bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stochasticity of Bacterial Attachment and Its Predictability by the Extended Derjaguin-Landau-Verwey-Overbeek Theory
Authors: Chia Teck Wah R. , Nguyen Vu Tuan , McMeekin Thomas , Fegan Narelle , Dykes Gary A. 
Published: April 2011

ABSTRACT

Bacterial attachment onto materials has been suggested to be stochastic by some authors but nonstochastic and based on surface properties by others. We investigated this by attaching pairwise combinations of two
Salmonella enterica
serovar Sofia (
S
. Sofia) strains (with different physicochemical and attachment properties) with one strain each of
S. enterica
serovar Typhimurium,
S. enterica
serovar Infantis, or
S. enterica
serovar Virchow (all with similar physicochemical and attachment abilities) in ratios of 0.428, 1, and 2.333 onto glass, stainless steel, Teflon, and polysulfone. Attached bacterial cells were recovered and counted. If the ratio of attached cells of each
Salmonella
serovar pair recovered was the same as the initial inoculum ratio, the attachment process was deemed stochastic. Experimental outcomes from the study were compared to those predicted by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory. Significant differences (
P
< 0.05) between the initial and the attached ratios for serovar pairs containing
S
. Sofia S1296a for all different ratios were apparent for all materials. For
S
. Sofia S1635-containing pairs, 7 out of 12 combinations of serovar pairs and materials had attachment ratios not significantly different (
P
> 0.05) from the initial ratio of 0.428. Five out of 12 and 10 out of 12 samples had attachment ratios not significantly different (
P
> 0.05) from the initial ratios of 1 and 2.333, respectively. These results demonstrate that bacterial attachment to different materials is likely to be nonstochastic only when the key physicochemical properties of the bacteria were significantly different (
P
< 0.05) from each other. XDLVO theory could successfully predict the attachment of some individual isolates to particular materials but could not be used to predict the likelihood of stochasticity in pairwise attachment experiments.
Distinct Acid Resistance and Survival Fitness Displayed by Curli Variants of Enterohemorrhagic Escherichia coli O157:H7
Authors: Carter Michelle Q. , Brandl Maria T. , Louie Jacqueline W. , Kyle Jennifer L. , Carychao Diana K. , Cooley Michael B. , Parker Craig T. , Bates Anne H. , Mandrell Robert E. 
Published: April 2011

ABSTRACT

Curli are adhesive fimbriae of
Enterobacteriaceae
and are involved in surface attachment, cell aggregation, and biofilm formation. Here, we report that both inter- and intrastrain variations in curli production are widespread in enterohemorrhagic
Escherichia coli
O157:H7. The relative proportions of curli-producing variants (C
+
) and curli-deficient variants (C
−
) in an
E. coli
O157:H7 cell population varied depending on the growth conditions. In variants derived from the 2006 U.S. spinach outbreak strains, the shift between the C
+
and C
−
subpopulations occurred mostly in response to starvation and was unidirectional from C
−
to C
+
; in variants derived from the 1993 hamburger outbreak strains, the shift occurred primarily in response to oxygen depletion and was bidirectional. Furthermore, curli variants derived from the same strain displayed marked differences in survival fitness: C
+
variants grew to higher concentrations in nutrient-limited conditions than C
−
variants, whereas C
−
variants were significantly more acid resistant than C
+
variants. This difference in acid resistance does not appear to be linked to the curli fimbriae
per se
, since a
csgA
deletion mutant in either a C
+
or a C
−
variant exhibited an acid resistance similar to that of its parental strain. Our data suggest that natural curli variants of
E. coli
O157:H7 carry several distinct physiological properties that are important for their environmental survival. Maintenance of curli variants in an
E. coli
O157:H7 population may provide a survival strategy in which C
+
variants are selected in a nutrient-limited environment, whereas C
−
variants are selected in an acidic environment, such as the stomach of an animal host, including that of a human.
Physiological Adaptation of Desulfitobacterium hafniense Strain TCE1 to Tetrachloroethene Respiration
Authors: Prat Laure , Maillard Julien , Grimaud Régis , Holliger Christof 
Published: April 2011

