bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Virulence Genes Associated with Pathogenic Escherichia coli Strains Isolated from Domestically Harvested Rainwater during Low- and High-Rainfall Periods
Authors: Dobrowsky P. H. , van Deventer A. , De Kwaadsteniet M. , Ndlovu T. , Khan S. , Cloete T. E. , Khan W. 
Published: December 2013

ABSTRACT

The possible health risks associated with the consumption of harvested rainwater remains one of the major obstacles hampering its large-scale implementation in water limited countries such as South Africa. Rainwater tank samples collected on eight occasions during the low- and high-rainfall periods (March to August 2012) in Kleinmond, South Africa, were monitored for the presence of virulence genes associated with
Escherichia coli
. The identity of presumptive
E. coli
isolates in rainwater samples collected from 10 domestic rainwater harvesting (DRWH) tanks throughout the sampling period was confirmed through universal 16S rRNA PCR with subsequent sequencing and phylogenetic analysis. Species-specific primers were also used to routinely screen for the virulent genes,
aggR
,
stx
,
eae
, and
ipaH
found in enteroaggregative
E. coli
(EAEC), enterohemorrhagic
E. coli
(EHEC), enteropathogenic
E. coli
(EPEC), and enteroinvasive
E. coli
, respectively, in the rainwater samples. Of the 92
E. coli
strains isolated from the rainwater using culture based techniques, 6% were presumptively positively identified as
E. coli
O157:H7 using 16S rRNA. Furthermore, virulent pathogenic
E. coli
genes were detected in 3% (EPEC and EHEC) and 16% (EAEC) of the 80 rainwater samples collected during the sampling period from the 10 DRWH tanks. This study thus contributes valuable information to the limited data available regarding the ongoing prevalence of virulent pathotypes of
E. coli
in harvested rainwater during a longitudinal study in a high-population-density, periurban setting.
Culture Volume and Vessel Affect Long-Term Survival, Mutation Frequency, and Oxidative Stress of Escherichia coli
Authors: Kram Karin E. , Finkel Steven E. 
Published: December 2013

ABSTRACT

Bacteria such as
Escherichia coli
are frequently studied during exponential- and stationary-phase growth. However, many strains can survive in long-term stationary phase (LTSP), without the addition of nutrients, from days to several years. During LTSP, cells experience a variety of stressors, including reactive oxidative species, nutrient depletion, and metabolic toxin buildup, that lead to physiological responses and changes in genetic stability. In this study, we monitored survival during LTSP, as well as reporters of genetic and physiological change, to determine how the physical environment affects
E. coli
during long-term batch culture. We demonstrate differences in yield during LTSP in cells incubated in LB medium in test tubes versus Erlenmeyer flasks, as well as growth in different volumes of medium. We determined that these differences are only partially due to differences in oxygen levels by incubating the cells in different volumes of media under anaerobic conditions. Since we hypothesized that differences in long-term survival are the result of changes in physiological outputs during the late log and early stationary phases, we monitored alkalization, mutation frequency, oxidative stress response, and glycation. Although initial cell yields are essentially equivalent under each condition tested, physiological responses vary greatly in response to culture environment. Incubation in lower-volume cultures leads to higher
oxyR
expression but lower mutation frequency and glycation levels, whereas incubation in high-volume cultures has the opposite effect. We show here that even under commonly used experimental conditions that are frequently treated as equivalent, the stresses experienced by cells can differ greatly, suggesting that culture vessel and incubation conditions should be carefully considered in the planning or analysis of experiments.
Production of Lycopene in the Non-Carotenoid-Producing Yeast Yarrowia lipolytica
Authors: Matthäus Falk , Ketelhot Markus , Gatter Michael , Barth Gerold 
Published: December 2013

