bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drosophila melanogasterMounts a Unique Immune Response to the RhabdovirusSigma virus
Authors: Tsai C. W. , McGraw E. A. , Ammar E.-D. , Dietzgen R. G. , Hogenhout S. A. 
Published: April 2008

ABSTRACTRhabdoviruses are important pathogens of humans, livestock, and plants that are often vectored by insects. Rhabdovirus particles have a characteristic bullet shape with a lipid envelope and surface-exposed transmembrane glycoproteins.Sigma virus(SIGMAV) is a member of theRhabdoviridaeand is a naturally occurring disease agent ofDrosophila melanogaster. The infection is maintained inDrosophilapopulations through vertical transmission via germ cells. We report here the nature of theDrosophilainnate immune response to SIGMAV infection as revealed by quantitative reverse transcription-PCR analysis of differentially expressed genes identified by microarray analysis. We have also compared and contrasted the immune response of the host with respect to two nonenveloped viruses,DrosophilaC virus (DCV) andDrosophilaX virus (DXV). We determined that SIGMAV infection upregulates expression of the peptidoglycan receptor protein genesPGRP-SB1andPGRP-SDand the antimicrobial peptide (AMP) genesDiptericin-A,Attacin-A,Attacin-B,Cecropin-A1, andDrosocin. SIGMAV infection did not inducePGRP-SAand the AMP genesDrosomycin-B,Metchnikowin, andDefensinthat are upregulated in DCV and/or DXV infections. Expression levels of the Toll and Imd signaling cascade genes are not significantly altered by SIGMAV infection. These results highlight shared and unique aspects of theDrosophilaimmune response to the three viruses and may shed light on the nature of the interaction with the host and the evolution of these associations.
Comparison of Transcription-Mediated Amplification and Growth-Based Methods for the Quantitation of
Enterococcus
Bacteria in Environmental Waters
Authors: Morris Ceri A. , Blackwood A. Denene , Kirs Marek , Buttigieg Neil D. , Morgan Rhian R. , Hogan James J. , Weeks Ian , Noble Rachel T. 
Published: April 2008

ABSTRACT

An assay based on transcription-mediated amplification (TMA) technology was used to quantitate
Enterococcus
fecal indicator bacteria in environmental water samples. The results generated by this and two growth-based methods relative to the 104 most-probable-number or CFU-per-100-ml threshold show that the three methods are in good qualitative agreement when tested against a range of water samples taken from different locations. The results demonstrate sensitive and rapid detection (approximately 4 h from sample collection to result) and quantitation of
Enterococcus
bacteria compared to the results with the growth-based methods.
Factors Contributing to Heat Resistance ofClostridium perfringensEndospores
Authors: Orsburn Benjamin , Melville Stephen B. , Popham David L. 
Published: April 2008

ABSTRACTThe endospores formed by strains of type AClostridium perfringensthat produce theC. perfringensenterotoxin (CPE) are known to be more resistant to heat and cold than strains that do not produce this toxin. The high heat resistance of these spores allows them to survive the cooking process, leading to a large number of food-poisoning cases each year. The relative importance of factors contributing to the establishment of heat resistance in this species is currently unknown. The present study examines the spores formed by both CPE+and CPE−strains for factors known to affect heat resistance in other species. We have found that the concentrations of DPA and metal ions, the size of the spore core, and the protoplast-to-sporoplast ratio are determining factors affecting heat resistance in these strains. While the overall thickness of the spore peptidoglycan was found to be consistent in all strains, the relative amounts of cortex and germ cell wall peptidoglycan also appear to play a role in the heat resistance of these strains.
Characterization of Diazotrophs Containing Mo-Independent Nitrogenases, Isolated from Diverse Natural Environments
Authors: Betancourt Doris A. , Loveless Telisa M. , Brown James W. , Bishop Paul E. 
Published: April 2008

