bluuebunny/crossref_metadata_2025 huggingface dataset:
Methodological issues in the epidemiological study of the teratogenicity of drugs
Authors: Källén Bengt A.J.
Published: May 2005

ABSTRACT The review presented here discusses and exemplifies problems in epidemiological studies of drug teratogenesis according to methodology: case–control studies, cohort studies, or total population studies. Sources of errors and the possibility of confounding are underlined. The review stresses the caution with which conclusions have to be drawn when exposure data are retrospective or other possible bias exists. It also stresses the problem with the multiple testing situation that is usually present in the studies. It is therefore difficult to draw any firm conclusion from single studies and still more difficult to draw conclusions on causality. As randomized studies are in most cases out of the question, one has to rely on the type of studies which can be made, but the interpretation of the results should be cautious. The ideal study, next to a randomized one, is a large prospective study with detailed exposure information and detailed and unbiased outcome data. Even so, such a study can mainly be used for identifying possible associations which have to be verified or rejected in new studies. Nearly every finding of a risk increase, if not extremely strong, should only be regarded as a tentative signal to be tested in independent studies.
Morphological differences in cardiovascular anomalies induced by bis‐diamine between Sprague–Dawley and Wistar rats
Authors: Fujino Hidetoshi , Nakagawa Masao , Nishijima Setsuko , Okamoto Nobuhiko , Hanato Takashi , Watanabe Noriko , Shirai Takeaki , Kamiya Hiroshi , Takeuchi Yoshihiro
Published: May 2005

ABSTRACT  It is known that animals show different responses to the same teratogen between different strains. We examined cardiac malformations in Sprague–Dawley (SD) and Wistar rats induced by bis‐diamine, which produced conotruncal anomalies and aortic arch malformations in embryos when administered to the dams, to elucidate the morphological differences and pathogenesis in the two strains. Two hundred milligrams of bis‐diamine dissolved in 1% gum‐tragacanth was administered to pregnant rats on embryonic day (ED) 9.5, 10.5 and 11.5 in each strain. The embryos were removed on ED 20.5. External appearances, cardiovascular morphology and associated anomalies were examined under a dissecting microscope. An immunohistological study with an anti‐N‐CAM antibody, an excellent marker for neural crest cells, was performed on ED 12.5 embryos. Isolated aortic arch anomalies were common features of malformations induced by bis‐diamine in SD rats and intracardiac defects were found in a small number of the embryos. Wistar rats showed more serious cardiovascular anomalies, such as persistent truncus arteriosus and tetralogy of Fallot, especially when dams were treated on ED 10.5 and isolated arch anomalies were significantly less prevalent than in SD rats. Immunohistology demonstrated that there were fewer N‐CAM positive cells in the conotruncal region in Wistar rats than in SD rats. Bis‐diamine induced more critical cardiovascular malformations in Wistar rats because neural crest cells, which play an important role in conotruncal septation, were more extensively damaged. Different susceptibility to bis‐diamine and/or different time of neural crest cell emigration from the hindbrain might explain those morphological differences.
Refining chromosomal region critical for Down syndrome‐related heart defects with a case of cryptic 21q22.2 duplication
Authors: Kosaki Rika , Kosaki Kenjiro , Matsushima Kazushige , Mitsui Norimasa , Matsumoto Naomichi , Ohashi Hirofumi
Published: May 2005

ABSTRACT  We report here a patient with features of Down syndrome and tetralogy of Fallot who had a 21q22 duplication. The extent of the duplication was defined using fluorescent hybridization probes that map to the critical region on chromosome 21. Included within the interval was the cell adhesion molecule DSCAM but not the collagen COL6A1. The present case provides further support to the concept that there exists Down syndrome‐associated congenital heart disease gene(s) on chromosome 21q22 and that over‐expression of DSCAM may contribute to the cardiac defects of Down syndrome.
Amphibian Declines in Latin America: Widespread Population Declines, Extinctions, and Impacts1
Authors: Lips Karen R. , Burrowes Patricia A. , Mendelson Joseph R. , Parra‐Olea Gabriela
Published: May 2005

Amphibian populations are in decline throughout Latin America; all families of frogs have experienced declines, but the species associated with aquatic habitats in upland areas have been most affected. Declines in Latin America were most common during the 1980s, but new declines continue to be reported. The causes of declines are varied, but they have most often been associated with habitat loss, a pathogenic fungus, and climate change. Scientists are just beginning to grasp the ethical and biological implications of losses of this magnitude. In this Special Section, we provide a general summary of the phenomenon and introduce five contributed papers that provide new data and new insights into Latin American declines.
Predicting the Distribution of the Amphibian Pathogen Batrachochytrium dendrobatidis in the New World1
Authors: Ron Santiago R.
Published: May 2005

