bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Genes and Proteins Necessary for Catabolism of Acyclic Terpenes and Leucine/Isovalerate in
Pseudomonas aeruginosa
Authors: Förster-Fromme Karin , Höschle Birgit , Mack Christina , Bott Michael , Armbruster Wolfgang , Jendrossek Dieter 
Published: July 2006

ABSTRACT

Geranyl-coenzyme A (CoA)-carboxylase (GCase; AtuC/AtuF) and methylcrotonyl-CoA-carboxylase (MCase; LiuB/LiuD) are characteristic enzymes of the catabolic pathway of acyclic terpenes (citronellol and geraniol) and of saturated methyl-branched compounds, such as leucine or isovalerate, respectively. Proteins encoded by two gene clusters (
atuABCDEFGH
and
liuRABCDE
) of
Pseudomonas aeruginosa
PAO1 were essential for acyclic terpene utilization (Atu) and for leucine and isovalerate utilization (Liu), respectively, as revealed by phenotype analysis of 10 insertion mutants, two-dimensional gel electrophoresis, determination of GCase and MCase activities, and Western blot analysis of wild-type and mutant strains. Analysis of the genome sequences of other pseudomonads (
P. putida
KT2440 and
P. fluorescens
Pf-5) revealed candidate genes for Liu proteins for both species and candidate genes for Atu proteins in
P. fluorescens
. This result concurred with the finding that
P. fluorescens
, but not
P. putida
, could grow on acyclic terpenes (citronellol and citronellate), while both species were able to utilize leucine and isovalerate. A regulatory gene,
atuR
, was identified upstream of
atuABCDEFGH
and negatively regulated expression of the
atu
gene cluster.
Molecular Epidemiology of Group A Rotaviruses in Water Sources and Selected Raw Vegetables in Southern Africa
Authors: van Zyl W. B. , Page N. A. , Grabow W. O. K. , Steele A. D. , Taylor M. B. 
Published: July 2006

ABSTRACT
Group A rotaviruses (RVs) are the most important cause of acute viral gastroenteritis in infants and young children. In this study raw and treated drinking water supplies at plants in two geographic areas, as well as selected irrigation water and corresponding raw vegetables in three regions of southern Africa, were screened for the presence of RVs using molecular techniques. Group A RVs were detected in 11.8% of partially treated and 1.7% of finally treated drinking water samples and in 14% of irrigation water samples and 1.7% of corresponding raw vegetable samples. Type-specific reverse transcriptase-PCR and sequence analysis revealed the presence of multiple types (G1, G2, G8, and G9) in irrigation water and single types (G1 or G3) in raw and treated drinking water. Group A RVs detected in all samples consisted of mixed P types (P[4], P[6], P[8], and P[9]), with P[6] predominating. The detection of types G8, G9, and P[6] reflects the emergence of these types in clinical infections. The similarity of environmental types to those in patients with clinical RV infections confirms the value of wastewater screening as a tool for assessing RVs circulating in communities, with the benefit of detecting types that cause both clinical and subclinical infections. The results provide new information on RV types in water and related environments and identify the potential risk of waterborne transmission. In addition, the presence of RVs in drinking water underlines shortcomings in quality specifications. These data provide valuable information regarding the prevalence of RVs in environmental sources, with important implications for vaccine development.
Influences of Biofilm Structure and Antibiotic Resistance Mechanisms on Indirect Pathogenicity in a Model Polymicrobial Biofilm
Authors: O'Connell Heather A. , Kottkamp Greg S. , Eppelbaum James L. , Stubblefield Bryan A. , Gilbert Sarah E. , Gilbert Eric S. 
Published: July 2006

ABSTRACT

Indirect pathogenicity (IP), the commensal protection of antibiotic-sensitive pathogens by resistant microorganisms of low intrinsic virulence, can prevent the eradication of polymicrobial infections. The contributions of antibiotic resistance mechanisms and biofilm structure to IP within polymicrobial biofilms were investigated using a model two-member consortium.
Escherichia coli
ATCC 33456 was transformed with vectors conferring either ampicillin or spectinomycin resistance, creating two distinct populations with different resistance mechanisms. Each strain alone or the consortium was grown as biofilms in flow cells and planktonically in chemostats. Comparisons in survival and activity were made on the basis of MICs and minimum biofilm preventative concentrations, a newly introduced descriptor. In ampicillin-containing medium, commensal interactions were evident during both modes of cultivation, but the sensitive strain experienced a greater benefit in the chemostat, indicating that the biofilm environment limited the commensal interaction between the Amp
r
and Spt
r
strains. In spectinomycin-containing medium, growth of the sensitive strain in chemostats and biofilms was not aided by the resistant strain. However, green fluorescent protein expression by the sensitive strain was greater in mixed-population biofilms (9% ± 1%) than when the strain was grown alone (2% ± 0%). No comparable benefit was evident during growth in the chemostat, indicating that the biofilm structure contributed to enhanced activity of the sensitive strain.
Use of a Nonmedicated Dietary Supplement Correlates with Increased Prevalence of Streptomycin-Sulfa-Tetracycline-Resistant
Escherichia coli
on a Dairy Farm
Authors: Khachatryan Artashes R. , Besser Thomas E. , Hancock Dale D. , Call Douglas R. 
Published: July 2006

