bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics and Biodiversity of Populations of Lactic Acid Bacteria andAcetic Acid Bacteria Involved in Spontaneous Heap Fermentation of Cocoa Beans inGhana
Authors: Camu Nicholas , De Winter Tom , Verbrugghe Kristof , Cleenwerck Ilse , Vandamme Peter , Takrama Jemmy S. , Vancanneyt Marc , De Vuyst Luc 
Published: February 2007

ABSTRACT

The Ghanaian cocoa bean heap fermentation process was studied through a
multiphasic approach, encompassing both microbiological and metabolite
target analyses. A culture-dependent (plating and incubation, followed
by repetitive-sequence-based PCR analyses of picked-up
colonies) and culture-independent (denaturing gradient gel
electrophoresis [DGGE] of 16S rRNA gene amplicons, PCR-DGGE) approach
revealed a limited biodiversity and targeted population dynamics of
both lactic acid bacteria (LAB) and acetic acid bacteria (AAB) during
fermentation. Four main clusters were identified among the LAB
isolated:
Lactobacillus plantarum
,
Lactobacillus
fermentum
,
Leuconostoc pseudomesenteroides
, and
Enterococcus casseliflavus
. Other taxa encompassed, for
instance,
Weissella
. Only four clusters were found
among the AAB identified:
Acetobacter pasteurianus
,
Acetobacter syzygii
-like bacteria, and two small clusters of
Acetobacter tropicalis
-like bacteria. Particular strains of
L. plantarum
,
L. fermentum
, and
A.
pasteurianus
, originating from the environment, were well adapted
to the environmental conditions prevailing during Ghanaian cocoa bean
heap fermentation and apparently played a significant role in the cocoa
bean fermentation process. Yeasts produced ethanol from
sugars, and LAB produced lactic acid, acetic acid, ethanol, and
mannitol from sugars and/or citrate. Whereas
L. plantarum
strains were abundant in the beginning of the fermentation,
L.
fermentum
strains converted fructose into mannitol upon prolonged
fermentation.
A. pasteurianus
grew on ethanol, mannitol, and
lactate and converted ethanol into acetic acid. A newly proposed
Weissella
sp., referred to as “
Weissella
ghanaensis
,” was detected through PCR-DGGE analysis in
some of the fermentations and was only occasionally picked up through
culture-based isolation. Two new species of
Acetobacter
were
found as well, namely, the species tentatively named“
Acetobacter senegalensis
” (
A.
tropicalis
-like) and “
Acetobacter
ghanaensis
” (
A.
syzygii
-like).
A Novel
lux
Operon in the Cryptically Bioluminescent Fish Pathogen
Vibrio salmonicida
Is Associated with Virulence
Authors: Nelson Eric J. , Tunsjø Hege S. , Fidopiastis Pat M. , Sørum Henning , Ruby Edward G. 
Published: February 2007

ABSTRACT

The cold-water-fish pathogen
Vibrio salmonicida
expresses a functional bacterial luciferase but produces insufficient levels of its aliphatic-aldehyde substrate to be detectably luminous in culture. Our goals were to (i) better explain this cryptic bioluminescence phenotype through molecular characterization of the
lux
operon and (ii) test whether the bioluminescence gene cluster is associated with virulence. Cloning and sequencing of the
V. salmonicida lux
operon revealed that homologs of all of the genes required for luminescence are present:
luxAB
(luciferase) and
luxCDE
(aliphatic-aldehyde synthesis). The arrangement and sequence of these structural
lux
genes are conserved compared to those in related species of luminous bacteria. However,
V. salmonicida
strains have a novel arrangement and number of homologs of the
luxR
and
luxI
quorum-sensing regulatory genes. Reverse transcriptase PCR analysis suggests that this novel arrangement of quorum-sensing genes generates antisense transcripts that may be responsible for the reduced production of bioluminescence. In addition, infection with a strain in which the
luxA
gene was mutated resulted in a marked delay in mortality among Atlantic salmon relative to infection with the wild-type parent in single-strain challenge experiments. In mixed-strain competition between the
luxA
mutant and the wild type, the mutant was attenuated up to 50-fold. It remains unclear whether the attenuation results from a direct loss of luciferase or a polar disturbance elsewhere in the
lux
operon. Nevertheless, these findings document for the first time an association between a mutation in a structural
lux
gene and virulence, as well as provide a new molecular system to study
Vibrio
pathogenesis in a natural host.
Tropheryma whipplei
in the Environment: Survey of Sewage Plant Influxes and Sewage Plant Workers
Authors: Schöniger-Hekele Maximilian , Petermann Dagmar , Weber Beate , Müller Christian 
Published: February 2007

ABSTRACT

We studied the prevalence of
Tropheryma whipplei
in influxes to 46 sewage treatment plants and in stool, mouthwash fluids, and dental plaques of 64 healthy workers in those facilities and 146 disease control patients.
T. whipplei
was found in sewage water, in stool of healthy individuals, and significantly more often in stool of workers exposed to sewage water.
Use of High-Affinity Cell Wall-Binding Domains of Bacteriophage Endolysins for Immobilization and Separation of Bacterial Cells
Authors: Kretzer Jan W. , Lehmann Rainer , Schmelcher Mathias , Banz Manuel , Kim Kwang-Pyo , Korn Corinna , Loessner Martin J. 
Published: February 2007