One application of ecological niche modeling is predicting suitable areas for the establishment of invasive species. Herein, I model the fundamental niche of the chytrid fungus Batrachochytrium dendrobatidis, a pathogen linked to amphibian declines on several continents. Niche models were generated with the Genetic Algorithm of Rule‐Set Prediction using point distribution data of the pathogen and digital maps of environmental variables integrated in a GIS environment. The distribution of regions suitable for B. dendrobatidis in the New World is extensive and includes significant portions of: (1) Sierra Madre Occidental pine‐oak forest; (2) Sonoran and Sinaloan dry forest; (3) Veracruz moist forest; (4) Central America east from the Isthmus of Tehuantepec; (5) Caribbean Islands; (6) temperate forest in Chile and western Argentina south of latitude 30°S; (7) Andes above 1000 m of altitude in Venezuela, Colombia, and Ecuador; (8) eastern slopes of the Andes in Peru and Bolivia; (9) Brazilian Atlantic forest; (10) Uruguay, Paraguay, and northeastern Argentina; (11) southwestern and Madeira‐Tapajós Amazonian tropical rainforests. The regions with the highest suitability for B. dendrobatidis include habitats that contain the world's most diverse amphibian faunas. Models were built with New World localities, but also showed strong predictability for B. dendrobatidis localities in the Old World. Out of a total of 59 reported Old World localities for B. dendrobatidis, 56 occurred within regions with high predicted suitability. I also present analyses of the environmental envelope of B. dendrobatidis and discuss the implications of the results for the conservation of amphibians in the neotropics.
Amphibian Population Declines in Latin America: A Synthesis1
Authors: Lips Karen R. , Burrowes Patricia A. , Mendelson Joseph R. , Parra‐Olea Gabriela
Published: May 2005

The loss of global amphibian biodiversity has been well documented in recent years. The greatest information from Latin America came from countries such as Costa Rica, Panama, Ecuador, and Puerto Rico. The five papers in this special section illustrate the critical status of Latin American amphibians and further demonstrate certain commonalities of amphibian population declines within the region. These studies provide a framework by which future research and management could proceed in all tropical regions.
Effects of Light Gaps and Litter Removal on the Seedling Performance of Six African Timber Species1
Authors: Makana Jean‐Remy , Thomas Sean C.
Published: May 2005

Valuable timber tree species frequently show poor regeneration after selective logging in tropical forests. Small size of logging gaps, lack of soil disturbance, and limited seed availability have each been blamed for observed regeneration failures. We investigated seed germination and seedling performance using a split‐plot factorial design involving light availability and litter removal for six Central African timber tree species, hypothesizing that canopy gaps and litter removal would improve seedling establishment, and that less shade‐tolerant species would show stronger responses to both factors. Contrary to our expectations, significantly more germinants established on intact litter than on exposed mineral soil 3 mo after seeding. After 18 mo, seedling survival, height and diameter growth, leaf area, and rooting depth were all much higher in gap plots than in the understory for all species, with the exception of Gilbertiodendron dewevrei, a highly shade‐tolerant species whose survival was higher in the understory. Leaf production was negatively influenced by litter removal in the least shade‐tolerant species, Nauclea diderrichii, with weak or positive effects in other species. G. dewevrei, while displaying a low‐light threshold for growth, exhibited a surprisingly high growth response to increasing light comparable to more shade‐intolerant species, a response that may help explain its local competitive dominance in the region. Due to the rapid closure of small gaps, we suggest that shade‐intolerant species such as N. diderrichii, Khaya anthotheca, and Entandrophragma utile might benefit from more intensive silvicultural practices that create larger canopy gaps.
Artificial Defoliation Induces Trichome Production in the Tropical Shrub Cnidoscolus aconitifolius (Euphorbiaceae)1
Authors: Abdala‐Roberts Luis , Parra‐Tabla Víctor
Published: May 2005

Induction of plant defenses and their spatial variability are key subjects in the field of ecology and evolution of defensive traits in plants. Nevertheless, induction has been more commonly studied under controlled environments, ignoring other factors that might influence this process in natural settings. The main goal of this study was to determine if artificial defoliation induces trichome production in three natural populations of the tropical shrub Cnidoscolus aconitifolius. First, we performed trichome counts for each population before imposing artificial defoliation to assess differences in trichome loads between populations. Trichome densities (trichomes/cm2) were quantified for leaf blades, petioles, and flower stalks. To determine if defoliation induced trichome production, three defoliation treatments (0% leaves defoliated or controls, 50% of total leaves defoliated, and 100% defoliation) were applied once at the beginning of the reproductive season. Trichome counts were performed on each structure every ∼20 d during a 3‐mo period after the application of treatments. Trichome counts showed significant differences in trichome densities between populations for all three structures. In turn, artificial defoliation increased trichome density. Significant differences among treatments were found for trichome densities on leaf blades and petioles. In both these structures, the 100 percent defoliation treatment differed significantly from control plants, presenting higher trichome densities. In addition, the treatment × population interaction was not significant for leaf blades and petioles, indicating that induction is a generalized response in this species, at least at the study sites. These results indicate that trichomes in C. aconitifolius are inducible due to defoliation.
Massive Destruction of Symphonia globulifera (Clusiaceae) Flowers by Central American Spider Monkeys (Ateles geoffroyi)1
Authors: Riba‐Hernández Pablo , Stoner Kathryn E.
Published: May 2005

