bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inorganic Phosphate and Sodium Ions Are Cogerminants for Spores of
Clostridium perfringens
Type A Food Poisoning-Related Isolates
Authors: Paredes-Sabja Daniel , Udompijitkul Pathima , Sarker Mahfuzur R. 
Published: August 2009

ABSTRACT

Clostridium perfringens
type A isolates carrying a chromosomal copy of the enterotoxin (
cpe
) gene are involved in the majority of food poisoning (FP) outbreaks, while type A isolates carrying a plasmid-borne
cpe
gene are involved in
C. perfringens
-associated non-food-borne (NFB) gastrointestinal diseases. To cause diseases,
C. perfringens
spores must germinate and return to active growth. Previously, we showed that only spores of FP isolates were able to germinate with K
+
ions. We now found that the spores of the majority of FP isolates, but none of the NFB isolates, germinated with the cogerminants Na
+
and inorganic phosphate (NaP
i
) at a pH of ∼6.0. Spores of
gerKA-KC
and
gerAA
mutants germinated to a lesser extent and released less dipicolinic acid (DPA) than did wild-type spores with NaP
i
. Although
gerKB
spores germinated to a similar extent as wild-type spores with NaP
i
, their rate of germination was lower. Similarly,
gerO
and
gerO gerQ
mutant spores germinated slower and released less DPA than did wild-type spores with NaP
i
. In contrast,
gerQ
spores germinated to a slightly lesser extent than wild-type spores but released all of their DPA during NaP
i
germination. In sum, this study identified NaP
i
as a novel nutrient germinant for spores of most FP isolates and provided evidence that proteins encoded by the
gerKA-KC
operon,
gerAA
, and
gerO
are required for NaP
i
-induced spore germination.
Transcriptomic Response of
Escherichia coli
O157:H7 to Oxidative Stress
Authors: Wang Siyun , Deng Kaiping , Zaremba Sam , Deng Xiangyu , Lin Chiahui , Wang Qian , Tortorello Mary Lou , Zhang Wei 
Published: August 2009

ABSTRACT

Chlorinated water is commonly used in industrial operations to wash and sanitize fresh-cut, minimally processed produce. Here we compared 42 human outbreak strains that represented nine distinct
Escherichia coli
O157:H7 genetic lineages (or clades) for their relative resistance to chlorine treatment. A quantitative measurement of resistance was made by comparing the extension of the lag phase during growth of each strain under exposure to sublethal concentrations of sodium hypochlorite in Luria-Bertani or brain heart infusion broth. Strains in clade 8 showed significantly (
P
< 0.05) higher resistance to chlorine than strains from other clades of
E. coli
O157:H7. To further explore how
E. coli
O157:H7 responds to oxidative stress at transcriptional levels, we analyzed the global gene expression profiles of two strains, TW14359 (clade 8; associated with the 2006 spinach outbreak) and Sakai (clade 1; associated with the 1996 radish sprout outbreak), under sodium hypochlorite or hydrogen peroxide treatment. We found over 380 genes were differentially expressed (more than twofold;
P
< 0.05) after exposure to low levels of chlorine or hydrogen peroxide. Significantly upregulated genes included several regulatory genes responsive to oxidative stress, genes encoding putative oxidoreductases, and genes associated with cysteine biosynthesis, iron-sulfur cluster assembly, and antibiotic resistance. Identification of
E. coli
O157:H7 strains with enhanced resistance to chlorine decontamination and analysis of their transcriptomic response to oxidative stress may improve our basic understanding of the survival strategy of this human enteric pathogen on fresh produce during minimal processing.
Quantification of Horizontal Transmission of
Salmonella enterica
Serovar Enteritidis Bacteria in Pair-Housed Groups of Laying Hens
Authors: Thomas M. E. , Klinkenberg D. , Ejeta G. , Van Knapen F. , Bergwerff A. A. , Stegeman J. A. , Bouma A. 
Published: August 2009

