bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential improvements of design parameters by taking block samples of soft marine Norwegian clays
Authors: Berre Toralv , Lunne Tom , Andersen Knut H , Strandvik Stein , Sjursen Morten
Published: July 2007

Undrained triaxial and direct simple shear tests on samples reconsolidated to the in situ effective stresses and oedometer tests have been carried out on standard piston tube and on high quality block samples from 12 deposits of soft Norwegian marine clays. Based on the results of a selected number of these tests, empirical procedures for estimating the effect of sample disturbance have been developed. These procedures can be used to show the potential increase that may be achieved in undrained shear strength and apparent preconsolidation stress by taking high quality block samples. Suggestions are also given regarding corrections for rate of loading and temperature effects; as well, examples are given regarding possible consequences for design if higher strengths are utilized.Key words: soft clays, sample disturbance, consolidation procedures, stress–strain–strength behaviour.
Evaluation of a simplified small-strain soil model for analysis of excavation-induced movements
Authors: Kung Gordon Tung-Chin , Hsiao Evan Cheng-Liang , Juang C Hsein
Published: July 2007

A simplified small-strain soil model, referred to herein as the modified pseudoplasticity (MPP) model, developed based on the small-strain behavior of clay measured from the triaxial tests is evaluated in this study. The simulation of the small-strain triaxial tests by the MPP model shows that nonlinear stress–strain characteristics of clays can be adequately accounted for at small strain, including the characteristic of high initial Young's modulus. Two well-documented excavation case histories are used to assess the MPP model. Satisfactory predictions are obtained of the excavation-induced wall deflection and ground surface settlement by finite element method (FEM) that incorporates the MPP model. The lateral soil deformation behind the wall can also be reasonably predicted. The simplified MPP model is shown to be effective for modeling the excavation-induced wall and ground movements.Key words: braced excavation, wall deflection, ground settlement, finite element method, stress-strain relationship, case histories.
Nonlinear consolidation of thin layers subjected to time-dependent loading
Authors: Conte Enrico , Troncone Antonello
Published: July 2007

The paper deals with one-dimensional consolidation of saturated clays with variable compressibility and permeability. A formulation is developed to analyse the consolidation of thin clay layers subjected to time-dependent loading. Moreover, a simple solution procedure is presented, which makes use of some analytical expressions derived in this study in conjunction with the Fourier series. Comparisons with other analytical and numerical solutions are shown, and some aspects of the nonlinear consolidation caused by time-dependent loading are highlighted.Key words: one-dimensional consolidation, nonlinear theory, time-dependent loading, excess pore-water pressure, settlement rate.
Experimental and numerical analysis of desiccation of a mining waste
Authors: Rodríguez R , Sánchez M , Ledesma A , Lloret A
Published: July 2007

The paper presents an analysis of the desiccation process in mining materials, based on physical laws. Due to the process complexity, most of the previous approaches used have an empirical basis. In this case, however, a formulation using coupled hydromechanical equations has been considered. To show the capabilities of the theoretical framework, several laboratory tests were performed, and afterwards a numerical simulation of the measured variables was attempted. The material tested was a metallurgical waste in tailings form and it was exposed to atmospheric desiccation. Further cracking will eventually change its properties, and this may have an environmental impact. Some of the experiments were devoted to material characterization, including the water retention curve, the hydraulic conductivity, and the tensile strength. In addition, laboratory drying tests open to the atmosphere or in hermetically closed containers were also performed. The numerical analyses carried out attempted to simulate some of these tests. One of the main outcomes of the analyses was the prediction of the time and the location of crack initiation. Finally, it should be pointed out that good agreement between the experiments and numerical simulations indicates that the formulation is taking into account the fundamental mechanisms involved in the desiccation process.Key words: desiccation, drying cracks, unsaturated soils, waste material, coupled phenomena, modelling.
Investigating ground movements caused by the construction of multiple tunnels in soft ground using laboratory model tests
Authors: Chapman D N , Ahn S K , Hunt D VL
Published: July 2007

The prediction of the ground movements above single tunnels in soft ground is well established and can be estimated using semi-empirical methods based on the Gaussian curve. However, the prediction of ground movements associated with closely spaced multiple tunnels, in particular side-by-side (sbs) tunnels, is not as well understood, and therefore simple predictive methods for this application are currently quite limited in terms of their accuracy. This paper describes results from a series of small-scale (1/50) laboratory model tests (conducted at 1g) carried out in Speswhite kaolin clay. These tests have been conducted to gain a greater understanding of the short-term ground movements associated with closely spaced multiple (sbs) tunnels. The observed ground movement results from these tests have shown many of the characteristics observed at full-scale in the published case studies. These results are compared to the commonly used Gaussian curve prediction method and demonstrate the potential inaccuracy in this approach for predicting ground movements associated with closely spaced multiple tunnels. A method that modifies the Gaussian curve approach is also applied to the laboratory data and shows improved predictions.Key words: tunnelling, ground movements, multiple side-by-side tunnels, physical modelling, settlement prediction.
Seismic monitoring short-duration events: liquefaction in 1gmodels
Authors: Lee Jong-Sub , Santamarina J Carlos
Published: July 2007