ABSTRACT

The codon-optimized genes
crtB
and
crtI
of
Pantoea ananatis
were expressed in
Yarrowia lipolytica
under the control of the
TEF1
promoter of
Y. lipolytica
. Additionally, the rate-limiting genes for isoprenoid biosynthesis in
Y. lipolytica
,
GGS1
and
HMG1
, were overexpressed to increase the production of lycopene. All of the genes were also expressed in a
Y. lipolytica
strain with
POX1
to
POX6
and
GUT2
deleted, which led to an increase in the size of lipid bodies and a further increase in lycopene production. Lycopene is located mainly within lipid bodies, and increased lipid body formation leads to an increase in the lycopene storage capacity of
Y. lipolytica
. Growth-limiting conditions increase the specific lycopene content. Finally, a yield of 16 mg g
−1
(dry cell weight) was reached in fed-batch cultures, which is the highest value reported so far for a eukaryotic host.
The Sialidases of Clostridium perfringens Type D Strain CN3718 Differ in Their Properties and Sensitivities to Inhibitors
Authors: Li Jihong , McClane Bruce A. 
Published: December 2013

ABSTRACT

Clostridium perfringens
causes histotoxic infections and diseases originating in animal or human intestines. A prolific toxin producer, this bacterium also produces numerous enzymes, including sialidases, that may facilitate infection.
C. perfringens
type D strain CN3718 carries genes encoding three sialidases, including two large secreted sialidases (named NanI and NanJ) and one small sialidase (named NanH) that has an intracellular location in log-phase cultures but is present in supernatants of death phase cultures. Using isogenic mutants of CN3718 that are capable of expressing only NanJ, NanI, or NanH, the current study characterized the properties and activities of each sialidase. The optimal temperature determined for NanJ or NanH enzymatic activity was 37°C or 43°C, respectively, while NanI activity increased until temperature reached 48°C. NanI activity was also the most resistant against higher temperatures. All three sialidases showed optimal activities at pH 5.5. Compared to NanJ or NanH, NanI contributed most to the sialidase activity in CN3718 culture supernatants, regardless of the substrate sialic acid linkage; NanI also released the most sialic acid from Caco-2 cells. Only NanI activity was enhanced by trypsin pretreatment and then only for substrates with an α-2,3- or α-2,6-sialic acid linkage. NanJ and NanI activities were more sensitive than NanH activity to two sialidase inhibitors (N-acetyl-2,3-dehydro-2-deoxyneuraminic acid and siastatin B). The activities of the three sialidases were affected differently by several metal ions. These results indicated that each
C. perfringens
sialidase has distinct properties, which may allow these enzymes to play different roles depending upon environmental conditions.
Infection Dynamics of the Tick-Borne Pathogen “Candidatus Neoehrlichia mikurensis” and Coinfections with Borrelia afzelii in Bank Voles in Southern Sweden
Authors: Andersson Martin , Scherman Kristin , Råberg Lars 
Published: December 2013

ABSTRACT

The tick-borne bacterium “
Candidatus
Neoehrlichia mikurensis” has recently been recognized as a human pathogen. Together with
Borrelia afzelii
, it is one of the most common pathogens found in the tick
Ixodes ricinus
. Here, we compared the epidemiologies of “
Ca
. Neoehrlichia mikurensis” and
B. afzelii
by longitudinal sampling from May to September in one of their most abundant vertebrate hosts, the bank vole (
Myodes glareolus
), using real-time PCR for detection and quantification. The prevalences of “
Ca
. Neoehrlichia mikurensis” and
B. afzelii
were determined to be 19% (50/261) and 22% (56/261), respectively. The prevalence of “
Ca
. Neoehrlichia mikurensis” increased significantly during the sampling season. The clearance rate of “
Ca
. Neoehrlichia mikurensis” was significantly higher than that of
B. afzelii
. We found a high frequency of double infections; 46% of all samples infected with “
Ca
. Neoehrlichia mikurensis” also had a coinfection with
B. afzelii
. The frequency of coinfections was significantly higher than expected from the prevalence of each pathogen. The high level of coinfections can be caused by interactions between the pathogens or might reflect variation in general susceptibility among voles.
Nanoscale Structural and Mechanical Analysis of Bacillus anthracis Spores Inactivated with Rapid Dry Heating
Authors: Xing Yun , Li Alex , Felker Daniel L. , Burggraf Larry W. 
Published: December 2013