Although more than 39 primate species have been described as nectar feeders, no studies have documented the negative affect this behavior may have on the reproductive success of the plants they consume. Here we report, for the first time, massive flower destruction of the tropical tree Symphonia globulifera by the frugivorous spider monkey, Ateles geoffroyi, and document the detrimental effect this behavior has on fruit set. Foraging behavior was collected from one troop of A. geoffroyi during 460 contact hours from June 1999 to May 2000 in the tropical humid forest at the Refugio de Vida Silvestre Punta Rio Claro (8°39′N, 83°44′E) in the Osa Peninsula in Southwestern Costa Rica. Detailed phenological data were collected from ten S. globulifera trees that the monkeys fed upon and ten trees that were outside of their home range, but in the Refugio. From July to September 1999 S. globulifera was the most important species consumed, representing from 86 to 100 percent of the total feeding time each month. Monkey foraging on S. globulifera flowers was destructive, detaching the flowers completely from the branches in 80 percent of the foraging bouts, and leaving flowers without petals and with damaged reproductive parts in 20 percent of the bouts. None of the ten trees where the monkeys were foraging set fruit, but seven of ten trees outside of their home range set fruit in November and December 1999. These results suggest that some primates may play an important role in floral herbivory in tropical forests and the subsequent reduction in reproductive success. Future studies should focus on evaluating the long‐term effect this foraging behavior may have on the population structure of this species and evaluate the effect of primate floral herbivory on the reproductive success of other plant species.
Trap Spacing and Transect Design for Dung Beetle Biodiversity Studies1
Authors: Larsen Trond H. , Forsyth Adrian
Published: May 2005

Standardized sampling methods are essential for comparing species diversity and abundance patterns across different studies and sites. Although dung beetles are widely used as a focal taxon in biodiversity studies, nothing appears to be known about the effective sampling area of dung‐baited traps. Mark‐recapture experiments using Canthon acutus showed that at least 50 m between traps should minimize trap interference, and that wind affects trap detectability. Consequently, we propose a standardized dung beetle sampling design.
Nonisothermal Compressor Station Optimization
Authors: Abbaspour M. , Chapman K. S. , Krishnaswami P.
Published: May 2005

A detailed mathematical model of compressor stations and pipes is essential for optimizing the performance of the gas pipeline system. Most of the available literature on compressor station modeling is based on isothermal solutions for pipe flow, which is inadequate for our purposes. In the present work, the pipe flow is treated as nonisothermal unsteady one-dimensional compressible flow. This is accomplished by treating the compressibility factor as a function of pressure and temperature, and the friction factor as a function of Reynolds number. The solution method is the fully implicit finite difference method that provides solution stability, even for relatively large time steps. The compressors within the compressor station are modeled using centrifugal compressor map-based polynomial equations. This modeling technique permits the designation of different models of compressors in the compressor station. The method can be easily extended to include other types of compressors. Using this mathematical model as a basis, a nonlinear programing problem (NLP) is set up wherein the design variables are the compressor speeds and the objective function to be minimized is the total fuel consumption. The minimum acceptable throughput is imposed as a constraint. This NLP is solved numerically by a sequential unconstrained minimization technique, using the mathematical model of the system for the required function evaluations. The results show that this approach is very effective in reducing fuel consumption. An application of this methodology for selecting the number of compressors to be shut down for the most fuel-efficient operation is also presented. Our results further indicate that station-level optimization produces results comparable to those obtained by network-level optimization. This is very significant because it implies that the optimization can be done locally at the station level, which is computationally much easier.
Underground Gas Storage Inventory Analysis by a Noniterative Method
Authors: Liu Ning , Civan Faruk
Published: May 2005

Underground gas storage inventory and conditions are predicted using a practical model and a noniterative solution algorithm. Various simulation scenarios concerning underground gas storage in depleted reservoirs with variable production rate and temperature conditions demonstrate the effectiveness of this approach. It is shown that the gas storage parameters can be determined conveniently by solving the system model directly without resorting to the tedious procedures of the previous approaches.
Organic Working Fluids for a Combined Power and Cooling Cycle
Authors: Vijayaraghavan Sanjay , Goswami D. Y.
Published: May 2005

A new thermodynamic cycle has been developed for the simultaneous production of power and cooling from low-temperature heat sources. The proposed cycle combines the Rankine and absorption refrigeration cycles, providing power and cooling as useful outputs. Initial studies were performed with an ammonia-water mixture as the working fluid in the cycle. This work extends the application of the cycle to working fluids consisting of organic fluid mixtures. Organic working fluids have been used successfully in geothermal power plants, as working fluids in Rankine cycles. An advantage of using organic working fluids is that the industry has experience with building turbines for these fluids. A commercially available optimization program has been used to maximize the thermodynamic performance of the cycle. The advantages and disadvantages of using organic fluid mixtures as opposed to an ammonia-water mixture are discussed. It is found that thermodynamic efficiencies achievable with organic fluid mixtures, under optimum conditions, are lower than those obtained with ammonia-water mixtures. Further, the refrigeration temperatures achievable using organic fluid mixtures are higher than those using ammonia-water mixtures.
An Advanced Strategy for Detecting Impulses in Mechanical Signals
Authors: Yang Wen-xian , Tse Peter W.
Published: May 2005