ABSTRACT

We examined how a dietary supplement affects the prevalence of antibiotic-resistant
Escherichia coli
on a dairy farm in Washington State. Between 2001 and 2004 the prevalence of fecal
E. coli
strains resistant to streptomycin, sulfadiazine, and tetracycline (SSuT strains) declined from 59.2% to 26.1% in the calf population. In 2003 the dairy discontinued use of a dietary supplement, and we hypothesized that the decline in prevalence of SSuT strains was related to this change in management. To test this we established three treatments in which calves received no supplement, the dietary supplement with oxytetracycline, or the dietary supplement without oxytetracycline. Calves receiving either dietary supplement had a significantly higher prevalence of SSuT
E. coli
than the no-supplement control group (≈37% versus 20%, respectively;
P
= 0.03). Importantly, there was no evidence that oxytetracycline contributed to an increased prevalence of fecal SSuT
E. coli
. We compared the growth characteristics of SSuT and non-SSuT
E. coli
in LB broth enriched with either the complete dietary supplement or its individual constituents. Both the complete dietary supplement and its vitamin D component supported a significantly higher cell density of SSuT strains (
P
= 0.003 and
P
= 0.001, respectively). The dry milk and vitamin A components of the dietary supplement did not support different cell densities. These results were consistent with selection and maintenance of SSuT
E. coli
due to environmental components independent of antibiotic selection.
Purification and Characterization of Two Enantioselective α-Ketoglutarate-Dependent Dioxygenases, RdpA and SdpA, fromSphingomonas herbicidovoransMH
Authors: Müller Tina A. , Fleischmann Thomas , van der Meer Jan Roelof , Kohler Hans-Peter E. 
Published: July 2006

ABSTRACTα-Ketoglutarate-dependent (R)-dichlorprop dioxygenase (RdpA) and α-ketoglutarate-dependent (S)-dichlorprop dioxygenase (SdpA), which are involved in the degradation of phenoxyalkanoic acid herbicides inSphingomonas herbicidovoransMH, were expressed and purified as His6-tagged fusion proteins fromEscherichia coliBL21(DE3)(pLysS). RdpA and SdpA belong to subgroup II of the α-ketoglutarate-dependent dioxygenases and share the specific motif HXDX24TX131HX10R. Amino acids His-111, Asp-113, and His-270 and amino acids His-102, Asp-104, and His 257 comprise the 2-His-1-carboxylate facial triads and were predicted to be involved in iron binding in RdpA and SdpA, respectively. RdpA exclusively transformed the (R) enantiomers of mecoprop [2-(4-chloro-2-methylphenoxy)propanoic acid] and dichlorprop [2-(2,4-dichlorophenoxy)propanoic acid], whereas SdpA was specific for the (S) enantiomers. The apparentKmvalues were 99 μM for (R)-mecoprop, 164 μM for (R)-dichlorprop, and 3 μM for α-ketoglutarate for RdpA and 132 μM for (S)-mecoprop, 495 μM for (S)-dichlorprop, and 20 μM for α-ketoglutarate for SdpA. Both enzymes had high apparentKmvalues for oxygen; these values were 159 μM for SdpA and >230 μM for RdpA, whose activity was linearly dependent on oxygen at the concentration range measured. Both enzymes had narrow cosubstrate specificity; only 2-oxoadipate was able to replace α-ketoglutarate, and the rates were substantially diminished. Ferrous iron was necessary for activity of the enzymes, and other divalent cations could not replace it. Although the results of growth experiments suggest that strain MH harbors a specific 2,4-dichlorophenoxyacetic acid-converting enzyme,tfdA-,tfdAα-, orcadAB-like genes were not discovered in a screening analysis in which heterologous hybridization and PCR were used.
Modification of Sexual Development and Carotene Production by Acetate and Other Small Carboxylic Acids in
Blakeslea trispora
and
Phycomyces blakesleeanus
Authors: Kuzina Vera , Cerdá-Olmedo Enrique 
Published: July 2006

