bluuebunny/crossref_metadata_2025 huggingface dataset:
Source Zone Natural Attenuation at Petroleum Hydrocarbon Spill Sites—II: Application to a Former Oil Field
Authors: Lundegard Paul D. , Johnson Paul C.
Published: November 2006

Petroleum spills often create persistent “source zones” of hydrocarbon‐impacted soils that are either in direct contact with ground water or in indirect contact through soil moisture infiltration and dissolution. Understanding the natural attenuation of source zones is critical to anticipating their longevity and the future chemical composition of their associated dissolved ground water and vapor plumes. A companion paper to this work presents an approach for site‐specific assessment of source zone natural attenuation (SZNA), based on three levels of data collection and analysis oriented toward answering common questions of interest. Use of this SZNA assessment approach is illustrated here through application to the 3000‐acre former Guadalupe Oil Field in California, where numerous petroleum source zones are present within a dune sand aquifer system. SZNA processes and mass loss rates are assessed through use of data from geochemical profiles of continuous cores, nested ground water wells, and soil‐gas probes. Mass loss rates are estimated by quantifying fluxes of dissolved electron acceptors and degradation products in ground water and in soil gas. Under current conditions, gas transport processes coupled with aerobic and anaerobic biodegradation acting on exposed portions (above the water table) of source zones are the most significant loss mechanisms. Depending on the depth of contamination and other factors, the mass loss rate per unit surface area for those processes varies from approximately 0.1 to 1.0 kg total petroleum hydrocarbons per m2/year. In comparison, mass losses from the submerged part of the source zone and involving ground water transport processes (i.e., dissolution and biodegradation) were estimated to be about approximately 2 orders of magnitude lower. Once aerobically degradable hydrocarbons above the water table are depleted, the slower mass loss processes operating on the submerged parts of the source will control source zone mass loss.
International Production and Distribution Networks in East Asia: Eighteen Facts, Mechanics, and Policy Implications*
Authors: KIMURA Fukunari
Published: November 2006

International production/distribution networks in East Asia developed in the 1990s and after have distinctive features in their significance, extensiveness, and sophistication. This paper first lists “18 facts” on production/distribution networks in East Asia that have been identified by a number of studies using international trade data, microdata of Japanese multinational enterprises, and casual observations. It then presents a concept of two‐dimensional fragmentation as a starting point of theoretically formalizing the phenomena of fragmentation and agglomeration. It finally discusses the policy environment in which the formation of production/distribution networks has been accelerated and policy implications of the existence of such networks for economic integration in East Asia.
What's new about wandering behaviour? An assessment of recent studies
Authors: Algase Donna L.
Published: November 2006

Problem.  The number and quality of studies on wandering and other behaviours has lagged that of biological sciences in the field of dementia research. Recent studies of wandering are examined for quantity, rigour, and findings.

Approach.  Medline, CINAHL and PsychInfo were searched systematically for studies of wandering. Research reports were reviewed and data was abstracted to characterise quantity and rigour. Study findings were organised by topic and summarised.

Results.  Between 2003 and 2005 inclusive, 47 studies met inclusion criteria. The largest proportion of studies was quantitative and descriptive; an explicit theory or framework guided about half of the studies. Major findings encompassed quantification and description, epidemiology, associated factors, and intervention and management of wandering.

Conclusions.  The growing body of research on wandering in becoming more rigorous. Newer measures of wandering have strong psychometric properties. Wandering occurs in multiple dementias and affects patients in larger numbers as dementia worsens. Wandering manifests similarly across cultural/ethnic groups and care settings and is associated with falls and increased mortality. A variety of interventions have been evaluated, but studies lack rigour.
Evaluation of Solanum xanthocarpum extract as a synergist for cypermethrin against larvae of the filarial vector Culex quinquefasciatus (Say)
Authors: MOHAN Lalit , SHARMA Preeti , SRIVASTAVA C. N.
Published: November 2006

Cypermethrin and crude extracts of Solanum xanthocarpum were both observed for their larvicidal activity against Culex quinquefasciatus. Petroleum ether extract with lethal concentration (LC)50 and LC90 of 41.28 and 111.16 p.p.m. after 24 h and LC50 38.48 and LC90 80.83 p.p.m. after 48 h, respectively, was found to be the most effective, followed by carbon tetrachloride and methanol extracts. LC50 and LC90 for cypermethrin were 0.0027 and 0.0097 p.p.m. after 24 h and 0.0013 and 0.0092 p.p.m. after 48 h of exposure, respectively. Combined formulations were evaluated for synergistic activity and a 1:1 ratio of cypermethrin and petroleum ether extract was observed to be more effective than 1:2 and 1:4 ratios. Combinations of S. xanthocarpum extracts and cypermethrin demonstrated higher larvicidal activity, indicating synergistic activity. These results demonstrate the need for further studies on the effectiveness and toxicity to humans and animals, particularly aquatic forms.
A Failure Assessment Method for a Pipe Bend Subjected to Both a Bending Moment and Internal Pressure
Authors: Yoshikawa Masaki , Katoh Akihiko , Sasaki Kazuaki
Published: November 2006

