bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromosome-encoded gene cluster for the metabolic pathway that converts aniline to TCA-cycle intermediates in Delftia tsuruhatensis AD9
Authors: Liang Quanfeng , Takeo Masahiro , Chen Ming , Zhang Wei , Xu Yuquan , Lin Min
Published: October 2005

Delftia tsuruhatensis AD9 was isolated as an aniline-degrading bacterium from the soil surrounding a textile dyeing plant. The gene cluster involved in aniline degradation was cloned from the total DNA of strain AD9 into Escherichia coli JM109. After shotgun cloning, two recombinant E. coli strains showing aniline oxidation activity or catechol meta-cleavage activity were obtained by simple plate assays. These strains contained 9·3 kb and 15·4 kb DNA fragments, respectively. Sequence analysis of the total 24·7 kb region revealed that this region contains a gene cluster (consisting of at least 17 genes, named tadQTA1A2BRD1C1D2C2EFGIJKL) responsible for the complete metabolism of aniline to TCA-cycle intermediates. In the gene cluster, the first five genes (tadQTA1A2B) and the subsequent gene (tadR) were predicted to encode a multi-component aniline dioxygenase and a LysR-type regulator, respectively, while the others (tadD1C1D2C2EFGIJKL) were expected to encode meta-cleavage pathway enzymes for catechol degradation. In addition, it was found that the gene cluster is surrounded by two IS1071 sequences, indicating that it has a class I transposon-like structure. PFGE and Southern hybridization analyses confirmed that the tad gene cluster is encoded on the chromosome of strain AD9 in a single copy. These results suggest that, in strain AD9, aniline is degraded via catechol through a meta-cleavage pathway by the chromosome-encoded tad gene cluster. The tad gene cluster showed significant similarity in nucleotide sequence and genetic organization to the plasmid-encoded aniline degradation gene cluster of Pseudomonas putida UCC22.
A Continent of Plant Defense Peptide Diversity: Cyclotides in AustralianHybanthus(Violaceae)
Authors: Simonsen Shane M. , Sando Lillian , Ireland David C. , Colgrave Michelle L. , Bharathi Rekha , Göransson Ulf , Craik David J.
Published: October 2005

Cyclotides are plant-derived miniproteins that have the unusual features of a head-to-tail cyclized peptide backbone and a knotted arrangement of disulfide bonds. It had been postulated that they might be an especially large family of host defense agents, but this had not yet been tested by field data on cyclotide variation in wild plant populations. In this study, we sampled Australian Hybanthus (Violaceae) to gain an insight into the level of variation within populations, within species, and between species. A wealth of cyclotide diversity was discovered: at least 246 new cyclotides are present in the 11 species sampled, and 26 novel sequences were characterized. A new approach to the discovery of cyclotide sequences was developed based on the identification of a conserved sequence within a signal sequence in cyclotide precursors. The number of cyclotides in the Violaceae is now estimated to be >9000. Cyclotide physicochemical profiles were shown to be a useful taxonomic feature that reflected species and their morphological relationships. The novel sequences provided substantial insight into the tolerance of the cystine knot framework in cyclotides to amino acid substitutions and will facilitate protein engineering applications of this framework.
Auxin Response Factors MediateArabidopsisOrgan Asymmetry via Modulation of KANADI Activity
Authors: Pekker Irena , Alvarez John Paul , Eshed Yuval
Published: October 2005

Members of the KANADI gene family in Arabidopsis thaliana regulate abaxial identity and laminar growth of lateral organs. Promoter APETALA3-mediated ectopic expression of KANADI restricts petal expansion and was used in a genetic screen for factors involved in KANADI-mediated signaling. Through this screen, mutations in ETTIN (ETT; also known as Auxin Response Factor3 [ARF3]) were isolated as second site suppressors and found to ameliorate ectopic KANADI activity throughout the plant as well. Mutant phenotypes of ett are restricted to flowers; however, double mutants with a closely related gene ARF4 exhibit transformation of abaxial tissues into adaxial ones in all aerial parts, resembling mutations in KANADI. Accordingly, the common RNA expression domain of both ARFs was found to be on the abaxial side of all lateral organs. Truncated, negatively acting gene products of strong ett alleles map to an ARF-specific, N-terminal domain of ETT. Such gene products strongly enhance abaxial tissue loss only when ARF activities are compromised. As KANADI is not required for either ETT or ARF4 transcription, and their overexpression cannot rescue kanadi mutants, cooperative activity is implied. ARF proteins are pivotal in mediating auxin responses; thus, we present a model linking transient local auxin gradients and gradual partitioning of lateral organs along the abaxial/adaxial axis.
RNA Interference Identifies a Calcium-Dependent Protein Kinase Involved inMedicago truncatulaRoot Development
Authors: Ivashuta Sergey , Liu Jinyuan , Liu Junqi , Lohar Dasharath P. , Haridas Sajeet , Bucciarelli Bruna , VandenBosch Kathryn A. , Vance Carroll P. , Harrison Maria J. , Gantt J. Stephen
Published: October 2005

