinsic biological variance inherent in microarray data. Furthermore, efficient integration with current biological knowledge

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

Science.gov (United States)

Sloma, Michael F.; Mathews, David H.

2016-01-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes

DEFF Research Database (Denmark)

Knoch, Tobias A; Wachsmuth, Malte; Kepper, Nick

2016-01-01

BACKGROUND: The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture...... of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture (T2C), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence. RESULTS: The genome is compacted...... into a chromatin quasi-fibre with ~5 ± 1 nucleosomes/11 nm, folded into stable ~30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types and functional states. The architecture and the DNA sequence...

Integrative Functional Genomics for Systems Genetics in GeneWeaver.org.

Science.gov (United States)

Bubier, Jason A; Langston, Michael A; Baker, Erich J; Chesler, Elissa J

2017-01-01

The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data. GeneWeaver contains curated experimental data together with resource-level data such as GO annotations, MP annotations, and KEGG pathways, along with persistent stores of user entered data sets. These can be entered directly into GeneWeaver or transferred from widely used resources such as GeneNetwork.org. Data are analyzed using statistical tools and advanced graph algorithms to discover new relations, prioritize candidate genes, and generate function hypotheses. Here we use GeneWeaver to find genes common to multiple gene sets, prioritize candidate genes from a quantitative trait locus, and characterize a set of differentially expressed genes. Coupling a large multispecies repository curated and empirical functional genomics data to fast computational tools allows for the rapid integrative analysis of heterogeneous data for interpreting and extrapolating systems genetics results.

Two-loop beam and soft functions for rapidity-dependent jet vetoes

Energy Technology Data Exchange (ETDEWEB)

Gangal, Shireen [Theory Group, Deutsches Elektronen-Synchrotron (DESY),Notkestraße 85, D-22607 Hamburg (Germany); Gaunt, Jonathan R. [Nikhef Theory Group and VU University Amsterdam,De Boelelaan 1081, NL-1081 HV Amsterdam (Netherlands); Stahlhofen, Maximilian [PRISMA Cluster of Excellence, Institute of Physics, Johannes Gutenberg University,Staudingerweg 7, D-55128 Mainz (Germany); Tackmann, Frank J. [Theory Group, Deutsches Elektronen-Synchrotron (DESY),Notkestraße 85, D-22607 Hamburg (Germany)

2017-02-06

Jet vetoes play an important role in many analyses at the LHC. Traditionally, jet vetoes have been imposed using a restriction on the transverse momentum p{sub Tj} of jets. Alternatively, one can also consider jet observables for which p{sub Tj} is weighted by a smooth function of the jet rapidity y{sub j} that vanishes as |y{sub j}|→∞. Such observables are useful as they provide a natural way to impose a tight veto on central jets but a looser one at forward rapidities. We consider two such rapidity-dependent jet veto observables, T{sub Bj} and T{sub Cj}, and compute the required beam and dijet soft functions for the jet-vetoed color-singlet production cross section at two loops. At this order, clustering effects from the jet algorithm become important. The dominant contributions are computed fully analytically while corrections that are subleading in the limit of small jet radii are expressed in terms of finite numerical integrals. Our results enable the full NNLL{sup ′} resummation and are an important step towards N{sup 3}LL resummation for cross sections with a T{sub Bj} or T{sub Cj} jet veto.

The ALMT Gene Family Performs Multiple Functions in Plants

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Jie Liu

2018-02-01

Full Text Available The aluminium activated malate transporter (ALMT gene family is named after the first member of the family identified in wheat (Triticum aestivum L.. The product of this gene controls resistance to aluminium (Al toxicity. ALMT genes encode transmembrane proteins that function as anion channels and perform multiple functions involving the transport of organic anions (e.g., carboxylates and inorganic anions in cells. They share a PF11744 domain and are classified in the Fusaric acid resistance protein-like superfamily, CL0307. The proteins typically have five to seven transmembrane regions in the N-terminal half and a long hydrophillic C-terminal tail but predictions of secondary structure vary. Although widely spread in plants, relatively little information is available on the roles performed by other members of this family. In this review, we summarized functions of ALMT gene families, including Al resistance, stomatal function, mineral nutrition, microbe interactions, fruit acidity, light response and seed development.

Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains

Science.gov (United States)

Zhang, Shuangshuang; Qi, Shuanhu; Klushin, Leonid I.; Skvortsov, Alexander M.; Yan, Dadong; Schmid, Friederike

2018-01-01

We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an attraction parameter ɛ and the other is the loop-stretch transition in a chain with one end attached to a repulsive substrate, driven by an external end-force F applied to the free end. Specifically, we compare the behavior of the respective order parameters of the transitions, i.e., the mean number of surface contacts in the case of the adsorption transition and the mean position of the chain end in the case of the loop-stretch transition. Close to the transition points, both the static behavior and the dynamic behavior of chains with different length N are very well described by a scaling ansatz with the scaling parameters (ɛ - ɛ*)Nϕ (adsorption transition) and (F - F*)Nν (loop-stretch transition), respectively, where ϕ is the crossover exponent of the adsorption transition and ν is the Flory exponent. We show that both the loop-stretch and the loop adsorption transitions provide an exceptional opportunity to construct explicit analytical expressions for the crossover functions which perfectly describe all simulation results on static properties in the finite-size scaling regime. Explicit crossover functions are based on the ansatz for the analytical form of the order parameter distributions at the respective transition points. In contrast to the close similarity in equilibrium static behavior, the dynamic relaxation at the two transitions shows qualitative differences, especially in the strongly ordered regimes. This is attributed to the fact that the surface contact dynamics in a strongly adsorbed chain is governed by local processes, whereas the end height relaxation of a strongly stretched chain involves the full spectrum of Rouse modes.

Cosmological perturbation theory using the FFTLog: formalism and connection to QFT loop integrals

Science.gov (United States)

Simonović, Marko; Baldauf, Tobias; Zaldarriaga, Matias; Carrasco, John Joseph; Kollmeier, Juna A.

2018-04-01

We present a new method for calculating loops in cosmological perturbation theory. This method is based on approximating a ΛCDM-like cosmology as a finite sum of complex power-law universes. The decomposition is naturally achieved using an FFTLog algorithm. For power-law cosmologies, all loop integrals are formally equivalent to loop integrals of massless quantum field theory. These integrals have analytic solutions in terms of generalized hypergeometric functions. We provide explicit formulae for the one-loop and the two-loop power spectrum and the one-loop bispectrum. A chief advantage of our approach is that the difficult part of the calculation is cosmology independent, need be done only once, and can be recycled for any relevant predictions. Evaluation of standard loop diagrams then boils down to a simple matrix multiplication. We demonstrate the promise of this method for applications to higher multiplicity/loop correlation functions.

Liquid Lead-Bismuth Materials Test Loop

International Nuclear Information System (INIS)

Tcharnotskaia, Valentina; Ammerman, Curtt; Darling, Timothy; King, Joe; Li, Ning; Shaw, Don; Snodgrass, Leon; Woloshun, Keith

2002-01-01

We designed and built the Liquid Lead-Bismuth Materials Test Loop (MTL) to study the materials behavior in a flow of molten lead-bismuth eutectic (LBE). In this paper we present a description of the loop with main components and their functions. Stress distribution in the piping due to sustained, occasional and expansion loads is shown. The loop is designed so that a difference of 100 deg. C can be attained between the coldest and the hottest parts at a nominal flow rate of 8.84 GPM. Liquid LBE flow can be activated by a mechanical sump pump or by natural convection. In order to maintain a self-healing protective film on the surface of the stainless steel pipe, a certain concentration of oxygen has to be maintained in the liquid metal. We developed oxygen sensors and an oxygen control system to be implemented in the loop. The loop is outfitted with a variety of instruments that are controlled from a computer based data acquisition system. Initial experiments include preconditioning the loop, filling it up with LBE, running at uniform temperature and tuning the oxygen control system. We will present some preliminary results and discuss plans for the future tests. (authors)

The FUN of identifying gene function in bacterial pathogens; insights from Salmonella functional genomics.

Science.gov (United States)

Hammarlöf, Disa L; Canals, Rocío; Hinton, Jay C D

2013-10-01

The availability of thousands of genome sequences of bacterial pathogens poses a particular challenge because each genome contains hundreds of genes of unknown function (FUN). How can we easily discover which FUN genes encode important virulence factors? One solution is to combine two different functional genomic approaches. First, transcriptomics identifies bacterial FUN genes that show differential expression during the process of mammalian infection. Second, global mutagenesis identifies individual FUN genes that the pathogen requires to cause disease. The intersection of these datasets can reveal a small set of candidate genes most likely to encode novel virulence attributes. We demonstrate this approach with the Salmonella infection model, and propose that a similar strategy could be used for other bacterial pathogens. Copyright © 2013 Elsevier Ltd. All rights reserved.

On Resumming Inflationary Perturbations beyond One-loop

DEFF Research Database (Denmark)

Riotto, Antonio; Sloth, Martin Snoager

2008-01-01

It is well known that the correlation functions of a scalar field in a quasi-de Sitter space exhibit at the loop level cumulative infra-red effects proportional to the total number of e-foldings of inflation. Using the in-in formalism, we explore the behavior of these infra-red effects in the large...... N limit of an O(N) invariant scalar field theory with quartic self-interactions. By resumming all higher-order loop diagrams non-perturbatively, we show that the connected four-point correlation function, which is a signal of non-Gaussianity, is non-perturbatively enhanced with respect to its tree-level...

A comparative approach to closed-loop computation.

Science.gov (United States)

Roth, E; Sponberg, S; Cowan, N J

2014-04-01

Neural computation is inescapably closed-loop: the nervous system processes sensory signals to shape motor output, and motor output consequently shapes sensory input. Technological advances have enabled neuroscientists to close, open, and alter feedback loops in a wide range of experimental preparations. The experimental capability of manipulating the topology-that is, how information can flow between subsystems-provides new opportunities to understand the mechanisms and computations underlying behavior. These experiments encompass a spectrum of approaches from fully open-loop, restrained preparations to the fully closed-loop character of free behavior. Control theory and system identification provide a clear computational framework for relating these experimental approaches. We describe recent progress and new directions for translating experiments at one level in this spectrum to predictions at another level. Operating across this spectrum can reveal new understanding of how low-level neural mechanisms relate to high-level function during closed-loop behavior. Copyright © 2013 Elsevier Ltd. All rights reserved.

Alternative loop rings

CERN Document Server

Goodaire, EG; Polcino Milies, C

1996-01-01

For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

Functionally enigmatic genes: a case study of the brain ignorome.

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Ashutosh K Pandey

Full Text Available What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.

Functionally enigmatic genes: a case study of the brain ignorome.

Science.gov (United States)

Pandey, Ashutosh K; Lu, Lu; Wang, Xusheng; Homayouni, Ramin; Williams, Robert W

2014-01-01

What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.

One-loop effective lagrangians after matching

Energy Technology Data Exchange (ETDEWEB)

Aguila, F. del; Santiago, J. [Universidad de Granada, Departamento de Fisica Teorica y del Cosmos and CAFPE, Granada (Spain); Kunszt, Z. [ETH Zuerich, Institute for Theoretical Physics, Zuerich (Switzerland)

2016-05-15

We discuss the limitations of the covariant derivative expansion prescription advocated to compute the one-loop Standard Model (SM) effective lagrangian when the heavy fields couple linearly to the SM. In particular, one-loop contributions resulting from the exchange of both heavy and light fields must be explicitly taken into account through matching because the proposed functional approach alone does not account for them. We review a simple case with a heavy scalar singlet of charge -1 to illustrate the argument. As two other examples where this matching is needed and this functional method gives a vanishing result, up to renormalization of the heavy sector parameters, we re-evaluate the one-loop corrections to the T-parameter due to a heavy scalar triplet with vanishing hypercharge coupling to the Brout-Englert-Higgs boson and to a heavy vector-like quark singlet of charged 2/3 mixing with the top quark, respectively. In all cases we make use of a new code for matching fundamental and effective theories in models with arbitrary heavy field additions. (orig.)

Loop-Mediated Isothermal Amplification Assay Targeting the MOMP Gene for Rapid Detection of Chlamydia psittaci Abortus Strain

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Guo-Zhen Lin, Fu-Ying Zheng, Ji-Zhang Zhou, Guang-Hua Wang, Xiao-An Cao, Xiao-Wei Gong and Chang-Qing Qiu*

2012-05-01

Full Text Available For rapid detection of the Chlamydia psittaci abortus strain, a loop-mediated isothermal amplification (LAMP assay was developed and evaluated in this study. The primers for the LAMP assay were designed on the basis of the main outer membrane protein (MOMP gene sequence of C. psittaci. Analysis showed that the assay could detect the abortus strain of C. psittaci with adequate specificity. The sensitivity of the test was the same as that of the nested-conventional PCR and higher than that of chick embryo isolation. Testing of 153 samples indicated that the LAMP assay could detect the genome of the C. psittaci abortus strain effectively in clinical samples. This assay is a useful tool for rapid diagnosis of C. psittaci infection in sheep, swine and cattle.

Baryon considered as a soliton in loop space

International Nuclear Information System (INIS)

Kazakov, V.A.; Migdal, A.A.