This paper proposes a new failure assessment method for a steel pipe bend subjected to both a bending moment and internal pressure. Consistent with previous studies, it was shown that the maximum bending moment of a pipe bend subjected to a bending moment increases with the addition of internal pressure. However, it was experimentally confirmed that the addition of this internal pressure has the detrimental effect of significantly reducing the critical deformation (maximum bending angle) of the pipe bend. In addition, it was found that, subsequent to the application of a large deflection, cracks initiate at the most deformed part of the pipe bend during the process of unloading the internal pressure and then the applied load. Herein, the authors propose a practical failure assessment method which uses small-scale tests and nonlinear finite element (FE) analyses to predict the critical deformation and crack initiation position for a full-scale pipe bend. The failure criterion, which uses principal stress, mean stress, and equivalent plastic strain, was developed using small-scale tests. A failure assessment was conducted by comparing the predictions of this criterion with stress and strain histories obtained from FE analyses. Also, the authors’ failure criterion was compared with previous failure criteria, and the advantages/disadvantages discussed.
Rotational Buoyancy Effects on Heat Transfer in Five Different Aspect-Ratio Rectangular Channels With Smooth Walls and 45Degree Ribbed Walls
Authors: Fu Wen-Lung , Wright Lesley M. , Han Je-Chin
Published: November 2006

This paper experimentally studies the effects of the buoyancy force and channel aspect ratio (W:H) on heat transfer in two-pass rotating rectangular channels with smooth walls and 45deg ribbed walls. The channel aspect ratios include 4:1, 2:1, 1:1, 1:2, and 1:4. Four Reynolds numbers are studied: 5000, 10,000, 25,000, and 40,000. The rotation speed is fixed at 550rpm for all tests, and for each channel, two channel orientations are studied: 90deg and 45 or 135deg, with respect to the plane of rotation. The maximum inlet coolant-to-wall density ratio (Δρ∕ρ)inlet is maintained around 0.12. Rib turbulators are placed on the leading and trailing walls of the channels at an angle of 45deg to the flow direction. The ribs have a 1.59 by 1.59mm square cross section, and the rib pitch-to-height ratio (P∕e) is 10 for all tests. Under the fixed rotation speed (550rpm) and fixed inlet coolant-to-wall density ratio (0.12), the local buoyancy parameter is varied with different Reynolds numbers, local rotating radius, local coolant-to-wall density ratio, and channel hydraulic diameter. The effects of the local buoyancy parameter and channel aspect ratio on the regional Nusselt number ratio are presented. The results show that increasing the local buoyancy parameter increases the Nusselt number ratio on the trailing surface and decreases the Nusselt number ratio on the leading surface in the first pass for all channels. However, the trend of the Nusselt number ratio in the second pass is more complicated due to the strong effect of the 180deg turn. Results are also presented for this critical turn region of the two-pass channels. In addition to these regions, the channel averaged heat transfer, friction factor, and thermal performance are determined for each channel. With the channels having comparable Nusselt number ratios, the 1:4 channel has the superior thermal performance because it incurs the least pressure penalty.
Quadrupole mass spectrometry desorption analysis of Ga adsorbate on AlN (0001)
Authors: Brown Jay S. , Koblmüller Gregor , Averbeck Robert , Riechert Henning , Speck James S.
Published: November 2006

The authors have investigated the adsorption and subsequent desorption of Ga on AlN (0001) with line-of-sight quadrupole mass spectrometry (QMS). The authors present desorption data consistent with a continuous Ga-flux dependent accumulation of a laterally contracted Ga bilayer on AlN (0001) from 0 to 2.7±0.3 ML GaN equivalent coverage, and further Ga accumulation in macroscopic Ga droplets. The temperature dependence of Ga-adsorbate QMS desorption transients was investigated and the authors determined that the desorption activation energies for individual monolayers of the Ga adsorbate on AlN (0001) were similar to Ga desorption from GaN (0001). For the (first) pseudomorphic Ga-adsorbate monolayer on AlN, the authors measured a maximum Ga coverage of 1.0±0.1 ML and desorption activation energy of 6.2±0.3eV. For the (second) laterally contracted Ga monolayer (1.7±0.3 ML) the desorption activation energy was 3.8±0.1eV.
Time-resolved measurements of the E-to-H mode transition in electronegative pulse-modulated inductively coupled plasmas
Authors: Edamura Manabu , Benck Eric C. , Wang Yicheng
Published: November 2006

Time-resolved measurements of electronegative pulse-modulated inductively coupled plasmas (ICPs) were carried out using various measurement techniques. In order to explain the experimentally observed results, it is proposed that the structure of an Ar∕CF4 plasma during an afterglow dynamically changes, passing through three stages when the period of the afterglow is long enough: (1) The first stage is the initial afterglow where the electron temperature suddenly decreases due to inelastic collision with CF4. Electron density decreases and the density of fluorine negative ions increases by electron attachment, but the sheath potential still exists and the negative ions are confined in the bulk plasma region. Since charge neutrality should be maintained, the density of positive ions is almost constant during this stage. (2) The second stage is the intermediate afterglow where the plasma consists mainly of negative and positive ions but sheath potentials remain, reducing the negative ion flux from the plasma. The sheath potential gradually disappears and the densities of all the charged particles (electrons and positive and negative ions) decrease because of increased loss to the wall surface. (3) The third stage is where the sheath structure has disappeared completely, and the plasma consists of mainly positive and negative ions and losses are dominated by ambipolar diffusion. The presence of these stages during the afterglow is very important in understanding the behavior of pulsed ICPs with E-to-H mode transitions. The state of an afterglow plasma at the moment power is reapplied determines the discharge characteristics of the pulsed ICPs (e.g., the appearance of an E mode, the duration of the E mode, stability of the plasma).
Interarticulator programming: Effects of closure duration on lip and tongue coordination in Japanese
Authors: Löfqvist Anders
Published: November 2006