ABSTRACT

Desulfitobacterium
spp. are ubiquitous organisms with a broad metabolic versatility, and some isolates have the ability to use tetrachloroethene (PCE) as terminal electron acceptor. In order to identify proteins involved in this organohalide respiration process, a comparative proteomic analysis was performed. Soluble and membrane-associated proteins obtained from cells of
Desulfitobacterium hafniense
strain TCE1 that were growing on different combinations of the electron donors lactate and hydrogen and the electron acceptors PCE and fumarate were analyzed. Among proteins increasingly expressed in the presence of PCE compared to fumarate as electron acceptor, a total of 57 proteins were identified by mass spectrometry analysis, revealing proteins involved in stress response and associated regulation pathways, such as PspA, GroEL, and CodY, and also proteins potentially participating in carbon and energy metabolism, such as proteins of the Wood-Ljungdahl pathway and electron transfer flavoproteins. These proteomic results suggest that
D. hafniense
strain TCE1 adapts its physiology to face the relative unfavorable growth conditions during an apparent opportunistic organohalide respiration.
Increase of Eicosapentaenoic Acid in Thraustochytrids through Thraustochytrid Ubiquitin Promoter-Driven Expression of a Fatty Acid Δ5 Desaturase Gene
Authors: Kobayashi Takumi , Sakaguchi Keishi , Matsuda Takanori , Abe Eriko , Hama Yoichiro , Hayashi Masahiro , Honda Daiske , Okita Yuji , Sugimoto Shinichi , Okino Nozomu , Ito Makoto 
Published: April 2011

ABSTRACT

Thraustochytrids, marine protists known to accumulate polyunsaturated fatty acids (PUFAs) in lipid droplets, are considered an alternative to fish oils as a source of PUFAs. The major fatty acids produced in thraustochytrids are palmitic acid (C
16:0
),
n
− 6 docosapentaenoic acid (DPA) (C
22:5

n

− 6
), and docosahexaenoic acid (DHA) (C
22:6

n

− 3
), with eicosapentaenoic acid (EPA) (C
20:5

n

− 3
) and arachidonic acid (AA) (C
20:4

n

− 6
) as minor constituents. We attempted here to alter the fatty acid composition of thraustochytrids through the expression of a fatty acid Δ5 desaturase gene driven by the thraustochytrid ubiquitin promoter. The gene was functionally expressed in
Aurantiochytrium limacinum
mh0186, increasing the amount of EPA converted from eicosatetraenoic acid (ETA) (C
20:4

n

− 3
) by the Δ5 desaturase. The levels of EPA and AA were also increased by 4.6- and 13.2-fold in the transgenic thraustochytrids compared to levels in the mock transfectants when ETA and dihomo-γ-linolenic acid (DGLA) (C
20:3

n

− 6
) were added to the culture at 0.1 mM. Interestingly, the amount of EPA in the transgenic thraustochytrids increased in proportion to the amount of ETA added to the culture up to 0.4 mM. The rates of conversion and accumulation of EPA were much higher in the thraustochytrids than in baker's yeasts when the desaturase gene was expressed with the respective promoters. This report describes for the first time the finding that an increase of EPA could be accomplished by introducing the Δ5 desaturase gene into thraustochytrids and indicates that molecular breeding of thraustochytrids is a promising strategy for generating beneficial PUFAs.
Bottom-Up versus Top-Down Control of Hypo- and Epilimnion Free-Living Bacterial Community Structures in Two Neighboring Freshwater Lakes
Authors: Berdjeb Lyria , Ghiglione Jean-François , Jacquet Stéphan 
Published: April 2011

ABSTRACT
Bacterioplankton plays a central role in the microbial functioning of lacustrine ecosystems; however, factors that constrain its structural variation are still poorly understood. Here we evaluated the driving forces exerted by a large set of environmental and biological parameters on the temporal and spatial dynamics of free-living bacterial community structures (BCS) in two neighboring perialpine lakes, Lake Bourget and Lake Annecy, which differ in trophic status. We analyzed monthly data from a 1-year sampling period at two depths situated in the epi- and hypolimnia for each lake. Overall, denaturing gradient gel electrophoresis (DGGE) revealed significant differences in the BCS in the two lakes, characterized by a higher number of bands in the oligotrophic ecosystem (i.e., Lake Annecy). The temporal dynamics of BCS differed greatly between depths and lakes, with temporal scale patterns being much longer in the mesotrophic Lake Bourget. Direct-gradient multivariate ordination analyses showed that a complex array of biogeochemical parameters was the driving force behind BCS shifts in both lakes. Our results indicated that 60 to 80% of the variance was explained only by the bottom-up factors in both lakes, indicating the importance of nutrients and organic matter from autotrophic origin in controlling the BCS. Top-down regulation by flagellates together with ciliates or viruses was found only in the hypolimnion and not in the epilimnion for both lakes and explained less than 18% of the bacterial community changes during the year. Our study suggests that the temporal dynamics of the free-living bacterial community structure in deep perialpine lakes are dependent mainly on bottom-up factors and to a lesser extent on top-down factors, whatever the specific environmental conditions of these lakes.
Fecal Carriage and Shedding Density of CTX-M Extended-Spectrum β-Lactamase-Producing Escherichia coli in Cattle, Chickens, and Pigs: Implications for Environmental Contamination and Food Production
Authors: Horton R. A. , Randall L. P. , Snary E. L. , Cockrem H. , Lotz S. , Wearing H. , Duncan D. , Rabie A. , McLaren I. , Watson E. , La Ragione R. M. , Coldham N. G. 
Published: April 2011