ABSTRACT

An important source of human salmonellosis is the consumption of table eggs contaminated with
Salmonella enterica
serovar Enteritidis. Optimization of the various surveillance programs currently implemented to reduce human exposure requires knowledge of the dynamics of
S.
Enteritidis infection within flocks. The aim of this study was to provide parameter estimates for a transmission model of
S.
Enteritidis in laying-type chicken flocks. An experiment was carried out with 60 pairs of laying hens. Per pair, one hen was inoculated with
S.
Enteritidis and the other was contact exposed. After inoculation, cloacal swab samples from all hens were collected over 18 days and tested for the presence of
S.
Enteritidis. On the basis of this test, it was determined if and when each contact-exposed hen became colonized. A transmission model including a latency period of 1 day and a slowly declining infectivity level was fitted. The mean initial transmission rate was estimated to be 0.47 (95% confidence interval [CI], 0.30 to 0.72) per day. The reproduction number
R
0
, the average number of hens infected by one colonized hen in a susceptible population, was estimated to be 2.8 (95% CI, 1.9 to 4.2). The generation time, the average time between colonization of a “primary” hen and colonization of contact-exposed hens, was estimated to be 7.0 days (95% CI, 5.0 to 11.6 days). Simulations using these parameters showed that a flock of 20,000 hens would reach a maximum colonization level of 92% within 80 days after colonization of the first hen. These results can be used, for example, to evaluate the effectiveness of control and surveillance programs and to optimize these programs in a cost-benefit analysis.
Impaired Uptake and/or Utilization of Leucine bySaccharomyces cerevisiaeIs Suppressed by theSPT15-300Allele of the TATA-Binding Protein Gene
Authors: Baerends Richard J. S. , Qiu Jin-Long , Rasmussen Simon , Nielsen Henrik Bjørn , Brandt Anders 
Published: August 2009

ABSTRACTSuccessful fermentations to produce ethanol require microbial strains that have a high tolerance to glucose and ethanol. Enhanced glucose/ethanol tolerance of the laboratory yeastSaccharomyces cerevisiaestrain BY4741 under certain growth conditions as a consequence of the expression of a dominant mutant allele of theSPT15gene (SPT15-300) corresponding to the three amino acid changes F177S, Y195H, and K218R has been reported (H. Alper, J. Moxley, E. Nevoigt, G. R. Fink, and G. Stephanopoulos, Science 314:1565-1568, 2006). TheSPT15gene codes for the TATA-binding protein. This finding prompted us to examine the effect of expression of theSPT15-300allele in various yeast species of industrial importance. Expression ofSPT15-300in leucine-prototrophic strains ofS. cerevisiae,Saccharomyces bayanus, orSaccharomyces pastorianus(lager brewing yeast), however, did not improve tolerance to ethanol on complex rich medium (yeast extract-peptone-dextrose). The enhanced growth of the laboratory yeast strain BY4741 expressing theSPT15-300mutant allele was seen only on defined media with low concentrations of leucine, indicating that the apparent improved growth in the presence of ethanol was indeed associated with enhanced uptake and/or utilization of leucine. Reexamination of the microarray data published by Alper and coworkers likewise suggested that expression of genes coding for the leucine permeases, Tat1p and Bap3p, were upregulated in theSPT15-300mutant, as was expression of the genesARO10,ADH3,ADH5, andSFA1, involved in leucine degradation.
Poly(3-Hydroxybutyrate) Production from Glycerol by
Zobellella denitrificans
MW1 via High-Cell-Density Fed-Batch Fermentation and Simplified Solvent Extraction
Authors: Ibrahim Mohammad H. A. , Steinbüchel Alexander 
Published: August 2009

ABSTRACT

Industrial production of biodegradable polyesters such as polyhydroxyalkanoates is hampered by high production costs, among which the costs for substrates and for downstream processing represent the main obstacles. Inexpensive fermentable raw materials such as crude glycerol, an abundant by-product of the biodiesel industry, have emerged to be promising carbon sources for industrial fermentations. In this study,
Zobellella denitrificans
MW1, a recently isolated bacterium, was used for the production of poly(3-hydroxybutyrate) (PHB) from glycerol as the sole carbon source. Pilot-scale fermentations (42-liter scale) were conducted to scale up the high PHB accumulation capability of this strain. By fed-batch cultivation, at first a relatively high cell density (29.9 ± 1.3 g/liter) was obtained during only a short fermentation period (24 h). However, the PHB content was relatively low (31.0% ± 4.2% [wt/wt]). Afterwards, much higher concentrations of PHB (up to 54.3 ± 7.9 g/liter) and higher cell densities (up to 81.2 ± 2.5 g/liter) were obtained by further fed-batch optimization in the presence of 20 g/liter NaCl, with optimized feeding of glycerol and ammonia to support both cell growth and polymer accumulation over a period of 50 h. A high specific growth rate (0.422/h) and a short doubling time (1.64 h) were attained. The maximum PHB content obtained was 66.9% ± 7.6% of cell dry weight, and the maximum polymer productivity and substrate yield coefficient were 1.09 ± 0.16 g/liter/h and 0.25 ± 0.04 g PHB/g glycerol, respectively. Furthermore, a simple organic solvent extraction process was employed for PHB recovery during downstream processing: self-flotation of cell debris after extraction of PHB with chloroform allowed a convenient separation of a clear PHB-solvent solution from the cells. Maximum PHB recovery (85.0% ± 0.10% [wt/wt]) was reached after 72 h of extraction with chloroform at 30°C, with a polymer purity of 98.3% ± 1.3%.
Surface Colonization by Marine Roseobacters: Integrating Genotype and Phenotype
Authors: Slightom Rachael N. , Buchan Alison 
Published: August 2009

