bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of model root exudates on structure and activity of a soil diazotroph community
Authors: Bürgmann Helmut , Meier Stefan , Bunge Michael , Widmer Franco , Zeyer Josef 
Published: October 2005

SummaryNitrogen fixation is often enhanced in the rhizosphere as compared with bulk soil, due to asymbiotic microorganisms utilizing root exudates as an energy source. We have studied the activity and composition of asymbiotic soil diazotrophs following pulse additions of artificial root exudates and single carbon sources, simulating the situation of bulk soil coming into contact with exudates from growing roots. Artificial root exudates and single sugars rapidly induced nitrogen fixation. The population of potential diazotrophs was studied using universal and group‐specific nifH polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) analysis. Reverse transcription PCR of nifH mRNA confirmed that phylotypes with an apparently increasing population size also expressed the nitrogenase system. According to our results, the actively nitrogen‐fixing population represents only a fraction of the total diazotroph diversity, and the results of group‐specific nifH PCR and phylogenetic analysis of cloned nifH and 16S rRNA gene fragments identified active species that belonged to the genus Azotobacter. Rapid changes of transcriptional activity over time were observed, indicating different growth and activation strategies in different Azotobacter strains. Only sugar‐containing substrates were able to induce nitrogen fixation, but substrate concentration and the presence of organic acids may have additional selective effects on the active diazotroph population.
Influence of different Oryza cultivars on expression of nifH gene pools in roots of rice
Authors: Knauth Stefan , Hurek Thomas , Brar Darshan , Reinhold‐Hurek Barbara 
Published: October 2005

SummaryCultivation‐independent studies suggest that roots of rice (Oryza sativa) are colonized by a diverse community of nitrogen‐fixing bacteria. Here we report for the first time mRNA‐based profiling of nitrogenase (nifH) genes, to study the impact of lowland‐rice genotypes at the cultivar level on the functional diversity of root‐associated diazotrophs. Root RNA extracts from all plants contained nifH mRNA at levels detectable by reverse transcription polymerase chain reaction (RT‐PCR). Terminal restriction fragment length polymorphism (T‐RFLP) analysis of RT‐PCR products showed only small interplant variations. However, RNA‐ and DNA‐based profiles obtained from the same root extractions differed from each other, suggesting that presence of diazotrophs did not necessarily coincide with active transcription of nif genes. Application of N‐fertilizer at planting had a long‐term effect on the profile of expressed nitrogenase genes. Phylogenetic analysis of a clone library constructed for nifH fragments expressed in wild species of rice roots indicated that active diazotrophs were not related to cultured strains. The composition of active diazotrophic communities was compared for six related cultivars of O. sativa, wild species Oryza brachyantha, and a genetic cross between it and cv. IR56, grown under identical conditions in rice field soil in the Philippines without N‐fertilizer application. Remarkable varietal differences in root associated nifH‐gene expressing communities were detected. This underlines the importance of mRNA‐based approaches to study functional diversity and eventually identify key diazotrophs in a particular environment.
Establishment of DsRed.T3_S4T as an improved autofluorescent marker for microbial ecology applications
Authors: Dandie Catherine E. , Larrainzar Estibaliz , Mark G. Louise , O'Gara Fergal , Morrissey John P. 
Published: October 2005

SummaryAutofluorescent proteins (AFPs), such as green fluorescent protein (GFP) and DsRed, are valuable tools for studying plant–microbe interactions. Nevertheless, because of some limitations, efforts are ongoing to generate improved AFP variants. Several groups have generated variants of GFP with altered spectral characteristics, and faster maturing and brighter variants of DsRed. In this study we used plasmid and chromosomal constructs to test the efficacy of a new variant of DsRed, DsRed.T3_S4T, in Pseudomonas fluorescens F113rif. In addition, we compared the ecological fitness of strains carrying chromosomal copies of EGFP, DsRed or DsRed.T3_S4T. Strains expressing DsRed.T3_S4T fluoresced significantly brighter than strains expressing DsRed. Furthermore, it was found that although all strains grew equally well in vitro, only strains carrying DsRed.T3_S4T functioned as well as wild type in a competitive rhizosphere colonization assay. In particular, it was observed that DsRed.T3_S4T is an improved marker over DsRed for microbial ecology studies in this strain.
Bacterial diversity in the rhizosphere of Proteaceae species
Authors: Stafford William H. L. , Baker Gillian C. , Brown Susan A. , Burton Stephanie G. , Cowan Don A. 
Published: October 2005