ABSTRACT

Molybdenum-independent nitrogenases were first described in the nitrogen-fixing bacterium
Azotobacter vinelandii
and have since been described in other diazotrophic bacteria. Previously, we reported the isolation of seven diazotrophs with Mo-independent nitrogenases from aquatic environments. In the present study, we extend these results to include diazotrophs isolated from wood chip mulch, soil, “paraffin dirt,” and sediments from mangrove swamps. Mo-deficient, N-free media under both aerobic and anaerobic conditions were used for the isolations. A total of 26 isolates were genetically and physiologically characterized. Their phylogenetic placement was determined using 16S rRNA gene sequence analysis. Most of the isolates are members of the gamma subdivision of the class
Proteobacteria
and appear to be specifically related to fluorescent pseudomonads and azotobacteria. Two other isolates, AN1 and LPF4, are closely related to
Enterobacter
spp. and
Paenibacillus
spp., respectively. PCR and/or Southern hybridization were used to detect the presence of nitrogenase genes in the isolates. PCR amplification of
vnfG
and
anfG
was used to detect the genetic potential for the expression of the vanadium-containing nitrogenase and the iron-only nitrogenase in the isolates. This study demonstrates that diazotrophs with Mo-independent nitrogenases can be readily isolated from diverse natural environments.
Identification of Mobile Elements and Pseudogenes in theShewanella oneidensisMR-1 Genome
Authors: Romine Margaret F. , Carlson Timothy S. , Norbeck Angela D. , McCue Lee Ann , Lipton Mary S. 
Published: April 2008

ABSTRACTShewanella oneidensisMR-1 is the first of 22 differentShewanellaspp. whose genomes have been or are being sequenced and thus serves as the model organism for studying the functional repertoire of theShewanellagenus. The original MR-1 genome annotation revealed a large number of transposase genes and pseudogenes, indicating that many of the genome's functions may be decaying. Comparative analyses of the sequencedShewanellastrains suggest that 209 genes in MR-1 have in-frame stop codons, frameshifts, or interruptions and/or are truncated and that 65 of the original pseudogene predictions were erroneous. Among the decaying functions are that of one of three chemotaxis clusters, type I pilus production, starch utilization, and nitrite respiration. Many of the mutations could be attributed to members of 41 different types of insertion sequence (IS) elements and three types of miniature inverted-repeat transposable elements identified here for the first time. The high copy numbers of individual mobile elements (up to 71) are expected to promote large-scale genome recombination events, as evidenced by the displacement of thealgApromoter. The ability of MR-1 to acquire foreign genes via reactions catalyzed by both the integron integrase and the ISSod25-encoded integrases is suggested by the presence ofattCsites and genes whose sequences are characteristic of other species downstream of each site. This large number of mobile elements and multiple potential sites for integrase-mediated acquisition of foreign DNA indicate that the MR-1 genome is exceptionally dynamic, with many functions and regulatory control points in the process of decay or reinvention.
Discovering the Hidden Secondary Metabolome of
Myxococcus xanthus
: a Study of Intraspecific Diversity
Authors: Krug Daniel , Zurek Gabriela , Revermann Ole , Vos Michiel , Velicer Gregory J. , Müller Rolf 
Published: April 2008

ABSTRACT

As a monophyletic group, the myxobacteria are known to produce a broad spectrum of secondary metabolites. However, the degree of metabolic diversity that can be found within a single species remains unexplored. The model species
Myxococcus xanthus
produces several metabolites also present in other myxobacterial species, but only one compound unique to
M. xanthus
has been found to date. Here, we compare the metabolite profiles of 98
M. xanthus
strains that originate from 78 locations worldwide and include 20 centimeter-scale isolates from one location. This screen reveals a strikingly high level of intraspecific diversity in the
M. xanthus
secondary metabolome. The identification of 37 nonubiquitous candidate compounds greatly exceeds the small number of secondary metabolites previously known to derive from this species. These results suggest that
M. xanthus
may be a promising source of future natural products and that thorough intraspecific screens of other species could reveal many new compounds of interest.
Community-Level Assessment of the Effects of the Broad-Spectrum Antimicrobial Chlorhexidine on the Outcome of River Microbial Biofilm Development
Authors: Lawrence J. R. , Zhu B. , Swerhone G. D. W. , Topp E. , Roy J. , Wassenaar L. I. , Rema T. , Korber D. R. 
Published: April 2008