ABSTRACTTheRoseobacterclade is a broadly distributed, abundant, and biogeochemically relevant group of marine bacteria. Representatives are often associated with organic surfaces in disparate marine environments, suggesting that a sessile lifestyle is central to the ecology of lineage members. The importance of surface association and colonization has been demonstrated recently for select strains, and it has been hypothesized that production of antimicrobial agents, cell density-dependent regulatory mechanisms, and morphological features contribute to the colonization success of roseobacters. Drawing on these studies, insight into a broad representation of strains is facilitated by the availability of a substantial collection of genome sequences that provides a holistic view of these features among clade members. These genome data often corroborate phenotypic data but also reveal significant variation in terms of gene content and synteny among group members, even among closely related strains (congeners and conspecifics). Thus, while detailed studies of representative strains are serving as models for how roseobacters transition between planktonic and sessile lifestyles, it is becoming clear that additional studies are needed if we are to have a more comprehensive view of how these transitions occur in different lineage members. This is important if we are to understand how associations with surfaces influence metabolic activities contributing to the cycling of carbon and nutrients in the world's oceans.
Actions of
Mycobacterium
sp. Strain AP1 on the Saturated- and Aromatic-Hydrocarbon Fractions of Fuel Oil in a Marine Medium
Authors: Vila Joaquim , Grifoll Magdalena 
Published: August 2009

ABSTRACT

The pyrene-degrading
Mycobacterium
sp. strain AP1 grew in nutrient-supplemented artificial seawater with a heavy fuel oil as the sole carbon source, causing the complete removal of all linear (C
12
to C
40
) and branched alkanes from the aliphatic fraction, as well as an extensive degradation of the three- and four-ring polycyclic aromatic hydrocarbons (PAHs) phenanthrene (95%), anthracene (80%), fluoranthene (80%), pyrene (75%), and benzo(
a
)anthracene (30%). Alkylated PAHs, which are more abundant in crude oils than the nonsubstituted compounds, were selectively attacked at extents that varied from more than 90% for dimethylnaphthalenes, methylphenanthrenes, methylfluorenes, and methyldibenzothiophenes to about 30% for monomethylated fluoranthenes/pyrenes and trimethylated phenanthrenes and dibenzothiophenes. Identification of key metabolites indicated the utilization of phenanthrene, pyrene, and fluoranthene by known assimilatory metabolic routes, while other components were cooxidized. Detection of mono- and dimethylated phthalic acids demonstrated ring cleavage and further oxidation of alkyl PAHs. The extensive degradation of the alkanes, the two-, three-, and four-ring PAHs, and their 1-, 2-, and 3-methyl derivatives from a complex mixture of hydrocarbons by
Mycobacterium
sp. strain AP1 illustrates the great substrate versatility of alkane- and PAH-degrading mycobacteria.
Candida albicans
Hyphal Formation and Virulence Assessed Using a
Caenorhabditis elegans
Infection Model
Authors: Pukkila-Worley Read , Peleg Anton Y. , Tampakakis Emmanouil , Mylonakis Eleftherios 
Published: August 2009

ABSTRACT

Candida albicans
colonizes the human gastrointestinal tract and can cause life-threatening systemic infection in susceptible hosts. We study here
C. albicans
virulence determinants using the nematode
Caenorhabditis elegans
in a pathogenesis system that models candidiasis. The yeast form of
C. albicans
is ingested into the
C. elegans
digestive tract. In liquid media, the yeast cells then undergo morphological change to form hyphae, which results in aggressive tissue destruction and death of the nematode. Several lines of evidence demonstrate that hyphal formation is critical for
C. albicans
pathogenesis in
C. elegans
. First, two yeast species unable to form hyphae (
Debaryomyces hansenii
and
Candida lusitaniae
) were less virulent than
C. albicans
in the
C. elegans
assay. Second, three
C. albicans
mutant strains compromised in their ability to form hyphae (
efg1Δ/efg1Δ
,
flo8Δ/flo8Δ
, and
cph1Δ/cph1Δ efg1Δ/efg1Δ
) were dramatically attenuated for virulence. Third, the conditional
tet-NRG1
strain, which enables the external manipulation of morphogenesis in vivo, was more virulent toward
C. elegans
when the assay was conducted under conditions that permit hyphal growth. Finally, we demonstrate the utility of the
C. elegans
assay in a screen for
C. albicans
virulence determinants, which identified several genes important for both hyphal formation in vivo and the killing of
C. elegans
, including the recently described
CAS5
and
ADA2
genes. These studies in a
C. elegans-C. albicans
infection model provide insights into the virulence mechanisms of an important human pathogen.
Trypanosomatid Genomes Contain Several Subfamilies of ingi-Related Retroposons
Authors: Bringaud Frédéric , Berriman Matthew , Hertz-Fowler Christiane 
Published: August 2009