1981-01-01

The baryon mass for large N is expressed in QCD in terms of the collective field in loop space, which satisfies the nonlinear functional-integral equation. This collective loop field is a relativistic generalization of the self-consistent Witten field. Our approach confirms Witten's idea that a baryon is a soliton in 1/N expansion

All-loops calculation of the structure function x→0 in perturbative QCD

International Nuclear Information System (INIS)

Catani, S.

1991-01-01

We study in perturbative QCD the initial-state radiation associated to hadron processes in the semi-hard region of small x (x is the Bjorken variable). A recent analysis of the exclusive multi-gluon distributions to double (infrared and collinear) logarithmic accuracy is extended to the case of inclusive distributions, which we evaluate to single (infrared) logarithmic accuracy. Thus the resulting x→0 structure function or N→1 gluon anomalous dimension is computed to all-loops accuracy. For the inclusive distributions we are able to perform a calculation to such an accuracy by extensively using cancellations which originate from coherence of QCD radiation and the infrared regularity of real-virtual singularities. We find that the x→0 structure function satisfies the Lipatov equation. With the present study we therefore provide a new derivation of the Lipatov result in the context of hard collisions together with a fully exclusive description. We discuss the structure of the Lipatov equation in relation with the x→0 exclusive distributions previously obtained and with the Altarelli-Parisi equation valid for finite values of x. (orig.)

Proteins mediating DNA loops effectively block transcription.

Science.gov (United States)

Vörös, Zsuzsanna; Yan, Yan; Kovari, Daniel T; Finzi, Laura; Dunlap, David

2017-07-01

Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method.

Science.gov (United States)

Li, Yaohang; Rata, Ionel; Chiu, See-wing; Jakobsson, Eric

2010-07-20

Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction. We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy dominance relationship to the rest of the models. We apply the POC method to a large number of decoy sets for loops of 4- to 12-residue in length using a functional space composed of several carefully-selected scoring functions: Rosetta, DOPE, DDFIRE, OPLS-AA, and a triplet backbone dihedral potential developed in our lab. Our computational results show that the sets of Pareto-optimal decoys, which are typically composed of approximately 20% or less of the overall decoys in a set, have a good coverage of the best or near-best decoys in more than 99% of the loop targets. Compared to the individual scoring function yielding best selection accuracy in the decoy sets, the POC method yields 23%, 37%, and 64% less false positives in distinguishing the native conformation, indentifying a near-native model (RMSD Pareto optimality and fuzzy dominance, the POC method is effective in distinguishing the best loop models from the other ones within a loop model set.

One-loop matching and running with covariant derivative expansion

Science.gov (United States)

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

2018-01-01

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these "mixed" one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-known matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of "integrating out" heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.

On the One Loop Corrections to Inflation II

DEFF Research Database (Denmark)

Sloth, Martin Snoager

2006-01-01

In this paper we extend our previous treatment of the one-loop corrections to inflation. Previously we calculated the one-loop corrections to the background and the two-point correlation function of inflaton fluctuations in a specific model of chaotic inflation. We showed that the loop correction...... model of chaotic inflation with a quadratic inflationary potential. We discuss the physical interpretation of the effect in terms of the tensor-to-scalar consistency relation. Finally, we discuss the relation to the work of Weinberg on quantum contributions to cosmological correlators....

The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.

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Ana Rita Araújo

Full Text Available The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth, has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila, a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general.

Random walk loop soups and conformal loop ensembles

NARCIS (Netherlands)

van de Brug, T.; Camia, F.; Lis, M.

2016-01-01

The random walk loop soup is a Poissonian ensemble of lattice loops; it has been extensively studied because of its connections to the discrete Gaussian free field, but was originally introduced by Lawler and Trujillo Ferreras as a discrete version of the Brownian loop soup of Lawler and Werner, a

One-loop effective potential on hyperbolic manifolds

International Nuclear Information System (INIS)

Cognola, G.; Kirsten, K.; Zerbini, S.

1993-01-01

The one-loop effective potential for a scalar field defined on an ultrastatic space-time whose spatial part is a compact hyperbolic manifold is studied using ζ-function regularization for the one-loop effective action. Other possible regularizations are discussed in detail. The renormalization group equations are derived, and their connection with the conformal anomaly is pointed out. The symmetry breaking and the topological mass generation are also discussed

Three-loop corrections in a covariant effective field theory

International Nuclear Information System (INIS)

McIntire, Jeff

2008-01-01

Chiral effective field theories have been used with success in the study of nuclear structure. It is of interest to systematically improve these energy functionals (particularly that of quantum hadrodynamics) through the inclusion of many-body correlations. One possible source of improvement is the loop expansion. Using the techniques of Infrared Regularization, the short-range, local dynamics at each order in the loops is absorbed into the parameterization of the underlying effective Lagrangian. The remaining nonlocal, exchange correlations must be calculated explicitly. Given that the interactions of quantum hadrodynamics are relatively soft, the loop expansion may be manageable or even perturbative in nuclear matter. This work investigates the role played by the three-loop contributions to the loop expansion for quantum hadrodynamics

Biochemical mechanisms determine the functional compatibility of heterologous genes

DEFF Research Database (Denmark)

Porse, Andreas; Schou, Thea S.; Munck, Christian

2018-01-01

-gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts. In contrast...... factors governing the functionality and fitness of antibiotic resistance genes. These findings emphasize the importance of biochemical mechanism for heterologous gene compatibility, and suggest physiological constraints as a pivotal feature orienting the evolution of antibiotic resistance....

Loop Quantum Cosmology

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Bojowald Martin

2008-07-01

Full Text Available Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time.

Loop Quantum Cosmology

Directory of Open Access Journals (Sweden)

Bojowald Martin

2005-12-01

Full Text Available Quantum gravity is expected to be necessary in order to understand situations where classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical space-time inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding space-time is then modified. One particular realization is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. Main effects are introduced into effective classical equations which allow to avoid interpretational problems of quantum theory. They give rise to new kinds of early universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function which allows to extend space-time beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of space-time arising in loop quantum gravity and its application to cosmology sheds new light on more general issues such as time.

Taxonomic Evaluation of the Greater Horseshoe Bat Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae) in Iran Inferred from the Mitochondrial D-Loop Gene.

Science.gov (United States)

Shahabi, Saeed; Akmali, Vahid; Sharifi, Mozafar

2017-08-01

To examine the level of genetic differentiation in the sequences of the mitochondrial D-loop gene of Rhinolophus ferrumequinum, and to evaluate the current taxonomic status of this species, 50 tissue samples of greater horseshoe bats were collected in 2011-2015 from 21 different localities in northwest, northeast, west, central, and south regions of Iran. Twenty-two published D-loop sequences from Europe (Switzerland, United Kingdom, Bulgaria, and Tunisia), and Anatolia (south, west, and east Turkey) were downloaded from GenBank. Molecular genetic analyses revealed remarkable variation among populations of R. ferrumequinum. Two major clades with strong support were identified within the greater horseshoe bat. One of these clades consists of individuals of R. ferrumequinum from Iran and eastern Turkey, and is further subdivided into two subclades. A second clade includes samples from western Turkey and Europe. The two subclades from Iran and Turkey and the second clade from western Turkey and Europe represent three diagnosable categories, which most probably warrant three subspecies for the species. Thus, based on genetic differences, it is clear that two subspecific populations are found in Iran: R. f. irani (southern Iran) and R. f. proximus (northern Iran).

Exact results for ABJ Wilson loops and open-closed duality

Energy Technology Data Exchange (ETDEWEB)

Hatsuda, Yasuyuki [Département de Physique Théorique et section de Mathématiques, Université de Genève,Genève, CH-1211 (Switzerland); Okuyama, Kazumi [Department of Physics, Shinshu University,Matsumoto 390-8621 (Japan)

2016-10-24

We find new exact relations between the partition function and vacuum expectation values (VEVs) of 1/2 BPS Wilson loops in ABJ theory, which allow us to predict the large N expansions of the 1/2 BPS Wilson loops from known results of the partition function. These relations are interpreted as an open-closed duality where the closed string background is shifted by the insertion of Wilson loops due to a back-reaction. Using the connection between ABJ theory and the topological string on local ℙ{sup 1}×ℙ{sup 1}, we explicitly write down non-trivial relations between open and closed string amplitudes.

Open and Closed Loop Parametric System Identification in Compact Disk Players

DEFF Research Database (Denmark)

Vidal, Enrique Sanchez; Stoustrup, Jakob; Andersen, Palle

2001-01-01

By measuring the current through the coil of the actuators in the optical pick-up in a compact disk player, open loop parametric system identification can be performed. The parameters are identified by minimizing the least-squares loss function of the ARX model. The only parameter which cannot be...... be identified in open loop is the optical gain. This is therefore estimated in closed loop. Practical results are analyzed and show very accurate estimates of the real parameters.......By measuring the current through the coil of the actuators in the optical pick-up in a compact disk player, open loop parametric system identification can be performed. The parameters are identified by minimizing the least-squares loss function of the ARX model. The only parameter which cannot...

[Gene deletion and functional analysis of the heptyl glycosyltransferase (waaF) gene in Vibrio parahemolyticus O-antigen cluster].

Science.gov (United States)

Zhao, Feng; Meng, Songsong; Zhou, Deqing

2016-02-04

To construct heptyl glycosyltransferase gene II (waaF) gene deletion mutant of Vibrio parahaemolyticus, and explore the function of the waaF gene in Vibrio parahaemolyticus. The waaF gene deletion mutant was constructed by chitin-based transformation technology using clinical isolates, and then the growth rate, morphology and serotypes were identified. The different sources (O3, O5 and O10) waaF gene complementations were constructed through E. coli S17λpir strains conjugative transferring with Vibrio parahaemolyticus, and the function of the waaF gene was further verified by serotypes. The waaF gene deletion mutant strain was successfully constructed and it grew normally. The growth rate and morphology of mutant were similar with the wild type strains (WT), but the mutant could not occurred agglutination reaction with O antisera. The O3 and O5 sources waaF gene complementations occurred agglutination reaction with O antisera, but the O10 sources waaF gene complementations was not. The waaF gene was related with O-antigen synthesis and it was the key gene of O-antigen synthesis pathway in Vibrio parahaemolyticus. The function of different sources waaF gene were not the same.

The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli

Science.gov (United States)

Beisel, Chase L.; Storz, Gisela

2011-01-01

SUMMARY Bacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse non-preferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multi-output feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression. PMID:21292161

Methods for transient assay of gene function in floral tissues

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Pathirana Nilangani N

2007-01-01

Full Text Available Abstract Background There is considerable interest in rapid assays or screening systems for assigning gene function. However, analysis of gene function in the flowers of some species is restricted due to the difficulty of producing stably transformed transgenic plants. As a result, experimental approaches based on transient gene expression assays are frequently used. Biolistics has long been used for transient over-expression of genes of interest, but has not been exploited for gene silencing studies. Agrobacterium-infiltration has also been used, but the focus primarily has been on the transient transformation of leaf tissue. Results Two constructs, one expressing an inverted repeat of the Antirrhinum majus (Antirrhinum chalcone synthase gene (CHS and the other an inverted repeat of the Antirrhinum transcription factor gene Rosea1, were shown to effectively induce CHS and Rosea1 gene silencing, respectively, when introduced biolistically into petal tissue of Antirrhinum flowers developing in vitro. A high-throughput vector expressing the Antirrhinum CHS gene attached to an inverted repeat of the nos terminator was also shown to be effective. Silencing spread systemically to create large zones of petal tissue lacking pigmentation, with transmission of the silenced state spreading both laterally within the affected epidermal cell layer and into lower cell layers, including the epidermis of the other petal surface. Transient Agrobacterium-mediated transformation of petal tissue of tobacco and petunia flowers in situ or detached was also achieved, using expression of the reporter genes GUS and GFP to visualise transgene expression. Conclusion We demonstrate the feasibility of using biolistics-based transient RNAi, and transient transformation of petal tissue via Agrobacterium infiltration to study gene function in petals. We have also produced a vector for high throughput gene silencing studies, incorporating the option of using T-A cloning to

Stably Expressed Genes Involved in Basic Cellular Functions.

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Kejian Wang

Full Text Available Stably Expressed Genes (SEGs whose expression varies within a narrow range may be involved in core cellular processes necessary for basic functions. To identify such genes, we re-analyzed existing RNA-Seq gene expression profiles across 11 organs at 4 developmental stages (from immature to old age in both sexes of F344 rats (n = 4/group; 320 samples. Expression changes (calculated as the maximum expression / minimum expression for each gene of >19000 genes across organs, ages, and sexes ranged from 2.35 to >109-fold, with a median of 165-fold. The expression of 278 SEGs was found to vary ≤4-fold and these genes were significantly involved in protein catabolism (proteasome and ubiquitination, RNA transport, protein processing, and the spliceosome. Such stability of expression was further validated in human samples where the expression variability of the homologous human SEGs was significantly lower than that of other genes in the human genome. It was also found that the homologous human SEGs were generally less subject to non-synonymous mutation than other genes, as would be expected of stably expressed genes. We also found that knockout of SEG homologs in mouse models was more likely to cause complete preweaning lethality than non-SEG homologs, corroborating the fundamental roles played by SEGs in biological development. Such stably expressed genes and pathways across life-stages suggest that tight control of these processes is important in basic cellular functions and that perturbation by endogenous (e.g., genetics or exogenous agents (e.g., drugs, environmental factors may cause serious adverse effects.