ABSTRACT

Chlorhexidine is a common-use antibacterial agent found in a range of personal-care products. We used rotating annular reactors to cultivate river biofilms under the influence of chlorhexidine or its molar equivalent in nutrients. Studies of the degradation of [
14
C]chlorhexidine demonstrated that no mineralization of the compound occurred. During studies with 100 μg liter
−1
chlorhexidine, significant changes were observed in the protozoan and micrometazoan populations, the algal and cyanobacterial biomass, the bacterial biomass, and carbon utilization. Denaturing gradient gel electrophoresis (DGGE) in combination with statistical analyses showed that the communities developing under control and 100 μg liter
−1
chlorhexidine were significantly different. At 10 μg liter
−1
chlorhexidine, there was significantly increased algal and cyanobacterial biomass while the bacterial biomass was not significantly affected (
P
< 0.05). No significant effects on protozoan or metazoan grazing were detected at the 10-μg liter
−1
chlorhexidine level. Fluorescent in situ hybridization indicated a significant reduction in the abundance of betaproteobacteria and gammaproteobacteria (
P
< 0.05). Archaeal cell counts were significantly reduced by both chlorhexidine and nutrient treatments. DGGE and statistical analyses indicated that 10 μg liter
−1
chlorhexidine and molar equivalent nutrient treatments were significantly different from control communities. In contrast to community level observations, toxicological testing with a panel of cyanobacteria, algae, and protozoa indicated no detectable effects at 10, 50, and 100 μg liter
−1
chlorhexidine. Thus, community level assessment indicated a risk of low levels of chlorhexidine in aquatic habitats while conventional approaches did not.
Functional Diversity and Electron Donor Dependence of Microbial Populations Capable of U(VI) Reduction in Radionuclide-Contaminated Subsurface Sediments
Authors: Akob Denise M. , Mills Heath J. , Gihring Thomas M. , Kerkhof Lee , Stucki Joseph W. , Anastácio Alexandre S. , Chin Kuk-Jeong , Küsel Kirsten , Palumbo Anthony V. , Watson David B. , Kostka Joel E. 
Published: April 2008

ABSTRACT

In order to elucidate the potential mechanisms of U(VI) reduction for the optimization of bioremediation strategies, the structure-function relationships of microbial communities were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate. A polyphasic approach was used to assess the functional diversity of microbial populations likely to catalyze electron flow under conditions proposed for in situ uranium bioremediation. The addition of ethanol and glucose as supplemental electron donors stimulated microbial nitrate and Fe(III) reduction as the predominant terminal electron-accepting processes (TEAPs). U(VI), Fe(III), and sulfate reduction overlapped in the glucose treatment, whereas U(VI) reduction was concurrent with sulfate reduction but preceded Fe(III) reduction in the ethanol treatments. Phyllosilicate clays were shown to be the major source of Fe(III) for microbial respiration by using variable-temperature Mössbauer spectroscopy. Nitrate- and Fe(III)-reducing bacteria (FeRB) were abundant throughout the shifts in TEAPs observed in biostimulated microcosms and were affiliated with the genera
Geobacter, Tolumonas, Clostridium, Arthrobacter, Dechloromonas
, and
Pseudomonas
. Up to two orders of magnitude higher counts of FeRB and enhanced U(VI) removal were observed in ethanol-amended treatments compared to the results in glucose-amended treatments. Quantification of citrate synthase (
gltA
) levels demonstrated a stimulation of
Geobacteraceae
activity during metal reduction in carbon-amended microcosms, with the highest expression observed in the glucose treatment. Phylogenetic analysis indicated that the active FeRB share high sequence identity with
Geobacteraceae
members cultivated from contaminated subsurface environments. Our results show that the functional diversity of populations capable of U(VI) reduction is dependent upon the choice of electron donor.
Role of Intestinal Microbiota in Transformation of Bismuth and Other Metals and Metalloids into Volatile Methyl and Hydride Derivatives in Humans and Mice
Authors: Michalke Klaus , Schmidt Annette , Huber Britta , Meyer Jörg , Sulkowski Margareta , Hirner Alfred V. , Boertz Jens , Mosel Frank , Dammann Philip , Hilken Gero , Hedrich Hans J. , Dorsch Martina , Rettenmeier Albert W. , Hensel Reinhard 
Published: April 2008