This paper examines the coordination of lip and tongue movements in sequences of vowel-bilabial consonant-vowel where the duration of the oral closure for the consonant is varied for linguistic purposes. Native speakers of Japanese served as subjects. The linguistic material consisted of Japanese word pairs that only differed in the duration of the labial consonant, which was either long or short. Recordings were made of lip and tongue movements using a magnetometer system. Results show a robust difference in closure duration between the long and short consonants. The tongue movement from the first to the second vowel had a longer duration in the long than in the short consonants, and its average speed was slower in the long consonant. The size of the tongue movement path between the vowels did not consistently differ between the long and short consonants. The tongue movement almost always started before the oral closure for the consonant, while the onset of the lip movement towards oral closure mostly started before that of the tongue movement. The offset of the tongue movement occurred after the release of the closure, but there was no clear pattern for the long and short consonants.
Frequency and amplitude discrimination along the kinesthetic-cutaneous continuum in the presence of masking stimuli
Authors: Israr Ali , Tan Hong Z. , Reed Charlotte M.
Published: November 2006

Frequency and amplitude discrimination thresholds along the kinesthetic to cutaneous continuum were evaluated on the left index fingerpad using a multifinger tactual display. Target stimuli were presented either in isolation (no-masker condition) or in the presence of masking stimuli (one- or two-masker conditions). Six reference target signals in the frequency range 2–300Hz (two each from low-, medium-, and high-frequency regions) and at an amplitude of either 20 or 35dB sensation levels (SL) were used. In the no-masker condition, the range of frequency Weber fraction was 0.13–0.38 and 0.14–0.28, and the range of amplitude discrimination threshold was 1.82–2.98dB and 1.65–2.71dB, at 20 and 35dB SL, respectively. In the masking conditions, average frequency Weber fractions rose to 0.60 and 0.46, and average amplitude thresholds rose to 3.63 and 3.72dB, at 20 and 35dB SL, respectively. In general, thresholds were largest in the two-masker condition and lowest in the no-masker condition. Although the frequency and amplitude thresholds generally increased in the presence of masking stimuli, there was some indication of channel independence for low- and high-frequency target stimuli. The implications of the results for tactual communication of speech are discussed.
Multiple source localization using a maximuma posterioriGibbs sampling approach
Authors: Michalopoulou Zoi-Heleni
Published: November 2006

Multiple source localization in underwater environments is approached within a matched-field processing framework. A maximum a posteriori estimation method is proposed that estimates source location and spectral characteristics of multiple sources via Gibbs sampling. The method facilitates localization of weak sources which are typically masked by the presence of strong interferers. A performance evaluation study based on Monte Carlo simulations shows that the proposed maximum a posteriori estimation approach is superior to simple coherent matched-field interference cancellation. The proposed method is also tested on the estimation of the number of sources present, providing probability distributions in addition to point estimates for the number of sources.
Sound speed and attenuation measurements in unconsolidated glass-bead sediments saturated with viscous pore fluids
Authors: Hefner Brian T. , Williams Kevin L.
Published: November 2006

As part of a recent ocean sediment acoustics experiment, a number of independent sound speed and attenuation measurements were made in a well-characterized sandy sediment. These measurements covered a broad frequency range and were used to test both Biot-Stoll theory and Buckingham’s more recent grain-to-grain shearing model. While Biot theory was able to model the sound speed well, it was unable to predict the attenuation measured above 50kHz. This paper presents a series of measurements made in the laboratory on a simple glass-bead sediment. One goal of these measurements was to test the hypothesis that the attenuation measured at-sea was a result of scattering from shells within the sediment. The laboratory sediments used were saturated with fluids with different viscosities in order (assuming that Biot-Stoll theory is correct) to shift the dispersion into the frequency range of the measurement system. The measured attenuation in the glass-bead sediments exhibited the same frequency dependence as observed in the ocean experiment even though no shells were present. The laboratory results motivated development of a sediment model which incorporates both fluid viscosity and grain-to-grain interactions as embodied in a simple frequency-dependent, imaginary frame modulus first suggested by Biot.
New Strategies for the Elimination of Polio from India
Authors: Grassly Nicholas C. , Fraser Christophe , Wenger Jay , Deshpande Jagadish M. , Sutter Roland W. , Heymann David L. , Aylward R. Bruce
Published: November 2006

The feasibility of global polio eradication is being questioned as a result of continued transmission in a few localities that act as sources for outbreaks elsewhere. Perhaps the greatest challenge is in India, where transmission has persisted in Uttar Pradesh and Bihar despite high coverage with multiple doses of vaccine. We estimate key parameters governing the seasonal epidemics in these areas and show that high population density and poor sanitation cause persistence by not only facilitating transmission of poliovirus but also severely compromising the efficacy of the trivalent vaccine. We analyze strategies to counteract this and show that switching to monovalent vaccine may finally interrupt virus transmission.
Solar Wind Neon from Genesis: Implications for the Lunar Noble Gas Record
Authors: Grimberg Ansgar , Baur Heinrich , Bochsler Peter , Bühler Fritz , Burnett Donald S. , Hays Charles C. , Heber Veronika S. , Jurewicz Amy J. G. , Wieler Rainer
Published: November 2006