FUNCTIONAL IMPLICATIONS OF THE CLOCK 3111T/C SINGLE-NUCLEOTIDE POLYMORPHISM

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Angela Renee Ozburn

2016-04-01

Full Text Available Circadian rhythm disruptions are prominently associated with Bipolar Disorder (BD. Circadian rhythms are regulated by the molecular clock, a family of proteins that function together in a transcriptional-translational feedback loop. The CLOCK protein is a key transcription factor of this feedback loop, and previous studies have found that manipulations of the Clock gene are sufficient to produce manic-like behavior in mice (Roybal et al., 2007. The Clock 3111T/C single-nucleotide polymorphism (SNP; rs1801260 is a genetic variation of the human Clock gene that is significantly associated with increased frequency of manic episodes in BD patients (Benedetti et al., 2003. The 3111T/C SNP is located in the 3’ untranslated region of the Clock gene. In this study, we sought to examine the functional implications of the human Clock 3111T/C SNP by transfecting a mammalian cell line (mouse embryonic fibroblasts isolated from Clock -/- knockout mice with pcDNA plasmids containing the human Clock gene with either the T or C SNP at position 3111. We then measured circadian gene expression over a 24 hour time period. We found that the Clock3111C SNP resulted in higher mRNA levels than the Clock 3111T SNP. Further, we found that Per2, a transcriptional target of CLOCK, was also more highly expressed with Clock 3111C expression, indicating the 3’UTR SNP affects the expression, function and stability of Clock mRNA.

The two-loop master integrals for qq-bar→VV

International Nuclear Information System (INIS)

Gehrmann, Thomas; Manteuffel, Andreas von; Tancredi, Lorenzo; Weihs, Erich

2014-01-01

We compute the full set of two-loop Feynman integrals appearing in massless two-loop four-point functions with two off-shell legs with the same invariant mass. These integrals allow to determine the two-loop corrections to the amplitudes for vector boson pair production at hadron colliders, qq-bar→VV, and thus to compute this process to next-to-next-to-leading order accuracy in QCD. The master integrals are derived using the method of differential equations, employing a canonical basis for the integrals. We obtain analytical results for all integrals, expressed in terms of multiple polylogarithms. We optimize our results for numerical evaluation by employing functions which are real valued for physical scattering kinematics and allow for an immediate power series expansion

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.

Science.gov (United States)

Smith, Emily M; Lajoie, Bryan R; Jain, Gaurav; Dekker, Job

2016-01-07

Three-dimensional genome structure plays an important role in gene regulation. Globally, chromosomes are organized into active and inactive compartments while, at the gene level, looping interactions connect promoters to regulatory elements. Topologically associating domains (TADs), typically several hundred kilobases in size, form an intermediate level of organization. Major questions include how TADs are formed and how they are related to looping interactions between genes and regulatory elements. Here we performed a focused 5C analysis of a 2.8 Mb chromosome 7 region surrounding CFTR in a panel of cell types. We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture. Furthermore, we find that these TAD boundaries are present irrespective of the expression and looping of genes located between them. In contrast, looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs. This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell-type-specific regulatory elements that are all located within the same TAD. Finally, we find that long-range associations between loci located in different TADs are also detected, but these display much lower interaction frequencies than looping interactions within TADs. Interestingly, interactions between TADs are also highly cell-type-specific and often involve loci clustered around TAD boundaries. These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell-type-specific long-range interactions and gene regulation. Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Automatic assignment of prokaryotic genes to functional categories using literature profiling.

Directory of Open Access Journals (Sweden)

Raul Torrieri

Full Text Available In the last years, there was an exponential increase in the number of publicly available genomes. Once finished, most genome projects lack financial support to review annotations. A few of these gene annotations are based on a combination of bioinformatics evidence, however, in most cases, annotations are based solely on sequence similarity to a previously known gene, which was most probably annotated in the same way. As a result, a large number of predicted genes remain unassigned to any functional category despite the fact that there is enough evidence in the literature to predict their function. We developed a classifier trained with term-frequency vectors automatically disclosed from text corpora of an ensemble of genes representative of each functional category of the J. Craig Venter Institute Comprehensive Microbial Resource (JCVI-CMR ontology. The classifier achieved up to 84% precision with 68% recall (for confidence≥0.4, F-measure 0.76 (recall and precision equally weighted in an independent set of 2,220 genes, from 13 bacterial species, previously classified by JCVI-CMR into unambiguous categories of its ontology. Finally, the classifier assigned (confidence≥0.7 to functional categories a total of 5,235 out of the ∼24 thousand genes previously in categories "Unknown function" or "Unclassified" for which there is literature in MEDLINE. Two biologists reviewed the literature of 100 of these genes, randomly picket, and assigned them to the same functional categories predicted by the automatic classifier. Our results confirmed the hypothesis that it is possible to confidently assign genes of a real world repository to functional categories, based exclusively on the automatic profiling of its associated literature. The LitProf--Gene Classifier web server is accessible at: www.cebio.org/litprofGC.

Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

KAUST Repository

Ariel, Federico D.; Jé gu, Teddy; Latrasse, David; Romero-Barrios, Natali; Christ, Auré lie; Benhamed, Moussa; Crespi, Martí n D.

2014-01-01

The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

KAUST Repository

Ariel, Federico D.

2014-08-01

The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

Predictability of Genetic Interactions from Functional Gene Modules

Directory of Open Access Journals (Sweden)

Jonathan H. Young

2017-02-01

Full Text Available Characterizing genetic interactions is crucial to understanding cellular and organismal response to gene-level perturbations. Such knowledge can inform the selection of candidate disease therapy targets, yet experimentally determining whether genes interact is technically nontrivial and time-consuming. High-fidelity prediction of different classes of genetic interactions in multiple organisms would substantially alleviate this experimental burden. Under the hypothesis that functionally related genes tend to share common genetic interaction partners, we evaluate a computational approach to predict genetic interactions in Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae. By leveraging knowledge of functional relationships between genes, we cross-validate predictions on known genetic interactions and observe high predictive power of multiple classes of genetic interactions in all three organisms. Additionally, our method suggests high-confidence candidate interaction pairs that can be directly experimentally tested. A web application is provided for users to query genes for predicted novel genetic interaction partners. Finally, by subsampling the known yeast genetic interaction network, we found that novel genetic interactions are predictable even when knowledge of currently known interactions is minimal.

Generalized modal analysis for closed-loop piezoelectric devices

International Nuclear Information System (INIS)

Giraud-Audine, Christophe; Giraud, Frédéric; Amberg, Michel; Lemaire-Semail, Betty

2015-01-01

Stress in a piezoelectric material can be controlled by imposing an electrical field. Thanks to feedback, this electrical field can be a function of some strain-related measurement so as to confer on the piezoelectric device a closed-loop macroscopic behaviour. In this paper we address the modelling of such a system by extending the modal decomposition methods to account for the closed loop. To do so, the boundary conditions are modified to include the electrical feedback circuit, hence allowing a closed-loop modal analysis. A case study is used to illustrate the theory and to validate it. The main advantage of the method is that design issues such as the coupling factor of the device and closed-loop stability are simultaneously captured. (paper)

Cross-organism learning method to discover new gene functionalities.

Science.gov (United States)

Domeniconi, Giacomo; Masseroli, Marco; Moro, Gianluca; Pinoli, Pietro

2016-04-01

Knowledge of gene and protein functions is paramount for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. Analyses for biomedical knowledge discovery greatly benefit from the availability of gene and protein functional feature descriptions expressed through controlled terminologies and ontologies, i.e., of gene and protein biomedical controlled annotations. In the last years, several databases of such annotations have become available; yet, these valuable annotations are incomplete, include errors and only some of them represent highly reliable human curated information. Computational techniques able to reliably predict new gene or protein annotations with an associated likelihood value are thus paramount. Here, we propose a novel cross-organisms learning approach to reliably predict new functionalities for the genes of an organism based on the known controlled annotations of the genes of another, evolutionarily related and better studied, organism. We leverage a new representation of the annotation discovery problem and a random perturbation of the available controlled annotations to allow the application of supervised algorithms to predict with good accuracy unknown gene annotations. Taking advantage of the numerous gene annotations available for a well-studied organism, our cross-organisms learning method creates and trains better prediction models, which can then be applied to predict new gene annotations of a target organism. We tested and compared our method with the equivalent single organism approach on different gene annotation datasets of five evolutionarily related organisms (Homo sapiens, Mus musculus, Bos taurus, Gallus gallus and Dictyostelium discoideum). Results show both the usefulness of the perturbation method of available annotations for better prediction model training and a great improvement of the cross-organism models with respect to the single-organism ones

Data Integration and Applications of Functional Gene Networks in Drosophila Melanogaster

Science.gov (United States)

Costello, James Christopher

2009-01-01

Understanding the function of every gene in the genome is a central goal in the biological sciences. This includes full characterization of a genes phenotypic effects, molecular interactions, the evolutionary forces that shape its function(s), and how these functions interrelate. Despite a long history and considerable effort to understand all…

Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

Directory of Open Access Journals (Sweden)

van Hijum Sacha AFT

2008-10-01

Full Text Available Abstract Background Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict function on a large scale: genes exhibiting similar expression patterns are more likely to participate in shared biological processes. Results We developed Prosecutor, an application that enables researchers to rapidly infer gene function based on available gene expression data and functional annotations. Our parameter-free functional prediction method uses a sensitive algorithm to achieve a high association rate of linking genes with unknown function to annotated genes. Furthermore, Prosecutor utilizes additional biological information such as genomic context and known regulatory mechanisms that are specific for prokaryotes. We analyzed publicly available transcriptome data sets and used literature sources to validate putative functions suggested by Prosecutor. We supply the complete results of our analysis for 11 prokaryotic organisms on a dedicated website. Conclusion The Prosecutor software and supplementary datasets available at http://www.prosecutor.nl allow researchers working on any of the analyzed organisms to quickly identify the putative functions of their genes of interest. A de novo analysis allows new organisms to be studied.

Renormalization of vacuum expectation values in spontaneously broken gauge theories: two-loop results

International Nuclear Information System (INIS)

Sperling, Marcus; Stöckinger, Dominik; Voigt, Alexander

2014-01-01

We complete the two-loop calculation of β-functions for vacuum expectation values (VEVs) in gauge theories by the missing O(g 4 )-terms. The full two-loop results are presented for generic and supersymmetric theories up to two-loop level in arbitrary R ξ -gauge. The results are obtained by means of a scalar background field, identical to our previous analysis. As a by-product, the two-loop scalar anomalous dimension for generic supersymmetric theories is presented. As an application we compute the β-functions for VEVs and tan β in the MSSM, NMSSM, and E 6 SSM

An intronic microRNA silences genes that are functionally antagonistic to its host gene.

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Barik, Sailen

2008-09-01

MicroRNAs (miRNAs) are short noncoding RNAs that down-regulate gene expression by silencing specific target mRNAs. While many miRNAs are transcribed from their own genes, nearly half map within introns of 'host' genes, the significance of which remains unclear. We report that transcriptional activation of apoptosis-associated tyrosine kinase (AATK), essential for neuronal differentiation, also generates miR-338 from an AATK gene intron that silences a family of mRNAs whose protein products are negative regulators of neuronal differentiation. We conclude that an intronic miRNA, transcribed together with the host gene mRNA, may serve the interest of its host gene by silencing a cohort of genes that are functionally antagonistic to the host gene itself.

Increased heart rate caused by atrial pacing with the closed-loop stimulation function prevented micturition syncope

Directory of Open Access Journals (Sweden)

Tatsuo Haraki, MD,PhD

2013-10-01

Full Text Available A 70-year-old man had been experiencing syncope several times a year. We implanted a DDD pacemaker with closed-loop stimulation (CLS function. When he urinated early in the morning, his increased atrial pacing rates elevated his heart rate (HR during and after micturition. After implantation of the DDD-CLS mode, he did not experience symptoms. In contrast, in the DDD-R mode, his intrinsic HR changed to atrial pacing after micturition but decreased to the basal rate within 2 min, and he experienced a sense of cold perspiration and presyncope. Increased HRs caused by atrial pacing with the CLS function were useful in the prevention of micturition syncope.

Gene-specific function prediction for non-synonymous mutations in monogenic diabetes genes.

Directory of Open Access Journals (Sweden)

Quan Li

Full Text Available The rapid progress of genomic technologies has been providing new opportunities to address the need of maturity-onset diabetes of the young (MODY molecular diagnosis. However, whether a new mutation causes MODY can be questionable. A number of in silico methods have been developed to predict functional effects of rare human mutations. The purpose of this study is to compare the performance of different bioinformatics methods in the functional prediction of nonsynonymous mutations in each MODY gene, and provides reference matrices to assist the molecular diagnosis of MODY. Our study showed that the prediction scores by different methods of the diabetes mutations were highly correlated, but were more complimentary than replacement to each other. The available in silico methods for the prediction of diabetes mutations had varied performances across different genes. Applying gene-specific thresholds defined by this study may be able to increase the performance of in silico prediction of disease-causing mutations.

