bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence of an Environmental Acinetobacter baumannii Strain Similar to a Clinical Isolate in Paleosol from Croatia
Authors: Hrenovic Jasna , Durn Goran , Goic-Barisic Ivana , Kovacic Ana 
Published: March 2014

ABSTRACT

Over the past decade, bacteria of the genus
Acinetobacter
have emerged as a leading cause of hospital-acquired infections. Outbreaks of
Acinetobacter
infections are considered to be caused exclusively by contamination and transmission in hospital environments. The natural habitats of clinically important multiresistant
Acinetobacter
spp. remain to be defined. In this paper, we report an incidental finding of a viable multidrug-resistant strain of
Acinetobacter baumannii
, related to clinical isolates, in acid paleosol from Croatia. The environmental isolate of
A. baumannii
showed 87% similarity to a clinical isolate originating from a hospital in this geographic area and was resistant to gentamicin, trimethoprim-sulfamethoxazole, ciprofloxacin, and levofloxacin. In paleosol, the isolate was able to survive a low pH (3.37), desiccation, and a high temperature (50°C). The probable source of
A. baumannii
in paleosol is illegally disposed waste of external origin situated in the abandoned quarry near the sampling site. The bacteria could have been leached from waste by storm water and thus infiltrated the paleosol.
Establishment of Intestinal Microbiota during Early Life: a Longitudinal, Explorative Study of a Large Cohort of Danish Infants
Authors: Bergström Anders , Skov Thomas Hjort , Bahl Martin Iain , Roager Henrik Munch , Christensen Line Brinch , Ejlerskov Katrine Tschentscher , Mølgaard Christian , Michaelsen Kim F. , Licht Tine Rask 
Published: March 2014

ABSTRACTFecal samples were obtained from a cohort of 330 healthy Danish infants at 9, 18, and 36 months after birth, enabling characterization of interbacterial relationships by use of quantitative PCR targeting 31 selected bacterial 16S rRNA gene targets representing different phylogenetic levels. Nutritional parameters and measures of growth and body composition were determined and investigated in relation to the observed development in microbiota composition. We found that significant changes in the gut microbiota occurred, particularly from age 9 to 18 months, when cessation of breastfeeding and introduction of a complementary feeding induce replacement of a microbiota characterized by lactobacilli, bifidobacteria, andEnterobacteriaceaewith a microbiota dominated byClostridiumspp. andBacteroidesspp. Classification of samples by a proxy enterotype based on the relative levels ofBacteroidesspp. andPrevotellaspp. showed that enterotype establishment occurs between 9 and 36 months. Thirty percent of the individuals shifted enterotype between 18 and 36 months. The composition of the microbiota was most pronouncedly influenced by the time of cessation of breastfeeding. From 9 to 18 months, a positive correlation was observed between the increase in body mass index and the increase of the short-chain-fatty-acid-producing clostridia, theClostridum leptumgroup, andEubacterium hallii. Considering previously established positive associations between rapid infant weight gain, early breastfeeding discontinuation, and later-life obesity, the corresponding microbial findings seen here warrant attention.
Metabolic Changes in Klebsiella oxytoca in Response to Low Oxidoreduction Potential, as Revealed by Comparative Proteomic Profiling Integrated with Flux Balance Analysis
Authors: Zhu Yan , Li Dan , Bao Guanhui , Wang Shaohua , Mao Shaoming , Song Jiangning , Li Yin , Zhang Yanping 
Published: March 2014