Changes in cellular or subcellular Ca2+ concentrations play essential roles in plant development and in the responses of plants to their environment. However, the mechanisms through which Ca2+ acts, the downstream signaling components, as well as the relationships among the various Ca2+-dependent processes remain largely unknown. Using an RNA interference–based screen for gene function in Medicago truncatula, we identified a gene that is involved in root development. Silencing Ca2+-dependent protein kinase1 (CDPK1), which is predicted to encode a Ca2+-dependent protein kinase, resulted in significantly reduced root hair and root cell lengths. Inactivation of CDPK1 is also associated with significant diminution of both rhizobial and mycorrhizal symbiotic colonization. Additionally, microarray analysis revealed that silencing CDPK1 alters cell wall and defense-related gene expression. We propose that M. truncatula CDPK1 is a key component of one or more signaling pathways that directly or indirectly modulates cell expansion or cell wall synthesis, possibly altering defense gene expression and symbiotic interactions.
Mutation of the TGD1 Chloroplast Envelope Protein Affects Phosphatidate Metabolism inArabidopsis
Authors: Xu Changcheng , Fan Jilian , Froehlich John E. , Awai Koichiro , Benning Christoph
Published: October 2005

Phosphatidate (PA) is a central metabolite of lipid metabolism and a signaling molecule in many eukaryotes, including plants. Mutations in a permease-like protein, TRIGALACTOSYLDIACYLGLYCEROL1 (TGD1), in Arabidopsis thaliana caused the accumulation of triacylglycerols, oligogalactolipids, and PA. Chloroplast lipids were altered in their fatty acid composition consistent with an impairment of lipid trafficking from the endoplasmic reticulum (ER) to the chloroplast and a disruption of thylakoid lipid biosynthesis from ER-derived precursors. The process mediated by TGD1 appears to be essential as mutation of the protein caused a high incidence of embryo abortion. Isolated tgd1 mutant chloroplasts showed a decreased ability to incorporate PA into galactolipids. The TGD1 protein was localized to the inner chloroplast envelope and appears to be a component of a lipid transporter. As even partial disruption of TGD1 function has drastic consequences on central lipid metabolism, the tgd1 mutant provides a tool to explore regulatory mechanisms governing lipid homeostasis and lipid trafficking in plants.
Novel surfactant mixtures for NMR spectroscopy of encapsulated proteins dissolved in low‐viscosity fluids
Authors: Peterson Ronald W. , Pometun Maxim S. , Shi Zhengshuang , Wand A. Joshua
Published: October 2005

NMR spectroscopy of encapsulated proteins dissolved in low‐viscosity fluids is emerging as a tool for biophysical studies of proteins in atomic detail in a variety of otherwise inaccessible contexts. The central element of the approach is the encapsulation of the protein of interest within the aqueous core of a reverse micelle with high structural fidelity. The process of encapsulation is highly dependent upon the nature of the surfactant(s) employed. Here we describe novel mixtures of surfactants that are capable of successfully encapsulating a range of types of proteins under a variety of conditions.
Thermodynamic analysis of the aggregation propensity of oxidized Alzheimer's β‐amyloid variants
Authors: Hortschansky Peter , Christopeit Tony , Schroeckh Volker , Fändrich Marcus
Published: October 2005

We have determined the critical concentrations of a set of 18 variants of Alzheimer's Aβ(1–40) peptide, each carrying a different residue at position 18. We find that the critical concentrations depend on the hydrophobicity and β‐sheet propensity of residue 18, and therefore on properties that we identified previously to affect also the kinetics by which these peptides aggregate. Since the critical concentrations can be related to the Gibbs free energy of aggregation (ΔG), these data imply a link between the thermodynamics and the kinetics of aggregation in that sequences that form very stable aggregates are also those that form such aggregates very rapidly.
Identifying putative Mycobacterium tuberculosis Rv2004c protein sequences that bind specifically to U937 macrophages and A549 epithelial cells
Authors: Forero Martha , Puentes Álvaro , Cortés Jimena , Castillo Fabio , Vera Ricardo , Rodríguez Luis E. , Valbuena John , Ocampo Marisol , Curtidor Hernando , Rosas Jaiver , García Javier , Barrera Gloria , Alfonso Rosalba , Patarroyo Manuel A. , Patarroyo Manuel E.
Published: October 2005

Virulence and immunity are still poorly understood in Mycobacterium tuberculosis. The H37Rv M. tuberculosis laboratory strain genome has been completely sequenced, and this along with proteomic technology represent powerful tools contributing toward studying the biology of target cell interaction with a facultative bacillus and designing new strategies for controlling tuberculosis. Rv2004c is a putative M. tuberculosis protein that could have specific mycobacterial functions. This study has revealed that the encoding gene is present in all mycobacterium species belonging to the M. tuberculosis complex. Rv2004c gene transcription was observed in all of this complex's strains except Mycobacterium bovis and Mycobacterium microti. Rv2004c protein expression was confirmed by using antibodies able to recognize a 54‐kDa molecule by immunoblotting, and its location was detected on the M. tuberculosis surface by transmission electron microscopy, suggesting that it is a mycobacterial surface protein. Binding assays led to recognizing high activity binding peptides (HABP); five HABPs specifically bound to U937 cells, and six specifically bound to A549 cells. HABP circular dichroism suggested that they had an α‐helical structure. HABP–target cell interaction was determined to be specific and saturable; some of them also displayed greater affinity for A549 cells than U937 cells. The critical amino acids directly involved in their interaction with U937 cells were also determined. Two probable receptor molecules were found on U937 cells and five on A549 for the two HABPs analyzed. These observations have important biological significance for studying bacillus–target cell interactions and implications for developing strategies for controlling this disease.
High‐affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement
Authors: Dutta Sanjib , Batori Vincent , Koide Akiko , Koide Shohei
Published: October 2005