ABSTRACT

The number and proportion of CTX-M positive
Escherichia coli
organisms were determined in feces from cattle, chickens, and pigs in the United Kingdom to provide a better understanding of the risk of the dissemination of extended-spectrum β-lactamase (ESBL) bacteria to humans from food animal sources. Samples of bovine (
n
= 35) and swine (
n
= 20) feces were collected from farms, and chicken cecal contents (
n
= 32) were collected from abattoirs. There was wide variation in the number of CTX-M-positive
E. coli
organisms detected; the median (range) CFU/g were 100 (100 × 10
6
to 1 × 10
6
), 5,350 (100 × 10
6
to 3.1 × 10
6
), and 2,800 (100 × 10
5
to 4.7 × 10
5
) for cattle, chickens, and pigs, respectively. The percentages of
E. coli
isolates that were CTX-M positive also varied widely; median (range) values were 0.013% (0.001 to 1%) for cattle, 0.0197% (0.00001 to 28.18%) for chickens, and 0.121% (0.0002 to 5.88%) for pigs. The proportion of animals designated high-density shedders (≥1 × 10
4
CFU/g) of CTX-M
E. coli
was 3/35, 15/32, and 8/20 for cattle, chickens, and pigs, respectively. We postulate that high levels of CTX-M
E. coli
in feces facilitate the dissemination of
bla
CTX-M
genes during the rearing of animals for food, and that the absolute numbers of CTX-M bacteria should be given greater consideration in epidemiological studies when assessing the risks of food-borne transmission.
Infaunal Burrows Are Enrichment Zones for Vibrio parahaemolyticus
Authors: Gamble Megan D. , Lovell Charles R. 
Published: April 2011

ABSTRACT

Vibrio parahaemolyticus
, a species that includes strains known to be pathogenic in humans, and other
Vibrionaceae
are common, naturally occurring bacteria in coastal environments. Understanding the ecology and transport of these organisms within estuarine systems is fundamental to predicting outbreaks of pathogenic strains. Infaunal burrows serve as conduits for increased transport of tidal waters and
V. parahaemolyticus
cells by providing large open channels from the sediment to salt marsh tidal creeks. An extensive seasonal study was conducted at the North Inlet Estuary in Georgetown, SC, to quantify
Vibrionaceae
and specifically
V. parahaemolyticus
bacteria in tidal water, fiddler crab (
Uca pugilator
,
Uca pugnax
) burrow water, and interstitial pore water. Numbers of
V. parahaemolyticus
bacteria were significantly higher within burrow waters (4,875 CFU ml
−1
) than in creek water (193 CFU ml
−1
) and interstitial pore water (128 CFU ml
−1
), demonstrating that infaunal burrows are sites of
V. parahaemolyticus
enrichment. A strong seasonal trend of increased abundances of
Vibrionaceae
and
V. parahaemolyticus
organisms during the warmer months of May through September was observed. Multilocus sequence typing (MLST) analysis of isolates presumed to be
V. parahaemolyticus
from creek water, pore water, and burrow water identified substantial strain-level genetic variability among
V. parahaemolyticus
bacteria. Analysis of carbon substrate utilization capabilities of organisms presumed to be
V. parahaemolyticus
also indicated physiological diversity within this clade, which helps to explain the broad distribution of these strains within the estuary. These burrows are “hot spots” of
Vibrionaceae
and
V. parahaemolyticus
cell numbers and strain diversity and represent an important microhabitat.
Engineering Saccharomyces cerevisiae To Release 3-Mercaptohexan-1-ol during Fermentation through Overexpression of an S. cerevisiae Gene,
STR3
, for Improvement of Wine Aroma
Authors: Holt Sylvester , Cordente Antonio G. , Williams Simon J. , Capone Dimitra L. , Jitjaroen Wanphen , Menz Ian R. , Curtin Chris , Anderson Peter A. 
Published: April 2011

