bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Airborne Molds, Endotoxins, and Glucans in Homes in New Orleans after Hurricanes Katrina and Rita
Authors: Rao Carol Y. , Riggs Margaret A. , Chew Ginger L. , Muilenberg Michael L. , Thorne Peter S. , Van Sickle David , Dunn Kevin H. , Brown Clive 
Published: January 2007

ABSTRACT

In August and September 2005, Hurricanes Katrina and Rita caused breeches in the New Orleans, LA, levee system, resulting in catastrophic flooding. The city remained flooded for several weeks, leading to extraordinary mold growth in homes. To characterize the potential risks of mold exposures, we measured airborne molds and markers of molds and bacteria in New Orleans area homes. In October 2005, we collected air samples from 5 mildly water-damaged houses, 15 moderately to heavily water-damaged houses, and 11 outdoor locations. The air filters were analyzed for culturable fungi, spores, (1→3,1→6)-β-
d
-glucans, and endotoxins. Culturable fungi were significantly higher in the moderately/heavily water-damaged houses (geometric mean = 67,000 CFU/m
3
) than in the mildly water-damaged houses (geometric mean = 3,700 CFU/m
3
) (
P
= 0.02). The predominant molds found were
Aspergillus niger
,
Penicillium
spp.,
Trichoderma
, and
Paecilomyces
. The indoor and outdoor geometric means for endotoxins were 22.3 endotoxin units (EU)/m
3
and 10.5 EU/m
3
, respectively, and for (1→3,1→6)-β-
d
-glucans were 1.7 μg/m
3
and 0.9 μg/m
3
, respectively. In the moderately/heavily water-damaged houses, the geometric means were 31.3 EU/m
3
for endotoxins and 1.8 μg/m
3
for (1→3,1→6)-β-
d
-glucans. Molds, endotoxins, and fungal glucans were detected in the environment after Hurricanes Katrina and Rita in New Orleans at concentrations that have been associated with health effects. The species and concentrations were different from those previously reported for non-water-damaged buildings in the southeastern United States.
Quantitative Assessment of the Tetracycline Resistance Gene Pool in Cheese Samples by Real-Time TaqMan PCR
Authors: Manuzon Michele Y. , Hanna Scott E. , Luo Hongliang , Yu Zhongtang , Harper W. James , Wang Hua H. 
Published: January 2007

ABSTRACT

A TaqMan real-time PCR assay was developed to quantify the
tetS
gene pool present in retail cheeses. This protocol offers a rapid, specific, sensitive, and culture-independent method for assessing antibiotic resistance genes in food samples rich in fats and proteins.
Characterization of IS
Xax1
, a Novel Insertion Sequence Restricted to
Xanthomonas axonopodis
pv. phaseoli (Variants fuscans and non-fuscans) and
Xanthomonas axonopodis
pv. vesicatoria
Authors: Alavi Seyed Mehdi , Poussier Stéphane , Manceau Charles 
Published: January 2007

ABSTRACT

IS
Xax1
is a novel insertion sequence belonging to the IS
256
and
Mutator
families. Dot blot, Southern blot, and PCR analyses revealed that IS
Xax1
is restricted to
Xanthomonas axonopodis
pv. phaseoli (variants fuscans and non-fuscans) and
X. axonopodis
pv. vesicatoria strains. Directed AFLP also showed that a high degree of polymorphism is associated with IS
Xax1
insertion in these strains.
Photoreactivation and Dark Repair in UV-Treated Microorganisms: Effect of Temperature
Authors: Salcedo I. , Andrade J. A. , Quiroga J. M. , Nebot E. 
Published: January 2007

ABSTRACT

Because of the lack of readily available information about the influence of temperature on microorganism reactivation processes subsequent to inactivation with UV radiation, a series of batch reactivation studies were performed at 5, 10, 15, 20, 25, and 30°C. A special effort was made to model the reactivation process to enable the effect of the temperature variable to be quantified. Because an earlier-proposed kinetic model (K. Kashimada, N. Kamiko, K. Yamamoto, and S. Ohgaki, Water Sci. Technol. 33:261-269, 1996), a first-order saturation type, does not adequately fit the data obtained in experiments of reactivation in conditions of light and darkness, a modification of that model is proposed. The new model, which actually coincides with the classical logistic equation, incorporates two kinetic parameters: the maximum survival ratio (

S
m

) and the second-order reactivation rate constant (
k
2
). In order to interpret correctly the reactivation occurring in conditions of darkness, a new term for the decay is added to the logistic equation. The new model accurately fits the data obtained in reactivation experiments, permitting the interpretation of the kinetic parameters

