Structure and function of initiator methionine tRNA from the mitochondria of Neurospora crassa

International Nuclear Information System (INIS)

Heckman, J.E.; Hecker, L.I.; Schwartzbach, S.D.; Barnett, W.E.; Baumstark, B.; RajBhandary, U.L.

1978-01-01

Initiator methionine tRNA from the mitochondria of Neurospora crassa has been purified and sequenced. This mitochondrial tRNA can be aminoacylated and formylated by E. coli enzymes, and is capable of initiating protein synthesis in E. coli extracts. The nucleotide composition of the mitochondrial initiator tRNA (the first mitochondrial tRNA subjected to sequence analysis) is very rich in A + U, like that reported for total mitochondrial tRNA. In two of the unique features which differentiate procaryotic from eucaryotic cytoplasmic initiator tRNAs, the mitochondrial tRNA appears to resemble the eucaryotic initiator tRNAs. Thus unlike procaryotic initiator tRNAs in which the 5' terminal nucleotide cannot form a Watson-Crick base pair to the fifth nucleotide from 3' end, the mitochondrial tRNA can form such a base pair; and like the eucaryotic cytoplasmic initiator tRNAs, the mitochondrial initiator tRNA lacks the sequence - T psiCG(or A) in loop IV. The corresponding sequence in the mitochondrial tRNA, however, is -UGCA- and not -AU(or psi)CG- as found in all eucaryotic cytoplasmic initiator tRNAs. In spite of some similarity of the mitochondrial initiator tRNA to both eucaryotic and procaryotic initiator tRNAs, the mitochondrial initiator tRNA is basically different from both these tRNAs. Between these two classes of initiator tRNAs, however, it is more homologous in sequence to procaryotic (56 to 60%) than to eucaryotic cytoplasmic initiator tRNAs

Byrsonima crassa Niedenzu (IK: antimicrobial activity and chemical study

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W. Vilegas

2009-01-01

Full Text Available

The methanolic extract of leaves from Byrsonima crassa, a Brazilian medicinal plant, was analyzed by CC and HPLC. Four constituents were isolated and identified as quercetin, methyl gallate, (--epigallocatechin gallate and quercetin-3-O-(2”-galloyl-a-L-arabinopyranoside. The methanolic and hydromethanolic extract, as well as fractions, were evaluated regarding their possible antimicrobial activity using in vitro methods. Results showed that both extracts and fractions exhibited significant antimicrobial activity against all tested strains. Keywords: Byrsonima crassa, antimicrobial activity, Malpighiaceae.

A Mouse Neurodegenerative Dynein Heavy Chain Mutation Alters Dynein Motility and Localization in Neurospora crassa

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Sivagurunathan, Senthilkumar; Schnittker, Robert R.; Nandini, Swaran; Plamann, Michael D.; King, Stephen J.

2013-01-01

Cytoplasmic dynein is responsible for the transport and delivery of cargoes in organisms ranging from humans to fungi. Dysfunction of dynein motor machinery due to mutations in dynein or its activating complex dynactin can result in one of several neurological diseases in mammals. The mouse Legs at odd angles (Loa) mutation in the tail domain of the dynein heavy chain has been shown to lead to progressive neurodegeneration in mice. The mechanism by which the Loa mutation affects dynein function is just beginning to be understood. In this work, we generated the dynein tail mutation observed in Loa mice into the Neurospora crassa genome and utilized cell biological and complementing biochemical approaches to characterize how that tail mutation affected dynein function. We determined that the Loa mutation exhibits several subtle defects upon dynein function in N. crassa that were not seen in mice, including alterations in dynein localization, impaired velocity of vesicle transport, and in the biochemical properties of purified motors. Our work provides new information on the role of the tail domain on dynein function and points out areas of future research that will be of interest to pursue in mammalian systems. PMID:22991199

FIRST HOST RECORD FOR THE ROOT PARASITE CORYNAEA CRASSA (BALANOPHORACEAE

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Joel Tupac Otero

2009-09-01

Full Text Available Corynaea crassa es una planta hemiparásita de raiz poco común y de la cual sabemos muy poco acerca  de su historia natural y en particular sobre su rango de hospederos. En este estudio escabamos 32 tuberculos de dicha especie y seguimos las raíces que estaban parasitando para determinar su identidad. Encontramos Bocconia frutescens (Papaveraceae, Verbesina sp. (Asteraceae, Cayaponia sp. (Cucurbitaceae y Palicourea sp.(Rubiaceae. Este es el primer registro de hospederos disponible para la especies y es información de gran utilidad para las conservación de C. crassa en habitats naturales.

Alcohol consumption and tolerance of Neurospora crassa

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The alcohol consumption and tolerance of the ascomycete Neurospora crassa was investigated in this study. This fungus is able to utilize both native alcohol and non-native alcohols as carbon sources, yet little is known about the enzymes involved in these processes. The deletion of alcohol dehydroge...

Biotechnological production of ethanol from renewable resources by Neurospora crassa: an alternative to conventional yeast fermentations?

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Dogaris, Ioannis; Mamma, Diomi; Kekos, Dimitris

2013-02-01

Microbial production of ethanol might be a potential route to replace oil and chemical feedstocks. Bioethanol is by far the most common biofuel in use worldwide. Lignocellulosic biomass is the most promising renewable resource for fuel bioethanol production. Bioconversion of lignocellulosics to ethanol consists of four major unit operations: pretreatment, hydrolysis, fermentation, and product separation/distillation. Conventional bioethanol processes for lignocellulosics apply commercial fungal cellulase enzymes for biomass hydrolysis, followed by yeast fermentation of resulting glucose to ethanol. The fungus Neurospora crassa has been used extensively for genetic, biochemical, and molecular studies as a model organism. However, the strain's potential in biotechnological applications has not been widely investigated and discussed. The fungus N. crassa has the ability to synthesize and secrete all three enzyme types involved in cellulose hydrolysis as well as various enzymes for hemicellulose degradation. In addition, N. crassa has been reported to convert to ethanol hexose and pentose sugars, cellulose polymers, and agro-industrial residues. The combination of these characteristics makes N. crassa a promising alternative candidate for biotechnological production of ethanol from renewable resources. This review consists of an overview of the ethanol process from lignocellulosic biomass, followed by cellulases and hemicellulases production, ethanol fermentations of sugars and lignocellulosics, and industrial application potential of N. crassa.

[Organization of mitochondria in the growing hyphae of Neurospora crassa].

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Potapova, T V; Boĭtsova, L Iu; Golyshev, S A; Popinako, A V

2013-01-01

In vivo fluorescent labeling of mitochondria in Neurospora crassa showed the concentration of filamentous mitochondria within 30 μm of apex in growing hyphae. These mitochondrial assemblies propagated forward with the elongation of hyphae, split and segregated as the growing tip bifurcated and formed de novo when new branches formed farther away from the apex. The efficiency of the mitochondria concentration in the apical 30 μm zone is related to the growth rate and identical in hyphae cultivated in glucose- and sorbitol-containing media. The obtained data are discussed in connection with the behavior of microtubules in growing hyphae as well as with the electric heterogeneity of N. crassa hyphal apex described previously.

Stress-induced cell death is mediated by ceramide synthesis in Neurospora crassa

DEFF Research Database (Denmark)

Plesofsky, Nora S; Levery, Steven B; Castle, Sherry A

2008-01-01

The combined stresses of moderate heat shock (45 degrees C) and analog-induced glucose deprivation constitute a lethal stress for Neurospora crassa. We found that this cell death requires fatty acid synthesis and the cofactor biotin. In the absence of the cofactor, the stressed cells are particul......The combined stresses of moderate heat shock (45 degrees C) and analog-induced glucose deprivation constitute a lethal stress for Neurospora crassa. We found that this cell death requires fatty acid synthesis and the cofactor biotin. In the absence of the cofactor, the stressed cells...

Products of mitochondrial protein synthesis in neurospora crassa.

NARCIS (Netherlands)

Sant, Peter van 't

1982-01-01

Het onderzoek, dat in dit proefschrift wordt beschreven, omvat verschillende aspecten van de biogenese van de mitochondriën van de ascomyeet Neurospora crassa. Het eerste hoofdstuk bevat een overzicht van de huidige kennis van de verschillende processen, die betrokken zijn bij de opbouw en de

Anti-Helicobacter pylori activity and immunostimulatory effect of extracts from Byrsonima crassa Nied. (Malpighiaceae

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Vilegas Wagner

2009-01-01

Full Text Available Abstract Background Several in vitro studies have looked at the effect of medicinal plant extracts against Helicobacter pylori (H. pylori. Regardless of the popular use of Byrsonima crassa (B. crassa as antiemetic, diuretic, febrifuge, to treat diarrhea, gastritis and ulcers, there is no data on its effects against H. pylori. In this study, we evaluated the anti-H. pylori of B. crassa leaves extracts and its effects on reactive oxygen/nitrogen intermediates induction by murine peritoneal macrophages. Methods The minimal inhibitory concentration (MIC was determined by broth microdilution method and the production of hydrogen peroxide (H2O2 and nitric oxide (NO by the horseradish peroxidase-dependent oxidation of phenol red and Griess reaction, respectively. Results The methanolic (MeOH and chloroformic (CHCl3 extracts inhibit, in vitro, the growth of H. pylori with MIC value of 1024 μg/ml. The MeOH extract induced the production H2O2 and NO, but CHCl3 extract only NO. Conclusion Based in our results, B. crassa can be considered a source of compounds with anti-H. pylori activity, but its use should be done with caution in treatment of the gastritis and peptic ulcers, since the reactive oxygen/nitrogen intermediates are involved in the pathogenesis of gastric mucosal injury induced by ulcerogenic agents and H. pylori infections.

Functional Profiling of Transcription Factor Genes in Neurospora crassa

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Alexander J. Carrillo

2017-09-01

Full Text Available Regulation of gene expression by DNA-binding transcription factors is essential for proper control of growth and development in all organisms. In this study, we annotate and characterize growth and developmental phenotypes for transcription factor genes in the model filamentous fungus Neurospora crassa. We identified 312 transcription factor genes, corresponding to 3.2% of the protein coding genes in the genome. The largest class was the fungal-specific Zn2Cys6 (C6 binuclear cluster, with 135 members, followed by the highly conserved C2H2 zinc finger group, with 61 genes. Viable knockout mutants were produced for 273 genes, and complete growth and developmental phenotypic data are available for 242 strains, with 64% possessing at least one defect. The most prominent defect observed was in growth of basal hyphae (43% of mutants analyzed, followed by asexual sporulation (38%, and the various stages of sexual development (19%. Two growth or developmental defects were observed for 21% of the mutants, while 8% were defective in all three major phenotypes tested. Analysis of available mRNA expression data for a time course of sexual development revealed mutants with sexual phenotypes that correlate with transcription factor transcript abundance in wild type. Inspection of this data also implicated cryptic roles in sexual development for several cotranscribed transcription factor genes that do not produce a phenotype when mutated.

Bioconversion of dilute-acid pretreated sorghum bagasse to ethanol by Neurospora crassa

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Dogaris, Ioannis; Gkounta, Olga; Mamma, Diomi; Kekos, Dimitris [National Technical Univ. of Athens, Zografou (Greece). Biotechnology Lab.

2012-07-15

Bioethanol production from sweet sorghum bagasse (SB), the lignocellulosic solid residue obtained after extraction of sugars from sorghum stalks, can further improve the energy yield of the crop. The aim of the present work was to evaluate a cost-efficient bioconversion of SB to ethanol at high solids loadings (16 % at pretreatment and 8 % at fermentation), low cellulase activities (1-7 FPU/g SB) and co-fermentation of hexoses and pentoses. The fungus Neurospora crassa DSM 1129 was used, which exhibits both depolymerase and co-fermentative ability, as well as mixed cultures with Saccharomyces cerevisiae 2541. A dilute-acid pretreatment (sulfuric acid 2 g/100 g SB; 210 C; 10 min) was implemented, with high hemicellulose decomposition and low inhibitor formation. The bioconversion efficiency of N. crassa was superior to S. cerevisiae, while their mixed cultures had negative effect on ethanol production. Supplementing the in situ produced N. crassa cellulolytic system (1.0 FPU/g SB) with commercial cellulase and {beta}-glucosidase mixture at low activity (6.0 FPU/g SB) increased ethanol production to 27.6 g/l or 84.7 % of theoretical yield (based on SB cellulose and hemicellulose sugar content). The combined dilute-acid pretreatment and bioconversion led to maximum cellulose and hemicellulose hydrolysis 73.3 % and 89.6 %, respectively. (orig.)

Performa Ayam dan Kualitas Telur yang Menggunakan Ransum Mengandung Onggok Fermentasi dengan Neurospora crassa

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Nuraini

2008-12-01

Full Text Available An experiment was conducted to determine the effect of feeding tapioca by-products fermented by Neurospora crassa on layer performances and egg quality. Two hundred layers were randomly allocated into 20 pens. This experiment was arranged in a completely randomized design with four dietary treatments: 0%, 10%, 20% and 30% tapioca by product fermented by N. crassa in the diets and five replications. Variable measured were feed comsumption, egg production, feed conversion, egg cholesterol and egg yolk colour. Results of the experiment indicated that feed comsumption, egg production, feed conversion, egg cholesterol and egg yolk colour were affected (P<0.05 by using fermented tapioca by-product in the diets of layers. Results of Duncan multiple range test indicated that feed consumption, egg production, and egg yolk colour in D treatment (used 30% tapioca by-products fermented were the highest compared to those other treatments, but the lowest on feed conversion and egg cholesterol. The conclusion of the experiment that tapioca by-products fermented by N. crassa can be used up to 30% in the diet of layer.

The bZIP Transcription Factor HAC-1 Is Involved in the Unfolded Protein Response and Is Necessary for Growth on Cellulose in Neurospora crassa.

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Alejandro Montenegro-Montero

Full Text Available High protein secretion capacity in filamentous fungi requires an extremely efficient system for protein synthesis, folding and transport. When the folding capacity of the endoplasmic reticulum (ER is exceeded, a pathway known as the unfolded protein response (UPR is triggered, allowing cells to mitigate and cope with this stress. In yeast, this pathway relies on the transcription factor Hac1, which mediates the up-regulation of several genes required under these stressful conditions. In this work, we identified and characterized the ortholog of the yeast HAC1 gene in the filamentous fungus Neurospora crassa. We show that its mRNA undergoes an ER stress-dependent splicing reaction, which in N. crassa removes a 23 nt intron and leads to a change in the open reading frame. By disrupting the N. crassa hac-1 gene, we determined it to be crucial for activating UPR and for proper growth in the presence of ER stress-inducing chemical agents. Neurospora is naturally found growing on dead plant material, composed primarily by lignocellulose, and is a model organism for the study of plant cell wall deconstruction. Notably, we found that growth on cellulose, a substrate that requires secretion of numerous enzymes, imposes major demands on ER function and is dramatically impaired in the absence of hac-1, thus broadening the range of physiological functions of the UPR in filamentous fungi. Growth on hemicellulose however, another carbon source that necessitates the secretion of various enzymes for its deconstruction, is not impaired in the mutant nor is the amount of proteins secreted on this substrate, suggesting that secretion, as a whole, is unaltered in the absence of hac-1. The characterization of this signaling pathway in N. crassa will help in the study of plant cell wall deconstruction by fungi and its manipulation may result in important industrial biotechnological applications.

Bioconversion of dilute-acid pretreated sorghum bagasse to ethanol by Neurospora crassa.

Science.gov (United States)

Dogaris, Ioannis; Gkounta, Olga; Mamma, Diomi; Kekos, Dimitris

2012-07-01

Bioethanol production from sweet sorghum bagasse (SB), the lignocellulosic solid residue obtained after extraction of sugars from sorghum stalks, can further improve the energy yield of the crop. The aim of the present work was to evaluate a cost-efficient bioconversion of SB to ethanol at high solids loadings (16 % at pretreatment and 8 % at fermentation), low cellulase activities (1-7 FPU/g SB) and co-fermentation of hexoses and pentoses. The fungus Neurospora crassa DSM 1129 was used, which exhibits both depolymerase and co-fermentative ability, as well as mixed cultures with Saccharomyces cerevisiae 2541. A dilute-acid pretreatment (sulfuric acid 2 g/100 g SB; 210 °C; 10 min) was implemented, with high hemicellulose decomposition and low inhibitor formation. The bioconversion efficiency of N. crassa was superior to S. cerevisiae, while their mixed cultures had negative effect on ethanol production. Supplementing the in situ produced N. crassa cellulolytic system (1.0 FPU/g SB) with commercial cellulase and β-glucosidase mixture at low activity (6.0 FPU/g SB) increased ethanol production to 27.6 g/l or 84.7 % of theoretical yield (based on SB cellulose and hemicellulose sugar content). The combined dilute-acid pretreatment and bioconversion led to maximum cellulose and hemicellulose hydrolysis 73.3 % and 89.6 %, respectively.

Un poète grec francophone : Théo Crassas (entretien

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Daniel Aranjo

2012-10-01

Full Text Available Dans cet entretien, l’auteur interroge le poète grec Théo Crassas sur ses raisons d’écrire en français. Le contexte familial - un oncle poète et francophone, ainsi que ses parents, éclaire ce choix. S’il est vrai que le français n’est plus la langue impériale qu’il fut longtemps, il n’en demeure pas moins une école universelle, de par ses auteurs classiques qui ont consacré son universalité. À ce titre, le français demeurera aussi capital dans l’histoire des humanités que le grec ancien ou le latin. Crassas se définit comme un cas singulier, car il n’écrit ses textes qu’en français.

Inactivation of Neurospora crassa conidia by singlet molecular oxygen generated by a photosensitized reaction

International Nuclear Information System (INIS)

Shimizu, M.; Egashira, T.; Takahama, U.

1979-01-01

Photodynamic damage of Neurospora crassa conidia was studied in the presence of the photosensitizing dye, toluidine blue O. Conidia which germinated to form colonies decreased in number as irradiation time became longer. The photoinactivation of conidia was suppressed by azide, bovine serum albumin, and histidine, and was stimulated in deuterium oxide. Wild-type conidia were less sensitive to the irradiation that albino conidia. In the wild type, carotenoid-enriched conidia were more resistant against the lethal damage than the conidia which contained small amounts of carotenoids. These results suggest that singlet molecular oxygen causes photodynamic lethal damage to N. crassa conidia and that singlet molecular oxygen is quenched by endogenous carotenoids

Phylogenetics and Gene Structure Dynamics of Polygalacturonase Genes in Aspergillus and Neurospora crassa

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Jin-Sung Hong

2013-09-01

Full Text Available Polygalacturonase (PG gene is a typical gene family present in eukaryotes. Forty-nine PGs were mined from the genomes of Neurospora crassa and five Aspergillus species. The PGs were classified into 3 clades such as clade 1 for rhamno-PGs, clade 2 for exo-PGs and clade 3 for exo- and endo-PGs, which were further grouped into 13 sub-clades based on the polypeptide sequence similarity. In gene structure analysis, a total of 124 introns were present in 44 genes and five genes lacked introns to give an average of 2.5 introns per gene. Intron phase distribution was 64.5% for phase 0, 21.8% for phase 1, and 13.7% for phase 2, respectively. The introns varied in their sequences and their lengths ranged from 20 bp to 424 bp with an average of 65.9 bp, which is approximately half the size of introns in other fungal genes. There were 29 homologous intron blocks and 26 of those were sub-clade specific. Intron losses were counted in 18 introns in which no obvious phase preference for intron loss was observed. Eighteen introns were placed at novel positions, which is considerably higher than those of plant PGs. In an evolutionary sense both intron loss and gain must have taken place for shaping the current PGs in these fungi. Together with the small intron size, low conservation of homologous intron blocks and higher number of novel introns, PGs of fungal species seem to have recently undergone highly dynamic evolution.

Neurospora crassa female development requires the PACC and other signal transduction pathways, transcription factors, chromatin remodeling, cell-to-cell fusion, and autophagy.

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Jennifer L Chinnici

Full Text Available Using a screening protocol we have identified 68 genes that are required for female development in the filamentous fungus Neurospora crassa. We find that we can divide these genes into five general groups: 1 Genes encoding components of the PACC signal transduction pathway, 2 Other signal transduction pathway genes, including genes from the three N. crassa MAP kinase pathways, 3 Transcriptional factor genes, 4 Autophagy genes, and 5 Other miscellaneous genes. Complementation and RIP studies verified that these genes are needed for the formation of the female mating structure, the protoperithecium, and for the maturation of a fertilized protoperithecium into a perithecium. Perithecia grafting experiments demonstrate that the autophagy genes and the cell-to-cell fusion genes (the MAK-1 and MAK-2 pathway genes are needed for the mobilization and movement of nutrients from an established vegetative hyphal network into the developing protoperithecium. Deletion mutants for the PACC pathway genes palA, palB, palC, palF, palH, and pacC were found to be defective in two aspects of female development. First, they were unable to initiate female development on synthetic crossing medium. However, they could form protoperithecia when grown on cellophane, on corn meal agar, or in response to the presence of nearby perithecia. Second, fertilized perithecia from PACC pathway mutants were unable to produce asci and complete female development. Protein localization experiments with a GFP-tagged PALA construct showed that PALA was localized in a peripheral punctate pattern, consistent with a signaling center associated with the ESCRT complex. The N. crassa PACC signal transduction pathway appears to be similar to the PacC/Rim101 pathway previously characterized in Aspergillus nidulans and Saccharomyces cerevisiae. In N. crassa the pathway plays a key role in regulating female development.

Neurospora crassa female development requires the PACC and other signal transduction pathways, transcription factors, chromatin remodeling, cell-to-cell fusion, and autophagy.

Science.gov (United States)

Chinnici, Jennifer L; Fu, Ci; Caccamise, Lauren M; Arnold, Jason W; Free, Stephen J

2014-01-01

Using a screening protocol we have identified 68 genes that are required for female development in the filamentous fungus Neurospora crassa. We find that we can divide these genes into five general groups: 1) Genes encoding components of the PACC signal transduction pathway, 2) Other signal transduction pathway genes, including genes from the three N. crassa MAP kinase pathways, 3) Transcriptional factor genes, 4) Autophagy genes, and 5) Other miscellaneous genes. Complementation and RIP studies verified that these genes are needed for the formation of the female mating structure, the protoperithecium, and for the maturation of a fertilized protoperithecium into a perithecium. Perithecia grafting experiments demonstrate that the autophagy genes and the cell-to-cell fusion genes (the MAK-1 and MAK-2 pathway genes) are needed for the mobilization and movement of nutrients from an established vegetative hyphal network into the developing protoperithecium. Deletion mutants for the PACC pathway genes palA, palB, palC, palF, palH, and pacC were found to be defective in two aspects of female development. First, they were unable to initiate female development on synthetic crossing medium. However, they could form protoperithecia when grown on cellophane, on corn meal agar, or in response to the presence of nearby perithecia. Second, fertilized perithecia from PACC pathway mutants were unable to produce asci and complete female development. Protein localization experiments with a GFP-tagged PALA construct showed that PALA was localized in a peripheral punctate pattern, consistent with a signaling center associated with the ESCRT complex. The N. crassa PACC signal transduction pathway appears to be similar to the PacC/Rim101 pathway previously characterized in Aspergillus nidulans and Saccharomyces cerevisiae. In N. crassa the pathway plays a key role in regulating female development.

Isolation, Fractionation and Characterization of Catalase from Neurospora crassa (InaCC F226)

Science.gov (United States)

Suryani; Ambarsari, L.; Lindawati, E.

2017-03-01

Catalase from Indigenous isolate Neurospora crassa InaCC F226 has been isolated, fractionated and characterized. Production of catalase by Neurospora crassa was done by using PDA medium (Potato Dextrosa Agar) and fractionated with ammonium sulphate with 20-80% saturation. Fraction 60% was optimum saturation of ammonium sulphate and had highest specific activity 3339.82 U/mg with purity 6.09 times, total protein 0.920 mg and yield 88.57%. The optimum pH and temperature for catalase activity were at 40°C and pH 7.0, respectively. The metal ions that stimulated catalase activity acted were Ca2+, Mn2+ and Zn2+, and inhibitors were EDTA, Mg2+ and Cu2+. Based on Km and Vmax values were 0.2384 mM and 13.3156 s/mM.

Differential gene expression in Neurospora crassa cell types: heterogeneity and amplification of rRNA genes. Progress report, July 1980-June 30, 1981

International Nuclear Information System (INIS)

Dutta, S.K.

1981-01-01

The significant results obtained during 1980-1981 year of the current research program are as follows: I. Studies on heterogeneity of multiple copies of rDNAs from N. crassa cell types are being continued, such as: (1) Autoradiographs of Southern transfers of EcoR 1 restricted fragments of nuclear DNA from conidia, germinated conidia (sprouts) and mycelia of N. crassa were compared after hybridization with 32 P-rDNA probe. The nuclear DNA of two hours sprout and of 16 hours mycelia gave similar hybridization patterns with EcoR 1 digest, but no such hybridization pattern was evident in conidial DNA digest; (2) Procedure for concentration of rDNAs from Neurospora species and cell types was standardized; restriction analysis of purified rDNAs is being done; (3) 35S total rDNA clone, 17S rDNA clone and 26S rDNA subclone are being used to see gross differences in the precursor rRNAs of different cell types; (4) Comparison of DNA:DNA homologies of rRNA genes with different Neurospora species. II. Post-mitochondrial DNAs of N. crassa are found to be rDNA-like and were further characterized by electron microscopic studies and are found to be approximately twice the size of SV-40 DNAs. These N. crassa post-mitochondrial DNAs hybridized with 32 P-labeled N. crassa nuclear DNAs. III. Previous studies on differential RNase sensitive DNA polymerase activity in N. Crassa cell types and on evolution of sexual morphogenesis in the genus Neurospora are completed and published. RNase sensitive DNA polymerase activity is found to be in the post-mitochondrial fraction. Heterothallism in the genus Neurospora is evolved from homothallism

The Effect of Chrysonilia crassa Additive on Duodenal & Caecal Morphology, Bacterial & Fungal Number, and Productivity of Ayam Kampung

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Turrini Yudiarti

2012-10-01

Full Text Available Fungi is a microorganism that can live in gastrointestinal tract of chicken. One type of fungi is multicellular or filamentous fungi. C.crassa is a species of filamentous fungi that has been isolated in the earlier study and it showed the best probiotic potency in vitro. The obyective of this research was to study the effect of addition of dried culture of  C.crassa in feed on intestinal & caecal morphology, bacterial & fungal number, and  productivity of indigenous chicken (ayam kampung. Research used completely randomized design with four treatments. The treatments were the level of  dried culture in basal diet (0%, 0.25 %,  0.50 % and 0.75 %. Each treatment was replicated 5 times and each replicate consists of 10 chickens. The parameters observed were : villi morphology, number of bacteria and fungi in the duodenum and cecum of chickens aged 1, 21 and 35 days and productivity i.e. feed intake, final body weight and feed conversion. The results showed that 0.50% dried culture of C.crassa could increase the duodenal villi width, decreased the number of bacterial and fungal colonies in duodenum and caecum, but it did not increase productivity. The conclusion : C.crassa could stimulate the duodenal villi development and decreased the number of the bacteria and fungi in the gastrointestinal tract, yet it has no positive impact on the chicken productivity.

The Effect of Chrysonilia crassa Additive on Duodenal & Caecal Morphology, Bacterial & Fungal Number, and Productivity of Ayam Kampung

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T. Yudiarti

2012-10-01

Full Text Available Fungi is a microorganism that can live in gastrointestinal tract of chicken. One type of fungi is multicellular or filamentous fungi. C.crassa is a species of filamentous fungi that has been isolated in the earlier study and it showed the best probiotic potency in vitro. The obyective of this research was to study the effect of addition of dried culture of C.crassa in feed on intestinal & caecal morphology, bacterial & fungal number, and productivity of indigenous chicken (ayam kampung. Research used completely randomized design with four treatments. The treatments were the level of dried culture in basal diet (0%, 0.25 %, 0.50 % and 0.75 %. Each treatment was replicated 5 times and each replicate consists of 10 chickens. The parameters observed were : villi morphology, number of bacteria and fungi in the duodenum and cecum of chickens aged 1, 21 and 35 days and productivity i.e. feed intake, final body weight and feed conversion. The results showed that 0.50% dried culture of C.crassa could increase the duodenal villi width, decreased the number of bacterial and fungal colonies in duodenum and caecum, but it did not increase productivity. The conclusion : C.crassa could stimulate the duodenal villi development and decreased the number of the bacteria and fungi in the gastrointestinal tract, yet it has no positive impact on the chicken productivity

The Effect of Chrysonilia crassa Additive on Duodenal & Caecal Morphology, Bacterial & Fungal Number, and Productivity of Ayam Kampung

OpenAIRE

Turrini Yudiarti; V. D. Yunianto B.I; R. Murwani; E. Kusdiyantini

2012-01-01

Fungi is a microorganism that can live in gastrointestinal tract of chicken. One type of fungi is multicellular or filamentous fungi. C.crassa is a species of filamentous fungi that has been isolated in the earlier study and it showed the best probiotic potency in vitro. The obyective of this research was to study the effect of addition of dried culture of  C.crassa in feed on intestinal & caecal morphology, bacterial & fungal number, and  productivity of indigenous chicken (ayam kamp...

Multiple layers of temporal and spatial control regulate accumulation of the fruiting body-specific protein APP in Sordaria macrospora and Neurospora crassa.

Science.gov (United States)

Nowrousian, Minou; Piotrowski, Markus; Kück, Ulrich

2007-07-01

During fungal fruiting body development, specialized cell types differentiate from vegetative mycelium. We have isolated a protein from the ascomycete Sordaria macrospora that is not present during vegetative growth but accumulates in perithecia. The protein was sequenced by mass spectrometry and the corresponding gene was termed app (abundant perithecial protein). app transcript occurs only after the onset of sexual development; however, the formation of ascospores is not a prerequisite for APP accumulation. The transcript of the Neurospora crassa ortholog is present prior to fertilization, but the protein accumulates only after fertilization. In crosses of N. crassa Deltaapp strains with the wild type, APP accumulates when the wild type serves as female parent, but not in the reciprocal cross; thus, the presence of a functional female app allele is necessary and sufficient for APP accumulation. These findings highlight multiple layers of temporal and spatial control of gene expression during fungal development.

Morphological mutants of Neurospora crassa: possible evidence of abnormal morphology due to changes in DNA composition

Energy Technology Data Exchange (ETDEWEB)

Chaudhuri, R K; Dutta, S.K. Ojha, M.

1973-01-01

DNA from seven experimentally induced morphological mutants and the wild type strain 74A of Neurospora crassa showed typical bimodal denaturation profiles in a Gilford 2400 spectrophotometer. The ''slime'' and ''ropy'' mutants showed a comparatively high proportion of A + T rich DNA sequences. Studies on thermal denaturation, percent hybridization, and thermal stability indicate the DNA sequences of the slime mutant were distinctly different from the normal genomes of parental DNA as well as other wild type DNAs. No such difference was noticed in any other mutant and natural isolate of the species N. crassa tested. These studies indicate possible correlation between a change in DNA nucleotide sequences and abnormal morphogenesis.

Neurospora crassa ncs-1, mid-1 and nca-2 double-mutant ...

Indian Academy of Sciences (India)

logue of Neuronal Calcium Sensor-1 has a role in growth, cal- cium stress tolerance, and ultraviolet survival. Genetica 139,. 885–894. Lew R. R., Abbas Z., Anderca M. I. and Free S. J. 2008 Phe- notype of a mechanosensitive channel mutant, mid-1, in a fil- amentous fungus, Neurospora crassa. Eukaryot. Cell. 7, 647–. 655.

Molecular Diversity of Lactic Acid Bacteria on Ileum and Coecum Broiler Chicken Fed by Chrysonilia crassa Fermentation

Science.gov (United States)

Nur Jannah, Siti; Khotimah, Husnul; Siti Ferniah, Rejeki; Sugiharto

2018-05-01

The Lactid Acid Bakteria (LAB) are microflora in the digestive tract which has positive roles in poultry’s health. One of the factors diversity of LAB in the gatrointestinal tract are influenced by feeding factor. The purpose of this study was to analyze the LAB diversity in ileum and coecum after being fed on fermented Chrysonilia crassa molecularly. LAB species diversity was analysed to provide a baseline profile of the microbial community database on the ileum and coecum digestive tract of broiler chicken of control (commercial feed) and treatment (feed with Chrysonilia crassa fermentation) by the method of Terminal Restriction Fragment Lenght Polymorphism The calculated values werethe number of phylotypes, relative abundace, Shannon-Wiener diversity index (H’), evennes index (E’), and similarity. Group of LAB detected in the control group were Lactobacillus delbrueckii (180 bp), Lactobacillus sp. (187 bp), Lactobacillus plantarum (572 bp), uncultured bacterium (87 bp) and unidentified (50 bp, 582bp). The result of this study showed that by feeding on the fermented Chrysonilia crassa feed had resulted in the decreasing of LAB diversity, i.e. ileum (0.66), coecum (0.48) compared with commercial feed (control) that was ileum (0.84), coecum (1.05).

Growth responses of Neurospora crassa to increased partial pressures of the noble gases and nitrogen.

Science.gov (United States)

Buchheit, R G; Schreiner, H R; Doebbler, G F

1966-02-01

Buchheit, R. G. (Union Carbide Corp., Tonawanda, N.Y.), H. R. Schreiner, and G. F. Doebbler. Growth responses of Neurospora crassa to increased partial pressures of the noble gases and nitrogen. J. Bacteriol. 91:622-627. 1966.-Growth rate of the fungus Neurospora crassa depends in part on the nature of metabolically "inert gas" present in its environment. At high partial pressures, the noble gas elements (helium, neon, argon, krypton, and xenon) inhibit growth in the order: Xe > Kr> Ar > Ne > He. Nitrogen (N(2)) closely resembles He in inhibitory effectiveness. Partial pressures required for 50% inhibition of growth were: Xe (0.8 atm), Kr (1.6 atm), Ar (3.8 atm), Ne (35 atm), and He ( approximately 300 atm). With respect to inhibition of growth, the noble gases and N(2) differ qualitatively and quantitatively from the order of effectiveness found with other biological effects, i.e., narcosis, inhibition of insect development, depression of O(2)-dependent radiation sensitivity, and effects on tissue-slice glycolysis and respiration. Partial pressures giving 50% inhibition of N. crassa growth parallel various physical properties (i.e., solubilities, solubility ratios, etc.) of the noble gases. Linear correlation of 50% inhibition pressures to the polarizability and of the logarithm of pressure to the first and second ionization potentials suggests the involvement of weak intermolecular interactions or charge-transfer in the biological activity of the noble gases.

Conidiation of Neurospora crassa induced by treatment with natrium fluoride in submerged culture

Energy Technology Data Exchange (ETDEWEB)

Timberlake, W E; Turian, G

1975-01-01

A transient treatment of pregerminated conidia of Neurospora crassa with NaF induced young, submerged cultures to prematurely differentiate conidia. The inductive treatment decreased the rate of respiration (with lower RQ), reduced the relative concentration of nucleoside triphosphates, and inhibited leucine incorporation into protein and adenosine incorporation into RNA.

The synthesis of Phosphate-repressible alkaline phosphatase do not appear to be regulated by ambient pH in the filamentous mould Neurospora crassa

Directory of Open Access Journals (Sweden)

Nozawa Sérgio R.

2002-01-01

Full Text Available In order to investigate further the adaptive response of moulds to ambient pH, we have measured by ELISA the pho-2-encoded Pi-repressible alkaline phosphatase synthesised by Neurospora crassa. We showed that the 74A and pho-2A strains of this mould secrete similar amounts of the pho-2-encoded enzyme irrespective of ambient pH, when both the preg and pgov genes are not functional, i.e., in strains nuc-2+ growing under Pi-starvation. This suggests that pho-2, which is responsive to Pi starvation via the action of genes nuc-2, preg, pgov and nuc-1, is not a gene responsive to ambient pH and that the differential glycosylation observed for the Pi-repressible alkaline phosphatase retained by the mycelium at pH 5.6 or secreted into the growth medium at pH 8.0 is the genetic response to ambient pH sensing in N. crassa.

Alternative Oxidase Transcription Factors AOD2 and AOD5 of Neurospora crassa Control the Expression of Genes Involved in Energy Production and Metabolism.

Science.gov (United States)

Qi, Zhigang; Smith, Kristina M; Bredeweg, Erin L; Bosnjak, Natasa; Freitag, Michael; Nargang, Frank E

2017-02-09

In Neurospora crassa , blocking the function of the standard mitochondrial electron transport chain results in the induction of an alternative oxidase (AOX). AOX transfers electrons directly from ubiquinol to molecular oxygen. AOX serves as a model of retrograde regulation since it is encoded by a nuclear gene that is regulated in response to signals from mitochondria. The N. crassa transcription factors AOD2 and AOD5 are necessary for the expression of the AOX gene. To gain insight into the mechanism by which these factors function, and to determine if they have roles in the expression of additional genes in N. crassa , we constructed strains expressing only tagged versions of the proteins. Cell fractionation experiments showed that both proteins are localized to the nucleus under both AOX inducing and noninducing conditions. Furthermore, chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) analysis revealed that the proteins are bound to the promoter region of the AOX gene under both conditions. ChIP-seq also showed that the transcription factors bind to the upstream regions of a number of genes that are involved in energy production and metabolism. Dependence on AOD2 and AOD5 for the expression of several of these genes was verified by quantitative PCR. The majority of ChIP-seq peaks observed were enriched for both AOD2 and AOD5. However, we also observed occasional sites where one factor appeared to bind preferentially. The most striking of these was a conserved sequence that bound large amounts of AOD2 but little AOD5. This sequence was found within a 310 bp repeat unit that occurs at several locations in the genome. Copyright © 2017 Qi et al.

Engineering Neurospora crassa for cellobionate production directly from cellulose without any enzyme addition

Science.gov (United States)

A previously engineered strain of N. crassa F5'ace-1'cre-1'ndvB) with six out of seven ß-glucosidase (bgl) genes, two transcription factors (cre1 and ace-1) and cellobionate phosphorylase (ndvB) deleted was able to produce cellobiose and cellobionate directly from cellulose without the addition of e...

Neurospora crassa ASM-1 complements the conidiation defect in a stuA mutant of Aspergillus nidulans.

Science.gov (United States)

Chung, Dawoon; Upadhyay, Srijana; Bomer, Brigitte; Wilkinson, Heather H; Ebbole, Daniel J; Shaw, Brian D

2015-01-01

Aspergillus nidulans StuA and Neurospora crassa ASM-1 are orthologous APSES (ASM-1, PHD1, SOK2, Efg1, StuA) transcription factors conserved across a diverse group of fungi. StuA and ASM-1 have roles in asexual (conidiation) and sexual (ascospore formation) development in both organisms. To address the hypothesis that the last common ancestor of these diverse fungi regulated conidiation with similar genes, asm-1 was introduced into the stuA1 mutant of A. nidulans. Expression of asm-1 complemented defective conidiophore morphology and restored conidia production to wild type levels in stuA1. Expression of asm-1 in the stuA1 strain did not rescue the defect in sexual development. When the conidiation regulator AbaA was tagged at its C-terminus with GFP in A. nidulans, it localized to nuclei in phialides. When expressed in the stuA1 mutant, AbaA::GFP localized to nuclei in conidiophores but no longer was confined to phialides, suggesting that expression of AbaA in specific cell types of the conidiophore was conditioned by StuA. Our data suggest that the function in conidiation of StuA and ASM-1 is conserved and support the view that, despite the great morphological and ontogenic diversity of their condiphores, the last common ancestor of A. nidulans and N. crassa produced an ortholog of StuA that was involved in conidiophore development. © 2015 by The Mycological Society of America.

Localization and role of MYO-1, an endocytic protein in hyphae of Neurospora crassa.

Science.gov (United States)

Lara-Rojas, Fernando; Bartnicki-García, Salomón; Mouriño-Pérez, Rosa R

2016-03-01

The subapical endocytic collar is a prominent feature of hyphae of Neurospora crassa. It comprises a dynamic collection of actin patches associated with a number of proteins required for endocytosis, namely, ARP-2/3 complex, fimbrin, coronin, etc. We presently show that MYO-1 is another key component of this endocytic collar. A myo-1 sequence was identified in the genome of N. crassa and used it to generate a strain with a myo-1-sgfp allele under the ccg1 promoter. Examination of living hyphae by confocal microscopy, revealed MYO-1-GFP located mainly as a dynamic collection of small patches arranged in collar-like fashion in the hyphal subapex. Dual tagging showed MYO-1-GFP partially colocalized with two other endocytic proteins, fimbrin and coronin. MYO-1 was also present during septum formation. By recovering a viable strain, albeit severely inhibited, after deletion of myo-1, it was possible to investigate the phenotypic consequences of the elimination of MYO-1. Deletion of myo-1 caused a severe reduction in growth rate (95%), near absence of aerial mycelium and no conidiation. A reduced uptake of the lipophilic dye FM4-64 indicated a deficiency in endocytosis in the Δmyo-1 mutant. Hyphae were produced by the Δmyo-1 mutant but their morphogenesis was severely affected; hyphal morphology was distorted displaying irregular periods of isotropic and polarized growth. The morphological alterations were accompanied, and presumably caused, by a disruption in the organization and dynamics of a myosin-deprived actin cytoskeleton that, ultimately, compromised the stability and function of the Spitzenkörper as a vesicle supply center. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of the temperature-sensitive mutations un-7 and png-1 in Neurospora crassa.

Science.gov (United States)

Dieterle, Michael G; Wiest, Aric E; Plamann, Mike; McCluskey, Kevin

2010-05-18

The model filamentous fungus Neurospora crassa has been studied for over fifty years and many temperature-sensitive mutants have been generated. While most of these have been mapped genetically, many remain anonymous. The mutation in the N. crassa temperature-sensitive lethal mutant un-7 was identified by a complementation based approach as being in the open reading frame designated NCU00651 on linkage group I. Other mutations in this gene have been identified that lead to a temperature-sensitive morphological phenotype called png-1. The mutations underlying un-7 result in a serine to phenylalanine change at position 273 and an isoleucine to valine change at position 390, while the mutation in png-1 was found to result in a serine to leucine change at position 279 although there were other conservative changes in this allele. The overall morphology of the strain carrying the un-7 mutation is compared to strains carrying the png-1 mutation and these mutations are evaluated in the context of other temperature-sensitive mutants in Neurospora.

Cell Wall Composition of Neurospora crassa Under Conditions of Copper Toxicity

OpenAIRE

Subramanyam, C.; Venkateswerlu, G.; Rao, S. L. N.

1983-01-01

The mycelia of Neurospora crassa grown in the presence of high concentrations of copper were blue in color, but only on a medium containing inorganic nitrate and phosphate as the nitrogen and phosphate sources, respectively. The cell wall isolate of the blue mycelia contained large amounts (12%) of copper and higher amounts of chitosan, phosphate, and amino groups, with a 42% decrease in the chitin content. Although all the glucosamine of the cell wall of control cultures could be released wi...

A Eukaryote without Catalase-Containing Microbodies : Neurospora crassa Exhibits a Unique Cellular Distribution of Its Four Catalases

NARCIS (Netherlands)

Schliebs, Wolfgang; Würtz, Christian; Kunau, Wolf-Hubert; Veenhuis, Marten; Rottensteiner, Hanspeter; Wuertz, Christian

2006-01-01

Microbodies usually house catalase to decompose hydrogen peroxide generated within the organelle by the action of various oxidases. Here we have analyzed whether peroxisomes (i.e., catalase-containing microbodies) exist in Neurospora crassa. Three distinct catalase isoforms were identified by native

Deletion of pH Regulator pac-3 Affects Cellulase and Xylanase Activity during Sugarcane Bagasse Degradation by Neurospora crassa.

Directory of Open Access Journals (Sweden)

Amanda Cristina Campos Antoniêto

Full Text Available Microorganisms play a vital role in bioethanol production whose usage as fuel energy is increasing worldwide. The filamentous fungus Neurospora crassa synthesize and secrete the major enzymes involved in plant cell wall deconstruction. The production of cellulases and hemicellulases is known to be affected by the environmental pH; however, the regulatory mechanisms of this process are still poorly understood. In this study, we investigated the role of the pH regulator PAC-3 in N. crassa during their growth on sugarcane bagasse at different pH conditions. Our data indicate that secretion of cellulolytic enzymes is reduced in the mutant Δpac-3 at alkaline pH, whereas xylanases are positively regulated by PAC-3 in acidic (pH 5.0, neutral (pH 7.0, and alkaline (pH 10.0 medium. Gene expression profiles, evaluated by real-time qPCR, revealed that genes encoding cellulases and hemicellulases are also subject to PAC-3 control. Moreover, deletion of pac-3 affects the expression of transcription factor-encoding genes. Together, the results suggest that the regulation of holocellulase genes by PAC-3 can occur as directly as in indirect manner. Our study helps improve the understanding of holocellulolytic performance in response to PAC-3 and should thereby contribute to the better use of N. crassa in the biotechnology industry.

Epigenetic and Posttranslational Modifications in Light Signal Transduction and the Circadian Clock in Neurospora crassa

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Marco Proietto

2015-07-01

Full Text Available Blue light, a key abiotic signal, regulates a wide variety of physiological processes in many organisms. One of these phenomena is the circadian rhythm presents in organisms sensitive to the phase-setting effects of blue light and under control of the daily alternation of light and dark. Circadian clocks consist of autoregulatory alternating negative and positive feedback loops intimately connected with the cellular metabolism and biochemical processes. Neurospora crassa provides an excellent model for studying the molecular mechanisms involved in these phenomena. The White Collar Complex (WCC, a blue-light receptor and transcription factor of the circadian oscillator, and Frequency (FRQ, the circadian clock pacemaker, are at the core of the Neurospora circadian system. The eukaryotic circadian clock relies on transcriptional/translational feedback loops: some proteins rhythmically repress their own synthesis by inhibiting the activity of their transcriptional factors, generating self-sustained oscillations over a period of about 24 h. One of the basic mechanisms that perpetuate self-sustained oscillations is post translation modification (PTM. The acronym PTM generically indicates the addition of acetyl, methyl, sumoyl, or phosphoric groups to various types of proteins. The protein can be regulatory or enzymatic or a component of the chromatin. PTMs influence protein stability, interaction, localization, activity, and chromatin packaging. Chromatin modification and PTMs have been implicated in regulating circadian clock function in Neurospora. Research into the epigenetic control of transcription factors such as WCC has yielded new insights into the temporal modulation of light-dependent gene transcription. Here we report on epigenetic and protein PTMs in the regulation of the Neurospora crassa circadian clock. We also present a model that illustrates the molecular mechanisms at the basis of the blue light control of the circadian clock.