The appearance of overlapping in the results derived by continuous wavelet transform (CWT) smears the spectral features and makes the results difficult to interpret. This will significantly affect the accuracy of analysis of anomalous signals. Aiming at minimizing the undesired effect of overlapping, a new soft-thresholding method in terms of exponential functions is proposed. Using the proposed soft-threshold and combining with Donoho’s approach for reducing the structures induced by noise, a strategy for purifying the results derived by the CWT is designed. A series of simulated and practical experiments show that, after adopting the proposed strategy, the results of CWT are further purified and thereby the spectral features of the inspected signal become more explicit and much more easily identified.
Discrete-Time Sliding Mode Control on a Flexible Truss Structure
Authors: Su Wu-Chung , Drakunov Sergey V. , O¨zgu¨ner U¨mit , Redmill Keith
Published: May 2005

Implementation of discrete-time sliding mode control on a sampled-data system leads to sliding motion in an OT2 boundary layer of the discontinuity surface, where T is the sampling period. A truss panel structure vibration control experiment is conducted to demonstrate the effectiveness of the proposed method. This paper utilizes a truncated model to characterize the models of interest and treats all the high frequency modes as disturbances. The experiment includes system identification, state observer design, and discrete-time sliding mode control.
Scaling Laws for Ultra-Short Hydrostatic Gas Journal Bearings
Authors: Spakovszky Z. S. , Liu L. X.
Published: May 2005

The journal bearings of the MIT micro-devices are located at the outer periphery of the rotor and are designed to operate at rotational speeds of order two million rpm in order to enable high-power densities with turbomachinery tip speeds near 500m/s. These journal bearings are very short compared to their relatively large bearing diameters such that the bearing L/D is typically less than 0.1, that is at least one order of magnitude smaller than in conventional gas bearings. Thus, the ultra-short micro gas journal bearings essentially act as short annular seals and operate at Reynolds numbers of order 300, two orders of magnitude lower than conventional annular seals. The concepts that hold for turbulent flow, large scale annular seals do not apply to micro bearings and the laminar flow regime sets new challenges in the design, implementation and operation of ultra-short, high-speed gas bearings. In order to reach the goal of operating the MIT micro devices at full design speed, the micro-bearing design must be improved and engineering solutions need to be found to overcome the challenges of high-speed bearing operation. This paper is the first to derive the scaling laws for the dynamics of ultra-short hydrostatic gas journal bearings. The theory is established from first principles and enables a physics based characterization of the dynamic behavior of ultra-short hydrostatic gas bearings. The derived scaling laws for natural frequency and damping ratio show good agreement with experimental data. A simple criterion for whirl instability is found that only depends on bearing geometry. The scaling laws together with this criterion are used to delineate engineering solutions critical for stable high-speed bearing operation. Design charts are developed which provide the link between fabrication tolerances, bearing performance, and the tolerable level of rotor unbalance for a minimum required whirl ratio.
Time-Varying Controller for Temperature-Dependent Viscoelasticity
Authors: Silva Luciano A. , Austin Eric M. , Inman Daniel J.
Published: May 2005

There are internal-variable techniques that account for the frequency-dependent behavior of viscoelastic materials, but the temperature dependence of these materials has received much less attention. Two methods for designing controllers robust to temperature disturbances are given: (1) Modal reference adaptive control and (2) time-varying pole placement control. Examples that demonstrate the strengths and weaknesses of each are given. The results show that it is possible to achieve vibration reduction while simultaneously rejecting the effects of a temperature disturbance. This work shows that both the frequency and temperature dependence of viscoelastic materials can be modeled with internal variables.
Active Vibration Isolation of Metrology Frames; A Modal Decoupled Control Design
Authors: Heertjes Marcel , de Graaff Koen , van der Toorn Jan-Gerard
Published: May 2005

For a six degree-of-freedom active vibration isolation system, a control strategy based on modal decoupling is proposed. This has the advantage of controlling the modal directions on a centralized single-input single-output basis. As a consequence, stability and performance can be imposed in each of the modal directions separately. An experimental demonstration is given using a dummy metrology frame. That is, a 1600 kg payload mass supported by three combined pneumatic and Lorentz controlled isolators. With this setup, two unstable modal directions resulting from a high center of gravity are stabilized without compromising performance in any of the remaining directions. In fact, performance in the remaining directions is enhanced using manual loop shaping.
Biosynthetic Pathway of
Pseudomonas aeruginosa
4-Hydroxy-2-Alkylquinolines
Authors: Bredenbruch Florian , Nimtz Manfred , Wray Victor , Morr Michael , Müller Rolf , Häussler Susanne
Published: May 2005

The role of intercellular communication in the regulation of bacterial multicellular behavior has received widespread attention, and a variety of signal molecules involved in bacterial communication have been discovered. In addition to the
N
-acyl-homoserine lactones, 4-hydroxy-2-alkylquinolines (HAQs), including the
Pseudomonas
quinolone signal, have been shown to function as signal molecules in
Pseudomonas aeruginosa
. In this study we unraveled the biosynthetic pathway of HAQs using feeding experiments with isotope-labeled precursors and analysis of extracted HAQs by gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy. Our results show that the biosynthesis of various HAQ metabolites is directed via a common metabolic pathway involving a “head-to-head” condensation of anthranilic acid and β-keto fatty acids. Moreover, we provide evidence that the β-keto-(do)decanoic acids, crucial for the biosynthesis of the heptyl and nonyl derivatives of the 4-hydroxyquinolines in
P. aeruginosa
, are at least in part derived from a common pool of β-hydroxy(do)decanoic acids involved in rhamnolipid biosynthesis.
Recycling of the Anhydro-
N
-Acetylmuramic Acid Derived from Cell Wall Murein Involves a Two-Step Conversion to
N
-Acetylglucosamine-Phosphate
Authors: Uehara Tsuyoshi , Suefuji Kyoko , Valbuena Noelia , Meehan Brian , Donegan Michael , Park James T.
Published: May 2005