ABSTRACT

Retroposons are ubiquitous transposable elements found in the genomes of most eukaryotes, including trypanosomatids. The African and American trypanosomes (
Trypanosoma brucei
and
Trypanosoma cruzi
) contain long autonomous retroposons of the ingi clade (Tbingi and L1Tc, respectively) and short nonautonomous truncated versions (TbRIME and NARTc, respectively), as well as degenerate ingi-related retroposons devoid of coding capacity (DIREs). In contrast,
Leishmania major
contains only remnants of extinct retroposons (LmDIREs) and of short nonautonomous heterogeneous elements (LmSIDERs). We extend this comparative and evolutionary analysis of retroposons to the genomes of two other African trypanosomes (
Trypanosoma congolense
and
Trypanosoma vivax
) and another
Leishmania
sp. (
Leishmania braziliensis
). Three new potentially functional retroposons of the ingi clade have been identified: Tvingi in
T. vivax
and Tcoingi and L1Tco in
T. congolense. T. congolense
is the first trypanosomatid containing two classes of potentially active retroposons of the ingi clade. We analyzed sequences located upstream of these new long autonomous ingi-related elements, which code for the recognition site of the retroposon-encoded endonuclease. The closely related Tcoingi and Tvingi elements show the same conserved pattern, indicating that the Tcoingi- and Tvingi-encoded endonucleases share site specificity. Similarly, the conserved pattern previously identified upstream of L1Tc has also been detected at the same relative position upstream of L1Tco elements. A phylogenetic analysis of all ingi-related retroposons identified so far, including DIREs, clearly shows that several distinct subfamilies have emerged and coexisted, though in the course of trypanosomatid evolution, only a few have been maintained as active elements in modern trypanosomatid (sub)species.
A Single
dicer
Gene Is Required for Efficient Gene Silencing Associated with Two Classes of Small Antisense RNAs in
Mucor circinelloides
Authors: de Haro Juan P. , Calo Silvia , Cervantes María , Nicolás Francisco E. , Torres-Martínez Santiago , Ruiz-Vázquez Rosa M. 
Published: August 2009

ABSTRACT

RNA silencing in the zygomycete
Mucor circinelloides
exhibits uncommon features, such as induction by self-replicative sense transgenes and the accumulation of two size classes of antisense small interfering RNAs (siRNAs). To investigate whether this silencing phenomenon follows the rules of a canonical RNA-silencing mechanism, we used hairpin RNA (hpRNA)-producing constructs as silencing triggers and analyzed the efficiency and stability of silencing in different genetic backgrounds. We show here that the dsRNA-induced silencing mechanism is also associated with the accumulation of two sizes of antisense siRNAs and that this mechanism is not mediated by the previously known
dcl-1
(
dicer
-like) gene, which implies the existence of an additional
dicer
gene. An
M. circinelloides dcl-2
gene was cloned and characterized, and the corresponding null mutant was generated by gene replacement. This mutant is severely impaired in the silencing mechanism induced by self-replicative sense or inverted-repeat transgenes, providing the first genetic evidence of a canonical silencing mechanism in this class of fungus and pointing to a role for
dcl-2
in the mechanism. Moreover, a functional
dcl-2
gene is required for the normal accumulation of the two sizes of antisense RNAs, as deduced from the analysis of
dcl-2

−

transformants containing hpRNA-expressing plasmids. In addition to its critical role in transgene-induced silencing, the
dcl-2
gene seems to play a role in the control of vegetative development, since the
dcl-2
null mutants showed a significant decrease in their production of asexual spores.
Generation of Metabolically Diverse Strains ofStreptococcus pyogenesduring Survival in Stationary Phase
Authors: Wood Daniel N. , Weinstein Kathryn E. , Podbielski Andreas , Kreikemeyer Berndt , Gaughan John P. , Valentine Samara , Buttaro Bettina A. 
Published: August 2009