The duration of liquefaction in small models is very short, therefore special monitoring systems are required. In an exploratory sequence of liquefaction tests, S-wave transillumination is implemented with a high repetition rate to provide detailed information on the evolution of shear stiffness during liquefaction. These data are complemented with measurements of acceleration, time-varying settlement, excess pore pressure, and resistivity profiles. Measurements show that excess pore pressure migration from liquefied deep layers may cause or sustain a zero effective stress condition in shallow layers, that multiple liquefaction events may take place in a given formation for a given excitation level, and that unsaturated layers may also reach a zero effective stress condition. The time scale for excess pore pressure dissipation in fully submerged specimens is related to particle resedimentation and pressure diffusion; downward drainage from unsaturated shallow layers may contribute an additional time scale. High resolution resistivity profiling reveals the gradual homogenization of the soil bed that takes place during subsequent liquefaction events. The S-wave transillumination technique can be extended to field applications and implemented with tomographic coverage to gain a comprehensive understanding of the spatial and temporal evolution of liquefaction.Key words: densification, electrical resistivity, multiple liquefaction, pore pressure, shear wave, spatial variability.
Preparation of ABC triblock copolymers of N-alkyl substituted acrylamides by RAFT polymerization
Authors: Cao Ya , Zhu X X
Published: July 2007

Reversible addition-fragmentation chain transfer (RAFT) polymerization of N-alkyl substituted acrylamides has been carried out by the use of a trithiocarbonate (2-dodecylsulfanylthiocarbonyl-sulfanyl-2-methyl propionic acid) as the RAFT reagent. The N-alkyl groups of the acrylamide monomers are important in the RAFT process. N-alkyl monosubstituted polyacrylamides are found to be active macro-chain transfer agents, while N,N-disubstituted monomers can react easily with them to form a sequent block. We have designed a synthetic pathway to successfully prepare ABC triblock copolymers of N-alkyl substituted acrylamides with low polydispersities (PDI < 1.20) by a three-step RAFT polymerization process.Key words: block copolymers, RAFT polymerization, N-alkyl substituted acrylamides, thermosensitive polymers.
Zinc oxide as a new, highly efficient, green, and reusable catalyst for microwave-assisted Michael addition of sulfonamides to α,β-unsaturated esters in ionic liquids
Authors: Zare Abdolkarim , Hasaninejad Alireza , Zare Ahmad Reza Moosavi , Parhami Abolfath , Sharghi Hashem , Khalafi-Nezhad Ali
Published: July 2007

A simple, clean, and efficient procedure for the green synthesis of some N-alkyl derivatives of sulfonamides is described. Microwave-assisted Michael addition of sulfonamides to α,β-unsaturated esters, in the presence of catalytic amount of zinc oxide (ZnO) in 1-butyl-3-methylimidazolium bromide ([bmim]Br), affords the title compounds in high yields and short reaction times.Key words: zinc oxide, green chemistry, microwave, Michael addition, sulfonamide, ionic liquid.
A reinterpretation of the unusual barochromism of azulene
Authors: Okamoto Masami , Hirayama Satoshi , Steer Ronald P
Published: July 2007

The UV–vis spectra of azulene in methylcyclohexane and acetonitrile solution at room temperature have been measured as a function of applied pressure in the 0.1–600 MPa range. The solvatochromic shifts are normal, but the barochromic shifts are unusual (hypsochromic shift in the S1–S0absorption bands vs. normal bathochromic shifts in its S2–S0and S3–S0absorption bands). An analytical relationship between the barochromic shift and the differences in the polarizabilities and dipole moments of the two radiatively coupled electronic states has been derived. The unusual barochromism of azulene has been reinterpreted in terms of differences in the polarizabilities of azulene in its ground and excited states and the dominance of dispersive interactions in barochromism.Key words: barochromism, solvatochromism, azulene, polarizability, dipole moment.
Identification and characterization of the regulatory elements of the inducible acetamidase operon from Mycobacterium smegmatis
Authors: Subbian Selvakumar , Narayanan Sujatha
Published: July 2007

The highly inducible acetamidase promoter from Mycobacterium smegmatis has been used as a tool in the study of mycobacterial genetics. The 4.2 kb acetamidase operon contains four putative open reading frames (ORFs) (amiC, amiA, amiD, and amiS) upstream of the 1.2 kb acetamidase ORF (amiE). In this article, using electrophoretic mobility shift assay and promoter probe analyses with a lacZ reporter system, we show the position of three putative operators within the acetamidase operon in M. smegmatis. Results from these studies reinforce previous findings about the involvement of multiple promoters in the regulation of acetamidase gene expression. Each of the identified operators are positioned upstream of the respective promoter reported in previous studies. We also found that the crude cell lysate of M. smegmatis containing potential regulators, obtained from bacteria grown under inducing or noninducing conditions, binds to specific operators. The binding affinity of each operator with its cognate regulator is significantly different from the other. This supports not only the previous model of acetamidase gene regulation in M. smegmatis but also explains the role of these operators in controlling the expression of respective promoters under different growth conditions.
Ophiostoma species (Ascomycetes: Ophiostomatales) associated with bark beetles (Coleoptera: Scolytinae) colonizing Pinus radiata in northern Spain
Authors: Romón Pedro , Zhou XuDong , Iturrondobeitia Juan Carlos , Wingfield Michael J. , Goldarazena Arturo
Published: July 2007