Lunar soils have been thought to contain two solar noble gas components with distinct isotopic composition. One has been identified as implanted solar wind, the other as higher-energy solar particles. The latter was puzzling because its relative amounts were much too large compared with present-day fluxes, suggesting periodic, very high solar activity in the past. Here we show that the depth-dependent isotopic composition of neon in a metallic glass exposed on NASA's Genesis mission agrees with the expected depth profile for solar wind neon with uniform isotopic composition. Our results strongly indicate that no extra high-energy component is required and that the solar neon isotope composition of lunar samples can be explained as implantation-fractionated solar wind.
Diguanylate Cyclases Control Magnesium-Dependent Motility ofVibrio fischeri
Authors: O'Shea Therese M. , Klein Adam H. , Geszvain Kati , Wolfe Alan J. , Visick Karen L.
Published: November 2006

Flagellar biogenesis and hence motility ofVibrio fischeridepends upon the presence of magnesium. In the absence of magnesium, cells contain few or no flagella and are poorly motile or nonmotile. To dissect the mechanism by which this regulation occurs, we screened transposon insertion mutants for those that could migrate through soft agar medium lacking added magnesium. We identified mutants with insertions in two distinct genes, VF0989 and VFA0959, which we termedmifAandmifB, respectively, formagnesium-dependentinduction offlagellation. Each gene encodes a predicted membrane-associated protein with diguanylate cyclase activity. Consistent with that activity, introduction intoV. fischeriof medium-copy plasmids carrying these genes inhibited motility. Furthermore, multicopy expression ofmifAinduced other phenotypes known to be correlated with diguanylate cyclase activity, including cellulose biosynthesis and biofilm formation. To directly test their function, we introduced the wild-type genes on high-copy plasmids intoEscherichia coli. We assayed for the production of cyclic di-GMP using two-dimensional thin-layer chromatography and found that strains carrying these plasmids produced a small but reproducible spot that migrated with anRfvalue consistent with cyclic di-GMP that was not produced by strains carrying the vector control. Disruptions ofmifAormifBincreased flagellin levels, while multicopy expression decreased them. Semiquantitative reverse transcription-PCR experiments revealed no significant difference in the amount of flagellin transcripts produced in either the presence or absence of Mg2+by either vector control ormifA-overexpressing cells, indicating that the impact of magnesium and cyclic-di-GMP primarily acts following transcription. Finally, we present a model for the roles of magnesium and cyclic di-GMP in the control of motility ofV. fischeri.
Experimental and Computational Assessment of Conditionally Essential Genes inEscherichia coli
Authors: Joyce Andrew R. , Reed Jennifer L. , White Aprilfawn , Edwards Robert , Osterman Andrei , Baba Tomoya , Mori Hirotada , Lesely Scott A. , Palsson Bernhard Ø. , Agarwalla Sanjay
Published: November 2006

Genome-wide gene essentiality data sets are becoming available forEscherichia coli, but these data sets have yet to be analyzed in the context of a genome scale model. Here, we present an integrative model-driven analysis of the KeioE. colimutant collection screened in this study on glycerol-supplemented minimal medium. Out of 3,888 single-deletion mutants tested, 119 mutants were unable to grow on glycerol minimal medium. These conditionally essential genes were then evaluated using a genome scale metabolic and transcriptional-regulatory model ofE. coli, and it was found that the model made the correct prediction in ∼91% of the cases. The discrepancies between model predictions and experimental results were analyzed in detail to indicate where model improvements could be made or where the current literature lacks an explanation for the observed phenotypes. The identified set of essential genes and their model-based analysis indicates that our current understanding of the roles these essential genes play is relatively clear and complete. Furthermore, by analyzing the data set in terms of metabolic subsystems across multiple genomes, we can project which metabolic pathways are likely to play equally important roles in other organisms. Overall, this work establishes a paradigm that will drive model enhancement while simultaneously generating hypotheses that will ultimately lead to a better understanding of the organism.
GroES/GroEL and DnaK/DnaJ Have Distinct Roles in Stress Responses and during Cell Cycle Progression inCaulobacter crescentus
Authors: Susin Michelle F. , Baldini Regina L. , Gueiros-Filho Frederico , Gomes Suely L.
Published: November 2006

Misfolding and aggregation of protein molecules are major threats to all living organisms. Therefore, cells have evolved quality control systems for proteins consisting of molecular chaperones and proteases, which prevent protein aggregation by either refolding or degrading misfolded proteins. DnaK/DnaJ and GroES/GroEL are the best-characterized molecular chaperone systems in bacteria. InCaulobacter crescentusthese chaperone machines are the products of essential genes, which are both induced by heat shock and cell cycle regulated. In this work, we characterized the viabilities of conditionaldnaKJandgroESLmutants under different types of environmental stress, as well as under normal physiological conditions. We observed thatC. crescentuscells with GroES/EL depleted are quite resistant to heat shock, ethanol, and freezing but are sensitive to oxidative, saline, and osmotic stresses. In contrast, cells with DnaK/J depleted are not affected by the presence of high concentrations of hydrogen peroxide, NaCl, and sucrose but have a lower survival rate after heat shock, exposure to ethanol, and freezing and are unable to acquire thermotolerance. Cells lacking these chaperones also have morphological defects under normal growth conditions. The absence of GroE proteins results in long, pinched filamentous cells with several Z-rings, whereas cells lacking DnaK/J are only somewhat more elongated than normal predivisional cells, and most of them do not have Z-rings. These findings indicate that there is cell division arrest, which occurs at different stages depending on the chaperone machine affected. Thus, the two chaperone systems have distinct roles in stress responses and during cell cycle progression inC. crescentus.
DNA Adenine Methylation Regulates Virulence Gene Expression in
Salmonella enterica
Serovar Typhimurium
Authors: Balbontín Roberto , Rowley Gary , Pucciarelli M. Graciela , López-Garrido Javier , Wormstone Yvette , Lucchini Sacha , García-del Portillo Francisco , Hinton Jay C. D. , Casadesús Josep
Published: November 2006