The tenth fibronectin type III (FN3) domain of human fibronectin (FNfn10), a prototype of the ubiquitous FN3 domain, is a small, monomeric β‐sandwich protein. In this study, we have bisected FNfn10 in each loop to generate a total of six fragment pairs. We found that fragment pairs bisected at multiple loops of FNfn10 show complementation in vivo as tested with a yeast two‐hybrid system. The dissociation constant of these fragment pairs determined in vitro were as low as 3 nM, resulting in one of the tightest fragment complementation systems reported so far. Furthermore, we show that the affinity of fragment complementation is correlated with the stability of the uncut parent protein. Exploring this correlation, we screened a yeast two‐hybrid library of one fragment and identified mutations that suppress the effect of a destabilizing mutation in the other fragment. One of the identified mutations significantly increased the stability of the uncut wild‐type protein, proving that fragment complementation can be used as a novel strategy for the selection of proteins with enhanced stability.
The crystal structure of the cis‐proline to glycine variant (P114G) of ribonuclease A
Authors: Schultz David A. , Friedman Alan M. , White Mark A. , Fox Robert O.
Published: October 2005

Replacement of a cis‐proline by glycine at position 114 in ribonuclease A leads to a large decrease in thermal stability and simplifies the refolding kinetics. A crystallographic approach was used to determine whether the decrease in thermal stability results from the presence of a cis glycine peptide bond, or from a localized structural rearrangement caused by the isomerization of the mutated cis 114 peptide bond. The structure was solved at 2.0 Å resolution and refined to an R‐factor of 19.5% and an Rfree of 21.9%. The overall conformation of the protein was similar to that of wild‐type ribonuclease A; however, there was a large localized rearrangement of the mutated loop (residues 110–117—a 9.3 Å shift of the Cα atom of residue 114). The peptide bond before Gly114 is in the trans configuration. Interestingly, a large anomalous difference density was found near residue 114, and was attributed to a bound cesium ion present in the crystallization experiment. The trans isomeric configuration of the peptide bond in the folded state of this mutant is consistent with the refolding kinetics previously reported, and the associated protein conformational change provides an explanation for the decreased thermal stability.
Misfolding of a bacterial autotransporter
Authors: Mogensen Jesper E. , Kleinschmidt Jörg H. , Schmidt M. Alexander , Otzen Daniel E.
Published: October 2005

The adhesin involved in diffuse adherence (AIDA) is an autotransporter protein that confers the diffuse adherence phenotype to certain diarrheagenic Escherichia coli strains. It consists of a 49 amino acid signal peptide, a 797 amino acid passenger domain, and a 440 amino acid β‐domain integrated into the outer membrane. The β‐domain consists of two parts: the β1‐domain, which is predicted to form two β‐strands on the bacterial cell surface, and the β2‐domain, which constitutes the transmembrane domain. We have previously shown that the β‐domain can be folded from the urea‐denatured state when bound to a nickel column during purification. It has not been possible to achieve proper refolding of the β‐domain in solution; instead, a misfolded state C is formed. Here, we characterize this misfolded state in greater detail, showing that despite being misfolded, C can be analyzed as a conventional conformational state, with cooperative unfolding in urea and SDS as well as showing simple exponential kinetics during its formation in the presence of lipid vesicles and detergent micelles. The kinetics of formation of C is sensitive to the lipid composition in vesicles. We have also attempted to identify biological factors that might aid folding of the β‐domain to the properly folded state. However, no purified periplasmic or cytosolic chaperone was found to increase folding yields, and no factor in a periplasmic extract was identified that could bind to C. We conclude that it is the exposure to the unique spatial arrangement of the bacterial cell that leads to proper refolding of the β‐domain.
Conformational changes accompany phosphorylation of the epidermal growth factor receptor C‐terminal domain
Authors: Lee Nam Y. , Koland John G.
Published: October 2005

The precise regulation of epidermal growth factor receptor (EGFR) signaling is crucial to its function in cellular growth control. Various studies have suggested that the C‐terminal phosphorylation domain, itself a substrate for the EGFR kinase activity, exerts a regulatory influence upon it, although the molecular mechanism for this regulation is unknown. The fluorescence resonance energy transfer (FRET) technique was employed to examine how C‐terminal domain conformational changes in the context of receptor activation and autophosphorylation might regulate EGFR enzymatic activity. A novel FRET reporter system was devised in which recombinant purified EGFR intracellular domain (ICD) proteins of varying C‐terminal lengths were site‐specifically labeled at their extreme C termini with blue fluorescent protein (BFP) and a fluorescent nucleotide analog, 2′(3′)‐O‐(2,4,6‐trinitrophenyl)‐adenosine 5′‐triphosphate (TNP‐ATP), binding at their active sites. This novel BFP/TNP‐ATP FRET pair demonstrated efficient energy transfer as evidenced by appreciable BFP‐donor quenching by bound TNP‐ATP. In particular, a marked reduction in energy transfer was observed for the full‐length BFP‐labeled EGFR‐ICD protein upon phosphorylation, likely reflecting its movement away from the active site. The estimated distances from the BFP module to the TNP‐ATP‐occupied active site for the full‐length and C‐terminally truncated proteins also reveal the possible folding geometry of this domain with respect to the kinase core. The present studies demonstrate the first use of BFP/TNP‐ATP as a FRET reporter system. Furthermore, the results described here provide biophysical evidence for phosphorylation‐dependent conformational changes in the C‐terminal phosphorylation domain and its likely interaction with the kinase core.
Specificity and reversibility of the transpeptidation reaction catalyzed by the Streptomyces R61 D‐Ala‐D‐Ala peptidase
Authors: Rhazi Noureddine , Delmarcelle Michael , Sauvage Eric , Jacquemotte Françoise , Devriendt Kris , Tallon Valérie , Ghosez Léon , Frère Jean‐Marie
Published: October 2005