Bark beetles (Coleoptera: Scolytinae) are known to be associated with fungi, especially species of Ophiostoma sensu lato and Ceratocystis . However, very little is known about these fungi in Spain. In this study, we examined the fungi associated with 13 bark beetle species and one weevil (Coleoptera: Entiminae) infesting Pinus radiata in the Basque Country of northern Spain. This study included an examination of 1323 bark beetles or their galleries in P. radiata. Isolations yielded a total of 920 cultures, which included 16 species of Ophiostoma sensu lato or their asexual states. These 16 species included 69 associations between fungi and bark beetles and weevils that have not previously been recorded. The most commonly encountered fungal associates of the bark beetles were Ophiostoma ips , Leptographium guttulatum , Ophiostoma stenoceras , and Ophiostoma piceae . In most cases, the niche of colonization had a significant effect on the abundance and composition of colonizing fungi. This confirms that resource overlap between species is reduced by partial spatial segregation. Interaction between niche and time seldom had a significant effect, which suggests that spatial colonization patterns are rarely flexible throughout timber degradation. The differences in common associates among the bark beetle species could be linked to the different niches that these beetles occupy.
Survival ofEscherichia coliO157:H7 in soil and on lettuce after soil fumigation
Authors: Ibekwe A.  Mark , Grieve Catherine M. , Yang Ching-Hong
Published: July 2007

Long-term survival of Escherichia coli O157:H7 in soil and in the rhizosphere of many crops after fumigation is relatively unknown. One of the critical concerns with food safety is the transfer of pathogens from contaminated soil to the edible portion of the plants. Multiplex fluorogenic polymerase chain reaction was used in conjunction with plate counts to quantify the survival of E. coli O157:H7 in soil after fumigation with methyl bromide and methyl iodide in growth chamber and microcosm laboratory experiments. Plants were grown at 20 °C in growth chambers during the first experiment and soils were irrigated with water contaminated with E. coli O157:H7. For the second experiment, soil microcosms were used in the laboratory without plants and were inoculated with E. coli O157:H7 and spiked with the two fumigants. Primers and probes were designed to amplify and quantify the Shiga-like toxin 1 (stx1) and 2 (stx2) genes and the intimin (eae) gene of E. coli O157:H7. Both fumigants were effective in reducing pathogen concentrations in soil, and when fumigated soils were compared with nonfumigated soils, pathogen concentrations were significantly higher in the nonfumigated soils throughout the study. This resulted in a longer survival of the pathogen on the leaf surface especially in sandy soil than observed in fumigated soils. Therefore, application of fumigant may play some roles in reducing the transfer of E. coli O157:H7 from soil to leaf. Regression models showed that survival of the pathogen in the growth chamber study followed a linear model while that of the microcosm followed a curvilinear model, suggesting long-term survival of the pathogen in soil. Both experiments showed that E. coli O157:H7 can survive in the environment for a long period of time, even under harsh conditions, and the pathogen can survive in soil for more than 90 days. This provides a very significant pathway for pathogen recontamination in the environment.
Citrate metabolism by Enterococcus faecium and Enterococcus durans isolated from goat’s and ewe’s milk: influence of glucose and lactose
Authors: Cabral María E. , Mukdsi María C. Abeijón , Medina de Figueroa Roxana B. , González Silvia N.
Published: July 2007

Citrate metabolism by Enterococcus faecium ET C9 and Enterococcus durans Ov 421 was studied as sole energy source and in presence of glucose or lactose. Both strains utilized citrate as the sole energy source. Enterococcus faecium ET C9 showed diauxic growth in the presence of a limiting concentration of glucose. Neither strain used citrate until glucose was fully metabolized. The strains showed co-metabolism of citrate and lactose. Lactate, acetate, formate, and flavour compounds (diacetyl, acetoin, and 2,3-butanediol) were detected in both strains. The highest production of flavour compounds was detected during growth of E. durans Ov 421 in media supplemented with citrate–glucose and citrate–lactose. Citrate lyase was inducible in both strains. Acetate kinase activities presented the highest values in LAPTc medium, with E. faecium ET C9 displaying a specific activity 2.4-fold higher than E. durans. The highest levels of α-acetolactate synthase specific activity were detected in E. durans grown in LAPTc+g, in accordance with the maximum production of flavour compounds detected in this medium. Diacetyl and acetoinreductases displayed lower specific activity values in the presence of citrate. Enterococcus faecium and E. durans displayed citrate lyase, acetate kinase, α-acetolactate synthase, and diacetyl and acetoin reductase activities. These enzymes are necessary for conversion of citrate to flavour compounds that are important in fermented dairy products.
Evaluation of quantitative polymerase chain reaction to assessnosZgene prevalence in mixed microbial communities
Authors: Siciliano Steven D. , Ma Wai , Powell Shane
Published: July 2007

The usefulness of quantitative polymerase chain reaction (QPCR) to measure nosZ gene prevalence in a multi-template reaction was assessed by comparing 19 nosZ template DNA samples and 91 model communities. Efficiencies of the QPCR varied but were not significantly different among nosZ genotypes and were not linked to genetic distance from Ralstonia eutropha . nosZ genotype QPCR efficiencies obtained from isolated denitrifiers were higher (84.8%) than those obtained from excised denaturing gradient gel electrophoresis bands or clones of PCR products from total community DNA (ca. 60%). Analysis of the model communities indicated that QPCR accurately predicts gene prevalence in communities composed of up to six templates.
Optimization of medium composition for lipase production byCandida rugosaNCIM 3462 using response surface methodology
Authors: Rajendran Aravindan , Thangavelu Viruthagiri
Published: July 2007