Escherichia coli
breaks down over 60% of the murein of its side wall and reuses the component amino acids to synthesize about 25% of the cell wall for the next generation. The amino sugars of the murein are also efficiently recycled. Here we show that the 1,6-anhydro-
N
-acetylmuramic acid (anhMurNAc) is returned to the biosynthetic pathway by conversion to
N
-acetylglucosamine-phosphate (GlcNAc-P). The sugar is first phosphorylated by
a
nhydro-

N

-acetyl
m
uramic acid
k
inase (AnmK), yielding MurNAc-P, and this is followed by action of an etherase which cleaves the bond between
d
-lactic acid and the
N
-acetylglucosamine moiety of MurNAc-P, yielding GlcNAc-P. The kinase gene has been identified by a reverse genetics method. The enzyme was overexpressed, purified, and characterized. The cell extract of an
anmK
deletion mutant totally lacked activity on anhMurNAc. Surprisingly, in the
anmK
mutant, anhMurNAc did not accumulate in the cytoplasm but instead was found in the medium, indicating that there was rapid efflux of free anhMurNAc.
16S rRNA Mutations That Confer Tetracycline Resistance inHelicobacter pyloriDecrease Drug Binding inEscherichia coliRibosomes
Authors: Nonaka Lisa , Connell Sean R. , Taylor Diane E.
Published: May 2005

Tetracycline resistance in clinical isolates ofHelicobacter pylorihas been associated with nucleotide substitutions at positions 965 to 967 in the 16S rRNA. We constructed mutants which had different sequences at 965 to 967 in the 16S rRNA gene present on a multicopy plasmid inEscherichia colistrain TA527, in which all sevenrrngenes were deleted. The MICs for tetracycline of all mutants having single, double, or triple substitutions at the 965 to 967 region that were previously found in highly resistantH. pyloriisolates were higher than that of the mutant exhibiting the wild-type sequence of tetracycline-susceptibleH. pylori. The MIC of the mutant with the 965TTC967 triple substitution was 32 times higher than that of theE. colimutant with the 965AGA967 substitution present in wild-typeH. pylori. The ribosomes extracted from the tetracycline-resistantE. coli965TTC967 variant bound less tetracycline thanE. coliwith the wild-typeH. pylorisequence at this region. The concentration of tetracycline bound to the ribosome was 40% that of the wild type. The results of this study suggest that tetracycline binding to the primary binding site (Tet-1) of the ribosome at positions 965 to 967 is influenced by its sequence patterns, which form the primary binding site for tetracycline.
Regulation of
mtrF
Expression in
Neisseria gonorrhoeae
and Its Role in High-Level Antimicrobial Resistance
Authors: Folster Jason P. , Shafer William M.
Published: May 2005

The obligate human pathogen
Neisseria gonorrhoeae
uses the MtrC-MtrD-MtrE efflux pump to resist structurally diverse hydrophobic antimicrobial agents (HAs), some of which bathe mucosal surfaces that become infected during transmission of gonococci. Constitutive high-level HA resistance occurs by the loss of a repressor (MtrR) that negatively controls transcription of the
mtrCDE
operon. This high-level HA resistance also requires the product of the
mtrF
gene, which is located downstream and transcriptionally divergent from
mtrCDE
. MtrF is a putative inner membrane protein, but its role in HA resistance mediated by the MtrC-MtrD-MtrE efflux pump remains to be determined. High-level HA resistance can also be mediated through an induction process that requires enhanced transcription of
mtrCDE
when gonococci are grown in the presence of a sublethal concentration of Triton X-100. We now report that inactivation of
mtrF
results in a significant reduction in the induction of HA resistance and that the expression of
mtrF
is enhanced when gonococci are grown under inducing conditions. However, no effect was observed on the induction of
mtrCDE
expression in an MtrF-negative strain. The expression of
mtrF
was repressed by MtrR, the major repressor of
mtrCDE
expression. In addition to MtrR, another repressor (MpeR) can downregulate the expression of
mtrF
. Repression of
mtrF
by MtrR and MpeR was additive, demonstrating that the repressive effects mediated by these regulators are independent processes.
Fructose Utilization inLactococcus lactisas a Model for Low-GC Gram-Positive Bacteria: Its Regulator, Signal, and DNA-Binding Site
Authors: Barrière Charlotte , Veiga-da-Cunha Maria , Pons Nicolas , Guédon Eric , van Hijum Sacha A. F. T. , Kok Jan , Kuipers Oscar P. , Ehrlich Dusko S. , Renault Pierre
Published: May 2005