S
m

,
k
2
, and
M
(for only repair in darkness), where
M
is mortality, a zero-order decay rate constant, and their relationship with various environmental conditions, such as microbial type, light, and temperature. The parameters

S
m

and
k
2
(and
M
for reactivation in conditions of darkness) show exponential dependence on the reactivating temperature, and it is possible to predict their values and hence the reactivation curve from the equations proposed in this work.
Individual and Combined Effects of pH and Lactic Acid Concentration on
Listeria innocua
Inactivation: Development of a Predictive Model and Assessment of Experimental Variability
Authors: Janssen M. , Geeraerd A. H. , Cappuyns A. , Garcia-Gonzalez L. , Schockaert G. , Van Houteghem N. , Vereecken K. M. , Debevere J. , Devlieghere F. , Van Impe J. F. 
Published: January 2007

ABSTRACT

In food technology, organic acids (e.g., lactic acid, acetic acid, and citric acid) are popular preservatives. The purpose of this study was to separate the individual effects of the influencing factors pH and undissociated lactic acid on
Listeria innocua
inactivation. Therefore, the inactivation process was investigated under controlled, initial conditions of pH (pH
0
) and undissociated lactic acid ([LaH]
0
). The resulting inactivation curves consisted of a (sometimes negligible) shoulder period followed by a descent phase. In a few cases, a tailing phase was observed. Depending on the conditions, the descent phase contained one or two log-linear parts or had a convex or concave shape. In addition, the inactivation process was characterized by a certain variability, dependent on the severity of the conditions. Furthermore, in the neighborhood of the growth/no growth interface sometimes contradictory observations occurred. Overall, the individual effects of the influencing factors pH and undissociated lactic acid could clearly be distinguished and were also apparent based on fluorescence microscopy. Appropriate model types were developed and enabled prediction of which conditions of pH
0
and [LaH]
0
are necessary to obtain a predetermined inactivation (number of decimal reductions) within a predetermined time range.
Strong Impact on the Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Community of a PAH-Polluted Soil but Marginal Effect on PAH Degradation when Priming with Bioremediated Soil Dominated by Mycobacteria
Authors: Johnsen Anders R. , Schmidt Stine , Hybholt Trine K. , Henriksen Sidsel , Jacobsen Carsten S. , Andersen Ole 
Published: January 2007

ABSTRACT

Bioaugmentation of soil polluted with polycyclic aromatic hydrocarbons (PAHs) is often disappointing because of the low survival rate and low activity of the introduced degrader bacteria. We therefore investigated the possibility of priming PAH degradation in soil by adding 2% of bioremediated soil with a high capacity for PAH degradation. The culturable PAH-degrading community of the bioremediated primer soil was dominated by
Mycobacterium
spp. A microcosm containing pristine soil artificially polluted with PAHs and primed with bioremediated soil showed a fast, 100- to 1,000-fold increase in numbers of culturable phenanthrene-, pyrene-, and fluoranthene degraders and a 160-fold increase in copy numbers of the mycobacterial PAH dioxygenase gene
pdo1
. A nonpolluted microcosm primed with bioremediated soil showed a high rate of survival of the introduced degrader community during the 112 days of incubation. A nonprimed control microcosm containing pristine soil artificially polluted with PAHs showed only small increases in the numbers of culturable PAH degraders and no
pdo1
genes. Initial PAH degradation rates were highest in the primed microcosm, but later, the degradation rates were comparable in primed and nonprimed soil. Thus, the proliferation and persistence of the introduced, soil-adapted degraders had only a marginal effect on PAH degradation. Given the small effect of priming with bioremediated soil and the likely presence of PAH degraders in almost all PAH-contaminated soils, it seems questionable to prime PAH-contaminated soil with bioremediated soil as a means of large-scale soil bioremediation.
Identification of Bacterial DNA Markers for the Detection of Human Fecal Pollution in Water
Authors: Shanks Orin C. , Domingo Jorge W. Santo , Lu Jingrang , Kelty Catherine A. , Graham James E. 
Published: January 2007