A sequential optimization approach using statistical design of experiments was employed to enhance the lipase production by Candida rugosa in submerged batch fermentation. Twelve medium components were evaluated initially using the Plackett–Burman 2-level factorial design. The significant variables affecting lipase production were found to be glucose, olive oil, peptone, (NH4)2SO4, and FeCl3·6H2O. Various vegetable oils were tested in the second step, and among them, groundnut oil was found to be the best inducer for lipase production by C. rugosa. The third step was to identify the optimal values of the significant medium components with groundnut oil as the inducer using response surface methodology. The regression equation obtained from the experimental data designed using a central composite design was solved, and analyzing the response surface contour plots, the optimal concentrations of the significant variables were determined. A maximum lipase activity of 5.95 U·mL–1, which is 1.64 times the maximum activity obtained in the Plackett–Burman experimental trials, was observed. The optimum combination of medium constituents contained 19.604 g·L–1glucose, 13.065 mL·L–1groundnut oil, 7.473 g·L–1peptone, 0.962 g·L–1(NH4)2SO4, 0.0019 g·L–1FeCl3·6H2O, and other insignificant components at the fixed level. A predictive model of the combined effects of the independent variables using response surface methodology and an artificial neural network was proposed. The unstructured kinetic models, logistic model, and Luedeking–Piret model were used to describe cell mass and lipase production. The parameters of the models were evaluated and the lipase production by C. rugosa was found to be growth associated.
Effect of protease mutations on the production of xylanases in Streptomyces lividans
Authors: Arias Éliana , Li Haiming , Morosoli Rolf
Published: July 2007

Three protease mutants — 7 (tap–), 12 (tap–, ssp–), and 17 (multiple mutations) — of Streptomyces lividans were tested for their influence on protein secretion. Streptomyces lividans grown in xylan secretes 3 xylanases (A, B, and C). Xylanases A (XlnA) and B (XlnB) are secreted by the Sec pathway, whereas xylanase C (XlnC) is secreted by the Tat pathway. The production of XlnA and XlnC was affected in the mutants, suggesting that the mutations interfered with both Sec- and Tat-secretion systems. However, the processing rate for the Sec and Tat precursor was similar to the wild-type strain, indicating that the mutations had no direct effect on secretion. Streptomyces lividans naturally produced 2 forms of XlnB: XlnB1, which contains the catalytic and the xylan-binding domains, and XlnB2, which contains the catalytic domain only. There was no change from the wild-type strain in the ratio of XlnB1/XlnB2 produced by the mutants, indicating that these proteases are not involved in this process. Although XlnA1, partially truncated in its xylan-binding domain, was rapidly degraded to its catalytic domain (XlnA2) in the wild-type strain, the rate of conversion was reduced in the 3 mutants, indicating that the proteases participated to some extent in this proteolytic process.
Myrothecium roridum Tri4 encodes a multifunctional oxygenase required for three oxygenation steps
Authors: McCormick Susan P. , Alexander Nancy J.
Published: July 2007

The biosyntheses of both macrocyclic trichothecenes in Myrothecium roridum and simple trichothecenes in Fusarium species begin with the cyclization of farnesyl pyrophosphate to form the sesquiterpene hydrocarbon trichodiene. A previous study showed that Myrothecium has a cluster of 3 genes that are homologous with Fusarium trichothecene genes: Tri4, a P450 oxygenase; Tri5, the sesquiterpene cyclase; and Tri6, a zinc-finger regulatory gene. Fusarium graminearum Tri4 (FgTri4) and M. roridum MrTri4 (MrTri4) have 66.9% identity. In this study, MrTri4 was expressed in Fusarium verticillioides . Liquid cultures of transformant strains expressing MrTri4 converted exogenous trichodiene to isotrichodiol, indicating that MrTri4 controls 3 oxygenation steps and that the product of MrTRI4 is isotrichodiol.
Impact of protozoan grazing on nitrification and the ammonia- and nitrite-oxidizing bacterial communities in activated sludge
Authors: Pogue Amy J. , Gilbride Kimberley A.
Published: July 2007

In activated sludge, protozoa feed on free-swimming bacteria and suspended particles, inducing flocculation and increasing the turnover rate of nutrients. In this study, the effect of protozoan grazing on nitrification rates under various conditions in municipal activated sludge batch reactors was examined, as was the spatial distribution of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) within the activated sludge. The reactors were monitored for ammonia, nitrite, nitrate, and total nitrogen concentrations, and bacterial numbers in the presence and absence of cycloheximide (a protozoan inhibitor), allylthiourea (an inhibitor of ammonia oxidation), and EDTA (a deflocculating agent). The accumulations of nitrate, nitrite, and ammonia were lower in batches without than with protozoa grazing. Inhibition of ammonia oxidation also decreased the amount of nitrite and nitrate accumulation. Inhibiting protozoan grazing along with ammonia oxidation further decreased the amounts of nitrite and nitrate accumulated. Induction of deflocculation led to high nitrate accumulation, indicating high levels of nitrification; this effect was lessened in the absence of protozoan grazing. Using fluorescent in situ hybridization and confocal laser scanning microscopy, AOB and NOB were found clustered within the floc, and inhibiting the protozoa, inhibiting ammonia oxidation, or inducing flocculation did not appear to lower the number of AOB and NOB present or affect their position within the floc. These results suggest that the AOB and NOB are present but less active in the absence of protozoa.
Metabolism of fatty acid in yeast: addition of reducing agents to the reaction medium influences β-oxidation activities, γ-decalactone production, and cell ultrastructure inSporidiobolus ruineniicultivated on ricinoleic acid methyl ester
Authors: Feron Gilles , Mauvais Geneviève , Lherminier Jeanine , Michel Joël , Wang Xiao-Dong , Viel Christophe , Cachon Rémy
Published: July 2007