The specificity of the Streptomyces R61 penicillin‐sensitive D‐Ala‐D‐Ala peptidase has been re‐examined with the help of synthetic substrates. The products of the transpeptidation reactions obtained with Gly‐L‐Xaa dipeptides as acceptor substrates are themselves poor substrates of the enzyme. This is in apparent contradiction with the classically accepted specificity rules for D‐Ala‐D‐Ala peptidases. The Gly‐L‐Xaa dipeptide is regenerated by both the hydrolysis and transpeptidation reactions. The latter reaction is observed when another Gly‐L‐Xaa peptide or D‐Alanine are supplied as acceptors. Utilization of substrates in which the terminal ‐COO− group has been esterified or amidated shows that a free carboxylate is not an absolute prerequisite for activity. The results are discussed in the context of the expected reversibilty of the transpeptidation reaction.
Structure of a shark IgNAR antibody variable domain and modeling of an early‐developmental isotype
Authors: Streltsov Victor A. , Carmichael Jennifer A. , Nuttall Stewart D.
Published: October 2005

The new antigen receptor (IgNAR) antibodies from sharks are disulphide bonded dimers of two protein chains, each containing one variable and five constant domains. Three types of IgNAR variable domains have been discovered, with Type 3 appearing early in shark development and being overtaken by the antigen‐driven affinity‐matured Type 1 and 2 response. Here, we have determined the first structure of a naturally occurring Type 2 IgNAR variable domain, and identified the disulphide bond that links and stabilizes the CDR1 and CDR3 loops. This disulphide bridge locks the CDR3 loop in an “upright” conformation in contrast to other shark antibody structures, where a more lateral configuration is observed. Further, we sought to model the Type 3 isotype based on the crystallographic structure reported here. This modeling indicates (1) that internal Type 3‐specific residues combine to pack into a compact immunoglobulin core that supports the CDR loop regions, and (2) that despite apparent low‐sequence variability, there is sufficient plasticity in the CDR3 loop to form a conformationally diverse antigen‐binding surface.
Crystal structure of the N‐terminal domain of E. coli Lon protease
Authors: Li Mi , Rasulova Fatima , Melnikov Edward E. , Rotanova Tatyana V. , Gustchina Alla , Maurizi Michael R. , Wlodawer Alexander
Published: October 2005

We report here the first crystal structure of the N‐terminal domain of an A‐type Lon protease. Lon proteases are ubiquitous, multidomain, ATP‐dependent enzymes with both highly specific and non‐specific protein binding, unfolding, and degrading activities. We expressed and purified a stable, monomeric 119‐amino acid N‐terminal subdomain of the Escherichia coli A‐type Lon protease and determined its crystal structure at 2.03 Å (Protein Data Bank [PDB] code 2ANE). The structure was solved in two crystal forms, yielding 14 independent views. The domain exhibits a unique fold consisting primarily of three twisted β‐sheets and a single long α‐helix. Analysis of recent PDB depositions identified a similar fold in BPP1347 (PDB code 1ZBO), a 203‐amino acid protein of unknown function from Bordetella parapertussis, crystallized as part of a structural genomics effort. BPP1347 shares sequence homology with Lon N‐domains and with a family of other independently expressed proteins of unknown functions. We postulate that, as is the case in Lon proteases, this structural domain represents a general protein and polypeptide interaction domain.
NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: Implications for 216 homologous DUF59 proteins
Authors: Almeida Marcius S. , Herrmann Torsten , Peti Wolfgang , Wilson Ian A. , Wüthrich Kurt
Published: October 2005

The NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima represents an α/β‐topology formed by the regular secondary structures α1–β1–β2–α2–β3–β4–α3– β5–310–α4, with a small anti‐parallel β‐sheet of β‐strands 1 and 2, and a mixed parallel/anti‐parallel β‐sheet of β‐strands 3–5. Similar folds have previously been observed in other proteins, with amino acid sequence identity as low as 3% and a variety of different functions. There are also 216 sequence homologs of TM0487, which all have the signature sequence of domains of unknown function 59 (DUF59), for which no three‐dimensional structures have as yet been reported. The TM0487 structure thus presents a platform for homology modeling of this large group of DUF59 proteins. Conserved among most of the DUF59s are 13 hydrophobic residues, which are clustered in the core of TM0487. A putative active site of TM0487 consisting of residues D20, E22, L23, T51, T52, and C55 is conserved in 98 of the 216 DUF59 sequences. Asp20 is buried within the proposed active site without any compensating positive charge, which suggests that its pKa value may be perturbed. Furthermore, the DUF59 family includes ORFs that are part of a conserved chromosomal group of proteins predicted to be involved in Fe–S cluster metabolism.
Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily
Authors: Caruthers Jonathan , Zucker Frank , Worthey Elizabeth , Myler Peter J. , Buckner Fred , Van Voorhuis Wes , Mehlin Chris , Boni Erica , Feist Tiffany , Luft Joseph , Gulde Stacey , Lauricella Angela , Kaluzhniy Oleksandr , Anderson Lori , Le Trong Isolde , Holmes Margaret A. , Earnest Thomas , Soltis Michael , Hodgson Keith O. , Hol Wim G.J. , Merritt Ethan A.
Published: October 2005