ABSTRACT

Effective killing of
Bacillus anthracis
spores is of paramount importance to antibioterrorism, food safety, environmental protection, and the medical device industry. Thus, a deeper understanding of the mechanisms of spore resistance and inactivation is highly desired for developing new strategies or improving the known methods for spore destruction. Previous studies have shown that spore inactivation mechanisms differ considerably depending upon the killing agents, such as heat (wet heat, dry heat), UV, ionizing radiation, and chemicals. It is believed that wet heat kills spores by inactivating critical enzymes, while dry heat kills spores by damaging their DNA. Many studies have focused on the biochemical aspects of spore inactivation by dry heat; few have investigated structural damages and changes in spore mechanical properties. In this study, we have inactivated
Bacillus anthracis
spores with rapid dry heating and performed nanoscale topographical and mechanical analysis of inactivated spores using atomic force microscopy (AFM). Our results revealed significant changes in spore morphology and nanomechanical properties after heat inactivation. In addition, we also found that these changes were different under different heating conditions that produced similar inactivation probabilities (high temperature for short exposure time versus low temperature for long exposure time). We attributed the differences to the differential thermal and mechanical stresses in the spore. The buildup of internal thermal and mechanical stresses may become prominent only in ultrafast, high-temperature heat inactivation when the experimental timescale is too short for heat-generated vapor to efficiently escape from the spore. Our results thus provide direct, visual evidences of the importance of thermal stresses and heat and mass transfer to spore inactivation by very rapid dry heating.
Zebrafish as a Natural Host Model for Vibrio cholerae Colonization and Transmission
Authors: Runft Donna L. , Mitchell Kristie C. , Abuaita Basel H. , Allen Jonathan P. , Bajer Sarah , Ginsburg Kevin , Neely Melody N. , Withey Jeffrey H. 
Published: December 2013

ABSTRACT

The human diarrheal disease cholera is caused by the aquatic bacterium
Vibrio cholerae
.
V. cholerae
in the environment is associated with several varieties of aquatic life, including insect egg masses, shellfish, and vertebrate fish. Here we describe a novel animal model for
V. cholerae
, the zebrafish. Pandemic
V. cholerae
strains specifically colonize the zebrafish intestinal tract after exposure in water with no manipulation of the animal required. Colonization occurs in close contact with the intestinal epithelium and mimics colonization observed in mammals. Zebrafish that are colonized by
V. cholerae
transmit the bacteria to naive fish, which then become colonized. Striking differences in colonization between
V. cholerae
classical and El Tor biotypes were apparent. The zebrafish natural habitat in Asia heavily overlaps areas where cholera is endemic, suggesting that zebrafish and
V. cholerae
evolved in close contact with each other. Thus, the zebrafish provides a natural host model for the study of
V. cholerae
colonization, transmission, and environmental survival.
NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum
Authors: Si Mei-Ru , Zhang Lei , Yang Zhi-Fang , Xu Yi-Xiang , Liu Ying-Bao , Jiang Cheng-Ying , Wang Yao , Shen Xi-Hui , Liu Shuang-Jiang 
Published: December 2013