The sensitivity of Sporidiobolus ruinenii yeast to the use of reducing agents, reflected in changes in the oxidoreduction potential at pH 7 (Eh7) environment, ricinoleic acid methyl ester catabolism, γ-decalactone synthesis, cofactor level, β-oxidation activity, and ultrastructure of the cell, was studied. Three environmental conditions (corresponding to oxidative, neutral, and reducing conditions) were fixed with the use of air or air and reducing agents (hydrogen and dithiothreitol). Lowering Eh7to neutral conditions (Eh7 = +30 mV and +2.5 mV) favoured the production of lactone more than the more oxidative condition (Eh7 = +350 mV). In contrast, when a reducing condition was used (Eh7= –130 mV), the production of γ-decalactone was very low. These results were linked to changes in the cofactor ratio during lactone production, to the β-oxidation activity involved in decanolide synthesis, and to ultrastructural modification of the cell.
Blind trials evaluating in vitro infectivity ofCryptosporidiumoocysts using cell culture immunofluorescence
Authors: Bukhari Zia , Holt David M. , Ware Michael W. , Schaefer Frank W.
Published: July 2007

An optimized cell culture immunofluorescence (IFA) procedure, using the HCT-8 cell line, was evaluated in blind trials to determine the sensitivity and reproducibility of measuring the infectivity of flow-cytometry-prepared inocula of Cryptosporidium parvum oocysts. In separate trials, suspensions consisting of between 0% and 100% viable oocysts were prepared at the US Environmental Protection Agency, shipped to the American Water Laboratory, and analyzed blindly by cell culture IFA. Data indicated the control (100% live) oocyst suspensions yielded statistically similar results to cell culture dose–response curve data developed previously at the American Water Laboratory. For test samples containing oocyst suspensions of unknown infectivity, cell culture IFA analyses indicated a high degree of correlation (r2= 0.89; n = 26) with the values expected by the US Environmental Protection Agency. Cell culture infectivity correlates well with neonatal mouse infectivity assays, and these blind validation trials provide credibility for the cell culture IFA procedure as a cost-effective and expedient alternative to mouse infectivity assays for determining in vitro infectivity of C. parvum oocysts.
Purification and characterization ofEnterobacter sakazakiienterotoxin
Authors: Raghav Mamta , Aggarwal P.K.
Published: July 2007

Enterobacter sakazakii has recently been recognized as an often fatal neonatal pathogen that rarely infects adults. Although not much is known about factors involved in its pathogenicity, the organism has been reported to produce enterotoxin. Currently, no information is available in the literature about the production and characterization of the enterotoxin. This report is the first attempt regarding purification and biochemical characterization of the enterotoxin produced from E. sakazakii. The toxin was purified by ammonium sulfate precipitation, followed by DEAE cellulose ion exchange and desalting by Sephadex™ G-100. The 66 kDa toxin was most active at pH 6 and was stable at 90 °C for 30 min. This stability combined with the potent activity of the toxin (LD50= 56 pg) emphasizes the potential risk to neonates fed infant milk formula contaminated with E. sakazakii. Further detailed molecular biological studies on the toxin are warranted in view of its stability and activity.
Detection of filamentous genus Gordonia in foam samples using genus-specific primers combined with PCR – denaturing gradient gel electrophoresis analysis
Authors: Shen Fo-Ting , Huang Hsuan-Ru , Arun A.B. , Lu Hui-Ling , Lin Ta-Chen , Rekha P.D. , Young Chiu-Chung
Published: July 2007

A nested-PCR amplification combined with denaturing gradient gel electrophoresis (PCR–DGGE) approach was used to detect and identify Gordonia populations from wastewater treatment plant foam samples. The PCR-amplified region (position 722–1119) by specifically designed primers G699F and G1096R covered the hypervariable region of the Gordonia 16S rRNA gene sequence. This approach successfully distinguished Gordonia species to the interspecies level. The differential ability of PCR–DGGE analysis was effectively used to separate 12 Gordonia species belonging to different 16S rRNA gene-based phylogenetic lineages into 8 groups. Based on this method, the minimum limit of Gordonia detection was 5 × 104CFU·g–1in the seeded soil samples. The PCR–DGGE bands obtained were excised and identified by sequence analysis. Gordonia polyisoprenivorans , Gordonia amicalis , DGGE type II Gordonia species, and an uncertain Gordonia species dominated the activated sludge foam samples. Results of this study indicate that the detection and analyses of genus Gordonia within a complex microbial community could be accomplished using the PCR–DGGE approach to a larger extent, with certain limitations. Detection of diverse Gordonia populations in foam samples from wastewater treatment plants revealed the significant role of Gordonia in biological foaming during wastewater treatment. The nested-PCR amplification and DGGE can be used as a diagnostic tool for the early detection of foaming incidents in wastewater treatment plants using Gordonia as indicator organism.
Characterization ofBacillusandPseudomonasstrains with suppressive traits isolated from tomato hydroponic-slow filtration unit
Authors: Renault D. , Déniel F. , Benizri E. , Sohier D. , Barbier G. , Rey P.
Published: July 2007