Production of cellobionate from cellulose using an engineered Neurospora crassa strain with laccase and redox mediator addition

Science.gov (United States)

We report a novel production process for cellobionic acid from cellulose using an engineered fungal strain with the exogenous addition of laccase and a redox mediator. A previously engineered strain of Neurospora crassa (F5'ace-1'cre-1'ndvB) was shown to produce cellobionate directly from cellulose ...

The putative cellodextrin transporter-like protein CLP1 is involved in cellulase induction in Neurospora crassa.

Science.gov (United States)

Cai, Pengli; Wang, Bang; Ji, Jingxiao; Jiang, Yongsheng; Wan, Li; Tian, Chaoguang; Ma, Yanhe

2015-01-09

Neurospora crassa recently has become a novel system to investigate cellulase induction. Here, we discovered a novel membrane protein, cellodextrin transporter-like protein 1 (CLP1; NCU05853), a putative cellodextrin transporter-like protein that is a critical component of the cellulase induction pathway in N. crassa. Although CLP1 protein cannot transport cellodextrin, the suppression of cellulase induction by this protein was discovered on both cellobiose and Avicel. The co-disruption of the cellodextrin transporters cdt2 and clp1 in strain Δ3βG formed strain CPL7. With induction by cellobiose, cellulase production was enhanced 6.9-fold in CPL7 compared with Δ3βG. We also showed that the suppression of cellulase expression by CLP1 occurred by repressing the expression of cellodextrin transporters, particularly cdt1 expression. Transcriptome analysis of the hypercellulase-producing strain CPL7 showed that the cellulase expression machinery was dramatically stimulated, as were the cellulase enzyme genes including the inducer transporters and the major transcriptional regulators. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

The Putative Cellodextrin Transporter-like Protein CLP1 Is Involved in Cellulase Induction in Neurospora crassa*

Science.gov (United States)

Cai, Pengli; Wang, Bang; Ji, Jingxiao; Jiang, Yongsheng; Wan, Li; Tian, Chaoguang; Ma, Yanhe

2015-01-01

Neurospora crassa recently has become a novel system to investigate cellulase induction. Here, we discovered a novel membrane protein, cellodextrin transporter-like protein 1 (CLP1; NCU05853), a putative cellodextrin transporter-like protein that is a critical component of the cellulase induction pathway in N. crassa. Although CLP1 protein cannot transport cellodextrin, the suppression of cellulase induction by this protein was discovered on both cellobiose and Avicel. The co-disruption of the cellodextrin transporters cdt2 and clp1 in strain Δ3βG formed strain CPL7. With induction by cellobiose, cellulase production was enhanced 6.9-fold in CPL7 compared with Δ3βG. We also showed that the suppression of cellulase expression by CLP1 occurred by repressing the expression of cellodextrin transporters, particularly cdt1 expression. Transcriptome analysis of the hypercellulase-producing strain CPL7 showed that the cellulase expression machinery was dramatically stimulated, as were the cellulase enzyme genes including the inducer transporters and the major transcriptional regulators. PMID:25398875

Structural studies of the vacuolar membrane ATPase from Neurospora crassa and comparison with the tonoplast membrane ATPase and Zea mays

International Nuclear Information System (INIS)

Bowman, E.J.; Mandala, S.; Taiz, L.; Bowman, B.J.

1986-01-01

The H + translocating ATPase located on vacuolar membranes of Neurospora crassa was partially purified by solubilization in two detergents, Triton X-100 and N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate, followed by centrifugation on sucrose density gradients. Two polypeptides of M/sub r/ ≅ 70,000 and ≅ 62,000 consistently migrated with activity, along with several minor bands of lower molecular weight. Radioactively labeled inhibitors of ATPase activity, N-[ 14 C]ethylmaleimide and 7-chloro-4-nitro[ 14 C]benzo-2-oxa-1,3-diazole, labeled the M/sub r/ ≅ 70,000 polypeptide; this labeling was reduced in the presence of ATP. N,N'-[ 14 C]dicyclohexylcarbodiimide labeled a polypeptide of M/sub r/ ≅ 15,000. Estimation of the functional size of the vacuolar membrane ATPase by radiation inactivation gave a value of M/sub r/ 5.2 x 10 5 , 10-15% larger than the mitochondrial ATPase. The Neurospora vacuolar ATPase showed no crossreactivity with antiserum to plasma membrane or mitochrondrial ATPase but stongly crossreacted with antiserum against a polypeptide of M/sub r/ ≅ 70,000 associated with the tonoplast ATPase of corn coleoptiles. These results suggest that fungal and plant vacuolar ATPases may be large multisubunit complexes, somewhat similar to, but immunologically distinct from, known F 0 F 1 ATPases

Selection and evaluation of reference genes for expression studies with quantitative PCR in the model fungus Neurospora crassa under different environmental conditions in continuous culture.

Directory of Open Access Journals (Sweden)

Kathleen D Cusick

Full Text Available Neurospora crassa has served as a model organism for studying circadian pathways and more recently has gained attention in the biofuel industry due to its enhanced capacity for cellulase production. However, in order to optimize N. crassa for biotechnological applications, metabolic pathways during growth under different environmental conditions must be addressed. Reverse-transcription quantitative PCR (RT-qPCR is a technique that provides a high-throughput platform from which to measure the expression of a large set of genes over time. The selection of a suitable reference gene is critical for gene expression studies using relative quantification, as this strategy is based on normalization of target gene expression to a reference gene whose expression is stable under the experimental conditions. This study evaluated twelve candidate reference genes for use with N. crassa when grown in continuous culture bioreactors under different light and temperature conditions. Based on combined stability values from NormFinder and Best Keeper software packages, the following are the most appropriate reference genes under conditions of: (1 light/dark cycling: btl, asl, and vma1; (2 all-dark growth: btl, tbp, vma1, and vma2; (3 temperature flux: btl, vma1, act, and asl; (4 all conditions combined: vma1, vma2, tbp, and btl. Since N. crassa exists as different cell types (uni- or multi-nucleated, expression changes in a subset of the candidate genes was further assessed using absolute quantification. A strong negative correlation was found to exist between ratio and threshold cycle (CT values, demonstrating that CT changes serve as a reliable reflection of transcript, and not gene copy number, fluctuations. The results of this study identified genes that are appropriate for use as reference genes in RT-qPCR studies with N. crassa and demonstrated that even with the presence of different cell types, relative quantification is an acceptable method for measuring

Selection and evaluation of reference genes for expression studies with quantitative PCR in the model fungus Neurospora crassa under different environmental conditions in continuous culture.

Science.gov (United States)

Cusick, Kathleen D; Fitzgerald, Lisa A; Pirlo, Russell K; Cockrell, Allison L; Petersen, Emily R; Biffinger, Justin C

2014-01-01

Neurospora crassa has served as a model organism for studying circadian pathways and more recently has gained attention in the biofuel industry due to its enhanced capacity for cellulase production. However, in order to optimize N. crassa for biotechnological applications, metabolic pathways during growth under different environmental conditions must be addressed. Reverse-transcription quantitative PCR (RT-qPCR) is a technique that provides a high-throughput platform from which to measure the expression of a large set of genes over time. The selection of a suitable reference gene is critical for gene expression studies using relative quantification, as this strategy is based on normalization of target gene expression to a reference gene whose expression is stable under the experimental conditions. This study evaluated twelve candidate reference genes for use with N. crassa when grown in continuous culture bioreactors under different light and temperature conditions. Based on combined stability values from NormFinder and Best Keeper software packages, the following are the most appropriate reference genes under conditions of: (1) light/dark cycling: btl, asl, and vma1; (2) all-dark growth: btl, tbp, vma1, and vma2; (3) temperature flux: btl, vma1, act, and asl; (4) all conditions combined: vma1, vma2, tbp, and btl. Since N. crassa exists as different cell types (uni- or multi-nucleated), expression changes in a subset of the candidate genes was further assessed using absolute quantification. A strong negative correlation was found to exist between ratio and threshold cycle (CT) values, demonstrating that CT changes serve as a reliable reflection of transcript, and not gene copy number, fluctuations. The results of this study identified genes that are appropriate for use as reference genes in RT-qPCR studies with N. crassa and demonstrated that even with the presence of different cell types, relative quantification is an acceptable method for measuring gene

Analyses of Dynein Heavy Chain Mutations Reveal Complex Interactions Between Dynein Motor Domains and Cellular Dynein Functions

Science.gov (United States)

Sivagurunathan, Senthilkumar; Schnittker, Robert R.; Razafsky, David S.; Nandini, Swaran; Plamann, Michael D.; King, Stephen J.

2012-01-01

Cytoplasmic dynein transports cargoes for a variety of crucial cellular functions. However, since dynein is essential in most eukaryotic organisms, the in-depth study of the cellular function of dynein via genetic analysis of dynein mutations has not been practical. Here, we identify and characterize 34 different dynein heavy chain mutations using a genetic screen of the ascomycete fungus Neurospora crassa, in which dynein is nonessential. Interestingly, our studies show that these mutations segregate into five different classes based on the in vivo localization of the mutated dynein motors. Furthermore, we have determined that the different classes of dynein mutations alter vesicle trafficking, microtubule organization, and nuclear distribution in distinct ways and require dynactin to different extents. In addition, biochemical analyses of dynein from one mutant strain show a strong correlation between its in vitro biochemical properties and the aberrant intracellular function of that altered dynein. When the mutations were mapped to the published dynein crystal structure, we found that the three-dimensional structural locations of the heavy chain mutations were linked to particular classes of altered dynein functions observed in cells. Together, our data indicate that the five classes of dynein mutations represent the entrapment of dynein at five separate points in the dynein mechanochemical and transport cycles. We have developed N. crassa as a model system where we can dissect the complexities of dynein structure, function, and interaction with other proteins with genetic, biochemical, and cell biological studies. PMID:22649085

A circadian rhythm of conidiation in Neurospora crassa (L-12)

Science.gov (United States)

Miyoshi, Yashuhiro

1993-01-01

Two fungi growth chambers containing six growth tubes each are used in this experiment. One chamber is for the space experiment; the other is for the simultaneous ground control experiment. The hyphae of Neurospora crassa band A mutant are inoculated at one end of each tube. Both the chambers are kept at 3 C plus or minus 1.5 C to stop hyphae growth until the Spacelab is activated. After the activation, each chamber is transferred simultaneously to the Spacelab and a phytotron in KSC and kept in continuous light at the same temperature. After about 24 hours of light exposure, each chamber is inserted into a growth chamber bag to keep it in constant darkness. The circadian rhythm of conidiation is initiated by this light to dark transition. After the dark incubation for 5 days at room temperature, both the growth chambers are kept at 3 C plus or minus 1.5 C to stop growth of the hyphae. After the space shuttle lands, both conidiation patterns are compared and analyzed. It has been known that numerous physiological phenomena show circadian rhythms. They are characterized by the fact that the oscillation can persist under constant conditions of light and temperature. Therefore, it has been accepted by most investigators that the generation mechanism of the circadian rhythm is endogeneous. However, one cannot reject the possibility that these rhythms are caused by some geophysical exogeneous factor having a 24-hour period, such as atmospheric pressure, gravity, or electromagnetic radiation. We use Neurospora crassa band A mutual which shows an obvious circadian rhythm in its spore-forming (conidiation) on the ground, and we intend to attempt the conidation of this mutant in the Spacelab where 24-hour periodicity is severely attenuated and to elucidate the effect of the geophysical exogeneous factor in the generation mechanism of the circadian rhythm.

X-ray-induced specific-locus mutations in the ad-3 region of two-component heterokaryons of Neurospora crassa

International Nuclear Information System (INIS)

Serres, F.J. de

1989-01-01

More extensive genetic tests have been preformed on a series of 832 X-ray-induced specific-locus mutations in the ad-3 region of a 2-component heterokaryon of Neurospora crassa, reported earlier. Using new tester strains and techniques for performing large-scale genetic tests to characterize ad-3 mutants induced in 2-component heterokaryons, new data have been obtained on this sample of X-ray-induced mutants. These new data show that unexpectedly high frequencies of both single-locus mutations and multilocus deletions in the ad-3 region have addition, but separate, sites of recessive lethal damage in the imeediately adjacent genetic regions. The frequencies of these X-ray-induced multiple-locus mutants in the ad-3 region are orders of magnitude higher than expected on the basis of target theory and classical models of chromosome structure during interphase. Current models of interphase chromosome structure in higher eukaryotes as revealed by chromosome 'painting' offer a possible explanation of the Neurospora data. (author). 25 refs.; 5 figs

La formacion de anillos de crecimiento en Fissurella crassa en el norte de Chile

OpenAIRE

Bretos, Marta

1980-01-01

Growth discontinuity in molluscs result in the formation of rings on their shells. Two kind of rings may be formed: disturbance and growth rings. Growth rings can be used to determine the age of molluscs with long life span. For this, it is necessary to know how many growth rings are formed per year. It has been demonstrated experimentally, using marked specimens, that F. crassa forms two growth rings per year at Huayquique, Northern Chile. They are formed during winter and summer. Disturbanc...

Effect of dietary supplementation with Rhizopus oryzae or Chrysonilia crassa on growth performance, blood profile, intestinal microbial population, and carcass traits in broilers exposed to heat stress

OpenAIRE

S. Sugiharto; T. Yudiarti; I. Isroli; E. Widiastuti; F. D. Putra

2017-01-01

Dietary supplementation of additives has recently been part of strategies to deal with the detrimental effects of heat stress (HS) on the performance and carcass traits in broiler chicks. This study aimed to investigate the effect of dietary supplementation with the fungi Rhizopus oryzae or Chrysonilia crassa on growth, blood profile, intestinal microbial population and carcass traits in broiler chicks subjected to HS. R. oryzae and C. crassa are filamentous fungi isolated from...

Proteomic alterations induced by ionic liquids in Aspergillus nidulans and Neurospora crassa.

Science.gov (United States)

Martins, Isabel; Hartmann, Diego O; Alves, Paula C; Planchon, Sébastien; Renaut, Jenny; Leitão, M Cristina; Rebelo, Luís P N; Silva Pereira, Cristina

2013-12-06

This study constitutes the first attempt to understand at the proteomic level the fungal response to ionic liquid stress. Ascomycota are able to grow in media supplemented with high concentrations of an ionic liquid, which, in turn, lead to major alterations in the fungal metabolic footprint. Herein, we analysed the differential accumulation of mycelial proteins in Aspergillus nidulans and Neurospora crassa after their exposure to two of the most commonly used ionic liquids: 1-ethyl-3-methylimidazolium chloride or cholinium chloride. Data obtained showed that numerous stress-responsive proteins (e.g. anti-ROS defence proteins) as well as several critical biological processes and/or pathways were affected by either ionic liquid. Amongst other changes, these compounds altered developmental programmes in both fungi (e.g. promoting the development of Hülle cells or conidiation) and led to accumulation of osmolytes, some of which may play an important role in multiple stress responses. In particular, in N. crassa, both ionic liquids increased the levels of proteins which are likely involved in the biosynthesis of unusual metabolites. These data potentially open new perspectives on ionic liquid research, furthering their conscious design and their use to trigger production of targeted metabolites. The present study emphasises the importance of understanding ionic liquid's stress responses, crucial to further their safe large-scale usage. Knowledge of the alterations prompted at a cellular and biochemical level gives also fresh perspectives on how to employ these "novel" compounds to manipulate proteins or pathways of biotechnological value. The results presented here provide meaningful insights into the understanding of fungi stress and adaptation responses to anthropogenic chemicals used in industry. © 2013.

Inactivation of carotenoid-producing and albino strains of Neurospora crassa by visible light, blacklight, and ultraviolet radiation

International Nuclear Information System (INIS)

Blanc, P.L.; Tuveson, R.W.; Sargent, M.L.

1976-01-01

Suspensions of Neurospora crassa conidia were inactivated by blacklight (BL) radiation (300 to 425 nm) in the absence of exogenous photosensitizing compounds. Carotenoid-containing wild-type conidia were less sensitive to BL radiation than albino conidia, showing a dose enhancement factor (DEF) of 1.2 for dose levels resulting in less than 10 percent survival. The same strains were about equally sensitive to shortwave ultraviolet (uv) inactivation. The kinetics of BL inactivation are similar to those of photodynamic inactivation by visible light in the presence of a photosensitizing dye (methylene blue). Only limited inactivation by visible light in the absence of exogenous photosensitizers was observed. BL and UV inactivations are probably caused by different mechanisms since wild-type conidia are only slightly more resistant to BL radiation (DEF = 1.2 at 1.0 percent survival) than are conidia from a uv-sensitive strain (upr-1, uvs-3). The BL-induced lethal lesions are probably not cyclobutyl pyrimidine dimers since BL-inactivated Haemophilus influenzae transforming deoxyribonucleic acid is not photoreactivated by N. crassa wild-type enzyme extracts, whereas uv-inactivated transforming deoxyribonucleic acid is photoreactivable with this treatment

Functional characterization of the Woronin body protein WscA of the pathogenic mold Aspergillus fumigatus.

Science.gov (United States)

Leonhardt, Yannik; Beck, Julia; Ebel, Frank

2016-05-01

Woronin bodies are fungal-specific organelles that seal damaged hyphal compartments and thereby contribute to the stress resistance and virulence of filamentous fungi. In this study, we have characterized the Aspergillus fumigatus Woronin body protein WscA. WscA is homologous to Neurospora crassa WSC, a protein that was shown to be important for biogenesis, segregation and positioning of Woronin bodies. WscA and WSC both belong to the Mpv17/PMP22 family of peroxisomal membrane proteins. An A. fumigatus ΔwscA mutant is unable to form Woronin bodies, and HexA, the protein that forms the crystal-like core of Woronin bodies, accumulates in large peroxisomes instead. The ΔwscA mutant showed no defect in segregation of HexA containing organelles, as has been reported for the corresponding N. crassa mutant. In the peroxisomes of the A. fumigatus mutant, HexA assembles into compact, donut-shaped structures. Experiments with GFP fusion proteins revealed that WscA function is highly sensitive to these modifications, in particular to an N-terminal fusion of GFP. In N. crassa, WSC was shown to be essentially required for Woronin body positioning, but the respective domain is not conserved in most other Pezizomycotina, including A. fumigatus. We have recently found evidence that HexA may have a direct role in WB positioning, since a HexA-GFP fusion protein, lacking a functional PTS1 motif, is efficiently recruited to the septal pore. In the current study we show that this targeting of HexA-GFP is independent of WscA. Copyright © 2016 Elsevier GmbH. All rights reserved.

La formación de anillos de crecimiento en Fissurella crassa en el norte de Chile

OpenAIRE

Marta Bretos

1980-01-01

Growth discontinuity in molluscs result in the formation of rings on their shells. Two kind of rings may be formed: disturbance and growth rings. Growth rings can be used to determine the age of molluscs with long life span. For this, it is necessary to know how many growth rings are formed per year. It has been demonstrated experimentally, using marked specimens, that F. crassa forms two growth rings per year at Huayquique, Northern Chile. They are formed during winter and summer. Disturbanc...

Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa

Energy Technology Data Exchange (ETDEWEB)

McCluskey, Kevin; Wiest, Aric E.; Grigoriev, Igor V.; Lipzen, Anna; Martin, Joel; Schackwitz, Wendy; Baker, Scott E.

2011-06-02

Classical forward genetics has been foundational to modern biology, and has been the paradigm for characterizing the role of genes in shaping phenotypes for decades. In recent years, reverse genetics has been used to identify the functions of genes, via the intentional introduction of variation and subsequent evaluation in physiological, molecular, and even population contexts. These approaches are complementary and whole genome analysis serves as a bridge between the two. We report in this article the whole genome sequencing of eighteen classical mutant strains of Neurospora crassa and the putative identification of the mutations associated with corresponding mutant phenotypes. Although some strains carry multiple unique nonsynonymous, nonsense, or frameshift mutations, the combined power of limiting the scope of the search based on genetic markers and of using a comparative analysis among the eighteen genomes provides strong support for the association between mutation and phenotype. For ten of the mutants, the mutant phenotype is recapitulated in classical or gene deletion mutants in Neurospora or other filamentous fungi. From thirteen to 137 nonsense mutations are present in each strain and indel sizes are shown to be highly skewed in gene coding sequence. Significant additional genetic variation was found in the eighteen mutant strains, and this variability defines multiple alleles of many genes. These alleles may be useful in further genetic and molecular analysis of known and yet-to-be-discovered functions and they invite new interpretations of molecular and genetic interactions in classical mutant strains.

Characterization of MMS-sensitive mutants of Neurospora crassa

Energy Technology Data Exchange (ETDEWEB)

DeLange, A.M.; Mishra, N.C.

1982-01-01

Several MMS-sensitive mutants of Neurospora crassa were compared with the wild-type strain for their relative sensitivities to UV, X-ray, and histidine. They were also compared for the frequency of spontaneous mutation at the loci which confer resistance to p-fluorophenylalanine. The mutants were also examined for possible defects in meiotic behavior in homozygous crosses and for any change in the inducible DNA salvage pathways. On the basis of these characterizations, the present MMS-sensitive mutants of Neurospora can be placed into three groups. On the basis of data presented, the MMS sensitivity of the first group mutants cannot be ascertained to arise from a defect in the DNA repair pathways; instead, it may stem from altered cell permeability or other pleotropic effects of the mus mutations. However, it can be suggested that the second and third group of mus mutants may indeed result from a defect in the DNA repair pathways controlled by the mus genes; this conclusion is based on their cross-sensitivity to a number of DNA-damaging agents such as MMS, UV and/or X-rays, high frequencies of spontaneous mutation and defects in meiotic behavior.

Identification of TTAGGG-binding proteins in Neurospora crassa, a fungus with vertebrate-like telomere repeats.

Science.gov (United States)

Casas-Vila, Núria; Scheibe, Marion; Freiwald, Anja; Kappei, Dennis; Butter, Falk

2015-11-17

To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical TTAGGG motif found in vertebrates and also several other fungi. Using label-free quantitative proteomics, we here investigate the telosome of Neurospora crassa, a fungus with canonical telomeric repeats. We show that at least six of the candidates detected in our screen are direct TTAGGG-repeat binding proteins. While three of the direct interactors (NCU03416 [ncTbf1], NCU01991 [ncTbf2] and NCU02182 [ncTay1]) feature the known myb/homeobox DNA interaction domain also found in the vertebrate telomeric factors, we additionally show that a zinc-finger protein (NCU07846) and two proteins without any annotated DNA-binding domain (NCU02644 and NCU05718) are also direct double-strand TTAGGG binders. We further find two single-strand binders (NCU02404 [ncGbp2] and NCU07735 [ncTcg1]). By quantitative label-free interactomics we identify TTAGGG-binding proteins in Neurospora crassa, suggesting candidates for telomeric factors that are supported by phylogenomic comparison with yeast species. Intriguingly, homologs in yeast species with degenerated telomeric repeats are also TTAGGG-binding proteins, e.g. in S. cerevisiae Tbf1 recognizes the TTAGGG motif found in its subtelomeres. However, there is also a subset of proteins that is not conserved. While a rudimentary core TTAGGG-recognition machinery may be conserved across yeast species, our data suggests Neurospora as an emerging model organism with unique features.

Genetic and biochemical characterization of the GH72 family of cell wall transglycosylases in Neurospora crassa.

Science.gov (United States)

Ao, Jie; Free, Stephen J

2017-04-01

The Neurospora crassa genome encodes five GH72 family transglycosylases, and four of these enzymes (GEL-1, GEL-2, GEL-3 and GEL-5) have been found to be present in the cell wall proteome. We carried out an extensive genetic analysis on the role of these four transglycosylases in cell wall biogenesis and demonstrated that the transglycosylases are required for the formation of a normal cell wall. As suggested by the proteomic analysis, we found that multiple transglycosylases were being expressed in N. crassa cells and that different combinations of the enzymes are required in different cell types. The combination of GEL-1, GEL-2 and GEL-5 is required for the growth of vegetative hyphae, while the GEL-1, GEL-2, GEL-3 combination is needed for the production of aerial hyphae and conidia. Our data demonstrates that the enzymes are redundant with partially overlapping enzymatic activities, which provides the fungus with a robust cell wall biosynthetic system. Characterization of the transglycosylase-deficient mutants demonstrated that the incorporation of cell wall proteins was severely compromised. Interestingly, we found that the transglycosylase-deficient mutant cell walls contained more β-1,3-glucan than the wild type cell wall. Our results demonstrate that the GH72 transglycosylases are not needed for the incorporation of β-1,3-glucan into the cell wall, but they are required for the incorporation of cell wall glycoprotein into the cell wall. Copyright © 2017 Elsevier Inc. All rights reserved.

High-resolution autoradiography of nuclear modifications during and after heat treatment of neurospora crassa

Energy Technology Data Exchange (ETDEWEB)

Ton-That, C.; Turian, G. (Geneva Univ. (Switzerland))

1984-01-01

The appearance of perinucleolar electron-dense spots in the nuclei of macroconidia of Neurospora crassa incubated at 46/sup 0/C and their disaggregation after shift-down to 25/sup 0/C have been investigated by high-resolution autoradiography after (5-/sup 3/H) uridine pulses with or without chase periods. The RNA of these ribonucleoprotein-rich dense spots has been found to originate mainly from the heat-sensitive nucleolus; after return to 25/sup 0/C, the nucleolar activity was recovered and the RNA material stored either in an unprocessed or a mature rRNA form in the dense spots was found to be progressively extruded into the cytoplasm.

High-resolution autoradiography of nuclear modifications during and after heat treatment of neurospora crassa

International Nuclear Information System (INIS)

Ton-That, C.; Turian, G.

1984-01-01

The appearance of perinucleolar electron-dense spots in the nuclei of macroconidia of Neurospora crassa incubated at 46 0 C and their disaggregation after shift-down to 25 0 C have been investigated by high-resolution autoradiography after (5- 3 H) uridine pulses with or without chase periods. The RNA of these ribonucleoprotein-rich dense spots has been found to originate mainly from the heat-sensitive nucleolus; after return to 25 0 C, the nucleolar activity was recovered and the RNA material stored either in an unprocessed or a mature rRNA form in the dense spots was found to be progressively extruded into the cytoplasm. (Author)

Progenesis in Proctoeces lintoni (Fellodistomidae), a parasite of Fissurella crassa (Archaeogastropoda) in a latitudinal gradient in the Pacific Coast of South America.

Science.gov (United States)

Oliva, M E; Huaquin, L G

2000-08-01

The fellodistomid Proctoeces lintoni is a common parasite of the gonads of key-hole limpets Fissurella spp. (Archaeogastropoda). It has also been found in the mantle of Octopus vulgaris and as an intestinal parasite of haemulid and gobiesocid fishes. Fissurella crassa, a host for progenetic P. lintoni, can be found from Huarmey, Peni (10 degrees S) to Chiloé, Chile (42 degrees S). Proctoeces lintoni has been found parasitizing fishes and molluscs from Callao, Peni (12 degrees S) to Valdivia, Chile (39 degrees S). Progenesis is thought to be a latitude-dependent phenomenon, and high progenesis is expected at higher latitude. In the present article, the association between latitude and progenesis was examined over a latitudinal gradient of about 3,000 km. Data suggest that progenesis of P. lintoni infecting F. crassa was not associated with latitude. Low levels of progenesis found in the Peruvian population could be a consequence of parasite-induced mortality rather than of low latitude, as would be predicted by the latitude dependence hypothesis.

Live imaging of β-1,3-glucan synthase FKS-1 in Neurospora crassa hyphae.

Science.gov (United States)

Sánchez-León, Eddy; Riquelme, Meritxell

2015-09-01

The subcellular localization and dynamics of FKS-1, the putative catalytic subunit of the β-1,3-glucan synthase complex, was analyzed in growing hyphae of Neurospora crassa by live confocal microscopy. GFP-tagged FKS-1 accumulated at the outer layer of the Spitzenkörper (Spk), and at the apical plasma membrane (PM). Fluorescence recovery after photobleaching analysis revealed arrival of FKS-1-containing carriers first at the immediate surroundings of the core region of the Spk, and thereafter to the Spk most outer region. The results obtained here and previous data suggest that FKS-1 is transported to the Spk in macrovesicles. Copyright © 2015 Elsevier Inc. All rights reserved.

Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

International Nuclear Information System (INIS)

Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank

2013-01-01

Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

Energy Technology Data Exchange (ETDEWEB)

Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank, E-mail: fkempken@bot.uni-kiel.de

2013-08-30

Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

Direct electrochemistry of nitrate reductase from the fungus Neurospora crassa.

Science.gov (United States)

Kalimuthu, Palraj; Ringel, Phillip; Kruse, Tobias; Bernhardt, Paul V

2016-09-01

We report the first direct (unmediated) catalytic electrochemistry of a eukaryotic nitrate reductase (NR). NR from the filamentous fungus Neurospora crassa, is a member of the mononuclear molybdenum enzyme family and contains a Mo, heme and FAD cofactor which are involved in electron transfer from NAD(P)H to the (Mo) active site where reduction of nitrate to nitrite takes place. NR was adsorbed on an edge plane pyrolytic graphite (EPG) working electrode. Non-turnover redox responses were observed in the absence of nitrate from holo NR and three variants lacking the FAD, heme or Mo cofactor. The FAD response is due to dissociated cofactor in all cases. In the presence of nitrate, NR shows a pronounced cathodic catalytic wave with an apparent Michaelis constant (KM) of 39μM (pH7). The catalytic cathodic current increases with temperature from 5 to 35°C and an activation enthalpy of 26kJmol(-1) was determined. In spite of dissociation of the FAD cofactor, catalytically activity is maintained. Copyright © 2016. Published by Elsevier B.V.

Early days of tRNA research: Discovery, function, purification and ...

Indian Academy of Sciences (India)

Madhu

2006-10-04

Oct 4, 2006 ... function in protein synthesis and methods for its purification ... intermediate carrier of the amino acid in protein synthesis. (table 1). .... 14C-leucine were incubated with GTP, PEP, and pyruvate kinase as indicated (adapted from: Hoagland et al 1958). .... Purification of N. crassa mitochondrial initiator tRNA.

Neurospora crassa glucose - repressible gene -1(Grg-1) promoter controls the expression of neurospora tyrosinase gene in a clock-controlled manner

International Nuclear Information System (INIS)

Tarawneh, A. K

1997-01-01

In this study sphareroplastes of white Neurospora crassa mutant auxotroph for aromatic am no acids a rom 9 q a-2 inv, was transformed by the pKF-Tyr7-wt DNA construct. This construct contains the promoter of neurospora crassa glucose-repressible gene-1 (G rg-1) usp stream of Neurospora tyrosinase gene. The co transformation of this mutant with pKF-Tyr-7-wt cincture's and the pKAL-1, a plasmid which contains the Neurospora q a-2+ gene transform it to photophor. The transform ant contains the tyrosinase gene which catalyzes the unique step in the synthesis of the black pigment melanin. The activity of the tyrosinase in this transform ant was followed by measuring the absorbance of the dark coloured pigment at 332 nm. The maximum of the tyrosinase activity was shown at 16.36 and 56 hours after the shift of the transformed mycelia from constant light (L L) to constant dark (Dd). The rate of the enzyme activity was changed according to ci radian cycle of 20 hours. This G rg 1/tyrosinase construct provides a good system to study to study the temporal control of gene expression and the interaction between the different environmental c uses that affects gene expression. (author). 20 refs., 4 figs

Influence of point mutations near the active site on the catalytic properties of fungal arylacetonitrilases from Aspergillus niger and Neurospora crassa

Czech Academy of Sciences Publication Activity Database

Petříčková, Alena; Sosedov, O.; Baum, S.; Stolz, A.; Martínková, Ludmila

2012-01-01

Roč. 77, MAY 2012 (2012), s. 74-80 ISSN 1381-1177 R&D Projects: GA ČR(CZ) GAP504/11/0394; GA ČR GD305/09/H008; GA AV ČR IAA500200708; GA MŠk(CZ) LC06010; GA MŠk OC09046 Institutional research plan: CEZ:AV0Z50200510 Keywords : Arylacetonitrilase variants * Aspergillus niger * Neurospora crassa Subject RIV: CE - Biochemistry Impact factor: 2.823, year: 2012

The Oxygenase CAO-1 of Neurospora crassa Is a Resveratrol Cleavage Enzyme

KAUST Repository

Diaz-Sanchez, V.; F. Estrada, A.; Limon, M. C.; Al-Babili, Salim; Avalos, J.

2013-01-01

The genome of the ascomycete Neurospora crassa encodes CAO-1 and CAO-2, two members of the carotenoid cleavage oxygenase family that target double bonds in different substrates. Previous studies demonstrated the role of CAO-2 in cleaving the C40 carotene torulene, a key step in the synthesis of the C35 apocarotenoid pigment neurosporaxanthin. In this work, we investigated the activity of CAO-1, assuming that it may provide retinal, the chromophore of the NOP-1 rhodopsin, by cleaving β-carotene. For this purpose, we tested CAO-1 activity with carotenoid substrates that were, however, not converted. In contrast and consistent with its sequence similarity to family members that act on stilbenes, CAO-1 cleaved the interphenyl Cα-Cβ double bond of resveratrol and its derivative piceatannol. CAO-1 did not convert five other similar stilbenes, indicating a requirement for a minimal number of unmodified hydroxyl groups in the stilbene background. Confirming its biological function in converting stilbenes, adding resveratrol led to a pronounced increase in cao-1 mRNA levels, while light, a key regulator of carotenoid metabolism, did not alter them. Targeted Δcao-1 mutants were not impaired by the presence of resveratrol, a phytoalexin active against different fungi, which did not significantly affect the growth and development of wild-type Neurospora. However, under partial sorbose toxicity, the Δcao-1 colonies exhibited faster radial growth than control strains in the presence of resveratrol, suggesting a moderate toxic effect of resveratrol cleavage products.

The Oxygenase CAO-1 of Neurospora crassa Is a Resveratrol Cleavage Enzyme

KAUST Repository

Diaz-Sanchez, V.

2013-07-26

The genome of the ascomycete Neurospora crassa encodes CAO-1 and CAO-2, two members of the carotenoid cleavage oxygenase family that target double bonds in different substrates. Previous studies demonstrated the role of CAO-2 in cleaving the C40 carotene torulene, a key step in the synthesis of the C35 apocarotenoid pigment neurosporaxanthin. In this work, we investigated the activity of CAO-1, assuming that it may provide retinal, the chromophore of the NOP-1 rhodopsin, by cleaving β-carotene. For this purpose, we tested CAO-1 activity with carotenoid substrates that were, however, not converted. In contrast and consistent with its sequence similarity to family members that act on stilbenes, CAO-1 cleaved the interphenyl Cα-Cβ double bond of resveratrol and its derivative piceatannol. CAO-1 did not convert five other similar stilbenes, indicating a requirement for a minimal number of unmodified hydroxyl groups in the stilbene background. Confirming its biological function in converting stilbenes, adding resveratrol led to a pronounced increase in cao-1 mRNA levels, while light, a key regulator of carotenoid metabolism, did not alter them. Targeted Δcao-1 mutants were not impaired by the presence of resveratrol, a phytoalexin active against different fungi, which did not significantly affect the growth and development of wild-type Neurospora. However, under partial sorbose toxicity, the Δcao-1 colonies exhibited faster radial growth than control strains in the presence of resveratrol, suggesting a moderate toxic effect of resveratrol cleavage products.

PcMtr, an aromatic and neutral aliphatic amino acid permease of Penicillium chrysogenum

NARCIS (Netherlands)

Trip, H; Evers, ME; Driessen, AJM

2004-01-01

The gene encoding an aromatic and neutral aliphatic amino acid permease of Penicillium chrysogenum was cloned, functionally expressed and characterized in Saccharomyces cerevisiae M4276. The permease, designated PcMtr, is structurally and functionally homologous to Mtr of Neurospora crassa, and

Effect of benzene compounds from plants on the growth and hyphal morphology in Neurospora crassa Efeito de compostos benzênicos de plantas sobre o crescimento e a morfologia das hifas em Neurospora crassa

Directory of Open Access Journals (Sweden)

Fabrícia Mendonça Neves

2005-06-01

Full Text Available The effects of the benzene compounds from plants, respectively cinnamic acid, coumaric acid, ferulic acid, caffeic acid, and cinnamic aldehyde on growth and hyphal morphology of Neurospora crassa, were investigated. Cinnamic acid, ferulic acid and cinnamic aldehyde inhibited colony growth, but produced no visible alterations on hyphae. Caffeic acid and coumaric acid did not inhibit growth, but changed hyphal morphology. The results suggest that caffeic and coumaric acids probably affect polarity maintenance (the continued deposition of wall material at the extending tip, while cinnamic aldehyde, ferulic and cinnamic acids decrease growth rate, but did not change hyphal polarity. The actin cytoskeleton and the Spitzenkörper appeared diffuse and not clearly visible when one of the benzene compounds was present in the culture.Os efeitos de compostos benzênicos de plantas, respectivamente ácido cinâmico, ácido coumárico, ácido ferúlico, ácido cafeico e aldeído cinâmico, sobre o crescimento da colônia e a morfologia das hifas de Neurospora crassa foram investigados. Ácido cinâmico, ácido ferúlico e aldeído cinâmico inibiram o crescimento colonial, mas não produziram diferenças visíveis sobre as hifas. Ácido cafeico e ácido coumárico não inibiram o crescimento, mas alteraram a morfologia das hifas. Os resultados sugerem que os ácidos cafeico e coumárico afetam provavelmente a manutenção da polaridade (a contínua deposição de material da parede na ponta em extensão, enquanto aldeído cinâmico e os ácidos cinâmicos e ferúlico diminuem a velocidade de crescimento, mas não alteram a polaridade das hifas. Actina no citoesqueleto e no Spitzenkörper apareceu difuso e não estava claramente visível na presença de um dos compostos benzênicos na cultura.

Effect of dietary supplementation with Rhizopus oryzae or Chrysonilia crassa on growth performance, blood profile, intestinal microbial population, and carcass traits in broilers exposed to heat stress

Directory of Open Access Journals (Sweden)

S. Sugiharto

2017-09-01

Full Text Available Dietary supplementation of additives has recently been part of strategies to deal with the detrimental effects of heat stress (HS on the performance and carcass traits in broiler chicks. This study aimed to investigate the effect of dietary supplementation with the fungi Rhizopus oryzae or Chrysonilia crassa on growth, blood profile, intestinal microbial population and carcass traits in broiler chicks subjected to HS. R. oryzae and C. crassa are filamentous fungi isolated from the ileum of indigenous Indonesian chickens which exhibited probiotic and antioxidant properties. Two hundred and forty 21-day-old male broiler chicks were randomly allotted into six groups, including birds reared under normal temperature (28 ± 2 °C (CONT, birds reared under HS conditions (35 ± 2 °C (HS-CONT, birds reared under HS and provided with commercial anti-stress formula (HS-VIT, birds reared under HS and provided with R. oryzae (HS-RO, birds reared under HS and provided with C. crassa (HS-CC and birds reared under HS and provided with rice bran (HS-RB. Body weight gain was highest (P < 0. 01 and lowest (P < 0. 01 in CONT and HS-CONT birds, respectively. The heart was heavier (P < 0. 05 in CONT than in HS-CONT and HS-VIT birds. CONT birds had heavier duodenum (P < 0. 05 and jejunum (P < 0. 01 than other birds. Eosinophils was higher (P < 0. 05 in HS-CC than in other birds. Low-density lipoprotein (LDL was higher (P < 0. 05 in HS-CONT than in CONT, HS-VIT and HS-CC birds. Total triglyceride was highest (P < 0. 05 and lowest (P < 0. 05 in HS-RB and HS-RO birds, respectively. Alanine aminotransferase (ALT was higher (P < 0. 05 in HS-CONT than in other HS birds. Total protein was lowest and highest (P < 0. 05 in CONT and HS-CONT birds, respectively. Albumin was higher (P < 0. 05 in HS-CONT and HS-VIT than in HS-RO birds. Globulin was lower (P < 0. 05 in CONT than in HS

Regulation of glycogen metabolism by the CRE-1, RCO-1 and RCM-1 proteins in Neurospora crassa. The role of CRE-1 as the central transcriptional regulator.

Science.gov (United States)

Cupertino, Fernanda Barbosa; Virgilio, Stela; Freitas, Fernanda Zanolli; Candido, Thiago de Souza; Bertolini, Maria Célia

2015-04-01

The transcription factor CreA/Mig1/CRE-1 is a repressor protein that regulates the use of alternative carbon sources via a mechanism known as Carbon Catabolite Repression (CCR). In Saccharomyces cerevisiae, Mig1 recruits the complex Ssn6-Tup1, the Neurospora crassa RCM-1 and RCO-1 orthologous proteins, respectively, to bind to promoters of glucose-repressible genes. We have been studying the regulation of glycogen metabolism in N. crassa and the identification of the RCO-1 corepressor as a regulator led us to investigate the regulatory role of CRE-1 in this process. Glycogen content is misregulated in the rco-1(KO), rcm-1(RIP) and cre-1(KO) strains, and the glycogen synthase phosphorylation is decreased in all strains, showing that CRE-1, RCO-1 and RCM-1 proteins are involved in glycogen accumulation and in the regulation of GSN activity by phosphorylation. We also confirmed the regulatory role of CRE-1 in CCR and its nuclear localization under repressing condition in N. crassa. The expression of all glycogenic genes is misregulated in the cre-1(KO) strain, suggesting that CRE-1 also controls glycogen metabolism by regulating gene expression. The existence of a high number of the Aspergillus nidulans CreA motif (5'-SYGGRG-3') in the glycogenic gene promoters led us to analyze the binding of CRE-1 to some DNA motifs both in vitro by DNA gel shift and in vivo by ChIP-qPCR analysis. CRE-1 bound in vivo to all motifs analyzed demonstrating that it down-regulates glycogen metabolism by controlling gene expression and GSN phosphorylation. Copyright © 2015 Elsevier Inc. All rights reserved.

La formación de anillos de crecimiento en Fissurella crassa en el norte de Chile

Directory of Open Access Journals (Sweden)

Marta Bretos

1980-12-01

Full Text Available Growth discontinuity in molluscs result in the formation of rings on their shells. Two kind of rings may be formed: disturbance and growth rings. Growth rings can be used to determine the age of molluscs with long life span. For this, it is necessary to know how many growth rings are formed per year. It has been demonstrated experimentally, using marked specimens, that F. crassa forms two growth rings per year at Huayquique, Northern Chile. They are formed during winter and summer. Disturbance ring formation has also been observed as a result of sawing marks on their shells. A growth curve for this species is proposed on the basis of Walford's line.

Identification and characterization of the genes encoding the core histones and histone variants of Neurospora crassa.

OpenAIRE

Hays, Shan M; Swanson, Johanna; Selker, Eric U

2002-01-01

We have identified and characterized the complete complement of genes encoding the core histones of Neurospora crassa. In addition to the previously identified pair of genes that encode histones H3 and H4 (hH3 and hH4-1), we identified a second histone H4 gene (hH4-2), a divergently transcribed pair of genes that encode H2A and H2B (hH2A and hH2B), a homolog of the F/Z family of H2A variants (hH2Az), a homolog of the H3 variant CSE4 from Saccharomyces cerevisiae (hH3v), and a highly diverged ...

Intergeneric complementation of a circadian rhythmicity defect : phylogenetic conservation of structure and function of the clock gene frequency

NARCIS (Netherlands)

Merrow, Martha W.; Dunlap, Jay C.; Dover, G.

1994-01-01

The Neurospora crassa frequency locus encodes a 989 amino acid protein that is a central component, a state variable, of the circadian biological clock. We have determined the sequence of all or part of this protein and surrounding regulatory regions from additional fungi representing three genera

Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

OpenAIRE

Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R.; Turner, Gloria E.; Sachs, Matthew S.; Glass, N. Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E.; Birren, Bruce W.; Weiss, Richard L.; Townsend, Jeffrey P.; Loros, Jennifer J.; Nelson, Mary Anne; Lambreghts, Randy

2007-01-01

A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building fr...

Neurospora COP9 signalosome integrity plays major roles for hyphal growth, conidial development, and circadian function.

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Zhipeng Zhou

Full Text Available The COP9 signalosome (CSN is a highly conserved multifunctional complex that has two major biochemical roles: cleaving NEDD8 from cullin proteins and maintaining the stability of CRL components. We used mutation analysis to confirm that the JAMM domain of the CSN-5 subunit is responsible for NEDD8 cleavage from cullin proteins in Neurospora crassa. Point mutations of key residues in the metal-binding motif (EX(nHXHX(10D of the CSN-5 JAMM domain disrupted CSN deneddylation activity without interfering with assembly of the CSN complex or interactions between CSN and cullin proteins. Surprisingly, CSN-5 with a mutated JAMM domain partially rescued the phenotypic defects observed in a csn-5 mutant. We found that, even without its deneddylation activity, the CSN can partially maintain the stability of the SCF(FWD-1 complex and partially restore the degradation of the circadian clock protein FREQUENCY (FRQ in vivo. Furthermore, we showed that CSN containing mutant CSN-5 efficiently prevents degradation of the substrate receptors of CRLs. Finally, we found that deletion of the CAND1 ortholog in N. crassa had little effect on the conidiation circadian rhythm. Our results suggest that CSN integrity plays major roles in hyphal growth, conidial development, and circadian function in N. crassa.

Maternal parentage influences spore production but not spore pigmentation in the anisogamous and hermaphroditic fungus Neurospora crassa

DEFF Research Database (Denmark)

Zimmerman, Kolea; Levitis, Daniel; Pringle, Anne

2014-01-01

. In this fungus, pigmented spores are viable and unpigmented spores are inviable. These results show that while both parents influence all these traits, maternal influence is strongest on both fertility and mortality traits until the spores are physiologically independent of the maternal cytoplasm.......In this study, we tested the hypothesis that maternal effects on offspring production and quality are greater than paternal effects in both offspring number (fertility) and offspring viability (mortality). We used the model filamentous fungus Neurospora crassa. This fungus is anisogamous......, and various ascospore characteristics. Mixed effects models of these data show that the female parent accounts for the majority of variation in perithecial production, number of spores produced, and spore germination. Surprisingly, both sexes equally influence the percentage of spores that are pigmented...

Neurospora crassa tox-1 Gene Encodes a pH- and Temperature-Tolerant Mini-Cellulase.