ABSTRACT

Oxidoreduction potential (ORP) is an important physiological parameter for biochemical production in anaerobic or microaerobic processes. However, the effect of ORP on cellular physiology remains largely unknown, which hampers the design of engineering strategies targeting proteins associated with ORP response. Here we characterized the effect of altering ORP in a 1,3-propanediol producer,
Klebsiella oxytoca
, by comparative proteomic profiling combined with flux balance analysis. Decreasing the extracellular ORP from −150 to −240 mV retarded cell growth and enhanced 1,3-propanediol production. Comparative proteomic analysis identified 61 differentially expressed proteins, mainly involved in carbohydrate catabolism, cellular constituent biosynthesis, and reductive stress response. A hypothetical oxidoreductase (HOR) that catalyzes 1,3-propanediol production was markedly upregulated, while proteins involved in biomass precursor synthesis were downregulated. As revealed by subsequent flux balance analysis, low ORP induced a metabolic shift from glycerol oxidation to reduction and rebalancing of redox and energy metabolism. From the integrated protein expression profiles and flux distributions, we can construct a rational analytic framework that elucidates how (facultative) anaerobes respond to extracellular ORP changes.
Effects of Leachate from Crumb Rubber and Zinc in Green Roofs on the Survival, Growth, and Resistance Characteristics of Salmonella enterica subsp. enterica Serovar Typhimurium
Authors: Crampton Mollee , Ryan Allayna , Eckert Cori , Baker Katherine H. , Herson Diane S. 
Published: March 2014

ABSTRACT

The use of green roofs is a growing practice worldwide, particularly in densely populated areas. In an attempt to find new methods for recycling crumb rubber, incorporation of crumb rubber into artificial medium for plant growth in green roofs and similar engineered environments has become an attractive option for the recycling of waste tires. Though this approach decreases waste in landfills, there are concerns about the leaching of zinc and other heavy metals, as well as nutrient and organic compounds, into the environment. The present study analyzed the impact of leachate from crumb rubber and zinc on the growth and viability of
Salmonella enterica
subsp.
enterica
serovar Typhimurium. Zinc was chosen for further studies since it has been previously implicated with other biological functions, including biofilm formation, motility, and possible cross-resistance to antimicrobial agents. The study showed that
Salmonella
can colonize crumb rubber and that crumb rubber extract may provide nutrients that are usable by this bacterium.
Salmonella
strains with reduced susceptibility (SRS) to zinc were obtained after subculturing in increasing concentrations of zinc. The SRS exhibited differences in gene expression of flux pump genes
zntA
and
znuA
compared to that of the parent when exposed to 20 mM added zinc. In biofilm formation studies, the SRS formed less biofilm but was more motile than the parental strain.
Abiotic Factors Affecting the Persistence of Avian Influenza Virus in Surface Waters of Waterfowl Habitats
Authors: Keeler Shamus P. , Dalton Melinda S. , Cressler Alan M. , Berghaus Roy D. , Stallknecht David E. 
Published: March 2014

ABSTRACT
Avian influenza (AI) virus can remain infectious in water for months, and virus-contaminated surface water is considered to be a source of infection within wild waterfowl populations. Previous work has characterized the effects of pH, salinity, and temperature on viral persistence in water, but most of that work was done with modified distilled water. The objective of this study was to identify the abiotic factors that influence the duration of AI virus persistence in natural surface water. Surface water samples were collected from 38 waterfowl habitats distributed across the United States. Samples were submitted to the U.S. Geological Survey National Water Quality Laboratory for chemical analysis and the University of Georgia for viral reduction time analysis. Samples were filtered with 0.22-μm filters, and the durations of persistence of three wild-bird-derived influenza A viruses within each water sample at 10, 17, and 28°C were determined. The effects of the surface water physicochemical factors on the duration of AI viral persistence in laboratory experiments were evaluated by multivariable linear regression with robust standard errors. The duration of AI virus persistence was determined to be longest in filtered surface water with a low temperature (<17°C), a neutral-to-basic pH (7.0 to 8.5), low salinity (<0.5 ppt), and a low ammonia concentration (<0.5 mg/liter). Our results also highlighted potential strain-related variation in the stability of AI virus in surface water. These results bring us closer to being able to predict the duration of AI virus persistence in surface water of waterfowl habitats.
Adaptation of Escherichia coli to Elevated Sodium Concentrations Increases Cation Tolerance and Enables Greater Lactic Acid Production
Authors: Wu Xianghao , Altman Ronni , Eiteman Mark A. , Altman Elliot 
Published: March 2014