Bacillus and Pseudomonas spp. are known to be involved in plant pathogenic fungi elimination during the slow filtration process used in tomato soilless cultures. We isolated 6–8 strains of both Bacillus and Pseudomonas from the top, middle, and bottom sections of filters and identified them after 16S rDNA sequencing. Four Pseudomonas strains were identified as Pseudomonas fulva , 5 as Pseudomonas plecoglossicida , and 12 as Pseudomonas putida . The use of specific oligonucleotide polymerase chain reaction primer sets designed from gyrB gene sequences additionally permitted the identification of 17 Bacillus cereus and 3 Bacillus thuringiensis strains. Ribotyping with EcoRI pointed out an important polymorphism within Bacillus and Pseudomonas strains. Molecular characterization did not reveal a correlation between the location of isolates within the filter (top, middle, or bottom) and bacterial identification or riboclusters. Functional aspects assessed by community-level physiological profiling showed marked phenotypic differences between Pseudomonas communities isolated from the top and bottom filter layers; differences were lower between Bacillus communities of different layers and far less noticeable between mixed communities of Bacillus and Pseudomonas. These strains were tested for several suppressive activities. Conversely to most Bacillus, the majority of Pseudomonas strains were auxin producers and promoted the growth of tomato plantlet roots. On the other hand, only Bacillus strains displayed antagonistic activities by inhibiting the growth of pathogenic fungi frequently detected in soilless cultures. Siderophores were produced by nearly all bacteria, but at higher amounts by Pseudomonas than Bacillus strains. The biocontrol agent potentiality of certain strains to optimize the slow filtration process and to promote the suppressive potential of nutrient solution is discussed.
Predicting green and dry mass of yellow-poplar: an integral approachWest Virginia Agriculture and Forestry Experiment Station Scientific Article 2962.
Authors: Brooks John R. , Jiang Lichun , Zhang  Yujia
Published: July 2007

An integral approach to estimating stem green and dry masses for yellow-poplar (Liriodendron tulipifera L.) in West Virginia was compared with traditional ratio equation methods. The data were based on stem analysis of 26 trees from the Central Appalachian Broadleaf Forest province in northern West Virginia and 18 trees from the Eastern Broadleaf Forest province in west-central West Virginia. Sample disks were extracted from 0.3 m, 0.6 m, 1.37 m, 1.8 m, and then every 1.2 m to an approximate 7.6 cm top diameter outside bark. Sample trees ranged from 17.3 cm to 56.1 cm in diameter and from 18.8 m to 38.5 m in total height. The proposed equation generally performed better for the whole tree as well as for sections within the tree based on the nine relative height classes examined. A constant wood-density equation was superior to the use of a linear wood-density equation as a function of height above the ground. The proposed equation explained over 90% of the variation in stem mass and compared favorably with existing fixed merchantable top mass equations.
Competitive responses of seedlings and understory plants in longleaf pine woodlands: separating canopy influences above and below ground
Authors: Pecot Stephen D. , Mitchell Robert J. , Palik Brian J. , Moser E. Barry , Hiers J. Kevin
Published: July 2007

A trenching study was used to investigate above- and below-ground competition in a longleaf pine ( Pinus palustris P. Mill.) woodland. Trenched and nontrenched plots were replicated in the woodland matrix, at gap edges, and in gap centers representing a range of overstory stocking. One-half of each plot received a herbicide treatment to remove the understory. We monitored pine survival and growth, understory productivity, light level (gap fraction), and soil resources. The overstory facilitated pine seedling survival. Pine seedling growth was reduced as overstory stocking increased. Reduced growth of seedlings was also observed in gaps when the understory was left intact. Understory plants competed with seedlings by filling the root gaps that developed as a result of overstory disturbance. Hardwood growth increased in gaps, owing to decreased belowground competition with adult pines, while growth of herbaceous plants and pine seedlings increased with light availability. Large overstory gaps are not required to initiate regeneration in longleaf pine woodlands. Retaining overstory dispersed throughout the stand but variable in density, through single-tree selection approaches, may be an alternative to gap-based approaches. This approach would allow for the fuel continuity needed to sustain the frequent fire required to maintain the diversity characteristic of this type of woodland.
Clonal-row versus random seed orchard designs: interior spruce mating system evaluation
Authors: El-Kassaby Y.A. , Stoehr M.U. , Reid D. , Walsh C.G. , Lee T.E.
Published: July 2007