Functional Potential of Bacterial Communities using Gene Context Information

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Anwesha Mohapatra

2017-12-01

Full Text Available Estimation of the functional potential of a bacterial genome can be determined by accurate annotation of its metabolic pathways. Existing homology based methods for pathway annotation fail to account for homologous genes that participate in multiple pathways, causing overestimation of gene copy number. Mere presence of constituent genes of a candidate pathway which are dispersed on a genome often results in incorrect annotation, thereby leading to erroneous gene abundance and pathway estimation. Clusters of evolutionarily conserved coregulated genes are characteristic features in bacterial genomes and their spatial arrangement in the genome is constrained by the pathway encoded by them. Thus, in order to improve the accuracy of pathway prediction, it is important to augment homology based annotation with gene organization information. In this communication, we present a methodology considering prioritization of gene context for improved pathway annotation. Extensive literature mining was performed to confirm conserved juxtaposed arrangement of gene components of various pathways. Our method was utilized to identify and analyse the functional potential of all available completely sequenced bacterial genomes. The accuracy of the predicted gene clusters and their importance in metabolic pathways will be demonstrated using a few case studies. One of such case study corresponds to butyrate production pathways in gut bacteria where it was observed that gut pathogens and commensals possess a distinct set of pathway components. In another example, we will demonstrate how our methodology improves the prediction accuracy of carbohydrate metabolic potential in human microbial communities. Applicability of our method for estimation of functional potential in bacterial communities present in diverse environments will also be illustrated.

Functional validation of GWAS gene candidates for abnormal liver function during zebrafish liver development

Directory of Open Access Journals (Sweden)

Leah Y. Liu

2013-09-01

Genome-wide association studies (GWAS have revealed numerous associations between many phenotypes and gene candidates. Frequently, however, further elucidation of gene function has not been achieved. A recent GWAS identified 69 candidate genes associated with elevated liver enzyme concentrations, which are clinical markers of liver disease. To investigate the role of these genes in liver homeostasis, we narrowed down this list to 12 genes based on zebrafish orthology, zebrafish liver expression and disease correlation. To assess the function of gene candidates during liver development, we assayed hepatic progenitors at 48 hours post fertilization (hpf and hepatocytes at 72 hpf using in situ hybridization following morpholino knockdown in zebrafish embryos. Knockdown of three genes (pnpla3, pklr and mapk10 decreased expression of hepatic progenitor cells, whereas knockdown of eight genes (pnpla3, cpn1, trib1, fads2, slc2a2, pklr, mapk10 and samm50 decreased cell-specific hepatocyte expression. We then induced liver injury in zebrafish embryos using acetaminophen exposure and observed changes in liver toxicity incidence in morphants. Prioritization of GWAS candidates and morpholino knockdown expedites the study of newly identified genes impacting liver development and represents a feasible method for initial assessment of candidate genes to instruct further mechanistic analyses. Our analysis can be extended to GWAS for additional disease-associated phenotypes.

One-loop calculations of photon splitting in relativistic quantum plasma by Green's function technique

International Nuclear Information System (INIS)

De la Incera, V.; Ferrer, E.; Shalad, A.Y.

1987-01-01

A homogeneous and isotropic plasma made up of electrons and positrons is examined. The coefficients of the covariant expansion of the three-photon vertex are calculated in the one-loop approximation of the Green's function technique, together with the probability amplitudes of various processes involving three photons that produce information on the probability of the polarization states of the incoming and outgoing photons in the splitting process. The calculation results are used to verify the consequences of all exact symmetries which must be done for the vertex tensor. The case of a charge-symmetric plasma is considered together with the special case of photon collinearity

Enhanced limbic/impaired cortical-loop connection onto the hippocampus of NHE rats: Application of resting-state functional connectivity in a preclinical ADHD model.

Science.gov (United States)

Zoratto, F; Palombelli, G M; Ruocco, L A; Carboni, E; Laviola, G; Sadile, A G; Adriani, W; Canese, R

2017-08-30

Due to a hyperfunctioning mesocorticolimbic system, Naples-High-Excitability (NHE) rats have been proposed to model for the meso-cortical variant of attention deficit/hyperactivity disorder (ADHD). Compared to Naples Random-Bred (NRB) controls, NHE rats show hyperactivity, impaired non-selective attention (Aspide et al., 1998), and impaired selective spatial attention (Ruocco et al., 2009a, 2014). Alteration in limbic functions has been proposed; however, resulting unbalance among forebrain areas has not been assessed yet. By resting-state functional Magnetic-Resonance Imaging (fMRI) in vivo, we investigated the connectivity of neuronal networks belonging to limbic vs. cortical loops in NHE and NRB rats (n=10 each). Notably, resting-state fMRI was applied using a multi-slice sagittal, gradient-echo sequence. Voxel-wise connectivity maps at rest, based on temporal correlation among fMRI time-series, were computed by seeding the hippocampus (Hip), nucleus accumbens (NAcc), dorsal striatum (dStr), amygdala (Amy) and dorsal/medial prefrontal cortex (PFC), both hemispheres. To summarize patterns of altered connection, clearly directional connectivity was evident within the cortical loop: bilaterally and specularly, from orbital and dorsal PFCs through dStr and hence towards Hip. Such network communication was reduced in NHE rats (also, with less mesencephalic/pontine innervation). Conversely, enhanced network activity emerged within the limbic loop of NHE rats: from left PFC, both through the NAcc and directly, to the Hip (all of which received greater ventral tegmental innervation, likely dopamine). Together with tuned-down cortical loop, this potentiated limbic loop may serve a major role in controlling ADHD-like behavioral symptoms in NHE rats. Copyright © 2017 Elsevier B.V. All rights reserved.

Contrasting HIV phylogenetic relationships and V3 loop protein similarities

Energy Technology Data Exchange (ETDEWEB)

Korber, B. (Los Alamos National Lab., NM (United States) Santa Fe Inst., NM (United States)); Myers, G. (Los Alamos National Lab., NM (United States))

1992-01-01

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

Contrasting HIV phylogenetic relationships and V3 loop protein similarities

Energy Technology Data Exchange (ETDEWEB)

Korber, B. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Myers, G. [Los Alamos National Lab., NM (United States)

1992-12-31

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

Principles of agonist recognition in Cys-loop receptors

Directory of Open Access Journals (Sweden)

Timothy eLynagh

2014-04-01

Full Text Available Cys-loop receptors are ligand-gated ion channels that are activated by a structurally diverse array of neurotransmitters, including acetylcholine, serotonin, glycine and GABA. After the term chemoreceptor emerged over 100 years ago, there was some wait until affinity labeling, molecular cloning, functional studies and X-ray crystallography experiments identified the extracellular interface of adjacent subunits as the principal site of agonist binding. The question of how subtle differences at and around agonist-binding sites of different Cys-loop receptors can accommodate transmitters as chemically diverse as glycine and serotonin has been subject to intense research over the last three decades. This review outlines the functional diversity and current structural understanding of agonist-binding sites, including those of invertebrate Cys-loop receptors. Together, this provides a framework to understand the atomic determinants involved in how these valuable therapeutic targets recognize and bind their ligands.

A Resource of Quantitative Functional Annotation for Homo sapiens Genes.

Science.gov (United States)

Taşan, Murat; Drabkin, Harold J; Beaver, John E; Chua, Hon Nian; Dunham, Julie; Tian, Weidong; Blake, Judith A; Roth, Frederick P

2012-02-01

The body of human genomic and proteomic evidence continues to grow at ever-increasing rates, while annotation efforts struggle to keep pace. A surprisingly small fraction of human genes have clear, documented associations with specific functions, and new functions continue to be found for characterized genes. Here we assembled an integrated collection of diverse genomic and proteomic data for 21,341 human genes and make quantitative associations of each to 4333 Gene Ontology terms. We combined guilt-by-profiling and guilt-by-association approaches to exploit features unique to the data types. Performance was evaluated by cross-validation, prospective validation, and by manual evaluation with the biological literature. Functional-linkage networks were also constructed, and their utility was demonstrated by identifying candidate genes related to a glioma FLN using a seed network from genome-wide association studies. Our annotations are presented-alongside existing validated annotations-in a publicly accessible and searchable web interface.

Electron-positron annihilation into hadrons at the higher-loop levels

Energy Technology Data Exchange (ETDEWEB)

Nesterenko, A.V. [Joint Institute for Nuclear Research, Bogoliubov Laboratory of Theoretical Physics, Dubna (Russian Federation)

2017-12-15

The strong corrections to the R-ratio of electron-positron annihilation into hadrons are studied at the higher-loop levels. Specifically, the derivation of a general form of the commonly employed approximate expression for the R-ratio (which constitutes its truncated re-expansion at high energies) is delineated, the appearance of the pertinent π{sup 2}-terms is expounded, and their basic features are examined. It is demonstrated that the validity range of such approximation is strictly limited to √(s)/Λ > exp(π/2) ≅ 4.81 and that it converges rather slowly when the energy scale approaches this value. The spectral function required for the proper calculation of the R-ratio is explicitly derived and its properties at the higher-loop levels are studied. The developed method of calculation of the spectral function enables one to obtain the explicit expression for the latter at an arbitrary loop level. By making use of the derived spectral function the proper expression for the R-ratio is calculated up to the five-loop level and its properties are examined. It is shown that the loop convergence of the proper expression for the R-ratio is better than that of its commonly employed approximation. The impact of the omitted higher-order π{sup 2}-terms on the latter is also discussed. (orig.)

Very high order lattice perturbation theory for Wilson loops

International Nuclear Information System (INIS)

Horsley, R.

2010-10-01

We calculate perturbativeWilson loops of various sizes up to loop order n=20 at different lattice sizes for pure plaquette and tree-level improved Symanzik gauge theories using the technique of Numerical Stochastic Perturbation Theory. This allows us to investigate the behavior of the perturbative series at high orders. We observe differences in the behavior of perturbative coefficients as a function of the loop order. Up to n=20 we do not see evidence for the often assumed factorial growth of the coefficients. Based on the observed behavior we sum this series in a model with hypergeometric functions. Alternatively we estimate the series in boosted perturbation theory. Subtracting the estimated perturbative series for the average plaquette from the non-perturbative Monte Carlo result we estimate the gluon condensate. (orig.)

Human ribonuclease H1 resolves R-loops and thereby enables progression of the DNA replication fork.

Science.gov (United States)

Parajuli, Shankar; Teasley, Daniel C; Murali, Bhavna; Jackson, Jessica; Vindigni, Alessandro; Stewart, Sheila A

2017-09-15

Faithful DNA replication is essential for genome stability. To ensure accurate replication, numerous complex and redundant replication and repair mechanisms function in tandem with the core replication proteins to ensure DNA replication continues even when replication challenges are present that could impede progression of the replication fork. A unique topological challenge to the replication machinery is posed by RNA-DNA hybrids, commonly referred to as R-loops. Although R-loops play important roles in gene expression and recombination at immunoglobulin sites, their persistence is thought to interfere with DNA replication by slowing or impeding replication fork progression. Therefore, it is of interest to identify DNA-associated enzymes that help resolve replication-impeding R-loops. Here, using DNA fiber analysis, we demonstrate that human ribonuclease H1 (RNH1) plays an important role in replication fork movement in the mammalian nucleus by resolving R-loops. We found that RNH1 depletion results in accumulation of RNA-DNA hybrids, slowing of replication forks, and increased DNA damage. Our data uncovered a role for RNH1 in global DNA replication in the mammalian nucleus. Because accumulation of RNA-DNA hybrids is linked to various human cancers and neurodegenerative disorders, our study raises the possibility that replication fork progression might be impeded, adding to increased genomic instability and contributing to disease. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology.

Science.gov (United States)

Hu, Yang; Zhou, Wenyang; Ren, Jun; Dong, Lixiang; Wang, Yadong; Jin, Shuilin; Cheng, Liang

2016-01-01

Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol. After annotating all the records about human genes of GeneRIFs, 288,869 associations between 13,148 mRNAs and 7,182 terms, 9,496 associations between 948 microRNAs and 533 terms, and 901 associations between 139 long noncoding RNAs (lncRNAs) and 297 terms were obtained as a comprehensive annotation resource of human genome. High consistency of term frequency of individual gene (Pearson correlation = 0.6401, p = 2.2e - 16) and gene frequency of individual term (Pearson correlation = 0.1298, p = 3.686e - 14) in GeneRIFs and GOA shows our annotation resource is very reliable.

Non-commutative flux representation for loop quantum gravity

Science.gov (United States)

Baratin, A.; Dittrich, B.; Oriti, D.; Tambornino, J.