ABSTRACT

The present study shows that feces samples of 14 human volunteers and isolated gut segments of mice (small intestine, cecum, and large intestine) are able to transform metals and metalloids into volatile derivatives ex situ during anaerobic incubation at 37°C and neutral pH. Human feces and the gut of mice exhibit highly productive mechanisms for the formation of the toxic volatile derivative trimethylbismuth [(CH
3
)
3
Bi] at rather low concentrations of bismuth (0.2 to 1 μmol kg
−1
[dry weight]). An increase of bismuth up to 2 to 14 mmol kg
−1
(dry weight) upon a single (human volunteers) or continuous (mouse study) administration of colloidal bismuth subcitrate resulted in an average increase of the derivatization rate from approximately 4 pmol h
−1
kg
−1
(dry weight) to 2,100 pmol h
−1
kg
−1
(dry weight) in human feces samples and from approximately 5 pmol h
−1
kg
−1
(dry weight) to 120 pmol h
−1
kg
−1
(dry weight) in mouse gut samples, respectively. The upshift of the bismuth content also led to an increase of derivatives of other elements (such as arsenic, antimony, and lead in human feces or tellurium and lead in the murine large intestine). The assumption that the gut microbiota plays a dominant role for these transformation processes, as indicated by the production of volatile derivatives of various elements in feces samples, is supported by the observation that the gut segments of germfree mice are unable to transform administered bismuth to (CH
3
)
3
Bi.
A Diversity-Covering Approach to Immunization with
Plasmodium falciparum
Apical Membrane Antigen 1 Induces Broader Allelic Recognition and Growth Inhibition Responses in Rabbits
Authors: Remarque Edmond J. , Faber Bart W. , Kocken Clemens H. M. , Thomas Alan W. 
Published: April 2008

ABSTRACT

Plasmodium falciparum
apical membrane antigen 1 (PfAMA1), a candidate malaria vaccine, is polymorphic. This polymorphism is believed to be generated predominantly under immune selection pressure and, as a result, may compromise attempts at vaccination. Alignment of 355 PfAMA1 sequences shows that around 10% of the 622 amino acid residues can vary between alleles and that linkages between polymorphic residues occur. Using this analysis, we have designed three diversity-covering (DiCo) PfAMA1 sequences that take account of these linkages and, when taken together, on average incorporate 97% of amino acid variability observed. For each of the three DiCo sequences, a synthetic gene was constructed and used to transform the methylotrophic yeast
Pichia pastoris
, allowing recombinant expression. All three DiCo proteins were reactive with the reduction-sensitive monoclonal antibody 4G2, suggesting the DiCo sequences had conformations similar to those of naturally occurring PfAMA1. Rabbits were immunized with FVO strain PfAMA1 or with the DiCo proteins either individually or as a mixture. Antibody titers and the ability to inhibit parasite growth in vitro were determined. Animals immunized with the DiCo mix performed similarly to animals immunized with FVO AMA1 when measured against FCR3 strain parasites but outperformed animals immunized with FVO AMA1 when assessed against other strains. The levels of growth inhibition (∼70%) induced by the mix of three DiCo proteins were comparable for FVO, 3D7, and HB3, suggesting that a considerable degree of diversity in AMA1 is adequately covered. This suggests that vaccines based upon the DiCo mix approach provide a broader functional immunity than immunization with a single allele.
Role of Integrin αvβ6 in Acute Lung Injury Induced byPseudomonas aeruginosa
Authors: Song Yuanlin , Pittet Jean Francois , Huang Xiaozhu , He Hong , Lynch Susan V. , Violette Shelia M. , Weinreb Paul H. , Horan Gerald S. , Carmago Amua , Sawa Yoriko , Bernstein Xin Liu , Wiener-Kronish Jeanine P. 
Published: April 2008

ABSTRACTDeletion of integrin αvβ6 has been associated with significant protection in experiments where lung injury was induced by bleomycin, lipophilic polysaccharides, and high tidal volume ventilation. This has led to the suggestion that antibody blockade of this integrin is a novel therapy for acute lung injury. We questioned whether β6 gene deletion would also protect againstPseudomonas aeruginosa-induced acute lung injury. Wild-type and littermate β6-null mice, as well as recombinant soluble TGF-β receptor type II-Fc (rsTGF-βRII-Fc) and anti-αvβ6 treated wild-type mice, were instilled with liveP. aeruginosa. Four or 8 h after bacterial instillation, the mice were euthanized, and either bronchoalveolar lavage fluid or lung homogenates were obtained. Deletion of the β6 gene resulted in an overall increase in inflammatory cells in the lungs. Bacterial numbers from the lung homogenates of infected β6-null mice were significantly decreased compared to the numbers in the wild-type mice (1.6 × 106CFU versus 4.2 × 106CFU [P< 0.01]). There were no significant differences inP. aeruginosa-mediated increases in lung endothelial permeability between wild-type and β6-null mice. Similarly, pretreatment with the αvβ6 antibody or with rsTGF-βRII-Fc did not significantly affect theP. aeruginosa-induced lung injury or rate of survival compared to pretreatment with control immunoglobulin G. We conclude that deletion or inhibition of the integrin αvβ6 didnotprotect animals fromP. aeruginosa-induced lung injury. However, these therapies also did not increase the lung injury, suggesting that host defense was not compromised by this promising new therapy.
Statistical Geometry and Cavity Correlations in the Hard Sphere Fluid
Authors: Speedy Robin J. , Bowles Richard K. 
Published: April 2008