Mating system pattern (selfing or outcrossing and correlated matings levels) comparisons between two interior spruce seed orchard designs (clonal-row and random) managed under intensive crown and pollen management were conducted. Crown manipulation consisted of tree topping and branch pruning, while pollen management involved multiple supplemental mass-pollination applications during peak seed-cone reproductive receptivity and pollen agitation using helicopters. Significant differences between orchards’ multilocus outcrossing rate estimates were observed, and both estimates significantly departed from complete outcrossing (t = 1.0). Clonal arrangements in the clonal-row design permitted higher chances for selfing (t = 0.948) in comparison with those of the random design (t = 0.989). Intensive pollen management, while effective, still produced a minor component of selfing. Both orchard designs produced similar individual tree's outcrossing rate trends with the majority showing high outcrossing, while few individuals showed high selfing propensity. Estimates of correlated mating varied substantially between the two seed orchard designs with 9.3% and 4.3% for the clonal-row and random seed orchards, respectively. While small but significant differences in the genetic quality of the seed crops were observed between the two orchard designs, the establishment of clonal-row seed orchards should be given serious considerations specifically under committed pollen and crown management. The ease of crop and orchard management in the clonal-row design outweighs the observed differences in the seed crop genetic quality. A slight modification to the clonal-row design is proposed and is expected to reduce the observed minor genetic quality differences between the two orchard designs.
Modeling corewood–outerwood transition in loblolly pine using wood specific gravity
Authors: Mora Christian R. , Allen H. Lee , Daniels Richard F. , Clark Alexander
Published: July 2007

A modified logistic function was used for modeling specific-gravity profiles obtained from X-ray densitometry analysis in 675 loblolly pine ( Pinus taeda L.) trees in four regeneration trials. Trees were 21 or 22 years old at the time of the study. The function was used for demarcating corewood, transitional, and outerwood zones. Site and silvicultural effects were incorporated into the model. Heteroscedasticity and within-group correlation were accounted for by specifying the variance and serial-correlation structure, respectively. The estimated transition zone was located between rings 5 and 15, and the outerwood demarcation point varied from rings 12 to 15. No effects of treatments on the demarcation points were observed; however, site preparation and fertilization affected the lower asymptotes of the curves in all sites. A geographical trend for the demarcation point was observed, with the northern site requiring more time to reach a plateau in specific gravity compared with the southern sites. The diameter of the juvenile core was increased as a result of the treatments. However, the amount of corewood was not statistically affected, ranging from 55% in the north to 75% in the south, except at one site where fertilization decreased the percentage of corewood.
Bridging native and scientific observations of snowshoe hare habitat restoration after clearcutting to set wildlife habitat management guidelines on Waswanipi Cree land
Authors: Jacqmain Hugo , Bélanger Louis , Hilton Susanne , Bouthillier Luc
Published: July 2007

Large-scale timber harvesting in the northern black spruce forest, on Quebec Cree territory, causes immediate loss of productive wildlife habitat for Cree hunters. Duration of this impact is key information to improve forest management. The objective here was to examine the postharvesting habitat restoration delay for snowshoe hare, a species valuable to Cree hunters, as well as a wildlife indicator of the sapling stage. A minimum threshold for vegetation development was established, at which the return of hare populations is considered acceptable by Cree hunters. To do so, an adaptive approach was used, combining Cree hunter knowledge and biological assessment. Hare populations were monitored in 36 cut blocks, ranging from 0 to 30 years after harvest. Cree hunters were interviewed to determine when a cut block becomes adequate for snaring. The combined analysis of the two knowledge sources indicated that stands that meet the threshold average 4 m in height, 6300 trees/ha in density, and are aged between 13 and 27 years. Current regulation sets this threshold at 3 m in height, regardless of cut block scale, and at 20 years postcut when considering family hunting ground scale, and thus, does not fully meet sustainable resource development objectives.
Modelling the influence of weed competition on growth of young Pinus radiata. Development and parameterization of a hybrid model across an environmental gradient
Authors: Watt Michael S. , Kimberley Mark O. , Coker Graham , Richardson Brian , Estcourt George
Published: July 2007

A hybrid tree growth model sensitive to competition from a diverse range of weed species was developed and validated using data from a nationwide series of 24 plots covering an extensive environmental gradient. Tree growth in plots with weeds over the first 3 years following establishment was predicted by reducing potential growth from an empirically determined optimum rate for the site (weed free) using a competition modifier, which accounts for the degree of weed competition for both light and water availability. Diameter growth of trees in plots with weeds was initially predicted by including a light competition modifier into the model developed for weed-free plots. This model accounted for 87% of the variance in diameter of trees growing with weeds. Although inclusion of this modifier provided unbiased predictions of tree diameter growth on wet sites, model predictions overestimated diameter growth on dryland sites by on average 11%. Addition of a competition index for water based on treatment differences in average fractional available root-zone volumetric water content significantly (p < 0.001) improved the precision (R2 = 0.96) and reduced the bias of the overall model. A cross validation of this final model indicated it was unbiased and relatively accurate (R2 = 0.95).
Winter conditions in eastern hemlock and mixed-hardwood deer wintering areas of Vermont
Authors: Lishawa Shane C. , Bergdahl Dale R. , Costa Scott D.
Published: July 2007