SummaryThe Cape Floral Kingdom is an area of unique plant biodiversity in South Africa with exceptional concentrations of rare and endemic species and experiencing drastic habitat loss. Here we present the first molecular study of the microbial diversity associated with the rhizosphere soil of endemic plants of the Proteaceae family (Leucospermum truncatulum and Leucadendron xanthoconus). Genomic DNA was extracted from L. truncatulum rhizosphere soil, L. xanthoconus rhizosphere and non‐rhizosphere soil and used as a template for the polymerase chain reaction (PCR) amplification of the 16S ribosomal RNA gene (rDNA). Construction and sequencing of 16S rDNA libraries revealed a high level of biodiversity and led to the identification of several novel bacterial phylotypes. The bacterial community profiles were compared by 16S rDNA denaturing gradient gel electrophoresis (DGGE). Cluster analysis and biodiversity indices revealed that the rhizosphere soil samples were more similar to each other than to non‐rhizosphere soil and the rhizosphere soil contained a bacterial diversity that was richer and more equitable compared with non‐rhizosphere soil. A Chloroflexus and an Azospirillum genospecies were restricted to the L. xanthoconus rhizosphere soil and Stenotrophomonas genospecies was identified in all rhizosphere soil samples but was not present in the non‐rhizosphere soil. Taxon‐specific nested PCR and DGGE‐identified differences between the Proteaceae plant rhizosphere soil with a Frankia genospecies restricted the L. truncatulum rhizosphere. Archaea‐specific rDNA PCR, DGGE and DNA sequencing revealed that Crenarcheote genospecies were excluded from the plant rhizosphere soil and only present in non‐rhizosphere soil.
Fracture‐induced Physical Phenomena and Memory Effects in Rocks: A Review
Authors: Lavrov A. 
Published: October 2005

Losing stability, the earth split;
Losing strength, the mountains sank. Tao De Ching
Abstract:  Fracture‐induced physical phenomena allow a real‐time monitoring of damage evolution in rocks induced by mechanical loading. Some of these phenomena, e.g. plastic deformation, changes in permeability and electric resistivity, provide an overall estimate of damage as a function of stress. Others, such as acoustic emission or electromagnetic emission, allow an exact location of cracks in space and time. Being nondestructive, monitoring techniques based on fracture‐induced physical phenomena, are a basis for prediction of earthquakes and rockbursts in underground mines. They are also crucial for a fundamental understanding of rock fracture mechanisms and for developing constitutive models of rock behaviour. Memory effects take place in rocks subjected to cyclic loading with the peak stress (strain) value increasing from cycle to cycle. The effects are represented by certain characteristic changes in rock properties and parameters that are observed when the stress (strain) reaches its previous peak value. Potential applications of memory effects range from stress measurement techniques to earthquake prediction to damage surface scanning. Essential experimental and theoretical results on fracture‐induced physical phenomena and memory effects in rocks are considered in the article. Possible applications as well as not‐yet‐clear points are discussed.
Effect of dynamic fluid compressibility and permeability on porous piezoelectric ceramics
Authors: Lacour Olivier , Lagier Michel , Sornette Didier 
Published: October 2005