We have determined the crystal structures of three homologous proteins from the pathogenic protozoans Leishmania donovani, Leishmania major, and Trypanosoma cruzi. We propose that these proteins represent a new subfamily within the isochorismatase superfamily (CDD classification cd004310). Their overall fold and key active site residues are structurally homologous both to the biochemically well‐characterized N‐carbamoylsarcosine‐amidohydrolase, a cysteine hydrolase, and to the phenazine biosynthesis protein PHZD (isochorismase), an aspartyl hydrolase. All three proteins are annotated as mitochondrial‐associated ribonuclease Mar1, based on a previous characterization of the homologous protein from L. tarentolae. This would constitute a new enzymatic activity for this structural superfamily, but this is not strongly supported by the observed structures. In these protozoan proteins, the extended active site is formed by inter‐subunit association within a tetramer, which implies a distinct evolutionary history and substrate specificity from the previously characterized members of the isochorismatase superfamily. The characterization of the active site is supported crystallographically by the presence of an unidentified ligand bound at the active site cysteine of the T. cruzi structure.
Novel sequence insertion in a Mâori patient with transfusion‐dependent β‐thalassaemia
Authors: Blacklock Hilary A. , Case Jacqui , Chan Tim , Raizis Tony , Doocey Richard , Fellowes Andrew , Royle Gordon , Jackson Sharon , Brennan Stephen , George Peter
Published: October 2005

Although β‐thalassaemia is common throughout the world, it has not been previously described in Polynesia. We report a novel sequence insertion where homozygosity for the defect results in transfusion‐dependent anaemia. The repeated 45 base pair (bp) insertion causes duplication of the start codon and consequent transcription from the original initiation code would be predicted to lead to the production of an irrelevant seven‐residue peptide, while residual translation from the novel initiation site would result in diminished yields of β‐globin and consequent clinical β+‐thalassaemia.
The development of esters in filtered and unfiltered wines that have been aged in oak barrels
Authors: Moreno Nerea Jiménez , Azpilicueta Carmen Ancín
Published: October 2005

Esters are quite important for the aroma of aged red wine as they contribute to the fruity complex nature of this wine. This research paper measured the development of esters during maturation of Merlot red wines. These wines had different amounts of turbidity. The wine was aged for 18 months either after filtration with diatomaceous earth or without filtration. Both American and French oak barrel were used for storage. The results obtained showed that the unfiltered wine had a greater concentration of esters at the end of the storage period than the filtered wine. Fatty acid and ethanol esters decreased more than isoamyl acetate, independently of filtration. Ethyl octanoate and ethyl decanoate decreased both in filtered and unfiltered wine. Isoamyl acetate was formed in unfiltered wine and ethyl butyrate and ethyl hexanoate decreased in filtered wine while they remained constant in unfiltered wine.
Hierarchical analysis of population genetic structure in the monogynous ant Cataglyphis cursor using microsatellite and mitochondrial DNA markers
Authors: CLÉMENCET J. , VIGINIER B. , DOUMS C.
Published: October 2005

Despite having winged queens, female dispersal in the monogynous ant Cataglyphis cursor is likely to be restricted because colonies reproduce by fission. We investigated the pattern of population genetic structure of this species using eight microsatellite markers and a mitochondrial DNA (mtDNA) sequence, in order to examine the extent of female and nuclear gene flow in two types of habitat. Sampling was carried out at a large spatial scale (16 sites from 2.5 to 120 km apart) as well as at a fine spatial scale (two 4.5‐km transects, one in each habitat type). The strong spatial clustering of mtDNA observed at the fine spatial scale strongly supported a restricted effective female dispersal. In agreement, patterns of the mtDNA haplotypes observed at large and fine spatial scales suggested that new sites are colonized by nearby sites. Isolation by distance and significant nuclear genetic structure have been detected at all the spatial scales investigated. The level of local genetic differentiation for mitochondrial marker was 15 times higher than for the nuclear markers, suggesting differences in dispersal pattern between the two sexes. However, male gene flow was not sufficient to prevent significant nuclear genetic differentiation even at short distances (500 m). Isolation‐by‐distance patterns differed between the two habitat types, with a linear decrease of genetic similarities with distance observed only in the more continuous of the two habitats. Finally, despite these low dispersal capacities and the potential use of parthenogenesis to produce new queens, no signs of reduction of nuclear genetic diversity was detected in C. cursor populations.
‘In vivo’ time course of plasma myeloperoxidase levels after granulocyte colony‐stimulating factor‐induced stem cell mobilization
Authors: Morabito F. , Tomaino A. , Cristani M. , Martino M. , Minciullo P. L. , Saija A. , Gangemi S.
Published: October 2005

summary.  Administration of granulocyte colony‐stimulating factor (G‐CSF) is widely used for harvesting an adequate number of CD34+ stem cells by leukapheresis in normal donors. G‐CSF is the most established agent for the mobilization of stem cells in current clinical practice, because it has been proven to be superior to any other agent tested to date in terms of not only mobilization capacity, but also of tolerance. However, although regulatory and accrediting agencies have provided guidelines to protect donors, the short‐ and long‐term side effects of G‐CSF need to be further studied.