ABSTRACT
We used genome fragment enrichment and bioinformatics to identify several microbial DNA sequences with high potential for use as markers in PCR assays for detection of human fecal contamination in water. Following competitive solution-phase hybridization of total DNA from human and pig fecal samples, 351 plasmid clones were sequenced and were determined to define 289 different genomic DNA regions. These putative human-specific fecal bacterial DNA sequences were then analyzed by dot blot hybridization, which confirmed that 98% were present in the source human fecal microbial community and absent from the original pig fecal DNA extract. Comparative sequence analyses of these sequences suggested that a large number (43.5%) were predicted to encode bacterial secreted or surface-associated proteins. Deoxyoligonucleotide primers capable of annealing to a subset of 26 of the candidate sequences predicted to encode factors involved in interactions with host cells were then used in the PCR and did not amplify markers in DNA from any additional pig fecal specimens. These 26 PCR assays exhibited a range of specificity in tests with 11 other animal sources, with more than half amplifying markers only in specimens from dogs or cats. Four assays were more specific, detecting markers only in specimens from humans, including those from 18 different human populations examined. We then demonstrated the potential utility of these assays by using them to detect human fecal contamination in several impacted watersheds.
Growth Yields in Bacterial Denitrification and Nitrate Ammonification
Authors: Strohm Tobin O. , Griffin Ben , Zumft Walter G. , Schink Bernhard 
Published: January 2007

ABSTRACT

Denitrification and nitrate ammonification are considered the highest-energy-yielding respiration systems in anoxic environments after oxygen has been consumed. The corresponding free energy changes are 7 and 35% lower than that of aerobic respiration, respectively. Growth yield determinations with pure cultures of
Paracoccus denitrificans
and
Pseudomonas stutzeri
revealed that far less energy is converted via ATP into cell mass than expected from the above calculations. Denitrification with formate or hydrogen as electron donor yielded about 2.4 to 3.0 g dry matter per mol formate or hydrogen and 15 to 18 g dry matter per mol acetate. Similar yields with acetate were obtained with
Pseudomonas stutzeri. Wolinella succinogenes
and
Sulfurospirillum deleyianum
, which reduce nitrate to ammonia, both exhibited similar yield values with formate or H
2
plus nitrate. The results indicate that ATP synthesis in denitrification is far lower than expected from the free energy changes and even lower than in nitrate ammonification. The results are discussed against the background of our present understanding of electron flow in denitrification and with respect to the importance of denitrification and nitrate ammonification in the environment.
Structure and Function Analysis of CaMdr1p, a Major Facilitator Superfamily Antifungal Efflux Transporter Protein of
Candida albicans
: Identification of Amino Acid Residues Critical for Drug/H
+
Transport
Authors: Pasrija Ritu , Banerjee Dibyendu , Prasad Rajendra 
Published: January 2007

ABSTRACT

We have cloned and overexpressed multidrug transporter CaMdr1p as a green fluorescent protein-tagged protein to show its capability to extrude drug substrates. The drug extrusion was sensitive to pH and energy inhibitors and displayed selective substrate specificity. CaMdr1p has a unique and conserved antiporter motif, also called motif C [G(X
6
)G(X
3
)GP(X
2
)GP(X
2
)G], in its transmembrane segment 5 (TMS 5). Alanine scanning of all the amino acids of the TMS 5 by site-directed mutagenesis highlighted the importance of the motif, as well as that of other residues of TMS 5, in drug transport. The mutant variants of TMS 5 were placed in four different categories. The first category had four residues, G244, G251, G255, and G259, which are part of the conserved motif C, and their substitution with alanine resulted in increased sensitivity to drugs and displayed impaired efflux of drugs. Interestingly, first category mutants, when replaced with leucine, resulted in more dramatic loss of drug resistance and efflux. Notwithstanding the location in the core motif, the second category included residues which are part of the motif, such as P260, and those which were not part of the motif, such as L245, W248, P256, and F262, whose substitution with alanine resulted in a severe loss of drug resistance and efflux. The third category included G263, which is a part of motif C, but unlike other conserved glycines, its replacement with alanine or leucine showed no change in the phenotype. The replacement of the remaining 11 residues of the fourth category did not result in any change. The putative helical wheel projection showed clustering of functionally critical residues to one side and thus suggests an asymmetric nature of TMS 5.
Biosynthesis of the Thioquinolobactin Siderophore: an Interesting Variation on Sulfur Transfer
Authors: Godert Amy M. , Jin Mi , McLafferty Fred W. , Begley Tadhg P. 
Published: January 2007

ABSTRACT

The thioquinolobactin siderophore from
Pseudomonas fluorescens
ATCC 17400 utilizes a variation of the sulfur transfer chemistry found in thiamine and molydobterin biosynthesis. A JAMM motif protein cleaves the C-terminal amino acid residues following a diglycine moiety on a small sulfur carrier protein, and the modified C terminus is activated and sulfurylated, forming a thiocarboxylate.
Role of an FtsK-Like Protein in Genetic Stability inStreptomyces coelicolorA3(2)
Authors: Wang Lei , Yu Yanfei , He Xinyi , Zhou Xiufen , Deng Zixin , Chater Keith F. , Tao Meifeng 
Published: January 2007