Transcriptomic analyses during growth in Luria-Bertani medium were performed in strain SL1344 of
Salmonella enterica
serovar Typhimurium and in two isogenic derivatives lacking Dam methylase. More genes were repressed than were activated by Dam methylation (139 versus 37). Key genes that were differentially regulated by Dam methylation were verified independently. The largest classes of Dam-repressed genes included genes belonging to the SOS regulon, as previously described in
Escherichia coli
, and genes of the SOS-inducible
Salmonella
prophages ST64B, Gifsy-1, and Fels-2. Dam-dependent virulence-related genes were also identified. Invasion genes in pathogenicity island SPI-1 were activated by Dam methylation, while the fimbrial operon
std
was repressed by Dam methylation. Certain flagellar genes were repressed by Dam methylation, and Dam
−
mutants of
S. enterica
showed reduced motility. Altered expression patterns in the absence of Dam methylation were also found for the chemotaxis genes
cheR
(repressed by Dam) and STM3216 (activated by Dam) and for the Braun lipoprotein gene,
lppB
(activated by Dam). The requirement for DNA adenine methylation in the regulation of specific virulence genes suggests that certain defects of
Salmonella
Dam
−
mutants in the mouse model may be caused by altered patterns of gene expression.
Characterization of
myo
-Inositol Utilization by
Corynebacterium glutamicum
: the Stimulon, Identification of Transporters, and Influence on
l
-Lysine Formation
Authors: Krings Eva , Krumbach Karin , Bathe Brigitte , Kelle Ralf , Wendisch Volker F. , Sahm Hermann , Eggeling Lothar
Published: November 2006

Although numerous bacteria possess genes annotated
iol
in their genomes, there have been very few studies on the possibly associated
myo
-inositol metabolism and its significance for the cell. We found that
Corynebacterium glutamicum
utilizes
myo
-inositol as a carbon and energy source, enabling proliferation with a high maximum rate of 0.35 h
−1
. Whole-genome DNA microarray analysis revealed that 31 genes respond to
myo
-inositol utilization, with 21 of them being localized in two clusters of >14 kb. A set of genomic mutations and functional studies yielded the result that some genes in the two clusters are redundant, and only cluster I is necessary for catabolizing the polyol. There are three genes which encode carriers belonging to the major facilitator superfamily and which exhibit a >12-fold increased mRNA level on
myo
-inositol. As revealed by mutant characterizations, one carrier is not involved in
myo
-inositol uptake whereas the other two are active and can completely replace each other with apparent

K
m

s for
myo
-inositol as a substrate of 0.20 mM and 0.45 mM, respectively. Interestingly, upon utilization of
myo
-inositol, the
l
-lysine yield is 0.10 mol/mol, as opposed to 0.30 mol/mol, with glucose as the substrate. This is probably not only due to
myo
-inositol metabolism alone since a mixture of 187 mM glucose and 17 mM
myo
-inositol, where the polyol only contributes 8% of the total carbon, reduced the
l
-lysine yield by 29%. Moreover, genome comparisons with other bacteria highlight the core genes required for growth on
myo
-inositol, whose metabolism is still weakly defined.
In Silico Prediction and Functional Validation of σ
28
-Regulated Genes in
Chlamydia
and
Escherichia coli
Authors: Yu Hilda Hiu Yin , Kibler Dennis , Tan Ming
Published: November 2006

σ
28
RNA polymerase is an alternative RNA polymerase that has been proposed to have a role in late developmental gene regulation in
Chlamydia
, but only a single target gene has been identified. To discover additional σ
28
-dependent genes in the
Chlamydia trachomatis
genome, we applied bioinformatic methods using a probability weight matrix based on known σ
28
promoters in other bacteria and a second matrix based on a functional analysis of the σ
28
promoter. We tested 16 candidate σ
28
promoters predicted with these algorithms and found that 5 were active in a chlamydial σ
28
in vitro transcription assay.
hctB
, the known σ
28
-regulated gene, is only expressed late in the chlamydial developmental cycle only, and two of the newly identified σ
28
target genes (
tsp
and
tlyC_1
) also have late expression profiles, providing support for σ
28
as a regulator of late gene expression. One of the other novel σ
28
-regulated genes is
dnaK
, a known heat shock-responsive gene, suggesting that σ
28
RNA polymerase may be involved in the response to cellular stress. Our σ
28
prediction algorithm can be applied to other bacteria, and by performing a similar analysis on the
Escherichia coli
genome, we have predicted and functionally identified five previously unknown σ
28
-regulated genes in
E. coli
.
The ERK Mitogen-Activated Protein Kinase Pathway Contributes to Ebola Virus Glycoprotein-Induced Cytotoxicity
Authors: Zampieri Carisa A. , Fortin Jean-Francois , Nolan Garry P. , Nabel Gary J.
Published: November 2006