ABSTRACT

Sulfur-containing aroma compounds are key contributors to the flavor of a diverse range of foods and beverages. The tropical fruit characters of
Vitis vinifera
L. cv. Sauvignon blanc wines are attributed to the presence of the aromatic thiols 3-mercaptohexan-1-ol (3MH), 3-mercaptohexan-1-ol-acetate, and 4-mercapto-4-methylpentan-2-one (4MMP). These volatile thiols are found in small amounts in grape juice and are formed from nonvolatile cysteinylated precursors during fermentation. In this study, we overexpressed a
Saccharomyces cerevisiae
gene,
STR3
, which led to an increase in 3MH release during fermentation of a
V. vinifera
L. cv. Sauvignon blanc juice. Characterization of the enzymatic properties of Str3p confirmed it to be a pyridoxal-5′-phosphate-dependent cystathionine β-lyase, and we demonstrated that this enzyme was able to cleave the cysteinylated precursors of 3MH and 4MMP to release the free thiols. These data provide direct evidence for a yeast enzyme able to release aromatic thiols
in vitro
that can be applied in the development of self-cloned yeast to enhance wine flavor.
Association of the Skn7 and Yap1 Transcription Factors in the Saccharomyces cerevisiae Oxidative Stress Response
Authors: Mulford K. E. , Fassler J. S. 
Published: April 2011

ABSTRACT

Saccharomyces cerevisiae
Skn7p is a stress response transcription factor that undergoes aspartyl phosphorylation by the Sln1p histidine kinase. Aspartyl phosphorylation of Skn7p is required for activation of genes required in response to wall stress, but Skn7p also activates oxidative stress response genes in an aspartyl phosphorylation-independent manner. The presence of binding sites for the Yap1p and Skn7p transcription factors in oxidative stress response promoters and the oxidative stress-sensitive phenotypes of
SKN7
and
YAP1
mutants suggest that these two factors work together. We present here evidence for a DNA-independent interaction between the Skn7 and Yap1 proteins that involves the receiver domain of Skn7p and the cysteine-rich domains of Yap1p. The interaction with Yap1p may help partition the Skn7 protein to oxidative stress response promoters when the Yap1 protein accumulates in the nucleus.
The Major Autolysin of Streptococcus gordonii Is Subject to Complex Regulation and Modulates Stress Tolerance, Biofilm Formation, and Extracellular-DNA Release
Authors: Liu Yaling , Burne Robert A. 
Published: April 2011

ABSTRACT

A gene, designated
atlS
, encoding a major autolysin from
Streptococcus gordonii
, was identified and characterized. The predicted AtlS protein is 1,160 amino acids and 127 kDa and has a conserved β1,4-
N
-acetylmuramidase domain. Zymographic analysis of wild-type
S. gordonii
revealed peptidoglycan hydrolase activities with molecular masses of 130 and 90 kDa that were absent in an
atlS
deletion mutant. Western blotting revealed that the 90-kDa band was derived from the 130-kDa protein. Inactivation of
atlS
resulted in formation of long chains by the cells, markedly decreased autolytic capacity, poor biofilm formation, diminished tolerance of acid and oxidative stress, and decreased production of extracellular DNA (eDNA). The biofilm-forming capacity of the
atlS
mutant could be almost completely restored to that of the wild-type strain by adding purified recombinant AtlA autolysin of
S. mutans
but was only partially restored by addition of eDNA. Autolysis, eDNA release, and
atlS
expression increased sharply when cells entered stationary phase and were greatly enhanced in cells growing with aeration. The LytST and VicRK two-component systems were both required for the induction of
atlS
by aeration, and purified LytT was able to bind to the promoter region of
atlS in vitro
. Thus, AtlS and its associated regulatory cascade dominantly control phenotypes of
S. gordonii
that are critical to colonization, persistence, and competition with other commensal and pathogenic oral bacteria in response to the redox environment and growth domain.
Progesterone Analogs Influence Germination of Clostridium sordellii and Clostridium difficile Spores In Vitro
Authors: Liggins Marc , Ramirez Norma , Magnuson Natiera , Abel-Santos Ernesto 
Published: April 2011