In addition to its role as carbon and energy source, fructose metabolism was reported to affect other cellular processes, such as biofilm formation by streptococci and bacterial pathogenicity in plants. Fructose genes encoding a 1-phosphofructokinase and a phosphotransferase system (PTS) fructose-specific enzyme IIABC component reside commonly in a gene cluster with a DeoR family regulator in various gram-positive bacteria. We present a comprehensive study of fructose metabolism inLactococcus lactis, including a systematic study offrumutants, global messenger analysis, and a molecular characterization of its regulation. Thefruoperon is regulated at the transcriptional level by both FruR and CcpA and at the metabolic level by inducer exclusion. The FruR effector is fructose-1-phosphate (F1P), as shown by combined analysis of transcription and measurements of the intracellular F1P pools in mutants either unable to produce this metabolite or accumulating it. The regulation of thefruoperon by FruR requires four adjacent 10-bp direct repeats. The well-conserved organization of thefrupromoter region in various low-GC gram-positive bacteria, including CRE boxes as well as the newly defined FruR motif, suggests that the regulation scheme defined inL. lactiscould be applied to these bacteria. Transcriptome profiling offruRandfruCmutants revealed that the effect of F1P and FruR regulation is limited to thefruoperon inL. lactis. This result is enforced by the fact that no other targets for FruR were found in the available low-GC gram-positive bacteria genomes, suggesting that additional phenotypical effects due to fructose metabolism do not rely directly on FruR control, but rather on metabolism.
Sulfur Amino Acid Metabolism and Its Control in
Lactococcus lactis
IL1403
Authors: Sperandio Brice , Polard Patrice , Ehrlich Dusko S. , Renault Pierre , Guédon Eric
Published: May 2005

Cysteine and methionine availability influences many processes in the cell. In bacteria, transcription of the specific genes involved in the synthesis of these two amino acids is usually regulated by different mechanisms or regulators. Pathways for the synthesis of cysteine and methionine and their interconversion were experimentally determined for
Lactococcus lactis
, a lactic acid bacterium commonly found in food. A new gene,
yhcE
, was shown to be involved in methionine recycling to cysteine. Surprisingly, 18 genes, representing almost all genes of these pathways, are under the control of a LysR-type activator, FhuR, also named CmbR. DNA microarray experiments showed that FhuR targets are restricted to this set of 18 genes clustered in seven transcriptional units, while cysteine starvation modifies the transcription level of several other genes potentially involved in oxidoreduction processes. Purified FhuR binds a 13-bp box centered 46 to 53 bp upstream of the transcriptional starts from the seven regulated promoters, while a second box with the same consensus is present upstream of the first binding box, separated by 8 to 10 bp.
O
-Acetyl serine increases FhuR binding affinity to its binding boxes. The overall view of sulfur amino acid metabolism and its regulation in
L. lactis
indicates that CysE could be a master enzyme controlling the activity of FhuR by providing its effector, while other controls at the enzymatic level appear to be necessary to compensate the absence of differential regulation of the genes involved in the interconversion of methionine and cysteine and other biosynthesis genes.
Characterization of Methionine Export in
Corynebacterium glutamicum
Authors: Trötschel Christian , Deutenberg Dietrich , Bathe Brigitte , Burkovski Andreas , Krämer Reinhard
Published: May 2005

Corynebacterium glutamicum
is known for its effective excretion of amino acids under particular metabolic conditions. Concomitant activities of uptake and excretion systems would create an energy-wasting futile cycle; amino acid export systems are therefore tightly regulated. We have used a DNA microarray approach to identify genes for membrane proteins which are overexpressed under conditions of elevated cytoplasmic concentrations of methionine. One of these genes was
brnF
, coding for the larger subunit of BrnFE, a previously identified two-component isoleucine export system. By deletion, complementation, and overexpression of the
brnFE
genes in a
C. glutamicum
strain, in which the two uptake systems for methionine were inactivated, we identified BrnFE as being responsible for methionine export. In the presence of both substrates in the cytoplasm, BrnFE was found to transport isoleucine and methionine at similar rates. The expression of the
brnFE
gene cluster depends on an Lrp-type transcription factor and was shown to be strongly induced by increasing cytoplasmic methionine concentration. Methionine was a better inducer than isoleucine, indicating that methionine rather than isoleucine might be the native substrate of BrnFE. When the synthesis of BrnFE was blocked by chloramphenicol, fast methionine export was still observed, but only at greatly increased cytoplasmic levels of this amino acid. This indicates the presence of at least one other methionine export system, presumably with low affinity but high capacity. Under conditions where cytoplasmic methionine does not exceed a concentration of 50 mM, BrnFE is the dominant export system for this amino acid.
Identification of a Turnover Element in Region 2.1 of
Escherichia coli
σ
32
by a Bacterial One-Hybrid Approach
Authors: Obrist Markus , Narberhaus Franz
Published: May 2005

Induction of the heat shock response in
Escherichia coli
requires the alternative sigma factor σ
32
(RpoH). The cellular concentration of σ
32
is controlled by proteolysis involving FtsH, other proteases, and the DnaKJ chaperone system. To identify individual σ
32
residues critical for degradation, we used a recently developed bacterial one-hybrid system and screened for stabilized versions of σ
32
. The five single point mutations that rendered the sigma factor more stable mapped to positions L47, A50, and I54 in region 2.1. Strains expressing the stabilized σ
32
variants exhibited elevated transcriptional activity, as determined by a
groE
-
lacZ
fusion. Structure calculations predicted that the three mutated residues line up on the same face of an α-helix in region 2.1, suggesting that they are positioned to interact with proteins of the degradation machinery.
Kinetic Studies of Polyhydroxybutyrate Granule Formation in
Wautersia eutropha
H16 by Transmission Electron Microscopy
Authors: Tian Jiamin , Sinskey Anthony J. , Stubbe JoAnne
Published: May 2005