The statistical geometry of a system of hard spheres is discussed in terms of the volumes Vj that lie with a sphere diameter, σ, of exactly j sphere centres. A site that has no sphere centre within σ is called a cavity site. We focus on the probability n00(r) that two sites separated by r are both cavity sites. n00(0), n00(σ), and the limiting slope (d ln n00(r)/dr)r=0, are all known in terms of the thermodynamic properties. The Vj and n00(r) are measured by computer simulation and an empirical expression, which satisfies the known exact relations, is shown to represent n00(r) precisely in the range 0 ≤ r ≤ σ.
Influence of transverse crack width on reinforcement corrosion initiation and propagation in mortar beams
Authors: Şahmaran Mustafa , Yaman İ. Özgür 
Published: April 2008

This paper discusses the relationship between crack widths, chloride diffusivity, and corrosion rate of cracked mortar beams. Flexural loads are introduced to generate crack widths ranging from 29 to 390 µm. The specimens were subjected to accelerated corrosion by immersion in a 5% NaCl solution and a constant voltage of 12 V. In addition, salt ponding tests were conducted to determine the chloride ion transport properties. The results showed that as the crack width increased, the effective diffusion coefficient (corrosion initiation) and mass loss of steel reinforcing bars due to the accelerated corrosion (corrosion propagation) also increased. For crack widths less than about 135 µm, the effect of crack width on the effective diffusion coefficient and mass loss of steel reinforcing bars embedded in mortar specimens was found to be marginal when compared with the virgin specimens. Therefore, it was concluded that the effect of crack width on the corrosion initiation and propagation period was more pronounced when the crack width is greater than about 135 µm. Moreover, a significant amount of self-healing was observed for the cracks that have widths below 50 µm when subjected to the NaCl solution exposure.
MC1R variants correlate with thinhorn sheep colour cline but not individual colour
Authors: Loehr J. , Worley K. , Moe J. , Carey J. , Coltman D. W. 
Published: April 2008

The melanocortin 1 receptor (MC1R) gene has provided a window on the evolution of colour polymorphisms. Recent studies have demonstrated associations between MC1R and melanism in a number of wildlife species. Thinhorn sheep ( Ovis dalli Nelson, 1884) are a possible species to test for association between MC1R polymorphisms and melanism. Across their range the pelage colour of thinhorn sheep intergrades between all white phenotypes to very dark phenotypes. Most thinhorn sheep are white; however, there is a 1200 km cline from light to dark sheep that occurs over three genetically distinct polymorphic populations. We sequenced the entire MC1R gene from 40 individuals across the range of thinhorn sheep. We found a single nucleotide polymorphism in MC1R at base pair position 921 that coincided with the geographic cline. However, at the individual level we found no relationship between individual melanism and genotype.
Effect of forest management on a rare habitat specialist, the Bicknell's Thrush (Catharus bicknelli)
Authors: Chisholm S. E. , Leonard M. L. 
Published: April 2008

Forest dwelling birds with narrow habitat preferences may be vulnerable to habitat changes from forest management. The Bicknell’s Thrush ( Catharus bicknelli (Ridgway, 1882)), a rare habitat specialist, occupies dense regenerating forest, including stands managed for timber. However, little is known of the impact of various forestry practices on Bicknell’s Thrush abundance. The purpose of our study was to determine how Bicknell’s Thrush abundance varied across the stages of a managed forest and to determine if abundance was affected by precommercial thinning, a practice that reduces stem density. Bicknell’s Thrush was most abundant in stands that were regenerating after being clear-cut 11–13 years earlier and of sufficient height and stem density to undergo thinning. Thrush abundance declined following thinning and was positively related to the amount of unthinned area remaining in the stand. Over all stand types, thrush abundance increased with increasing elevation and with the density of stems between 5 and 10 cm in diameter, but decreased with increasing amounts of bare ground. The results of this study suggest that Bicknell’s Thrush may benefit from the early successional habitat associated with managed forests, but may be negatively affected by treatments such as precommercial thinning that reduce stem densities.