In regions experiencing harsh winter, eastern hemlock ( Tsuga canadensis (L.) Carrière) is thought to moderate winter conditions and provide cover for white-tailed deer ( Odocoileus virginianus Zimmerman, 1780). In Vermont, USA, eastern hemlock is the dominant tree in many white-tailed deer wintering areas. Hemlock woolly adelgid ( Adelges tsugae Annand; HWA), an insect introduced from Asia, is causing widespread mortality of eastern hemlock. HWA cold-hardiness research and cold-hardiness zone climate models predict that HWA is capable of winter survival in portions of southern Vermont. This study quantifies the effects of eastern hemlock cover on winter temperatures and snow depths and assesses the effect of hemlock dominance on the winter severity values for white-tailed deer and on cold hardiness zone designations. Within site-paired eastern hemlock and hardwood stands, temperatures were recorded at 30 min intervals and snow depths were recorded every 2 weeks in the winters of 2003–2004 and 2004–2005. Extreme temperatures and snow depths were significantly moderated within hemlock stands. In southern Vermont, eastern hemlock mortality caused by HWA will alter these pockets of moderated microclimate, adding additional stress to white-tailed deer. Furthermore, the magnitude of temperature buffering in hemlock stands suggests that HWA may be capable of winter survival farther north than previously estimated.
Dwarf mistletoe effects on fuel loadings in ponderosa pine forests in northern Arizona
Authors: Hoffman Chad , Mathiasen Robert , Sieg Carolyn Hull
Published: July 2007

Southwestern dwarf mistletoe ( Arceuthobium vaginatum (Willd.) J. Presl ssp. cryptopodum ) infests about 0.9 million ha in the southwestern United States. Several studies suggest that dwarf mistletoes affect forest fuels and fire behavior; however, few studies have quantified these effects. We compared surface fuel loadings and predicted fire behavior among four levels of dwarf mistletoe infestation (none, light, moderate, and severe) in a total of 239 plots on 11 sites on basaltic soils in northern Arizona. In each plot we measured tree attributes, dwarf mistletoe rating and surface fuel loading. Stands severely infested by dwarf mistletoe had lower (P < 0.05) tree density and higher snag density, but higher (P < 0.05) total surface fuel loadings and total fuel loadings >7.62 cm and <7.62 cm, than non-infested stands. However, there were no statistical differences in any canopy fuel variables among infestation classes. Predicted fire behavior indicated that the wind speed required to promote the spread of a surface fire into the canopy was lower in severely infested stands than in non-infested stands. These results suggest that stands in northern Arizona that are severely infested with dwarf mistletoe should be priority areas for fuels treatments.
Combining microsatellites, growth, and adaptive traits for managing in situ genetic resources ofEucalyptus urophylla
Authors: Tripiana Vincent , Bourgeois Michaël , Verhaegen Daniel , Vigneron Philippe , Bouvet Jean-Marc
Published: July 2007

Genetic diversity and structure of 17 populations representative of the natural range of Eucalyptus urophylla S.T. Blake in Indonesia were analysed with 10 microsatellite markers. Two provenance and progeny trials, using the same populations, were established in the Republic of the Congo and analysed for growth and survival at 37 months. Observed microsatellite heterozygosity (Ho) was moderate to high within populations (Ho= 0.51–0.72). The index of fixation (FIS) was significantly different from zero for all populations (FIS= 0.13–0.31) and possibly resulted from a Wahlund effect. The differentiation parameter was low (FST= 0.04) and not significantly different from zero, which can be explained by effective gene flow via pollen. The genetic variances within and among provenances for survival and growth traits were significantly different from zero, representing 13%–23% and 14%–50% of the total variation, respectively. The differentiation between populations based on quantitative traits was marked (QST= 0.07–0.33). A negative relationship between altitude of the seed source and its performance in the Congo was observed (R2= 0.59–0.67) and could be explained by the effect of natural selection along the altitudinal gradient. This marked differentiation for quantitative traits despite high apparent gene flow results in a clinal variation, which suggests the use of altitude of seed source as an important principle for in situ or ex situ management of E. urophylla genetic resources.
The relationship between tree growth patterns and likelihood of mortality: a study of two tree species in the Sierra Nevada
Authors: Das Adrian J. , Battles John J. , Stephenson Nathan L. , van Mantgem Phillip J.
Published: July 2007

We examined mortality of Abies concolor (Gord. & Glend.) Lindl. (white fir) and Pinus lambertiana Dougl. (sugar pine) by developing logistic models using three growth indices obtained from tree rings: average growth, growth trend, and count of abrupt growth declines. For P. lambertiana, models with average growth, growth trend, and count of abrupt declines improved overall prediction (78.6% dead trees correctly classified, 83.7% live trees correctly classified) compared with a model with average recent growth alone (69.6% dead trees correctly classified, 67.3% live trees correctly classified). For A. concolor, counts of abrupt declines and longer time intervals improved overall classification (trees with DBH ≥20 cm: 78.9% dead trees correctly classified and 76.7% live trees correctly classified vs. 64.9% dead trees correctly classified and 77.9% live trees correctly classified; trees with DBH <20 cm: 71.6% dead trees correctly classified and 71.0% live trees correctly classified vs. 67.2% dead trees correctly classified and 66.7% live trees correctly classified). In general, count of abrupt declines improved live-tree classification. External validation of A. concolor models showed that they functioned well at stands not used in model development, and the development of size-specific models demonstrated important differences in mortality risk between understory and canopy trees. Population-level mortality-risk models were developed for A. concolor and generated realistic mortality rates at two sites. Our results support the contention that a more comprehensive use of the growth record yields a more robust assessment of mortality risk.