2011-09-01

The Hilbert space of loop quantum gravity is usually described in terms of cylindrical functionals of the gauge connection, the electric fluxes acting as non-commuting derivation operators. It has long been believed that this non-commutativity prevents a dual flux (or triad) representation of loop quantum gravity to exist. We show here, instead, that such a representation can be explicitly defined, by means of a non-commutative Fourier transform defined on the loop gravity state space. In this dual representation, flux operators act by sstarf-multiplication and holonomy operators act by translation. We describe the gauge invariant dual states and discuss their geometrical meaning. Finally, we apply the construction to the simpler case of a U(1) gauge group and compare the resulting flux representation with the triad representation used in loop quantum cosmology.

Loop Quantum Cosmology.

Science.gov (United States)

Bojowald, Martin

2008-01-01

Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time. Supplementary material is available for this article at 10.12942/lrr-2008-4.

Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination.

Science.gov (United States)

Jie, Shiqi; Li, Mingming; Gan, Min; Zhu, Jianyu; Yin, Huaqun; Liu, Xueduan

2016-08-08

Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. A total of 25595 functional genes involved in different biogeochemical processes have been detected in three sites, and different diversities and structures of microbial functional genes were observed. The analysis of gene overlapping, unique genes, and various diversity indices indicated a significant correlation between the level of heavy metal contamination and the functional diversity. Plentiful resistant genes related to various metal were detected, such as copper, arsenic, chromium and mercury. The results indicated a significantly higher abundance of genes involved in metal resistance including sulfate reduction genes (dsr) in studied site with most serious heavy metal contamination, such as cueo, mer, metc, merb, tehb and terc gene. With regard to the relationship between the environmental variables and microbial functional structure, S, Cu, Cd, Hg and Cr were the dominating factor shaping the microbial distribution pattern in three sites. This study suggests that high level of heavy metal contamination resulted in higher functional diversity and the abundance of metal resistant genes. These variation therefore significantly contribute to the resistance, resilience and stability of the microbial community subjected to the gradient of heavy metals contaminant in Xiangjiang River.

Progress in design and development of series liquid lithium-lead expeirmental loops in China

International Nuclear Information System (INIS)

Wu Yican; Huang Qunying; Zhu Zhiqiang; Gao Sheng; Song Yong; Li Chunjing; Peng Lei; Liu Shaojun; Wu qingsheng; Liu Songlin; Chen Hongli; Bai Yunqing; Jin Ming; Lv Ruojun; Wang Weihua; Guo Zhihui; Chen Yaping; Ling Xinzhen; Zhang Maolian; Wang Yongliang; Wu Zhaoyang; Wang Hongyan

2009-01-01

Liquid LiPb (lithium-lead) experimental loops are the important platforms to investigate the key technologies of liquid LiPb breeder blankets for fusion reactors. Based on the development strategy for liquid LiPb breeder blankets, the technologies development of liquid LiPb experimental loops have been explored by the FDS Team for years, and a series of LiPb experimental loops named DRAGON have been designed and developed, which have independence intellectual property and multi-functional parameters. In this paper, the development route suggestion of Chinese LiPb experimental loops was elaborated, and some information for the senes experimental loops were introduced, such as the design principles, structural features, functions and related experimental researches, etc. (authors)

FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets.

Science.gov (United States)

Tiys, Evgeny S; Ivanisenko, Timofey V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2018-02-09

Estimation of functional connectivity in gene sets derived from genome-wide or other biological experiments is one of the essential tasks of bioinformatics. A promising approach for solving this problem is to compare gene networks built using experimental gene sets with random networks. One of the resources that make such an analysis possible is CrossTalkZ, which uses the FunCoup database. However, existing methods, including CrossTalkZ, do not take into account individual types of interactions, such as protein/protein interactions, expression regulation, transport regulation, catalytic reactions, etc., but rather work with generalized types characterizing the existence of any connection between network members. We developed the online tool FunGeneNet, which utilizes the ANDSystem and STRING to reconstruct gene networks using experimental gene sets and to estimate their difference from random networks. To compare the reconstructed networks with random ones, the node permutation algorithm implemented in CrossTalkZ was taken as a basis. To study the FunGeneNet applicability, the functional connectivity analysis of networks constructed for gene sets involved in the Gene Ontology biological processes was conducted. We showed that the method sensitivity exceeds 0.8 at a specificity of 0.95. We found that the significance level of the difference between gene networks of biological processes and random networks is determined by the type of connections considered between objects. At the same time, the highest reliability is achieved for the generalized form of connections that takes into account all the individual types of connections. By taking examples of the thyroid cancer networks and the apoptosis network, it is demonstrated that key participants in these processes are involved in the interactions of those types by which these networks differ from random ones. FunGeneNet is a web tool aimed at proving the functionality of networks in a wide range of sizes of

Small, synthetic, GC-rich mRNA stem-loop modules 5' proximal to the AUG start-codon predictably tune gene expression in yeast.

Science.gov (United States)

Lamping, Erwin; Niimi, Masakazu; Cannon, Richard D

2013-07-29

A large range of genetic tools has been developed for the optimal design and regulation of complex metabolic pathways in bacteria. However, fewer tools exist in yeast that can precisely tune the expression of individual enzymes in novel metabolic pathways suitable for industrial-scale production of non-natural compounds. Tuning expression levels is critical for reducing the metabolic burden of over-expressed proteins, the accumulation of toxic intermediates, and for redirecting metabolic flux from native pathways involving essential enzymes without negatively affecting the viability of the host. We have developed a yeast membrane protein hyper-expression system with critical advantages over conventional, plasmid-based, expression systems. However, expression levels are sometimes so high that they adversely affect protein targeting/folding or the growth and/or phenotype of the host. Here we describe the use of small synthetic mRNA control modules that allowed us to predictably tune protein expression levels to any desired level. Down-regulation of expression was achieved by engineering small GC-rich mRNA stem-loops into the 5' UTR that inhibited translation initiation of the yeast ribosomal 43S preinitiation complex (PIC). Exploiting the fact that the yeast 43S PIC has great difficulty scanning through GC-rich mRNA stem-loops, we created yeast strains containing 17 different RNA stem-loop modules in the 5' UTR that expressed varying amounts of the fungal multidrug efflux pump reporter Cdr1p from Candida albicans. Increasing the length of mRNA stem-loops (that contained only GC-pairs) near the AUG start-codon led to a surprisingly large decrease in Cdr1p expression; ~2.7-fold for every additional GC-pair added to the stem, while the mRNA levels remained largely unaffected. An mRNA stem-loop of seven GC-pairs (∆G = -15.8 kcal/mol) reduced Cdr1p expression levels by >99%, and even the smallest possible stem-loop of only three GC-pairs (∆G = -4.4 kcal/mol) inhibited

Two-loop hard-thermal-loop thermodynamics with quarks

International Nuclear Information System (INIS)

Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

2004-01-01

We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for N f =2 and with exact numerical results obtained in the large-N f limit

Multi-loop positivity of the planar N=4 SYM six-point amplitude

Energy Technology Data Exchange (ETDEWEB)

Dixon, Lance J. [SLAC National Accelerator Laboratory,Stanford University, Stanford, CA 94309 (United States); Hippel, Matt von [Perimeter Institute for Theoretical Physics,Waterloo, Ontario N2L 2Y5 (Canada); McLeod, Andrew J. [SLAC National Accelerator Laboratory,Stanford University, Stanford, CA 94309 (United States); Trnka, Jaroslav [Center for Quantum Mathematics and Physics (QMAP),Department of Physics, University of California, Davis, CA 95616 (United States)

2017-02-22

We study the six-point NMHV ratio function in planar N=4 SYM theory in the context of positive geometry. The Amplituhedron construction of the integrand for the amplitudes provides a kinematical region in which the integrand was observed to be positive. It is natural to conjecture that this property survives integration, i.e. that the final result for the ratio function is also positive in this region. Establishing such a result would imply that preserving positivity is a surprising property of the Minkowski contour of integration and it might indicate some deeper underlying structure. We find that the ratio function is positive everywhere we have tested it, including analytic results for special kinematical regions at one and two loops, as well as robust numerical evidence through five loops. There is also evidence for not just positivity, but monotonicity in a “radial” direction. We also investigate positivity of the MHV six-gluon amplitude. While the remainder function ceases to be positive at four loops, the BDS-like normalized MHV amplitude appears to be positive through five loops.

A self-adaptive genetic algorithm to estimate JA model parameters considering minor loops

Energy Technology Data Exchange (ETDEWEB)

Lu, Hai-liang; Wen, Xi-shan; Lan, Lei; An, Yun-zhu; Li, Xiao-ping

2015-01-15

A self-adaptive genetic algorithm for estimating Jiles–Atherton (JA) magnetic hysteresis model parameters is presented. The fitness function is established based on the distances between equidistant key points of normalized hysteresis loops. Linearity function and logarithm function are both adopted to code the five parameters of JA model. Roulette wheel selection is used and the selection pressure is adjusted adaptively by deducting a proportional which depends on current generation common value. The Crossover operator is established by combining arithmetic crossover and multipoint crossover. Nonuniform mutation is improved by adjusting the mutation ratio adaptively. The algorithm is used to estimate the parameters of one kind of silicon-steel sheet’s hysteresis loops, and the results are in good agreement with published data. - Highlights: • We present a method to find JA parameters for both major and minor loops. • Fitness function is based on distances between key points of normalized loops. • The selection pressure is adjusted adaptively based on generations.

A self-adaptive genetic algorithm to estimate JA model parameters considering minor loops

International Nuclear Information System (INIS)

Lu, Hai-liang; Wen, Xi-shan; Lan, Lei; An, Yun-zhu; Li, Xiao-ping

2015-01-01

A self-adaptive genetic algorithm for estimating Jiles–Atherton (JA) magnetic hysteresis model parameters is presented. The fitness function is established based on the distances between equidistant key points of normalized hysteresis loops. Linearity function and logarithm function are both adopted to code the five parameters of JA model. Roulette wheel selection is used and the selection pressure is adjusted adaptively by deducting a proportional which depends on current generation common value. The Crossover operator is established by combining arithmetic crossover and multipoint crossover. Nonuniform mutation is improved by adjusting the mutation ratio adaptively. The algorithm is used to estimate the parameters of one kind of silicon-steel sheet’s hysteresis loops, and the results are in good agreement with published data. - Highlights: • We present a method to find JA parameters for both major and minor loops. • Fitness function is based on distances between key points of normalized loops. • The selection pressure is adjusted adaptively based on generations

LoopIng: a template-based tool for predicting the structure of protein loops.

KAUST Repository

Messih, Mario Abdel; Lepore, Rosalba; Tramontano, Anna

2015-01-01

) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has

Switch loop flexibility affects substrate transport of the AcrB efflux pump

International Nuclear Information System (INIS)

Muller, Reinke T.; Travers, Timothy; Cha, Hi-jea; Phillips, Joshua L.

2017-01-01

The functionally important switch-loop of the trimeric multidrug transporter AcrB separates the access and deep drug binding pockets in every protomer. This loop, comprising 11 amino acid residues, has been shown to be crucial for substrate transport, as drugs have to travel past the loop to reach the deep binding pocket and from there are transported outside the cell via the connected AcrA and TolC channels. It contains four symmetrically arranged glycine residues suggesting that flexibility is a key feature for pump activity. Upon combinatorial substitution of these glycine residues to proline, functional and structural asymmetry was observed. Proline substitutions on the PC1 proximal side completely abolished transport and reduced backbone flexibility of the switch loop, which adopted a conformation restricting the pathway towards the deep binding pocket. Here, two phenylalanine residues located adjacent to the substitution sensitive glycine residues play a role in blocking the pathway upon rigidification of the loop, since the removal of the phenyl rings from the rigid loop restores drug transport activity.

A Statistical Model of Current Loops and Magnetic Monopoles

International Nuclear Information System (INIS)

Ayyer, Arvind

2015-01-01

We formulate a natural model of loops and isolated vertices for arbitrary planar graphs, which we call the monopole-dimer model. We show that the partition function of this model can be expressed as a determinant. We then extend the method of Kasteleyn and Temperley-Fisher to calculate the partition function exactly in the case of rectangular grids. This partition function turns out to be a square of a polynomial with positive integer coefficients when the grid lengths are even. Finally, we analyse this formula in the infinite volume limit and show that the local monopole density, free energy and entropy can be expressed in terms of well-known elliptic functions. Our technique is a novel determinantal formula for the partition function of a model of isolated vertices and loops for arbitrary graphs

Genome-wide identification, classification, and functional analysis of the basic helix-loop-helix transcription factors in the cattle, Bos Taurus.

Science.gov (United States)

Li, Fengmei; Liu, Wuyi

2017-06-01

The basic helix-loop-helix (bHLH) transcription factors (TFs) form a huge superfamily and play crucial roles in many essential developmental, genetic, and physiological-biochemical processes of eukaryotes. In total, 109 putative bHLH TFs were identified and categorized successfully in the genomic databases of cattle, Bos Taurus, after removing redundant sequences and merging genetic isoforms. Through phylogenetic analyses, 105 proteins among these bHLH TFs were classified into 44 families with 46, 25, 14, 3, 13, and 4 members in the high-order groups A, B, C, D, E, and F, respectively. The remaining 4 bHLH proteins were sorted out as 'orphans.' Next, these 109 putative bHLH proteins identified were further characterized as significantly enriched in 524 significant Gene Ontology (GO) annotations (corrected P value ≤ 0.05) and 21 significantly enriched pathways (corrected P value ≤ 0.05) that had been mapped by the web server KOBAS 2.0. Furthermore, 95 bHLH proteins were further screened and analyzed together with two uncharacterized proteins in the STRING online database to reconstruct the protein-protein interaction network of cattle bHLH TFs. Ultimately, 89 bHLH proteins were fully mapped in a network with 67 biological process, 13 molecular functions, 5 KEGG pathways, 12 PFAM protein domains, and 25 INTERPRO classified protein domains and features. These results provide much useful information and a good reference for further functional investigations and updated researches on cattle bHLH TFs.