ABSTRACTStreptomyces coelicolorA3(2) does not have a canonical cell division cycle during most of its complex life cycle, yet it contains a gene (ftsKSC) encoding a protein similar to FtsK, which couples the completion of cell division and chromosome segregation in unicellular bacteria such asEscherichia coli. Here, we show that various constructedftsKSCmutants all grew apparently normally and sporulated but upon restreaking gave rise to many aberrant colonies and to high frequencies of chloramphenicol-sensitive mutants, a phenotype previously associated with large terminal deletions from the linear chromosome. Indeed, most of the aberrant colonies had lost large fragments near one or both chromosomal termini, as if chromosome ends had failed to reach their prespore destination before the closure of sporulation septa. A constructed FtsKSC-enhanced green fluorescent protein fusion protein was particularly abundant in aerial hyphae, forming distinctive complexes before localizing to each sporulation septum, suggesting a role for FtsKSCin chromosome segregation during sporulation. Use of a fluorescent reporter showed that whenftsKSCwas deleted, several spore compartments in most spore chains failed to express the late-sporulation-specific sigma factor genesigF, even though they contained chromosomal DNA. This suggested thatsigFexpression is autonomously activated in each spore compartment in response to completion of chromosome transfer, which would be a previously unknown checkpoint for late-sporulation-specific gene expression. These results provide new insight into the genetic instability prevalent among streptomycetes, including those used in the industrial production of antibiotics.
Reassessment of the Late Steps of Coenzyme B
12
Synthesis in
Salmonella enterica
: Evidence that Dephosphorylation of Adenosylcobalamin-5′-Phosphate by the CobC Phosphatase Is the Last Step of the Pathway
Authors: Zayas Carmen L. , Escalante-Semerena Jorge C. 
Published: January 2007

ABSTRACT

We report that
cobC
strains of
Salmonella enterica
serovar Typhimurium are impaired in the ability to salvage cobyric acid (Cby), a de novo corrin ring biosynthetic intermediate, under aerobic growth conditions. In vivo and in vitro evidence support the conclusion that this new phenotype of
cobC
strains is due to the inability of serovar Typhimurium to dephosphorylate adenosylcobalamin-5′-phosphate (AdoCbl-5′-P), the product of the condensation of α-ribazole-5′-phosphate (α-RP) and adenosylcobinamide-GDP by the AdoCbl-5′-P synthase (CobS, EC 2.7.8.26) enzyme. Increased flux through the 5,6-dimethylbenzimidazole and cobinamide (Cbi) activation branches of the nucleotide loop assembly pathway in
cobC
strains restored AdoCbl-5′-P synthesis from Cby in a
cobC
strain. The rate of the CobS-catalyzed reaction was at least 2 orders of magnitude higher with α-RP than with α-ribazole as substrate. On the basis of the data reported herein, we conclude that removal of the phosphoryl group from AdoCbl-5′-P is the last step in AdoCbl biosynthesis in serovar Typhimurium and that the reaction is catalyzed by the AdoCbl-5′-P phosphatase (CobC) enzyme. Explanations for the correction of the Cby salvaging phenotype are discussed.
Evidence for Type III Restriction and Modification Systems in
Mycoplasma pulmonis
Authors: Dybvig Kevin , Cao Z. , French C. Todd , Yu Huilan 
Published: January 2007

ABSTRACT

Mycoplasma pulmonis
possesses a cassette of genes that are predicted to code for type III restriction and modification (R-M) enzymes. Transposon disruption of a gene predicted to code for the endonuclease subunit of the enzyme resulted in loss of R-M activity. Genomic data indicate that the cassette was acquired by horizontal gene transfer and possibly located on a mobile element.
Genes Required for Glycolipid Synthesis and Lipoteichoic Acid Anchoring in
Staphylococcus aureus
Authors: Gründling Angelika , Schneewind Olaf 
Published: January 2007