ABSTRACTAdaptive evolution was employed to generate sodium (Na+)-tolerant mutants ofEscherichia coliMG1655. Four mutants with elevated sodium tolerance, designated ALS1184, ALS1185, ALS1186, and ALS1187, were independently isolated after 73 days of serial transfer in medium containing progressively greater Na+concentrations. The isolates also showed increased tolerance of K+, although this cation was not used for selective pressure. None of the adapted mutants showed increased tolerance to the nonionic osmolyte sucrose. Several physiological parameters ofE. coliMG1655 and ALS1187, the isolate with the greatest Na+tolerance, were calculated and compared using glucose-limited chemostats. Genome sequencing showed that the ALS1187 isolate contained mutations in five genes,emrR,hfq,kil,rpsG, andsspA, all of which could potentially affect the ability ofE. colito tolerate Na+. Two of these genes,hfqandsspA, are known to be involved in global regulatory processes that help cells endure a variety of cellular stresses. Pyruvate formate lyase knockouts were constructed in strains MG1655 and ALS1187 to determine whether increased Na+tolerance afforded increased anaerobic generation of lactate. In fed-batch fermentations,E. coliALS1187pflBgenerated 76.2 g/liter lactate compared to MG1655pflB, which generated only 56.3 g/liter lactate.
Microaerobic Conversion of Glycerol to Ethanol in Escherichia coli
Authors: Wong Matthew S. , Li Mai , Black Ryan W. , Le Thao Q. , Puthli Sharon , Campbell Paul , Monticello Daniel J. 
Published: March 2014

ABSTRACT

Glycerol has become a desirable feedstock for the production of fuels and chemicals due to its availability and low price, but many barriers to commercialization remain. Previous investigators have made significant improvements in the yield of ethanol from glycerol. We have developed a fermentation process for the efficient microaerobic conversion of glycerol to ethanol by
Escherichia coli
that presents solutions to several other barriers to commercialization: rate, titer, specific productivity, use of inducers, use of antibiotics, and safety. To increase the rate, titer, and specific productivity to commercially relevant levels, we constructed a plasmid that overexpressed glycerol uptake genes
dhaKLM
,
gldA
, and
glpK
, as well as the ethanol pathway gene
adhE
. To eliminate the cost of inducers and antibiotics from the fermentation, we used the
adhE
and
icd
promoters from
E. coli
in our plasmid, and we implemented glycerol addiction to retain the plasmid. To address the safety issue of off-gas flammability, we optimized the fermentation process with reduced-oxygen sparge gas to ensure that the off-gas remained nonflammable. These advances represent significant progress toward the commercialization of an
E. coli
-based glycerol-to-ethanol process.
Genetic Diversity Analysis Reveals that Geographical Environment Plays a More Important Role than Rice Cultivar in Villosiclava virens Population Selection
Authors: Wang Fei , Zhang Shu , Liu Mei-Gang , Lin Xian-Song , Liu Hui-Jiang , Peng You-Liang , Lin Yang , Huang Jun-Bin , Luo Chao-Xi 
Published: March 2014

ABSTRACT

Rice false smut caused by
Villosiclava virens
is an economically important disease of grains worldwide. The genetic diversity of 153 isolates from six fields located in Wuhan (WH), Yichang Wangjia (YCW), Yichang Yaohe (YCY), Huanggang (HG), Yangxin (YX), and Jingzhou (JZ) in Hubei province of China were phylogenetically analyzed to evaluate the influence of environments and rice cultivars on the
V. virens
populations. Isolates (43) from Wuhan were from two rice cultivars, Wanxian 98 and Huajing 952, while most of the other isolates from fields YCW, YCY, HG, YX, and JZ originated from different rice cultivars with different genetic backgrounds. Genetic diversity of isolates was analyzed using random amplified polymorphic DNA (RAPD) and single-nucleotide polymorphisms (SNP). The isolates from the same cultivars in Wuhan tended to group together, indicating that the cultivars had an important impact on the fungal population. The 110 isolates from individual fields tended to cluster according to geographical origin. The values of Nei's gene diversity (
H
) and Shannon's information index (
I
) showed that the genetic diversity among isolates was higher between than within geographical populations. Furthermore, mean genetic distance between groups (0.006) was higher than mean genetic distance within groups (0.0048) according to MEGA 5.2. The pairwise population fixation index (
F
ST
) values also showed significant genetic differentiation between most populations. Higher genetic similarity of isolates from individual fields but different rice cultivars suggested that the geographical factor played a more important role in the selection of
V. virens
isolates than rice cultivars. This information could be used to improve the management strategy for rice false smut by adjusting the cultivation measures, such as controlling fertilizer, water, and planting density, in the rice field to change the microenvironment.
Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase
Authors: Inoue Kengo , Usami Yusuke , Ashikawa Yuji , Noguchi Haruko , Umeda Takashi , Yamagami-Ashikawa Aiko , Horisaki Tadafumi , Uchimura Hiromasa , Terada Tohru , Nakamura Shugo , Shimizu Kentaro , Habe Hiroshi , Yamane Hisakazu , Fujimoto Zui , Nojiri Hideaki 
Published: March 2014