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.

Science.gov (United States)

Wang, Jun; Tao, Feng; Marowsky, Nicholas C; Fan, Chuanzhu

2016-09-01

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. © 2016 American Society of Plant Biologists. All rights reserved.

One-loop regularization of the Polyakov string functional

International Nuclear Information System (INIS)

Cohen, E.; Kluberg-Stern, H.; Peschanski, R.

1989-01-01

The divergences of the vacuum amplitude for the bosonic Polyakov string are studied at the one-loop level in a modular invariant regularization scheme, characterized by a dimensional cutoff analogous to proper time. As a result, the singular behaviour in the cutoff is not uniform in the range of the modulus variable and this yields a control on the singularities induced by the tachyon and the dilaton. The divergences are those of a sigma model, but the coefficients of the sigma-model counter-terms are different for the sphere and the flat torus. (orig.)

Conformal Behavior at Four Loops and Scheme (In)Dependence

DEFF Research Database (Denmark)

Ryttov, Thomas

2014-01-01

We search for infrared zeros of the beta function and evaluate the anomalous dimension of the mass at the associated fixed point for asymptotically free vector-like fermionic gauge theories with gauge group SU(N). The fixed points of the beta function are studied at the two, three and four loop l...... by the minimum and maximum value respectively over all three schemes and at three and four loops. Our analysis suggests that the former two theories lie in the conformal window while the latter belongs to the chirally broken phase....

IGF-I Gene Therapy in Aging Rats Modulates Hippocampal Genes Relevant to Memory Function.

Science.gov (United States)

Pardo, Joaquín; Abba, Martin C; Lacunza, Ezequiel; Ogundele, Olalekan M; Paiva, Isabel; Morel, Gustavo R; Outeiro, Tiago F; Goya, Rodolfo G

2018-03-14

In rats, learning and memory performance decline during normal aging, which makes this rodent species a suitable model to evaluate therapeutic strategies. In aging rats, insulin-like growth factor-I (IGF-I), is known to significantly improve spatial memory accuracy as compared to control counterparts. A constellation of gene expression changes underlie the hippocampal phenotype of aging but no studies on the effects of IGF-I on the hippocampal transcriptome of old rodents have been documented. Here, we assessed the effects of IGF-I gene therapy on spatial memory performance in old female rats and compared them with changes in the hippocampal transcriptome. In the Barnes maze test, experimental rats showed a significantly higher exploratory frequency of the goal hole than controls. Hippocampal RNA-sequencing showed that 219 genes are differentially expressed in 28-month-old rats intracerebroventricularly injected with an adenovector expressing rat IGF-I as compared with placebo adenovector-injected counterparts. From the differentially expressed genes, 81 were down and 138 upregulated. From those genes, a list of functionally relevant genes, concerning hippocampal IGF-I expression, synaptic plasticity as well as neuronal function was identified. Our results provide an initial glimpse at the molecular mechanisms underlying the neuroprotective actions of IGF-I in the aging brain.

Statistical indicators of collective behavior and functional clusters in gene networks of yeast

Science.gov (United States)

Živković, J.; Tadić, B.; Wick, N.; Thurner, S.

2006-03-01

We analyze gene expression time-series data of yeast (S. cerevisiae) measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene interaction networks based on correlation coefficients and study the formation of the corresponding giant components and minimum spanning trees. By coloring genes according to their cell function we find functional clusters in the correlation networks and functional branches in the associated trees. Our results suggest that a percolation point of functional clusters can be identified on these gene expression correlation networks.

Hox gene function and interaction in the milkweed bug Oncopeltus fasciatus (Hemiptera).

Science.gov (United States)

Angelini, David R; Liu, Paul Z; Hughes, Cynthia L; Kaufman, Thomas C

2005-11-15

Studies in genetic model organisms such as Drosophila have demonstrated that the homeotic complex (Hox) genes impart segmental identity during embryogenesis. Comparative studies in a wide range of other insect taxa have shown that the Hox genes are expressed in largely conserved domains along the anterior-posterior body axis, but whether they are performing the same functions in different insects is an open question. Most of the Hox genes have been studied functionally in only a few holometabolous insects that undergo metamorphosis. Thus, it is unclear how the Hox genes are functioning in the majority of direct-developing insects and other arthropods. To address this question, we used a combination of RNAi and in situ hybridization to reveal the expression, functions, and regulatory interactions of the Hox genes in the milkweed bug Oncopeltus fasciatus. Our results reveal many similarities and some interesting differences compared to Drosophila. We find that the gene Antennapedia is required for the identity of all three thoracic segments, while Ultrabithorax, abdominal-A and Abdominal-B cooperate to pattern the abdomen. The three abdominal genes exhibit posterior prevalence like in Drosophila, but apparently via some post-transcriptional mechanism. The functions of the head genes proboscipedia, Deformed, and Sex combs reduced were shown previously, and here we find that the complex temporal expression of pb in the labium is like that of other insects, but its regulatory relationship with Scr is unique. Overall, our data reveal that the evolution of insect Hox genes has included many small changes within general conservation of expression and function, and that the milkweed bug provides a useful model for understanding the roles of Hox genes in a direct-developing insect.

A theory of loop formation and elimination by spike timing-dependent plasticity

Directory of Open Access Journals (Sweden)

James Kozloski

2010-03-01

Full Text Available We show that the local Spike Timing-Dependent Plasticity (STDP rule has the effect of regulating the trans-synaptic weights of loops of any length within a simulated network of neurons. We show that depending on STDP's polarity, functional loops are formed or eliminated in networks driven to normal spiking conditions by random, partially correlated inputs, where functional loops comprise synaptic weights that exceed a non-zero threshold. We further prove that STDP is a form of loop-regulating plasticity for the case of a linear network driven by noise. Thus a notable local synaptic learning rule makes a specific prediction about synapses in the brain in which standard STDP is present: that under normal spiking conditions, they should participate in predominantly feed-forward connections at all scales. Our model implies that any deviations from this prediction would require a substantial modification to the hypothesized role for standard STDP. Given its widespread occurrence in the brain, we predict that STDP could also regulate long range functional loops among individual neurons across all brain scales, up to, and including, the scale of global brain network topology.

Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer

Directory of Open Access Journals (Sweden)

Koen M.A. Dreijerink

2017-03-01

Full Text Available While the multiple endocrine neoplasia type 1 (MEN1 gene functions as a tumor suppressor in a variety of cancer types, we explored its oncogenic role in breast tumorigenesis. The MEN1 gene product menin is involved in H3K4 trimethylation and co-activates transcription. We integrated ChIP-seq and RNA-seq data to identify menin target genes. Our analysis revealed that menin-dependent target gene promoters display looping to distal enhancers that are bound by menin, FOXA1 and GATA3. In this fashion, MEN1 co-regulates a proliferative breast cancer-specific gene expression program in ER+ cells. In primary mammary cells, MEN1 exerts an anti-proliferative function by regulating a distinct expression signature. Our findings clarify the cell-type-specific functions of MEN1 and inform the development of menin-directed treatments for breast cancer.

Protein functional links in Trypanosoma brucei, identified by gene fusion analysis

Directory of Open Access Journals (Sweden)

Trimpalis Philip

2011-07-01

Full Text Available Abstract Background Domain or gene fusion analysis is a bioinformatics method for detecting gene fusions in one organism by comparing its genome to that of other organisms. The occurrence of gene fusions suggests that the two original genes that participated in the fusion are functionally linked, i.e. their gene products interact either as part of a multi-subunit protein complex, or in a metabolic pathway. Gene fusion analysis has been used to identify protein functional links in prokaryotes as well as in eukaryotic model organisms, such as yeast and Drosophila. Results In this study we have extended this approach to include a number of recently sequenced protists, four of which are pathogenic, to identify fusion linked proteins in Trypanosoma brucei, the causative agent of African sleeping sickness. We have also examined the evolution of the gene fusion events identified, to determine whether they can be attributed to fusion or fission, by looking at the conservation of the fused genes and of the individual component genes across the major eukaryotic and prokaryotic lineages. We find relatively limited occurrence of gene fusions/fissions within the protist lineages examined. Our results point to two trypanosome-specific gene fissions, which have recently been experimentally confirmed, one fusion involving proteins involved in the same metabolic pathway, as well as two novel putative functional links between fusion-linked protein pairs. Conclusions This is the first study of protein functional links in T. brucei identified by gene fusion analysis. We have used strict thresholds and only discuss results which are highly likely to be genuine and which either have already been or can be experimentally verified. We discuss the possible impact of the identification of these novel putative protein-protein interactions, to the development of new trypanosome therapeutic drugs.

Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks.

Science.gov (United States)

Zhou, Xuezhong; Liu, Baoyan; Wu, Zhaohui; Feng, Yi

2007-10-01

The amount of biomedical data in different disciplines is growing at an exponential rate. Integrating these significant knowledge sources to generate novel hypotheses for systems biology research is difficult. Traditional Chinese medicine (TCM) is a completely different discipline, and is a complementary knowledge system to modern biomedical science. This paper uses a significant TCM bibliographic literature database in China, together with MEDLINE, to help discover novel gene functional knowledge. We present an integrative mining approach to uncover the functional gene relationships from MEDLINE and TCM bibliographic literature. This paper introduces TCM literature (about 50,000 records) as one knowledge source for constructing literature-based gene networks. We use the TCM diagnosis, TCM syndrome, to automatically congregate the related genes. The syndrome-gene relationships are discovered based on the syndrome-disease relationships extracted from TCM literature and the disease-gene relationships in MEDLINE. Based on the bubble-bootstrapping and relation weight computing methods, we have developed a prototype system called MeDisco/3S, which has name entity and relation extraction, and online analytical processing (OLAP) capabilities, to perform the integrative mining process. We have got about 200,000 syndrome-gene relations, which could help generate syndrome-based gene networks, and help analyze the functional knowledge of genes from syndrome perspective. We take the gene network of Kidney-Yang Deficiency syndrome (KYD syndrome) and the functional analysis of some genes, such as CRH (corticotropin releasing hormone), PTH (parathyroid hormone), PRL (prolactin), BRCA1 (breast cancer 1, early onset) and BRCA2 (breast cancer 2, early onset), to demonstrate the preliminary results. The underlying hypothesis is that the related genes of the same syndrome will have some biological functional relationships, and will constitute a functional network. This paper presents

Drosha regulates gene expression independently of RNA cleavage function

DEFF Research Database (Denmark)

Gromak, Natalia; Dienstbier, Martin; Macias, Sara

2013-01-01

Drosha is the main RNase III-like enzyme involved in the process of microRNA (miRNA) biogenesis in the nucleus. Using whole-genome ChIP-on-chip analysis, we demonstrate that, in addition to miRNA sequences, Drosha specifically binds promoter-proximal regions of many human genes in a transcription......-dependent manner. This binding is not associated with miRNA production or RNA cleavage. Drosha knockdown in HeLa cells downregulated nascent gene transcription, resulting in a reduction of polyadenylated mRNA produced from these gene regions. Furthermore, we show that this function of Drosha is dependent on its N......-terminal protein-interaction domain, which associates with the RNA-binding protein CBP80 and RNA Polymerase II. Consequently, we uncover a previously unsuspected RNA cleavage-independent function of Drosha in the regulation of human gene expression....

Supersymmetric Regularization Two-Loop QCD Amplitudes and Coupling Shifts

Energy Technology Data Exchange (ETDEWEB)

Dixon, Lance

2002-03-08

We present a definition of the four-dimensional helicity (FDH) regularization scheme valid for two or more loops. This scheme was previously defined and utilized at one loop. It amounts to a variation on the standard 't Hooft-Veltman scheme and is designed to be compatible with the use of helicity states for ''observed'' particles. It is similar to dimensional reduction in that it maintains an equal number of bosonic and fermionic states, as required for preserving supersymmetry. Supersymmetry Ward identities relate different helicity amplitudes in supersymmetric theories. As a check that the FDH scheme preserves supersymmetry, at least through two loops, we explicitly verify a number of these identities for gluon-gluon scattering (gg {yields} gg) in supersymmetric QCD. These results also cross-check recent non-trivial two-loop calculations in ordinary QCD. Finally, we compute the two-loop shift between the FDH coupling and the standard {bar M}{bar S} coupling, {alpha}{sub s}. The FDH shift is identical to the one for dimensional reduction. The two-loop coupling shifts are then used to obtain the three-loop QCD {beta} function in the FDH and dimensional reduction schemes.