In this study, we evaluated the time course of plasma myeloperoxidase (MPO) levels measured in a group of donors given recombinant human G‐CSF (rHuG‐CSF) at different intervals: (i) before starting rHuG‐CSF administration, (ii) on day 5 of rHuG‐CSF administration, (iii) on the same day soon after the end of the first leukapheresis procedure and (iv) 1 week after rHuG‐CSF withdrawal.

Plasma MPO levels significantly increased in the donors after 5 days of rHuG‐CSF treatment, returning to the baseline values within 7 days following rHuG‐CSF withdrawal.

These findings may contribute to a better understanding of G‐CSF safety profile in stem cell donors.
hDAF porcine cardiac xenograft maintains cardiac output after orthotopic transplantation into baboon – a perioperative study
Authors: Bauer Andreas , Baschnegger Heiko , Abicht Jan M. , Brandl Ulrike , Brenner Paolo , Thein Eckart , Hammer Claus , Reichart Bruno , Peter Klaus , Schmoeckel Michael , Christ Frank
Published: October 2005

Abstract:  Background:  Only limited data are available on the physiological functional compatibility of cardiac xenografts after orthotopic pig to baboon transplantation (oXHTx). Thus we investigated hemodynamic parameters including cardiac output (CO) before and after oXHTx.

Methods:  Orthotopic xenogeneic heart transplantation from nine hDAF transgeneic piglets to baboons was performed. We used femoral arterial thermodilution for the invasive assessment of CO and stroke volume.

Results:  Baseline CO of the baboons after induction of anesthesia was 1.36 (1.0–1.9) l/min. 30 to 60 min after termination of the cardiopulmonary bypass, CO of the cardiac xenograft was significantly increased to 1.72 (1.3–2.1) l/min (P < 0.01). The stroke volumes of the baboon heart before transplantation and the cardiac xenograft was comparable [14.9 (11–26) vs. 11.8 (10–23) ml]. Thus the higher CO was achieved by an increase in heart rate after oXHTx [75.0 (69–110) vs. 140.0 (77–180)/min; P < 0.01]. Despite the increased CO, oxygen delivery was reduced [256 (251–354) vs. 227 (172–477) ml/min; P < 0.01] due to the inevitable hemodilution during the cardiopulmonary bypass and the blood loss caused by the surgical procedures.

Conclusion:  Our results demonstrate that in the early phase after orthotopic transplantation of hDAF pig hearts to baboons, cardiac function of the donor heart is maintained and exceeds baseline CO. However, in the early intraoperative phase this was only possible by using inotropic substances and vasopressors due to the inevitable blood loss and dilution by the priming of the bypass circuit.
A Risk Analysis Model of the Relationship Between Beverage Consumption from School Vending Machines and Risk of Adolescent Overweight
Authors: Forshee Richard A. , Storey Maureen L. , Ginevan Michael E.
Published: October 2005

Risk analysis is a widely used tool to understand problems in food safety policy, but it is seldom applied to nutrition policy. We propose that risk analysis be applied more often to inform debates on nutrition policy, and we conduct a risk assessment of the relationship of regular carbonated soft drink (RCSD) consumption in schools and body mass index (BMI) as a case study. Data for RCSD consumption in schools were drawn from three data sets: the Continuing Survey of Food Intake by Individuals 1994–1996, 1998 (CSFII), the National Health and Nutrition Examination Survey 1999–2000 (NHANES), and the National Family Opinion (NFO) WorldGroup Share of Intake Panel (SIP) study. We used the largest relationship between RCSD and BMI that was published by prospective observational studies to characterize the maximum plausible relationship in our study. Consumption of RCSD in schools was low in all three data sets, ranging from 15 g/day in NFO‐SIP to 60 g/day in NHANES. There was no relationship between RCSD consumption from all sources and BMI in either the CSFII or the NHANES data. The risk assessment showed no impact on BMI by removing RCSD consumption in school. These findings suggest that focusing adolescent overweight prevention programs on RCSD in schools will not have a significant impact on BMI.
Daily physical activity in Swedish children aged 8–11 years
Authors: Dencker M. , Thorsson O. , Karlsson M. K. , Lindén C. , Svensson J. , Wollmer P. , Andersen L. B.
Published: October 2005

Introduction: Physical inactivity is hypothesized to be a contributing factor in the development of a variety of diseases. Recommendations for an adequate level of physical activity have been proposed. There are few studies in which the physical activity in children has been objectively assessed. The purpose of this study was to estimate objectively the level of physical activity in Swedish children.

Materials and methods: We studied 248 children (140 boys and 108 girls) aged 7.9–11.1 years from Malmö, Sweden. Physical activity was measured with accelerometers. Children were instructed to wear the accelerometers for 4 days. The mean daily activity was expressed as the mean counts per minute of recording. The time that the child spent performing moderate or vigorous activity was calculated by using previously established cutoff points.

Results: The mean daily activity was higher in boys than in girls, 751±243 vs 618±154 counts/min (P<0.001). All children fulfilled the recommendation for moderate physical activity for 60 min or more per day. Ninety‐two percent of the boys and 86% of the girls performed vigorous activity, for 20 min or more per day.