ABSTRACT

NrdH redoxins are small protein disulfide oxidoreductases behaving like thioredoxins but sharing a high amino acid sequence similarity to glutaredoxins. Although NrdH redoxins are supposed to be another candidate in the antioxidant system, their physiological roles in oxidative stress remain unclear. In this study, we confirmed that the
Corynebacterium glutamicum
NrdH redoxin catalytically reduces the disulfides in the class Ib ribonucleotide reductases (RNR), insulin and 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB), by exclusively receiving electrons from thioredoxin reductase. Overexpression of NrdH increased the resistance of
C. glutamicum
to multiple oxidative stresses by reducing ROS accumulation. Accordingly, elevated expression of the
nrdH
gene was observed when the
C. glutamicum
wild-type strain was exposed to oxidative stress conditions. It was discovered that the NrdH-mediated resistance to oxidative stresses was largely dependent on the presence of the thiol peroxidase Prx, as the increased resistance to oxidative stresses mediated by overexpression of NrdH was largely abrogated in the
prx
mutant. Furthermore, we showed that NrdH facilitated the hydroperoxide	reduction activity of Prx by directly targeting and serving as its electron donor. Thus, we present evidence that the NrdH redoxin can protect against the damaging effects of reactive oxygen species (ROS) induced by various exogenous oxidative stresses by acting as a peroxidase cofactor.
Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics
Authors: Luo Chengwei , Rodriguez-R Luis M. , Johnston Eric R. , Wu Liyou , Cheng Lei , Xue Kai , Tu Qichao , Deng Ye , He Zhili , Shi Jason Zhou , Yuan Mengting Maggie , Sherry Rebecca A. , Li Dejun , Luo Yiqi , Schuur Edward A. G. , Chain Patrick , Tiedje James M. , Zhou Jizhong , Konstantinidis Konstantinos T. 
Published: December 2013

ABSTRACT

Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO
2
production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.
Evaluation of Non-Saccharomyces Yeasts for the Reduction of Alcohol Content in Wine
Authors: Contreras A. , Hidalgo C. , Henschke P. A. , Chambers P. J. , Curtin C. , Varela C. 
Published: December 2013

ABSTRACT

Over recent decades, the average ethanol concentration of wine has increased, largely due to consumer preference for wine styles associated with increased grape maturity; sugar content increases with grape maturity, and this translates into increased alcohol content in wine. However, high ethanol content impacts wine sensory properties, reducing the perceived complexity of flavors and aromas. In addition, for health and economic reasons, the wine sector is actively seeking technologies to facilitate the production of wines with lower ethanol content. Nonconventional yeast species, in particular, non-
Saccharomyces
yeasts, have shown potential for producing wines with lower alcohol content. These yeast species, which are largely associated with grapes preharvest, are present in the early stages of fermentation but, in general, are not capable of completing alcoholic fermentation. We have evaluated 50 different non-
Saccharomyces
isolates belonging to 24 different genera for their capacity to produce wine with a lower ethanol concentration when used in sequential inoculation regimes with a
Saccharomyces cerevisiae
wine strain. A sequential inoculation of
Metschnikowia pulcherrima
AWRI1149 followed by an
S. cerevisiae
wine strain was best able to produce wine with an ethanol concentration lower than that achieved with the single-inoculum, wine yeast control. Sequential fermentations utilizing AWRI1149 produced wines with 0.9% (vol/vol) and 1.6% (vol/vol) (corresponding to 7.1 g/liter and 12.6 g/liter, respectively) lower ethanol concentrations in Chardonnay and Shiraz wines, respectively. In Chardonnay wine, the total concentration of esters and higher alcohols was higher for wines generated from sequential inoculations, whereas the total concentration of volatile acids was significantly lower. In sequentially inoculated Shiraz wines, the total concentration of higher alcohols was higher and the total concentration of volatile acids was reduced compared with those in control
S. cerevisiae
wines, whereas the total concentrations of esters were not significantly different.
The Ancient Small GTPase Rab21 Functions in Intermediate Endocytic Steps in Trypanosomes
Authors: Ali Moazzam , Leung Ka Fai , Field Mark C. 
Published: December 2013