ABSTRACT

Staphylococcus aureus
lipoteichoic acid (LTA) is composed of a linear 1,3-linked polyglycerolphosphate chain and is tethered to the bacterial membrane by a glycolipid (diglucosyl-diacylglycerol [Glc
2
-DAG]). Glc
2
-DAG is synthesized in the bacterial cytoplasm by YpfP, a processive enzyme that transfers glucose to diacylglycerol (DAG), using UDP-glucose as its substrate. Here we present evidence that the
S. aureus
α-phosphoglucomutase (PgcA) and UTP:α-glucose 1-phosphate uridyltransferase (GtaB) homologs are required for the synthesis of Glc
2
-DAG. LtaA (
l
ipo
t
eichoic
a
cid protein
A
), a predicted membrane permease whose structural gene is located in an operon with
ypfP
, is not involved in Glc
2
-DAG synthesis but is required for synthesis of glycolipid-anchored LTA. Our data suggest a model in which LtaA facilitates the transport of Glc
2
-DAG from the inner (cytoplasmic) leaflet to the outer leaflet of the plasma membrane, delivering Glc
2
-DAG as a substrate for LTA synthesis, thereby generating glycolipid-anchored LTA. Glycolipid anchoring of LTA appears to play an important role during infection, as
S. aureus
variants lacking
ltaA
display defects in the pathogenesis of animal infections.
S-Layer Anchoring and Localization of an S-Layer-Associated Protease in
Caulobacter crescentus
Authors: Ford Matthew J. , Nomellini John F. , Smit John 
Published: January 2007

ABSTRACT

The S-layer of the gram-negative bacterium
Caulobacter crescentus
is composed of a single protein, RsaA, that is secreted and assembled into a hexagonal crystalline array that covers the organism. Despite the widespread occurrence of comparable bacterial S-layers, little is known about S-layer attachment to cell surfaces, especially for gram-negative organisms. Having preliminary indications that the N terminus of RsaA anchors the monomer to the cell surface, we developed an assay to distinguish direct surface attachment from subunit-subunit interactions where small RsaA fragments are incubated with S-layer-negative cells to assess the ability of the fragments to reattach. In doing so, we found that the RsaA anchoring region lies in the first ∼225 amino acids and that this RsaA anchoring region requires a smooth lipopolysaccharide species found in the outer membrane. By making mutations at six semirandom sites, we learned that relatively minor perturbations within the first ∼225 amino acids of RsaA caused loss of anchoring. In other studies, we confirmed that only this N-terminal region has a direct role in S-layer anchoring. As a by-product of the anchoring studies, we discovered that Sap, the
C. crescentus
S-layer-associated protease, recognized a cleavage site in the truncated RsaA fragments that is not detected by Sap in full-length RsaA. This, in turn, led to the discovery that Sap was an extracellular membrane-bound protease, rather than intracellular, as previously proposed. Moreover, Sap was secreted to the cell surface primarily by the S-layer type I secretion apparatus.
The
cymA
Gene, Encoding a Tetraheme
c
-Type Cytochrome, Is Required for Arsenate Respiration in
Shewanella
Species
Authors: Murphy Julie N. , Saltikov Chad W. 
Published: January 2007

ABSTRACT

In
Shewanella
sp. strain ANA-3, utilization of arsenate as a terminal electron acceptor is conferred by a two-gene operon,
arrAB
, which lacks a gene encoding a membrane-anchoring subunit for the soluble ArrAB protein complex. Analysis of the genome sequence of
Shewanella putrefaciens
strain CN-32 showed that it also contained the same
arrAB
operon with 100% nucleotide identity. Here, we report that CN-32 respires arsenate and that this metabolism is dependent on
arrA
and an additional gene encoding a membrane-associated tetraheme
c
-type cytochrome,
cymA
. Deletion of
cymA
in ANA-3 also eliminated growth on and reduction of arsenate. The Δ
cymA
strains of CN-32 and ANA-3 negatively affected the reduction of Fe(III) and Mn(IV) but not growth on nitrate. Unlike the CN-32 Δ
cymA
strain, growth on fumarate was absent in the Δ
cymA
strain of ANA-3. Both homologous and heterologous complementation of
cymA
in
trans
restored growth on arsenate in Δ
cymA
strains of both CN-32 and ANA-3. Transcription patterns of
cymA
showed that it was induced under anaerobic conditions in the presence of fumarate and arsenate. Nitrate-grown cells exhibited the greatest level of
cymA
expression in both wild-type strains. Lastly, site-directed mutagenesis of the first Cys to Ser in each of the four CXXCH
c
-heme binding motifs of the CN-32 CymA nearly eliminated growth on and reduction of arsenate. Together, these results indicate that the biochemical mechanism of arsenate respiration and reduction requires the interactions of ArrAB with a membrane-associated tetraheme cytochrome, which in the non-arsenate-respiring
Shewanella
species
Shewanella oneidensis
strain MR-1, has pleiotropic effects on Fe(III), Mn(IV), dimethyl sulfoxide, nitrate, nitrite, and fumarate respiration.