Science.gov (United States)

Xiao, Yue; Zhang, Qiongsi; Luo, Yiquan; Zhang, Ying; Luo, Xi; Wang, Yuchuan; Cao, Weiguo; Pinto, Vito De; Liu, Qiuyun; Li, Gang

2016-06-15

Cellulases that endure extreme conditions are essential in various industrial sectors. This study reports a mini-cellulase gene tox-1 from Neurospora crassa. The gene tox-1 was cloned in Escherichia coli after chimerization with the YebF gene and substitutions of certain isoleucine and valine with leucine residues. The yeast transformants could grow on rice straw-agar medium. The 44-amino acid peptide and its two mutant variants displayed potent cellulase activities in Congo Red assay and enzymatic assays. Conservative replacements with leucine have substantially increased the stabilities and half-lives of the peptides at alkaline pH and low and high temperatures and also the tolerance to organic solvents and surfactants, on the basis of activities toward cellose. The small size of the mini-cellulase would allow for commercially viable automatic chemical peptide synthesis. This work suggests that conservative leucine replacements may serve as a general strategy in the engineering of more robust enzymes with special features with little loss of activities.

Mating-type genes from the homothallic fungus Sordaria macrospora are functionally expressed in a heterothallic ascomycete.

Science.gov (United States)

Pöggeler, S; Risch, S; Kück, U; Osiewacz, H D

1997-10-01

Homokaryons from the homothallic ascomycte Sordaria macrospora are able to enter the sexual pathway and to form fertile fruiting bodies. To analyze the molecular basis of homothallism and to elucidate the role of mating-products during fruiting body development, we cloned and sequenced the entire S. macrospora mating-type locus. Comparison of the Sordaria mating-type locus with mating-type idiomorphs from the heterothallic ascomycetes Neurospora crassa and Podospora anserina revealed that sequences from both idiomorphs (A/a and mat-/mat+, respectively) are contiguous in S. macrospora. DNA sequencing of the S. macrospora mating-type region allowed the identification of four open reading frames (ORFs), which were termed Smt-a1, SmtA-1, SmtA-2 and SmtA-3. While Smt-a1, SmtA-1, and SmtA-2 show strong sequence similarities with the corresponding N. crassa mating-type ORFs, SmtA-3 has a chimeric character. It comprises sequences that are similar to the A and a mating-type idiomorph from N. crassa. To determine functionality of the S. macrospora mating-type genes, we show that all ORFs are transcriptionally expressed. Furthermore, we transformed the S. macrospora mating-type genes into mat- and mat+ strains of the closely related heterothallic fungus P. anserina. The transformation experiments show that mating-type genes from S. macrospora induce fruiting body formation in P. anserina.

High spin structure functions

International Nuclear Information System (INIS)

Khan, H.

1990-01-01

This thesis explores deep inelastic scattering of a lepton beam from a polarized nuclear target with spin J=1. After reviewing the formation for spin-1/2, the structure functions for a spin-1 target are defined in terms of the helicity amplitudes for forward compton scattering. A version of the convolution model, which incorporates relativistic and binding energy corrections is used to calculate the structure functions of a neutron target. A simple parameterization of these structure functions is given in terms of a few neutron wave function parameters and the free nucleon structure functions. This allows for an easy comparison of structure functions calculated using different neutron models. (author)

Alteration of light-dependent gene regulation by the absence of the RCO-1/RCM-1 repressor complex in the fungus Neurospora crassa.

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Carmen Ruger-Herreros

Full Text Available The activation of transcription by light in the fungus Neurospora crassa requires the White Collar Complex (WCC, a photoreceptor and transcription factor complex. After light reception two WCCs interact and bind the promoters of light-regulated genes to activate transcription. This process is regulated by VVD, a small photoreceptor that disrupts the interaction between WCCs and leads to a reduction in transcription after long exposures to light. The N. crassa RCO-1/RCM-1 repressor complex is the homolog of the Tup1-Ssn6 repressor complex in yeast, and its absence modifies photoadaptation. We show that the absence of the RCO-1/RCM-1 repressor complex leads to several alterations in transcription that are gene-specific: an increase in the accumulation of mRNAs in the dark, a repression of transcription, and a derepression of transcription after long exposures to light. The absence of the RCO-1/RCM-1 repressor complex leads to lower VVD levels that are available for the regulation of the activity of the WCC. The reduction in the amount of VVD results in increased WCC binding to the promoters of light-regulated genes in the dark and after long exposures to light, leading to the modification of photoadaptation that has been observed in rco-1 and rcm-1 mutants. Our results show that the photoadaptation phenotype of mutants in the RCO-1/RCM-1 repressor complex is, at least in part, an indirect consequence of the reduction of vvd transcription, and the resulting modification in the regulation of transcription by the WCC.

Hadron structure functions

International Nuclear Information System (INIS)

Martin, F.

1981-03-01

The x dependence of hadron structure functions is investigated. If quarks can exist in very low mass states (10 MeV for d and u quarks) the pion structure function is predicted to behave like (1-x) and not (1-x) 2 in a x-region around 1. Relativistic and non-relativistic quark bound state pictures of hadrons are considered together with their relation with the Q 2 evolution of structure functions. Good agreement with data is in general obtained

Photon structure function

International Nuclear Information System (INIS)

Bardeen, W.A.

1980-11-01

Theoretical understanding of the photon structure function is reviewed. As an illustration of the pointlike component, the parton model is briefly discussed. However, the systematic study of the photon structure function is presented through the framework of the operator product expansion. Perturbative QCD is used as the theoretical basis for the calculation of leading contributions to the operator product expansion. The influence of higher order QCD effects on these results is discussed. Recent results for the polarized structure functions are discussed

Alterations in growth and branching of Neurospora crassa caused by sub-inhibitory concentrations of antifungal agents Alteraciones de crecimiento y ramificación en Neurospora crassa provocadas por concentraciones subinhibitorias de agentes antimicóticos

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R. C. Pereira

2009-03-01

Full Text Available Six antifungal agents at subinhibitory concentrations were used for investigating their ability to affect the growth and branching in Neurospora crassa. Among the antifungals herein used, the azole agent ketoconazole at 0.5 μg/ml inhibited radial growth more than fluconazole at 5.0 μg/ml while amphotericin B at 0.05 μg/ml was more effective than nystatin at 0.05 μg/ml. Morphological alterations in hyphae were observed in the presence of griseofulvin, ketoconazole and terbinafine at the established concentrations. The antifungal agents were more effective on vegetative growth than on conidial germination. Terbinafine markedly reduced growth unit length (GU by 54.89%, and caused mycelia to become hyperbranched. In all cases, there was a high correlation between hyphal length and number of tips (r > 0.9. All our results showed highly significant differences by ANOVA, (p Se investigó el efecto de seis agentes antimicóticos en concentraciones subinhibitorias sobre el crecimiento y la ramificación en Neurospora crassa. El agente azólico ketoconazol a la concentración de 0,5 μg/ml inhibió el crecimiento radial más que el fluconazol a 5,0 μg/ml, y la anfotericina B a 0,05 μg/ ml fue más eficiente que 0,05 μg/ml de nistatina, entre los agentes poliénicos usados. En presencia de griseofulvina, ketoconazol y terbinafina a las concentraciones establecidas se observaron alteraciones morfológicas en las hifas. Los agentes antimicóticos fueron más eficientes sobre el crecimiento vegetativo que sobre la germinación conidial. La terbinafina redujo marcadamente (54,89% la longitud de la unidad de crecimiento y provocó la hiperramificación del micelio. En todos los casos, existió gran correlación entre la longitud y el número de ápices de las hifas (r > 0,9. Todos los resultados mostraron diferencias altamente significativas de acuerdo con ANOVA (p < 0,001, α = 0,05. Considerando que el ápice de la hifa es la principal interfase entre

The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa.

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Carla J Eaton

Full Text Available Heterotrimeric G protein signaling is essential for normal hyphal growth in the filamentous fungus Neurospora crassa. We have previously demonstrated that the non-receptor guanine nucleotide exchange factor RIC8 acts upstream of the Gα proteins GNA-1 and GNA-3 to regulate hyphal extension. Here we demonstrate that regulation of hyphal extension results at least in part, from an important role in control of asexual spore (conidia germination. Loss of GNA-3 leads to a drastic reduction in conidial germination, which is exacerbated in the absence of GNA-1. Mutation of RIC8 leads to a reduction in germination similar to that in the Δgna-1, Δgna-3 double mutant, suggesting that RIC8 regulates conidial germination through both GNA-1 and GNA-3. Support for a more significant role for GNA-3 is indicated by the observation that expression of a GTPase-deficient, constitutively active gna-3 allele in the Δric8 mutant leads to a significant increase in conidial germination. Localization of the three Gα proteins during conidial germination was probed through analysis of cells expressing fluorescently tagged proteins. Functional TagRFP fusions of each of the three Gα subunits were constructed through insertion of TagRFP in a conserved loop region of the Gα subunits. The results demonstrated that GNA-1 localizes to the plasma membrane and vacuoles, and also to septa throughout conidial germination. GNA-2 and GNA-3 localize to both the plasma membrane and vacuoles during early germination, but are then found in intracellular vacuoles later during hyphal outgrowth.

Multi-functional composite structures

Science.gov (United States)

Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

2004-10-19

Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

Identification of two products of mitochondrial protein synthesis associated with mitochondrial adenosine triphosphatase from Neurospora crassa

International Nuclear Information System (INIS)

Jackl, G.; Sebald, W.

1975-01-01

Soluble mitochondrial ATPase (F 1 ) isolated from Neurospora crassa is resolved by dodecyl-sulfate-gel electrophoresis into five polypeptide bands with apparent molecular weights of 59,000, 55,000, 36,000, 15,000 and 12,000. At least nine further polypeptides remain associated with ATPase after disintegration of mitochondria with Triton X-100 as shown by the analysis of an immunoprecipitate obtained with antiserum to F 1 ATPase. Two of the associated polypeptides with apparent molecular weights of 19,000 and 11,000 are translated on mitochondrial ribosomes, as demonstrated by incorporation in vivo of radioactive leucine in the presence of specific inhibitors of mitochondrial (chloramphenicol) and extramitochondrial (cycloheximide) protein synthesis. The appearance of mitochondrial translation products in the immunoprecipitated ATPase complex is inhibited by cycloheximide. The same applies for some of the extramitochondrial translation products in the presence of chloramphenicol. This suggests that both types of polypeptides are necessary for the assembly of the ATPase complex. (orig.) [de

Screening of agricultural wastes as a medium production of catalase for enzymatic fuel cell by Neurospora crassa InaCC F226

Science.gov (United States)

Santoso, Pugoh; Yopi

2017-12-01

Explorations of local microorganisms from Indonesia that can produce of catalase are still limited. Neurospora crassa is a fungus which resulting of two kinds of catalase, namely catalase-1 and catalase-3. We studied the production of catalase by Neurospora crassa (no. F226) from Indonesia Culture Collection (InaCC) in Solid State Fermentation (SSF). Among four screened agro wastes (corn cob, rice straw, oil palm empty fruit bunches, and bagasse), rice straw and oil palm empty fruit bunches (OPEFB) were remarked as the most promising substrate suited for the excellent growth and adequate production of catalase. Based on the result, the method of solid state fermentation was suitable to production of catalase. It is caused that the medium served to maintain microbial growth and metabolism. The filamentous filament is more suitable for living on solid media because it has a high tolerance to low water activity, and it has a high potential to excrete hydrolytic enzymes that caused of its morphology. The filamentous filament morphology allows the fungus to form colonies and penetrate the solid substrates in order to obtain nutrients. The results showed that the highest catalase activity was obtained on rice straw and oil palm empty fruit bunches medium with catalase activity of 39.1 U/mL and 37,7 U/mL in 50% moisture content medium, respectively. Optimization of humidity and pH medium in the rice straw were investigated which is the highest activity obtained in 30% moisture content and pH medium of 6. The catalase activity was reached in the value of 53.761 U/mL and 56.903 U/mL by incubated 48 hours and 96 hours, respectively.

Unpolarized Structure Functions

International Nuclear Information System (INIS)

Christy, M.E.; Melnitchouk, W.

2011-01-01

Over the past decade measurements of unpolarized structure functions with unprecedented precision have significantly advanced our knowledge of nucleon structure. These have for the first time allowed quantitative tests of the phenomenon of quark-hadron duality, and provided a deeper understanding of the transition from hadron to quark degrees of freedom in inclusive scattering. Dedicated Rosenbluth-separation experiments have yielded high-precision transverse and longitudinal structure functions in regions previously unexplored, and new techniques have enabled the first glimpses of the structure of the free neutron, without contamination from nuclear effects.

VIB1, a link between glucose signaling and carbon catabolite repression, is essential for plant cell wall degradation by Neurospora crassa.

Directory of Open Access Journals (Sweden)

Yi Xiong

2014-08-01

Full Text Available Filamentous fungi that thrive on plant biomass are the major producers of hydrolytic enzymes used to decompose lignocellulose for biofuel production. Although induction of cellulases is regulated at the transcriptional level, how filamentous fungi sense and signal carbon-limited conditions to coordinate cell metabolism and regulate cellulolytic enzyme production is not well characterized. By screening a transcription factor deletion set in the filamentous fungus Neurospora crassa for mutants unable to grow on cellulosic materials, we identified a role for the transcription factor, VIB1, as essential for cellulose utilization. VIB1 does not directly regulate hydrolytic enzyme gene expression or function in cellulosic inducer signaling/processing, but affects the expression level of an essential regulator of hydrolytic enzyme genes, CLR2. Transcriptional profiling of a Δvib-1 mutant suggests that it has an improper expression of genes functioning in metabolism and energy and a deregulation of carbon catabolite repression (CCR. By characterizing new genes, we demonstrate that the transcription factor, COL26, is critical for intracellular glucose sensing/metabolism and plays a role in CCR by negatively regulating cre-1 expression. Deletion of the major player in CCR, cre-1, or a deletion of col-26, did not rescue the growth of Δvib-1 on cellulose. However, the synergistic effect of the Δcre-1; Δcol-26 mutations circumvented the requirement of VIB1 for cellulase gene expression, enzyme secretion and cellulose deconstruction. Our findings support a function of VIB1 in repressing both glucose signaling and CCR under carbon-limited conditions, thus enabling a proper cellular response for plant biomass deconstruction and utilization.

An F-actin-depleted zone is present at the hyphal tip of invasive hyphae of Neurospora crassa.

Science.gov (United States)

Suei, S; Garrill, A

2008-01-01

The distribution of filamentous actin (F-actin) in invasive and noninvasive hyphae of the ascomycete Neurospora crassa was investigated. Eighty six percent of noninvasive hyphae had F-actin in the tip region compared to only 9% of invasive hyphae. The remaining 91% of the invasive hyphae had no obvious tip high concentration of F-actin staining; instead they had an F-actin-depleted zone in this region, although some F-actin, possibly associated with the Spitzenkörper, remained at the tip. The size of the F-actin-depleted zone in invasive hyphae increased with an increase in agar concentration. The membrane stain FM 4-64 reveals a slightly larger accumulation of vesicles at the tips of invasive hyphae relative to noninvasive hyphae, although this difference is unlikely to be sufficient to account for the exclusion of F-actin from the depleted zone. Antibodies raised against the actin filament-severing protein cofilin from both yeast and human cells localize to the tips of invasive hyphae. The human cofilin antibody shows a more random distribution in noninvasive hyphae locating primarily at the hyphal periphery but with some diffuse cytoplasmic staining. This antibody also identifies a single band at 21 kDa in immunoblots of whole hyphal fractions. These data suggest that a protein with epitopic similarity to cofilin may function in F-actin dynamics that underlie invasive growth. The F-actin-depleted zone may play a role in the regulation of tip yielding to turgor pressure, thus increasing the protrusive force necessary for invasive growth.

Acetylglutamate synthase in Neurospora crassa: characterization, localization, and genetic behavior of a regulatory enzyme of arginine biosynthesis

International Nuclear Information System (INIS)

Jacobson, J.A.

1988-01-01

This study describes the characterization and localization of the first enzyme of arginine biosynthesis in Neurospora crassa. A radioactive assay was developed to detect this enzyme whereby radioactive substrate and product molecules could be separated by ion-exchange chromatography. The enzyme was found to have a pH optimum of 9.0 and K/sub m/ values for glutamate and acetyl-CoA of approximately 4.7 and 0.45 mM, respectively. The enzyme was shown to be feedback inhibited by arginine. Half-maximal inhibition was observed at 0.13 mM arginine, a concentration which is similar to be in vivo cytosolic concentration of 0.2 mM. Arginine was found to act as a competitive inhibitor with respect to acetyl-CoA. Acetylglutamate synthase was localized to the mitochondrion. However, in contrast to the mitochondrial matrix location of the other ornithine biosynthetic enzymes, this enzyme was found to reside on the mitochondrial inner membrane

Photon structure function - theory

International Nuclear Information System (INIS)

Bardeen, W.A.

1984-12-01

The theoretical status of the photon structure function is reviewed. Particular attention is paid to the hadronic mixing problem and the ability of perturbative QCD to make definitive predictions for the photon structure function. 11 references

Nuclear correlations and structure functions

International Nuclear Information System (INIS)

Hu Guoju; Irvine, J.M.

1989-01-01

It is argued that the search for a mass number dependence of the nuclear structure function per nucleon is profitably directed to the region of Bjorken scaling variable x > 1. We show that in the convolution model of the nuclear structure function the nuclear momentum distribution and energy spectrum generated by cluster expansion techniques, here realised in the correlated basis function method, invoking tensor correlations and short-range density-dependent repulsions adequately describes the structure function for 12 C in the region x > 1. The results of structure functions for a number of light-, medium- and heavy-mass nuclei are presented. (author)

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Energy Technology Data Exchange (ETDEWEB)

Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

2007-09-02

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

Involvement of mitochondrial proteins in calcium signaling and cell death induced by staurosporine in Neurospora crassa.

Science.gov (United States)

Gonçalves, A Pedro; Cordeiro, J Miguel; Monteiro, João; Lucchi, Chiara; Correia-de-Sá, Paulo; Videira, Arnaldo

2015-10-01

Staurosporine-induced cell death in Neurospora crassa includes a well defined sequence of alterations in cytosolic calcium levels, comprising extracellular Ca(2+) influx and mobilization of Ca(2+) from internal stores. Here, we show that cells undergoing respiratory stress due to the lack of certain components of the mitochondrial complex I (like the 51kDa and 14kDa subunits) or the Ca(2+)-binding alternative NADPH dehydrogenase NDE-1 are hypersensitive to staurosporine and incapable of setting up a proper intracellular Ca(2+) response. Cells expressing mutant forms of NUO51 that mimic human metabolic diseases also presented Ca(2+) signaling deficiencies. Accumulation of reactive oxygen species is increased in cells lacking NDE-1 and seems to be required for Ca(2+) oscillations in response to staurosporine. Measurement of the mitochondrial levels of Ca(2+) further supported the involvement of these organelles in staurosporine-induced Ca(2+) signaling. In summary, our data indicate that staurosporine-induced fungal cell death involves a sophisticated response linking Ca(2+) dynamics and bioenergetics. Copyright © 2015 Elsevier B.V. All rights reserved.

Reorganization of plasma membrane lipid domains during conidial germination.

Science.gov (United States)

Santos, Filipa C; Fernandes, Andreia S; Antunes, Catarina A C; Moreira, Filipe P; Videira, Arnaldo; Marinho, H Susana; de Almeida, Rodrigo F M

2017-02-01

Neurospora crassa, a filamentous fungus, in the unicellular conidial stage has ideal features to study sphingolipid (SL)-enriched domains, which are implicated in fundamental cellular processes ranging from antifungal resistance to apoptosis. Several changes in lipid metabolism and in the membrane composition of N. crassa occur during spore germination. However, the biophysical impact of those changes is unknown. Thus, a biophysical study of N. crassa plasma membrane, particularly SL-enriched domains, and their dynamics along conidial germination is prompted. Two N. crassa strains, wild-type (WT) and slime, which is devoid of cell wall, were studied. Conidial growth of N. crassa WT from a dormancy state to an exponential phase was accompanied by membrane reorganization, namely an increase of membrane fluidity, occurring faster in a supplemented medium than in Vogel's minimal medium. Gel-like domains, likely enriched in SLs, were found in both N. crassa strains, but were particularly compact, rigid and abundant in the case of slime cells, even more than in budding yeast Saccharomyces cerevisiae. In N. crassa, our results suggest that the melting of SL-enriched domains occurs near growth temperature (30°C) for WT, but at higher temperatures for slime. Regarding biophysical properties strongly affected by ergosterol, the plasma membrane of slime conidia lays in between those of N. crassa WT and S. cerevisiae cells. The differences in biophysical properties found in this work, and the relationships established between membrane lipid composition and dynamics, give new insights about the plasma membrane organization and structure of N. crassa strains during conidial growth. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional materials discovery using energy-structure-function maps.

Science.gov (United States)

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

2017-03-30

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Structure function monitor

Science.gov (United States)

McGraw, John T [Placitas, NM; Zimmer, Peter C [Albuquerque, NM; Ackermann, Mark R [Albuquerque, NM

2012-01-24

Methods and apparatus for a structure function monitor provide for generation of parameters characterizing a refractive medium. In an embodiment, a structure function monitor acquires images of a pupil plane and an image plane and, from these images, retrieves the phase over an aperture, unwraps the retrieved phase, and analyzes the unwrapped retrieved phase. In an embodiment, analysis yields atmospheric parameters measured at spatial scales from zero to the diameter of a telescope used to collect light from a source.

Functional Insights from Structural Genomics

Energy Technology Data Exchange (ETDEWEB)

Forouhar,F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Montelione, G.; Tong, L.; et al

2007-01-01

Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).

Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.

Science.gov (United States)

Bausewein, Thomas; Mills, Deryck J; Langer, Julian D; Nitschke, Beate; Nussberger, Stephan; Kühlbrandt, Werner

2017-08-10

The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7. Tom22, the central preprotein receptor, connects the two Tom40 pores at the dimer interface. Our structure offers detailed insights into the molecular architecture of the mitochondrial preprotein import machinery. Copyright © 2017 Elsevier Inc. All rights reserved.

Spin dependent photon structure functions

International Nuclear Information System (INIS)

Manohar, A.V.; Massachusetts Inst. of Tech., Cambridge

1989-01-01

Spin dependent structure functions of the photon are studied using the operator product expansion. There are new twist-two photon and gluon operators which contribute. The structure functions g 1 and F 3 are calculable in QCD, but differ from their free quark values. The corrections to F 3 are suppressed by 1/log Q 2 . The calculation is an extension of the analysis of Witten for the spin averaged structure functions F 1 and F 2 . (orig.)

Calculations of nucleon structure functions

International Nuclear Information System (INIS)

Signal, A.I.

1990-01-01

We present a method of calculating deep inelastic nucleon structure functions using bag model wavefunctions. Our method uses the Peierls - Yoccoz projection to form translation invariant bag states. We obtain the correct support for the structure functions and satisfy the positivity requirements for quark and anti-quark distribution functions. (orig.)

Nucleon structure functions

International Nuclear Information System (INIS)

Virchaux, M.

1992-11-01

The present status of experimental measurements of the nucleon structure functions is reviewed. The results from nearly all deep inelastic experiments are in good mutual agreement. Principles of the analysis of these structure function data in the framework of QCD are described. The specific features of the perturbative QCD predictions are observed in the data. This provides quantitative tests of the validity of QCD as well as determinations of the various parton distributions in the nucleon and some of the most precise measurements of the strong coupling constant αs. The future of this field of experimental physics is sketched

Chromatin Structure and Function

CERN Document Server

Wolffe, Alan P

1999-01-01

The Third Edition of Chromatin: Structure and Function brings the reader up-to-date with the remarkable progress in chromatin research over the past three years. It has been extensively rewritten to cover new material on chromatin remodeling, histone modification, nuclear compartmentalization, DNA methylation, and transcriptional co-activators and co-repressors. The book is written in a clear and concise fashion, with 60 new illustrations. Chromatin: Structure and Function provides the reader with a concise and coherent account of the nature, structure, and assembly of chromatin and its active

Mutagenesis at the ad-3A and ad-3B loci in haploid UV-sensitive strains of Neurospora crassa. Pt. 2

International Nuclear Information System (INIS)

Serres, F.J. de

1980-01-01

UV-induced inactivation and induction of mutations at the ad-3A and ad-3B loci of Neurospora crassa have been compared among 7 different UV-sensitive strains and a standard wild-type strain. The 7 strains show varying degrees of sensitivity to UV-induced inactivation, with the relative sensitivity being: uvs-2 > uvs-3 > uvs-4 > uvs-6 > upr-1 > uvs-5 > uvs-1. Studies on the induction of ad-3 mutants by UV show that the 2 excision-repair deficient mutants uvs-2 and upr-1 exhibit enhanced ad-3 mutant frequencies, while uvs-4 and uvs-5 exhibit reduced ad-3 mutant frequencies, and uvs-3 completely eliminates UV mutagenesis. The ad-3 mutation-induction curves obtained with uvs-1 or uvs-6 are not significantly different from that found with the wild-type strain. (orig.)

Dual chromatin recognition by the histone deacetylase complex HCHC is required for proper DNA methylation in Neurospora crassa

Science.gov (United States)

Honda, Shinji; Bicocca, Vincent T.; Gessaman, Jordan D.; Rountree, Michael R.; Yokoyama, Ayumi; Yu, Eun Y.; Selker, Jeanne M. L.; Selker, Eric U.

2016-01-01

DNA methylation, heterochromatin protein 1 (HP1), histone H3 lysine 9 (H3K9) methylation, histone deacetylation, and highly repeated sequences are prototypical heterochromatic features, but their interrelationships are not fully understood. Prior work showed that H3K9 methylation directs DNA methylation and histone deacetylation via HP1 in Neurospora crassa and that the histone deacetylase complex HCHC is required for proper DNA methylation. The complex consists of the chromodomain proteins HP1 and chromodomain protein 2 (CDP-2), the histone deacetylase HDA-1, and the AT-hook motif protein CDP-2/HDA-1–associated protein (CHAP). We show that the complex is required for proper chromosome segregation, dissect its function, and characterize interactions among its components. Our analyses revealed the existence of an HP1-based DNA methylation pathway independent of its chromodomain. The pathway partially depends on CHAP but not on the CDP-2 chromodomain. CDP-2 serves as a bridge between the recognition of H3K9 trimethylation (H3K9me3) by HP1 and the histone deacetylase activity of HDA-1. CHAP is also critical for HDA-1 localization to heterochromatin. Specifically, the CHAP zinc finger interacts directly with the HDA-1 argonaute-binding protein 2 (Arb2) domain, and the CHAP AT-hook motifs recognize heterochromatic regions by binding to AT-rich DNA. Our data shed light on the interrelationships among the prototypical heterochromatic features and support a model in which dual recognition by the HP1 chromodomain and the CHAP AT-hooks are required for proper heterochromatin formation. PMID:27681634

Purely Functional Structured Programming

OpenAIRE

Obua, Steven

2010-01-01

The idea of functional programming has played a big role in shaping today's landscape of mainstream programming languages. Another concept that dominates the current programming style is Dijkstra's structured programming. Both concepts have been successfully married, for example in the programming language Scala. This paper proposes how the same can be achieved for structured programming and PURELY functional programming via the notion of LINEAR SCOPE. One advantage of this proposal is that m...

Proton and neutron structure functions

International Nuclear Information System (INIS)

Rock, S.

1991-01-01

New result on charged lepton scattering from hydrogen and deuterium targets by the BCDMS, NMC and SLAC collaborations have greatly increased our knowledge of the structure functions of protons and neutrons. The disagreement between the high energy muon scattering cross sections obtained by the EMC and BCDMS collaborations have been almost completely resolved by comparison with a global analysis of old and new SLAC data and a reanalysis of EMC data. We now have a consistent set of structure functions which covers an approximate range 1 ≤ Q 2 ≤ 200 (GeV/c) 2 and 0.07 ≤ x ≤ 0.7. The ratio of neutron to proton structure functions decreases with increasing Q 2 for values of x ≥ 0.1. The difference between proton and neutron structure functions approaches zero as x decreases, consistent with the expected √x behavior. (orig.)

Mutagenesis at the ad-3A and ad-3B loci in haploid UV-sensitive strains of Neurospora crassa. Pt. 3

International Nuclear Information System (INIS)

Schuepbach, M.E.; Serres, F.J. de

1981-01-01

γ-ray-induced inactivation and induction of mutations at the ad-3A and ad-3B loci of Neurospora crassa have been compared among 6 different UV- sensitive strains and a standard wild-type strain. The 6 strains show varying degrees of sensitivy to γ-ray-induced inactivation, with the relative sensitivy at 37% survival being uvs-6 > upr-1 > uvs-2 UE uvs-3 > wild-type > uvs-5 > uvs-4. Studies on the induction of ad-3 mutants by γ-rays show that when the dose-response curves (expressed in terms of ad-3 mutants among the surving colonies) of the UV-sensitive strains are compared with wild-type, the excision-repair-deficient mutants uvs-2 and upr-1 exhibit enhanced ad-3 mutant frequencies, uvs-3 exibits reduced ad-3 mutant frequencies whereas both uvs-4 and uvs-5 show lower mutant frequencies than wild-type. (orig.)

Regge behaviour of structure functions and evolution of gluon structure function upto next-to-leading order at low-x

International Nuclear Information System (INIS)

Jamil, U.; Sarma, J.K.

2011-01-01

Evolution of gluon structure function from Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution equations upto next-to-leading order at low-x is presented assuming the Regge behaviour of structure functions. We compare our results of gluon structure function with GRV 98 global parameterization and show the compatibility of Regge behaviour of structure functions with PQCD. (author)

Structure functions from chiral soliton models

International Nuclear Information System (INIS)

Weigel, H.; Reinhardt, H.; Gamberg, L.

1997-01-01

We study nucleon structure functions within the bosonized Nambu-Jona-Lasinio (NJL) model where the nucleon emerges as a chiral soliton. We discuss the model predictions on the Gottfried sum rule for electron-nucleon scattering. A comparison with a low-scale parametrization shows that the model reproduces the gross features of the empirical structure functions. We also compute the leading twist contributions of the polarized structure functions g 1 and g 2 in this model. We compare the model predictions on these structure functions with data from the E143 experiment by GLAP evolving them from the scale characteristic for the NJL-model to the scale of the data

Comparative live-cell imaging analyses of SPA-2, BUD-6 and BNI-1 in Neurospora crassa reveal novel features of the filamentous fungal polarisome.

Directory of Open Access Journals (Sweden)

Alexander Lichius

Full Text Available A key multiprotein complex involved in regulating the actin cytoskeleton and secretory machinery required for polarized growth in fungi, is the polarisome. Recognized core constituents in budding yeast are the proteins Spa2, Pea2, Aip3/Bud6, and the key effector Bni1. Multicellular fungi display a more complex polarized morphogenesis than yeasts, suggesting that the filamentous fungal polarisome might fulfill additional functions. In this study, we compared the subcellular organization and dynamics of the putative polarisome components BUD-6 and BNI-1 with those of the bona fide polarisome marker SPA-2 at various developmental stages of Neurospora crassa. All three proteins exhibited a yeast-like polarisome configuration during polarized germ tube growth, cell fusion, septal pore plugging and tip repolarization. However, the localization patterns of all three proteins showed spatiotemporally distinct characteristics during the establishment of new polar axes, septum formation and cytokinesis, and maintained hyphal tip growth. Most notably, in vegetative hyphal tips BUD-6 accumulated as a subapical cloud excluded from the Spitzenkörper (Spk, whereas BNI-1 and SPA-2 partially colocalized with the Spk and the tip apex. Novel roles during septal plugging and cytokinesis, connected to the reinitiation of tip growth upon physical injury and conidial maturation, were identified for BUD-6 and BNI-1, respectively. Phenotypic analyses of gene deletion mutants revealed additional functions for BUD-6 and BNI-1 in cell fusion regulation, and the maintenance of Spk integrity. Considered together, our findings reveal novel polarisome-independent functions of BUD-6 and BNI-1 in Neurospora, but also suggest that all three proteins cooperate at plugged septal pores, and their complex arrangement within the apical dome of mature hypha might represent a novel aspect of filamentous fungal polarisome architecture.

The NDR kinase scaffold HYM1/MO25 is essential for MAK2 map kinase signaling in Neurospora crassa.

Directory of Open Access Journals (Sweden)

Anne Dettmann

2012-09-01

Full Text Available Cell communication is essential for eukaryotic development, but our knowledge of molecules and mechanisms required for intercellular communication is fragmentary. In particular, the connection between signal sensing and regulation of cell polarity is poorly understood. In the filamentous ascomycete Neurospora crassa, germinating spores mutually attract each other and subsequently fuse. During these tropic interactions, the two communicating cells rapidly alternate between two different physiological states, probably associated with signal delivery and response. The MAK2 MAP kinase cascade mediates cell-cell signaling. Here, we show that the conserved scaffolding protein HYM1/MO25 controls the cell shape-regulating NDR kinase module as well as the signal-receiving MAP kinase cascade. HYM1 functions as an integral part of the COT1 NDR kinase complex to regulate the interaction with its upstream kinase POD6 and thereby COT1 activity. In addition, HYM1 interacts with NRC1, MEK2, and MAK2, the three kinases of the MAK2 MAP kinase cascade, and co-localizes with MAK2 at the apex of growing cells. During cell fusion, the three kinases of the MAP kinase module as well as HYM1 are recruited to the point of cell-cell contact. hym-1 mutants phenocopy all defects observed for MAK2 pathway mutants by abolishing MAK2 activity. An NRC1-MEK2 fusion protein reconstitutes MAK2 signaling in hym-1, while constitutive activation of NRC1 and MEK2 does not. These data identify HYM1 as a novel regulator of the NRC1-MEK2-MAK2 pathway, which may coordinate NDR and MAP kinase signaling during cell polarity and intercellular communication.

A Mapping Between Structural and Functional Brain Networks.

Science.gov (United States)

Meier, Jil; Tewarie, Prejaas; Hillebrand, Arjan; Douw, Linda; van Dijk, Bob W; Stufflebeam, Steven M; Van Mieghem, Piet

2016-05-01

The relationship between structural and functional brain networks is still highly debated. Most previous studies have used a single functional imaging modality to analyze this relationship. In this work, we use multimodal data, from functional MRI, magnetoencephalography, and diffusion tensor imaging, and assume that there exists a mapping between the connectivity matrices of the resting-state functional and structural networks. We investigate this mapping employing group averaged as well as individual data. We indeed find a significantly high goodness of fit level for this structure-function mapping. Our analysis suggests that a functional connection is shaped by all walks up to the diameter in the structural network in both modality cases. When analyzing the inverse mapping, from function to structure, longer walks in the functional network also seem to possess minor influence on the structural connection strengths. Even though similar overall properties for the structure-function mapping are found for different functional modalities, our results indicate that the structure-function relationship is modality dependent.

Proton structure functions at small x

International Nuclear Information System (INIS)

Hentschinski, Martin

2015-01-01

Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recent result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F 2 and F L , which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F 2 . We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F 2 in the small x region, as measured at HERA. Predictions for the structure function F L are found to be in agreement with the existing HERA data. (paper)

Elimination of active tad elements during the sexual phase of the Neurospora crassa life cycle.

Science.gov (United States)

Anderson, C; Tang, Q; Kinsey, J A

2001-06-01

Tad is an active LINE-like retrotransposon isolated from the Adiopodoumé strain of Neurospora crassa. Extensive analysis of other Neurospora strains has revealed no other strain with active Tad, but all strains tested have multiple copies of defective Tad elements. We have examined the ability of Tad to survive during the sexual cycle of Neurospora and find that active Tad is rapidly eliminated. The characteristics of this elimination suggest that the repeat-induced point mutation (RIP) mechanism was responsible. By the use of transformation to switch the mating type of the Adiopodoumé strain we concluded that this strain is not defective in the RIP process. Analysis of defective Tad elements isolated from a variety of strains indicates that the major difference between these elements and active Tad is due to the presence of a large number of G-C to A-T transition mutations. This would be expected if the changes were due primarily to the RIP process. Mapping of a selection of defective Tad elements reveals that they are present on all of the chromosomes; however, many of the elements are not widely shared among strains. This suggests that repeated introduction and elimination of Tad elements has occurred. Mechanisms that might be responsible for this repeated introduction are discussed. Copyright 2001 Academic Press.

Diquarks and nucleon structure functions

International Nuclear Information System (INIS)

Linkevich, A.D.; Savrin, V.I.; Skachkov, N.B.

1982-01-01

Formulae for structure functions of the deep-inelastic lepton-nucleon scattering are obtained through relativistic wave functions of systems composed of particles with spins 0, 1/2 and 1, 1/2. These wave functions are solutions of covariant two-particle single-time equations describing the nucleon as a system formed out of a quark and a diquark. Diquark is considered as a boson with the spin 0 and 1. The expressions for the nucleon structure functions are obtained by using the matrix elements of the current operator corresponding to the elastic scattering of the photon on a quark and on a diquark [ru

Study of quark structure functions

International Nuclear Information System (INIS)

Dao, F.T.; Flaminio, E.; Lai, K.; Metcalf, M.; Wang, L.

1977-01-01

The quark structure functions of the proton are determined through a combined analysis of the reactions pN → ll-barX and eN → eX. The valence-quark structure function of the pion is also given by analyzing the πN → μμ-barX data measured by the Branson et al

Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates.

Science.gov (United States)

Ellison, Christopher E; Kowbel, David; Glass, N Louise; Taylor, John W; Brem, Rachel B

2014-04-01

Most fungal genomes are poorly annotated, and many fungal traits of industrial and biomedical relevance are not well suited to classical genetic screens. Assigning genes to phenotypes on a genomic scale thus remains an urgent need in the field. We developed an approach to infer gene function from expression profiles of wild fungal isolates, and we applied our strategy to the filamentous fungus Neurospora crassa. Using transcriptome measurements in 70 strains from two well-defined clades of this microbe, we first identified 2,247 cases in which the expression of an unannotated gene rose and fell across N. crassa strains in parallel with the expression of well-characterized genes. We then used image analysis of hyphal morphologies, quantitative growth assays, and expression profiling to test the functions of four genes predicted from our population analyses. The results revealed two factors that influenced regulation of metabolism of nonpreferred carbon and nitrogen sources, a gene that governed hyphal architecture, and a gene that mediated amino acid starvation resistance. These findings validate the power of our population-transcriptomic approach for inference of novel gene function, and we suggest that this strategy will be of broad utility for genome-scale annotation in many fungal systems. IMPORTANCE Some fungal species cause deadly infections in humans or crop plants, and other fungi are workhorses of industrial chemistry, including the production of biofuels. Advances in medical and industrial mycology require an understanding of the genes that control fungal traits. We developed a method to infer functions of uncharacterized genes by observing correlated expression of their mRNAs with those of known genes across wild fungal isolates. We applied this strategy to a filamentous fungus and predicted functions for thousands of unknown genes. In four cases, we experimentally validated the predictions from our method, discovering novel genes involved in the

Structure functions and correlations in nuclei

International Nuclear Information System (INIS)

Fantoni, S.

1988-01-01

In this paper the results obtained for the static structure function S(k) and the longitudinal structure function S L (k) of 3 H, 3 He and 4 He nuclei and nuclear matter are presented and discussed. The calculations have been performed using realistic wave functions obtained from Faddeev and variational theories. The Monte Carlo method has been used to calculate the structure functions of finite systems, and the FHNC/SOC method for nuclear matter. The results for the 3 He nucleus are in agreement with the recent Saclay data. The results for nuclear matter are compared with the experimental data relative to heavier nuclei, like e.g. 40 Ca

Resonance contribution to electromagnetic structure functions

International Nuclear Information System (INIS)

Bowling, A.L. Jr.

1974-01-01

The part of the pion and proton electromagnetic structure functions due to direct channel resonances in the virtual Compton amplitude is discussed. After a phenomenological discussion, based on the work of Bloom and Gilman, of resonance production in inelastic electroproduction, the single resonance contribution to the pion and proton structure functions is expressed in terms of transition form factors. Froissart-Gribov representations of the Compton amplitude partial waves are presented and are used to specify the spin dependence of the transition form factors. The dependence of the form factors on momentum transfer and resonance mass is assumed on the basis of the behavior of exclusive resonance electroproduction. The single resonance contributions are summed in the Bjorken limit, and the result exhibits Bjorken scaling. Transverse photons are found to dominate in the Bjorken limit, and the threshold behavior of the resonant part of the structure functions is related to the asymptotic behavior of exclusive form factors at large momentum transfer. The resonant parts of the annihilation structure functions are not in general given by simple analytic continuation in the scaling vari []ble ω' of the electroproduction structure functions. (Diss. Abstr. Int., B)

Phenomenology of the electron structure function

International Nuclear Information System (INIS)

Slominski, W.; Szwed, J.

2001-01-01

The advantages of introducing the electron structure function (ESF) in electron induced processes are demonstrated. Contrary to the photon structure function it is directly measured in such processes. At present energies, a simultaneous analysis of both the electron and the photon structure functions gives an important test of the experimentally applied methods. Estimates of the ESF at LEP momenta are given. At very high momenta contributions from W and Z bosons together with γ-Z interference can be observed. Predictions for the next generation of experiments are given. (orig.)

Structure and Structure-activity Relationship of Functional Organic Molecules

Institute of Scientific and Technical Information of China (English)

2011-01-01

@@ Research theme The group is made up of junior scientists from the State Key Laboratory of Elemento-organic Chemistry, Nankai University.The scientists focus their studis on the structure and structure-activity relationship of functional organic molecules not only because it has been the basis of their research, but also because the functional study of organic compounds is now a major scientific issue for organic chemists around the world.

The Structure-Function Linkage Database.

Science.gov (United States)

Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E; Barber, Alan E; Custer, Ashley F; Hicks, Michael A; Huang, Conrad C; Lauck, Florian; Mashiyama, Susan T; Meng, Elaine C; Mischel, David; Morris, John H; Ojha, Sunil; Schnoes, Alexandra M; Stryke, Doug; Yunes, Jeffrey M; Ferrin, Thomas E; Holliday, Gemma L; Babbitt, Patricia C

2014-01-01

The Structure-Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure-function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies 'look alike', making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity.

Polarized DIS Structure Functions from Neural Networks

International Nuclear Information System (INIS)

Del Debbio, L.; Guffanti, A.; Piccione, A.

2007-01-01

We present a parametrization of polarized Deep-Inelastic-Scattering (DIS) structure functions based on Neural Networks. The parametrization provides a bias-free determination of the probability measure in the space of structure functions, which retains information on experimental errors and correlations. As an example we discuss the application of this method to the study of the structure function g 1 p (x,Q 2 )

Structure functions and correlations in nuclei

International Nuclear Information System (INIS)

Schiavilla, R.; Lewart, D.S.; Pandharipande, V.R.

1987-01-01

The static longitudinal structure function S l (k) and the static structure function S(k) of 3 H, 3 He and 4 He nuclei and nuclear matter are calculated using realistic wave functions obtained from Faddeev and variational calculations. In order to study the variation of the structure function with the number of particles in the system we also calculate S(k) of atomic helium liquid drops containing 4, 8, 20, 40, 70, 168 and 240 atoms. Monte Carlo integration is used to calculate the structure functions of finite systems, while those of nuclear matter are calculated with chain summation methods. The behaivior of S(k) and S l (k) at small values of k is discussed. We find that the recent Saclay data on S l (k) of the 3 He nucleus are in agreement with theory. Though the data indicate the the existence of correlations between the two protons in the 3 He nucleus, they are not accurate enough to draw interesting conclusions about the repulsive core in the nucleon-nucleon interaction. The structure functions of atomic helium liquid drops indicate a smooth variation of S(k) with the number of atoms in the drop. The S L (k) of the 4 He nucleus and nuclear matter are very similar for k > 1.5 fm -1 , and it appears plausible that S L (k) of nuclei having A > 3 may not depend significantly on A when k > 1.5 fm -1 . (orig.)

A possible form of the pion's structure function

International Nuclear Information System (INIS)

Long Ming; Huang Tao

1986-01-01

The pion's structure function behaviour is discussed by using the Fock state expansion of the hadronic wave function in QCD in this paper. As an example, we employ a model wave function of the Fock state in the light-cone and assume a Regge behaviour of a weight function for higher Fock states, and we get a possible form of the pion's structure function. This form is consistent with experimental data of the pion's structure function

Functional nanometer-scale structures

Science.gov (United States)

Chan, Tsz On Mario

Nanometer-scale structures have properties that are fundamentally different from their bulk counterparts. Much research effort has been devoted in the past decades to explore new fabrication techniques, model the physical properties of these structures, and construct functional devices. The ability to manipulate and control the structure of matter at the nanoscale has made many new classes of materials available for the study of fundamental physical processes and potential applications. The interplay between fabrication techniques and physical understanding of the nanostructures and processes has revolutionized the physical and material sciences, providing far superior properties in materials for novel applications that benefit society. This thesis consists of two major aspects of my graduate research in nano-scale materials. In the first part (Chapters 3--6), a comprehensive study on the nanostructures based on electrospinning and thermal treatment is presented. Electrospinning is a well-established method for producing high-aspect-ratio fibrous structures, with fiber diameter ranging from 1 nm--1 microm. A polymeric solution is typically used as a precursor in electrospinning. In our study, the functionality of the nanostructure relies on both the nanostructure and material constituents. Metallic ions containing precursors were added to the polymeric precursor following a sol-gel process to prepare the solution suitable for electrospinning. A typical electrospinning process produces as-spun fibers containing both polymer and metallic salt precursors. Subsequent thermal treatments of the as-spun fibers were carried out in various conditions to produce desired structures. In most cases, polymer in the solution and the as-spun fibers acted as a backbone for the structure formation during the subsequent heat treatment, and were thermally removed in the final stage. Polymers were also designed to react with the metallic ion precursors during heat treatment in some

Structure-function relationships during segregated and integrated network states of human brain functional connectivity.

Science.gov (United States)

Fukushima, Makoto; Betzel, Richard F; He, Ye; van den Heuvel, Martijn P; Zuo, Xi-Nian; Sporns, Olaf

2018-04-01

Structural white matter connections are thought to facilitate integration of neural information across functionally segregated systems. Recent studies have demonstrated that changes in the balance between segregation and integration in brain networks can be tracked by time-resolved functional connectivity derived from resting-state functional magnetic resonance imaging (rs-fMRI) data and that fluctuations between segregated and integrated network states are related to human behavior. However, how these network states relate to structural connectivity is largely unknown. To obtain a better understanding of structural substrates for these network states, we investigated how the relationship between structural connectivity, derived from diffusion tractography, and functional connectivity, as measured by rs-fMRI, changes with fluctuations between segregated and integrated states in the human brain. We found that the similarity of edge weights between structural and functional connectivity was greater in the integrated state, especially at edges connecting the default mode and the dorsal attention networks. We also demonstrated that the similarity of network partitions, evaluated between structural and functional connectivity, increased and the density of direct structural connections within modules in functional networks was elevated during the integrated state. These results suggest that, when functional connectivity exhibited an integrated network topology, structural connectivity and functional connectivity were more closely linked to each other and direct structural connections mediated a larger proportion of neural communication within functional modules. Our findings point out the possibility of significant contributions of structural connections to integrative neural processes underlying human behavior.