Supersymmetric Regularization Two-Loop QCD Amplitudes and Coupling Shifts

International Nuclear Information System (INIS)

Dixon, Lance

2002-01-01

We present a definition of the four-dimensional helicity (FDH) regularization scheme valid for two or more loops. This scheme was previously defined and utilized at one loop. It amounts to a variation on the standard 't Hooft-Veltman scheme and is designed to be compatible with the use of helicity states for ''observed'' particles. It is similar to dimensional reduction in that it maintains an equal number of bosonic and fermionic states, as required for preserving supersymmetry. Supersymmetry Ward identities relate different helicity amplitudes in supersymmetric theories. As a check that the FDH scheme preserves supersymmetry, at least through two loops, we explicitly verify a number of these identities for gluon-gluon scattering (gg → gg) in supersymmetric QCD. These results also cross-check recent non-trivial two-loop calculations in ordinary QCD. Finally, we compute the two-loop shift between the FDH coupling and the standard MS coupling, α s . The FDH shift is identical to the one for dimensional reduction. The two-loop coupling shifts are then used to obtain the three-loop QCD β function in the FDH and dimensional reduction schemes

Shortening a loop can increase protein native state entropy.

Science.gov (United States)

Gavrilov, Yulian; Dagan, Shlomi; Levy, Yaakov

2015-12-01

Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. © 2015 Wiley Periodicals, Inc.

Functional clustering of time series gene expression data by Granger causality

Science.gov (United States)

2012-01-01

Background A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them. PMID:23107425

Amiloride-enhanced gene transfection of octa-arginine functionalized calcium phosphate nanoparticles.

Directory of Open Access Journals (Sweden)

Juan Ramón Vanegas Sáenz

Full Text Available Nanoparticles represent promising gene delivery systems in biomedicine to facilitate prolonged gene expression with low toxicity compared to viral vectors. Specifically, nanoparticles of calcium phosphate (nCaP, the main inorganic component of human bone, exhibit high biocompatibility and good biodegradability and have been reported to have high affinity for protein or DNA, having thus been used as gene transfer vectors. On the other hand, Octa-arginine (R8, which has a high permeability to cell membrane, has been reported to improve intracellular delivery systems. Here, we present an optimized method for nCaP-mediated gene delivery using an octa-arginine (R8-functionalized nCaP vector containing a marker or functional gene construct. nCaP particle size was between 220-580 nm in diameter and all R8-functionalized nCaPs carried a positive charge. R8 concentration significantly improved nCaP transfection efficiency with high cell compatibility in human mesenchymal stem cells (hMSC and human osteoblasts (hOB in particular, suggesting nCaPs as a good option for non-viral vector gene delivery. Furthermore, pre-treatment with different endocytosis inhibitors identified that the endocytic pathway differed among cell lines and functionalized nanoparticles, with amiloride increasing transfection efficiency of R8-functionalized nCaPs in hMSC and hOB.

Design of a PWR emergency core cooling simulator loop

International Nuclear Information System (INIS)

Melo, C.A. de.

1982-12-01

The preliminary design of a PWR Emergency Core Cooling Simulator Loop for investigations of the phenomena involved in a postulated Loss-of-Coolant Accident, during the Reflooding Phase, is presented. The functions of each component of the loop, the design methods and calculations, the specification of the instrumentation, the system operation sequence, the materials list and a cost assessment are included. (Author) [pt

Weighted functional linear regression models for gene-based association analysis.

Science.gov (United States)

Belonogova, Nadezhda M; Svishcheva, Gulnara R; Wilson, James F; Campbell, Harry; Axenovich, Tatiana I

2018-01-01

Functional linear regression models are effectively used in gene-based association analysis of complex traits. These models combine information about individual genetic variants, taking into account their positions and reducing the influence of noise and/or observation errors. To increase the power of methods, where several differently informative components are combined, weights are introduced to give the advantage to more informative components. Allele-specific weights have been introduced to collapsing and kernel-based approaches to gene-based association analysis. Here we have for the first time introduced weights to functional linear regression models adapted for both independent and family samples. Using data simulated on the basis of GAW17 genotypes and weights defined by allele frequencies via the beta distribution, we demonstrated that type I errors correspond to declared values and that increasing the weights of causal variants allows the power of functional linear models to be increased. We applied the new method to real data on blood pressure from the ORCADES sample. Five of the six known genes with P models. Moreover, we found an association between diastolic blood pressure and the VMP1 gene (P = 8.18×10-6), when we used a weighted functional model. For this gene, the unweighted functional and weighted kernel-based models had P = 0.004 and 0.006, respectively. The new method has been implemented in the program package FREGAT, which is freely available at https://cran.r-project.org/web/packages/FREGAT/index.html.

Covariant diagrams for one-loop matching

International Nuclear Information System (INIS)

Zhang, Zhengkang

2016-10-01

We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gaugecovariant quantities and are thus dubbed ''covariant diagrams.'' The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

Defect networks and supersymmetric loop operators

Energy Technology Data Exchange (ETDEWEB)

Bullimore, Mathew [Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo, ON N2L 2Y5 (Canada)

2015-02-10

We consider topological defect networks with junctions in A{sub N−1} Toda CFT and the connection to supersymmetric loop operators in N=2 theories of class S on a four-sphere. Correlation functions in the presence of topological defect networks are computed by exploiting the monodromy of conformal blocks, generalising the notion of a Verlinde operator. Concentrating on a class of topological defects in A{sub 2} Toda theory, we find that the Verlinde operators generate an algebra whose structure is determined by a set of generalised skein relations that encode the representation theory of a quantum group. In the second half of the paper, we explore the dictionary between topological defect networks and supersymmetric loop operators in the N=2{sup ∗} theory by comparing to exact localisation computations. In this context, the the generalised skein relations are related to the operator product expansion of loop operators.

Covariant diagrams for one-loop matching

Energy Technology Data Exchange (ETDEWEB)

Zhang, Zhengkang [Michigan Center for Theoretical Physics (MCTP), University of Michigan,450 Church Street, Ann Arbor, MI 48109 (United States); Deutsches Elektronen-Synchrotron (DESY),Notkestraße 85, 22607 Hamburg (Germany)

2017-05-30

We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed “covariant diagrams.” The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

Covariant diagrams for one-loop matching

Energy Technology Data Exchange (ETDEWEB)

Zhang, Zhengkang [Michigan Univ., Ann Arbor, MI (United States). Michigan Center for Theoretical Physics; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2016-10-15

We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gaugecovariant quantities and are thus dubbed ''covariant diagrams.'' The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

Covariant diagrams for one-loop matching

International Nuclear Information System (INIS)

Zhang, Zhengkang

2017-01-01

We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed “covariant diagrams.” The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

A multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors for functional gene analysis.

Science.gov (United States)

Weber, Kristoffer; Bartsch, Udo; Stocking, Carol; Fehse, Boris

2008-04-01

Functional gene analysis requires the possibility of overexpression, as well as downregulation of one, or ideally several, potentially interacting genes. Lentiviral vectors are well suited for this purpose as they ensure stable expression of complementary DNAs (cDNAs), as well as short-hairpin RNAs (shRNAs), and can efficiently transduce a wide spectrum of cell targets when packaged within the coat proteins of other viruses. Here we introduce a multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors designed according to the "building blocks" principle. Using a wide spectrum of different fluorescent markers, including drug-selectable enhanced green fluorescent protein (eGFP)- and dTomato-blasticidin-S resistance fusion proteins, LeGO vectors allow simultaneous analysis of multiple genes and shRNAs of interest within single, easily identifiable cells. Furthermore, each functional module is flanked by unique cloning sites, ensuring flexibility and individual optimization. The efficacy of these vectors for analyzing multiple genes in a single cell was demonstrated in several different cell types, including hematopoietic, endothelial, and neural stem and progenitor cells, as well as hepatocytes. LeGO vectors thus represent a valuable tool for investigating gene networks using conditional ectopic expression and knock-down approaches simultaneously.

New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

Science.gov (United States)

Imhoff, Johannes F.

2016-01-01

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane

New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

Directory of Open Access Journals (Sweden)

Johannes F. Imhoff

2016-05-01

Full Text Available During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA as target for the green sulfur bacteria and of two reaction center proteins (pufLM for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS reductase (aprA, sulfate thioesterase (soxB and dissimilatory sulfite reductase (dsrAB for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK for denitrifying bacteria and with genes

Neocortical electrical stimulation for epilepsy : Closed-loop versus open-loop

NARCIS (Netherlands)

Vassileva, Albena; van Blooijs, Dorien; Leijten, Frans; Huiskamp, Geertjan

2018-01-01

The aim of this review is to evaluate whether open-loop or closed-loop neocortical electrical stimulation should be the preferred approach to manage seizures in intractable epilepsy. Twenty cases of open-loop neocortical stimulation with an implanted device have been reported, in 5 case studies.

Functional requirements driving the gene duplication in 12 Drosophila species.

Science.gov (United States)

Zhong, Yan; Jia, Yanxiao; Gao, Yang; Tian, Dacheng; Yang, Sihai; Zhang, Xiaohui

2013-08-15

Gene duplication supplies the raw materials for novel gene functions and many gene families arisen from duplication experience adaptive evolution. Most studies of young duplicates have focused on mammals, especially humans, whereas reports describing their genome-wide evolutionary patterns across the closely related Drosophila species are rare. The sequenced 12 Drosophila genomes provide the opportunity to address this issue. In our study, 3,647 young duplicate gene families were identified across the 12 Drosophila species and three types of expansions, species-specific, lineage-specific and complex expansions, were detected in these gene families. Our data showed that the species-specific young duplicate genes predominated (86.6%) over the other two types. Interestingly, many independent species-specific expansions in the same gene family have been observed in many species, even including 11 or 12 Drosophila species. Our data also showed that the functional bias observed in these young duplicate genes was mainly related to responses to environmental stimuli and biotic stresses. This study reveals the evolutionary patterns of young duplicates across 12 Drosophila species on a genomic scale. Our results suggest that convergent evolution acts on young duplicate genes after the species differentiation and adaptive evolution may play an important role in duplicate genes for adaption to ecological factors and environmental changes in Drosophila.

Large-scale gene function analysis with the PANTHER classification system.

Science.gov (United States)

Mi, Huaiyu; Muruganujan, Anushya; Casagrande, John T; Thomas, Paul D

2013-08-01

The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.

Gene expression and functional annotation of the human ciliary body epithelia.

Directory of Open Access Journals (Sweden)

Sarah F Janssen

Full Text Available PURPOSE: The ciliary body (CB of the human eye consists of the non-pigmented (NPE and pigmented (PE neuro-epithelia. We investigated the gene expression of NPE and PE, to shed light on the molecular mechanisms underlying the most important functions of the CB. We also developed molecular signatures for the NPE and PE and studied possible new clues for glaucoma. METHODS: We isolated NPE and PE cells from seven healthy human donor eyes using laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44×k Agilent microarrays. For microarray conformations, we used a literature study, RT-PCRs, and immunohistochemical stainings. We analyzed the gene expression data with R and with the knowledge database Ingenuity. RESULTS: The gene expression profiles and functional annotations of the NPE and PE were highly similar. We found that the most important functionalities of the NPE and PE were related to developmental processes, neural nature of the tissue, endocrine and metabolic signaling, and immunological functions. In total 1576 genes differed statistically significantly between NPE and PE. From these genes, at least 3 were cell-specific for the NPE and 143 for the PE. Finally, we observed high expression in the (NPE of 35 genes previously implicated in molecular mechanisms related to glaucoma. CONCLUSION: Our gene expression analysis suggested that the NPE and PE of the CB were quite similar. Nonetheless, cell-type specific differences were found. The molecular machineries of the human NPE and PE are involved in a range of neuro-endocrinological, developmental and immunological functions, and perhaps glaucoma.

A loop-based neural architecture for structured behavior encoding and decoding.

Science.gov (United States)

Gisiger, Thomas; Boukadoum, Mounir

2018-02-01

We present a new type of artificial neural network that generalizes on anatomical and dynamical aspects of the mammal brain. Its main novelty lies in its topological structure which is built as an array of interacting elementary motifs shaped like loops. These loops come in various types and can implement functions such as gating, inhibitory or executive control, or encoding of task elements to name a few. Each loop features two sets of neurons and a control region, linked together by non-recurrent projections. The two neural sets do the bulk of the loop's computations while the control unit specifies the timing and the conditions under which the computations implemented by the loop are to be performed. By functionally linking many such loops together, a neural network is obtained that may perform complex cognitive computations. To demonstrate the potential offered by such a system, we present two neural network simulations. The first illustrates the structure and dynamics of a single loop implementing a simple gating mechanism. The second simulation shows how connecting four loops in series can produce neural activity patterns that are sufficient to pass a simplified delayed-response task. We also show that this network reproduces electrophysiological measurements gathered in various regions of the brain of monkeys performing similar tasks. We also demonstrate connections between this type of neural network and recurrent or long short-term memory network models, and suggest ways to generalize them for future artificial intelligence research. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mining protein loops using a structural alphabet and statistical exceptionality

Directory of Open Access Journals (Sweden)

Martin Juliette

2010-02-01

Full Text Available Abstract Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times. Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words. These structural words have low structural variability (mean RMSd of 0.85 Å. As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues and long loops. Moreover, half of

Mining protein loops using a structural alphabet and statistical exceptionality.