ABSTRACT

In
Phycomyces blakesleeanus
and
Blakeslea trispora
(order Mucorales, class Zygomycetes), sexual interaction on solid substrates leads to zygospore development and to increased carotene production (sexual carotenogenesis). Addition of small quantities of acetate, propionate, lactate, or leucine to mated cultures on minimal medium stimulated zygospore production and inhibited sexual carotenogenesis in both
Phycomyces
and
Blakeslea
. In
Blakeslea
, the threshold acetate concentration was <1 mmol/liter for both effects, and the concentrations that had one-half of the maximal effect were <2 mmol/liter for carotenogenesis and >7 mmol/liter for zygosporogenesis. The effects on
Phycomyces
were similar, but the concentrations of acetate had to be multiplied by ca. 3 to obtain the same results. Inhibition of sexual carotenogenesis by acetate occurred normally in
Phycomyces
mutants that cannot use acetate as a carbon source and in mutants whose dormant spores cannot be activated by acetate. Small carboxylic acids may be signals that, independent of their ability to trigger spore germination in
Phycomyces
, modify metabolism and development during the sexual cycle of
Phycomyces
and
Blakeslea
, uncoupling two processes that were thought to be linked and mediated by a common mechanism.
Suspension Array Analysis of 16S rRNA from Fe- and SO
4
2
-Reducing Bacteria in Uranium-Contaminated Sediments Undergoing Bioremediation
Authors: Chandler Darrell P. , Jarrell Ann E. , Roden Eric R. , Golova Julia , Chernov Boris , Schipma Matthew J. , Peacock Aaron D. , Long Philip E. 
Published: July 2006

ABSTRACT

A 16S rRNA-targeted tunable bead array was developed and used in a retrospective analysis of metal- and sulfate-reducing bacteria in contaminated subsurface sediments undergoing in situ U(VI) bioremediation. Total RNA was extracted from subsurface sediments and interrogated directly, without a PCR step. Bead array validation studies with total RNA derived from 24 isolates indicated that the behavior and response of the 16S rRNA-targeted oligonucleotide probes could not be predicted based on the primary nucleic acid sequence. Likewise, signal intensity (absolute or normalized) could not be used to assess the abundance of one organism (or rRNA) relative to the abundance of another organism (or rRNA). Nevertheless, the microbial community structure and dynamics through time and space and as measured by the rRNA-targeted bead array were consistent with previous data acquired at the site, where indigenous sulfate- and iron-reducing bacteria and near neighbors of
Desulfotomaculum
were the organisms that were most responsive to a change in injected acetate concentrations. Bead array data were best interpreted by analyzing the relative changes in the probe responses for spatially and temporally related samples and by considering only the response of one probe to itself in relation to a background (reference) environmental sample. By limiting the interpretation of the data in this manner and placing it in the context of supporting geochemical and microbiological analyses, we concluded that ecologically relevant and meaningful information can be derived from direct microarray analysis of rRNA in uncharacterized environmental samples, even with the current analytical uncertainty surrounding the behavior of individual probes on tunable bead arrays.
Helicobacter anseris
sp. nov. and
Helicobacter brantae
sp. nov., Isolated from Feces of Resident Canada Geese in the Greater Boston Area
Authors: Fox James G. , Taylor Nancy S. , Howe Shelly , Tidd Michele , Xu Shilu , Paster Bruce J. , Dewhirst Floyd E. 
Published: July 2006

ABSTRACT

Numbers of nonmigratory Canada geese have increased substantially in the past decade, and they have become a nuisance in some urban areas. Because of their close contact with humans in parks and areas adjacent to surface waterways, contact with their feces poses a zoonotic risk. A total of 97 geese from 10 separate geographic locales in the greater Boston area had their feces sampled for detection of
Helicobacter
spp. Identification of
Helicobacter
spp. based on 16S rRNA genus-specific helicobacter primers was noted in 39 of 97 (40.2%) DNA fecal extracts. Twenty-seven (27.8%) of these geese had helicobacters isolated from their feces. A urease-positive novel species,
Helicobacter anseris
, based on phenotypic, biochemical, and 16S rRNA analyses, was isolated from 20 geese from seven different flocks. A second, novel, urease-negative
Helicobacter
sp.,
H. brantae
, was identified in seven geese. Four geese had both novel
Helicobacter
spp. cultured from their feces. Whether these two novel helicobacters pose a zoonotic risk, similar to other enteric helicobacters (e.g.,
H. canadensis
, previously isolated from diarrheic and bacteremic humans and from geese in Europe), will require further studies.
Intrinsic Properties of So-Called Dormant Probiotic Bacteria, Determined by Flow Cytometric Viability Assays
Authors: Lahtinen Sampo J. , Ouwehand Arthur C. , Reinikainen Johanna P. , Korpela Jaakko M. , Sandholm Jouko , Salminen Seppo J. 
Published: July 2006