Clustering aspects in nuclear structure functions

International Nuclear Information System (INIS)

Hirai, M.; Saito, K.; Watanabe, T.; Kumano, S.

2011-01-01

For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility, clustering aspects are studied in structure functions of deep inelastic lepton-nucleus scattering by using momentum distributions calculated in antisymmetrized (or fermionic) molecular dynamics (AMD) and also in a simple shell model for comparison. According to AMD, the 9 Be nucleus consists of two α-like clusters with a surrounding neutron. The clustering produces high-momentum components in nuclear wave functions, which affects nuclear modifications of the structure functions. We investigated whether clustering features could appear in the structure function F 2 of 9 Be along with studies for other light nuclei. We found that nuclear modifications of F 2 are similar in both AMD and shell models within our simple convolution description although there are slight differences in 9 Be. It indicates that the anomalous 9 Be result should be explained by a different mechanism from the nuclear binding and Fermi motion. If nuclear-modification slopes d(F 2 A /F 2 D )/dx are shown by the maximum local densities, the 9 Be anomaly can be explained by the AMD picture, namely by the clustering structure, whereas it certainly cannot be described in the simple shell model. This fact suggests that the large nuclear modification in 9 Be should be explained by large densities in the clusters. For example, internal nucleon structure could be modified in the high-density clusters. The clustering aspect of nuclear structure functions is an unexplored topic which is interesting for future investigations.

Chemotropism and Cell Fusion in Neurospora crassa Relies on the Formation of Distinct Protein Complexes by HAM-5 and a Novel Protein HAM-14.

Science.gov (United States)

Jonkers, Wilfried; Fischer, Monika S; Do, Hung P; Starr, Trevor L; Glass, N Louise

2016-05-01

In filamentous fungi, communication is essential for the formation of an interconnected, multinucleate, syncytial network, which is constructed via hyphal fusion or fusion of germinated asexual spores (germlings). Anastomosis in filamentous fungi is comparable to other somatic cell fusion events resulting in syncytia, including myoblast fusion during muscle differentiation, macrophage fusion, and fusion of trophoblasts during placental development. In Neurospora crassa, fusion of genetically identical germlings is a highly dynamic and regulated process that requires components of a MAP kinase signal transduction pathway. The kinase pathway components (NRC-1, MEK-2 and MAK-2) and the scaffold protein HAM-5 are recruited to hyphae and germling tips undergoing chemotropic interactions. The MAK-2/HAM-5 protein complex shows dynamic oscillation to hyphae/germling tips during chemotropic interactions, and which is out-of-phase to the dynamic localization of SOFT, which is a scaffold protein for components of the cell wall integrity MAP kinase pathway. In this study, we functionally characterize HAM-5 by generating ham-5 truncation constructs and show that the N-terminal half of HAM-5 was essential for function. This region is required for MAK-2 and MEK-2 interaction and for correct cellular localization of HAM-5 to "fusion puncta." The localization of HAM-5 to puncta was not perturbed in 21 different fusion mutants, nor did these puncta colocalize with components of the secretory pathway. We also identified HAM-14 as a novel member of the HAM-5/MAK-2 pathway by mining MAK-2 phosphoproteomics data. HAM-14 was essential for germling fusion, but not for hyphal fusion. Colocalization and coimmunoprecipitation data indicate that HAM-14 interacts with MAK-2 and MEK-2 and may be involved in recruiting MAK-2 (and MEK-2) to complexes containing HAM-5. Copyright © 2016 by the Genetics Society of America.

Magnetism and Structure in Functional Materials

CERN Document Server

Planes, Antoni; Saxena, Avadh

2005-01-01

Magnetism and Structure in Functional Materials addresses three distinct but related topics: (i) magnetoelastic materials such as magnetic martensites and magnetic shape memory alloys, (ii) the magnetocaloric effect related to magnetostructural transitions, and (iii) colossal magnetoresistance (CMR) and related magnanites. The goal is to identify common underlying principles in these classes of materials that are relevant for optimizing various functionalities. The emergence of apparently different magnetic/structural phenomena in disparate classes of materials clearly points to a need for common concepts in order to achieve a broader understanding of the interplay between magnetism and structure in this general class of new functional materials exhibiting ever more complex microstructure and function. The topic is interdisciplinary in nature and the contributors correspondingly include physicists, materials scientists and engineers. Likewise the book will appeal to scientists from all these areas.

Summary of the Photon Structure Functions - Measurements at LEP

International Nuclear Information System (INIS)

Przybycien, M.

2002-01-01

The present status of the photon structure functions measurements at LEP is discussed. The short introduction to the kinematics and theoretical framework of the structure functions measurements at LEP is given first. Then follow presentations of the most important measurements, ranging from the QED photon structure function, through the hadronic structure functions of real and virtual photons, and at the end the first measurement of the electron structure function is shown. (author)

Effective constraint algebras with structure functions

International Nuclear Information System (INIS)

Bojowald, Martin; Brahma, Suddhasattwa

2016-01-01

This article presents the result that fluctuations and higher moments of a state, by themselves, do not imply quantum corrections in structure functions of constrained systems. Moment corrections are isolated from other types of quantum effects, such as factor-ordering choices and regularization, by introducing a new condition with two parts: (i) having a direct (or faithful) quantization of the classical structure functions, (ii) free of factor-ordering ambiguities. In particular, it is assumed that the classical constraints can be quantized in an anomaly free way, so that properties of the resulting constraint algebras can be derived. If the two-part condition is not satisfied, effective constraints can still be evaluated, but quantum effects may be stronger. Consequences for canonical quantum gravity, whose structure functions encode space–time structure, are discussed. In particular, deformed algebras found in models of loop quantum gravity provide reliable information even in the Planck regime. (paper)

Biochemical genetics of the circadian rhythm in Neurospora crassa: studies on the cel strain

International Nuclear Information System (INIS)

Lakin-Thomas, P.L.

1985-01-01

In Neurospora crassa, the cel mutation lengthens the period of the circadian rhythm when the medium is supplemented with linoleic acid (18:2). Double mutant strains were constructed between cel and the clock mutants prd-1 and four alleles at the frq locus. It was found that: (1) the effect of 18:2 on cel was blocked by prd-1, i.e., prd-1 is epistatic to cel. (2) cel and frq interact such that the percent increase in the period produced by 18:2 was inversely proportional to the period of the frq parent. (3) Data from the literature on period effects in double mutant strains support a multiplicative rather than an additive model. A biochemical interpretation of these interactions is discussed, based on the control of flux through metabolic pathways. Because the cel strain is known to be deficient in the pantothenate derivative normally attached to the fatty acid synthetase (FAS) complex, the possibility that cel may affect other pantothenate-modified proteins was investigated. It was found that in the cel + strain, five proteins of molecular weights (M/sub r/) 9000, 19,000, 22,000, 140,000, and 200,000 were labelled with [ 14 C]pantothenate. In the cel strain, only the 200 k (FAS) label was reduced in amount. Therefore, there is no evidence that cel affects circadian rhythmicity through any deficiency other than FAS. A biochemical model for circadian rhythmicity in Neurospora is presented. Oscillations in cytoplasmic and mitochondrial Ca 2+ are proposed; clock mutations are postulated to affect Ca 2+ transporters and the mitochondrial membrane; and phase-shifting effects are accounted for by changes in Ca 2+ or ATP levels

The notochord: structure and functions.

Science.gov (United States)

Corallo, Diana; Trapani, Valeria; Bonaldo, Paolo

2015-08-01

The notochord is an embryonic midline structure common to all members of the phylum Chordata, providing both mechanical and signaling cues to the developing embryo. In vertebrates, the notochord arises from the dorsal organizer and it is critical for proper vertebrate development. This evolutionary conserved structure located at the developing midline defines the primitive axis of embryos and represents the structural element essential for locomotion. Besides its primary structural function, the notochord is also a source of developmental signals that patterns surrounding tissues. Among the signals secreted by the notochord, Hedgehog proteins play key roles during embryogenesis. The Hedgehog signaling pathway is a central regulator of embryonic development, controlling the patterning and proliferation of a wide variety of organs. In this review, we summarize the current knowledge on notochord structure and functions, with a particular emphasis on the key developmental events that take place in vertebrates. Moreover, we discuss some genetic studies highlighting the phenotypic consequences of impaired notochord development, which enabled to understand the molecular basis of different human congenital defects and diseases.

Introduction to structure functions

International Nuclear Information System (INIS)

Kwiecinski, J.

1996-07-01

The theory of deep inelastic scattering structure functions is reviewed with an emphasis put on the QCD expectations of their behaviour in the region of small values of Bjorken parameter x. (author). 56 refs

A density functional study of backbone structures of polydiacetylene: destabilization of butatriene structure

International Nuclear Information System (INIS)

Katagiri, Hideki; Shimoi, Yukihiro; Abe, Shuji

2004-01-01

Backbone structures of polydiacetylene are studied with first-principles electronic structure method using plane-waves within generalized gradient approximation (GGA) of density functional theory. In spin-restricted calculations a coarse k-point sampling gives a potential energy curve with two local minima corresponding to acetylene and butatriene structures. However, the potential barrier between the two structures rapidly decreases with increasing number of k-points, which results in destabilization of the butatriene structure. Spin polarization effects also destabilize the butatriene structure, inducing atom-centered spin-density-wave state. These potential energies were compared with those obtained by Hartree-Fock, density functional within local density approximation (LDA) and GGA, and hybrid density functional methods using a gaussian basis set. The comparison shows that the density functional methods within LDA and GGA favor the destabilization of the butatriene structure in contrast to the Hartree-Fock method

Network structure shapes spontaneous functional connectivity dynamics.

Science.gov (United States)

Shen, Kelly; Hutchison, R Matthew; Bezgin, Gleb; Everling, Stefan; McIntosh, Anthony R

2015-04-08

The structural organization of the brain constrains the range of interactions between different regions and shapes ongoing information processing. Therefore, it is expected that large-scale dynamic functional connectivity (FC) patterns, a surrogate measure of coordination between brain regions, will be closely tied to the fiber pathways that form the underlying structural network. Here, we empirically examined the influence of network structure on FC dynamics by comparing resting-state FC (rsFC) obtained using BOLD-fMRI in macaques (Macaca fascicularis) to structural connectivity derived from macaque axonal tract tracing studies. Consistent with predictions from simulation studies, the correspondence between rsFC and structural connectivity increased as the sample duration increased. Regions with reciprocal structural connections showed the most stable rsFC across time. The data suggest that the transient nature of FC is in part dependent on direct underlying structural connections, but also that dynamic coordination can occur via polysynaptic pathways. Temporal stability was found to be dependent on structural topology, with functional connections within the rich-club core exhibiting the greatest stability over time. We discuss these findings in light of highly variable functional hubs. The results further elucidate how large-scale dynamic functional coordination exists within a fixed structural architecture. Copyright © 2015 the authors 0270-6474/15/355579-10$15.00/0.

Mind, brain, structure and function

Energy Technology Data Exchange (ETDEWEB)

Aleksander, I

1982-01-01

The author discusses the type of problem one encounters when trying to formalise the nature of a state structure associated with the brain and the origins of this state structure. The paper first defines in broad terms the nature of the structure function problem, and then goes on to separate out those parts of a structure that lead to the variational and adaptive nature of the state structure. It is argued that the relationship between the structure that leads to adaptation and its embedding in an external environment are crucial areas for further study. 4 references.

Photon-photon collisions and photon structure functions at LEP

CERN Document Server

Patt, J

2000-01-01

The present knowledge of the structure of the photon based on measurements of photon structure functions is discussed. This review covers recent results on QED structure functions and on the hadronic structure function F/sub 2//sup gamma /. (13 refs).

Structure functions are not parton probabilities

International Nuclear Information System (INIS)

Brodsky, Stanley J.; Hoyer, Paul; Sannino, Francesco; Marchal, Nils; Peigne, Stephane

2002-01-01

The common view that structure functions measured in deep inelastic lepton scattering are determined by the probability of finding quarks and gluons in the target is not correct in gauge theory. We show that gluon exchange between the fast, outgoing partons and target spectators, which is usually assumed to be an irrelevant gauge artifact, affects the leading twist structure functions in a profound way. This observation removes the apparent contradiction between the projectile (eikonal) and target (parton model) views of diffractive and small x B phenomena. The diffractive scattering of the fast outgoing quarks on spectators in the target causes shadowing in the DIS cross section. Thus the depletion of the nuclear structure functions is not intrinsic to the wave function of the nucleus, but is a coherent effect arising from the destructive interference of diffractive channels induced by final state interactions. This is consistent with the Glauber-Gribov interpretation of shadowing as a rescattering effect

QCD predictions for weak neutral current structure functions

International Nuclear Information System (INIS)

Wu Jimin

1987-01-01

Employing the analytic expression (to the next leading order) for non-singlet component of structure function which the author got from QCD theory and putting recent experiment result of neutral current structure function at Q 2 = 11 (GeV/C) 2 as input, the QCD prediction for neutral current structure function of their scaling violation behaviours was given

QCD dipole predictions for DIS and diffractive structure functions

International Nuclear Information System (INIS)

Royon, C.

1997-01-01

The proton structure function F 2 , the gluon density F G , and the longitudinal structure function F L are derived in the QCD dipole picture of BFKL dynamics. We use a three parameter fit to describe the 1994 H1 proton structure function F 2 data in the low x, moderate Q 2 range. Without any additional parameter, the gluon density and the longitudinal structure functions are predicted. The diffractive dissociation processes are also discussed within the same framework, and a new prediction for the proton diffractive structure function is obtained

An approach to the structure function for nucleon

International Nuclear Information System (INIS)

Long Ming

1986-01-01

The structure function for nucleon is discussed by using the method given in a previous paper. The formula are compared with the experimental data from low Q 2 to high Q 2 . The results show that the way that the structure function for nucleon can be obtained from the hadronic wavefunction is a possible approach of investigating structure functions for hadron

Four RNA families with functional transient structures.

Science.gov (United States)

Zhu, Jing Yun A; Meyer, Irmtraud M

2015-01-01

Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5' flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5' UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All

Using the structure-function linkage database to characterize functional domains in enzymes.

Science.gov (United States)

Brown, Shoshana; Babbitt, Patricia

2014-12-12

The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. Copyright © 2014 John Wiley & Sons, Inc.

Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.

Directory of Open Access Journals (Sweden)

2005-08-01

Full Text Available The bias in protein structure and function space resulting from experimental limitations and targeting of particular functional classes of proteins by structural biologists has long been recognized, but never continuously quantified. Using the Enzyme Commission and the Gene Ontology classifications as a reference frame, and integrating structure data from the Protein Data Bank (PDB, target sequences from the structural genomics projects, structure homology derived from the SUPERFAMILY database, and genome annotations from Ensembl and NCBI, we provide a quantified view, both at the domain and whole-protein levels, of the current and projected coverage of protein structure and function space relative to the human genome. Protein structures currently provide at least one domain that covers 37% of the functional classes identified in the genome; whole structure coverage exists for 25% of the genome. If all the structural genomics targets were solved (twice the current number of structures in the PDB, it is estimated that structures of one domain would cover 69% of the functional classes identified and complete structure coverage would be 44%. Homology models from existing experimental structures extend the 37% coverage to 56% of the genome as single domains and 25% to 31% for complete structures. Coverage from homology models is not evenly distributed by protein family, reflecting differing degrees of sequence and structure divergence within families. While these data provide coverage, conversely, they also systematically highlight functional classes of proteins for which structures should be determined. Current key functional families without structure representation are highlighted here; updated information on the "most wanted list" that should be solved is available on a weekly basis from http://function.rcsb.org:8080/pdb/function_distribution/index.html.

Functional classification of protein structures by local structure matching in graph representation.

Science.gov (United States)

Mills, Caitlyn L; Garg, Rohan; Lee, Joslynn S; Tian, Liang; Suciu, Alexandru; Cooperman, Gene; Beuning, Penny J; Ondrechen, Mary Jo

2018-03-31

As a result of high-throughput protein structure initiatives, over 14,400 protein structures have been solved by structural genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP-Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP-Func method to our previously reported method, structurally aligned local sites of activity (SALSA), using the ribulose phosphate binding barrel (RPBB), 6-hairpin glycosidase (6-HG), and Concanavalin A-like Lectins/Glucanase (CAL/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP-Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP-Func methods to predict function. Forty-one SG proteins in the RPBB superfamily, nine SG proteins in the 6-HG superfamily, and one SG protein in the CAL/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Structure and Functions of Linker Histones.

Science.gov (United States)

Lyubitelev, A V; Nikitin, D V; Shaytan, A K; Studitsky, V M; Kirpichnikov, M P

2016-03-01

Linker histones such as variants H1, H5, and other similar proteins play an important role in regulation of chromatin structure and dynamics. However, interactions of linker histones with DNA and proteins, as well as specific functions of their different variants, are poorly studied. This is because they acquire tertiary structure only when interacting with a nucleosome, and because of limitations of currently available methods. However, deeper investigation of linker histones and their interactions with other proteins will address a number of important questions - from structure of compacted chromatin to regulation of early embryogenesis. In this review, structures of histone H1 variants and its interaction with chromatin DNA are considered. A possible functional significance of different H1 variants, a role of these proteins in maintaining interphase chromatin structure, and interactions of linker histones with other cellular proteins are also discussed.

Functional Generalized Structured Component Analysis.

Science.gov (United States)

Suk, Hye Won; Hwang, Heungsun

2016-12-01

An extension of Generalized Structured Component Analysis (GSCA), called Functional GSCA, is proposed to analyze functional data that are considered to arise from an underlying smooth curve varying over time or other continua. GSCA has been geared for the analysis of multivariate data. Accordingly, it cannot deal with functional data that often involve different measurement occasions across participants and a large number of measurement occasions that exceed the number of participants. Functional GSCA addresses these issues by integrating GSCA with spline basis function expansions that represent infinite-dimensional curves onto a finite-dimensional space. For parameter estimation, functional GSCA minimizes a penalized least squares criterion by using an alternating penalized least squares estimation algorithm. The usefulness of functional GSCA is illustrated with gait data.

Collagens--structure, function, and biosynthesis.

Science.gov (United States)

Gelse, K; Pöschl, E; Aigner, T

2003-11-28

The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified so far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. This review focuses on the distribution and function of various collagen types in different tissues. It introduces their basic structural subunits and points out major steps in the biosynthesis and supramolecular processing of fibrillar collagens as prototypical members of this protein family. A final outlook indicates the importance of different collagen types not only for the understanding of collagen-related diseases, but also as a basis for the therapeutical use of members of this protein family discussed in other chapters of this issue.

Structure and Function of Your Skin

Science.gov (United States)

... Name: Category: Share: Yes No, Keep Private Structure & Function of Your Skin Share | What It Looks Like . . . ... in the dermis. What It Does . . . The major function of skin is to provide a barrier between ...

The structural science of functional materials.

Science.gov (United States)

Catlow, C Richard A

2018-01-01

The growing complexity of functional materials and the major challenges this poses to structural science are discussed. The diversity of structural materials science and the contributions that computation is making to the field are highlighted.

QCD dipole prediction for dis and diffractive structure functions

International Nuclear Information System (INIS)

Royon, CH.

1996-01-01

The F 2 , F G , R = F L /F T proton structure functions are derived in the QCD dipole picture of BFKL dynamics. We get a three parameter fit describing the 1994 H1 proton structure function F 2 data in the low x, moderate Q 2 range. Without any additional parameter, the gluon density and the longitudinal structure functions are predicted. The diffractive dissociation processes are also discussed, and a new prediction for the proton diffractive structure function is obtained. (author)

Nuclear enhanced power corrections to DIS structure functions

OpenAIRE

Guo, Xiaofeng; Qiu, Jianwei; Zhu, Wei

2001-01-01

We calculate nuclear enhanced power corrections to structure functions measured in deeply inelastic lepton-nucleus scattering in Quantum Chromodynamics (QCD). We find that the nuclear medium enhanced power corrections at order of $O(\\alpha_s/Q^2)$ enhance the longitudinal structure function $F_L$, and suppress the transverse structure function $F_1$. We demonstrate that strong nuclear effects in $\\sigma_A/\\sigma_D$ and $R_A/R_D$, recently observed by HERMES Collaboration, can be explained in ...

Second-order QCD analysis of the photon structure function

International Nuclear Information System (INIS)

Antoniadis, I.; Grunberg, G.

1983-01-01

The QCD predictions for the photon structure function are reexamined with particular emphasis on the small-x behavior. A simple parametrization of the real photon structure function, free of 1/x singularity, is derived. The structure function is found to be sensitive at small x to the non-perturbatively calculable constant term in the n=2 moment, and we show that the problem of a negative structure function can be solved on the basis of the knowledge of this single non-perturbative parameter. (orig.)

AGE STRUCTURE OR FUNCTIONAL RESPONSE? RECONCILING ...

African Journals Online (AJOL)

... surplus production that differ from traditional single-species management models. ... Specifically, while the ECOSIM “Arena” functional response and the von ... as a proxy for age structure rather than as a function of predator/prey behaviour, ...

EFFECTIVE HYPERFINE-STRUCTURE FUNCTIONS OF AMMONIA

Energy Technology Data Exchange (ETDEWEB)

Augustovičová, L.; Soldán, P.; Špirko, V., E-mail: spirko@marge.uochb.cas.cz [Charles University in Prague, Faculty of Mathematics and Physics, Department of Chemical Physics and Optics, Ke Karlovu 3, CZ-12116 Prague 2 (Czech Republic)

2016-06-20

The hyperfine structure of the rotation-inversion ( v {sub 2} = 0{sup +}, 0{sup −}, 1{sup +}, 1{sup −}) states of the {sup 14}NH{sub 3} and {sup 15}NH{sub 3} ammonia isotopomers is rationalized in terms of effective (ro-inversional) hyperfine-structure (hfs) functions. These are determined by fitting to available experimental data using the Hougen’s effective hyperfine-structure Hamiltonian within the framework of the non-rigid inverter theory. Involving only a moderate number of mass independent fitting parameters, the fitted hfs functions provide a fairly close reproduction of a large majority of available experimental data, thus evidencing adequacy of these functions for reliable prediction. In future experiments, this may help us derive spectroscopic constants of observed inversion and rotation-inversion transitions deperturbed from hyperfine effects. The deperturbed band centers of ammonia come to the forefront of fundamental physics especially as the probes of a variable proton-to-electron mass ratio.

Nucleon structure functions, resonance form factors, and duality

International Nuclear Information System (INIS)

Davidovsky, V.V.; Struminsky, B.V.

2003-01-01

The behavior of nucleon structure functions in the resonance region is explored. For form factors that describe resonance production, expressions are obtained that are dependent on the photon virtuality Q 2 , which have a correct threshold behavior, and which take into account available experimental data on resonance decay. Resonance contributions to nucleon structure functions are calculated. The resulting expressions are used to investigate quark-hadron duality in electron-nucleon scattering by taking the example of the structure function F 2

DNA: Structure and function

DEFF Research Database (Denmark)

Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir

1998-01-01

This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...

Deep inelastic singlet structure functions and scaling violation

Energy Technology Data Exchange (ETDEWEB)

Wen-zhu, Li; Bing-xun, Hu

1984-02-01

The flavour singlet structure functions of deep inelastic scattering processes can yield more decisive tests of QCD than the non-singlet. We give analytical expression for flavour singlet structure functions through analysing the lepton-nucleon deep inelastic scattering processes by means of QCD and using Jacobi polynomials. This expression contains 4 to 5 parameters and shows the changes of the singlet structure functions with x and Q/sup 2/ very well. In QCD leading order, the conclusion is in reasonable agreement with experimental data.

Functional and planning structures of education institutions areas

OpenAIRE

Соколова, Юлія Віталіївна; Ковальська, Гелена Леонідівна

2014-01-01

The article discusses the main aspects of functional and planning organization of the education institutions. The features of the schools stationing in the city structure and its future extension are also defined. The major functional subdivisions are considered and the role of each of it in the education institution structure is investigated. The ratio of the functional zones depending on the specialization of educational institution is determined. The advantages of the functional zone coope...

Generalized fluid impulse functions for oscillating marine structures

Science.gov (United States)

Janardhanan, K.; Price, W. G.; Wu, Y.

1992-03-01

A selection of generalized impulse response functions is presented for a variety of rigid and flexible marine structures (i.e. mono-hull, SWATH, floating drydock and twin dock, fixed flexible pile). These functions are determined from calculated and experimental frequency-dependent hydrodynamic data, and the characteristics of these data depend on the type of structure considered. This information is reflected in the shape and duration of the generalized impulse response functions which are pre-requisites for a generalized integro-differential mathematical model describing the dynamic behaviour of the structures to seaway excitation.

Structure functions in the chiral bag model

International Nuclear Information System (INIS)

Sanjose, V.; Vento, V.; Centro Mixto CSIC/Valencia Univ., Valencia

1989-01-01

We calculate the structure functions of an isoscalar nuclear target for the deep inelastic scattering by leptons in an extended version of the chiral bag model which incorporates the qanti q structure of the pions in the cloud. Bjorken scaling and Regge behavior are satisfied. The model calculation reproduces the low-x behavior of the data but fails to explain the medium- to large-x behavior. Evolution of the quark structure functions seem inevitable to attempt a connection between the low-energy models and the high-energy behavior of quantum chromodynamics. (orig.)

Structure functions in the chiral bag model

Energy Technology Data Exchange (ETDEWEB)

Sanjose, V.; Vento, V.

1989-07-13

We calculate the structure functions of an isoscalar nuclear target for the deep inelastic scattering by leptons in an extended version of the chiral bag model which incorporates the qanti q structure of the pions in the cloud. Bjorken scaling and Regge behavior are satisfied. The model calculation reproduces the low-x behavior of the data but fails to explain the medium- to large-x behavior. Evolution of the quark structure functions seem inevitable to attempt a connection between the low-energy models and the high-energy behavior of quantum chromodynamics. (orig.).

Progress on nuclear modifications of structure functions

Directory of Open Access Journals (Sweden)

Kumano S.

2016-01-01

Full Text Available We report progress on nuclear structure functions, especially on their nuclear modifications and a new tensor structure function for the deuteron. To understand nuclear structure functions is an important step toward describing nuclei and QCD matters from low to high densities and from low to high energies in terms of fundamental quark and gluon degrees of freedom beyond conventional hadron and nuclear physics. It is also practically important for understanding new phenomena in high-energy heavy-ion collisions at RHIC and LHC. Furthermore, since systematic errors of current neutrinooscillation experiments are dominated by uncertainties of neutrino-nucleus interactions, such studies are valuable for finding new physics beyond current framework. Next, a new tensor-polarized structure function b1 is discussed for the deuteron. There was a measurement by HERMES; however, its data are inconsistent with the conventional convolution estimate based on the standard deuteron model with D-state admixture. This fact suggests that a new hadronic phenomenon should exist in the tensor-polarized deuteron at high energies, and it will be experimentally investigated at JLab from the end of 2010’s.

Kinetic-energy density functional: Atoms and shell structure

International Nuclear Information System (INIS)

Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E.

1996-01-01

We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. copyright 1996 The American Physical Society

The contact activation proteins: a structure/function overview

NARCIS (Netherlands)

Meijers, J. C.; McMullen, B. A.; Bouma, B. N.

1992-01-01

In recent years, extensive knowledge has been obtained on the structure/function relationships of blood coagulation proteins. In this overview, we present recent developments on the structure/function relationships of the contact activation proteins: factor XII, high molecular weight kininogen,

Nucleon structure functions in noncommutative space-time

Energy Technology Data Exchange (ETDEWEB)

Rafiei, A.; Rezaei, Z.; Mirjalili, A. [Yazd University, Physics Department, Yazd (Iran, Islamic Republic of)

2017-05-15

In the context of noncommutative space-time we investigate the nucleon structure functions which play an important role in identifying the internal structure of nucleons. We use the corrected vertices and employ new vertices that appear in two approaches of noncommutativity and calculate the proton structure functions in terms of the noncommutative tensor θ{sub μν}. To check our results we plot the nucleon structure function (NSF), F{sub 2}(x), and compare it with experimental data and the results from the GRV, GJR and CT10 parametrization models. We show that with the new vertex that arises the noncommutativity correction will lead to a better consistency between theoretical results and experimental data for the NSF. This consistency will be better for small values of the Bjorken variable x. To indicate and confirm the validity of our calculations we also act conversely. We obtain a lower bound for the numerical values of Λ{sub NC} scale which correspond to recent reports. (orig.)

Collagens - structure, function and biosynthesis.

OpenAIRE

Gelse, K; Poschl, E; Aigner, T

2003-01-01

The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified so far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. This review focuses on the dis...

Solving crystal structures with the symmetry minimum function

International Nuclear Information System (INIS)

Estermann, M.A.

1995-01-01

Unravelling the Patterson function (the auto-correlation function of the crystal structure) (A.L. Patterson, Phys. Rev. 46 (1934) 372) can be the only way of solving crystal structures from neutron and incomplete diffraction data (e.g. powder data) when direct methods for phase determination fail. The negative scattering lengths of certain isotopes and the systematic loss of information caused by incomplete diffraction data invalidate the underlying statistical assumptions made in direct methods. In contrast, the Patterson function depends solely on the quality of the available diffraction data. Simpson et al. (P.G. Simpson et al., Acta Crystallogr. 18 (1965) 169) showed that solving a crystal structure with a particular superposition of origin-shifted Patterson functions, the symmetry minimum function, is advantageous over using the Patterson function alone, for single-crystal X-ray data.This paper describes the extension of the Patterson superposition approach to neutron data and powder data by (a) actively using the negative regions in the Patterson map caused by negative scattering lengths and (b) using maximum entropy Patterson maps (W.I.F. David, Nature 346 (1990) 731). Furthermore, prior chemical knowledge such as bond lengths and angles from known fragments have been included. Two successful structure solutions of a known and a previously unknown structure (M. Hofmann, J. Solid State Chem., in press) illustrate the potential of this new development. ((orig.))

Small-x Resummation and HERA Structure Function Data

CERN Document Server

Altarelli, Guido; Forte, Stefano; Altarelli, Guido; Ball, Richard D.; Forte, Stefano

2001-01-01

We apply our systematic NLO small x resummation of singlet splitting functions to the scaling violations of structure functions and compare the results with data. We develop various theoretical tools which are needed in order to relate resummed parton distributions to measurable structure functions, and we present results from a variety of fits to HERA data for the structure functions F_2 and F_L using the resummation. The behaviour of the singlet splitting functions at small x and fixed Q^2 is effectively parametrized as x^{-lambda}. We find that, for lambda small or negative, the resummed description of scaling violations may be phenomenologically as good as or even better than the standard next-to-leading order treatment. However, the best fit gluon density and value of alpha_s can be significantly modified by the resummation.

Characterization of technical surfaces by structure function analysis

Science.gov (United States)

Kalms, Michael; Kreis, Thomas; Bergmann, Ralf B.

2018-03-01

The structure function is a tool for characterizing technical surfaces that exhibits a number of advantages over Fourierbased analysis methods. So it is optimally suited for analyzing the height distributions of surfaces measured by full-field non-contacting methods. The structure function is thus a useful method to extract global or local criteria like e. g. periodicities, waviness, lay, or roughness to analyze and evaluate technical surfaces. After the definition of line- and area-structure function and offering effective procedures for their calculation this paper presents examples using simulated and measured data of technical surfaces including aircraft parts.

Structure functions and parton distributions

International Nuclear Information System (INIS)

Martin, A.D.; Stirling, W.J.; Roberts, R.G.

1995-01-01

The MRS parton distribution analysis is described. The latest sets are shown to give an excellent description of a wide range of deep-inelastic and other hard scattering data. Two important theoretical issues-the behavior of the distributions at small x and the flavor structure of the quark sea-are discussed in detail. A comparison with the new structure function data from HERA is made, and the outlook for the future is discussed

An impedance function approach for soil-structure interaction analyses including structure-to-structure interaction effects

International Nuclear Information System (INIS)

Gantayat, A.; Kamil, H.

1981-01-01

The dynamic soil-structure and structure-to-structure interaction effects may be determined in one of the two ways: by modeling the entire soil-structure system by a finite-element model, or by using a frequency-dependent (or frequency-independent) impedance function approach. In seismic design of nuclear power plant structures, the normal practice is to use the first approach because of its simplicity and easy availability of computer codes to perform such analyses. However, in the finite-element approach, because of the size and cost restrictions, the three-dimensional behavior of the entire soil-structure system and the radiation damping in soil are only approximately included by using a two-dimensional finite-element mesh. In using the impedance function approach, the soil-structure analyses can be performed in four steps: (a) determination of the dynamic properties of the fixed base superstructure, (b) determination of foundation and structure impedance matrices and input motions, (c) evaluation of foundation motion, (d) analysis of the fixed base superstructure using computed foundation motion. (orig./RW)

Connectivity and functional profiling of abnormal brain structures in pedophilia.

Science.gov (United States)

Poeppl, Timm B; Eickhoff, Simon B; Fox, Peter T; Laird, Angela R; Rupprecht, Rainer; Langguth, Berthold; Bzdok, Danilo

2015-06-01

Despite its 0.5-1% lifetime prevalence in men and its general societal relevance, neuroimaging investigations in pedophilia are scarce. Preliminary findings indicate abnormal brain structure and function. However, no study has yet linked structural alterations in pedophiles to both connectional and functional properties of the aberrant hotspots. The relationship between morphological alterations and brain function in pedophilia as well as their contribution to its psychopathology thus remain unclear. First, we assessed bimodal connectivity of structurally altered candidate regions using meta-analytic connectivity modeling (MACM) and resting-state correlations employing openly accessible data. We compared the ensuing connectivity maps to the activation likelihood estimation (ALE) maps of a recent quantitative meta-analysis of brain activity during processing of sexual stimuli. Second, we functionally characterized the structurally altered regions employing meta-data of a large-scale neuroimaging database. Candidate regions were functionally connected to key areas for processing of sexual stimuli. Moreover, we found that the functional role of structurally altered brain regions in pedophilia relates to nonsexual emotional as well as neurocognitive and executive functions, previously reported to be impaired in pedophiles. Our results suggest that structural brain alterations affect neural networks for sexual processing by way of disrupted functional connectivity, which may entail abnormal sexual arousal patterns. The findings moreover indicate that structural alterations account for common affective and neurocognitive impairments in pedophilia. The present multimodal integration of brain structure and function analyses links sexual and nonsexual psychopathology in pedophilia. © 2015 Wiley Periodicals, Inc.

Photon structure functions at small x in holographic QCD

International Nuclear Information System (INIS)

Watanabe, Akira; Li, Hsiang-nan

2015-01-01

We investigate the photon structure functions at small Bjorken variable x in the framework of the holographic QCD, assuming dominance of the Pomeron exchange. The quasi-real photon structure functions are expressed as convolution of the Brower–Polchinski–Strassler–Tan (BPST) Pomeron kernel and the known wave functions of the U(1) vector field in the five-dimensional AdS space, in which the involved parameters in the BPST kernel have been fixed in previous studies of the nucleon structure functions. The predicted photon structure functions, as confronted with data, provide a clean test of the BPST kernel. The agreement between theoretical predictions and data is demonstrated, which supports applications of holographic QCD to hadronic processes in the nonperturbative region. Our results are also consistent with those derived from the parton distribution functions of the photon proposed by Glück, Reya, and Schienbein, implying realization of the vector meson dominance in the present model setup.

Structure functions of hadrons in the QCD effective theory

International Nuclear Information System (INIS)

Shigetani, Takayuki

1996-01-01

We study the structure functions of hadrons with the low energy effective theory of QCD. We try to clarify a link between the low energy effective theory, where non-perturbative dynamics is essential, and the high energy deep inelastic scattering experiment. We calculate the leading twist matrix elements of the structure function at the low energy model scale within the effective theory. Calculated structure functions are evoluted to the high momentum scale with the help of the perturbative QCD, and compared with the experimental data. Through the comparison of the model calculations with the experiment, we discuss how the non-perturbative dynamics of the effective theory is reflected in the deep inelastic phenomena. We first evaluate the structure functions of the pseudoscalar mesons using the NJL model. The resulting structure functions show reasonable agreements with experiments. We study then the quark distribution functions of the nucleon using a covariant quark-diquark model. We calculate three leading twist distribution functions, spin-independent f 1 (x), longitudinal spin distribution g 1 (x), and chiral-odd transversity spin distribution h 1 (x). The results for f 1 (x) and g 1 (x) turn out to be consistent with available experiments because of the strong spin-0 diquark correlation. (author)

Structure function measurements in the deep inelastic muon-nucleon scattering

International Nuclear Information System (INIS)

Peschel, H.

1990-03-01

Measurements of deep inelastic scattering events on a combined copper and deuterium target were performed by the European Muon Collaboration (EMC) using a muon beam at CERN's SPS with energies at 100 GeV and 280 GeV. The data are analysed and compared with a detailed Monte-Carlo simulation and allow the determination of structure functions from both targets. In the light of the present discrepancy between EMC's and BCDMS's structure functions, stringend cuts were applied to the data. The results confirm the EMC structure function measurements on unbound nucleons. The comparison between the copper structure function from this experiment and the NA2 iron structure function shows a trend to lower values at low x Bj . (orig.) [de

Structure functions of electroweak boson and leptons

International Nuclear Information System (INIS)

Slominski, W.; Szwed, J.

1996-01-01

The QCD structure of the electroweak bosons is reviewed and the lepton structure function is defined and calculated. The leading order splitting functions of electron into quarks are extracted, showing an important contribution from γ-Z interference. Leading logarithmic QCD evolution equations are constructed and solved in the asymptotic region where log 2 behavior of the Parton densities is observed. Possible applications with clear manifestation of ''resolved'' photon and weak bosons are discussed. 8 refs., 3 figs

Boson structure functions from inelastic electron scattering

International Nuclear Information System (INIS)

De Jager, C.W.

1986-01-01

The even /sup 104-110/Pd isotopes and /sup 196/Pt have been investigated at NIKHEF-K by high-resolution inelastic electron scattering. A new IBA-2 calculation has been performed for the Pd isotopes, in which the ratio of the proton and neutron coupling constants is taken from pion scattering. One set of boson structure functions sufficed for the description of the first and second E2-excitations in all Pd isotopes. The data showed no sensitivity for different structure functions for proton and neutron bosons. A preliminary analysis of a number of negative parity states (3/sup -/,5/sup -/ and 7/sup -/), observed in /sup 196/Pt, was performed through the introduction of an f-boson. The first E4-excitation in the palladium isotopes can be reasonably described with a β-structure function, but all other E4-excitations require the introduction of g-boson admixtures

2004 Structural, Function and Evolutionary Genomics

Energy Technology Data Exchange (ETDEWEB)

Douglas L. Brutlag Nancy Ryan Gray

2005-03-23

This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

Structure-Function Network Mapping and Its Assessment via Persistent Homology

Science.gov (United States)

2017-01-01

Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience. This work deals with the general method of structure-function mapping at the whole-brain level. We formulate the problem as a topological mapping of structure-function connectivity via matrix function, and find a stable solution by exploiting a regularization procedure to cope with large matrices. We introduce a novel measure of network similarity based on persistent homology for assessing the quality of the network mapping, which enables a detailed comparison of network topological changes across all possible thresholds, rather than just at a single, arbitrary threshold that may not be optimal. We demonstrate that our approach can uncover the direct and indirect structural paths for predicting functional connectivity, and our network similarity measure outperforms other currently available methods. We systematically validate our approach with (1) a comparison of regularized vs. non-regularized procedures, (2) a null model of the degree-preserving random rewired structural matrix, (3) different network types (binary vs. weighted matrices), and (4) different brain parcellation schemes (low vs. high resolutions). Finally, we evaluate the scalability of our method with relatively large matrices (2514x2514) of structural and functional connectivity obtained from 12 healthy human subjects measured non-invasively while at rest. Our results reveal a nonlinear structure-function relationship, suggesting that the resting-state functional connectivity depends on direct structural connections, as well as relatively parsimonious indirect connections via polysynaptic pathways. PMID:28046127

Structure functions of nucleons and nuclei

Energy Technology Data Exchange (ETDEWEB)

Bentz, Wolfgang; Ito, Takuya [Department of Physics, Tokai University, Kanagawa (Japan); Cloet, Ian [Department of Physics, University of Washington, Seattle (United States); Thomas, Anthony [Jefferson Lab., Newport News, VA (United States); Yazaki, Koichi [RIKEN, Wako-shi, Saitama (Japan)

2009-07-01

We use an effective chiral quark theory to calculate the quark distributions and structure functions of nucleons and nuclei. The description of the single nucleon is based on the Faddeev framework, and nuclear systems are described in the mean field approximation. Particular amphasis is put on the prediction of the polarized EMC effect in nuclei, and on applications to deep inelastic neutrino-nucleus scattering. Concerning the polarized EMC effect, we discuss the quenching of the quark spin sum in nuclei and its implications for the spin dependent nuclear structure functions, and present results for several nuclei where an experimental observation is feasible. Concerning the case of deep inelastic neutrino-nucleus scattering, we estimate the effect of medium modifications of the quark distribution functions on the measured cross sections, and discuss an interesting resolution of the so called NuTeV anomaly. Finally, we discuss extensions of our model to describe fragmentation functions for semi-inclusive processes. The connection between our effective quark model description and the jet model of Field and Feynman is discussed.

Animal Structures and Functions, Science (Experimental): 5314.13.

Science.gov (United States)

Silver, Barbara A.

This unit of instruction was designed to introduce the student to the relationship between structure and function in the animal kingdom, with emphasis given to: (1) the evolution of physiological systems in the major animal phyla, (2) the complementarity of structure and function, and (3) the concept of homeostasis. The booklet lists the relevant…

Ontogenetic functional diversity: size structure of a keystone predator drives functioning of a complex ecosystem.

Science.gov (United States)

Rudolf, Volker H W; Rasmussen, Nick L

2013-05-01

A central challenge in community ecology is to understand the connection between biodiversity and the functioning of ecosystems. While traditional approaches have largely focused on species-level diversity, increasing evidence indicates that there exists substantial ecological diversity among individuals within species. By far, the largest source of this intraspecific diversity stems from variation among individuals in ontogenetic stage and size. Although such ontogenetic shifts are ubiquitous in natural communities, whether and how they scale up to influence the structure and functioning of complex ecosystems is largely unknown. Here we take an experimental approach to examine the consequences of ontogenetic niche shifts for the structure of communities and ecosystem processes. In particular we experimentally manipulated the stage structure in a keystone predator, larvae of the dragonfly Anax junius, in complex experimental pond communities to test whether changes in the population stage or size structure of a keystone species scale up to alter community structure and ecosystem processes, and how functional differences scale with relative differences in size among stages. We found that the functional role of A. junius was stage-specific. Altering what stages were present in a pond led to concurrent changes in community structure, primary producer biomass (periphyton and phytoplankton), and ultimately altered ecosystem processes (respiration and net primary productivity), indicating a strong, but stage-specific, trophic cascade. Interestingly, the stage-specific effects did not simply scale with size or biomass of the predator, but instead indicated clear ontogenetic niche shifts in ecological interactions. Thus, functional differences among stages within a keystone species scaled up to alter the functioning of entire ecosystems. Therefore, our results indicate that the classical approach of assuming an average functional role of a species can be misleading because

Analysis of Lamellar Structures with Application of Generalized Functions

Directory of Open Access Journals (Sweden)

Kipiani Gela

2016-12-01

Full Text Available Theory of differential equations in respect of the functional area is based on the basic concepts on generalized functions and splines. There are some basic concepts related to the theory of generalized functions and their properties are considered in relation to the rod systems and lamellar structures. The application of generalized functions gives the possibility to effectively calculate step-variable stiffness lamellar structures. There are also widely applied structures, in that several in which a number of parallel load bearing layers are interconnected by discrete-elastic links. For analysis of system under study, such as design diagrams, there are applied discrete and discrete-continual models.

Vortex structure and characterization of quasiperiodic functions

International Nuclear Information System (INIS)

Dana, Itzhack; Chernov, Vladislav E

2002-01-01

Quasiperiodic functions (QPFs) are characterized by their full vortex structure in one unit cell. This characterization is much finer and more sensitive than the topological one given by the total vorticity per unit cell (the 'Chern index'). It is shown that QPFs with an arbitrarily prescribed vortex structure exist by constructing explicitly such a 'standard' QPF. Two QPFs with the same vortex structure are equivalent, in the sense that their ratio is a function which is strictly periodic, nonvanishing and at least continuous. A general QPF can then be approximately reconstructed from its vortex structure on the basis of the standard QPF and the equivalence concept. As another application of this concept, a simple method is proposed for calculating the quasiperiodic eigenvectors of periodic matrices. Possible applications to the quantum-chaos problem on a phase-space torus are briefly discussed

Spin-dependent parton distributions and structure functions

International Nuclear Information System (INIS)

Bentz, W.; Ito, T.; Cloet, I.C.; Thomas, A.W.; Yazaki, K.

2008-01-01

Nuclear parton distributions and structure functions are determined in an effective chiral quark theory. We also discuss an extension of our model to fragmentation functions. Presented at the 20th Few-Body Conference, Pisa, Italy, 10-14 September 2007. (author)

Deep inelastic structure functions in the chiral bag model

International Nuclear Information System (INIS)

Sanjose, V.; Vento, V.; Centro Mixto CSIC/Valencia Univ., Valencia

1989-01-01

We calculate the structure functions for deep inelastic scattering on baryons in the cavity approximation to the chiral bag model. The behavior of these structure functions is analyzed in the Bjorken limit. We conclude that scaling is satisfied, but not Regge behavior. A trivial extension as a parton model can be achieved by introducing the structure function for the pion in a convolution picture. In this extended version of the model not only scaling but also Regge behavior is satisfied. Conclusions are drawn from the comparison of our results with experimental data. (orig.)

Deep inelastic structure functions in the chiral bag model

Energy Technology Data Exchange (ETDEWEB)

Sanjose, V. (Valencia Univ. (Spain). Dept. de Didactica de las Ciencias Experimentales); Vento, V. (Valencia Univ. (Spain). Dept. de Fisica Teorica; Centro Mixto CSIC/Valencia Univ., Valencia (Spain). Inst. de Fisica Corpuscular)

1989-10-02

We calculate the structure functions for deep inelastic scattering on baryons in the cavity approximation to the chiral bag model. The behavior of these structure functions is analyzed in the Bjorken limit. We conclude that scaling is satisfied, but not Regge behavior. A trivial extension as a parton model can be achieved by introducing the structure function for the pion in a convolution picture. In this extended version of the model not only scaling but also Regge behavior is satisfied. Conclusions are drawn from the comparison of our results with experimental data. (orig.).

A structural self-regulation of functioning macromolecules

International Nuclear Information System (INIS)

Khristoforov, L.N.