Science.gov (United States)

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of

Plant ion channels: gene families, physiology, and functional genomics analyses.

Science.gov (United States)

Ward, John M; Mäser, Pascal; Schroeder, Julian I

2009-01-01

Distinct potassium, anion, and calcium channels in the plasma membrane and vacuolar membrane of plant cells have been identified and characterized by patch clamping. Primarily owing to advances in Arabidopsis genetics and genomics, and yeast functional complementation, many of the corresponding genes have been identified. Recent advances in our understanding of ion channel genes that mediate signal transduction and ion transport are discussed here. Some plant ion channels, for example, ALMT and SLAC anion channel subunits, are unique. The majority of plant ion channel families exhibit homology to animal genes; such families include both hyperpolarization- and depolarization-activated Shaker-type potassium channels, CLC chloride transporters/channels, cyclic nucleotide-gated channels, and ionotropic glutamate receptor homologs. These plant ion channels offer unique opportunities to analyze the structural mechanisms and functions of ion channels. Here we review gene families of selected plant ion channel classes and discuss unique structure-function aspects and their physiological roles in plant cell signaling and transport.

Identification of a second flagellin gene and functional characterization of a sigma70-like promoter upstream of a Leptospira borgpetersenii flaB gene.

Science.gov (United States)

Lin, Min; Dan, Hanhong; Li, Yijing

2004-02-01

Leptospira borgpetersenii, one of the causative agents of leptospirosis in both animals and humans, is a bacterial pathogen with characteristic motility that is mediated by the rotation of two periplasmic flagella (PF). The flaB gene coding for a core polypeptide subunit of PF was previously characterized by sequence analysis of its open reading frame (ORF) (M. Lin, J Biochem Mol Biol Biophys 2:181-187, 1999). The present study was undertaken to isolate and clone the uncharacterized sequence upstream of the flaB gene by using a PCR-based genome walking procedure. This has resulted in a 1470-bp genomic DNA sequence in which an 846-bp ORF coding for a 281-amino acid polypeptide (31.3 kDa) is identified 455 bp upstream from the flaB start codon. The encoded protein exhibits 72% amino acid identity to the deduced FlaB protein sequence of L. borgpetersenii and a high degree of sequence homology to the FlaB proteins of other spirochaetes. This has demonstrated for the first time that a second flaB gene homolog is present in a Leptospira species. The newly identified gene is designated flaB1, and the previously cloned flaB renamed flaB2. Within the intergenic sequence between flaB1 and flaB2, a potential stem-loop structure (12-bp inverted repeats) was identified 25 bp downstream of the flaB1 stop codon; this could serve as a transcription terminator for the flaB1 mRNA. Three E. coli-like promoter regions (I, II, and III) for binding Esigma(70), a regulatory sequence uncommonly found in flagellar genes, were predicted upstream of the flaB2 ORF. Only promoter region II contains a promoter that is functional in E. coli, as revealed at phenotypic and transcriptional levels by its capability of directing the expression of the chloramphenicol acetyltransferase (CAT) gene in the promoter probe vector pKK232-8. These observations may suggest that flaB1 and flaB2 are transcribed separately and do not form a transcriptional operon controlled by a single promoter.

On the duality-transformed Wilson loop operator

International Nuclear Information System (INIS)

Mizrachi, L.

1981-08-01

Duality transformation of the vacuum expectation value of the Wilson loop operator is performed in the radial gauge (xsub(μ)Asub(μ)sup(a)(x) = 0). It is found to be equal, up to a multiplicative constant, to , where O(c) is a line integral along the loop c (defining the Wilson loop operator) of a function of the dual field variables. In the weak coupling region self duality is recovered in the sense that the Lagrangian is local gauge invariant defined in terms of the dual gauge potentials but with g (the coupling constant) replaced by 1/g, and O(c) is simply the line integral of the dual gauge potentials. For large g, a strong coupling expansion is suggested (but the theory is not local gauge invariant). (author)

Gene function analysis by artificial microRNAs in Physcomitrella patens.

KAUST Repository

Khraiwesh, Basel

2011-01-01

MicroRNAs (miRNAs) are ~21 nt long small RNAs transcribed from endogenous MIR genes which form precursor RNAs with a characteristic hairpin structure. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences resulting in cleavage or translational inhibition of the target RNA. Artificial miRNAs (amiRNAs) can be generated by exchanging the miRNA/miRNA sequence of endogenous MIR precursor genes, while maintaining the general pattern of matches and mismatches in the foldback. Thus, for functional gene analysis amiRNAs can be designed to target any gene of interest. During the last decade the moss Physcomitrella patens emerged as a model plant for functional gene analysis based on its unique ability to integrate DNA into the nuclear genome by homologous recombination which allows for the generation of targeted gene knockout mutants. In addition to this, we developed a protocol to express amiRNAs in P. patens that has particular advantages over the generation of knockout mutants and might be used to speed up reverse genetics approaches in this model species.

The 3-loop non-singlet heavy flavor contributions and anomalous dimensions for the structure function F2(x,Q2 and transversity

Directory of Open Access Journals (Sweden)

J. Ablinger

2014-09-01

Full Text Available We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the structure function F2(x,Q2 in the asymptotic region Q2≫m2 and the associated operator matrix element Aqq,Q(3,NS(N to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This matrix element is associated with the vector current and axial vector current for the even and the odd moments N, respectively. We also calculate the corresponding operator matrix elements for transversity, compute the contributions to the 3-loop anomalous dimensions to O(NF and compare to results in the literature. The 3-loop matching of the flavor non-singlet distribution in the variable flavor number scheme is derived. All results can be expressed in terms of nested harmonic sums in N space and harmonic polylogarithms in x-space. Numerical results are presented for the non-singlet charm quark contribution to F2(x,Q2.

The 3-loop non-singlet heavy flavor contributions and anomalous dimensions for the structure function F2(x,Q2) and transversity

International Nuclear Information System (INIS)

Ablinger, J.; Hasselhuhn, A.; Schneider, C.; Manteuffel, A. von

2014-06-01

We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the structure function F 2 (x,Q 2 ) in the asymptotic region Q 2 >>m 2 and the associated operator matrix element A (3),NS qq,Q (N) to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This matrix element is associated to the vector current and axial vector current for the even and the odd moments N, respectively. We also calculate the corresponding operator matrix elements for transversity, compute the contributions to the 3-loop anomalous dimensions to O(N F ) and compare to results in the literature. The 3-loop matching of the flavor non-singlet distribution in the variable flavor number scheme is derived. All results can be expressed in terms of nested harmonic sums in N space and harmonic polylogarithms in x-space. Numerical results are presented for the non-singlet charm quark contribution to F 2 (x,Q 2 ).

The 3-loop non-singlet heavy flavor contributions and anomalous dimensions for the structure function F2(x,Q2) and transversity

International Nuclear Information System (INIS)

Ablinger, J.; Behring, A.; Blümlein, J.; De Freitas, A.; Hasselhuhn, A.; Manteuffel, A. von; Round, M.; Schneider, C.; Wißbrock, F.

2014-01-01

We calculate the massive flavor non-singlet Wilson coefficient for the heavy flavor contributions to the structure function F 2 (x,Q 2 ) in the asymptotic region Q 2 ≫m 2 and the associated operator matrix element A qq,Q (3),NS (N) to 3-loop order in Quantum Chromodynamics at general values of the Mellin variable N. This matrix element is associated with the vector current and axial vector current for the even and the odd moments N, respectively. We also calculate the corresponding operator matrix elements for transversity, compute the contributions to the 3-loop anomalous dimensions to O(N F ) and compare to results in the literature. The 3-loop matching of the flavor non-singlet distribution in the variable flavor number scheme is derived. All results can be expressed in terms of nested harmonic sums in N space and harmonic polylogarithms in x-space. Numerical results are presented for the non-singlet charm quark contribution to F 2 (x,Q 2 )

Background-free propagation in loop quantum gravity

OpenAIRE

Speziale, Simone

2008-01-01

I review the definition of n-point functions in loop quantum gravity, discussing what has been done and what are the main open issues. Particular attention is dedicated to gauge aspects and renormalization.

Methods of Temperature and Emission Measure Determination of Coronal Loops

Science.gov (United States)

Cirtain, J. W.; Schmelz, J. T.; Martens, P. C. H.

2002-05-01

Recent observational results from both SOHO-EIT and TRACE indicate that coronal loops are isothermal along their length (axially). These results are obtained from a narrowband filter ratio method that assumes that the plasma is isothermal along the line of sight (radially). However, these temperatures vary greatly from those derived from differential emission measure (DEM) curves produced from spectral lines recorded by SOHO-CDS. The DEM results indicate that the loops are neither axially nor radially isothermal. This discrepancy was investigated by Schmelz et al. (2001). They chose pairs of iron lines from the same CDS data set to mimic the EIT and TRACE loop results. Ratios of different lines gave different temperatures, indicating that the plasma was not radially isothermal. In addition the results indicated that the loop was axially isothermal, even though the DEM analysis of the same data showed this result to be false. Here we have analyzed the EIT data for the CDS loop published by Schmelz et al. (2001). We took the ratios of the 171-to-195 and 195-to-284 filter data, and made temperature maps of the loop. The results indicate that the loop is axially isothermal, but different temperatures were found for each pair of filters. Both ratio techniques force the resultant temperature to lie within the range where the response functions (for filters) or the emissivity functions (for lines) overlap; isothermal loops are therefore a byproduct of the analysis. This conclusion strengthens support for the idea that temperature and emission measure results from filter ratio methods may be misleading or even drastically wrong. This research was funded in part by the NASA/TRACE MODA grant for Montana State University. Solar physics research at the University of Memphis is supported by NASA grant NAG5-9783.

Small, synthetic, GC-rich mRNA stem-loop modules 5′ proximal to the AUG start-codon predictably tune gene expression in yeast

Science.gov (United States)

2013-01-01

Background A large range of genetic tools has been developed for the optimal design and regulation of complex metabolic pathways in bacteria. However, fewer tools exist in yeast that can precisely tune the expression of individual enzymes in novel metabolic pathways suitable for industrial-scale production of non-natural compounds. Tuning expression levels is critical for reducing the metabolic burden of over-expressed proteins, the accumulation of toxic intermediates, and for redirecting metabolic flux from native pathways involving essential enzymes without negatively affecting the viability of the host. We have developed a yeast membrane protein hyper-expression system with critical advantages over conventional, plasmid-based, expression systems. However, expression levels are sometimes so high that they adversely affect protein targeting/folding or the growth and/or phenotype of the host. Here we describe the use of small synthetic mRNA control modules that allowed us to predictably tune protein expression levels to any desired level. Down-regulation of expression was achieved by engineering small GC-rich mRNA stem-loops into the 5′ UTR that inhibited translation initiation of the yeast ribosomal 43S preinitiation complex (PIC). Results Exploiting the fact that the yeast 43S PIC has great difficulty scanning through GC-rich mRNA stem-loops, we created yeast strains containing 17 different RNA stem-loop modules in the 5′ UTR that expressed varying amounts of the fungal multidrug efflux pump reporter Cdr1p from Candida albicans. Increasing the length of mRNA stem-loops (that contained only GC-pairs) near the AUG start-codon led to a surprisingly large decrease in Cdr1p expression; ~2.7-fold for every additional GC-pair added to the stem, while the mRNA levels remained largely unaffected. An mRNA stem-loop of seven GC-pairs (∆G = −15.8 kcal/mol) reduced Cdr1p expression levels by >99%, and even the smallest possible stem-loop of only three GC-pairs (�

Boundary string field theory and an open string one-loop

International Nuclear Information System (INIS)

Lee, Tae Jin; Viswanathan, K. S.; Yang, Yi

2003-01-01

We discuss the open string one-loop partition function in the tachyon condensation background of an unstable D-brane system. We evaluate the partition function by using the boundary-state formulation and find that it is in complete agreement with the result obtained in the boundary string field theory. This suggests that the open string higher loop diagrams may be produced consistently by using a closed string field theory, where the D-brane plays the role of a source for the closed string field

Analytic result for the two-loop six-point NMHV amplitude in N=4 super Yang-Mills theory

CERN Document Server

Dixon, Lance J.; Henn, Johannes M.

2012-01-01

We provide a simple analytic formula for the two-loop six-point ratio function of planar N = 4 super Yang-Mills theory. This result extends the analytic knowledge of multi-loop six-point amplitudes beyond those with maximal helicity violation. We make a natural ansatz for the symbols of the relevant functions appearing in the two-loop amplitude, and impose various consistency conditions, including symmetry, the absence of spurious poles, the correct collinear behaviour, and agreement with the operator product expansion for light-like (super) Wilson loops. This information reduces the ansatz to a small number of relatively simple functions. In order to fix these parameters uniquely, we utilize an explicit representation of the amplitude in terms of loop integrals that can be evaluated analytically in various kinematic limits. The final compact analytic result is expressed in terms of classical polylogarithms, whose arguments are rational functions of the dual conformal cross-ratios, plus precisely two function...

A multiple-pass ring oscillator based dual-loop phase-locked loop

International Nuclear Information System (INIS)