Ebola virus is a highly lethal pathogen that causes hemorrhagic fever in humans and nonhuman primates. Among the seven known viral gene products, the envelope glycoprotein (GP) alone induces cell rounding and detachment that ultimately leads to cell death. Cellular cytoxicity is not seen with comparable levels of expression of a mutant form of GP lacking a mucin-like domain (GPΔmuc). GP-induced cell death is nonapoptotic and is preceded by downmodulation of cell surface molecules involved in signaling pathways, including certain integrins and epidermal growth factor receptor. To investigate the mechanism of GP-induced cellular toxicity, we analyzed the activation of several signal transduction pathways involved in cell growth and survival. The active form of extracellular signal-regulated kinases types 1 and 2 (ERK1/2), phospho-ERK1/2, was reduced in cells expressing GP compared to those expressing GPΔmuc as determined by flow cytometry, in contrast to the case for several other signaling proteins. Subsequent analysis of the activation states and kinase activities of related kinases revealed a more pronounced effect on the ERK2 kinase isoform. Disruption of ERK2 activity by a dominant negative ERK or by small interfering RNA-mediated ERK2 knockdown potentiated the decrease in αV integrin expression associated with toxicity. Conversely, activation of the pathway through the expression of a constitutively active form of ERK2 significantly protected against this effect. These results indicate that the ERK signaling cascade mediates GP-mediated cytotoxicity and plays a role in pathogenicity induced by this gene product.
E6AP Ubiquitin Ligase Mediates Ubiquitylation and Degradation of Hepatitis C Virus Core Protein
Authors: Shirakura Masayuki , Murakami Kyoko , Ichimura Tohru , Suzuki Ryosuke , Shimoji Tetsu , Fukuda Kouichirou , Abe Katsutoshi , Sato Shigeko , Fukasawa Masayoshi , Yamakawa Yoshio , Nishijima Masahiro , Moriishi Kohji , Matsuura Yoshiharu , Wakita Takaji , Suzuki Tetsuro , Howley Peter M. , Miyamura Tatsuo , Shoji Ikuo
Published: November 2006

Hepatitis C virus (HCV) core protein is a major component of viral nucleocapsid and a multifunctional protein involved in viral pathogenesis and hepatocarcinogenesis. We previously showed that the HCV core protein is degraded through the ubiquitin-proteasome pathway. However, the molecular machinery for core ubiquitylation is unknown. Using tandem affinity purification, we identified the ubiquitin ligase E6AP as an HCV core-binding protein. E6AP was found to bind to the core protein in vitro and in vivo and promote its degradation in hepatic and nonhepatic cells. Knockdown of endogenous E6AP by RNA interference increased the HCV core protein level. In vitro and in vivo ubiquitylation assays showed that E6AP promotes ubiquitylation of the core protein. Exogenous expression of E6AP decreased intracellular core protein levels and supernatant HCV infectivity titers in the HCV JFH1-infected Huh-7 cells. Furthermore, knockdown of endogenous E6AP by RNA interference increased intracellular core protein levels and supernatant HCV infectivity titers in the HCV JFH1-infected cells. Taken together, our results provide evidence that E6AP mediates ubiquitylation and degradation of HCV core protein. We propose that the E6AP-mediated ubiquitin-proteasome pathway may affect the production of HCV particles through controlling the amounts of viral nucleocapsid protein.
Human Immunodeficiency Virus Type 1 Matrix Protein Assembles on Membranes as a Hexamer
Authors: Alfadhli Ayna , Huseby Doug , Kapit Eliot , Colman Dalbinder , Barklis Eric
Published: November 2006

The membrane-binding matrix (MA) domain of the human immunodeficiency virus type 1 (HIV-1) structural precursor Gag (PrGag) protein oligomerizes in solution as a trimer and crystallizes in three dimensions as a trimer unit. A number of models have been proposed to explain how MA trimers might align with respect to PrGag capsid (CA) N-terminal domains (NTDs), which assemble hexagonal lattices. We have examined the binding of naturally myristoylated HIV-1 matrix (MyrMA) and matrix plus capsid (MyrMACA) proteins on membranes in vitro. Unexpectedly, MyrMA and MyrMACA proteins both assembled hexagonal cage lattices on phosphatidylserine-cholesterol membranes. Membrane-bound MyrMA proteins did not organize into trimer units but, rather, organized into hexamer rings. Our results yield a model in which MA domains stack directly above NTD hexamers in immature particles, and they have implications for HIV assembly and interactions between MA and the viral membrane glycoproteins.
Differential duplication of an intronic region in the NFATC1 gene in patients with congenital heart disease
Authors: Yehya Amin , Souki Ramzi , Bitar Fadi , Nemer Georges
Published: November 2006