1998-01-01

An approach to describing the functional structural changes of macromolecules processing the flows of low-mass agents is formulated. The latter appear as a source of a discrete noise whose defining parameters depend on structural variables. We derive a forward evolution equation and then, by adiabatic elimination, effective Fokker-Planck's equation for the structural modes. Within the dichotomous case, we discuss noise-induced nonequilibrium phase transitions reflecting the regulatory role of the structural subsystem

Soil-Borne Microbial Functional Structure across Different Land Uses

NARCIS (Netherlands)

Kuramae, E.E.; Zhou, J.Z.; Kowalchuk, G.A.; van Veen, J.A..

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate

Soil-borne microbial functional structure across different land uses

NARCIS (Netherlands)

Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate

Pair distribution function and structure factor of spherical particles

International Nuclear Information System (INIS)

Howell, Rafael C.; Proffen, Thomas; Conradson, Steven D.

2006-01-01

The availability of neutron spallation-source instruments that provide total scattering powder diffraction has led to an increased application of real-space structure analysis using the pair distribution function. Currently, the analytical treatment of finite size effects within pair distribution refinement procedures is limited. To that end, an envelope function is derived which transforms the pair distribution function of an infinite solid into that of a spherical particle with the same crystal structure. Distributions of particle sizes are then considered, and the associated envelope function is used to predict the particle size distribution of an experimental sample of gold nanoparticles from its pair distribution function alone. Finally, complementing the wealth of existing diffraction analysis, the peak broadening for the structure factor of spherical particles, expressed as a convolution derived from the envelope functions, is calculated exactly for all particle size distributions considered, and peak maxima, offsets, and asymmetries are discussed

Molecular structures and functional relationships in clostridial neurotoxins.

Science.gov (United States)

Swaminathan, Subramanyam

2011-12-01

The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here. Journal compilation © 2011 FEBS. No claim to original US government works.

Structure functions at low x

International Nuclear Information System (INIS)

Roeck, A.De.

2000-01-01

Deep recent data and phenomenology on low-x structure functions are discussed inelastic scattering. We will be interested primordially in the regions Q 2 → 0 i.e. the transition from γp to, and x → 10 -4 - 10 -6 i.e. the region of high parton densities

Function-specific and Enhanced Brain Structural Connectivity Mapping via Joint Modeling of Diffusion and Functional MRI.

Science.gov (United States)

Chu, Shu-Hsien; Parhi, Keshab K; Lenglet, Christophe

2018-03-16

A joint structural-functional brain network model is presented, which enables the discovery of function-specific brain circuits, and recovers structural connections that are under-estimated by diffusion MRI (dMRI). Incorporating information from functional MRI (fMRI) into diffusion MRI to estimate brain circuits is a challenging task. Usually, seed regions for tractography are selected from fMRI activation maps to extract the white matter pathways of interest. The proposed method jointly analyzes whole brain dMRI and fMRI data, allowing the estimation of complete function-specific structural networks instead of interactively investigating the connectivity of individual cortical/sub-cortical areas. Additionally, tractography techniques are prone to limitations, which can result in erroneous pathways. The proposed framework explicitly models the interactions between structural and functional connectivity measures thereby improving anatomical circuit estimation. Results on Human Connectome Project (HCP) data demonstrate the benefits of the approach by successfully identifying function-specific anatomical circuits, such as the language and resting-state networks. In contrast to correlation-based or independent component analysis (ICA) functional connectivity mapping, detailed anatomical connectivity patterns are revealed for each functional module. Results on a phantom (Fibercup) also indicate improvements in structural connectivity mapping by rejecting false-positive connections with insufficient support from fMRI, and enhancing under-estimated connectivity with strong functional correlation.

Transcriptomic profiling-based mutant screen reveals three new transcription factors mediating menadione resistance in Neurospora crassa.

Science.gov (United States)

Zhu, Jufen; Yu, Xinxu; Xie, Baogui; Gu, Xiaokui; Zhang, Zhenying; Li, Shaojie

2013-06-01

To gain insight into the regulatory mechanisms of oxidative stress responses in filamentous fungi, the genome-wide transcriptional response of Neurospora crassa to menadione was analysed by digital gene expression (DGE) profiling, which identified 779 upregulated genes and 576 downregulated genes. Knockout mutants affecting 130 highly-upregulated genes were tested for menadione sensitivity, which revealed that loss of the transcription factor siderophore regulation (SRE) (a transcriptional repressor for siderophore biosynthesis), catatase-3, cytochrome c peroxidase or superoxide dismutase 1 copper chaperone causes hypersensitivity to menadione. Deletion of sre dramatically increased transcription of the siderophore biosynthesis gene ono and the siderophore iron transporter gene sit during menadione stress, suggesting that SRE is required for repression of iron uptake under oxidative stress conditions. Contrary to its phenotype, the sre deletion mutant showed higher transcriptional levels of genes encoding reactive oxygen species (ROS) scavengers than wild type during menadione stress, which implies that the mutant suffers a higher level of oxidative stress than wild type. Uncontrolled iron uptake in the sre mutant might exacerbate cellular oxidative stress. This is the first report of a negative regulator of iron assimilation participating in the fungal oxidative stress response. In addition to SRE, eight other transcription factor genes were also menadione-responsive but their single gene knockout mutants showed wild-type menadione sensitivity. Two of them, named as mit-2 (menadione induced transcription factor-2) and mit-4 (menadione induced transcription factor-4), were selected for double mutant analysis. The double mutant was hypersensitive to menadione. Similarly, the double mutation of mit-2 and sre also had additive effects on menadione sensitivity, suggesting multiple transcription factors mediate oxidative stress resistance in an additive manner

Functional Annotation of Ion Channel Structures by Molecular Simulation.

Science.gov (United States)

Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

2016-12-06

Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Studying Membrane Protein Structure and Function Using Nanodiscs

DEFF Research Database (Denmark)

Huda, Pie

The structure and dynamic of membrane proteins can provide valuable information about general functions, diseases and effects of various drugs. Studying membrane proteins are a challenge as an amphiphilic environment is necessary to stabilise the protein in a functionally and structurally relevant...... form. This is most typically achieved through the use of detergent based reconstitution systems. However, time and again such systems fail to provide a suitable environment causing aggregation and inactivation. Nanodiscs are self-assembled lipoproteins containing two membrane scaffold proteins...... and a lipid bilayer in defined nanometer size, which can act as a stabiliser for membrane proteins. This enables both functional and structural investigation of membrane proteins in a detergent free environment which is closer to the native situation. Understanding the self-assembly of nanodiscs is important...

Significance tests for functional data with complex dependence structure.

Science.gov (United States)

Staicu, Ana-Maria; Lahiri, Soumen N; Carroll, Raymond J

2015-01-01

We propose an L 2 -norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

Significance tests for functional data with complex dependence structure

KAUST Repository

Staicu, Ana-Maria

2015-01-01

We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

Many Activities, One Structure: Functional Plasticity of Ribozyme Folds

Directory of Open Access Journals (Sweden)

Matthew W.L. Lau

2016-11-01

Full Text Available Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation. The function of ribozymes requires the formation of active sites decorated with RNA functional groups within defined three-dimensional (3D structures. The genotype (sequence of RNAs ultimately determines what 3D structures they adopt (as a function of their environmental conditions. These 3D structures, in turn, give rise to biochemical activity, which can further elaborate them by catalytic rearrangements or association with other molecules. The fitness landscape of a non-periodic linear polymer, such as RNA, relates its primary structure to a phenotype. Two major challenges in the analysis of ribozymes is to map all possible genotypes to their corresponding catalytic activity (that is, to determine their fitness landscape experimentally, and to understand whether their genotypes and three-dimensional structures can support multiple different catalytic functions. Recently, the combined results of experiments that employ in vitro evolution methods, high-throughput sequencing and crystallographic structure determination have hinted at answers to these two questions: while the fitness landscape of ribozymes is rugged, meaning that their catalytic activity cannot be optimized by a smooth trajectory in sequence space, once an RNA achieves a stable three-dimensional fold, it can be endowed with distinctly different biochemical activities through small changes in genotype. This functional plasticity of highly structured RNAs may be particularly advantageous for the adaptation of organisms to drastic changes in selective pressure, or for the development of new biotechnological tools.

The photon structure function at large Q2

International Nuclear Information System (INIS)

Cordier, A.

1987-01-01

LEP II offers the unique opportunity to measure the photon structure function over a large Q 2 range up to ∼ 2000 GeV 2 . Two crucial predictions of QCD can be tested in this experiment: the linear rise in log Q 2 as a consequence of asymptotic freedom, and the large renormalization O(1) of the shape of the structure function due to gluon bremsstrahlung, unperturbed by higher-twist effects

The virtual photon structure functions and AdS/QCD correspondence

International Nuclear Information System (INIS)

Yoshida, Yutaka

2010-01-01

We study the virtual photons structure functions from gauge/string duality. If the Bjorken variable x is not small, supergravity approximation becomes good in dual string theory. We calculate the virtual photon structure functions at large 't Hooft coupling in a moderate x-region and determine x-behavior of the structure functions. We also show that the Callan-Gross relation F L =0 is satisfied to a good approximation in gravity calculation. (author)

Edge-functionalization of armchair graphene nanoribbons with pentagonal-hexagonal edge structures.

Science.gov (United States)

Ryou, Junga; Park, Jinwoo; Kim, Gunn; Hong, Suklyun

2017-06-21

Using density functional theory calculations, we have studied the edge-functionalization of armchair graphene nanoribbons (AGNRs) with pentagonal-hexagonal edge structures. While the AGNRs with pentagonal-hexagonal edge structures (labeled (5,6)-AGNRs) are metallic, the edge-functionalized (5,6)-AGNRs with substitutional atoms opens a band gap. We find that the band structures of edge-functionalized (5,6)-N-AGNRs by substitution resemble those of defect-free (N-1)-AGNR at the Γ point, whereas those at the X point show the original ones of the defect-free N-AGNR. The overall electronic structures of edge-functionalized (5,6)-AGNRs depend on the number of electrons, supplied by substitutional atoms, at the edges of functionalized (5,6)-AGNRs.

THE STRUCTURE AND FUNCTION OF DEPARTMENTS OF MEDICINE.

Science.gov (United States)

Landefeld, C Seth

2016-01-01

The structure and function of departments of medicine are important for several reasons. First, departments of medicine are the biggest departments in virtually every medical school and in most universities with a medical school, and they are the largest professional units in most academic medical centers. In fact, Petersdorf described them as "the linchpins of medical schools" (1). Departments of medicine account for one-fourth or more of the academic medical enterprise: they include about one-fourth of the faculty of medical school, account for roughly one-fourth of the patient care and clinical revenue of academic medical centers, and their faculty perform a disproportionate share of teaching and research, accounting for up to 45% of National Institutes of Health (NIH) - funded research in some medical schools. Second, the department's ability to fulfill its role and advance its mission depends on its structure and function. Finally, lessons learned from examining the structure and function of departments of medicine may guide other departments and schools of medicine themselves in improving their structure and function. This paper describes the issues that face departments of medicine in 2016. I begin by providing the context for these issues with a definition of a department of medicine, describing briefly the history of departments, and stating their mission.

Size of the plasma membrane H+-ATPase from Neurospora crassa determined by radiation inactivation and comparison with the sarcoplasmic reticulum Ca2+-ATPase from skeletal muscle

International Nuclear Information System (INIS)

Bowman, B.J.; Berenski, C.J.; Jung, C.Y.

1985-01-01

Using radiation inactivation, the authors have measured the size of the H + -ATPase in Neurospora crassa plasma membranes. Membranes were exposed to either high energy electrons from a Van de Graaff generator or to gamma irradiation from 60 Co. Both forms of radiation caused an exponential loss of ATPase activity in parallel with the physical destruction of the Mr = 104,000 polypeptide of which this enzyme is composed. By applying target theory, the size of the H + -ATPase in situ was found to be approximately 2.3 X 10(5) daltons. They also used radiation inactivation to measure the size of the Ca 2+ -ATPase of sarcoplasmic reticulum and got a value of approximately 2.4 X 10(5) daltons, in agreement with previous reports. By irradiating a mixture of Neurospora plasma membranes and rabbit sarcoplasmic reticulum, they directly compared the sizes of these two ATPases and found them to be essentially the same. The authors conclude that both H + -ATPase and Ca 2+ -ATPase are oligomeric enzymes, most likely composed of two approximately 100,000-dalton polypeptides

Rise in proton structure function

International Nuclear Information System (INIS)

Fazal-e-Aleem; Rashid, H.; Ali, S.

1996-08-01

By the choice of a new scale factor we obtain a good qualitative fit to the HERA data for the proton structure function in the small x region which exhibits double asymptotic scaling. Any scaling violations in the future measurements when made in smaller bins will be of immense value. (author). 19 refs, 6 figs

Quality assessment of protein model-structures based on structural and functional similarities.

Science.gov (United States)

Konopka, Bogumil M; Nebel, Jean-Christophe; Kotulska, Malgorzata

2012-09-21

Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. GOBA--Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and

MODY - calculation of ordered structures by symmetry-adapted functions

Science.gov (United States)

Białas, Franciszek; Pytlik, Lucjan; Sikora, Wiesława

2016-01-01

In this paper we focus on the new version of computer program MODY for calculations of symmetryadapted functions based on the theory of groups and representations. The choice of such a functional frame of coordinates for description of ordered structures leads to a minimal number of parameters which must be used for presentation of such structures and investigations of their properties. The aim of this work is to find those parameters, which are coefficients of a linear combination of calculated functions, leading to construction of different types of structure ordering with a given symmetry. A spreadsheet script for simplification of this work has been created and attached to the program.

The pmr gene, encoding a Ca2+-ATPase, is required for calcium and manganese homeostasis and normal development of hyphae and conidia in Neurospora crassa.

Science.gov (United States)

Bowman, Barry J; Abreu, Stephen; Johl, Jessica K; Bowman, Emma Jean

2012-11-01

The pmr gene is predicted to encode a Ca(2+)-ATPase in the secretory pathway. We examined two strains of Neurospora crassa that lacked PMR: the Δpmr strain, in which pmr was completely deleted, and pmr(RIP), in which the gene was extensively mutated. Both strains had identical, complex phenotypes. Compared to the wild type, these strains required high concentrations of calcium or manganese for optimal growth and had highly branched, slow-growing hyphae. They conidiated poorly, and the shape and size of the conidia were abnormal. Calcium accumulated in the Δpmr strains to only 20% of the wild-type level. High concentrations of MnCl(2) (1 to 5 mM) in growth medium partially suppressed the morphological defects but did not alter the defect in calcium accumulation. The Δpmr Δnca-2 double mutant (nca-2 encodes a Ca(2+)-ATPase in the plasma membrane) accumulated 8-fold more calcium than the wild type, and the morphology of the hyphae was more similar to that of wild-type hyphae. Previous experiments failed to show a function for nca-1, which encodes a SERCA-type Ca(2+)-ATPase in the endoplasmic reticulum (B. J. Bowman, S. Abreu, E. Margolles-Clark, M. Draskovic, and E. J. Bowman, Eukaryot. Cell 10:654-661, 2011). The pmr(RIP) Δnca-1 double mutant accumulated small amounts of calcium, like the Δpmr strain, but exhibited even more extreme morphological defects. Thus, PMR can apparently replace NCA-1 in the endoplasmic reticulum, but NCA-1 cannot replace PMR. The morphological defects in the Δpmr strain are likely caused, in part, by insufficient concentrations of calcium and manganese in the Golgi compartment; however, PMR is also needed to accumulate normal levels of calcium in the whole cell.

Bound-state quark and gluon contributions to structure functions in QCD

International Nuclear Information System (INIS)

Brodsky, S.J.

1991-01-01

One can distinguish two types of contributions to the quark and gluon structure functions of hadrons in quantum chromodynamics: 'intrinsic' contributions, which are due to the direct scattering on the bound-state constituents, and 'extrinsic' contributions, which are derived from particles created in the collision. In this talk, I discuss several aspects of deep inealstic structure functions in which the bound-state structure of the proton plays a crucial role: (1) the properties of the intrinsic gluon distribution associated with the proton bound-state wavefunction; (2) the separation of the quark structure function of the proton into intrinsic 'bound-valence' and extrinsic 'non-valence' components which takes into account the Pauli principle; (3) the properties and identification of intrinsic heavy quark structure functions; and (4) a theory of shadowing and anti-shadowing of nuclear structure functions, directly related to quark-nucleon interactions and the gluon saturation phenomenon. (orig.)

Bound-state quark and gluon contributions to structure functions in QCD

International Nuclear Information System (INIS)

Brodsky, S.J.

1990-08-01

One can distinguish two types of contributions to the quark and gluon structure functions of hadrons in quantum chromodynamics: ''intrinsic'' contributions, which are due to the direct scattering on the bound-state constituents, and ''extrinsic'' contributions, which are derived from particles created in the collision. In this talk, I discussed several aspects of deep inelastic structure functions in which the bound-state structure of the proton plays a crucial role: the properties of the intrinsic gluon distribution associated with the proton bound-state wavefunction; the separation of the quark structure function of the proton onto intrinsic ''bound-valence'' and extrinsic ''non-valence'' components which takes into account the Pauli principle; the properties and identification of intrinsic heavy quark structure functions; and a theory of shadowing and anti-shadowing of nuclear structure functions, directly related to quark-nucleon interactions and the gluon saturation phenomenon. 49 refs., 5 figs

Structure to function: Spider silk and human collagen

Science.gov (United States)

Rabotyagova, Olena S.

Nature has the ability to assemble a variety of simple molecules into complex functional structures with diverse properties. Collagens, silks and muscles fibers are some examples of fibrous proteins with self-assembling properties. One of the great challenges facing Science is to mimic these designs in Nature to find a way to construct molecules that are capable of organizing into functional supra-structures by self-assembly. In order to do so, a construction kit consisting of molecular building blocks along with a complete understanding on how to form functional materials is required. In this current research, the focus is on spider silk and collagen as fibrous protein-based biopolymers that can shed light on how to generate nanostructures through the complex process of self-assembly. Spider silk in fiber form offers a unique combination of high elasticity, toughness, and mechanical strength, along with biological compatibility and biodegrability. Spider silk is an example of a natural block copolymer, in which hydrophobic and hydrophilic blocks are linked together generating polymers that organize into functional materials with extraordinary properties. Since silks resemble synthetic block copolymer systems, we adopted the principles of block copolymer design from the synthetic polymer literature to build block copolymers based on spider silk sequences. Moreover, we consider spider silk to be an important model with which to study the relationships between structure and properties in our system. Thus, the first part of this work was dedicated to a novel family of spider silk block copolymers, where we generated a new family of functional spider silk-like block copolymers through recombinant DNA technology. To provide fundamental insight into relationships between peptide primary sequence, block composition, and block length and observed morphological and structural features, we used these bioengineered spider silk block copolymers to study secondary structure

Extraction of Structure Function and Gluon Distribution Function at Low-x from Cross Section Derivative by Regge Behavior

International Nuclear Information System (INIS)

Boroun, G.R.

2005-01-01

An approximation method based on Regge behavior is presented. This new method relates the reduced cross section derivative and the structure function Regge behavior at low x. With the use of this approximation method, the C and λ parameters are calculated from the HERA reduced cross section data taken at low-x. Also, we calculate the structure functions F 2 (x,Q 2 ) even for low-x values, which have not been investigated. To test the validity of calculated structure functions, we find the gluon distribution function in the Leading order approximation based on Regge behaviour of structure function and compare to the NLO QCD fit to H1 data and NLO parton distribution function.

Population structure analysis using rare and common functional variants

Directory of Open Access Journals (Sweden)

Ding Lili

2011-11-01

Full Text Available Abstract Next-generation sequencing technologies now make it possible to genotype and measure hundreds of thousands of rare genetic variations in individuals across the genome. Characterization of high-density genetic variation facilitates control of population genetic structure on a finer scale before large-scale genotyping in disease genetics studies. Population structure is a well-known, prevalent, and important factor in common variant genetic studies, but its relevance in rare variants is unclear. We perform an extensive population structure analysis using common and rare functional variants from the Genetic Analysis Workshop 17 mini-exome sequence. The analysis based on common functional variants required 388 principal components to account for 90% of the variation in population structure. However, an analysis based on rare variants required 532 significant principal components to account for similar levels of variation. Using rare variants, we detected fine-scale substructure beyond the population structure identified using common functional variants. Our results show that the level of population structure embedded in rare variant data is different from the level embedded in common variant data and that correcting for population structure is only as good as the level one wishes to correct.

Cardiac structure and function predicts functional decline in the oldest old.

Science.gov (United States)

Leibowitz, David; Jacobs, Jeremy M; Lande-Stessman, Irit; Gilon, Dan; Stessman, Jochanan

2018-02-01

Background This study examined the association between cardiac structure and function and the deterioration in activities of daily living (ADLs) in an age-homogenous, community-dwelling population of patients born in 1920-1921 over a five-year follow-up period. Design Longitudinal cohort study. Methods Patients were recruited from the Jerusalem Longitudinal Cohort Study, which has followed an age-homogenous cohort of Jerusalem residents born in 1920-1921. Patients underwent home echocardiography and were followed up for five years. Dependence was defined as needing assistance with one or more basic ADL. Standard echocardiographic assessment of cardiac structure and function, including systolic and diastolic function, was performed. Reassessment of ADLs was performed at the five-year follow-up. Results A total of 459 patients were included in the study. Of these, 362 (79%) showed a deterioration in at least one ADL at follow-up. Patients with functional deterioration had a significantly higher left ventricular mass index and left atrial volume with a lower ejection fraction. There was no significant difference between the diastolic parameters the groups in examined. When the data were examined categorically, a significantly larger percentage of patients with functional decline had an abnormal left ventricular ejection fraction and left ventricular hypertrophy. The association between left ventricular mass index and functional decline remained significant in all multivariate models. Conclusions In this cohort of the oldest old, an elevated left ventricular mass index, higher left atrial volumes and systolic, but not diastolic dysfunction, were predictive of functional disability.

Neuropsychological functioning and brain structure in schizophrenia.

Science.gov (United States)

Crespo-Facorro, Benedicto; Barbadillo, Laura; Pelayo-Terán, José Maria; Rodríguez-Sánchez, José Manuel

2007-08-01

Cognitive deficits are core features of schizophrenia that are already evident at early phases of the illness. The study of specific relationships between cognition and brain structure might provide valuable clues about neural basis of schizophrenia and its phenomenology. The aim of this article was to review the most consistent findings of the studies exploring the relationships between cognitive deficits and brain anomalies in schizophrenia. Besides several important methodological shortcomings to bear in mind before drawing any consistent conclusion from the revised literature, we have attempted to systematically summarize these findings. Thus, this review has revealed that whole brain volume tends to positively correlate with a range of cognitive domains in healthy volunteers and female patients. An association between prefrontal morphological characteristics and general inability to control behaviour seems to be present in schizophrenia patients. Parahippocampal volume is related to semantic cognitive functions. Thalamic anomalies have been associated with executive deficits specifically in patients. Available evidence on the relationship between cognitive functions and cerebellar structure is still contradictory. Nonetheless, a larger cerebellum appears to be associated with higher IQ in controls and in female patients. Enlarged ventricles, including lateral and third ventricles, are associated with deficits in attention, executive and premorbid cognitive functioning in patients. Several of these reported findings seem to be counterintuitive according to neural basis of cognitive functioning drawn from animal, lesion, and functional imaging investigations. Therefore, there is still a great need for more methodologically stringent investigations that would help in the advance of our understanding of the cognition/brain structure relationships in schizophrenia.

Altered resting brain function and structure in professional badminton players.

Science.gov (United States)

Di, Xin; Zhu, Senhua; Jin, Hua; Wang, Pin; Ye, Zhuoer; Zhou, Ke; Zhuo, Yan; Rao, Hengyi

2012-01-01

Neuroimaging studies of professional athletic or musical training have demonstrated considerable practice-dependent plasticity in various brain structures, which may reflect distinct training demands. In the present study, structural and functional brain alterations were examined in professional badminton players and compared with healthy controls using magnetic resonance imaging (MRI) and resting-state functional MRI. Gray matter concentration (GMC) was assessed using voxel-based morphometry (VBM), and resting-brain functions were measured by amplitude of low-frequency fluctuation (ALFF) and seed-based functional connectivity. Results showed that the athlete group had greater GMC and ALFF in the right and medial cerebellar regions, respectively. The athlete group also demonstrated smaller ALFF in the left superior parietal lobule and altered functional connectivity between the left superior parietal and frontal regions. These findings indicate that badminton expertise is associated with not only plastic structural changes in terms of enlarged gray matter density in the cerebellum, but also functional alterations in fronto-parietal connectivity. Such structural and functional alterations may reflect specific experiences of badminton training and practice, including high-capacity visuo-spatial processing and hand-eye coordination in addition to refined motor skills.

Functional evolution and structural conservation in chimeric cytochromes p450: calibrating a structure-guided approach.

Science.gov (United States)

Otey, Christopher R; Silberg, Jonathan J; Voigt, Christopher A; Endelman, Jeffrey B; Bandara, Geethani; Arnold, Frances H

2004-03-01

Recombination generates chimeric proteins whose ability to fold depends on minimizing structural perturbations that result when portions of the sequence are inherited from different parents. These chimeric sequences can display functional properties characteristic of the parents or acquire entirely new functions. Seventeen chimeras were generated from two CYP102 members of the functionally diverse cytochrome p450 family. Chimeras predicted to have limited structural disruption, as defined by the SCHEMA algorithm, displayed CO binding spectra characteristic of folded p450s. Even this small population exhibited significant functional diversity: chimeras displayed altered substrate specificities, a wide range in thermostabilities, up to a 40-fold increase in peroxidase activity, and ability to hydroxylate a substrate toward which neither parent heme domain shows detectable activity. These results suggest that SCHEMA-guided recombination can be used to generate diverse p450s for exploring function evolution within the p450 structural framework.

Therapeutic monoclonal antibody N-glycosylation - Structure, function and therapeutic potential.

Science.gov (United States)

Cymer, Florian; Beck, Hermann; Rohde, Adelheid; Reusch, Dietmar

2018-03-01

Therapeutic antibodies (IgG-type) contain several post-translational modifications (PTMs) whereby introducing a large heterogeneity, both structural and functional, into this class of therapeutics. Of these modifications, glycosylation in the fragment crystallizable (Fc) region is the most heterogeneous PTM, which can affect the stability of the molecule and interactions with Fc-receptors in vivo. Hence, the glycoform distribution can affect the mode of action and have implications for bioactivity, safety and efficacy of the drug. Main topics of the manuscript include: What factors influence the (Fc) glycan pattern in therapeutic antibodies and how can these glycans be characterized? How does structure of the Fc-glycan relate to function and what methods are available to characterize those functions? Although heterogeneous in their scope, the different sections are intended to combine current knowledge on structure-function correlations of IgG glycan structures with regard to Fc (effector) functions, as well as basic aspects and methodologies for their assessment. Copyright © 2017. Published by Elsevier Ltd.

Plasmodesmata: Structure and Function

Directory of Open Access Journals (Sweden)

Thomas David Geydan

2006-07-01

Full Text Available Plasmodesmata are channels that transverse the cell wall and membrane. These specialized and non passive channels act like gates that facilitate and regulate both communication and transportation of molecules such as water, nutrients, metabolites and macromolecules between plant cells. In the last decade a new point of view of plasmodesmata has emerged, and studies have  demonstrated that these channels are more complex. In this brief note, we pretend to expose the actual knowledge of plasmodesmata, focusing on their structure and function.

Structure functions and parton distributions

International Nuclear Information System (INIS)

Olness, F.; Tung, Wu-Ki

1991-04-01

Activities of the structure functions and parton distributions group is summarized. The impact of scheme-dependence of parton distributions (especially sea-quarks and gluons) on the quantitative formulation of the QCD parton model is highlighted. Recent progress on the global analysis of parton distributions is summarized. Issues on the proper use of the next-to-leading parton distributions are stressed

Analysis of the proton longitudinal structure function from the gluon distribution function

International Nuclear Information System (INIS)

Boroun, G.R.; Rezaei, B.

2012-01-01

We make a critical, next-to-leading order, study of the relationship between the longitudinal structure function F L and the gluon distribution proposed in Cooper-Sarkar et al. (Z. Phys. C 39:281, 1988; Acta Phys. Pol. B 34:2911 2003), which is frequently used to extract the gluon distribution from the proton longitudinal structure function at small x. The gluon density is obtained by expanding at particular choices of the point of expansion and compared with the hard Pomeron behavior for the gluon density. Comparisons with H1 data are made and predictions for the proposed best approach are also provided. (orig.)

MRI in Optic Neuritis: Structure, Function, Interactions

DEFF Research Database (Denmark)

Fuglø, Dan

2011-01-01

resonance imaging (MRI), and the visual evoked potential (VEP) continues to show a delayed P100 indicating persistent demyelination. The explanation for this apparent discrepancy between structure and function could be due to either a redundancy in the visual pathways so that some degree of signal loss...... will have very few or no clinical symptoms, or it could be due to compensatory mechanisms in the visual pathway or the visual cortex. In order to understand the pathophysiology and recovery processes in ON it is essential to have sensitive methods to asses both structure and function. These methods...... are low. Functional MRI (fMRI) is a non-invasive technique that can measure brain activity with a high spatial resolution. Recently, technical and methodological advancements have made it feasible to record VEPs and fMRI simultaneously and the relationship between averaged VEPs and averaged fMRI signals...

Performance analysis, quality function deployment and structured methods

Science.gov (United States)

Maier, M. W.

Quality function deployment, (QFD), an approach to synthesizing several elements of system modeling and design into a single unit, is presented. Behavioral, physical, and performance modeling are usually considered as separate aspects of system design without explicit linkages. Structured methodologies have developed linkages between behavioral and physical models before, but have not considered the integration of performance models. QFD integrates performance models with traditional structured models. In this method, performance requirements such as cost, weight, and detection range are partitioned into matrices. Partitioning is done by developing a performance model, preferably quantitative, for each requirement. The parameters of the model become the engineering objectives in a QFD analysis and the models are embedded in a spreadsheet version of the traditional QFD matrices. The performance model and its parameters are used to derive part of the functional model by recognizing that a given performance model implies some structure to the functionality of the system.

The spin-dependent structure function g1 of the deuteron

International Nuclear Information System (INIS)

Bueltmann, S.

1996-01-01

Results on the spin-dependent structure function g 1 d of the deuteron measured by the Spin Muon Collaboration at CERN are presented. They are based on deep-inelastic scattering of 190 GeV polarized muons off a polarized deuteron target in the kinematic range of 0.003 ≤ x Bj ≤ 0.7 and 1 GeV 2 ≤ Q 2 ≤ 60 GeV 2 . The structure function is found to be negative for small values of x Bj , while the proton structure function g 1 p measured earlier by the SMC is positive over the whole x Bj -range. The Bjorken sum rule is in good agreement with the first moments of the structure functions, while the Ellis-Jaffe sum rule is violated by more than three standard deviations for the deuteron measurement. (author)

Conflict between object structural and functional affordances in peripersonal space.

Science.gov (United States)

Kalénine, Solène; Wamain, Yannick; Decroix, Jérémy; Coello, Yann

2016-10-01

Recent studies indicate that competition between conflicting action representations slows down planning of object-directed actions. The present study aims to assess whether similar conflict effects exist during manipulable object perception. Twenty-six young adults performed reach-to-grasp and semantic judgements on conflictual objects (with competing structural and functional gestures) and non-conflictual objects (with similar structural and functional gestures) presented at difference distances in a 3D virtual environment. Results highlight a space-dependent conflict between structural and functional affordances. Perceptual judgments on conflictual objects were slower that perceptual judgments on non-conflictual objects, but only when objects were presented within reach. Findings demonstrate that competition between structural and functional affordances during object perception induces a processing cost, and further show that object position in space can bias affordance competition. Copyright © 2016 Elsevier B.V. All rights reserved.

Adaptation of brain functional and structural networks in aging.

Directory of Open Access Journals (Sweden)

Annie Lee

Full Text Available The human brain, especially the prefrontal cortex (PFC, is functionally and anatomically reorganized in order to adapt to neuronal challenges in aging. This study employed structural MRI, resting-state fMRI (rs-fMRI, and high angular resolution diffusion imaging (HARDI, and examined the functional and structural reorganization of the PFC in aging using a Chinese sample of 173 subjects aged from 21 years and above. We found age-related increases in the structural connectivity between the PFC and posterior brain regions. Such findings were partially mediated by age-related increases in the structural connectivity of the occipital lobe within the posterior brain. Based on our findings, it is thought that the PFC reorganization in aging could be partly due to the adaptation to age-related changes in the structural reorganization of the posterior brain. This thus supports the idea derived from task-based fMRI that the PFC reorganization in aging may be adapted to the need of compensation for resolving less distinctive stimulus information from the posterior brain regions. In addition, we found that the structural connectivity of the PFC with the temporal lobe was fully mediated by the temporal cortical thickness, suggesting that the brain morphology plays an important role in the functional and structural reorganization with aging.

Adaptation of brain functional and structural networks in aging.

Science.gov (United States)

Lee, Annie; Ratnarajah, Nagulan; Tuan, Ta Anh; Chen, Shen-Hsing Annabel; Qiu, Anqi

2015-01-01

The human brain, especially the prefrontal cortex (PFC), is functionally and anatomically reorganized in order to adapt to neuronal challenges in aging. This study employed structural MRI, resting-state fMRI (rs-fMRI), and high angular resolution diffusion imaging (HARDI), and examined the functional and structural reorganization of the PFC in aging using a Chinese sample of 173 subjects aged from 21 years and above. We found age-related increases in the structural connectivity between the PFC and posterior brain regions. Such findings were partially mediated by age-related increases in the structural connectivity of the occipital lobe within the posterior brain. Based on our findings, it is thought that the PFC reorganization in aging could be partly due to the adaptation to age-related changes in the structural reorganization of the posterior brain. This thus supports the idea derived from task-based fMRI that the PFC reorganization in aging may be adapted to the need of compensation for resolving less distinctive stimulus information from the posterior brain regions. In addition, we found that the structural connectivity of the PFC with the temporal lobe was fully mediated by the temporal cortical thickness, suggesting that the brain morphology plays an important role in the functional and structural reorganization with aging.

Photon structure functions with heavy particle mass effects

Energy Technology Data Exchange (ETDEWEB)

Uematsu, Tsuneo, E-mail: uematsu@scphys.kyoto-u.jp [Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 (Japan); Maskawa Institute for Science and Culture, Kyoto Sangyo University, Kamigamo, Kita-ku, Kyoto 603-8555 (Japan)

2013-01-15

In the framework of the perturbative QCD we investigate heavy particle mass effects on the unpolarized and polarized photon structure functions, F{sub 2}{sup γ} and g{sub 1}{sup γ}, respectively. We present our basic formalism to treat heavy particle mass effects to NLO in perturbative QCD. We also study heavy quark effects on the QCD sum rule for the first moment of g{sub 1}{sup γ}, which is related to axial anomaly. The photon structure function in supersymmetric QCD is also briefly discussed.

Network-level structure-function relationships in human neocortex

NARCIS (Netherlands)

Miŝic, Bratislav; Betzel, Richard F.; De Reus, Marcel A.; Van Den Heuvel, Martijn P.; Berman, Marc G.; McIntosh, Anthony R.; Sporns, Olaf

2016-01-01

The dynamics of spontaneous fluctuations in neural activity are shaped by underlying patterns of anatomical connectivity. While numerous studies have demonstrated edge-wise correspondence between structural and functional connections, much less is known about how large-scale coherent functional

Calculation of the nucleon structure function from the nucleon wave function

Science.gov (United States)

Hussar, Paul E.

1993-01-01

Harmonic oscillator wave functions have played an historically important role in our understanding of the structure of the nucleon, most notably by providing insight into the mass spectra of the low-lying states. High energy scattering experiments are known to give us a picture of the nucleon wave function at high-momentum transfer and in a frame in which the nucleon is traveling fast. A simple model that crosses the twin bridges of momentum scale and Lorentz frame that separate the pictures of the nucleon wave function provided by the deep inelastic scattering data and by the oscillator model is presented.

Longitudinal structure function from logarithmic slopes of F2 at low x

Science.gov (United States)

Boroun, G. R.

2018-01-01

Using Laplace transform techniques, I calculate the longitudinal structure function FL(x ,Q2) from the scaling violations of the proton structure function F2(x ,Q2) and make a critical study of this relationship between the structure functions at leading order (LO) up to next-to-next-to leading order (NNLO) analysis at small x . Furthermore, I consider heavy quark contributions to the relation between the structure functions, which leads to compact formula for Nf=3 +Heavy . The nonlinear corrections to the longitudinal structure function at LO up to NNLO analysis are shown in the Nf=4 (light quark flavor) based on the nonlinear corrections at R =2 and R =4 GeV-1 . The results are compared with experimental data of the longitudinal proton structure function FL in the range of 6.5 ≤Q2≤800 GeV2 .

Structure and function of wood

Science.gov (United States)

Alex Wiedenhoeft

2010-01-01

Wood is a complex biological structure, a composite of many chemistries and cell types acting together to serve the needs of a living plant. Attempting to understand wood in the context of wood technology, we have often overlooked the key and basic fact that wood evolved over the course of millions of years to serve three main functions in plants― conduction of water...

Significance tests for functional data with complex dependence structure

KAUST Repository

Staicu, Ana-Maria; Lahiri, Soumen N.; Carroll, Raymond J.

2015-01-01

We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a

Generalized functions, convergence structures, and their applications

CERN Document Server

Pap, Endre; Pilipović, Stevan; Vladimirov, Vasilij; International Conference "Generalized functions, convergence structures and their applications" (GFCA-87)

1988-01-01

This Proceedings consists of a collection of papers presented at the International Conference "Generalized functions, convergence structures and their applications" held from June 23-27, 1987 in Dubrovnik, Yugoslavia (GFCA-87): 71 participants from 21 countr~es from allover the world took part in the Conference. Proceedings reflects the work of the Conference. Plenary lectures of J. Burzyk, J. F. Colombeau, W. Gahler, H. Keiter, H. Komatsu, B. Stankovic, H. G. Tillman, V. S. Vladimirov provide an up-to-date account of the cur­ rent state of the subject. All these lectures, except H. G. Tillman's, are published in this volume. The published communications give the contemporary problems and achievements in the theory of generalized functions, in the theory of convergence structures and in their applications, specially in the theory of partial differential equations and in the mathematical physics. New approaches to the theory of generalized functions are presented, moti­ vated by concrete problems of applicat...

Nucleon structure functions from lattice operator product expansion

Energy Technology Data Exchange (ETDEWEB)

Chambers, A.J.; Somfleth, K.; Young, R.D.; Zanotti, J.M. [Adelaide Univ., SA (Australia). CSSM, Dept. of Physics; Horsley, R. [Edinburgh Univ. (United Kingdom). School of Physics and Astronomy; Nakamura, Y. [RIKEN Advanced Institute for Computational Science, Kobe (Japan); Perlt, H.; Schiller, A. [Leipzig Univ. (Germany). Inst. fuer Theoretische Physik; Rakow, P.E.L. [Liverpool Univ. (United Kingdom). Theoretical Physics Div.; Schierholz, G. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2017-03-15

Deep-inelastic scattering, in the laboratory and on the lattice, is most instructive for understanding how the nucleon is built from quarks and gluons. The long-term goal is to compute the associated structure functions from first principles. So far this has been limited to model calculations. In this Letter we propose a new method to compute the structure functions directly from the virtual, all-encompassing Compton amplitude, utilizing the operator product expansion. This overcomes issues of renormalization and operator mixing, which so far have hindered lattice calculations of power corrections and higher moments.

Nucleon structure functions from lattice operator product expansion

International Nuclear Information System (INIS)

Chambers, A.J.; Somfleth, K.; Young, R.D.; Zanotti, J.M.; Perlt, H.; Schiller, A.

2017-03-01

Deep-inelastic scattering, in the laboratory and on the lattice, is most instructive for understanding how the nucleon is built from quarks and gluons. The long-term goal is to compute the associated structure functions from first principles. So far this has been limited to model calculations. In this Letter we propose a new method to compute the structure functions directly from the virtual, all-encompassing Compton amplitude, utilizing the operator product expansion. This overcomes issues of renormalization and operator mixing, which so far have hindered lattice calculations of power corrections and higher moments.

Structure and function of nanoparticle-protein conjugates

International Nuclear Information System (INIS)

Aubin-Tam, M-E; Hamad-Schifferli, K

2008-01-01

Conjugation of proteins to nanoparticles has numerous applications in sensing, imaging, delivery, catalysis, therapy and control of protein structure and activity. Therefore, characterizing the nanoparticle-protein interface is of great importance. A variety of covalent and non-covalent linking chemistries have been reported for nanoparticle attachment. Site-specific labeling is desirable in order to control the protein orientation on the nanoparticle, which is crucial in many applications such as fluorescence resonance energy transfer. We evaluate methods for successful site-specific attachment. Typically, a specific protein residue is linked directly to the nanoparticle core or to the ligand. As conjugation often affects the protein structure and function, techniques to probe structure and activity are assessed. We also examine how molecular dynamics simulations of conjugates would complete those experimental techniques in order to provide atomistic details on the effect of nanoparticle attachment. Characterization studies of nanoparticle-protein complexes show that the structure and function are influenced by the chemistry of the nanoparticle ligand, the nanoparticle size, the nanoparticle material, the stoichiometry of the conjugates, the labeling site on the protein and the nature of the linkage (covalent versus non-covalent)

How to analyze Structure and Function in Tissue – based Diagnosis?

Directory of Open Access Journals (Sweden)

Klaus Kayser

2016-04-01

Full Text Available Background Tissue – based diagnosis (morphological analysis of human tissue judges, measures and interprets morphologic images which have been acquired from human tissue. It translates the findings into a diagnosis or description of biological functions. What are its principle algorithms and theoretical background? Theory Pathologists are used to distinguish between structure and function. Biological structures are ordered clusters of material (genes, nuclei, cells, organs, etc., which remain constant during the period of detection and observation. They are commonly embedded or appear in circumscribed spaces. These spaces are clearly separated from their environment (background. Functions are forces that act on structures. They modify their appearance, create and delete structures and their spatial relationship. The recognition of both structures and functions is dependent upon the observation time: Material that remains unchanged within the observation period is called structure, its changes between a series of observations a function. Derivatives Biological structures and functions should be interpreted in relation to the observation time. Functions can be considered structural gradients of time or of observation periods. Implementation The analysis of conventional stained histological slides reflects to a short non changeable observation time, which in reality cannot be repeated at different times on the same tissue. Acquired digital images such as virtual slides (VS offer the opportunity of simulating different observation times if object features are analyzed that reflect structural changes at different times. The measurement of immunohistochemal intensity levels performed on the same structure can be considered a time series of the binding or antigen – antibody process. The obtained frame of these measurements can be mapped on chemical significant descriptors such as Shannon’s and structural entropy, and their entropy flows. Material

General quadratic gauge theory: constraint structure, symmetries and physical functions

Energy Technology Data Exchange (ETDEWEB)

Gitman, D M [Institute of Physics, University of Sao Paulo (Brazil); Tyutin, I V [Lebedev Physics Institute, Moscow (Russian Federation)

2005-06-17

How can we relate the constraint structure and constraint dynamics of the general gauge theory in the Hamiltonian formulation to specific features of the theory in the Lagrangian formulation, especially relate the constraint structure to the gauge transformation structure of the Lagrangian action? How can we construct the general expression for the gauge charge if the constraint structure in the Hamiltonian formulation is known? Whether we can identify the physical functions defined as commuting with first-class constraints in the Hamiltonian formulation and the physical functions defined as gauge invariant functions in the Lagrangian formulation? The aim of the present paper is to consider the general quadratic gauge theory and to answer the above questions for such a theory in terms of strict assertions. To fulfil such a programme, we demonstrate the existence of the so-called superspecial phase-space variables in terms of which the quadratic Hamiltonian action takes a simple canonical form. On the basis of such a representation, we analyse a functional arbitrariness in the solutions of the equations of motion of the quadratic gauge theory and derive the general structure of symmetries by analysing a symmetry equation. We then use these results to identify the two definitions of physical functions and thus prove the Dirac conjecture.

Visual Restoration after Cataract Surgery Promotes Functional and Structural Brain Recovery

Directory of Open Access Journals (Sweden)

Haotian Lin

2018-04-01

Full Text Available Background: Visual function and brain function decline concurrently with aging. Notably, cataract patients often present with accelerated age-related decreases in brain function, but the underlying mechanisms are still unclear. Optical structures of the anterior segment of the eyes, such as the lens and cornea, can be readily reconstructed to improve refraction and vision quality. However, the effects of visual restoration on human brain function and structure remain largely unexplored. Methods: A prospective, controlled clinical trial was conducted. Twenty-six patients with bilateral age-related cataracts (ARCs who underwent phacoemulsification and intraocular lens implantation and 26 healthy controls without ARC, matched for age, sex, and education, were recruited. Visual functions (including visual acuity, visual evoke potential, and contrast sensitivity, the Mini-Mental State Examination and functional magnetic resonance imaging (including the fractional amplitude of low-frequency fluctuations and grey matter volume variation were assessed for all the participants and reexamined for ARC patients after cataract surgery. This trial was registered with ClinicalTrials.gov (NCT02644720. Findings: Compared with the healthy controls, the ARC patients presented decreased brain functionality as well as structural alterations in visual and cognitive-related brain areas preoperatively. Three months postoperatively, significant functional improvements were observed in the visual and cognitive-related brain areas of the patients. Six months postoperatively, the patients' grey matter volumes in these areas were significantly increased. Notably, both the function and structure in the visual and cognitive-related brain areas of the patients improved significantly and became comparable to those of the healthy controls 6 months postoperatively. Interpretation: We demonstrated that ocular reconstruction can functionally and structurally reverse cataract

Structure and function of mammalian cilia

DEFF Research Database (Denmark)

Satir, Peter; Christensen, Søren T

2008-01-01

In the past half century, beginning with electron microscopic studies of 9 + 2 motile and 9 + 0 primary cilia, novel insights have been obtained regarding the structure and function of mammalian cilia. All cilia can now be viewed as sensory cellular antennae that coordinate a large number...

Structure functions of longitudinal virtual photons at low virtualities

International Nuclear Information System (INIS)

Ioffe, B.L.; Shushpanov, I.A.