The ac piezoelectric properties of porous ceramics in the presence of compressible viscous fluids filling the pores inside the ceramics are studied. Above the Biot frequency fB, the fluid decouples from the solid and does not significantly affect the piezoelectric properties. Our study which is both experimental and theoretical focuses on the frequency domain below the Biot frequency, in which the fluid is in principle strongly coupled to the solid matrix for oscillations parallel to solid–fluid boundaries. Two regimes are found: (1) For frequencies smaller than a cross-over frequency fc∼(β/η)L−2, where L is the thickness of the sample, β the fluid bulk modulus, and η its viscosity, the piezoelectric coefficients dij are close to those of the dense nonporous ceramics weighted by the filling factor (1−φ); (2) for frequencies larger than fc, the dij tend to those of the empty porous ceramics for fluid bulk modulus significantly smaller than that of the ceramics, as is the case in our experiments. These observations are explained in terms of a frequency-dependent penetration of the acoustic fluid pressure inside the porous ceramics as a result of the interplay between fluid compressibility and viscosity.
The nature of the decoupling between solid and fluid at frequencies larger than fc but still smaller than fB is for motions, not parallel to their common boundaries (for which the Biot mechanism applies), but perpendicular to their common boundaries. This decoupling occurs due to the finite compressibility of the fluid and in details is controlled by the tube-cavity topological structure of the porous medium. The dependence of the hydrostatic piezoelectric coefficient dH=d33+d31+d32 as a function of frequency observed experimentally is compared to an effective medium theory for the piezoelectric properties coupled to a permeability model. The experimental dependence of the cross-over frequency fc on sample sizes and on the fluid viscosity are in good agreement with our theory. The study shows that it is thus possible to obtain the desirable property of a high piezoelectric coefficient dH, characteristic of light porous piezoelectric ceramics, and good mechanical properties under applied high hydrostatic pressure with the use of an internal fluid which allows the pressure to equilibrate without destroying the piezoelectric properties of the porous ceramics.
Dependence of distortion-product otoacoustic emissions on primary levels in normal and impaired ears. I. Effects of decreasing L2 below L1
Authors: Whitehead M. L. , McCoy M. J. , Lonsbury-Martin B. L. , Martin G. K. 
Published: October 2005

The 2f1−f2 distortion-product otoacoustic emission (DPOAE) is evoked by two primary tones of frequencies f1&lt;f2, and levels L1 and L2. Previous reports indicate that decreasing L2 below L1=L2 can; (1) increase DPOAE amplitude in normal ears, and (2) increase the degree to which DPOAE amplitudes are reduced by cochlear trauma. Although both of these factors could be advantageous for clinical applications of DPOAEs, neither has been explored in detail. In the present study, 2f1−f2 DPOAE-amplitude frequency functions were collected from normal and impaired ears of rabbits and humans, with L1=L2, and with L2&lt;L1, at each of three values of L1. In rabbits, controlled tonal or noise overexposures were used to produce permanent reductions of DPOAE amplitudes. Comparison of pre- and postexposure DPOAE-amplitude frequency functions demonstrated that the frequency-specific reductions of DPOAEs were enhanced by decreasing L2 below L1. In humans, DPOAE-amplitude frequency functions obtained with the various L1 and L2 combinations were collected from 16 normal ears to provide preliminary normative data for each stimulus-level condition.
The L1−L2 that produced the maximum DPOAE amplitude in normal ears was systematically dependent on L1. Thus at most frequencies, decreasing L2 below L1=L2 substantially reduced mean DPOAE amplitude when L1≥75 dB SPL, but increased mean DPOAE amplitudes at L1=65 dB SPL. However, the increase of mean DPOAE amplitude obtained by decreasing L2 below L1=65 dB SPL was small, being less than 3.5 dB at most frequencies. More importantly, at L1=65 dB SPL, L2 could be decreased considerably below L1=L2 without reducing mean DPOAE amplitude relative to that at L1=L2. Inspection of DPOAE-amplitude frequency functions obtained from subjects with mild or moderate sensorineural hearing losses indicated that, in frequency regions of hearing impairment, decreasing L2 below L1 can enhance the degree of reduction of DPOAEs below the corresponding normative amplitudes, without reducing the normative amplitudes. It is concluded that decreasing L2 below L1=L2 has the potential to enhance the performance of DPOAEs in clinical applications.
Approximate models for sound propagation above multi-impedance plane boundaries
Authors: Hothersall D. C. , Harriott J. N. B. 
Published: October 2005