Conclusion: All children, aged 8–11 years, who participated in this study reached the recommended level of physical activity, with boys being more active than girls.
Pumping Test in a Confined Aquifer Under Tidal Influence
Authors: Chapuis Robert P. , Bélanger Christian , Chenaf Djaouida
Published: October 2005

In a coastal environment, tide‐induced head fluctuations can complicate the interpretation of drawdown data from pumping tests. For confined aquifers and sinusoidal tides, the superposition principle can be used to obtain a closed‐form solution. After subtracting the net tidal effects, the drawdown data become amenable to the standard analyses. Numerical simulations have shown that the method is reliable when the distance of the monitoring well to the well does not exceed 10% of the distance between the well and the tidal boundary.
On the use of high-modulus graphite-epoxy materials for synthetic clarinet reeds
Authors: Backus John
Published: October 2005

The natural cane from which clarinet reeds are made is a material having a high modulus of elasticity and a low density. This ensures that under normal playing conditions the natural frequency of the reed is higher than the frequency of any played note; this is a necessary playing condition. Other materials such as plastics and most metals have densities that are too large to make clarinet reeds having a high enough natural frequency. Magnesium is an exception; it has a density sufficiently low, that reeds made from it are reasonably playable. However, magnesium is a low-loss material, and reeds made from it have a high Q; this results in an undesirable accentuation of the higher harmonics in the tone. Material is now available in the form of graphite filaments embedded in an epoxy matrix which when cured has a very high elastic modulus together with a low density. To make a reed from a solid piece of this material turns out to be impractical; the high elastic modulus requires that the reed be excessively thin. However, by using a structure consisting of ribs of the graphite material separated by a filler material of low density, it is possible to duplicate in the structure the elastic modulus and density of natural cane. Furthermore, the structure has a loss factor comparable to cane. Clarinet reeds made in this manner are found to play very well. [This work was supported by the NSF.]
Identification of sung vowels
Authors: Gottfried Terry L.
Published: October 2005

Identification of vowels sung by males, while not as difficult as when sung by sopranos, can still present problems for listeners. Ten American English vowels/i, I, e, ε, æ, a, ʌ, o, U, u/ in /b/ - vowel-/d/ syllables were sung by a trained male singer at seven different pitches: C3, E3, A3, C4, E4, A4, and C5 (131–524 Hz). The upper five pitches were sung with a counter-tenor head voice. The lower five pitches were sung with “full” pharyngeal voice. Subjects listened and identified randomized sets of tokens. Identification accuracy was lower for vowels sung at the higher pitches, regardless of vocal register. Errors for all pitches tended to be greatest for back vowels; confusions between /a/ and /ʌ/ were especially common. Acoustical analysis of the target formant frequencies were performed. The relationship between sung vowel identification and vocal production was examined. [Supported by MIMH, NICHHD, and NSF.].
The influence of shape of palate upon lingual articulation in the speech of children
Authors: Hiki Shizuo , Itoh Hidemi
Published: October 2005

Plaster casts of the hard palates of 30 children in six kinds of dental age and those of two children in various stages of growth were made and their three-dimensional shapes were measured. On the other hand, the patterns of lingual contact to palate in utterances of the consonants with frontal and middle tongue positions were observed in four children using the technique of electro-palatography. By comparing the results with those of adults previously studied by the authors [H. Itoh and S. Hiki: “Observation of personal characteristics of lingual articulation by use of electro-palatography,” J. Acoust. Soc. Am. 61, S31 (1977)], the lingual articulation characteristic of children was investigated.
Laryngeal airway resistance as a function of phonation type
Authors: Holmberg Eva
Published: October 2005

An indirect method to estimate laryngeal airway resistance was investigated. The ratio of the intraoral pressure (IOP) for the voiceless stop and the volume velocity air flow (V0) for the open vowel in the CV utterance /pa/ was suggested to give an estimate of the laryngeal airway resistance (Rlaw); Rlaw = IOP/V0. The primary variable was phonation type. It was hypothesized that the Rlaw value would reflect the laryngeal airway resistance during: (1) normal, (2) pressed, and (3) breathy phonation. Other controlled variables were intensity and fundamental frequency. The results suggested that the Rlaw value was highest for pressed phonation and lowest for breathy phonation irrespective of intensity and fundamental frequency. Good discrimination in the Rlaw value between high and low intensity was also found. These results were interpreted to give evidence that the Rlaw value obtained with this method was a good index of actual resistance.
Laryngeal-oral coordination in American English obstruent production
Authors: Löfqvist A. , Yoshioka H.
Published: October 2005

Voiceless obstruent production involves simultaneous activity at both laryngeal and supralaryngeal levels. The laryngeal and oral articulations have to be temporally coordinated, and the present experiment was designed to examine the nature of this coordination. Laryngeal activity was monitored by transillumination, and an artificial palate was used to obtain information on tongue-palate contact patterns. Voiceless obstruents in various positions and under different stress conditions spoken at two different rates provided the linguistic material. Preliminary results indicate a fixed relation between onset of glottal adduction and oral release in aspirated stops. In voiceless fricatives, peak glottal opening occurs close to the middle of the oral constriction. The results also suggest that temporal ratios between oral and laryngeal gestures tend to remain constant across changes in stress and speaking rate. [Work supported by NINCDS and BRSG.]
The response of a rectangular parallelepiped to a simulated acoustic emission burst
Authors: Hill E. V. K.
Published: October 2005