1996-01-01

The structure functions F L 1 and F L 2 of longitudinal virtual photons at low virtualities are calculated in the framework of chiral perturbation theory (ChPT) in the zero and first order of ChPT. It is assumed that the virtuality of a target longitudinal photon p 2 is much less than the virtuality of the hard projectile photon Q 2 and both are less than the characteristic ChPT scale. In this approximation the structure functions are determined by the production of two pions in γγ collisions. The numerical results for F L 2 and F L 1 are presented (the upper index refers to the longitudinal polarization of the virtual target photon). The possibilities of measurements of these structure functions are briefly discussed. copyright 1996 The American Physical Society

Measurement of the nucleon structure functions

International Nuclear Information System (INIS)

Gordon, B.A.; Loomis, W.A.; Pipkin, F.M.; Pordes, S.H.; Sessoms, A.L.; Shambroom, W.D.; Tao, C.; Verhey, L.J.; Wilson, R.; Anderson, H.L.; Fine, R.M.; Heisterberg, R.H.; Kinnison, W.W.; Matis, H.S.; Mo, L.W.; Myrianthopoulos, L.C.; Wright, S.C.; Francis, W.R.; Hicks, R.G.; Kirk, T.B.W.; Quirk, T.W.; Bharadwaj, V.K.; Booth, N.E.; Kirkbride, G.I.; Proudfoot, J.; Skuja, A.; Staton, M.A.; Williams, W.S.C.

1979-01-01

Measurements have been made of the inclusive scattering of 96, 147, and 219 GeV muons from hydrogen, and of 147 GeV muons from deuterium. Results are presented for the nucleon structure function F 2 (x,Q 2 ) [equivalentνW 2 (x,Q 2 )] for 10 2 2 . The value of F 2 rises with Q 2 at small x, and falls with Q 2 at large x, in agreement with the ideas of quantum chromodynamics. An average value of the ratio sigma/sub L//sigma/sub T/ equivalent R = 0.52 +- 0.35 has been obtained for the region 0.003 2 2 . The values of F 2 from this experiment have been combined with those from other charged-lepton scattering experiments to determine moments of the structure functions. The variation with Q 2 of these moments is used to derive values for Λ, taking into account corrections up to second order in α/sub s/. The fit to the data is very good

Measurement of the electron structure function F2e at LEP energies

Directory of Open Access Journals (Sweden)

J. Abdallah

2014-10-01

Full Text Available The hadronic part of the electron structure function F2e has been measured for the first time, using e+e− data collected by the DELPHI experiment at LEP, at centre-of-mass energies of s=91.2–209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The electron structure function F2e data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the contribution of large target photon virtualities is significant. The data presented can serve as a cross-check of the photon structure function F2γ analyses and help in refining existing parameterisations.

Recognition of functional sites in protein structures.

Science.gov (United States)

Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

2004-06-04

Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

Structure of BRS-invariant local functionals

International Nuclear Information System (INIS)

Brandt, F.

1993-01-01

For a large class of gauge theories a nilpotent BRS-operator s is constructed and its cohomology in the space of local functionals of the off-shell fields is shown to be isomorphic to the cohomology of s=s+d on functions f(C,T) of tensor fields T and of variables C which are constructed of the ghosts and the connection forms. The result allows general statements about the structure of invariant classical actions and anomaly cadidates whose BRS-variation vanishes off-shell. The assumptions under which the result holds are thoroughly discussed. (orig.)

Nonlinear correction to the longitudinal structure function at small x

International Nuclear Information System (INIS)

Boroun, G.R.

2010-01-01

We computed the longitudinal proton structure function F L , using the nonlinear Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (NLDGLAP) evolution equation approach at small x. For the gluon distribution, the nonlinear effects are related to the longitudinal structure function. As the very small-x behavior of the gluon distribution is obtained by solving the Gribov, Levin, Ryskin, Mueller and Qiu (GLR-MQ) evolution equation with the nonlinear shadowing term incorporated, we show that the strong rise that corresponds to the linear QCD evolution equations can be tamed by screening effects. Consequently, the obtained longitudinal structure function shows a tamed growth at small x. We computed the predictions for all details of the nonlinear longitudinal structure function in the kinematic range where it has been measured by the H1 Collaboration and made comparisons with the computation by Moch, Vermaseren and Vogt at the second order with input data from the MRST QCD fit. (orig.)

Relationships between structure and function: System structure matters whether you are in a wetland or a college classroom

Science.gov (United States)

Andrews, Sarah Elizabeth

Part I of this dissertation describes two research projects I undertook to understand how structure influences function in freshwater wetlands. In the first study I tested the hypothesis that wetland structure (created versus natural) would influence function (methane cycling). Created wetlands had reduced rates of potential methane production and potential methane oxidation compared to natural wetlands; this was most likely explained by differences in edaphic factors that characterized each wetland, particularly soil moisture and soil organic matter. In the second study (Andrews et al. 2013), I tested the hypothesis that plant community structure (functional group composition, richness, presence/absence) would influence function (methane and iron cycling) in wetland mesocosms. Plant functional group richness was less important than the type of vegetation present: the presence of perennial vegetation (reeds or tussocks) led to increased rates of potential iron reduction compared to when only annual vegetation was present. Part II of this dissertation describes research I undertook to understand how structure influences function in an undergraduate soil science course. In the first study I tested the hypothesis that course structure (traditional versus studio) would influence function (student performance) in the course. Students in the studio course outperformed students in the traditional course; there was also a decrease in the fail rate. In the second study I looked at students' perspectives on their learning and experiences (function) in the studio course and asked whether students' epistemological development influenced this function. Interviews with students revealed that active learning, the integrated nature of the course, community, and variety of learning and assessment methods helped student learning. Students' epistemological development (interpreted from the Measure of Epistemological Reflection) permeated much of what they spoke about during the

Functional clustering in hippocampal cultures: relating network structure and dynamics

International Nuclear Information System (INIS)

Feldt, S; Dzakpasu, R; Olariu, E; Żochowski, M; Wang, J X; Shtrahman, E

2010-01-01

In this work we investigate the relationship between gross anatomic structural network properties, neuronal dynamics and the resultant functional structure in dissociated rat hippocampal cultures. Specifically, we studied cultures as they developed under two conditions: the first supporting glial cell growth (high glial group), and the second one inhibiting it (low glial group). We then compared structural network properties and the spatio-temporal activity patterns of the neurons. Differences in dynamics between the two groups could be linked to the impact of the glial network on the neuronal network as the cultures developed. We also implemented a recently developed algorithm called the functional clustering algorithm (FCA) to obtain the resulting functional network structure. We show that this new algorithm is useful for capturing changes in functional network structure as the networks evolve over time. The FCA detects changes in functional structure that are consistent with expected dynamical differences due to the impact of the glial network. Cultures in the high glial group show an increase in global synchronization as the cultures age, while those in the low glial group remain locally synchronized. We additionally use the FCA to quantify the amount of synchronization present in the cultures and show that the total level of synchronization in the high glial group is stronger than in the low glial group. These results indicate an interdependence between the glial and neuronal networks present in dissociated cultures

Matrix Transfer Function Design for Flexible Structures: An Application

Science.gov (United States)

Brennan, T. J.; Compito, A. V.; Doran, A. L.; Gustafson, C. L.; Wong, C. L.

1985-01-01

The application of matrix transfer function design techniques to the problem of disturbance rejection on a flexible space structure is demonstrated. The design approach is based on parameterizing a class of stabilizing compensators for the plant and formulating the design specifications as a constrained minimization problem in terms of these parameters. The solution yields a matrix transfer function representation of the compensator. A state space realization of the compensator is constructed to investigate performance and stability on the nominal and perturbed models. The application is made to the ACOSSA (Active Control of Space Structures) optical structure.

Phenomenological study of the nucleon structure functions; Etude phenomenologique des fonctions de structure du nucleon

Energy Technology Data Exchange (ETDEWEB)

Bertini, M

1995-05-12

This thesis is devoted to the study of the deep inelastic scattering. Its purpose is the development of phenomenological models describing experimental results on unpolarized (F{sub 2}) and polarized (g{sub 1}) nucleon structure functions in the wide range of the kinematical domain. Special attention is paid to the small-x behaviour of F{sub 2} and to the link between deep inelastic scattering and photoproduction process. The investigation of the Pomeron in deep inelastic scattering shows that one single Pomeron compatible with the Froissard-Martin limit can account for all the present HERA data. A phenomenological model of the proton structure function is developed, based on a two-component structure including various features expected from both perturbative quantum chromodynamics and non perturbative Regge theory. A link with the photoproduction process is provided. A detailed analysis of the perturbative components, based on the Gribov-Lipatov-Altarelli-Parisi evolution equations is presented. Taking into account the different parton distribution, this approach allows to describe data on proton and neutron structure functions, on deep inelastic neutrino scattering, and to reproduce the gluons distribution extracted by the ZEUS collaboration. The model is applied to the polarized deep inelastic scattering and the axial anomaly effect appearing both in the description of results on the spin dependent structure functions g{sup p,n,d} and in the interpretation of the nucleon spin structure is discussed. (J.S.). 260 refs., 34 figs., 8 tabs., 6 appends.

Effective field theory approach to structure functions at small xBj

International Nuclear Information System (INIS)

Nachtmann, O.

2003-01-01

We relate the structure functions of deep inelastic lepton-nucleon scattering to current-current correlation functions in a Euclidean field theory depending on a parameter r. The r-dependent Hamiltonian of the theory is P 0 -(1-r)P 3 , with P 0 the usual Hamiltonian and P 3 the third component of the momentum operator. We show that a small x Bj in the structure functions corresponds to the small r limit of the effective theory. We argue that for r→0 there is a critical regime of the theory where simple scaling relations should hold. We show that in this framework Regge behaviour of the structure functions obtained with the hard pomeron ansatz corresponds to a scaling behaviour of the matrix elements in the effective theory where the intercept of the hard pomeron appears as a critical index. Explicit expressions for various analytic continuations of the structure functions and matrix elements are given as well as path integral representations for the matrix elements in the effective theory. Our aim is to provide a framework for truly non-perturbative calculations of the structure functions at small x Bj for arbitrary Q 2 . (orig.)

Structural and Functional Plasticity in the Maternal Brain Circuitry

Science.gov (United States)

Pereira, Mariana

2016-01-01

Parenting recruits a distributed network of brain structures (and neuromodulators) that coordinates caregiving responses attuned to the young's affect, needs, and developmental stage. Many of these structures and connections undergo significant structural and functional plasticity, mediated by the interplay between maternal hormones and social…

The identification and functional annotation of RNA structures conserved in vertebrates

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Mirza, Aashiq Hussain; Hansen, Claus

2017-01-01

Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure-b......-structured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.......Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure......-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins...

Factor structure of functional state of primary school age children

Directory of Open Access Journals (Sweden)

Davidenko O.V.

2011-02-01

Full Text Available The examination of primary school children to determine the ranking of significant factors that determine the structure of their functional state depending on the level of physical health. It is shown that the main factor in the structure of the functional state of younger schoolchildren in low-and lower-middle level of physical fitness is selected morpho-functional status, which characterizes the functions of the body at rest. For children with average or above average level of physical fitness is a leading factor in physical fitness of schoolchildren.

Inactivation of normal and mutant Neurospora crassa conidia by visible light and near-UV: role of 1O2, carotenoid composition and sensitizer location

International Nuclear Information System (INIS)

Thomas, S.A.; Sargent, M.L.; Tuveson, R.W.

1981-01-01

Inactivation of Neurospora crassa conidia from wild-type and mutant strains by visible and near-ultraviolet light was investigated in the presence and absence of photosensitizing dyes. Inactivation by near-UV was virtually unchanged by the presence of deuterium oxide or azide suggesting that, contrary to the situation with visible light and photosensitizing dyes, 1 O 2 is not involved in any substantial way in the formation of lethal lesions. Carotenoid deficient strains were similar to wild-type strains in sensitivity to near-UV inactivation which is consistent with 1 O 2 not being involved. Photodynamic inactivation of conidia by visible light occurred in the presence of methylene blue (MB), toluidine blue O (TB), or acridine orange (AO). Carotenoid deficient strains were more sensitive to such inactivation only when MB and TB were used. This suggests that MB and TB mediated damage involves the cell membrane where carotenoids are available for quenching, whereas AO mediated damage occurs in the nucleus sequestered from the protective influence of carotenoids. A newly isolated, lemon-yellow mutant exhibited sensitivities to photodynamic inactivation similar to other pure-white mutants. The sensitivity of this pigmented mutant is apparently related to insufficient unsaturation of the two coloured carotenoids produced by the mutant. (author)

Structure modification and functionality of whey proteins: quantitative structure-activity relationship approach.

Science.gov (United States)

Nakai, S; Li-Chan, E

1985-10-01

According to the original idea of quantitative structure-activity relationship, electric, hydrophobic, and structural parameters should be taken into consideration for elucidating functionality. Changes in these parameters are reflected in the property of protein solubility upon modification of whey proteins by heating. Although solubility is itself a functional property, it has been utilized to explain other functionalities of proteins. However, better correlations were obtained when hydrophobic parameters of the proteins were used in conjunction with solubility. Various treatments reported in the literature were applied to whey protein concentrate in an attempt to obtain whipping and gelling properties similar to those of egg white. Mapping simplex optimization was used to search for the best results. Improvement in whipping properties by pepsin hydrolysis may have been due to higher protein solubility, and good gelling properties resulting from polyphosphate treatment may have been due to an increase in exposable hydrophobicity. However, the results of angel food cake making were still unsatisfactory.

Cellular regulation of the structure and function of aortic valves

Directory of Open Access Journals (Sweden)

Ismail El-Hamamsy

2010-01-01

Full Text Available The aortic valve was long considered a passive structure that opens and closes in response to changes in transvalvular pressure. Recent evidence suggests that the aortic valve performs highly sophisticated functions as a result of its unique microscopic structure. These functions allow it to adapt to its hemodynamic and mechanical environment. Understanding the cellular and molecular mechanisms involved in normal valve physiology is essential to elucidate the mechanisms behind valve disease. We here review the structure and developmental biology of aortic valves; we examine the role of its cellular parts in regulating its function and describe potential pathophysiological and clinical implications.

Improving the precision of the structure-function relationship by considering phylogenetic context.

Directory of Open Access Journals (Sweden)

2005-06-01

Full Text Available Understanding the relationship between protein structure and function is one of the foremost challenges in post-genomic biology. Higher conservation of structure could, in principle, allow researchers to extend current limitations of annotation. However, despite significant research in the area, a precise and quantitative relationship between biochemical function and protein structure has been elusive. Attempts to draw an unambiguous link have often been complicated by pleiotropy, variable transcriptional control, and adaptations to genomic context, all of which adversely affect simple definitions of function. In this paper, I report that integrating genomic information can be used to clarify the link between protein structure and function. First, I present a novel measure of functional proximity between protein structures (F-score. Then, using F-score and other entirely automatic methods measuring structure and phylogenetic similarity, I present a three-dimensional landscape describing their inter-relationship. The result is a "well-shaped" landscape that demonstrates the added value of considering genomic context in inferring function from structural homology. A generalization of methodology presented in this paper can be used to improve the precision of annotation of genes in current and newly sequenced genomes.

Industrial entrepreneurial network: Structural and functional analysis

Science.gov (United States)

Medvedeva, M. A.; Davletbaev, R. H.; Berg, D. B.; Nazarova, J. J.; Parusheva, S. S.

2016-12-01

Structure and functioning of two model industrial entrepreneurial networks are investigated in the present paper. One of these networks is forming when implementing an integrated project and consists of eight agents, which interact with each other and external environment. The other one is obtained from the municipal economy and is based on the set of the 12 real business entities. Analysis of the networks is carried out on the basis of the matrix of mutual payments aggregated over the certain time period. The matrix is created by the methods of experimental economics. Social Network Analysis (SNA) methods and instruments were used in the present research. The set of basic structural characteristics was investigated: set of quantitative parameters such as density, diameter, clustering coefficient, different kinds of centrality, and etc. They were compared with the random Bernoulli graphs of the corresponding size and density. Discovered variations of random and entrepreneurial networks structure are explained by the peculiarities of agents functioning in production network. Separately, were identified the closed exchange circuits (cyclically closed contours of graph) forming an autopoietic (self-replicating) network pattern. The purpose of the functional analysis was to identify the contribution of the autopoietic network pattern in its gross product. It was found that the magnitude of this contribution is more than 20%. Such value allows using of the complementary currency in order to stimulate economic activity of network agents.

Puzzle Pieces: Neural Structure and Function in Prader-Willi Syndrome

Science.gov (United States)

Manning, Katherine E.; Holland, Anthony J.

2015-01-01

Prader-Willi syndrome (PWS) is a neurodevelopmental disorder of genomic imprinting, presenting with a behavioural phenotype encompassing hyperphagia, intellectual disability, social and behavioural difficulties, and propensity to psychiatric illness. Research has tended to focus on the cognitive and behavioural investigation of these features, and, with the exception of eating behaviour, the neural physiology is currently less well understood. A systematic review was undertaken to explore findings relating to neural structure and function in PWS, using search terms designed to encompass all published articles concerning both in vivo and post-mortem studies of neural structure and function in PWS. This supported the general paucity of research in this area, with many articles reporting case studies and qualitative descriptions or focusing solely on the overeating behaviour, although a number of systematic investigations were also identified. Research to date implicates a combination of subcortical and higher order structures in PWS, including those involved in processing reward, motivation, affect and higher order cognitive functions, with both anatomical and functional investigations indicating abnormalities. It appears likely that PWS involves aberrant activity across distributed neural networks. The characterisation of neural structure and function warrants both replication and further systematic study. PMID:28943631

Puzzle Pieces: Neural Structure and Function in Prader-Willi Syndrome

Directory of Open Access Journals (Sweden)

Katherine E. Manning

2015-12-01

Full Text Available Prader-Willi syndrome (PWS is a neurodevelopmental disorder of genomic imprinting, presenting with a behavioural phenotype encompassing hyperphagia, intellectual disability, social and behavioural difficulties, and propensity to psychiatric illness. Research has tended to focus on the cognitive and behavioural investigation of these features, and, with the exception of eating behaviour, the neural physiology is currently less well understood. A systematic review was undertaken to explore findings relating to neural structure and function in PWS, using search terms designed to encompass all published articles concerning both in vivo and post-mortem studies of neural structure and function in PWS. This supported the general paucity of research in this area, with many articles reporting case studies and qualitative descriptions or focusing solely on the overeating behaviour, although a number of systematic investigations were also identified. Research to date implicates a combination of subcortical and higher order structures in PWS, including those involved in processing reward, motivation, affect and higher order cognitive functions, with both anatomical and functional investigations indicating abnormalities. It appears likely that PWS involves aberrant activity across distributed neural networks. The characterisation of neural structure and function warrants both replication and further systematic study.

Renormalized sum rules for structure functions of heavy meson decays

International Nuclear Information System (INIS)

Grozin, A.G.; Korchemsky, G.P.

1996-01-01

We consider the properties of the structure functions of inclusive heavy meson decays B→X c and treat the c quark mass as a free parameter. We show that in two extreme cases of heavy and light c quarks the structure functions of heavy-heavy and heavy-light transitions are given by a Fourier transform of the matrix elements of Wilson lines containing a timelike and a lightlike segment, correspondingly. Using the renormalization properties of Wilson lines we find the dependence of the structure functions on the factorization scale, the structure function of the heavy-heavy transition is renormalized multiplicatively, while that of the heavy-light transition obeys the GLAP-type evolution equation. We propose a generalization of the sum rules for the moments of the structure functions (Bjorken, Voloshin, and the open-quote open-quote third close-quote close-quote sum rules) with a soft exponential factorization cutoff, which correctly incorporates both perturbative and nonperturbative effects. We analyze nonperturbative corrections by first considering infrared renormalon contributions to the Wilson lines. Uncertainties induced by the leading renormalon pole at u=1/2 are exactly canceled by a similar uncertainty in the heavy quark pole mass. The leading nonperturbative corrections associated with the next renormalon at u=1 are parametrized by the matrix element μ π 2 which is proportional to the heavy quark kinetic energy. copyright 1996 The American Physical Society

Multiscale Persistent Functions for Biomolecular Structure Characterization

Energy Technology Data Exchange (ETDEWEB)

Xia, Kelin [Nanyang Technological University (Singapore). Division of Mathematical Sciences, School of Physical, Mathematical Sciences and School of Biological Sciences; Li, Zhiming [Central China Normal University, Wuhan (China). Key Laboratory of Quark and Lepton Physics (MOE) and Institute of Particle Physics; Mu, Lin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division

2017-11-02

Here in this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al. in Pattern Recognit 48(2):391–401, 2015; Merelli et al. in Entropy 17(10):6872–6892, 2015; Rucco et al. in: Proceedings of ECCS 2014, Springer, pp 117–128, 2016), a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our MPE can be used in conformational entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of an MRF built from angular distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. Additionally, it is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the intermediate range. Moreover, by comparing with traditional entropies from various grid sizes, bond angle-based methods and a persistent homology-based support vector machine method (Cang et al. in Mol Based Math Biol 3:140–162, 2015), we find that our MPE method gives the best results in terms of average true positive rate in a classic protein structure classification test. More interestingly, all-alpha and all-beta protein classes can be clearly separated from each other with zero error only in our model. Finally, a special protein structure index (PSI) is proposed, for the first

Protein Function Prediction Based on Sequence and Structure Information

KAUST Repository

Smaili, Fatima Z.

2016-05-25

The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

DMPD: Structural and functional analyses of bacterial lipopolysaccharides. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 12106784 Structural and functional analyses of bacterial lipopolysaccharides. Carof...html) (.csml) Show Structural and functional analyses of bacterial lipopolysaccharides. PubmedID 12106784 Title Structural and functi...onal analyses of bacterial lipopolysaccharides. Authors

From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

Science.gov (United States)

Forman-Kay, Julie D.; Mittag, Tanja

2015-01-01

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

Psychedelics Promote Structural and Functional Neural Plasticity.

Science.gov (United States)

Ly, Calvin; Greb, Alexandra C; Cameron, Lindsay P; Wong, Jonathan M; Barragan, Eden V; Wilson, Paige C; Burbach, Kyle F; Soltanzadeh Zarandi, Sina; Sood, Alexander; Paddy, Michael R; Duim, Whitney C; Dennis, Megan Y; McAllister, A Kimberley; Ori-McKenney, Kassandra M; Gray, John A; Olson, David E

2018-06-12

Atrophy of neurons in the prefrontal cortex (PFC) plays a key role in the pathophysiology of depression and related disorders. The ability to promote both structural and functional plasticity in the PFC has been hypothesized to underlie the fast-acting antidepressant properties of the dissociative anesthetic ketamine. Here, we report that, like ketamine, serotonergic psychedelics are capable of robustly increasing neuritogenesis and/or spinogenesis both in vitro and in vivo. These changes in neuronal structure are accompanied by increased synapse number and function, as measured by fluorescence microscopy and electrophysiology. The structural changes induced by psychedelics appear to result from stimulation of the TrkB, mTOR, and 5-HT2A signaling pathways and could possibly explain the clinical effectiveness of these compounds. Our results underscore the therapeutic potential of psychedelics and, importantly, identify several lead scaffolds for medicinal chemistry efforts focused on developing plasticity-promoting compounds as safe, effective, and fast-acting treatments for depression and related disorders. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

The structure and function of presynaptic endosomes

Energy Technology Data Exchange (ETDEWEB)

Jähne, Sebastian, E-mail: sebastian.jaehne1@stud.uni-goettingen.de [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); International Max Planck Research School for Neurosciences, 37077 Göttingen (Germany); Rizzoli, Silvio O. [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); Helm, Martin S., E-mail: martin.helm@med.uni-goettingen.de [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); International Max Planck Research School for Molecular Biology, 37077 Göttingen (Germany)

2015-07-15

The function of endosomes and of endosome-like structures in the presynaptic compartment is still controversial. This is in part due to the absence of a consensus on definitions and markers for these compartments. Synaptic endosomes are sometimes seen as stable organelles, permanently present in the synapse. Alternatively, they are seen as short-lived intermediates in synaptic vesicle recycling, arising from the endocytosis of large vesicles from the plasma membrane, or from homotypic fusion of small vesicles. In addition, the potential function of the endosome is largely unknown in the synapse. Some groups have proposed that the endosome is involved in the sorting of synaptic vesicle proteins, albeit others have produced data that deny this possibility. In this review, we present the existing evidence for synaptic endosomes, we discuss their potential functions, and we highlight frequent technical pitfalls in the analysis of this elusive compartment. We also sketch a roadmap to definitely determine the role of synaptic endosomes for the synaptic vesicle cycle. Finally, we propose a common definition of synaptic endosome-like structures.

The structure and function of presynaptic endosomes

International Nuclear Information System (INIS)

Jähne, Sebastian; Rizzoli, Silvio O.; Helm, Martin S.

2015-01-01

The function of endosomes and of endosome-like structures in the presynaptic compartment is still controversial. This is in part due to the absence of a consensus on definitions and markers for these compartments. Synaptic endosomes are sometimes seen as stable organelles, permanently present in the synapse. Alternatively, they are seen as short-lived intermediates in synaptic vesicle recycling, arising from the endocytosis of large vesicles from the plasma membrane, or from homotypic fusion of small vesicles. In addition, the potential function of the endosome is largely unknown in the synapse. Some groups have proposed that the endosome is involved in the sorting of synaptic vesicle proteins, albeit others have produced data that deny this possibility. In this review, we present the existing evidence for synaptic endosomes, we discuss their potential functions, and we highlight frequent technical pitfalls in the analysis of this elusive compartment. We also sketch a roadmap to definitely determine the role of synaptic endosomes for the synaptic vesicle cycle. Finally, we propose a common definition of synaptic endosome-like structures

Geometrical scaling in charm structure function ratios

International Nuclear Information System (INIS)

Boroun, G.R.; Rezaei, B.

2014-01-01

By using a Laplace-transform technique, we solve the next-to-leading-order master equation for charm production and derive a compact formula for the ratio R c =F L cc ¯ /F 2 cc ¯ , which is useful for extracting the charm structure function from the reduced charm cross section, in particular, at DESY HERA, at small x. Our results show that this ratio is independent of x at small x. In this method of determining the ratios, we apply geometrical scaling in charm production in deep inelastic scattering (DIS). Our analysis shows that the renormalization scales have a sizable impact on the ratio R c at high Q 2 . Our results for the ratio of the charm structure functions are in a good agreement with some phenomenological models

Normal central retinal function and structure preserved in retinitis pigmentosa.

Science.gov (United States)

Jacobson, Samuel G; Roman, Alejandro J; Aleman, Tomas S; Sumaroka, Alexander; Herrera, Waldo; Windsor, Elizabeth A M; Atkinson, Lori A; Schwartz, Sharon B; Steinberg, Janet D; Cideciyan, Artur V

2010-02-01

To determine whether normal function and structure, as recently found in forms of Usher syndrome, also occur in a population of patients with nonsyndromic retinitis pigmentosa (RP). Patients with simplex, multiplex, or autosomal recessive RP (n = 238; ages 9-82 years) were studied with static chromatic perimetry. A subset was evaluated with optical coherence tomography (OCT). Co-localized visual sensitivity and photoreceptor nuclear layer thickness were measured across the central retina to establish the relationship of function and structure. Comparisons were made to patients with Usher syndrome (n = 83, ages 10-69 years). Cross-sectional psychophysical data identified patients with RP who had normal rod- and cone-mediated function in the central retina. There were two other patterns with greater dysfunction, and longitudinal data confirmed that progression can occur from normal rod and cone function to cone-only central islands. The retinal extent of normal laminar architecture by OCT corresponded to the extent of normal visual function in patients with RP. Central retinal preservation of normal function and structure did not show a relationship with age or retained peripheral function. Usher syndrome results were like those in nonsyndromic RP. Regional disease variation is a well-known finding in RP. Unexpected was the observation that patients with presumed recessive RP can have regions with functionally and structurally normal retina. Such patients will require special consideration in future clinical trials of either focal or systemic treatment. Whether there is a common molecular mechanism shared by forms of RP with normal regions of retina warrants further study.

Soil-borne microbial functional structure across different land uses.

Science.gov (United States)

Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

Toward a standardized structural-functional group connectome in MNI space.

Science.gov (United States)

Horn, Andreas; Blankenburg, Felix

2016-01-01

The analysis of the structural architecture of the human brain in terms of connectivity between its subregions has provided profound insights into its underlying functional organization and has coined the concept of the "connectome", a structural description of the elements forming the human brain and the connections among them. Here, as a proof of concept, we introduce a novel group connectome in standard space based on a large sample of 169 subjects from the Enhanced Nathan Kline Institute-Rockland Sample (eNKI-RS). Whole brain structural connectomes of each subject were estimated with a global tracking approach, and the resulting fiber tracts were warped into standard stereotactic (MNI) space using DARTEL. Employing this group connectome, the results of published tracking studies (i.e., the JHU white matter and Oxford thalamic connectivity atlas) could be largely reproduced directly within MNI space. In a second analysis, a study that examined structural connectivity between regions of a functional network, namely the default mode network, was reproduced. Voxel-wise structural centrality was then calculated and compared to others' findings. Furthermore, including additional resting-state fMRI data from the same subjects, structural and functional connectivity matrices between approximately forty thousand nodes of the brain were calculated. This was done to estimate structure-function agreement indices of voxel-wise whole brain connectivity. Taken together, the combination of a novel whole brain fiber tracking approach and an advanced normalization method led to a group connectome that allowed (at least heuristically) performing fiber tracking directly within MNI space. Such an approach may be used for various purposes like the analysis of structural connectivity and modeling experiments that aim at studying the structure-function relationship of the human connectome. Moreover, it may even represent a first step toward a standard DTI template of the human brain

Structure of β-decay strength functions

International Nuclear Information System (INIS)

Naumov, Y.V.; Bykov, A.A.; Izosimov, I.N.

1983-01-01

The experimental and theoretical studies on the structure of the Gamow--Teller β-decay strength functions are reviewed. Also considered are processes such as M1 γ decay of analog states, the emission of delayed protons, neutrons, and α particles, delayed fission, and the (p, n) reaction at proton energies 100--200 MeV. The results of measurements of the strength functions by γ-ray total absorption are analyzed. It is shown that the β + decay of nuclei far from the stability band exhibits a new type of collective charge-exchange excitation: Gamow--Teller resonance with μ/sub tau/ = +1

QCD analysis of structure functions in terms of Jacobi polynomials

International Nuclear Information System (INIS)

Krivokhizhin, V.G.; Kurlovich, S.P.; Savin, I.A.; Sidorov, A.V.; Skachkov, N.B.; Sanadze, V.V.

1987-01-01

A new method of QCD-analysis of singlet and nonsinglet structure functions based on their expansion in orthogonal Jacobi polynomials is proposed. An accuracy of the method is studied and its application is demonstrated using the structure function F 2 (x,Q 2 ) obtained by the EMC Collaboration from measurements with an iron target. (orig.)

Template-assisted growth of nano structured functional materials

International Nuclear Information System (INIS)

Ying, K.K.; Nur Ubaidah Saidin; Khuan, N.I.; Suhaila Hani Ilias; Foo, C.T.

2012-01-01

Template-assisted growth is an important nano electrochemical deposition technique for synthesizing one-dimensional (1-D) nano structures with uniformly well-controlled shapes and sizes. A good template with well-defined dimensions is imperative for realizing this task. Porous anodic alumina (PAA) has been a favorable candidate for this purpose as it can be tailor-made with precise pore geometries, such as pore length and diameter as well as inter-pore distances, via the anodization of pure aluminium. This paper reports the fabrication of PAA templates and electrochemical synthesis of functional nano structures in the form of nano wires using PAA templates as scaffolds. Axial heterostructure and homogeneous nano wires formed by engineering materials configuration via composition and/ or layer thickness variations were fabricated for different functionalities. X-ray diffraction and imaging techniques were used to alucidate the microstructures, morphologies and chemical compositions of the nano wires produced. Due to their large surface area-to-volume ratios, and therefore high sensitivities, these functional nano structures have useful applications as critical components in nano sensor devices and various areas of nano technology. Potential applications include as hydrogen gas sensors in nuclear power plant for monitoring structural integrity of reactor components and containment building, as well as environmental monitoring of air pollution and leakages of toxic gases and chemicals. (Author)

Density functional study of molecular interactions in secondary structures of proteins.

Science.gov (United States)

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Geometrical comparison of two protein structures using Wigner-D functions.

Science.gov (United States)

Saberi Fathi, S M; White, Diana T; Tuszynski, Jack A

2014-10-01

In this article, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root-mean-square deviation characterization and employs a series expansion of the protein's shape function in terms of the Wigner-D functions to define a new criterion, which is called a "similarity value." We further demonstrate that the expansion coefficients for the shape function obtained with the help of the Wigner-D functions correspond to structure factors. Our method addresses the common problem of comparing two proteins with different numbers of atoms. We illustrate it with a worked example. © 2014 Wiley Periodicals, Inc.

A knowledge representation view on biomedical structure and function.

Science.gov (United States)

Schulz, Stefan; Hahn, Udo

2002-01-01

In biomedical ontologies, structural and functional considerations are of outstanding importance, and concepts which belong to these two categories are highly interdependent. At the representational level both axes must be clearly kept separate in order to support disciplined ontology engineering. Furthermore, the biaxial organization of physical structure (both by a taxonomic and partonomic order) entails intricate patterns of inference. We here propose a layered encoding of taxonomic, partonomic and functional aspects of biomedical concepts using description logics. PMID:12463912

CYCLOPHILIN A: STRUCTURE AND FUNCTIONS

Directory of Open Access Journals (Sweden)

A. A. Kalinina

2017-01-01

Full Text Available Cyclophilins belong to a large family of ancient conservative proteins with peptidyl-prolyl-cis-trans isomerase activity. The main member of this family – cyclophilin A – was discovered as an intracellular ligand for cyclosporine A. Further investigations revealed a wide range of functions of cyclophilin A. Cyclophilin A is involved in T-cell signaling, it takes part in folding, assembly and intracellular transport of proteins, as well as acts as an antioxidant. Different cell types secrete cyclophilin A under infection or oxidative stress. Cyclophilin A is one of the main factors involved in inflammation and pathogenesis of autoimmune, cardiovascular and other diseases. This protein is thought to take part in tumor progression. In this review we describe the structure of cyclophilin A and its main known functions in health and disease.

Structure and functions of organizational trust in employees’ notions

Directory of Open Access Journals (Sweden)

Marina M. Zavartseva

2016-06-01

Full Text Available This article investigates the structure and functions of organizational trust, examining the content of employees’ subjective notions about organizational trust and it’s role in organization’s functioning. The combination of direct (R.B.Shaw’s trust assessment survey and indirect (the semantic differential scale; the contentanalysis of the checklist of trust structural components methods was used. Using data on 378 employees of different organizations (commercial, medical, educational we distinguished subjective images of organization in groups with opposite estimation of organizational trust’s level. The study indicated that organizational trust’s structure is not linear, and exposed two main functions of high level of organizational trust – idealization and positive emotional estimation both of actual organization (that is currently place of employment. Obtained data provide basis for express-diagnostic of trust in organization and might be used for design of psychological training aiming high organization’s efficacy.

Data Presentation Structures in Specialised Dictionaries: Law Dictionaries with Communicative Functions

DEFF Research Database (Denmark)

Nielsen, Sandro

2015-01-01

data stand out, lexicographers should prioritize functional data that are directly related to and support the function(s) of dictionaries on a need-to-have/nice-to have basis, because data presentation structures with functional focus may better help users achieve their intended goals, i.e. finding......Theoretical lexicographers have developed a range of elaborate structures to describe the arrangement of data inside dictionaries, in particular in dictionary articles. However, most of these structures have been developed on the basis of detailed analyses of print dictionaries and relatively...... little has been said about the arrangement of data in e-dictionaries. The relevant data types are lexicographical data providing help concerning the function(s) and use of dictionaries on search results pages. In order to create a visual hierarchy on screen that makes the most important search result...

Transparent wood for functional and structural applications

Science.gov (United States)

Li, Yuanyuan; Fu, Qiliang; Yang, Xuan; Berglund, Lars

2017-12-01

Optically transparent wood combines mechanical performance with optical functionalities is an emerging candidate for applications in smart buildings and structural optics and photonics. The present review summarizes transparent wood preparation methods, optical and mechanical performance, and functionalization routes, and discusses potential applications. The various challenges are discussed for the purpose of improved performance, scaled-up production and realization of advanced applications. This article is part of a discussion meeting issue `New horizons for cellulose nanotechnology'.

Less-structured time in children's daily lives predicts self-directed executive functioning.

Science.gov (United States)

Barker, Jane E; Semenov, Andrei D; Michaelson, Laura; Provan, Lindsay S; Snyder, Hannah R; Munakata, Yuko

2014-01-01

Executive functions (EFs) in childhood predict important life outcomes. Thus, there is great interest in attempts to improve EFs early in life. Many interventions are led by trained adults, including structured training activities in the lab, and less-structured activities implemented in schools. Such programs have yielded gains in children's externally-driven executive functioning, where they are instructed on what goal-directed actions to carry out and when. However, it is less clear how children's experiences relate to their development of self-directed executive functioning, where they must determine on their own what goal-directed actions to carry out and when. We hypothesized that time spent in less-structured activities would give children opportunities to practice self-directed executive functioning, and lead to benefits. To investigate this possibility, we collected information from parents about their 6-7 year-old children's daily, annual, and typical schedules. We categorized children's activities as "structured" or "less-structured" based on categorization schemes from prior studies on child leisure time use. We assessed children's self-directed executive functioning using a well-established verbal fluency task, in which children generate members of a category and can decide on their own when to switch from one subcategory to another. The more time that children spent in less-structured activities, the better their self-directed executive functioning. The opposite was true of structured activities, which predicted poorer self-directed executive functioning. These relationships were robust (holding across increasingly strict classifications of structured and less-structured time) and specific (time use did not predict externally-driven executive functioning). We discuss implications, caveats, and ways in which potential interpretations can be distinguished in future work, to advance an understanding of this fundamental aspect of growing up.

Climate extremes drive changes in functional community structure.

Science.gov (United States)

Boucek, Ross E; Rehage, Jennifer S

2014-06-01

The response of communities to climate extremes can be quite variable. Much of this variation has been attributed to differences in community-specific functional trait diversity, as well as community composition. Yet, few if any studies have explicitly tested the response of the functional trait structure of communities following climate extremes (CEs). Recently in South Florida, two independent, but sequential potential CEs took place, a 2010 cold front, followed by a 2011 drought, both of which had profound impacts on a subtropical estuarine fish community. These CEs provided an opportunity to test whether the structure of South Florida fish communities following each extreme was a result of species-specific differences in functional traits. From historical temperature (1927-2012) and freshwater inflows records into the estuary (1955-2012), we determined that the cold front was a statistically extreme disturbance, while the drought was not, but rather a decadal rare disturbance. The two disturbances predictably affected different parts of functional community structure and thus different component species. The cold front virtually eliminated tropical species, including large-bodied snook, mojarra species, nonnative cichlids, and striped mullet, while having little affect on temperate fishes. Likewise, the drought severely impacted freshwater fishes including Florida gar, bowfin, and two centrarchids, with little effect on euryhaline species. Our findings illustrate the ability of this approach to predict and detect both the filtering effects of different types of disturbances and the implications of the resulting changes in community structure. Further, we highlight the value of this approach to developing predictive frameworks for better understanding community responses to global change. © 2014 John Wiley & Sons Ltd.

TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

Science.gov (United States)

Wiebe, Nicholas J P; Meyer, Irmtraud M

2010-06-24

The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular

The ratio of structure functions for the neutron and the proton

International Nuclear Information System (INIS)

Ballintijn, M.K.

1994-01-01

The subject of this thesis is the ratio of the structure functions F 2 of the deuteron and the proton. The structure function ratio is measured by the NMC with high precision due to a dedicated target setup. In this thesis the analysis is presented of the data taken in 1989, which were obtained using incident muon energies of 120, 200 and 280 GeV. These data complement the results from earlier measurements performed in 1986 and 1987 which were obtained at 90 and 280 GeV incident muon energy. The newly determined structure function ratio, in a slightly extended range of the scaling parameter x, is compared to the previous one and is found to be in good agreement. All data are combined to give the most accurate determination of the structure function ratio to date. The results are used to determine the dependence of the structure function ratio on the value of Q 2 , the scale at which the nucleon is probed. Finally, the structure function ratios obtained at four different incident muon energies separately, are used to determine the difference R d -R p , where R is the ratio of cross sections for the absorption of longitudinally and transversely polarized virtual photons. The difference in R for the deuteron and the proton is related to differences in the gluon distribution. The result is compatible with a gluon distribution that is identical for the deuteron and the proton. The degree of equality of R d and R p is a measure for the correctness of the procedure to extract structure function ratios. The present result is R d -R p =0.02±0.02 and hence compatible with zero. (orig.)

The gluon contribution to polarised nucleon structure functions

International Nuclear Information System (INIS)

Ross, G.G.; Roberts, R.G.

1990-08-01

As with all parton distributions in quantum chromodynamics (QCD) the separation of polarised nucleon structure functions into gluon and quark contributions must be specified. We consider a definition of the gluon contribution to polarised nucleon structure functions based on exclusive processes which is explicitly gauge invariant, has no regularisation ambiguities, is insensitive to infrared singularities and can be related to other polarised scattering processes. We discuss the relationship of this gluon definition to others that have recently been used and to the estimates that have been made of the gluon contribution using current algebra and other methods. A quantitative analysis of the structure function g 1 (x,Q 2 ) for polarised deep inelastic scattering is carried out, with the aim of examining the importance of the gluon contribution. Using the positivity of parton distributions the magnitude of Δg(x,Q 2 ) is constrained by a realistic estimate of the unpolarised glue. With the appropriate choice of the hard scattering cross-section, Δσ γg , we find that even with a maximally polarised glue (for x > 0.1), some polarised strange quark contribution is still needed by the data of the EMC. (author)

Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

Directory of Open Access Journals (Sweden)

Vassilev Boris

2010-04-01

Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

Quark-hadron duality of nucleon spin structure function

International Nuclear Information System (INIS)

Dong, Y.B.

2005-01-01

Bloom-Gilman quark-hadron duality of nuclear spin structure function is studied by comparing the integral of g 1 from perturbative QCD prediction in the scaling region to the moment of g 1 in the resonance region. The spin structure function in the resonance region is estimated by the parametrization forms of non-resonance background and of resonance contributions. The uncertainties of our calculations due to those parametrization forms are discussed. Moreover, the effect of the Δ(1232)-resonance in the first resonance region and the role of the resonances in the second resonance region are explicitly shown. Elastic peak contribution to the duality is also analyzed. (orig.)

Proteins with Novel Structure, Function and Dynamics

Science.gov (United States)

Pohorille, Andrew

2014-01-01

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Analysis of structure-function network decoupling in the brain systems of spastic diplegic cerebral palsy.

Science.gov (United States)

Lee, Dongha; Pae, Chongwon; Lee, Jong Doo; Park, Eun Sook; Cho, Sung-Rae; Um, Min-Hee; Lee, Seung-Koo; Oh, Maeng-Keun; Park, Hae-Jeong

2017-10-01

Manifestation of the functionalities from the structural brain network is becoming increasingly important to understand a brain disease. With the aim of investigating the differential structure-function couplings according to network systems, we investigated the structural and functional brain networks of patients with spastic diplegic cerebral palsy with periventricular leukomalacia compared to healthy controls. The structural and functional networks of the whole brain and motor system, constructed using deterministic and probabilistic tractography of diffusion tensor magnetic resonance images and Pearson and partial correlation analyses of resting-state functional magnetic resonance images, showed differential embedding of functional networks in the structural networks in patients. In the whole-brain network of patients, significantly reduced global network efficiency compared to healthy controls were found in the structural networks but not in the functional networks, resulting in reduced structural-functional coupling. On the contrary, the motor network of patients had a significantly lower functional network efficiency over the intact structural network and a lower structure-function coupling than the control group. This reduced coupling but reverse directionality in the whole-brain and motor networks of patients was prominent particularly between the probabilistic structural and partial correlation-based functional networks. Intact (or less deficient) functional network over impaired structural networks of the whole brain and highly impaired functional network topology over the intact structural motor network might subserve relatively preserved cognitions and impaired motor functions in cerebral palsy. This study suggests that the structure-function relationship, evaluated specifically using sparse functional connectivity, may reveal important clues to functional reorganization in cerebral palsy. Hum Brain Mapp 38:5292-5306, 2017. © 2017 Wiley Periodicals

Functional and structural responses to marine urbanisation

Science.gov (United States)

Mayer-Pinto, M.; Cole, V. J.; Johnston, E. L.; Bugnot, A.; Hurst, H.; Airoldi, L.; Glasby, T. M.; Dafforn, K. A.

2018-01-01

Urban areas have broad ecological footprints with complex impacts on natural systems. In coastal areas, growing populations are advancing their urban footprint into the ocean through the construction of seawalls and other built infrastructure. While we have some understanding of how urbanisation might drive functional change in terrestrial ecosystems, coastal systems have been largely overlooked. This study is one of the first to directly assess how changes in diversity relate to changes in ecosystem properties and functions (e.g. productivity, filtration rates) of artificial and natural habitats in one of the largest urbanised estuaries in the world, Sydney Harbour. We complemented our surveys with an extensive literature search. We found large and important differences in the community structure and function between artificial and natural coastal habitats. However, differences in diversity and abundance of organisms do not necessarily match observed functional changes. The abundance and composition of important functional groups differed among habitats with rocky shores having 40% and 70% more grazers than seawalls or pilings, respectively. In contrast, scavengers were approximately 8 times more abundant on seawalls than on pilings or rocky shores and algae were more diverse on natural rocky shores and seawalls than on pilings. Our results confirm previous findings in the literature. Oysters were more abundant on pilings than on rocky shores, but were also smaller. Interestingly, these differences in oyster populations did not affect in situ filtration rates between habitats. Seawalls were the most invaded habitats while pilings supported greater secondary productivity than other habitats. This study highlights the complexity of the diversity-function relationship and responses to ocean sprawl in coastal systems. Importantly, we showed that functional properties should be considered independently from structural change if we are to design and manage artificial

NCACO-score: An effective main-chain dependent scoring function for structure modeling

Directory of Open Access Journals (Sweden)

Dong Xiaoxi

2011-05-01

Full Text Available Abstract Background Development of effective scoring functions is a critical component to the success of protein structure modeling. Previously, many efforts have been dedicated to the development of scoring functions. Despite these efforts, development of an effective scoring function that can achieve both good accuracy and fast speed still presents a grand challenge. Results Based on a coarse-grained representation of a protein structure by using only four main-chain atoms: N, Cα, C and O, we develop a knowledge-based scoring function, called NCACO-score, that integrates different structural information to rapidly model protein structure from sequence. In testing on the Decoys'R'Us sets, we found that NCACO-score can effectively recognize native conformers from their decoys. Furthermore, we demonstrate that NCACO-score can effectively guide fragment assembly for protein structure prediction, which has achieved a good performance in building the structure models for hard targets from CASP8 in terms of both accuracy and speed. Conclusions Although NCACO-score is developed based on a coarse-grained model, it is able to discriminate native conformers from decoy conformers with high accuracy. NCACO is a very effective scoring function for structure modeling.

UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

Science.gov (United States)

Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

2016-01-04

The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Adaptive Functional-Based Neuro-Fuzzy-PID Incremental Controller Structure

Directory of Open Access Journals (Sweden)

Ashraf Ahmed Fahmy

2014-03-01

Full Text Available This paper presents an adaptive functional-based Neuro-fuzzy-PID incremental (NFPID controller structure that can be tuned either offline or online according to required controller performance. First, differential membership functions are used to represent the fuzzy membership functions of the input-output space of the three term controller. Second, controller rules are generated based on the discrete proportional, derivative, and integral function for the fuzzy space. Finally, a fully differentiable fuzzy neural network is constructed to represent the developed controller for either offline or online controller parameter adaptation.  Two different adaptation methods are used for controller tuning, offline method based on controller transient performance cost function optimization using Bees Algorithm, and online method based on tracking error minimization using back-propagation with momentum algorithm. The proposed control system was tested to show the validity of the controller structure over a fixed PID controller gains to control SCARA type robot arm.

Comparison of parton distributions and structure functions for the proton

International Nuclear Information System (INIS)

Abramowicz, H.; Charchula, K.; Krawczyk, M.; Levy, A.

1990-09-01

A comparative study of the most popular parton parametrizations is presented. The individual parton distributions as well as the F 2 structure function are discussed with a particular emphasis on the low x region, 10 -4 -2 . The predictions of these parametrizations for the F 2 structure function have a wide spread which persists also in the HERA kinematical region. (orig.)

Intrinsic polarization of the high energy W-boson structure functions

International Nuclear Information System (INIS)

Ralston, J.P.; Olness, F.

1986-01-01

Several new issues are presented that are to be incorporated into a consistent treatment of high-energy transverse effective-W boson structure functions. The issues included the numerical importance of the proper choice of scale, and the q 2 evolution of the boson structure functions in an Altarelli-Parisi framework. We investigate a novel effect of the V-A coupling which produces a sizable intrinsic polarization of the W distributions. A preliminary estimate yields a left- to right-helicity structure function ratio W/sub L// + W/sub R/ + ≅ 1 - 21/(1 - x) + 21/(1 - x) 2 . For x ≥ 0.06, there are two lift-handed W + 's for every right-handed one in an unpolarized proton. 11 refs., 2 figs

DNA mimic proteins: functions, structures, and bioinformatic analysis.

Science.gov (United States)

Wang, Hao-Ching; Ho, Chun-Han; Hsu, Kai-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J

2014-05-13

DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.

Soil-Borne Microbial Functional Structure across Different Land Uses

Directory of Open Access Journals (Sweden)

Eiko E. Kuramae

2014-01-01

Full Text Available Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

Hierarchical structure of correlation functions for single jets

International Nuclear Information System (INIS)

Lupia, S.; Giovannini, A.; Ugoccioni, R.

1993-01-01

Theoretical basis of void scaling function properties of hierarchical structure in rapidity and p T intervals are explored. Their phenomenological consequences are analyzed at single jet level by using Monte Carlo methods in e + e - annihilation. It is found that void scaling function study provides an interesting alternative approach for characterizing single jets of different origin. (orig.)

nuvA, an Aspergillus nidulans gene involved in DNA repair and recombination, is a homologue of Saccharomyces cerevisiae RAD18 and Neurospora crassa uvs-2.

Science.gov (United States)

Iwanejko, L; Cotton, C; Jones, G; Tomsett, B; Strike, P

1996-03-01

A 40 kb genomic clone and 2.3 kb EcoRI subclone that rescued the DNA repair and recombination defects of the Aspergillus nidulans nuvA11 mutant were isolated and the subclone sequenced. The subclone hybridized to a cosmid in a chromosome-specific library confirming the assignment of nuvA to linkage group IV and indicating its closeness to bimD. Amplification by PCR clarified the relative positions of nuvA and bimD. A region identified within the subclone, encoding a C3HC4 zinc finger motif, was used as a probe to retrieve a cDNA clone. Sequencing of this clone showed that the nuvA gene has an ORF of 1329 bp with two introns of 51 bp and 60 bp. Expression of nuvA appears to be extremely low. The putative NUVA polypeptide has two zinc finger motifs, a molecular mass of 48906 Da and has 39% identity with the Neurospora crassa uvs-2 and 25% identity with the Saccharomyces cerevisiae RAD18 translation products. Although mutations in nuvA, uvs-2 and RAD18 produce similar phenotypes, only the nuvA11 mutation affects meiotic recombination. A role for nuvA in both DNA repair and genetic recombination is proposed.

Dipole rescattering and the nuclear structure function

Energy Technology Data Exchange (ETDEWEB)

Carvalho, F. [Depto de Ciencias Exatas e da Terra, Universidade Federal de Sao Paulo, SP (Brazil); Goncalves, V. P. [Instituto de Fisica e Matematica, Universidade Federal de Pelotas, Caixa Postal 354, CEP 96010-900, Pelotas, RS (Brazil); Navarra, F. S.; Oliveira, E. G. [Instituto de Fisica, Universidade de Sao Paulo Rua do Matao, Travessa R, 187, 05508-090 Sao Paulo, SP (Brazil)

2013-03-25

In the framework of the dipole model, we study the effects of the dipole multiple scatterings in a nuclear target and compute the nuclear structure function. We compare different unitarization schemes and confront our results with the E665 data.

Subjective Cognitive Decline: Mapping Functional and Structural Brain Changes-A Combined Resting-State Functional and Structural MR Imaging Study.

Science.gov (United States)

Sun, Yu; Dai, Zhengjia; Li, Yuxia; Sheng, Can; Li, Hongyan; Wang, Xiaoni; Chen, Xiaodan; He, Yong; Han, Ying

2016-10-01

Purpose To determine whether individuals with subjective cognitive decline (SCD) exhibit functional and structural brain alterations by using resting-state functional and structural magnetic resonance (MR) imaging. Materials and Methods This study received institutional review board approval, and all participants gave informed consent. Resting-state functional MR imaging and structural MR imaging techniques were used to measure amplitude of low-frequency fluctuations (ALFF) and regional gray matter volume in 25 subjects with SCD (mean age, 65.52 years ± 6.12) and 61 control subjects (mean age, 64.11 years ± 8.59). Voxel-wise general linear model analyses were used to examine between-group differences in ALFF or in gray matter volume and to further determine the brain-behavioral relationship. Results Subjects with SCD exhibited higher ALFF values than did control subjects in the bilateral inferior parietal lobule (left: 0.44 ± 0.25 vs 0.27 ± 0.18, respectively; P = .0003; right: 1.46 ± 0.45 vs 1.10 ± 0.37, respectively; P = .0015), right inferior (0.45 ± 0.15 vs 0.37 ± 0.08, repectively; P = .0106) and middle (1.03 ± 0.32 vs 0.83 ± 0.20, respectively; P = .0008) occipital gyrus, right superior temporal gyrus (0.11 ± 0.07 vs 0.07 ± 0.04, respectively; P = .0016), and right cerebellum posterior lobe (0.51 ± 0.27 vs 0.39 ± 0.15, respectively; P = .0010). In the SCD group, significant correlations were found between Auditory Verbal Learning Test recognition scores and ALFF in the left inferior parietal lobe (r = -0.79, P Learning Test immediate recall scores and ALFF values in the right middle occipital gyrus (r = -0.64, P = .002). Nonsignificant group differences were found in gray matter volume (P > .05, corrected). Conclusion Individuals with SCD had altered spontaneous functional activity, suggesting that resting-state functional MR imaging may be a noninvasive method for characterizing SCD. (©) RSNA, 2016 Online supplemental material is available for

Biomonitors and the assessment of ecological impacts: Distribution of herbivorous epifauna in contaminated macroalgal beds

International Nuclear Information System (INIS)

Roberts, David A.; Johnston, Emma L.; Poore, Alistair G.B.

2008-01-01

We determined metal contents of co-occurring algae Padina crassa and Sargassum sp. in Port Jackson (Australia), and relationships between metal levels and the abundance of epifaunal amphipods. Copper, lead and zinc concentrations were amongst the highest yet recorded in these algae. Copper, manganese and lead concentrations were far greater in P. crassa than Sargassum sp., possibly due to the low growth of P. crassa in proximity to contaminated sediments. However, in manipulative experiments the proximity of algae to sediments did not explain these differences. The abundance of herbivorous amphipods correlated negatively with the copper content of P. crassa, but not with the lower concentrations in Sargassum sp. The greater contamination of P. crassa led to patchy distributions of metals in algal beds and recolonisation experiments showed Sargassum sp. acts as a refuge from contaminants for epifauna. The contamination of macroalgae may pose threats to epifauna in harbours around the world. - The accumulation of metals by macroalgae may pose ecological threats to herbivorous epifauna in ports and harbours worldwide

Protein Function Prediction Based on Sequence and Structure Information

KAUST Repository

Smaili, Fatima Z.

2016-01-01

operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching

Structural and functional loss in restored wetland ecosystems.

Directory of Open Access Journals (Sweden)

David Moreno-Mateos

2012-01-01

Full Text Available Wetlands are among the most productive and economically valuable ecosystems in the world. However, because of human activities, over half of the wetland ecosystems existing in North America, Europe, Australia, and China in the early 20th century have been lost. Ecological restoration to recover critical ecosystem services has been widely attempted, but the degree of actual recovery of ecosystem functioning and structure from these efforts remains uncertain. Our results from a meta-analysis of 621 wetland sites from throughout the world show that even a century after restoration efforts, biological structure (driven mostly by plant assemblages, and biogeochemical functioning (driven primarily by the storage of carbon in wetland soils, remained on average 26% and 23% lower, respectively, than in reference sites. Either recovery has been very slow, or postdisturbance systems have moved towards alternative states that differ from reference conditions. We also found significant effects of environmental settings on the rate and degree of recovery. Large wetland areas (>100 ha and wetlands restored in warm (temperate and tropical climates recovered more rapidly than smaller wetlands and wetlands restored in cold climates. Also, wetlands experiencing more (riverine and tidal hydrologic exchange recovered more rapidly than depressional wetlands. Restoration performance is limited: current restoration practice fails to recover original levels of wetland ecosystem functions, even after many decades. If restoration as currently practiced is used to justify further degradation, global loss of wetland ecosystem function and structure will spread.

Surface structure and properties of functionalized nanodiamonds: a first-principles study

International Nuclear Information System (INIS)

Datta, Aditi; Kirca, Mesut; Fu Yao; To, Albert C

2011-01-01

The goal of this work is to gain fundamental understanding of the surface and internal structure of functionalized detonation nanodiamonds (NDs) using quantum mechanics based density functional theory (DFT) calculations. The unique structure of ND assists in the binding of different functional groups to its surface which in turn facilitates binding with drug molecules. The ability to comprehensively model the surface properties, as well as drug-ND interactions during functionalization, is a challenge and is the problem of our interest. First, the structure of NDs of technologically relevant size (∼5 nm) was optimized using classical mechanics based molecular mechanics simulations. Quantum mechanics based density functional theory (DFT) was then employed to analyse the properties of smaller relevant parts of the optimized cluster further to address the effect of functionalization on the stability of the cluster and reactivity at its surface. It is found that functionalization is preferred over reconstruction at the (100) surface and promotes graphitization in the (111) surface for NDs functionalized with the carbonyl oxygen (C = O) group. It is also seen that the edges of ND are the preferred sites for functionalization with the carboxyl group (-COOH) vis-a-vis the corners of ND.

Surface structure and properties of functionalized nanodiamonds: a first-principles study

Energy Technology Data Exchange (ETDEWEB)

Datta, Aditi; Kirca, Mesut; Fu Yao; To, Albert C, E-mail: albertto@pitt.edu [Department of Mechanical Engineering and Materials Science and Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261 (United States)

2011-02-11

The goal of this work is to gain fundamental understanding of the surface and internal structure of functionalized detonation nanodiamonds (NDs) using quantum mechanics based density functional theory (DFT) calculations. The unique structure of ND assists in the binding of different functional groups to its surface which in turn facilitates binding with drug molecules. The ability to comprehensively model the surface properties, as well as drug-ND interactions during functionalization, is a challenge and is the problem of our interest. First, the structure of NDs of technologically relevant size ({approx}5 nm) was optimized using classical mechanics based molecular mechanics simulations. Quantum mechanics based density functional theory (DFT) was then employed to analyse the properties of smaller relevant parts of the optimized cluster further to address the effect of functionalization on the stability of the cluster and reactivity at its surface. It is found that functionalization is preferred over reconstruction at the (100) surface and promotes graphitization in the (111) surface for NDs functionalized with the carbonyl oxygen (C = O) group. It is also seen that the edges of ND are the preferred sites for functionalization with the carboxyl group (-COOH) vis-a-vis the corners of ND.

Structural and functional cerebral correlates of hypnotic suggestibility.

Directory of Open Access Journals (Sweden)

Alexa Huber

Full Text Available Little is known about the neural bases of hypnotic suggestibility, a cognitive trait referring to the tendency to respond to hypnotic suggestions. In the present magnetic resonance imaging study, we performed regression analyses to assess hypnotic suggestibility-related differences in local gray matter volume, using voxel-based morphometry, and in waking resting state functional connectivity of 10 resting state networks, in 37 healthy women. Hypnotic suggestibility was positively correlated with gray matter volume in portions of the left superior and medial frontal gyri, roughly overlapping with the supplementary and pre-supplementary motor area, and negatively correlated with gray matter volume in the left superior temporal gyrus and insula. In the functional connectivity analysis, hypnotic suggestibility was positively correlated with functional connectivity between medial posterior areas, including bilateral posterior cingulate cortex and precuneus, and both the lateral visual network and the left fronto-parietal network; a positive correlation was also found with functional connectivity between the executive-control network and a right postcentral/parietal area. In contrast, hypnotic suggestibility was negatively correlated with functional connectivity between the right fronto-parietal network and the right lateral thalamus. These findings demonstrate for the first time a correlation between hypnotic suggestibility, the structural features of specific cortical regions, and the functional connectivity during the normal resting state of brain structures involved in imagery and self-monitoring activity.

Structural and functional cerebral correlates of hypnotic suggestibility.

Science.gov (United States)

Huber, Alexa; Lui, Fausta; Duzzi, Davide; Pagnoni, Giuseppe; Porro, Carlo Adolfo

2014-01-01

Little is known about the neural bases of hypnotic suggestibility, a cognitive trait referring to the tendency to respond to hypnotic suggestions. In the present magnetic resonance imaging study, we performed regression analyses to assess hypnotic suggestibility-related differences in local gray matter volume, using voxel-based morphometry, and in waking resting state functional connectivity of 10 resting state networks, in 37 healthy women. Hypnotic suggestibility was positively correlated with gray matter volume in portions of the left superior and medial frontal gyri, roughly overlapping with the supplementary and pre-supplementary motor area, and negatively correlated with gray matter volume in the left superior temporal gyrus and insula. In the functional connectivity analysis, hypnotic suggestibility was positively correlated with functional connectivity between medial posterior areas, including bilateral posterior cingulate cortex and precuneus, and both the lateral visual network and the left fronto-parietal network; a positive correlation was also found with functional connectivity between the executive-control network and a right postcentral/parietal area. In contrast, hypnotic suggestibility was negatively correlated with functional connectivity between the right fronto-parietal network and the right lateral thalamus. These findings demonstrate for the first time a correlation between hypnotic suggestibility, the structural features of specific cortical regions, and the functional connectivity during the normal resting state of brain structures involved in imagery and self-monitoring activity.

Gluon structure function for deeply inelastic scattering with nucleus in QCD

Energy Technology Data Exchange (ETDEWEB)

Ayala Filho, Alvaro L; Ducati, M.B. Gay [Rio Grande do Sul Univ., Porto Alegre, RS (Brazil). Inst. de Fisica; Levin, Eugene [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil); [Petersburg Nuclear Physics Institute, Gatchina (Russian Federation). Theory Dept.

1995-06-01

In this talk we present the first calculation of the gluon structure function for nucleus in QCD. We discuss the Glauber formula for the gluon structure function and the violation of this simple approach that we anticipate in QCD. (author). 10 refs, 4 figs.

Structure and Dynamics of Hydroxyl-Functionalized Protic Ammonium Carboxylate Ionic Liquids.

Science.gov (United States)

Thummuru, Dhileep Nagi Reddy; Mallik, Bhabani S

2017-10-26

We performed classical molecular dynamics simulations to investigate the structure and dynamics of protic ionic liquids, 2-hydroxy ethylammonium acetate, ethylammonium hydroxyacetate, and 2-hydroxyethylammonium hydroxyacetate at ambient conditions. Structural properties such as density, radial distribution functions, spatial distribution functions, and structure factors have been calculated. Dynamic properties such as mean square displacements, as well as residence and hydrogen bond dynamics have also been calculated. Hydrogen bond lifetimes and residence times change with the addition of hydroxyl groups. We observe that when a hydroxyl group is present on the cation, dynamics become very slow and it forms a strong hydrogen bond with carboxylate oxygen atoms of the anion. The hydroxyl functionalized ILs show more dynamic diversity than structurally similar ILs.

Hybrid functional calculation of electronic and phonon structure of BaSnO3

International Nuclear Information System (INIS)

Kim, Bog G.; Jo, J.Y.; Cheong, S.W.

2013-01-01

Barium stannate, BaSnO 3 (BSO), with a cubic perovskite structure, has been highlighted as a promising host material for the next generation transparent oxide electrodes. This study examined theoretically the electronic structure and phonon structure of BSO using hybrid density functional theory based on the HSE06 functional. The electronic structure results of BSO were corrected by extending the phonon calculations based on the hybrid density functional. The fundamental thermal properties were also predicted based on a hybrid functional calculation. Overall, a detailed understanding of the electronic structure, phonon modes and phonon dispersion of BSO will provide a theoretical starting-point for engineering applications of this material. - Graphical Abstract: (a) Crystal structure of BaSnO 3 . The center ball is Ba and small (red) ball on edge is oxygen and SnO 6 octahedrons are plotted as polyhedron. (b) Electronic band structure along the high symmetry point in the Brillouin zone using the HSE06 hybrid functional. (c) The phonon dispersion curve calculated using the HSE06 hybrid functional (d) Zone center lowest energy F 1u phonon mode. Highlights: ► We report the full hybrid functional calculation of not only the electronic structure but also the phonon structure for BaSnO 3 . ► The band gap calculation of HSE06 revealed an indirect gap with 2.48 eV. ► The effective mass at the conduction band minimum and valence band maximum was calculated. ► In addition, the phonon structure of BSO was calculated using the HSE06 functional. ► Finally, the heat capacity was calculated and compared with the recent experimental result.

An introduction about precise measurements of QED γ structure functions

International Nuclear Information System (INIS)

Courau, A.

1989-11-01

Pure QED processes are theoretically exactly computable. However precise measurements and theoretical expectations of QED γ structure functions within a given experimental acceptance are not so trivial. Yet such a study is quite interesting. It supplies on the one hand a good QED test and, on the other hand, a good exercise for testing the procedure used for the determination of the hadronic γ structure functions

Structural and functional correlates of epileptogenesis — Does gender matter?

Science.gov (United States)

Savic, Ivanka; Engel, Jerome

2016-01-01

In the majority of neuropsychiatric conditions, marked gender-based differences have been found in the epidemiology, clinical manifestations, and therapy of disease. One possible reason is that sex differences in cerebral morphology, structural and functional connections, render men and women differentially vulnerable to various disease processes. The present review addresses this issue with respect to the functional and structural correlates to some forms of epilepsy. PMID:24943053

Linking structural features of protein complexes and biological function.

Science.gov (United States)

Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

2015-09-01

Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

Phosphatidylinositol 4-kinases: Function, structure, and inhibition

International Nuclear Information System (INIS)

Boura, Evzen; Nencka, Radim

2015-01-01

The phosphatidylinositol 4-kinases (PI4Ks) synthesize phosphatidylinositol 4-phosphate (PI4P), a key member of the phosphoinositide family. PI4P defines the membranes of Golgi and trans-Golgi network (TGN) and regulates trafficking to and from the Golgi. Humans have two type II PI4Ks (α and β) and two type III enzymes (α and β). Recently, the crystal structures were solved for both type II and type III kinase revealing atomic details of their function. Importantly, the type III PI4Ks are hijacked by +RNA viruses to create so-called membranous web, an extensively phosphorylated and modified membrane system dedicated to their replication. Therefore, selective and potent inhibitors of PI4Ks have been developed as potential antiviral agents. Here we focus on the structure and function of PI4Ks and their potential in human medicine

Phosphatidylinositol 4-kinases: Function, structure, and inhibition

Energy Technology Data Exchange (ETDEWEB)

Boura, Evzen, E-mail: boura@uochb.cas.cz; Nencka, Radim, E-mail: nencka@uochb.cas.cz

2015-10-01

The phosphatidylinositol 4-kinases (PI4Ks) synthesize phosphatidylinositol 4-phosphate (PI4P), a key member of the phosphoinositide family. PI4P defines the membranes of Golgi and trans-Golgi network (TGN) and regulates trafficking to and from the Golgi. Humans have two type II PI4Ks (α and β) and two type III enzymes (α and β). Recently, the crystal structures were solved for both type II and type III kinase revealing atomic details of their function. Importantly, the type III PI4Ks are hijacked by +RNA viruses to create so-called membranous web, an extensively phosphorylated and modified membrane system dedicated to their replication. Therefore, selective and potent inhibitors of PI4Ks have been developed as potential antiviral agents. Here we focus on the structure and function of PI4Ks and their potential in human medicine.

Myoglobin Structure and Function: A Multiweek Biochemistry Laboratory Project

Science.gov (United States)

Silverstein, Todd P.; Kirk, Sarah R.; Meyer, Scott C.; Holman, Karen L. McFarlane

2015-01-01

We have developed a multiweek laboratory project in which students isolate myoglobin and characterize its structure, function, and redox state. The important laboratory techniques covered in this project include size-exclusion chromatography, electrophoresis, spectrophotometric titration, and FTIR spectroscopy. Regarding protein structure,…

Heme isomers substantially affect heme's electronic structure and function

DEFF Research Database (Denmark)

Kepp, Kasper Planeta

2017-01-01

Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as du...

Hierarchical structure of correlation functions for single jets

Energy Technology Data Exchange (ETDEWEB)

Lupia, S. (Dipt. di Fisica Teorica, Univ. di Torino, and INFN, Sezione di Torino (Italy)); Giovannini, A. (Dipt. di Fisica Teorica, Univ. di Torino, and INFN, Sezione di Torino (Italy)); Ugoccioni, R. (Dipt. di Fisica Teorica, Univ. di Torino, and INFN, Sezione di Torino (Italy))

1993-08-01

Theoretical basis of void scaling function properties of hierarchical structure in rapidity and p[sub T] intervals are explored. Their phenomenological consequences are analyzed at single jet level by using Monte Carlo methods in e[sup +]e[sup -] annihilation. It is found that void scaling function study provides an interesting alternative approach for characterizing single jets of different origin. (orig.)

Glutathione transferases are structural and functional outliers in the thioredoxin fold.

Science.gov (United States)

Atkinson, Holly J; Babbitt, Patricia C

2009-11-24

Glutathione transferases (GSTs) are ubiquitous scavengers of toxic compounds that fall, structurally and functionally, within the thioredoxin fold suprafamily. The fundamental catalytic capability of GSTs is catalysis of the nucleophilic addition or substitution of glutathione at electrophilic centers in a wide range of small electrophilic compounds. While specific GSTs have been studied in detail, little else is known about the structural and functional relationships between different groupings of GSTs. Through a global analysis of sequence and structural similarity, it was determined that variation in the binding of glutathione between the two major subgroups of cytosolic (soluble) GSTs results in a different mode of glutathione activation. Additionally, the convergent features of glutathione binding between cytosolic GSTs and mitochondrial GST kappa are described. The identification of these structural and functional themes helps to illuminate some of the fundamental contributions of the thioredoxin fold to catalysis in the GSTs and clarify how the thioredoxin fold can be modified to enable new functions.

Effect of acid hydrolysis on starch structure and functionality: a review.

Science.gov (United States)

Wang, Shujun; Copeland, Les

2015-01-01

Acid hydrolysis is an important chemical modification that can significantly change the structural and functional properties of starch without disrupting its granular morphology. A deep understanding of the effect of acid hydrolysis on starch structure and functionality is of great importance for starch scientific research and its industrial applications. During acid hydrolysis, amorphous regions are hydrolyzed preferentially, which enhances the crystallinity and double helical content of acid hydrolyzed starch. This review discusses current understanding of the effect of acid hydrolysis on starch structure and functionality. The effects of acid hydrolysis on amylose content, chain length distribution of amylopectin molecules, molecular and crystalline organization (including lamellar structure) and granular morphology are considered. Functional properties discussed include swelling power, gelatinization, retrogradation, pasting, gel texture, and in vitro enzyme digestibility. The paper also highlights some promising applications of acid hydrolyzed starch (starch nanocrystals) in the preparation of biodegradable nanocomposites, bio-hydrogen, and slowly digestible starch-based healthy foods.

Local quark-hadron duality of nucleon spin structure functions with target mass corrections

International Nuclear Information System (INIS)

Dong, Y.B. . E-mail dongyb@mail.ihep.ac.cn; Chen, D.Y.

2007-01-01

Target mass corrections to nucleon spin structure functions are analyzed. Our results show that the corrections are important to the structure functions in a large x region. Moreover, they play a remarkable role to the local quark-hadron duality of the nucleon spin structure functions in three individual inelastic resonance production regions

On relation of momenta of structure functions of the composite systems with their simultaneous wave functions

International Nuclear Information System (INIS)

Linkevich, A.D.; Savrin, V.I.; Sanadze, V.V.; Skachkov, N.B.

1984-01-01

Calculation of hadron structure function (SF) comprising point objects is carried out. The obtained hadron SF is expressed by means of simultaneous relativistic wave functions of a composite particle. Exact calculation of hadron SF momenta in simultaneous formulation of quantum field theory off-energy surface is conducted. The given calculation of hadron SF is shown to result in their dependence on momentum transferred square (or square of total vector of energy-momentum of Compton scattering on a quark) whih is determined by the set of simultaneous hadron wave functions as bound state of quark (partons) in the considered case of non-structural quarks

Evidence for the functional significance of diazotroph community structure in soil.

Science.gov (United States)

Hsu, Shi-Fang; Buckley, Daniel H

2009-01-01

Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.

Extinction order and altered community structure rapidly disrupt ecosystem functioning.

Science.gov (United States)

Larsen, Trond H; Williams, Neal M; Kremen, Claire

2005-05-01

By causing extinctions and altering community structure, anthropogenic disturbances can disrupt processes that maintain ecosystem integrity. However, the relationship between community structure and ecosystem functioning in natural systems is poorly understood. Here we show that habitat loss appeared to disrupt ecosystem functioning by affecting extinction order, species richness and abundance. We studied pollination by bees in a mosaic of agricultural and natural habitats in California and dung burial by dung beetles on recently created islands in Venezuela. We found that large-bodied bee and beetle species tended to be both most extinction-prone and most functionally efficient, contributing to rapid functional loss. Simulations confirmed that extinction order led to greater disruption of function than predicted by random species loss. Total abundance declined with richness and also appeared to contribute to loss of function. We demonstrate conceptually and empirically how the non-random response of communities to disturbance can have unexpectedly large functional consequences.

Regge analysis of diffractive and leading baryon structure functions from deep inelastic scattering

International Nuclear Information System (INIS)

Batista, M.; Covolan, R.J.M.; Montanha, J.

2002-01-01

In this paper we present a combined analysis of the H1 data on leading baryon and diffractive structure functions from DIS, which are handled as two components of the same semi-inclusive process. The available structure function data are analyzed in a series of fits in which three main exchanges are taken into account: the Pomeron, Reggeon, and pion. For each of these contributions, Regge factorization of the correspondent structure function is assumed. By this procedure, we extract information about the interface between the diffractive, Pomeron-dominated, region and the leading proton spectrum, which is mostly ruled by secondary exchanges. One of the main results is that the relative Reggeon contribution to the semi-inclusive structure function is much smaller than the one obtained from an analysis of the diffractive structure function alone

Oblique photon expansion of QED structure functions

International Nuclear Information System (INIS)

Chahine, C.

1986-01-01

In the oblique photon expansion, the collinear part of photon emission is summed up to all orders in perturbation theory. The number of oblique or non-collinear photons is the expansion order. Unlike in perturbation theory, every term of the expansion is both infrared finite and gauge invariant. The zero oblique photon contribution to the electromagnetic structure tensor in QED is computed in detail. The behaviors of the structure functions F1 and F2 are discussed in the soft and ultra-soft limits

Nucleon deep-inelastic structure functions in a quark model with factorizability assumptions

International Nuclear Information System (INIS)

Linkevich, A.D.; Skachkov, N.B.

1979-01-01

Formula for structure functions of deep-inelastic electron scattering on nucleon is derived. For this purpose the dynamic model of factorizing quark amplitudes is used. It has been found that with increase of Q 2 transferred pulse square at great values of x kinemastic variable the decrease of structure function values is observed. At x single values the increase of structure function values is found. The comparison With experimental data shows a good agreement of the model with experiment

Staphylococcal Immune Evasion Proteins: Structure, Function, and Host Adaptation.

Science.gov (United States)

Koymans, Kirsten J; Vrieling, Manouk; Gorham, Ronald D; van Strijp, Jos A G

2017-01-01

Staphylococcus aureus is a successful human and animal pathogen. Its pathogenicity is linked to its ability to secrete a large amount of virulence factors. These secreted proteins interfere with many critical components of the immune system, both innate and adaptive, and hamper proper immune functioning. In recent years, numerous studies have been conducted in order to understand the molecular mechanism underlying the interaction of evasion molecules with the host immune system. Structural studies have fundamentally contributed to our understanding of the mechanisms of action of the individual factors. Furthermore, such studies revealed one of the most striking characteristics of the secreted immune evasion molecules: their conserved structure. Despite high-sequence variability, most immune evasion molecules belong to a small number of structural categories. Another remarkable characteristic is that S. aureus carries most of these virulence factors on mobile genetic elements (MGE) or ex-MGE in its accessory genome. Coevolution of pathogen and host has resulted in immune evasion molecules with a highly host-specific function and prevalence. In this review, we explore how these shared structures and genomic locations relate to function and host specificity. This is discussed in the context of therapeutic options for these immune evasion molecules in infectious as well as in inflammatory diseases.

A Structure-Function Study of RecA: The Structural Basis for ATP Specificity in the Strand Exchange Reaction

Science.gov (United States)

Gegner, Julie; Spruill, Natalie; Plesniak, Leigh A.

1999-11-01

The terms "structure" and "function" can assume a variety of meanings. In biochemistry, the "structure" of a protein can refer to its sequence of amino acids, the three-dimensional arrangement of atoms within a subunit, or the arrangement of subunits into a larger oligomeric or filamentous state. Likewise, the function of biological macromolecules can be examined at many levels. The function of a protein can be described by its role in an organism's survival or by a chemical reaction that it promotes. We have designed a three-part biochemical laboratory experiment that characterizes the structure and function of the Escherichia coli RecA protein. The first part examines the importance of RecA in the survival of bacteria that have been exposed to UV light. This is the broadest view of function of the enzyme. Second, the students use an in vitro assay of RecA whereby the protein promotes homologous recombination. Because RecA functions not catalytically, but rather stoichiometrically, in this recombination reaction, the oligomeric state of RecA in complex with DNA must also be discussed. Finally, through molecular modeling of X-ray crystallographic structures, students identify functionally important features of the ATP cofactor binding site of RecA.

Whole-brain functional connectivity predicted by indirect structural connections

DEFF Research Database (Denmark)

Røge, Rasmus; Ambrosen, Karen Marie Sandø; Albers, Kristoffer Jon

2017-01-01

Modern functional and diffusion magnetic resonance imaging (fMRI and dMRI) provide data from which macro-scale networks of functional and structural whole brain connectivity can be estimated. Although networks derived from these two modalities describe different properties of the human brain, the...

Nuclear structure functions at a future electron-ion collider

Science.gov (United States)

Aschenauer, E. C.; Fazio, S.; Lamont, M. A. C.; Paukkunen, H.; Zurita, P.

2017-12-01

The quantitative knowledge of heavy nuclei's partonic structure is currently limited to rather large values of momentum fraction x —robust experimental constraints below x ˜10-2 at low resolution scale Q2 are particularly scarce. This is in sharp contrast to the free proton's structure which has been probed in Deep Inelastic Scattering (DIS) measurements down to x ˜10-5 at perturbative resolution scales. The construction of an electron-ion collider (EIC) with a possibility to operate with a wide variety of nuclei, will allow one to explore the low-x region in much greater detail. In the present paper we simulate the extraction of the nuclear structure functions from measurements of inclusive and charm reduced cross sections at an EIC. The potential constraints are studied by analyzing simulated data directly in a next-to-leading order global fit of nuclear Parton Distribution Functions based on the recent EPPS16 analysis. A special emphasis is placed on studying the impact an EIC would have on extracting the nuclear gluon parton distribution function, the partonic component most prone to nonlinear effects at low Q2. In comparison to the current knowledge, we find that the gluon parton distribution function can be measured at an EIC with significantly reduced uncertainties.

Golgi structure formation, function, and post-translational modifications in mammalian cells.

Science.gov (United States)

Huang, Shijiao; Wang, Yanzhuang

2017-01-01

The Golgi apparatus is a central membrane organelle for trafficking and post-translational modifications of proteins and lipids in cells. In mammalian cells, it is organized in the form of stacks of tightly aligned flattened cisternae, and dozens of stacks are often linked laterally into a ribbon-like structure located in the perinuclear region of the cell. Proper Golgi functionality requires an intact architecture, yet Golgi structure is dynamically regulated during the cell cycle and under disease conditions. In this review, we summarize our current understanding of the relationship between Golgi structure formation, function, and regulation, with focus on how post-translational modifications including phosphorylation and ubiquitination regulate Golgi structure and on how Golgi unstacking affects its functions, in particular, protein trafficking, glycosylation, and sorting in mammalian cells.

Theoretical analysis of polarized structure functions

International Nuclear Information System (INIS)

Altarelli, G.; ); Ball, R.D.; Forte, S.; Ridolfi, G.

1998-01-01

We review the analysis of polarized structure function data using perturbative QCD and NLO We use the most recent experimental data to obtain updated results for polarized parton distributions, first moments and the strong coupling. We also discuss several theoretical issues involving in this analysis and in the interpretation of its results. Finally, we compare our results with other similar analyses in the recent literature. (author)

RANDOM FUNCTIONS AND INTERVAL METHOD FOR PREDICTING THE RESIDUAL RESOURCE OF BUILDING STRUCTURES

Directory of Open Access Journals (Sweden)

Shmelev Gennadiy Dmitrievich

2017-11-01

Full Text Available Subject: possibility of using random functions and interval prediction method for estimating the residual life of building structures in the currently used buildings. Research objectives: coordination of ranges of values to develop predictions and random functions that characterize the processes being predicted. Materials and methods: when performing this research, the method of random functions and the method of interval prediction were used. Results: in the course of this work, the basic properties of random functions, including the properties of families of random functions, are studied. The coordination of time-varying impacts and loads on building structures is considered from the viewpoint of their influence on structures and representation of the structures’ behavior in the form of random functions. Several models of random functions are proposed for predicting individual parameters of structures. For each of the proposed models, its scope of application is defined. The article notes that the considered approach of forecasting has been used many times at various sites. In addition, the available results allowed the authors to develop a methodology for assessing the technical condition and residual life of building structures for the currently used facilities. Conclusions: we studied the possibility of using random functions and processes for the purposes of forecasting the residual service lives of structures in buildings and engineering constructions. We considered the possibility of using an interval forecasting approach to estimate changes in defining parameters of building structures and their technical condition. A comprehensive technique for forecasting the residual life of building structures using the interval approach is proposed.

Informing the Structure of Executive Function in Children: A Meta-Analysis of Functional Neuroimaging Data

Science.gov (United States)

McKenna, Róisín; Rushe, T.; Woodcock, Kate A.

2017-01-01

The structure of executive function (EF) has been the focus of much debate for decades. What is more, the complexity and diversity provided by the developmental period only adds to this contention. The development of executive function plays an integral part in the expression of children's behavioral, cognitive, social, and emotional capabilities. Understanding how these processes are constructed during development allows for effective measurement of EF in this population. This meta-analysis aims to contribute to a better understanding of the structure of executive function in children. A coordinate-based meta-analysis was conducted (using BrainMap GingerALE 2.3), which incorporated studies administering functional magnetic resonance imaging (fMRI) during inhibition, switching, and working memory updating tasks in typical children (aged 6–18 years). The neural activation common across all executive tasks was compared to that shared by tasks pertaining only to inhibition, switching or updating, which are commonly considered to be fundamental executive processes. Results support the existence of partially separable but partially overlapping inhibition, switching, and updating executive processes at a neural level, in children over 6 years. Further, the shared neural activation across all tasks (associated with a proposed “unitary” component of executive function) overlapped to different degrees with the activation associated with each individual executive process. These findings provide evidence to support the suggestion that one of the most influential structural models of executive functioning in adults can also be applied to children of this age. However, the findings also call for careful consideration and measurement of both specific executive processes, and unitary executive function in this population. Furthermore, a need is highlighted for a new systematic developmental model, which captures the integrative nature of executive function in children. PMID

Detailed measurements of structure functions from nucleons and nuclei

CERN Multimedia

2002-01-01

The experiment will study deep inelastic muon nucleon scattering in a wide range of $Q^{2}$(1-200 (GeV/c)$^{2}$) and $x(0.005-0.75)$. The main aims of the experiment are: \\\\\\\\ a) Detailed measurements of the nuclear dependence of the structure function $F_{2}^{A}$, of $R = \\sigma_/\\sigma_{T}$ and of the cross-section for $J/\\psi$ production. They will provide a basis for the understanding of the EMC effect: the modification of quark and gluon distributions due to the nuclear environment. \\\\b) A simultaneous high luminosity measurement of the structure function $F_{2}$ on hydrogen and deuterium. This will provide substantially improved accuracy in the knowledge of the neutron structure function $F_{2}^{n}$, of $F_{2}^{p}-F_{2}^{n}$ and $F_{2}^{n}/F_{2}^{p}$ and their $Q^{2}$ dependence. Furthermore, the data will allow a determination of the strong coupling constant $\\alpha_{S}(Q^{2})$ with reduced experimental and theoretical uncertainties as well as of the ratio of the down to up quark distributions in the v...

Structure-function relations in physiology education: Where's the mechanism?

Science.gov (United States)

Lira, Matthew E; Gardner, Stephanie M

2017-06-01

Physiology demands systems thinking: reasoning within and between levels of biological organization and across different organ systems. Many physiological mechanisms explain how structures and their properties interact at one level of organization to produce emergent functions at a higher level of organization. Current physiology principles, such as structure-function relations, selectively neglect mechanisms by not mentioning this term explicitly. We explored how students characterized mechanisms and functions to shed light on how students make sense of these terms. Students characterized mechanisms as 1 ) processes that occur at levels of organization lower than that of functions; and 2 ) as detailed events with many steps involved. We also found that students produced more variability in how they characterized functions compared with mechanisms: students characterized functions in relation to multiple levels of organization and multiple definitions. We interpret these results as evidence that students see mechanisms as holding a more narrow definition than used in the biological sciences, and that students struggle to coordinate and distinguish mechanisms from functions due to cognitive processes germane to learning in many domains. We offer the instructional suggestion that we scaffold student learning by affording students opportunities to relate and also distinguish between these terms so central to understanding physiology. Copyright © 2017 the American Physiological Society.

Design and synthesis of diverse functional kinked nanowire structures for nanoelectronic bioprobes.

Science.gov (United States)

Xu, Lin; Jiang, Zhe; Qing, Quan; Mai, Liqiang; Zhang, Qingjie; Lieber, Charles M

2013-02-13

Functional kinked nanowires (KNWs) represent a new class of nanowire building blocks, in which functional devices, for example, nanoscale field-effect transistors (nanoFETs), are encoded in geometrically controlled nanowire superstructures during synthesis. The bottom-up control of both structure and function of KNWs enables construction of spatially isolated point-like nanoelectronic probes that are especially useful for monitoring biological systems where finely tuned feature size and structure are highly desired. Here we present three new types of functional KNWs including (1) the zero-degree KNW structures with two parallel heavily doped arms of U-shaped structures with a nanoFET at the tip of the "U", (2) series multiplexed functional KNW integrating multi-nanoFETs along the arm and at the tips of V-shaped structures, and (3) parallel multiplexed KNWs integrating nanoFETs at the two tips of W-shaped structures. First, U-shaped KNWs were synthesized with separations as small as 650 nm between the parallel arms and used to fabricate three-dimensional nanoFET probes at least 3 times smaller than previous V-shaped designs. In addition, multiple nanoFETs were encoded during synthesis in one of the arms/tip of V-shaped and distinct arms/tips of W-shaped KNWs. These new multiplexed KNW structures were structurally verified by optical and electron microscopy of dopant-selective etched samples and electrically characterized using scanning gate microscopy and transport measurements. The facile design and bottom-up synthesis of these diverse functional KNWs provides a growing toolbox of building blocks for fabricating highly compact and multiplexed three-dimensional nanoprobes for applications in life sciences, including intracellular and deep tissue/cell recordings.

Foot Type Biomechanics Part 2: are structure and anthropometrics related to function?

Science.gov (United States)

Mootanah, Rajshree; Song, Jinsup; Lenhoff, Mark W; Hafer, Jocelyn F; Backus, Sherry I; Gagnon, David; Deland, Jonathan T; Hillstrom, Howard J

2013-03-01

Many foot pathologies are associated with specific foot types. If foot structure and function are related, measurement of either could assist with differential diagnosis of pedal pathologies. Biomechanical measures of foot structure and function are related in asymptomatic healthy individuals. Sixty-one healthy subjects' left feet were stratified into cavus (n=12), rectus (n=27) and planus (n=22) foot types. Foot structure was assessed by malleolar valgus index, arch height index, and arch height flexibility. Anthropometrics (height and weight), age, and walking speed were measured. Foot function was assessed by center of pressure excursion index, peak plantar pressure, maximum force, and gait pattern parameters. Foot structure and anthropometric variables were entered into stepwise linear regression models to identify predictors of function. Measures of foot structure and anthropometrics explained 10-37% of the model variance (adjusted R(2)) for gait pattern parameters. When walking speed was included, the adjusted R(2) increased to 45-77% but foot structure was no longer a factor. Foot structure and anthropometrics predicted 7-47% of the model variance for plantar pressure and 16-64% for maximum force parameters. All multivariate models were significant (pFoot structure and function are related in asymptomatic healthy individuals. The structural parameters employed are basic measurements that do not require ionizing radiation and could be used in a clinical setting. Further research is needed to identify additional predictive parameters (plantar soft tissue characteristics, skeletal alignment, and neuromuscular control) and to include individuals with pathology. Copyright © 2012. Published by Elsevier B.V.

Impact of age and sex on normal left heart structure and function.

Science.gov (United States)

Hagström, Linn; Henein, Michael Y; Karp, Kjell; Waldenström, Anders; Lindqvist, Per

2017-11-01

Accurate age- and sex-related normal reference values of ventricular structure and function are important to determine the level of dysfunction in patients. The aim of this study therefore was to document normal age range sex-related measurements of LV structural and functional measurements to serve such purpose. We evaluated left ventricular structure and function in 293 healthy subjects between 20 and 90 years with equally distributed gender. Doppler echocardiography was used including measure of both systolic and diastolic functions. Due to systolic LV function, only long axis function correlated with age (r = 0·55, P<0·01) and the correlation was stronger in females. Concerning diastolic function, there was a strong age correlation in all parameters used (r = 0·40-0·74, P<0·001). Due to LV structural changes over age, females showed a larger reduction in end-diastolic volumes, but no or trivial difference in wall thickness after the age of 60 years. Age is associated with significant normal changes in left ventricular structure and function, which should be considered when deciding on normality. These changes are related to systemic arterial changes as well as body stature, thus reflecting overall body ageing process. Furthermore, normal cardiac ageing in females might partly explain the higher prevalence of heart failure with preserved ejection in females. © 2016 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

Precision measurement of the neutron spin dependent structure functions

International Nuclear Information System (INIS)

Kolomensky, Y.G.

1997-02-01

In experiment E154 at the Stanford Linear Accelerator Center the spin dependent structure function g 1 n (x, Q 2 ) of the neutron was measured by scattering longitudinally polarized 48.3 GeV electrons off a longitudinally polarized 3 He target. The high beam energy allowed the author to extend the kinematic coverage compared to the previous SLAC experiments to 0.014 ≤ x ≤ 0.7 with an average Q 2 of 5 GeV 2 . The author reports the integral of the spin dependent structure function in the measured range to be ∫ 0.014 0.7 dx g 1 n (x, 5 GeV 2 ) = -0.036 ± 0.004(stat.) ± 0.005(syst.). The author observes relatively large values of g 1 n at low x that call into question the reliability of data extrapolation to x → 0. Such divergent behavior disagrees with predictions of the conventional Regge theory, but is qualitatively explained by perturbative QCD. The author performs a Next-to-Leading Order perturbative QCD analysis of the world data on the nucleon spin dependent structure functions g 1 p and g 1 n paying careful attention to the experimental and theoretical uncertainties. Using the parameterizations of the helicity-dependent parton distributions obtained in the analysis, the author evolves the data to Q 2 = 5 GeV 2 , determines the first moments of the polarized structure functions of the proton and neutron, and finds agreement with the Bjorken sum rule

Structure functions in electron-nucleon deep inelastic scattering

Energy Technology Data Exchange (ETDEWEB)

Saleem, M.; Fazal-E-Aleem (University of the Punjab, Lahore (Pakistan). Dept. of Physics)

1982-06-26

The phenomenological expressions for the structure functions in electron-nucleon deep inelastic scattering are proposed and are shown to satisfy the experimental data as well as a number of sum rules.

Functional brain connectivity is predictable from anatomic network's Laplacian eigen-structure.

Science.gov (United States)

Abdelnour, Farras; Dayan, Michael; Devinsky, Orrin; Thesen, Thomas; Raj, Ashish

2018-05-15

How structural connectivity (SC) gives rise to functional connectivity (FC) is not fully understood. Here we mathematically derive a simple relationship between SC measured from diffusion tensor imaging, and FC from resting state fMRI. We establish that SC and FC are related via (structural) Laplacian spectra, whereby FC and SC share eigenvectors and their eigenvalues are exponentially related. This gives, for the first time, a simple and analytical relationship between the graph spectra of structural and functional networks. Laplacian eigenvectors are shown to be good predictors of functional eigenvectors and networks based on independent component analysis of functional time series. A small number of Laplacian eigenmodes are shown to be sufficient to reconstruct FC matrices, serving as basis functions. This approach is fast, and requires no time-consuming simulations. It was tested on two empirical SC/FC datasets, and was found to significantly outperform generative model simulations of coupled neural masses. Copyright © 2018. Published by Elsevier Inc.