ABSTRACT
Plate counting and four culture-independent flow cytometric assays were used to determine the viability and intrinsic properties of three probiotic strains during storage. The strains showed reduction in plate counts but were able to maintain esterase activity, intact cytoplasmic membrane, and pH gradient. The apparently uncultivable probiotic cells were active and stress resistant.
Analysis of the Life Cycle of the Soil Saprophyte
Bacillus cereus
in Liquid Soil Extract and in Soil
Authors: Vilain Sébastien , Luo Yun , Hildreth Michael B. , Brözel Volker S. 
Published: July 2006

ABSTRACT

Bacillus
is commonly isolated from soils, with organisms of
Bacillus cereus
sensu lato being prevalent. Knowledge of the ecology of
B. cereus
and other
Bacillus
species in soil is far from complete. While the older literature favors a model of growth on soil-associated organic matter, the current paradigm is that
B. cereus
sensu lato germinates and grows in association with animals or plants, resulting in either symbiotic or pathogenic interactions. An in terra approach to study soil-associated bacteria is described, using filter-sterilized soil-extracted soluble organic matter (SESOM) and artificial soil microcosms (ASM) saturated with SESOM.
B. cereus
ATCC 14579 displayed a life cycle, with the ability to germinate, grow, and subsequently sporulate in both the liquid SESOM extract and in ASM inserted into wells in agar medium. Cells grew in liquid SESOM without separating, forming multicellular structures that coalesced to form clumps and encasing the ensuing spores in an extracellular matrix.
Bacillus
was able to translocate from the point of inoculation through soil microcosms as shown by the emergence of outgrowths on the surrounding agar surface. Microscopic inspection revealed bundles of parallel chains inside the soil. The motility inhibitor
l
-ethionine failed to suppress outgrowth, ruling out translocation by a flagellar-mediated mechanism such as swimming or swarming.
Bacillus subtilis
subsp.
subtilis
Marburg and four
Bacillus
isolates taken at random from soils also displayed a life cycle in SESOM and ASM and were all able to translocate through ASM, even in presence of
l
-ethionine. These data indicate that
B. cereus
is a saprophytic bacterium that is able to grow in soil and furthermore that it is adapted to translocate by employing a multicellular mode of growth.
Simian Immunodeficiency Virus (SIV)/Immunoglobulin G Immune Complexes in SIV-Infected Macaques Block Detection of CD16 but Not Cytolytic Activity of Natural Killer Cells
Authors: Wei Qing , Stallworth Jackie W. , Vance Patricia J. , Hoxie James A. , Fultz Patricia N. 
Published: July 2006

ABSTRACTNatural killer cells are components of the innate immune system that play an important role in eliminating viruses and malignant cells. Using simian immunodeficiency virus (SIV) infection of macaques as a model, flow cytometry revealed a gradual loss of CD16+NK cell numbers that was associated with disease progression. Of note, the apparent loss of NK cells was detected in whole-blood samples but not in isolated peripheral blood mononuclear cells (PBMC), suggesting that an inhibitor(s) of the antibody used to detect CD16, the low-affinity immunoglobulin G (IgG) receptor, was present in blood but was removed during PBMC isolation. (Actual decreases in CD16+cell numbers in PBMC generally were not detected until animals became lymphopenic.) The putative decrease in CD16+cell numbers in whole blood correlated with increasing SIV-specific antibody titers and levels of plasma virion RNA. With the addition of increasing amounts of plasma from progressor, but not nonprogressor, macaques to PBMC from an uninfected animal, the apparent percentage of CD16+cells and the mean fluorescence intensity of antibodies binding to CD16 declined proportionately. A similar decrease was observed with the addition of monomeric IgG (mIgG) and IgG immune complexes (IgG-ICs) purified from the inhibitory plasma samples; some of the ICs contained SIV p27gagantigen and/or virions. Of interest, addition of purified IgG/IgG-ICs to NK cell lytic assays did not inhibit killing of K562 cells. These results indicate that during progressive SIV and, by inference, human immunodeficiency virus disease, CD16+NK cell numbers can be underestimated, or the cells not detected at all, when one is using a whole-blood fluorescence-activated cell sorter assay and a fluorochrome-labeled antibody that can be blocked by mIgG or IgG-ICs. Although this blocking had no apparent effect on NK cell activity in vitro, the in vivo effects are unknown.
Different Levels of Immunogenicity of Two Strains of Fowlpox Virus as Recombinant Vaccine Vectors Eliciting T-Cell Responses in Heterologous Prime-Boost Vaccination Strategies
Authors: Cottingham Matthew G. , van Maurik Andre , Zago Manola , Newton Angela T. , Anderson Richard J. , Howard M. Keith , Schneider Jörg , Skinner Michael A. 
Published: July 2006