ABSTRACT

Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy-encoding gene from
Janthinobacterium
sp. strain J3 generated the I262V, F275W, Q282N, and Q282Y Oxy derivatives, which showed oxygenation capabilities different from those of the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. The I262V, F275W, and Q282Y derivatives catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15, 25, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and the imino nitrogen of carbazole. In the crystal structure of the F275W derivative complexed with fluorene, C-9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate-binding position that, in turn, favors specific oxygenation reactions toward various substrates.
Top-Down Proteomic Identification of Shiga Toxin 2 Subtypes from Shiga Toxin-Producing Escherichia coli by Matrix-Assisted Laser Desorption Ionization–Tandem Time of Flight Mass Spectrometry
Authors: Fagerquist Clifton K. , Zaragoza William J. , Sultan Omar , Woo Nathan , Quiñones Beatriz , Cooley Michael B. , Mandrell Robert E. 
Published: March 2014

ABSTRACT

We have analyzed 26 Shiga toxin-producing
Escherichia coli
(STEC) strains for Shiga toxin 2 (Stx2) production using matrix-assisted laser desorption ionization (MALDI)–tandem time of flight (TOF-TOF) tandem mass spectrometry (MS/MS) and top-down proteomic analysis. STEC strains were induced to overexpress Stx2 by overnight culturing on solid agar supplemented with either ciprofloxacin or mitomycin C. Harvested cells were lysed by bead beating, and unfractionated bacterial cell lysates were ionized by MALDI. The A2 fragment of the A subunit and the mature B subunit of Stx2 were analyzed by MS/MS. Sequence-specific fragment ions were used to identify amino acid subtypes of Stx2 using top-down proteomic analysis using software developed in-house at the U.S. Department of Agriculture (USDA). Stx2 subtypes (a, c, d, f, and g) were identified on the basis of the mass of the A2 fragment and the B subunit as well as from their sequence-specific fragment ions by MS/MS (postsource decay). Top-down proteomic identification was in agreement with DNA sequencing of the full Stx2 operon (
stx
2
) for all strains. Top-down results were also compared to a bioassay using a Vero-d2EGFP cell line. Our results suggest that top-down proteomic identification is a rapid, highly specific technique for distinguishing Stx2 subtypes.
Adaptation of the Wine Bacterium Oenococcus oeni to Ethanol Stress: Role of the Small Heat Shock Protein Lo18 in Membrane Integrity
Authors: Maitre Magali , Weidmann Stéphanie , Dubois-Brissonnet Florence , David Vanessa , Covès Jacques , Guzzo Jean 
Published: March 2014