ABSTRACT

Clostridium sordellii
and
Clostridium difficile
are closely related anaerobic Gram-positive, spore-forming human pathogens.
C. sordellii
and
C. difficile
form spores that are believed to be the infectious form of these bacteria. These spores return to toxin-producing vegetative cells upon binding to small molecule germinants. The endogenous compounds that regulate clostridial spore germination are not fully understood. While
C. sordellii
spores require three structurally distinct amino acids to germinate, the occurrence of postpregnancy
C. sordellii
infections suggests that steroidal sex hormones might regulate its capacity to germinate. On the other hand,
C. difficile
spores require taurocholate (a bile salt) and glycine (an amino acid) to germinate. Bile salts and steroid hormones are biosynthesized from cholesterol, suggesting that the common sterane structure can affect the germination of both
C. sordellii
and
C. difficile
spores. Therefore, we tested the effect of sterane compounds on
C. sordellii
and
C. difficile
spore germination. Our results show that both steroid hormones and bile salts are able to increase
C. sordellii
spore germination rates. In contrast, a subset of steroid hormones acted as competitive inhibitors of
C. difficile
spore germination. Thus, even though
C. sordellii
and
C. difficile
are phylogenetically related, the two species' spores respond differently to steroidal compounds.
Molecular Characterization of the Glycerol-Oxidative Pathway of Clostridium butyricum VPI 1718
Authors: Raynaud Céline , Lee Jieun , Sarçabal Patricia , Croux Christian , Meynial-Salles Isabelle , Soucaille Philippe 
Published: April 2011

ABSTRACT

The glycerol oxidative pathway of
Clostridium butyricum
VPI 1718 plays an important role in glycerol dissimilation. We isolated, sequenced, and characterized the region coding for the glycerol oxidation pathway. Five open reading frames (ORFs) were identified:
dhaR
, encoding a putative transcriptional regulator;
dhaD
(1,142 bp), encoding a glycerol dehydrogenase; and
dhaK
(995 bp),
dhaL
(629 bp), and
dhaM
(386 bp), encoding a phosphoenolpyruvate (PEP)-dependent dihydroxyacetone (DHA) kinase enzyme complex. Northern blot analysis demonstrated that the last four genes are transcribed as a 3.2-kb polycistronic operon only in glycerol-metabolizing cultures, indicating that the expression of this operon is regulated at the transcriptional level. The transcriptional start site of the operon was determined by primer extension, and the promoter region was deduced. The glycerol dehydrogenase activity of DhaD and the PEP-dependent DHA kinase activity of DhaKLM were demonstrated by heterologous expression in different
Escherichia coli
mutants. Based on our complementation experiments, we proposed that the HPr phosphoryl carrier protein and His9 residue of the DhaM subunit are involved in the phosphoryl transfer to dihydroxyacetone-phosphate. DhaR, a potential regulator of this operon, was found to contain conserved transmitter and receiver domains that are characteristic of two-component systems present in the AraC family. To the best of our knowledge, this is the first molecular characterization of a glycerol oxidation pathway in a Gram-positive bacterium.
The Interplay of mRNA Stimulatory Signals Required for AUU-Mediated Initiation and Programmed −1 Ribosomal Frameshifting in Decoding of Transposable Element IS
911
Authors: Prère Marie-Françoise , Canal Isabelle , Wills Norma M. , Atkins John F. , Fayet Olivier 
Published: April 2011

ABSTRACT

The IS
911
bacterial transposable element uses −1 programmed translational frameshifting to generate the protein required for its mobility: translation initiated in one gene (
orfA
) shifts to the −1 frame and continues in a second overlapping gene (
orfB
), thus generating the OrfAB transposase. The A-AAA-AAG frameshift site of IS
911
is flanked by two stimulatory elements, an upstream Shine-Dalgarno sequence and a downstream stem-loop. We show here that, while they can act independently, these stimulators have a synergistic effect when combined. Mutagenic analyses revealed features of the complex stem-loop that make it a low-efficiency stimulator. They also revealed the dual role of the upstream Shine-Dalgarno sequence as (i) a stimulator of frameshifting, by itself more potent than the stem-loop, and (ii) a mandatory determinant of initiation of OrfB protein synthesis on an AUU codon directly preceding the A6G motif. Both roles rely on transient base pairing of the Shine-Dalgarno sequence with the 3′ end of 16S rRNA. Because of its effect on frameshifting, the Shine-Dalgarno sequence is an important determinant of the level of transposase in IS
911
-containing cells, and hence of the frequency of transposition.