Wautersia eutropha
, formerly known as
Ralstonia eutropha
, a gram-negative bacterium, accumulates polyhydroxybutyrate (PHB) as insoluble granules inside the cell when nutrients other than carbon are limited. In this paper, we report findings from kinetic studies of granule formation and degradation in
W. eutropha
H16 obtained using transmission electron microscopy (TEM). In nitrogen-limited growth medium, the phenotype of the cells at the early stages of granule formation was revealed for the first time. At the center of the cells, dark-stained “mediation elements” with small granules attached were observed. These mediation elements are proposed to serve as nucleation sites for granule initiation. TEM images also revealed that when
W. eutropha
cells were introduced into nitrogen-limited medium from nutrient-rich medium, the cell size increased two- to threefold, and the cells underwent additional volume changes during growth. Unbiased stereology was used to analyze the two-dimensional TEM images, from which the average volume of a
W. eutropha
H16 cell and the total surface area of granules per cell in nutrient-rich and PHB production media were obtained. These parameters were essential in the calculation of the concentration of proteins involved in PHB formation and utilization and their changes with time. The extent of protein coverage of the granule surface area is presented in the accompanying paper (J. Tian, A. He, A. Lawrence, P. Liu, N. Watson, A. J. Sinskey, and J. Stubbe, J. Bacteriol.
187:
3825-3832, 2005).
Structure and Genome Organization of AFV2, a Novel Archaeal Lipothrixvirus with Unusual Terminal and Core Structures
Authors: Häring Monika , Vestergaard Gisle , Brügger Kim , Rachel Reinhard , Garrett Roger A. , Prangishvili David
Published: May 2005

A novel filamentous virus, AFV2, from the hyperthermophilic archaeal genus
Acidianus
shows structural similarity to lipothrixviruses but differs from them in its unusual terminal and core structures. The double-stranded DNA genome contains 31,787 bp and carries eight open reading frames homologous to those of other lipothrixviruses, a single tRNA
Lys
gene containing a 12-bp archaeal intron, and a 1,008-bp repeat-rich region near the center of the genome.
Alginate Lyase (AlgL) Activity Is Required for Alginate Biosynthesis in
Pseudomonas aeruginosa
Authors: Albrecht Mark T. , Schiller Neal L.
Published: May 2005

To determine whether AlgL's lyase activity is required for alginate production in
Pseudomonas aeruginosa
, an
algLΔ
::Gm
r
mutant (FRD-MA7) was created.
algL
complementation of FRD-MA7 restored alginate production, but
algL
constructs containing mutations inactivating lyase activity did not, demonstrating that the enzymatic activity of AlgL is required for alginate production.
Methylotrophic Autotrophy in
Beijerinckia mobilis
Authors: Dedysh Svetlana N. , Smirnova Ksenia V. , Khmelenina Valentina N. , Suzina Natalia E. , Liesack Werner , Trotsenko Yuri A.
Published: May 2005

Representatives of the genus
Beijerinckia
are known as heterotrophic, dinitrogen-fixing bacteria which utilize a wide range of multicarbon compounds. Here we show that at least one of the currently known species of this genus, i.e.,
Beijerinckia mobilis
, is also capable of methylotrophic metabolism coupled with the ribulose bisphosphate (RuBP) pathway of C
1
assimilation. A complete suite of dehydrogenases commonly involved in the sequential oxidation of methanol via formaldehyde and formate to CO
2
was detected in cell extracts of
B. mobilis
grown on CH
3
OH. Carbon dioxide produced by oxidation of methanol was further assimilated via the RuBP pathway as evidenced by reasonably high activities of phosphoribulokinase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Detection and partial sequence analysis of genes encoding the large subunits of methanol dehydrogenase (
mxaF
) and form I RubisCO (
cbbL
) provided genotypic evidence for methylotrophic autotrophy in
B. mobilis
.
The London Underground: dust and hazards to health
Authors: Seaton A , Cherrie J , Dennekamp M , Donaldson K , Hurley J F , Tran C L
Published: May 2005

Aims:To assess hazards associated with exposure to dust in the London Underground railway and to provide an informed opinion on the risks to workers and the travelling public of exposure to tunnel dust.

Methods:Concentrations of dust, as mass (PM2.5) and particle number, were measured at different underground stations and in train cabs; its size and composition were analysed; likely maximal exposures of staff and passengers were estimated; and in vitro toxicological testing of sample dusts in comparison with other dusts was performed.

Results:Concentrations on station platforms were 270–480 μg/m3PM2.5and 14 000–29 000 particles/cm3. Cab concentrations over a shift averaged 130–200 μg/m3and 17 000–23 000 particles/cm3. The dust comprised by mass approximately 67% iron oxide, 1–2% quartz, and traces of other metals, the residue being volatile matter. The finest particles are drawn underground from the surface while the coarser dust is generated by interaction of brakes, wheels, and rails. Taking account of durations of exposure, drivers and station staff would have maximum exposures of about 200 μg/m3over eight hours; the occupational exposure standard for welding fume, as iron oxide, is 5 mg/m3over an eight hour shift. Toxicology showed the dust to have cytotoxic and inflammatory potential at high doses, consistent with its composition largely of iron oxide.