ABSTRACT

Malolactic fermentation in wine is often carried out by
Oenococcus oeni
. Wine is a stressful environment for bacteria because ethanol is a toxic compound that impairs the integrity of bacterial membranes. The small heat shock protein (sHsp) Lo18 is an essential actor of the stress response in
O. oeni
. Lo18 prevents the thermal aggregation of proteins and plays a crucial role in membrane quality control. Here, we investigated the interaction between Lo18 and four types of liposomes: one was prepared from
O. oeni
grown under optimal growth conditions (here, control liposomes), one was prepared from
O. oeni
grown in the presence of 8% ethanol (here, ethanol liposomes), one was prepared from synthetic phospholipids, and one was prepared from phospholipids from
Bacillus subtilis
or
Lactococcus lactis
. We observed the strongest interaction between Lo18 and control liposomes. The lipid binding activity of Lo18 required the dissociation of oligomeric structures into dimers. Protein protection experiments carried out in the presence of the liposomes from
O. oeni
suggested that Lo18 had a higher affinity for control liposomes than for a model protein. In anisotropy experiments, we mimicked ethanol action by temperature-dependent fluidization of the liposomes. Results suggest that the principal determinant of Lo18-membrane interaction is lipid bilayer phase behavior rather than phospholipid composition. We suggest a model to describe the ethanol adaptation of
O. oeni
. This model highlights the dual role of Lo18 in the protection of proteins from aggregation and membrane stabilization and suggests how modifications of phospholipid content may be a key factor determining the balance between these two functions.
Phasin Proteins Activate Aeromonas caviae Polyhydroxyalkanoate (PHA) Synthase but Not Ralstonia eutropha PHA Synthase
Authors: Ushimaru Kazunori , Motoda Yoko , Numata Keiji , Tsuge Takeharu 
Published: March 2014

ABSTRACT

In this study, we performed
in vitro
and
in vivo
activity assays of polyhydroxyalkanoate (PHA) synthases (PhaCs) in the presence of phasin proteins (PhaPs), which revealed that PhaPs are activators of PhaC derived from
Aeromonas caviae
(PhaC
Ac
). In
in vitro
assays, among the three PhaCs tested, PhaC
Ac
was significantly activated when PhaPs were added at the beginning of polymerization (prepolymerization PhaC
Ac
), whereas the prepolymerization PhaC
Re
(derived from
Ralstonia eutropha
) and PhaC
Da
(
Delftia acidovorans
) showed reduced activity with PhaPs. The PhaP-activated PhaC
Ac
showed a slight shift of substrate preference toward 3-hydroxyhexanoyl-CoA (C
6
). PhaP
Ac
also activated PhaC
Ac
when it was added during polymerization (polymer-elongating PhaC
Ac
), while this effect was not observed for PhaC
Re
. In an
in vivo
assay using
Escherichia coli
TOP10 as the host strain, the effect of PhaP
Ac
expression on PHA synthesis by PhaC
Ac
or PhaC
Re
was examined. As PhaP
Ac
expression increased, PHA production was increased by up to 2.3-fold in the PhaC
Ac
-expressing strain, whereas it was slightly increased in the PhaC
Re
-expressing strain. Taken together, this study provides evidence that PhaPs function as activators for PhaC
Ac
both
in vitro
and
in vivo
but do not activate PhaC
Re
. This activating effect may be attributed to the new role of PhaPs in the polymerization reaction by PhaC
Ac
.
Analysis of the Microbial Community Structure by Monitoring an Hg Methylation Gene (
hgcA
) in Paddy Soils along an Hg Gradient
Authors: Liu Yu-Rong , Yu Ri-Qing , Zheng Yuan-Ming , He Ji-Zheng 
Published: March 2014

ABSTRACT

Knowledge of the diversity of mercury (Hg)-methylating microbes in the environment is limited due to a lack of available molecular biomarkers. Here, we developed novel degenerate PCR primers for a key Hg-methylating gene (
hgcA
) and amplified successfully the targeted genes from 48 paddy soil samples along an Hg concentration gradient in the Wanshan Hg mining area of China. A significant positive correlation was observed between
hgcA
gene abundance and methylmercury (MeHg) concentrations, suggesting that microbes containing the genes contribute to Hg methylation in the sampled soils. Canonical correspondence analysis (CCA) showed that the
hgcA
gene diversity in microbial community structures from paddy soils was high and was influenced by the contents of total Hg, SO
4
2−
, NH
4
+
, and organic matter. Phylogenetic analysis showed that
hgcA
microbes in the sampled soils likely were related to
Deltaproteobacteria
,
Firmicutes
,
Chloroflexi
,
Euryarchaeota
, and two unclassified groups. This is a novel report of
hgcA
diversity in paddy habitats, and results here suggest a link between Hg-methylating microbes and MeHg contamination
in situ
, which would be useful for monitoring and mediating MeHg synthesis in soils.