Most forms of congenital heart disease (CHD) result from aberrations in cardiac morphogenesis including errors in septation, valve formation, and proper patterning of the great vessels. Transcription factors are key proteins that dictate mRNA synthesis rate and subsequent protein production in most eukaryotes. NFATC1 belongs to the Rel family of transcription factors. In mice, it is expressed in the embryonic heart and is restricted to the endocardium where it plays a major role in valve formation. To establish a role for NFATC1 in CHD, we started screening for mutations in the exons encoding the DNA-binding domain of NFATC1 in patients enrolled in our study on CHD in Lebanon. DNA was extracted from patients with pulmonary stenosis (PS), tricuspid atresia (TA) and ventricular septal defect (VSD). PCR amplification and DNA sequencing were done on the patients and their parents and (or) siblings. PCR amplification of the exon 7 region showed that 2 bands are obtained in 57% of patients with CHD (32/56) and in 45% of their healthy parents and (or) siblings. Sequencing of the 2 bands revealed that both are amplicons of the exon 7 region, and that the additional band harbors an additional 44 nucleotides segment in the intronic region. The homozygous form of this allele was only present in patients with VSD (2/21). A screen of a pool of 81 healthy, unrelated individuals showed no presence for the homozygous form of this allele, suggesting that NFATC1 is a potential VSD-susceptibility gene.
Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research
Authors: Jiang Jiming , Gill Bikram S.
Published: November 2006

Fluorescence in situ hybridization (FISH), which allows direct mapping of DNA sequences on chromosomes, has become the most important technique in plant molecular cytogenetics research. Repetitive DNA sequence can generate unique FISH patterns on individual chromosomes for karyotyping and phylogenetic analysis. FISH on meiotic pachytene chromosomes coupled with digital imaging systems has become an efficient method to develop physical maps in plant species. FISH on extended DNA fibers provides a high-resolution mapping approach to analyze large DNA molecules and to characterize large genomic loci. FISH-based physical mapping provides a valuable complementary approach in genome sequencing and map-based cloning research. We expect that FISH will continue to play an important role in relating DNA sequence information to chromosome biology. FISH coupled with immunoassays will be increasingly used to study features of chromatin at the cytological level that control expression and regulation of genes.
Physiological characteristics of the best Eritrean runners—exceptional running economy
Authors: Lucia Alejandro , Esteve-Lanao Jonathan , Oliván Jesús , Gómez-Gallego Félix , San Juan Alejandro F. , Santiago Catalina , Pérez Margarita , Chamorro-Viña Carolina , Foster Carl
Published: November 2006

Despite their young age, limited training history, and lack of running tradition compared with other East African endurance athletes (e.g., Kenyans and Ethiopians), male endurance runners from Eritrea have recently attained important running successes. The purposes of our study were (i) to document the main physical and physiological characteristics of elite black Eritrean distance runners (n = 7; age: 22 ± 3 years) and (ii) to compare them with those of their elite white Spanish counterparts. For this second purpose we selected a control group of elite Spanish runners (n = 9; 24 ± 2 years), owing to the traditionally high success of Spanish athletes in long-distance running compared with other white runners, especially in cross-country competitions. The subjects’ main anthropometric characteristics were determined, together with their maximum oxygen uptake (VO2 max) and VO2(mL·kg–1·min–1), blood lactate, and ammonia concentrations while running at 17, 19, or 21 km·h–1. The body mass index (18.9 ± 1.5 kg·m–2) and maximal calf circumference (30.9 ± 1.5 cm) was lower in Eritreans than in Spaniards (20.5 ± 1.7 kg·m–2and 33.9 ± 2.0 cm, respectively) (p < 0.05 and p < 0.01, respectively) and their lower leg (shank) length was longer (44.1 ± 3.0 cm vs. 40.6 ± 2.7 cm, respectively) (p < 0.05). VO2 maxdid not differ significantly between Eritreans and Spaniards (73.8 ± 5.6 mL·kg–1·min–1vs. 77.8 ± 5.7 mL·kg–1·min–1, respectively), whereas the VO2cost of running was lower (p < 0.01) in the former (e.g., 65.9 ± 6.8 mL·kg–1·min–1vs. 74.8  ± 5.0 mL·kg–1·min–1when running at 21 km·h–1). Our data suggest that the excellent running economy of Eritreans is associated, at least partly, with anthropometric variables. Comparison of their submaximal running cost with other published data suggests that superior running economy, rather than enhanced aerobic capacity, may be the common denominator in the success of black endurance runners of East African origin.
The effect of dietary control and carbohydrate supplementation on the immune and hormonal responses to rowing exercise
Authors: Sellar Christopher M. , Syrotuik Daniel G. , Field Catherine J. , Bell Gordon J.
Published: November 2006

To determine the effect of carbohydrate supplementation on the immune and stress hormone responses to 1 h of strenuous rowing exercise, 22 male subjects were randomly assigned to a placebo (PLA, n = 11) or carbohydrate (CHO, n = 11) group. Subjects completed 3 d of modified dietary intake, a standardized pre-exercise meal, and consumed either a carbohydrate beverage (1 g·kg body mass–1) or a non-caloric placebo drink before, during, and after a 1 h rowing trial. Increases were observed in adrenocorticotrophic hormone, cortisol, blood leukocytes, neutrophils, and natural killer cell concentrations and activity, whereas the ability of peripheral blood monouclear cells (PBMCs) to respond (interleukin-2 (IL-2) production) to stimulation was reduced 5 min after exercise in both groups (p < 0.05). Lymphocytes were also elevated, but in the PLA group only (p < 0.05). One hour after exercise, blood leukocytes remained elevated owing to increased neutrophil concentrations, whereas a number of lymphocyte subsets (CD3+, CD3+/4+, CD3+/8+, CD20+, CD25+, CD4+/25+, CD8+/25+) and the ability of PBMCs to respond to stimulation (IL-2, interferon-γ (IFN-γ) production) were lower than resting values in both groups (p < 0.05). Carbohydrate supplementation to athletes in the post-prandial state undergoing a 1 h rowing trial resulted in attenuation of the post-exercise increase in peripheral blood lymphocyte concentration, but had little effect on the ability of PBMCs to produce cytokines following stimulation, natural killer cell activity, stress hormone concentrations, exercise performance, or self-reported incidence of illness during the 14 d period following the experimental trial.
UV inactivation of humic-coated bacteriophages MS2 and T4 in water
Authors: Templeton M R , Hofmann R , Andrews R C
Published: November 2006