Discussion:It is unjustifiable to compare PM2.5exposure underground with that on the surface, since the adverse effects of iron oxide and combustion generated particles differ. Concentrations of ultrafine particles are lower and of coarser (PM2.5) particles higher underground than on the surface. The concentrations underground are well below allowable workplace concentrations for iron oxide and unlikely to represent a significant cumulative risk to the health of workers or commuters.
Supermarket baker’s asthma: how accurate is routine health surveillance?
Authors: Brant A , Nightingale S , Berriman J , Sharp C , Welch J , Newman Taylor A J , Cullinan P
Published: May 2005

Background:Regular health surveillance is commonly recommended for workers exposed to occupational antigens but little is known about how effective it is in identifying cases.

Aims:To report one large company’s surveillance and compare its findings with those of a standard cross-sectional survey in the same workforce.

Methods:A supermarket company with 324 in-store bakeries producing bread from raw ingredients conducted a three-stage health surveillance programme in around 3000 bakery employees. The first stage involved the administration of a simple respiratory questionnaire. If chest symptoms were present a second questionnaire focusing on their work relationship was administered. If positive a blood sample was requested for the measurement of specific IgE to flour and fungal α-amylase. The results were compared to an independent cross-sectional survey of employees in 20 of the company’s stores.

Results:Two hundred and ninety nine (92%) of the company’s bakeries took part in surveillance. The overall employee response for the first stage was 77%; a quarter of those with respiratory symptoms reported that they were work related. Seventy four (61%) of those with work related chest symptoms had a measurement of specific IgE to either flour or fungal α-amylase, of whom 30 (41%) had a positive result. Surveillance estimated that 1% of bakery employees (1% bakers, 2% managers, 0.6% confectioners) had work related symptoms with specific IgE. This compared with 4% (7.5% bakers, 3.3% managers, 0% confectioners) in the cross-sectional survey (n = 166, 93% response).

Conclusion:Comparison with a standard cross-sectional survey suggests that routine surveillance can underestimate the workplace burden of disease. The reasons may include technical or resource issues and uncertainties over confidentiality or the perceived consequences of participation. More research needs to be done looking into the design and efficacy of surveillance in occupational asthma.
Required competencies of occupational physicians: a Delphi survey of UK customers
Authors: Reetoo K N , Harrington J M , Macdonald E B
Published: May 2005

Background:Occupational physicians can contribute to good management in healthy enterprises. The requirement to take into account the needs of the customers when planning occupational health services is well established.

Aims:To establish the priorities of UK employers, employees, and their representatives regarding the competencies they require from occupational physicians; to explore the reasons for variations of the priorities in different groups; and to make recommendations for occupational medicine training curricula in consideration of these findings.

Methods:This study involved a Delphi survey of employers and employees from public and private organisations of varying business sizes, and health and safety specialists as well as trade union representatives throughout the UK. It was conducted in two rounds by a combination of computer assisted telephone interview (CATI) and postal survey techniques, using a questionnaire based on the list of competencies described by UK and European medical training bodies.

Results:There was broad consensus about the required competencies of occupational physicians among the respondent subgroups. All the competencies in which occupational physicians are trained were considered important by the customers. In the order of decreasing importance, the competencies were: Law and Ethics, Occupational Hazards, Disability and Fitness for Work, Communication, Environmental Exposures, Research Methods, Health Promotion, and Management.

Conclusion:The priorities of customers differed from previously published occupational physicians’ priorities. Existing training programmes for occupational physicians should be regularly reviewed and where necessary, modified to ensure that the emphasis of training meets customer requirements.
Proximity of the home to roads and the risk of wheeze in an Ethiopian population
Authors: Venn A , Yemaneberhan H , Lewis S , Parry E , Britton J
Published: May 2005

Background:There is widespread public concern that exposure to road vehicle traffic pollution causes asthma, but epidemiological studies in developed countries have not generally confirmed a strong effect and may have underestimated the risk as a result of relatively high and widespread exposure to traffic in everyday life.

Aims:To investigate the effect of living close to a traffic bearing road on the risk of wheezing in Jimma, Ethiopia where road traffic is generally low and restricted to a limited network of roads.

Methods:Data have been previously collected on respiratory symptoms, allergic sensitisation, and numerous demographic and lifestyle factors in a systematic sample of inhabitants of Jimma town. In 2003 the homes of these people were retraced; the shortest distance to the nearest surfaced road, and traffic flows on these roads were measured.

Results:Distance measurements were collected for 7609 (80%) individuals. The overall prevalence of wheeze was similar in those living within 150 m of a road compared to those living further away (3.9%v3.7%), but among the 3592 individuals living within 150 m, the risk of wheeze increased significantly in linear relation to proximity to the road (adjusted odds ratio = 1.17 per 30 m proximity, 95% CI 1.01 to 1.36). This relation was stronger, though not significantly so, for roads with above median traffic flows.

Conclusion:These findings indicate that living in close proximity to road vehicle traffic is associated with an increased risk of wheeze, but that other environmental factors are also likely to be important.