The forced vibrational response of the rectangular parallelepiped is of particular interest in the study of wave propagation in three-dimensional solids and especially in the characterization of acoustic emission sources. There has been considerable interest in studying source mechanisms in order to predict, and perhaps eventually control, flaw growth in structural materials. The acoustic emission source waves generated by flaw growth are thought to be pulselike functions of stress (force) which are produced by the step displacements associated with material yielding. Much of this type of emission in solids is produced internally and can therefore be modeled as a body force phenomenon; as such, this paper presents a normal mode solution for the response of a rectangular parallelepiped to an impulsive body force. The numerical results prior to any reflections from the boundaries show good agreement with the infinite space solution.
New interpretations of shock-associated noise with and without screech
Authors: Glahn U. von
Published: October 2005

Anomalous trends in present convergent nozzle (Mach 1) shock-associated noise analyses and predictions, with particular emphasis on the roles of screech and jet temperature, are discussed. Experimentally measured values of shock-associated noise are used to reassess data trends, including both frequency and sound pressure level. The data band used includes both model-scale nozzles, varying in nominal diameter from 5 to 13 cm, and full-scale engine nozzles up to 48 cm. All data were obtained at static conditions. From this reassessment of the measured data, new empirical methods for the prediction of shock-associated noise are developed. Separate procedures are presented for screech-free and screech-contaminated shock-associated noise. In the present approach, shock-associated noise spectra are developed from considerations that include the peak frequency and sound pressure level of the shock noise, the low-frequency sound pressure level slope, and the high-frequency sound pressure level roll-off; the latter is shown to vary with directivity angle.
Effect of a boundary layer about a nozzle on jet noise in flight
Authors: Michel Ulf , Rawls John W.
Published: October 2005

It is demonstrated that the presence of a relatively thick boundary layer about the outside of a nozzle can explain observed differences in jet noise between flight simulation experiments (usually thick boundary layers) and flyover experiments with engines mounted in nacelles (thin boundary layers). To study the boundary layer influence, the uniform velocity profile of a single stream static jet is replaced by a coannular jet in flight. The momentum loss in flight due to the external boundary layer is considered by reducing the velocity of the annular portion of the jet properly. A scaling law that relates flyover to static coannular jet noise (A. Michalke and U. Michel, AIAA Paper 80-1031) and prediction methods for static coannular jet noise as implemented in the NASA Aircraft Noise Prediction Program are then used to study the effect of the external boundary layer on the flyover jet noise directivities. [Research was accomplished while the first author held an NRC Senior Research Associateship.]
Effect of facility variations on the acoustic characteristics of three single stream nozzles
Authors: Gutierrez Orlando A.
Published: October 2005

The characteristics of the jet noise produced by three single stream referee nozzles have been investigated statically at the NASA-Lewis Research Center outdoor jet acoustic facility. These nozzles were a 712-cm-diam conical convergent, a 10-cm-diem conical convergent, and an 8-lobe daisy nozzle with 712cm equivalent diameter flow area. The same nozzles have been previously tested in other facilities such as the Royal Aircraft Establishment 24-ft acoustic wind tunnel. The test conducted covered pressure ratios from 1.4 to 2.5 at total temperatures of 810°K and ambient. Data were obtained using four different acoustic arena arrangements. Data taken with the different arrangements are compared. The results obtained are also compared with data from other facilities and with a prediction procedure developed elsewhere [i.e., Stone and Montegani (1979).]
Core noise measurements on a small, general aviation class turbofan engine
Authors: Reshotko Meyer , Karchmer Allen
Published: October 2005

As part of a program to investigate core and combustor noise, simultaneous measurements were made of internal fluctuating pressure and farfield noise on a JT-15D turbofan engine. Acoustic waveguide probes, located in the engine at the combustor, in the turbine exit and in the core nozzle, were used to measure internal fluctuating pressures. Low-frequency acoustic power determined at the core nozzle exit corresponds in level to the farfield acoustic power at engine speeds below 70% of maximum, the approach condition. At engine speeds above 70% of maximum, the jet noise dominates in the farfield, greatly exceeding that of the core. From coherence measurements, it is shown that the combustor is the dominant source of the low-frequency core noise. The results obtained from the JT-15D engine compare favorably with those obtained previously from a YF-102 engine, both engines having reverse flow annular combustors and being in the same size class.
Aeroacoustic measurements on a lifting wing/flap at Reynolds numbers to 2.8 × 106
Authors: Kendall James M.
Published: October 2005

Progress in the control of airframe (nonpropulsive) noise rests upon identification of the several sources disposed about an aircraft. Acoustic measurements were made in the NASA Ames 7 × 10-ft wind tunnel on a 0.75-m chord wing/flap combination at speeds to 57 m/s. The flap was divided at mid-span, and the halves were set 0°-0°, 0°-35°, and 35°-35° with respect to the wing. A directional microphone system was placed outside the tunnel but in communication with the model through an opening. The microphone axis was scanned in a two-dimensional array of aiming points about the lower side of the wing to determine the locations of sources which radiate downward from an aircraft. The results show that the sites of noise production, and the spectra and intensity of these, differ considerably among the test configurations. Speculation is made on the fluid dynamic processes of generation.