ABSTRACTThe FP9 strain ofFowlpox virushas been described as a more immunogenic recombinant vaccine vector than the Webster FPV-M (FPW) strain (R. J. Anderson et al., J. Immunol. 172:3094-3100, 2004). This study expands the comparison to include two separate recombinant antigens and multiple, rather than single, independent viral clones derived from the two strains. Dual-poxvirus heterologous prime-boost vaccination regimens using individual clones of recombinant FP9 or FPW in combination with recombinant modifiedVaccinia virusAnkara expressing the same antigen were evaluated for their ability to elicit T-cell responses against recombinant antigens fromPlasmodium berghei(circumsporozoite protein) or human immunodeficiency virus type 1 (a Gag-Pol-Nef fusion protein). Gamma interferon enzyme-linked immunospot assay and fluorescence-activated cell sorting assays of the responses to specific epitopes confirmed the approximately twofold-greater cellular immunogenicity of FP9 compared to FPW, when given as the priming or boosting immunization. Equality of transgene expression in mouse cells infected with the two strains in vitro was verified by Western blotting. Directed partial sequence analysis and PCR analysis of FPW and comparison to available whole-genome sequences revealed that many loci that are mutated in the highly attenuated and culture-adapted FP9 strain are wild type in FPW, including the seven multikilobase deletions. These “passage-specific” alterations are hypothesized to be involved in determining the immunogenicity ofFowlpox virusas a recombinant vaccine vector.
Tuberculosis in Elephants: Antibody Responses to Defined Antigens of
Mycobacterium tuberculosis
, Potential for Early Diagnosis, and Monitoring of Treatment
Authors: Lyashchenko Konstantin P. , Greenwald Rena , Esfandiari Javan , Olsen John H. , Ball Ray , Dumonceaux Genevieve , Dunker Freeland , Buckley Carol , Richard Michael , Murray Suzan , Payeur Janet B. , Andersen Peter , Pollock John M. , Mikota Susan , Miller Michele , Sofranko Denise , Waters W. Ray 
Published: July 2006

ABSTRACT

Tuberculosis (TB) in elephants is a re-emerging zoonotic disease caused primarily by
Mycobacterium tuberculosis
. Current diagnosis relies on trunk wash culture, the only officially recognized test, which has serious limitations. Innovative and efficient diagnostic methods are urgently needed. Rapid identification of infected animals is a crucial prerequisite for more effective control of TB, as early diagnosis allows timely initiation of chemotherapy. Serology has diagnostic potential, although key antigens have not been identified and optimal immunoassay formats are not established. To characterize the humoral responses in elephant TB, we tested 143 serum samples collected from 15 elephants over time. These included 48 samples from five culture-confirmed TB cases, of which four were in Asian elephants infected with
M. tuberculosis
and one was in an African elephant with
Mycobacterium bovis
. Multiantigen print immunoassay (MAPIA) employing a panel of 12 defined antigens was used to identify serologic correlates of active disease. ESAT-6 was the immunodominant antigen recognized in elephant TB. Serum immunoglobulin G antibodies to ESAT-6 and other proteins were detected up to 3.5 years prior to culture of
M. tuberculosis
from trunk washes. Antibody levels to certain antigens gradually decreased in response to antitubercular therapy, suggesting the possibility of treatment monitoring. In addition to MAPIA, serum samples were evaluated with a recently developed rapid test (RT) based on lateral flow technology (ElephantTB STAT-PAK). Similarly to MAPIA, infected elephants were identified using the RT up to 4 years prior to positive culture. These findings demonstrate the potential for TB surveillance and treatment monitoring using the RT and MAPIA, respectively.