ABSTRACTStreptococcus pyogenes, in addition to causing fulminant disease, can be carried asymptomatically and may survive in the host without causing disease. Long-term stationary-phase cultures were used to characterize the metabolism of cultures surviving after glucose depletion. Survival of stationary-phase cultures in glucose-depleted rich medium was truncated by switching the cells to phosphate-buffered saline or by the addition of antibiotics, suggesting that survival depended on the presence of nutrients and metabolic activity. The metabolites of the pyruvate-to-acetate (PA) pathway (acetate and formate) and amino acid catabolic pathways (ammonia) accumulated throughout long-term stationary phase (12 weeks). Acid and ammonia production was balanced so that the culture pH was maintained above pH 5.6. Strains isolated from long-term stationary-phase cultures accumulated mutations that resulted in unique exponential-phase metabolisms, with some strains expressing the PA pathway, some strains producing ammonia, and some strains expressing both in the presence of glucose. Strains expressing high levels of PA pathway activity during exponential growth were unable to survive when regrown in pure culture due to the production of excess acid. These data suggest thatS. pyogenesdiversifies during survival in stationary phase into distinct strains with different metabolisms and that complementary metabolism is required to control the pH in stationary-phase cultures. One of three survivor strains isolated from tonsillar discard material from patients expressed high levels of the PA pathway during exponential growth. Sequencing of multiple group A streptococcus regulators revealed two different mutations in two different strains, suggesting that random mutation occurs during survival.
GuaA and GuaB Are Essential forBorrelia burgdorferiSurvival in the Tick-Mouse Infection Cycle
Authors: Jewett Mollie W. , Lawrence Kevin A. , Bestor Aaron , Byram Rebecca , Gherardini Frank , Rosa Patricia A. 
Published: August 2009

ABSTRACTPathogens lacking the enzymatic pathways for de novo purine biosynthesis are required to salvage purines and pyrimidines from the host environment for synthesis of DNA and RNA. Two key enzymes in purine salvage pathways are IMP dehydrogenase (GuaB) and GMP synthase (GuaA), encoded by theguaBandguaAgenes, respectively. While these genes are typically found on the chromosome in most bacterial pathogens, theguaABoperon ofBorrelia burgdorferiis present on plasmid cp26, which also harbors a number of genes critical forB. burgdorferiviability. Using molecular genetics and an experimental model of the tick-mouse infection cycle, we demonstrate that the enzymatic activities encoded by theguaABoperon are essential forB. burgdorferimouse infectivity and provide a growth advantage to spirochetes in the tick. These data indicate that the GuaA and GuaB proteins are critical for the survival ofB. burgdorferiin the infection cycle and highlight a potential difference in the requirements for purine salvage in the disparate mammalian and tick environments.
Autonomous and FliK-Dependent Length Control of the Flagellar Rod in
Salmonella enterica
Authors: Takahashi Noriko , Mizuno Shino , Hirano Takanori , Chevance Fabienne F. V. , Hughes Kelly T. , Aizawa Shin-Ichi 
Published: August 2009

ABSTRACT

Salmonella flgG
point mutations produce filamentous rod structures whose lengths are determined by FliK. FliK length variants produce rods with lengths proportional to the corresponding FliK molecular size, suggesting that FliK controls the length of not only the hook but also the rod by the same molecular mechanism.
The
Escherichia coli
Azoreductase AzoR Is Involved in Resistance to Thiol-Specific Stress Caused by Electrophilic Quinones
Authors: Liu Guangfei , Zhou Jiti , Fu Q. Shiang , Wang Jing 
Published: August 2009

ABSTRACT

The physiological role of
Escherichia coli
azoreductase AzoR was studied. It was found that AzoR was capable of reducing several benzo-, naphtho-, and anthraquinone compounds, which were better substrates for AzoR than the model azo substrate methyl red. The
ΔazoR
mutant displayed reduced viability when exposed to electrophilic quinones, which are capable of depleting cellular reduced glutathione (GSH). Externally added GSH can partially restore the impaired growth of the
ΔazoR
mutant caused by 2-methylhydroquinone. The transcription of
azoR
was induced by electrophiles, including 2-methylhydroquinone, catechol, menadione, and diamide. A transcription start point was identified 44 bp upstream from the translation start point. These data indicated that AzoR is a quinone reductase providing resistance to thiol-specific stress caused by electrophilic quinones.