An estimation of the structure function xF3 in neutrino-proton scattering

International Nuclear Information System (INIS)

Aoki, Kenzaburo; Arimoto, Shinsuke; Hoshino, Shigetoshi; Itoh, Nobuhisa; Konno, Toshiharu.

1981-01-01

The structure function xF 3 (x, Q 2 ) in the deep-inelastic neutrino-proton scattering was estimated without differentiating with respect to Q 2 in the evolution function. At first, the moment of the non-singlet structure function xF 3 (x, Q 2 ) is defined. Then, the kernel function f(z, Q 2 ) is presented. Finally, the expression for the structure function xF 3 is given. The values of the structure function for various Q 2 are shown in five figures. A peak is seen in each figure, and the highest peak is at about Q 2 = 14GeV 2 . The analysis suggests very small value of xF 3 in small Q 2 region. The kernel function f(x/y, Q 2 ) may be interpreted as the probability of finding a quark of momentum fraction x arising from that of y is quantum chromodynamics. (Kato, T.)

Proton structure functions in the dipole picture of BFKL dynamics

International Nuclear Information System (INIS)

Navelet, H.; Peschanski, R.; Wallon, S.; Royon, Ch.

1996-06-01

The proton structure functions are derived in the QCD dipole picture. Assuming k T and renormalization-group factorization, deep-inelastic proton scattering is related to deep-inelastic onium scattering. A three parameter fit of the 1994 H1 data in the low-x, moderate Q 2 range has been obtained. The dipole picture of BFKL dynamics is shown to provide a relevant model for quantitatively describing the proton structure functions at HERA. (author)

NAC transcription factors: structurally distinct, functionally diverse

DEFF Research Database (Denmark)

Olsen, Addie Nina; Ernst, Heidi A; Leggio, Leila Lo

2005-01-01

level and localization, and to the first indications of NAC participation in transcription factor networks. The recent determination of the DNA and protein binding NAC domain structure offers insight into the molecular functions of the protein family. Research into NAC transcription factors has......NAC proteins constitute one of the largest families of plant-specific transcription factors, and the family is present in a wide range of land plants. Here, we summarize the biological and molecular functions of the NAC family, paying particular attention to the intricate regulation of NAC protein...

Structure-function relationships of human meniscus.

Science.gov (United States)

Danso, Elvis K; Oinas, Joonas M T; Saarakkala, Simo; Mikkonen, Santtu; Töyräs, Juha; Korhonen, Rami K

2017-03-01

Biomechanical properties of human meniscus have been shown to be site-specific. However, it is not known which meniscus constituents at different depths and locations contribute to biomechanical properties obtained from indentation testing. Therefore, we investigated the composition and structure of human meniscus in a site- and depth-dependent manner and their relationships with tissue site-specific biomechanical properties. Elastic and poroelastic properties were analyzed from experimental stress-relaxation and sinusoidal indentation measurements with fibril reinforced poroelastic finite element modeling. Proteoglycan (PG) and collagen contents, as well as the collagen orientation angle, were determined as a function of tissue depth using microscopic and spectroscopic methods, and they were compared with biomechanical properties. For all the measurement sites (anterior, middle and posterior) of lateral and medial menisci (n=26), PG content and collagen orientation angle increased as a function of tissue depth while the collagen content had an initial sharp increase followed by a decrease across tissue depth. The highest values (pmeniscus. This location had also higher (pmeniscus, higher (pmeniscus) significantly higher (pmeniscus modulus and/or nonlinear permeability. This study suggests that nonlinear biomechanical properties of meniscus, caused by the collagen network and fluid, may be strongly influenced by tissue osmotic swelling from the deep meniscus caused by the increased PG content, leading to increased collagen fibril tension. These nonlinear biomechanical properties are suggested to be further amplified by higher collagen content at all tissue depths and superficial collagen fibril orientation. However, these structure-function relationships are suggested to be highly site-specific. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural and functional characterization of human complement factor P

DEFF Research Database (Denmark)

Pedersen, Dennis

not yet been resolved. This PhD-thesis provide structural understanding of the FP mediated stabilization of the AP C3 convertase. Furthermore, functional studies involving oligomeric and monomeric FP variants have helped us to understand the importance of FP oligomerization for the primary functions of FP...... of complement by stabilizing the C3 convertase complex (C3bBb). FP has also been suggested to serve as a pattern recognition molecule for the initiation of the alternative pathway. However, the molecular mechanisms of FP remain unclear due to its oligomeric nature and hence the atomic structure of FP has...

Functional and Structural Brain Changes Associated with Methamphetamine Abuse

Directory of Open Access Journals (Sweden)

Bruce R. Russell

2012-10-01

Full Text Available Methamphetamine (MA is a potent psychostimulant drug whose abuse has become a global epidemic in recent years. Firstly, this review article briefly discusses the epidemiology and clinical pharmacology of methamphetamine dependence. Secondly, the article reviews relevant animal literature modeling methamphetamine dependence and discusses possible mechanisms of methamphetamine-induced neurotoxicity. Thirdly, it provides a critical review of functional and structural neuroimaging studies in human MA abusers; including positron emission tomography (PET and functional and structural magnetic resonance imaging (MRI. The effect of abstinence from methamphetamine, both short- and long-term within the context of these studies is also reviewed.

Structural and regulatory functions of keratins

International Nuclear Information System (INIS)

Magin, Thomas M.; Vijayaraj, Preethi; Leube, Rudolf E.

2007-01-01

The diversity of epithelial functions is reflected by the expression of distinct keratin pairs that are responsible to protect epithelial cells against mechanical stress and to act as signaling platforms. The keratin cytoskeleton integrates these functions by forming a supracellular scaffold that connects at desmosomal cell-cell adhesions. Multiple human diseases and murine knockouts in which the integrity of this system is destroyed testify to its importance as a mechanical stabilizer in certain epithelia. Yet, surprisingly little is known about the precise mechanisms responsible for assembly and disease pathology. In addition to these structural aspects of keratin function, experimental evidence accumulating in recent years has led to a much more complex view of the keratin cytoskeleton. Distinct keratins emerge as highly dynamic scaffolds in different settings and contribute to cell size determination, translation control, proliferation, cell type-specific organelle transport, malignant transformation and various stress responses. All of these properties are controlled by highly complex patterns of phosphorylation and molecular associations

Towards aspect-oriented functional--structural plant modelling.

Science.gov (United States)

Cieslak, Mikolaj; Seleznyova, Alla N; Prusinkiewicz, Przemyslaw; Hanan, Jim

2011-10-01

Functional-structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty. The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element's function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module. The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes. This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In a future work, this approach could be further

Deep-inelastic structure functions in an approximation to the bag theory

International Nuclear Information System (INIS)

Jaffe, R.L.

1975-01-01

A cavity approximation to the bag theory developed earlier is extended to the treatment of forward virtual Compton scattering. In the Bjorken limit and for small values of ω (ω = vertical-bar2p center-dot q/q 2 vertical-bar) it is argued that the operator nature of the bag boundaries might be ignored. Structure functions are calculated in one and three dimensions. Bjorken scaling is obtained. The model provides a realization of light-cone current algebra and possesses a parton interpretation. The structure functions show a quasielastic peak. The spreading of the structure functions about the peak is associated with confinement. As expected, Regge behavior is not obtained for large ω. The ''momentum sum rule'' is saturated, indicating that the hadron's charged constituents carry all the momentum in this model. νW/subL/ is found to scale and is calculable. Application of the model to the calculation of spin-dependent and chiral-symmetry--violating structure functions is proposed. The nature of the intermediate states in this approximation is discussed. Problems associated with the cavity approximation are also discussed

Theoretical Analysis of Polarized Structure Functions

CERN Document Server

Altarelli, Guido; Forte, Stefano; Ridolfi, G

1998-01-01

We review the analysis of polarized structure function data using perturbative QCD at next-to-leading order. We use the most recent experimental data to obtain updated results for polarized parton distributions, first moments and the strong coupling. We also discuss several theoretical issues involved in this analysis and in the interpretation of its results. Finally, we compare our results with other similar analyses in the recent literature.

Leading twist moments of the neutron structure function F_2n

Energy Technology Data Exchange (ETDEWEB)

M. Osipenko; W. Melnitchouk; S. Simula; S. Kulagin; G. Ricco

2005-10-20

We perform a global analysis of neutron $F_2^n$ structure function data, obtained by combining proton and deuteron measurements over a large range of kinematics. From these data the lowest moments ($n \\leq 10$) of the leading twist neutron $F_2^n$ structure function are extracted. Particular attention is paid to nuclear effects in the deuteron, which become increasingly important for the higher moments. Our results for the nonsinglet, isovector $p - n$ combination of the leading twist moments are compared with those of available lattice simulations. We also determine the lowest few moments of the higher twist contributions, obtained by subtracting the leading twist from the total structure function, and analyze their isospin dependence.

Determination of the pion and kaon structure functions

International Nuclear Information System (INIS)

Aitkenhead, W.; Barton, D.S.; Brandenburg, G.W.; Busza, W.; Dobrowolski, T.; Friedman, J.I.; Kendall, H.W.; Lyons, T.; Nelson, B.; Rosenson, L.; Toy, W.; Verdier, R.; Votta, L.; Chiaradia, M.T.; DeMarzo, C.; Favuzzi, C.; Germinario, G.; Guerriero, L.; LaVopa, P.; Maggi, G.; Posa, F.; Selvaggi, G.; Spinelli, P.; Waldner, F.; Brenner, A.E.; Carey, D.C.; Elias, J.E.; Garbincius, P.H.; Mikenberg, G.; Polychronakos, V.A.; Meunier, R.; Cutts, D.; Dulude, R.S.; Lanou, R.E. Jr.; Massimo, J.T.

1980-01-01

Quark structure functions have been extracted from low-p/sub T/ inclusive hadron production data for the pion and kaon with use of the recombination model. n/sup π/=1.0 +- 0.1 and n/sup K/=2.5 +- 0.6 is obtained, where n is the leading (1-x) power of the nonstrange--valence-quark distribution. Both the pion and kaon nonstrange--sea-quark functions have napprox. =3.5

Structure functions and pair correlations of the quark-gluon plasma

International Nuclear Information System (INIS)

Thoma, Markus H.

2005-01-01

Recent experiments at RHIC and theoretical considerations indicate that the quark-gluon plasma, present in the fireball of relativistic heavy-ion collisions, might be in a liquid phase. The liquid state can be identified by characteristic correlation and structure functions. Here definitions of the structure functions and pair correlations of the quark-gluon plasma are presented as well as perturbative results. These definitions might be useful for verifying the quark-gluon-plasma liquid in QCD lattice calculations

Review: Evolution of GnIH structure and function

Directory of Open Access Journals (Sweden)

Tomohiro eOsugi

2014-08-01

Full Text Available Discovery of gonadotropin-inhibitory hormone (GnIH in the Japanese quail in 2000 was the first to demonstrate the existence of a hypothalamic neuropeptide inhibiting gonadotropin release. We now know that GnIH regulates reproduction by inhibiting gonadotropin synthesis and release via action on the gonadotropin-releasing hormone (GnRH system and the gonadotrope in various vertebrates. GnIH peptides identified in birds and mammals have a common LPXRF-amide (X = L or Q motif at the C-terminus and inhibits pituitary gonadotropin secretion. However, the function and structure of GnIH peptides were diverse in fish. Goldfish GnIHs possessing a C-terminal LPXRF-amide motif had both stimulatory and inhibitory effects on gonadotropin synthesis or release. The C-terminal sequence of grass puffer and medaka GnIHs were MPQRF-amide. To investigate the evolutionary origin of GnIH and its ancestral structure and function, we searched for GnIH in agnathans, the most ancient lineage of vertebrates. We identified GnIH precursor gene and mature GnIH peptides with C-terminal QPQRF-amide or RPQRF-amide from the brain of sea lamprey. Lamprey GnIH fibers were in close proximity to GnRH-III neurons. Further, one of lamprey GnIHs stimulated the expression of lamprey GnRH-III peptide in the hypothalamus and gonadotropic hormone β mRNA expression in the pituitary. We further identified the ancestral form of GnIH, which had a C-terminal RPQRF-amide, and its receptors in amphioxus, the most basal chordate species. The amphioxus GnIH inhibited cAMP signaling in vitro. In sum, the original forms of GnIH may date back to the time of the emergence of early chordates. GnIH peptides may have had various C-terminal structures slightly different from LPXRF-amide in basal chordates, which had stimulatory and/or inhibitory functions on reproduction. The C-terminal LPXRF-amide structure and its inhibitory function on reproduction may be selected in later-evolved vertebrates, such as

Phenomenological structure functions and Gribov-Lipatov relation

International Nuclear Information System (INIS)

Choudhary, D.K.; Misra, A.K.

1987-01-01

An analysis of the Giribov-Lipatov relation using the phenomenological forms of the structure function F 2 ep is made. The analysis indicate breakdown of the relation at PETRA energies. Plausible reasons of the breakdown of Gribov-Lipatov relation are discussed together with its phenomenological form. 33 refs., 6 figures. (author)

Class I Cytokine Receptors: Structure and function in the Membrane

DEFF Research Database (Denmark)

Bugge, Katrine Østergaard

bilayer via structural characterizations of TMD representatives. To enable structural studies of these domains, an organic-extraction based strategy for efficient production of isotope-labeled TMDs with or without short intrinsically disordered regions was developed. This strategy successfully provided...... of these challenging domains. Supplemented by a review of the current collection of TMD structures from single-pass transmembrane receptors, the thesis as a whole provides important insights on the structure and function in the membrane as well as highlight the open questions to be addressed in the years to come.......Class I cytokine receptors are involved in important biological functions of both physiological and pathological nature in mammals. However, the molecular details of the cross-membrane signal transduction through these receptors remain obscure. One of the major reasons for this is the lack...

When structure affects function--the need for partial volume effect correction in functional and resting state magnetic resonance imaging studies.

Science.gov (United States)

Dukart, Juergen; Bertolino, Alessandro

2014-01-01

Both functional and also more recently resting state magnetic resonance imaging have become established tools to investigate functional brain networks. Most studies use these tools to compare different populations without controlling for potential differences in underlying brain structure which might affect the functional measurements of interest. Here, we adapt a simulation approach combined with evaluation of real resting state magnetic resonance imaging data to investigate the potential impact of partial volume effects on established functional and resting state magnetic resonance imaging analyses. We demonstrate that differences in the underlying structure lead to a significant increase in detected functional differences in both types of analyses. Largest increases in functional differences are observed for highest signal-to-noise ratios and when signal with the lowest amount of partial volume effects is compared to any other partial volume effect constellation. In real data, structural information explains about 25% of within-subject variance observed in degree centrality--an established resting state connectivity measurement. Controlling this measurement for structural information can substantially alter correlational maps obtained in group analyses. Our results question current approaches of evaluating these measurements in diseased population with known structural changes without controlling for potential differences in these measurements.

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.

KAUST Repository

Kosinski, Jan; Barbato, Alessandro; Tramontano, Anna

2013-01-01

SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.

KAUST Repository

Kosinski, Jan

2013-02-08

SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Structure-function relationship in complex brain networks expressed by hierarchical synchronization

International Nuclear Information System (INIS)

Zhou Changsong; Zemanova, Lucia; Zamora-Lopez, Gorka; Hilgetag, Claus C; Kurths, Juergen

2007-01-01

The brain is one of the most complex systems in nature, with a structured complex connectivity. Recently, large-scale corticocortical connectivities, both structural and functional, have received a great deal of research attention, especially using the approach of complex network analysis. Understanding the relationship between structural and functional connectivity is of crucial importance in neuroscience. Here we try to illuminate this relationship by studying synchronization dynamics in a realistic anatomical network of cat cortical connectivity. We model the nodes (cortical areas) by a neural mass model (population model) or by a subnetwork of interacting excitable neurons (multilevel model). We show that if the dynamics is characterized by well-defined oscillations (neural mass model and subnetworks with strong couplings), the synchronization patterns are mainly determined by the node intensity (total input strengths of a node) and the detailed network topology is rather irrelevant. On the other hand, the multilevel model with weak couplings displays more irregular, biologically plausible dynamics, and the synchronization patterns reveal a hierarchical cluster organization in the network structure. The relationship between structural and functional connectivity at different levels of synchronization is explored. Thus, the study of synchronization in a multilevel complex network model of cortex can provide insights into the relationship between network topology and functional organization of complex brain networks

Structure-function relationship in complex brain networks expressed by hierarchical synchronization

Energy Technology Data Exchange (ETDEWEB)

Zhou Changsong [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Zemanova, Lucia [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Zamora-Lopez, Gorka [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Hilgetag, Claus C [Jacobs University Bremen, Campus Ring 6, Rm 116, D-28759 Bremen (Germany); Kurths, Juergen [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany)

2007-06-15

The brain is one of the most complex systems in nature, with a structured complex connectivity. Recently, large-scale corticocortical connectivities, both structural and functional, have received a great deal of research attention, especially using the approach of complex network analysis. Understanding the relationship between structural and functional connectivity is of crucial importance in neuroscience. Here we try to illuminate this relationship by studying synchronization dynamics in a realistic anatomical network of cat cortical connectivity. We model the nodes (cortical areas) by a neural mass model (population model) or by a subnetwork of interacting excitable neurons (multilevel model). We show that if the dynamics is characterized by well-defined oscillations (neural mass model and subnetworks with strong couplings), the synchronization patterns are mainly determined by the node intensity (total input strengths of a node) and the detailed network topology is rather irrelevant. On the other hand, the multilevel model with weak couplings displays more irregular, biologically plausible dynamics, and the synchronization patterns reveal a hierarchical cluster organization in the network structure. The relationship between structural and functional connectivity at different levels of synchronization is explored. Thus, the study of synchronization in a multilevel complex network model of cortex can provide insights into the relationship between network topology and functional organization of complex brain networks.

Multi-subject Manifold Alignment of Functional Network Structures via Joint Diagonalization.

Science.gov (United States)

Nenning, Karl-Heinz; Kollndorfer, Kathrin; Schöpf, Veronika; Prayer, Daniela; Langs, Georg

2015-01-01

Functional magnetic resonance imaging group studies rely on the ability to establish correspondence across individuals. This enables location specific comparison of functional brain characteristics. Registration is often based on morphology and does not take variability of functional localization into account. This can lead to a loss of specificity, or confounds when studying diseases. In this paper we propose multi-subject functional registration by manifold alignment via coupled joint diagonalization. The functional network structure of each subject is encoded in a diffusion map, where functional relationships are decoupled from spatial position. Two-step manifold alignment estimates initial correspondences between functionally equivalent regions. Then, coupled joint diagonalization establishes common eigenbases across all individuals, and refines the functional correspondences. We evaluate our approach on fMRI data acquired during a language paradigm. Experiments demonstrate the benefits in matching accuracy achieved by coupled joint diagonalization compared to previously proposed functional alignment approaches, or alignment based on structural correspondences.

Functional hypergraph uncovers novel covariant structures over neurodevelopment.

Science.gov (United States)

Gu, Shi; Yang, Muzhi; Medaglia, John D; Gur, Ruben C; Gur, Raquel E; Satterthwaite, Theodore D; Bassett, Danielle S

2017-08-01

Brain development during adolescence is marked by substantial changes in brain structure and function, leading to a stable network topology in adulthood. However, most prior work has examined the data through the lens of brain areas connected to one another in large-scale functional networks. Here, we apply a recently developed hypergraph approach that treats network connections (edges) rather than brain regions as the unit of interest, allowing us to describe functional network topology from a fundamentally different perspective. Capitalizing on a sample of 780 youth imaged as part of the Philadelphia Neurodevelopmental Cohort, this hypergraph representation of resting-state functional MRI data reveals three distinct classes of subnetworks (hyperedges): clusters, bridges, and stars, which respectively represent homogeneously connected, bipartite, and focal architectures. Cluster hyperedges show a strong resemblance to previously-described functional modules of the brain including somatomotor, visual, default mode, and salience systems. In contrast, star hyperedges represent highly localized subnetworks centered on a small set of regions, and are distributed across the entire cortex. Finally, bridge hyperedges link clusters and stars in a core-periphery organization. Notably, developmental changes within hyperedges are ordered in a similar core-periphery fashion, with the greatest developmental effects occurring in networked hyperedges within the functional core. Taken together, these results reveal a novel decomposition of the network organization of human brain, and further provide a new perspective on the role of local structures that emerge across neurodevelopment. Hum Brain Mapp 38:3823-3835, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Structural and functional networks in complex systems with delay.

Science.gov (United States)

Eguíluz, Víctor M; Pérez, Toni; Borge-Holthoefer, Javier; Arenas, Alex

2011-05-01

Functional networks of complex systems are obtained from the analysis of the temporal activity of their components, and are often used to infer their unknown underlying connectivity. We obtain the equations relating topology and function in a system of diffusively delay-coupled elements in complex networks. We solve exactly the resulting equations in motifs (directed structures of three nodes) and in directed networks. The mean-field solution for directed uncorrelated networks shows that the clusterization of the activity is dominated by the in-degree of the nodes, and that the locking frequency decreases with increasing average degree. We find that the exponent of a power law degree distribution of the structural topology γ is related to the exponent of the associated functional network as α=(2-γ)(-1) for γ<2. © 2011 American Physical Society

Structural and functional hyperconnectivity within the sensorimotor system in xenomelia.

Science.gov (United States)

Hänggi, Jürgen; Vitacco, Deborah A; Hilti, Leonie M; Luechinger, Roger; Kraemer, Bernd; Brugger, Peter

2017-03-01

Xenomelia is a rare condition characterized by the persistent and compulsive desire for the amputation of one or more physically healthy limbs. We highlight the neurological underpinnings of xenomelia by assessing structural and functional connectivity by means of whole-brain connectome and network analyses of regions previously implicated in empirical research in this condition. We compared structural and functional connectivity between 13 xenomelic men with matched controls using diffusion tensor imaging combined with fiber tractography and resting state functional magnetic resonance imaging. Altered connectivity in xenomelia within the sensorimotor system has been predicted. We found subnetworks showing structural and functional hyperconnectivity in xenomelia compared with controls. These subnetworks were lateralized to the right hemisphere and mainly comprised by nodes belonging to the sensorimotor system. In the connectome analyses, the paracentral lobule, supplementary motor area, postcentral gyrus, basal ganglia, and the cerebellum were hyperconnected to each other, whereas in the xenomelia-specific network analyses, hyperconnected nodes have been found in the superior parietal lobule, primary and secondary somatosensory cortex, premotor cortex, basal ganglia, thalamus, and insula. Our study provides empirical evidence of structural and functional hyperconnectivity within the sensorimotor system including those regions that are core for the reconstruction of a coherent body image. Aberrant connectivity is a common response to focal neurological damage. As exemplified here, it may affect different brain regions differentially. Due to the small sample size, our findings must be interpreted cautiously and future studies are needed to elucidate potential associations between hyperconnectivity and limb disownership reported in xenomelia.

On the twist-2 contributions to polarized structure functions and new sum rules

International Nuclear Information System (INIS)

Bluemlein, J.; Kochelev, N.

1996-03-01

The twist-2 contributions to the polarized structure functions in deep inelastic lepton-hadron scattering are calculated including the exchange of weak bosons and using both the operator product expansion and the covariant parton model. A new relation between two structure functions leading to a sequence of new sum rules is found. The light quark mass corrections to the structure functions are derived in lowest order QCD. (orig.)

Supramolecular Structure and Function 9

CERN Document Server

Pifat-Mrzljak, Greta

2007-01-01

The book is based on International Summer Schools on Biophysics held in Croatia which, contrary to other workshops centered mainly on one topic or technique, has very broad scope providing advanced training in areas related to biophysics. This volume is presenting papers in the field of biophysics for studying biological phenomena by using physical methods (NMR, EPR, FTIR, Mass Spectrometry, etc.) and/or concepts (predictions of protein-protein interactions, virtual ligand screening etc.). The interrelationship of supramolecular structures and there functions is enlightened by applications of principals of these physical methods in the biophysical and molecular biology context.

Measurement of the electron structure function F{sub 2}{sup e} at LEP energies

Energy Technology Data Exchange (ETDEWEB)

Abdallah, J. [LPNHE, IN2P3-CNRS, Univ. Paris VI et VII, 4 place Jussieu, FR-75252 Paris Cedex 05 (France); Abreu, P. [LIP, IST, FCUL, Av. Elias Garcia, 14-1" o, PT-1000 Lisboa Codex (Portugal); Adam, W. [Institut für Hochenergiephysik, Österr. Akad. d. Wissensch., Nikolsdorfergasse 18, AT-1050 Vienna (Austria); Adzic, P. [Institute of Nuclear Physics, N.C.S.R. Demokritos, P.O. Box 60228, GR-15310 Athens (Greece); Albrecht, T. [Institut für Experimentelle Kernphysik, Universität Karlsruhe, Postfach 6980, DE-76128 Karlsruhe (Germany); Alemany-Fernandez, R. [CERN, CH-1211 Geneva 23 (Switzerland); Allmendinger, T. [Institut für Experimentelle Kernphysik, Universität Karlsruhe, Postfach 6980, DE-76128 Karlsruhe (Germany); Allport, P.P. [Department of Physics, University of Liverpool, P.O. Box 147, Liverpool L69 3BX (United Kingdom); Amaldi, U. [Dipartimento di Fisica, Univ. di Milano-Bicocca and INFN-Milano, Piazza della Scienza 3, IT-20126 Milan (Italy); Amapane, N. [Dipartimento di Fisica Sperimentale, Università di Torino and INFN, Via P. Giuria 1, IT-10125 Turin (Italy); Amato, S. [Univ. Federal do Rio de Janeiro, C.P. 68528 Cidade Univ., Ilha do Fundão, BR-21945-970 Rio de Janeiro (Brazil); Anashkin, E. [Dipartimento di Fisica, Università di Padova and INFN, Via Marzolo 8, IT-35131 Padua (Italy); Andreazza, A. [Dipartimento di Fisica, Università di Milano and INFN-Milano, Via Celoria 16, IT-20133 Milan (Italy); Andringa, S.; Anjos, N. [LIP, IST, FCUL, Av. Elias Garcia, 14-1" o, PT-1000 Lisboa Codex (Portugal); Antilogus, P. [LPNHE, IN2P3-CNRS, Univ. Paris VI et VII, 4 place Jussieu, FR-75252 Paris Cedex 05 (France); and others

2014-10-07

The hadronic part of the electron structure function F{sub 2}{sup e} has been measured for the first time, using e{sup +}e{sup −} data collected by the DELPHI experiment at LEP, at centre-of-mass energies of √(s)=91.2–209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The electron structure function F{sub 2}{sup e} data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the contribution of large target photon virtualities is significant. The data presented can serve as a cross-check of the photon structure function F{sub 2}{sup γ} analyses and help in refining existing parameterisations.

Structural and functional properties of alkali-treated high-amylose rice starch.

Science.gov (United States)

Cai, Jinwen; Yang, Yang; Man, Jianmin; Huang, Jun; Wang, Zhifeng; Zhang, Changquan; Gu, Minghong; Liu, Qiaoquan; Wei, Cunxu

2014-02-15

Native starches were isolated from mature grains of high-amylose transgenic rice TRS and its wild-type rice TQ and treated with 0.1% and 0.4% NaOH for 7 and 14 days at 35 °C. Alkali-treated starches were characterised for structural and functional properties using various physical methods. The 0.1% NaOH treatment had no significant effect on structural and functional properties of starches except that it markedly increased the hydrolysis of starch by amylolytic enzymes. The 0.4% NaOH treatment resulted in some changes in structural and functional properties of starches. The alkali treatment affected granule morphology and decreased the electron density between crystalline and amorphous lamellae of starch. The effect of alkali on the crystalline structure including long- and short-range ordered structure was not pronounced. Compared with control starch, alkali-treated TRS starches had lower amylose content, higher onset and peak gelatinisation temperatures, and faster hydrolysis of starch by HCl and amylolytic enzymes. Copyright © 2013 Elsevier Ltd. All rights reserved.

The Candida albicans Biofilm Matrix: Composition, Structure and Function.

Science.gov (United States)

Pierce, Christopher G; Vila, Taissa; Romo, Jesus A; Montelongo-Jauregui, Daniel; Wall, Gina; Ramasubramanian, Anand; Lopez-Ribot, Jose L

2017-03-01

A majority of infections caused by Candida albicans -the most frequent fungal pathogen-are associated with biofilm formation. A salient feature of C. albicans biofilms is the presence of the biofilm matrix. This matrix is composed of exopolymeric materials secreted by sessile cells within the biofilm, in which all classes of macromolecules are represented, and provides protection against environmental challenges. In this review, we summarize the knowledge accumulated during the last two decades on the composition, structure, and function of the C. albicans biofilm matrix. Knowledge of the matrix components, its structure, and function will help pave the way to novel strategies to combat C. albicans biofilm infections.

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.

Science.gov (United States)

Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2015-01-01

Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and

FACTOR STRUCTURE OF FUNCTIONAL CAPABILITIES OF BODYBUILDERS

Directory of Open Access Journals (Sweden)

Predrag Milenović

2007-05-01

Full Text Available It is evident that researches in the fi eld of kineziology and sports sciences on the topic of body-building here are very rare mainly and probably because of its place in the system of hyerarchy of sports. Lack of interest in body-building and its insuffi cient popularization springs probably, among other things, from its different interpretation and, according to some people, from its ultimate goals which are not justifi ed by many. Others, experts from the fi eld of body-building, starting from the basic principles of its exercising point out its numerous positive characteristics and sides. Undoubtedly, characteristics of functional capabilities of sportspeople are specifi c for each sport or discipline. In body-building the functional sphere is bordered and defi ned by the nature of the sport’s activity itself, as well as by genetics and internal and external factors in a very complex training process of a bodu-builder. The goal of this research was determining the structure of the functional sphere of a body-builder. It was performed on the sample of 30 selected sportsmen, body-builders, of chronological age between 17 and 19 ( 6 months, members of the Sports' Club Strength ''Leskovac'', the Weight Lifters' Club '' Dubočica'' and the Body-building Club '' Dubočica'' from Leskovac. All the examiees have been submitted to training processes during a period longer than a year. For the purpose of determining the structure of the morphological sphere the Factor Analysis has been applied. Based on the data from the matrix of the Factor Structure the isolated factors can be interpreted in the following manner: The fi rst isolated factor in the sphere of applied functional variables is best defi ned by the variable of pulse under stress (FPUOP and the variable of maximum Oxygen consumption in liters per minute (FOLM. This isolated factor can be defi ned as a dimension of the transportation system of Oxygen. The second isolated factor in the

Soil-structure interaction analysis by Green function

International Nuclear Information System (INIS)

Muto, Kiyoshi; Kobayashi, Toshio; Nakahara, Mitsuharu.

1985-01-01

Using the method of discretized Green function which had been suggested by the authors, the parametric study of the effects of base mat foundation thickness and soil stiffness were conducted. There was no upper structure effects from the response and reaction stress of the soil by employing different base mat foundation thicknesses. However, the response stress of base mat itself had considerable effect on the base mat foundation stress. The harder the soil, became larger accelerations, and smaller displacements on the upper structure. The upper structure lines of force were directed onto the soil. In the case of soft soil, the reaction soil stress were distributed evenly over the entire reactor building area. Common characteristics of all cases, in-plane shear deformation of the upper floor occured and in-plane acceleration and displacement at the center of the structure become larger. Also, the soil stresses around the shield wall of the base mat foundation became large cecause of the effect of the shield wall bending. (Kubozono, M.)

Electron-beam induced structural and function change of microbial peroxiredoxin

Energy Technology Data Exchange (ETDEWEB)

Hong, S. H.; An, B. C.; Lee, S. S.; Lee, E. M.; Chung, B. Y. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2012-03-15

Pseudomonas aerogenes peroxiredoxin (PaPrx) has dual functions acting as thioredoxin (Trx)-dependent peroxidase and molecular chaperone. The function of PaPrx is controlled by its structural status. In this study, we examined the effect of electron beam on structural modification related to chaperone activity. When irradiated electron beam at 1 kGy, the structural and functional changes of PaPrx were initiated. The enhanced chaperone activity was increased about 3- 40 4-fold at 2 kGy compared with non-irradiated, while the peroxidase activity was decreased. We also investigated the influence of the electron beam on protein physical property factors such as hydrophobicity and secondary structure. The exposure of hydrophobic domains reached a peak at 2 kGy of electron beam and then dose-dependently decreased with increasing electron beam irradiation. In addition, the electron beam irradiated PaPrx significantly increased exposure of {beta}-sheet and random coil elements on the protein surface whereas exposure of {alpha}-helix and turn elements was decreased. Our results suggest that highly enhanced chaperone activity could be applied to use in bio-engineering system and various industrial applications.

Electron-beam induced structural and function change of microbial peroxiredoxin

International Nuclear Information System (INIS)

Hong, S. H.; An, B. C.; Lee, S. S.; Lee, E. M.; Chung, B. Y.

2012-01-01

Pseudomonas aerogenes peroxiredoxin (PaPrx) has dual functions acting as thioredoxin (Trx)-dependent peroxidase and molecular chaperone. The function of PaPrx is controlled by its structural status. In this study, we examined the effect of electron beam on structural modification related to chaperone activity. When irradiated electron beam at 1 kGy, the structural and functional changes of PaPrx were initiated. The enhanced chaperone activity was increased about 3- 40 4-fold at 2 kGy compared with non-irradiated, while the peroxidase activity was decreased. We also investigated the influence of the electron beam on protein physical property factors such as hydrophobicity and secondary structure. The exposure of hydrophobic domains reached a peak at 2 kGy of electron beam and then dose-dependently decreased with increasing electron beam irradiation. In addition, the electron beam irradiated PaPrx significantly increased exposure of β-sheet and random coil elements on the protein surface whereas exposure of α-helix and turn elements was decreased. Our results suggest that highly enhanced chaperone activity could be applied to use in bio-engineering system and various industrial applications

Psychedelics Promote Structural and Functional Neural Plasticity

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Calvin Ly

2018-06-01

Full Text Available Summary: Atrophy of neurons in the prefrontal cortex (PFC plays a key role in the pathophysiology of depression and related disorders. The ability to promote both structural and functional plasticity in the PFC has been hypothesized to underlie the fast-acting antidepressant properties of the dissociative anesthetic ketamine. Here, we report that, like ketamine, serotonergic psychedelics are capable of robustly increasing neuritogenesis and/or spinogenesis both in vitro and in vivo. These changes in neuronal structure are accompanied by increased synapse number and function, as measured by fluorescence microscopy and electrophysiology. The structural changes induced by psychedelics appear to result from stimulation of the TrkB, mTOR, and 5-HT2A signaling pathways and could possibly explain the clinical effectiveness of these compounds. Our results underscore the therapeutic potential of psychedelics and, importantly, identify several lead scaffolds for medicinal chemistry efforts focused on developing plasticity-promoting compounds as safe, effective, and fast-acting treatments for depression and related disorders. : Ly et al. demonstrate that psychedelic compounds such as LSD, DMT, and DOI increase dendritic arbor complexity, promote dendritic spine growth, and stimulate synapse formation. These cellular effects are similar to those produced by the fast-acting antidepressant ketamine and highlight the potential of psychedelics for treating depression and related disorders. Keywords: neural plasticity, psychedelic, spinogenesis, synaptogenesis, depression, LSD, DMT, ketamine, noribogaine, MDMA

Human astrocytes: structure and functions in the healthy brain.

Science.gov (United States)

Vasile, Flora; Dossi, Elena; Rouach, Nathalie

2017-07-01

Data collected on astrocytes' physiology in the rodent have placed them as key regulators of synaptic, neuronal, network, and cognitive functions. While these findings proved highly valuable for our awareness and appreciation of non-neuronal cell significance in brain physiology, early structural and phylogenic investigations of human astrocytes hinted at potentially different astrocytic properties. This idea sparked interest to replicate rodent-based studies on human samples, which have revealed an analogous but enhanced involvement of astrocytes in neuronal function of the human brain. Such evidence pointed to a central role of human astrocytes in sustaining more complex information processing. Here, we review the current state of our knowledge of human astrocytes regarding their structure, gene profile, and functions, highlighting the differences with rodent astrocytes. This recent insight is essential for assessment of the relevance of findings using animal models and for comprehending the functional significance of species-specific properties of astrocytes. Moreover, since dysfunctional astrocytes have been described in many brain disorders, a more thorough understanding of human-specific astrocytic properties is crucial for better-adapted translational applications.

Catchment Classification: Connecting Climate, Structure and Function

Science.gov (United States)

Sawicz, K. A.; Wagener, T.; Sivapalan, M.; Troch, P. A.; Carrillo, G. A.

2010-12-01

Hydrology does not yet possess a generally accepted catchment classification framework. Such a classification framework needs to: [1] give names to things, i.e. the main classification step, [2] permit transfer of information, i.e. regionalization of information, [3] permit development of generalizations, i.e. to develop new theory, and [4] provide a first order environmental change impact assessment, i.e., the hydrologic implications of climate, land use and land cover change. One strategy is to create a catchment classification framework based on the notion of catchment functions (partitioning, storage, and release). Results of an empirical study presented here connects climate and structure to catchment function (in the form of select hydrologic signatures), based on analyzing over 300 US catchments. Initial results indicate a wide assortment of signature relationships with properties of climate, geology, and vegetation. The uncertainty in the different regionalized signatures varies widely, and therefore there is variability in the robustness of classifying ungauged basins. This research provides insight into the controls of hydrologic behavior of a catchment, and enables a classification framework applicable to gauged and ungauged across the study domain. This study sheds light on what we can expect to achieve in mapping climate, structure and function in a top-down manner. Results of this study complement work done using a bottom-up physically-based modeling framework to generalize this approach (Carrillo et al., this session).

Hormonal regulation of alveolarization: structure-function correlation

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Godinez Marye H

2006-03-01

Full Text Available Abstract Background Dexamethasone (Dex limits and all-trans-retinoic acid (RA promotes alveolarization. While structural changes resulting from such hormonal exposures are known, their functional consequences are unclear. Methods Neonatal rats were treated with Dex and/or RA during the first two weeks of life or were given RA after previous exposure to Dex. Morphology was assessed by light microscopy and radial alveolar counts. Function was evaluated by plethysmography at d13, pressure volume curves at d30, and exercise swim testing and arterial blood gases at both d15 and d30. Results Dex-treated animals had simplified lung architecture without secondary septation. Animals given RA alone had smaller, more numerous alveoli. Concomitant treatment with Dex + RA prevented the Dex-induced changes in septation. While the results of exposure to Dex + RA were sustained, the effects of RA alone were reversed two weeks after treatment was stopped. At d13, Dex-treated animals had increased lung volume, respiratory rate, tidal volume, and minute ventilation. On d15, both RA- and Dex-treated animals had hypercarbia and low arterial pH. By d30, the RA-treated animals resolved this respiratory acidosis, but Dex-treated animals continued to demonstrate blood gas and lung volume abnormalities. Concomitant RA treatment improved respiratory acidosis, but failed to normalize Dex-induced changes in pulmonary function and lung volumes. No differences in exercise tolerance were noted at either d15 or d30. RA treatment after the period of alveolarization also corrected the effects of earlier Dex exposure, but the structural changes due to RA alone were again lost two weeks after treatment. Conclusion We conclude that both RA- and corticosteroid-treatments are associated with respiratory acidosis at d15. While RA alone-induced changes in structure andrespiratory function are reversed, Dex-treated animals continue to demonstrate increased respiratory rate, minute

A Determination of the Neutron Spin Structure Function

Energy Technology Data Exchange (ETDEWEB)

Hughes, Emlyn W

2003-08-18

The authors report the results of the experiment E142 which measured the spin dependent structure function of the neutron, g{sub 1}{sup n}(x, Q{sup 2}). The experiment was carried out at the Stanford Linear Accelerator Center by measuring an asymmetry in the deep inelastic scattering of polarized electrons from a polarized {sup 3}He target, at electron energies from 19 to 26 GeV. The structure function was determined over the kinematic range 0.03 < BJorken x < 0.6 and 1.0 < Q{sup 2} < 5.5 (GeV/c){sup 2}. An evaluation of the integral {integral}{sub 0}{sup 1} g{sub 1}{sup n}(x,Q{sup 2})dx at fixed Q{sup 2} = 2 (GeV/c){sup 2} yields the final result {Lambda}{sub 1}{sup n} = -0.032 {+-} 0.006 (stat.) {+-} 0.009 (syst.). This result, when combined with the integral of the proton spin structure function measured in other experiments, confirms the fundamental Bjorken sum rule with O({alpha}{sub s}{sup 3}) corrections to within one standard deviation. This is a major success for perturbative Quantum Chromodynamics. Some ancillary results include the findings that the Ellis-Jaffe sum rule for the neutron is violated at the 2 {sigma} level, and that the total contribution of the quarks to the helicity of the nucleon is 0.36 {+-} 0.10. The strange sea polarization is estimated to be small and negative, {Delta}s = -0.07 {+-} 0.04.

Integration of structural and functional magnetic resonance imaging in amyotrophic lateral sclerosis.

Science.gov (United States)

Douaud, Gwenaëlle; Filippini, Nicola; Knight, Steven; Talbot, Kevin; Turner, Martin R

2011-12-01

Amyotrophic lateral sclerosis as a system failure is a concept supported by the finding of consistent extramotor as well as motor cerebral pathology. The functional correlates of the structural changes detected using advanced magnetic resonance imaging techniques such as diffusion tensor imaging and voxel-based morphometry have not been extensively studied. A group of 25 patients with amyotrophic lateral sclerosis was compared to healthy control subjects using a multi-modal neuroimaging approach comprising T(1)-weighted, diffusion-weighted and resting-state functional magnetic resonance imaging. Using probabilistic tractography, a grey matter connection network was defined based upon the prominent corticospinal tract and corpus callosum involvement demonstrated by white matter tract-based spatial statistics. This 'amyotrophic lateral sclerosis-specific' network included motor, premotor and supplementary motor cortices, pars opercularis and motor-related thalamic nuclei. A novel analysis protocol, using this disease-specific grey matter network as an input for a dual-regression analysis, was then used to assess changes in functional connectivity directly associated with this network. A spatial pattern of increased functional connectivity spanning sensorimotor, premotor, prefrontal and thalamic regions was found. A composite of structural and functional magnetic resonance imaging measures also allowed the qualitative discrimination of patients from controls. An integrated structural and functional connectivity approach therefore identified apparently dichotomous processes characterizing the amyotrophic lateral sclerosis cerebral network failure, in which there was increased functional connectivity within regions of decreased structural connectivity. Patients with slower rates of disease progression showed connectivity measures with values closer to healthy controls, raising the possibility that functional connectivity increases might not simply represent a

Functional and structural balances of homologous sensorimotor regions in multiple sclerosis fatigue

DEFF Research Database (Denmark)

Cogliati Dezza, I; Zito, G; Tomasevic, L

2015-01-01

regions-known to be crucial for sensorimotor networks effectiveness-decrease with MS fatigue increase. Functional connectivity measures at rest and during a simple motor task (weak handgrip of either the right or left hand) were derived from primary sensorimotor areas electroencephalographic recordings......Fatigue in multiple sclerosis (MS) is a highly disabling symptom. Among the central mechanisms behind it, an involvement of sensorimotor networks is clearly evident from structural and functional studies. We aimed at assessing whether functional/structural balances of homologous sensorimotor...... in 27 mildly disabled MS patients. Structural MRI-derived inter-hemispheric asymmetries included the cortical thickness of Rolandic regions and the volume of thalami. Fatigue symptoms increased together with the functional inter-hemispheric imbalance of sensorimotor homologous areas activities at rest...

Political ideology: its structure, functions, and elective affinities.

Science.gov (United States)

Jost, John T; Federico, Christopher M; Napier, Jaime L

2009-01-01

Ideology has re-emerged as an important topic of inquiry among social, personality, and political psychologists. In this review, we examine recent theory and research concerning the structure, contents, and functions of ideological belief systems. We begin by defining the construct and placing it in historical and philosophical context. We then examine different perspectives on how many (and what types of) dimensions individuals use to organize their political opinions. We investigate (a) how and to what extent individuals acquire the discursive contents associated with various ideologies, and (b) the social-psychological functions that these ideologies serve for those who adopt them. Our review highlights "elective affinities" between situational and dispositional needs of individuals and groups and the structure and contents of specific ideologies. Finally, we consider the consequences of ideology, especially with respect to attitudes, evaluations, and processes of system justification.

Phenotypic analysis of newly isolated short-lifespan Neurospora crassa mutant deficient in a high mobility group box protein.

Science.gov (United States)

Yoshihara, Ryouhei; Li, ZhengHao; Ishimori, Keisuke; Kuwabara, Kazuki; Hatakeyama, Shin; Tanaka, Shuuitsu

2017-08-01

To elucidate genetic mechanisms affecting the lifespan of the filamentous fungus Neurospora crassa, we attempted to identify a gene of which a defect causes a short-lifespan. By screening a Neurospora knockout library, provided by the Fungal Genetics Stock Center at Kansas State University, several KO strains with a short-lifespan were isolated. FGSC#11693 is one of these, which shows similar phenotypes to known Neurospora short-lifespan mutants as follows: 1) hyphal growth ceases after about 2weeks of cultivation, despite that of the wild-type continuing for over 2years, 2) viability of conidia is lower than that of the wild-type, and 3) high sensitivity to mutagens such as methyl methanesulfonate, ultraviolet radiation, and hydroxyl urea is exhibited. The NCU number of the knocked-out gene in the KO strain is NCU02695, and recovery from the short-lifespan and mutagen sensitivity was achieved by the introduction of this gene from the wild-type. The putative amino acid sequence of the knocked-out gene contains two high mobility group box domains and a mitochondrial localization signal is found at the N-terminal of this sequence. Upon analyzing the subcellular localization of the gene product fused with GFP, GFP signals were detected in mitochondria. From these observations, the gene and KO strain were named mitochondrial high mobility group box protein 1 (MHG1) and mhg1 KO strain, respectively. The amount of mtDNA relative to the nuclear amount was lower in the mhg1 KO strain than in the wild-type. mtDNA aberration was also observed in the mhg1 KO strain. These results suggest that the MHG1 protein plays an important role in the maintenance of mitochondrial DNA, and mitochondrial abnormality caused by mtDNA aberration is responsible for the short-lifespan of the mhg1 KO strain. Copyright © 2017 Elsevier Inc. All rights reserved.