ABSTRACT

Endocytosis is an essential process in nearly all eukaryotic cells, including the African trypanosome
Trypanosoma brucei
. Endocytosis in these organisms is exclusively clathrin mediated, although several lineage-specific features indicate that precise mechanisms are distinct from those of higher eukaryotes.
T. brucei
Rab21 is a member of an ancient, pan-eukaryotic, endocytic Rab clade that is retained by trypanosomes. We show that
T. brucei
Rab21 (TbRab21) localizes to endosomes, partially colocalizing with TbRab5A, TbRab28, and TbVps23, the latter two being present at late endosomes. TbRab21 expression is essential for cellular proliferation, and its suppression results in a partial block in traffic to the lysosome. RNA interference (RNAi)-mediated knockdown of TbRab21 had no effect on TbRab5A expression or location but did result in decreased in
trans
expression of ESCRT (trypanosome endosomal sorting complex required for transport) components and TbRab28, while knockdown of ESCRT subunit TbVps23 resulted in decreased TbRab21 expression. These data suggest that TbRab21 acts downstream of TbRab5A and functions in intimate connection with the trypanosome ESCRT system.
Candida albicans Triggers NLRP3-Mediated Pyroptosis in Macrophages
Authors: Wellington Melanie , Koselny Kristy , Sutterwala Fayyaz S. , Krysan Damian J. 
Published: December 2013

ABSTRACTPyroptosis is an inflammasome-mediated programmed cell death pathway triggered in macrophages by a variety of stimuli, including intracellular bacterial pathogens. Activation of pyroptosis leads to the secretion of interleukin-1β (IL-1β) and pore-mediated cell lysis. Although not considered an intracellular pathogen,Candida albicansis able to kill and, thereby, escape from macrophages. Here, we show thatC. albicans-infected bone marrow-derived macrophages (BMDM) and murine J774 macrophages undergo pyroptotic cell death that is suppressed by glycine and pharmacologic inhibition of caspase-1. Infection of BMDM harvested from mice lacking components of the inflammasome revealed that pyroptosis was dependent on caspase-1, ASC, and NLRP3 and independent of NLRC4. In contrast to its role during intracellular bacterial infection, pyroptosis does not restrictC. albicansreplication. NonfilamentousCandidaspp. did not trigger pyroptosis, whileCandida krusei, which forms pseudohyphae in macrophages, triggered much lower levels than didC. albicans. Interestingly, aSaccharomyces cerevisiaestrain from the filamentous background Σ1278 also triggered low, but significant, levels of pyroptosis. We have found that deletion of the transcription factorUPC2decreases pyroptosis but has little effect on filamentation in the macrophage. In addition, a gain-of-function mutant ofUPC2induces higher levels of pyroptosis than does a matched control strain. Taken together, these data are most consistent with a model in which filamentation is necessary but not sufficient to trigger NLRP3 inflammasome-mediated pyroptosis. This is the first example of a fungal pathogen triggering pyroptosis and indicates thatC. albicans-mediated macrophage damage is not solely due to hypha-induced physical disruption of cellular integrity.
Physiological Framework for the Regulation of Quorum Sensing-Dependent Public Goods in Pseudomonas aeruginosa
Authors: Mellbye Brett , Schuster Martin 
Published: December 2013

ABSTRACT

Many bacteria possess cell density-dependent quorum-sensing (QS) systems that often regulate cooperative secretions involved in host-microbe or microbe-microbe interactions. These secretions, or “public goods,” are frequently coregulated by stress and starvation responses. Here we provide a physiological rationale for such regulatory complexity in the opportunistic pathogen
Pseudomonas aeruginosa
. Using minimal-medium batch and chemostat cultures, we comprehensively characterized specific growth rate-limiting macronutrients as key triggers for the expression of extracellular enzymes and metabolites directly controlled by the
las
and
rhl
QS systems. Expression was unrelated to cell density, depended on the secreted product's elemental composition, and was induced only when the limiting nutrient was not also a building block of the product;
rhl
-dependent products showed the strongest response, caused by the largely
las
-independent induction of the regulator RhlR and its cognate signal. In agreement with the prominent role of the
rhl
system, slow growth inverted the
las
-to-
rhl
signal ratio, previously considered a characteristic distinguishing between planktonic and biofilm lifestyles. Our results highlight a supply-driven, metabolically prudent regulation of public goods that minimizes production costs and thereby helps stabilize cooperative behavior. Such regulation would be beneficial for QS-dependent public goods that act broadly and nonspecifically, and whose need cannot always be accurately assessed by the producing cell. Clear differences in the capacities of the
las
and
rhl
systems to integrate starvation signals help explain the existence of multiple QS systems in one cell.