The propagation of sound over an infinite plane with various distributions of surface impedance is considered. Three methods are used to calculate the sound field. The first is a numerical solution based on a boundary integral equation formulation of the problem. Although involving some approximation this approach provides accurate results for a wide range of propagation conditions in a still homogeneous atmosphere but suffers from the need for large computing resources. The other two methods are approximate but have the advantage that they are easy and efficient to calculate. The first of these involves empirical modification of the equation for diffraction of monopole radiation by a rigid half-plane, proposed by de Jong. In the other the sound field at the receiver is assumed to be governed by the surface conditions in a region around the specular reflection point. This region is defined by a Fresnel-zone condition.
Results using the three approaches are compared for a large range of source and receiver positions and for the following boundary conditions: (i) A straight discontinuity between two surface impedances perpendicular to the source–receiver path, (ii) a straight discontinuity between two surface impedances parallel to the source–receiver path, and (iii) a strip of different impedance perpendicular to the source–receiver path. Comparison is also made with the results of model experiments for surface conditions when the discontinuity is parallel to the direction from source to receiver. The computational time for the boundary integral equation calculations is dependent on the frequency of the source and the site geometry, but in all cases was several orders of magnitude greater than the computation times for the other two methods. Calculation times for these two methods was very short since they essentially involved only the enumeration of a formula. The de Jong approach proved flexible in application to all the boundary conditions considered and agreed well with the boundary integral equation and the experimental results except in one case of propagation over a strip when the grazing angle was very small. The Fresnel-zone method adequately described the general trends in the results of the other two methods. Possible extensions of this method to more complex distributions of ground cover and allowance for atmospheric effects are discussed.
S-Phase-Dependent Enhancement of Dengue Virus 2 Replication in Mosquito Cells, but Not in Human Cells
Authors: Helt Anna-Marija , Harris Eva 
Published: October 2005

ABSTRACTDengue virus (DEN) is the most prevalent cause of arthropod-borne viral illness in humans. We determined the influence of cellular growth state on DEN type 2 (DEN2) replication in mosquito and human cells, based on the hypothesis that manipulation of cellular growth state will facilitate identification of viral and cellular determinants of productive infection. Comparison of density-arrested and cycling C6/36Aedes albopictuscells infected with a low-passage DEN2 isolate revealed that cycling cells generated higher virus titers per cell. When C6/36 cells were stalled in S-phase via a thymidine (THY) block, titers of low-passage DEN2 isolates and a high-passage strain, 16681, were increased approximately 30-fold and 10-fold, respectively. Moreover, virus release was earlier in THY-treated cells than in asynchronously cycling cells. Adsorption, entry, genome uncoating, and translation were not responsible for increased titers of virus from S-phase C6/36 cells. In contrast to the 30-fold increase in virus titers, intracellular levels of viral RNA were increased approximately 2-fold, suggesting that the S-phase-responsive step is late in the DEN2 replication cycle. Analysis of viral RNA and protein released from the cells indicated that enhanced DEN2 assembly is largely responsible for increased virus titers produced during S-phase. In contrast to C6/36 cells, DEN2 titers from S-phase human hepatoma cells or primary human fibroblasts were not increased. These results demonstrate a differential response of DEN2 to the mosquito and human cell cycle and provide a framework for detailed studies into the mechanisms mediating virus assembly.
Complex Determinants in Human Immunodeficiency Virus Type 1 Envelope gp120 Mediate CXCR4-Dependent Infection of Macrophages
Authors: Ghaffari Guity , Tuttle Daniel L. , Briggs Daniel , Burkhardt Brant R. , Bhatt Deepa , Andiman Warren A. , Sleasman John W. , Goodenow Maureen M. 
Published: October 2005

ABSTRACTHost cell range, or tropism, combined with coreceptor usage defines viral phenotypes as macrophage tropic using CCR5 (M-R5), T-cell-line tropic using CXCR4 (T-X4), or dually lymphocyte and macrophage tropic using CXCR4 alone or in combination with CCR5 (D-X4 or D-R5X4). Although envelope gp120 V3 is necessary and sufficient for M-R5 and T-X4 phenotypes, the clarity of V3 as a dominant phenotypic determinant diminishes in the case of dualtropic viruses. We evaluated D-X4 phenotype, pathogenesis, and emergence of D-X4 viruses in vivo and mapped genetic determinants in gp120 that mediate use of CXCR4 on macrophages ex vivo. Viral quasispecies with D-X4 phenotypes were associated significantly with advanced CD4+-T-cell attrition and commingled with M-R5 or T-X4 viruses in postmortem thymic tissue and peripheral blood. A D-X4 phenotype required complex discontinuous genetic determinants in gp120, including charged and uncharged amino acids in V3, the V5 hypervariable domain, and novel V1/V2 regions distinct from prototypic M-R5 or T-X4 viruses. The D-X4 phenotype was associated with efficient use of CXCR4 and CD4 for fusion and entry but unrelated to levels of virion-associated gp120, indicating that gp120 conformation contributes to cell-specific tropism. The D-X4 phenotype describes a complex and heterogeneous class of envelopes that accumulate multiple amino acid changes along an evolutionary continuum. Unique gp120 determinants required for the use of CXCR4 on macrophages, in contrast to cells of lymphocytic lineage, can provide targets for development of novel strategies to block emergence of X4 quasispecies of human immunodeficiency virus type 1.
N-Linked Glycosylation of West Nile Virus Envelope Proteins Influences Particle Assembly and Infectivity
Authors: Hanna Sheri L. , Pierson Theodore C. , Sanchez Melissa D. , Ahmed Asim A. , Murtadha Mariam M. , Doms Robert W. 
Published: October 2005