This bench-scale study investigated the hypothesis that humic acids may thinly coat the surfaces of viruses (bacteriophages MS2 and T4) and thereby protect them from inactivation by UV light (254 nm). The model viruses were mixed in buffered water (pH 5.5) that contained Aldrich® humic acid (AHA) concentrations of 0, 10, 50, and 150 mg/L and were exposed to UV light at 40 and 80 mJ/cm2 for bacteriophage MS2 and 2 and 7 mJ/cm2 for bacteriophage T4 using a low pressure UV collimated beam. No steps were taken to form particles (i.e., no coagulant was added). The UV inactivation of both bacteriophages decreased to a statistically significant degree (based on 95% confidence level, Student's t test) at a humic acid concentration of 150 mg/L at the higher UV doses for each phage. This was despite the increased UV absorbance at 254 nm (UV254) caused by the humic acid being taken into account in the UV dose calculation. It was therefore hypothesized that the humic acid was coating the phage surfaces with a thin UV-shielding layer. As a further investigation of this hypothesis, samples containing humic acid, both with and without phage, were pelletized by ultracentrifugation and re-suspended in pure Milli-Q® water and the resulting UV254 values were compared. It was anticipated that the re-suspended pellets from the solutions containing humic acid and phage would exhibit higher UV254 than those of the pellets from solutions containing either phage or humic acid, due to the coating interaction. While there were statistically significant differences in UV254 among some of the re-suspended pellets, the results were inconsistent due to limitations of the experiment. As such, while some supporting evidence for the humic coating hypothesis was provided by this initial proof of concept study, further research is needed to more fully understand this phenomenon. Key words: ultraviolet light, disinfection, humic acid, bacteriophage, MS2, T4.
Effect of process parameters on succinic acid production in Escherichia coli W3110 and enzymes involved in the reductive tricarboxylic acid cycle
Authors: Isar Jasmine , Agarwal Lata , Saran Saurabh , Gupta Pritesh , Saxena Rajendra Kumar
Published: November 2006

The effect of process optimization on succinic acid production by Escherichia coli W3110 and on enzymes involved in the reverse tricarboxylic acid cycle was studied. Approximately, 7.02 g L–1 of succinic acid was produced in 60 h at pH 7.0 in 500 mL anaerobic bottles containing 300 mL of the medium, wherein the sucrose concentration was 2.5%, the ratio of tryptone to ammonium hydrogen phosphate was 1:1, and the concentration of magnesium carbon ate was 1.5%. When these optimized fermentation conditions were employed in a 10 L bioreactor, 11.2 g L–1 of succinic acid was produced in 48 h. This is a 10-fold increase in succinic acid production from the initial titer of 0.94 g L–1. This clearly indicates the importance of process optimization, where by manipulating the media composition and production conditions, a remarkable increase in the production of the desired biomolecule can be obtained. The production of succinic acid is a multi-step reaction through the reverse tricarboxylic acid cycle. A linear relationship was observed between succinic acid production and the enzyme activities. The enzyme activities were found to increase in the order phospho-enol-pyruvate carboxylase < malate dehydrogenase < fumarase < fumarate reductase. The activity of phospho-enol-pyruvate carboxykinase was also estimated. Results indicate that this enzyme was not a very active participant in the production of succinic acid, since it catalyzes the phosphorylation of oxaloacetic acid to yield phospho-enol-pyruvate.Key words: anaerobic production, succinic acid, Escherichia coli, process optimization, reverse tricarboxylic acid cycle enzymes, fermentation.
In vitro susceptibility of isolates ofSporothrix schenckiito amphotericin B, itraconazole, and terbinafine: comparison of yeast and mycelial forms
Authors: Kohler Lidiane Meire , Soares Betânia Maria , de Assis Santos Daniel , Da Silva Barros Maria Elisabete , Hamdan Júnia Soares
Published: November 2006

Forty-three clinical isolates of Sporothrix schenckii derived from humans and animals were evaluated in vitro for their susceptibility to amphotericin B, itraconazole, and terbinafine. MICs were determined by the method of micro dilution in liquid media, using protocols M27-A2 for the yeast form and M38-A for the mycelial form, both standardized by the Clinical Laboratory Standards Institute. In general, higher MICs were found for the mycelial form (intervals of up to two dilutions). In the case of amphotericin B, a significant difference in activity was observed, with higher values (p < 0.05) found for the mycelial form. MICs for itraconazole and terbinafine were similar for both yeast and mycelial forms but slightly higher for mycelia. Although data presented here indicate different levels of susceptibility when both growth forms were compared, indicating an intrinsic difference between them, it is still difficult to draw a consensus as to which form correlates better with clinical findings. More studies are necessary to determine the criteria for in vitro tests that will lead to efficient therapeutic choices.Key words: Sporothrix schenckii, susceptibility testing, antifungal drug.