ABSTRACTWest Nile virus (WNV) encodes two envelope proteins, premembrane (prM) and envelope (E). While the prM protein of all WNV strains contains a single N-linked glycosylation site, not all strains contain an N-linked site in the E protein. The presence of N-linked glycosylation on flavivirus E proteins has been linked to virus production, pH sensitivity, and neuroinvasiveness. Therefore, we examined the impact of prM and E glycosylation on WNV assembly and infectivity. Similar to other flaviviruses, expression of WNV prM and E resulted in the release of subviral particles (SVPs). Removing the prM glycosylation site in a lineage I or II strain decreased SVP release, as did removal of the glycosylation site in a lineage I E protein. Addition of the E protein glycosylation site in a lineage II strain that lacked this site increased SVP production. Similar results were obtained in the context of either reporter virus particles (RVPs) or infectious lineage II WNV. RVPs or virions bearing combinations of glycosylated and nonglycosylated forms of prM and E could infect mammalian, avian, and mosquito cells (BHK-21, QT6, and C6/36, respectively). Those particles lacking glycosylation on the E protein were modestly more infectious per genome copy on BHK-21 and QT6 cells, while this absence greatly enhanced the infection of C6/36 cells. Thus, glycosylation of WNV prM and E proteins can affect the efficiency of virus release and infection in a manner that is cell type and perhaps species dependent. This suggests a multifaceted role for envelope N-linked glycosylation in WNV biology and tropism.
Recombinant Newcastle Disease Virus Expressing a Foreign Viral Antigen Is Attenuated and Highly Immunogenic in Primates
Authors: Bukreyev Alexander , Huang Zhuhui , Yang Lijuan , Elankumaran Subbiah , St. Claire Marisa , Murphy Brian R. , Samal Siba K. , Collins Peter L. 
Published: October 2005

ABSTRACT

Paramyxoviruses such as human parainfluenza viruses that bear inserts encoding protective antigens of heterologous viruses can induce an effective immunity against the heterologous viruses in experimental animals. However, vectors based on common human pathogens would be expected to be restricted in replication in the adult human population due to high seroprevalence, an effect that would reduce vector immunogenicity. To address this issue, we evaluated Newcastle disease virus (NDV), an avian paramyxovirus that is serotypically distinct from common human pathogens, as a vaccine vector. Two strains were evaluated: the attenuated vaccine strain LaSota (NDV-LS) that replicates mostly in the chicken respiratory tract and the Beaudette C (NDV-BC) strain of intermediate virulence that produces mild systemic infection in chickens. A recombinant version of each virus was modified by the insertion, between the P and M genes, of a gene cassette encoding the human parainfluenza virus type 3 (HPIV3) hemagglutinin-neuraminidase (HN) protein, a test antigen with considerable historic data. The recombinant viruses were administered to African green monkeys (NDV-BC and NDV-LS) and rhesus monkeys (NDV-BC only) by combined intranasal and intratracheal routes at a dose of 10
6.5
PFU per site, with a second equivalent dose administered 28 days later. Little or no virus shedding was detected in nose-throat swabs or tracheal lavages following immunization with either strain. In a separate experiment, direct examination of lung tissue confirmed a highly attenuated, restricted pattern of replication by parental NDV-BC. The serum antibody response to the foreign HN protein induced by the first immunization with either NDV vector was somewhat less than that observed following a wild-type HPIV3 infection; however, the titer following the second dose exceeded that observed with HPIV3 infection, even though HPIV3 replicates much more efficiently than NDV in these animals. NDV appears to be a promising vector for the development of vaccines for humans; one application would be in controlling localized outbreaks of emerging pathogens.