ABSTRACT

Immobilization and magnetic separation for specific enrichment of microbial cells, such as the pathogen
Listeria monocytogenes
, depends on the availability of suitable affinity molecules. We report here a novel concept for the immobilization and separation of bacterial cells by replacing antibodies with cell wall-binding domains (CBDs) of bacteriophage-encoded peptidoglycan hydrolases (endolysins). These polypeptide modules very specifically recognize and bind to ligands on the gram-positive cell wall with high affinity. With paramagnetic beads coated with recombinant
Listeria
phage endolysin-derived CBD molecules, more than 90% of the viable
L. monocytogenes
cells could be immobilized and recovered from diluted suspensions within 20 to 40 min. Recovery rates were similar for different species and serovars of
Listeria
and were not affected by the presence of other microorganisms. The CBD-based magnetic separation (CBD-MS) procedure was evaluated for capture and detection of
L. monocytogenes
from artificially and naturally contaminated food samples. The CBD separation method was shown to be superior to the established standard procedures; it required less time (48 h versus 96 h) and was the more sensitive method. Furthermore, the generalizability of the CBD-MS approach was demonstrated by using specific phage-encoded CBDs specifically recognizing
Bacillus cereus
and
Clostridium perfringens
cells, respectively. Altogether, CBD polypeptides represent novel and innovative tools for the binding and capture of bacterial cells, with many possible applications in microbiology and diagnostics.
Human Enteropathogen Load in Activated Sewage Sludge and Corresponding Sewage Sludge End Products
Authors: Graczyk Thaddeus K. , Lucy Frances E. , Tamang Leena , Miraflor Allen 
Published: February 2007

ABSTRACT

This study demonstrated a significant reduction in the concentrations of
Cryptosporidium parvum
and
Cryptosporidium hominis
oocysts,
Giardia lamblia
cysts, and spores of human-virulent microsporidia in dewatered and biologically stabilized sewage sludge cake end products compared to those of the respective pathogens in the corresponding samples collected during the sludge activation process.
The Antifungal Protein AFP from
Aspergillus giganteus
Inhibits Chitin Synthesis in Sensitive Fungi
Authors: Hagen Silke , Marx Florentine , Ram Arthur F. , Meyer Vera 
Published: February 2007

ABSTRACT

The antifungal protein AFP from
Aspergillus giganteus
is highly effective in restricting the growth of major human- and plant-pathogenic filamentous fungi. However, a fundamental prerequisite for the use of AFP as an antifungal drug is a complete understanding of its mode of action. In this study, we performed several analyses focusing on the assumption that the chitin biosynthesis of sensitive fungi is targeted by AFP. Here we show that the N-terminal domain of AFP (amino acids 1 to 33) is sufficient for efficient binding of AFP to chitin but is not adequate for inhibition of the growth of sensitive fungi. AFP susceptibility tests and SYTOX Green uptake experiments with class III and class V chitin synthase mutants of
Fusarium oxysporum
and
Aspergillus oryzae
showed that deletions made the fungi less sensitive to AFP and its membrane permeabilization effect. In situ chitin synthase activity assays revealed that chitin synthesis is specifically inhibited by AFP in sensitive fungi, indicating that AFP causes cell wall stress and disturbs cell integrity. Further evidence that there was AFP-induced cell wall stress was obtained by using an
Aspergillus niger
reporter strain in which the cell wall integrity pathway was strongly induced by AFP.
Water Transport in Intact Yeast Cells as Assessed by Fluorescence Self-Quenching
Authors: Soveral Graça , Madeira Ana , Loureiro-Dias Maria C. , Moura Teresa F. 
Published: February 2007

ABSTRACT

Intact yeast cells loaded with 5- and-6-carboxyfluorescein were used to assess water transport. The results were similar to those previously reported for protoplasts assessed by using either fluorescence or light scattering, and the activation energies were 8.0 and 15.1 kcal mol
−1
(33.4 and 63.2 kJ mol
−1
) for a strain overexpressing
AQY1
aquaporin and a parental strain, respectively.
Quantitative Real-Time PCR Detection of Toxic
Nodularia
Cyanobacteria in the Baltic Sea
Authors: Koskenniemi Kerttu , Lyra Christina , Rajaniemi-Wacklin Pirjo , Jokela Jouni , Sivonen Kaarina 
Published: February 2007

ABSTRACT

A specific quantitative real-time PCR (qPCR) method was developed for the quantification of hepatotoxin nodularin-producing
Nodularia
, one of the main bloom-forming cyanobacteria in the Baltic Sea. Specific PCR primers were designed for subunit F of the nodularin synthetase gene (
ndaF
), which encodes the NdaF subunit of the nodularin synthetase gene complex needed for nodularin production. The qPCR method was applied to water samples (a total of 120 samples) collected from the Baltic Sea in July 2004. As few as 30
ndaF
gene copies ml
−1
of seawater could be detected, and thus, the method was very sensitive. The
ndaF
gene copy numbers and nodularin concentrations were shown to correlate in the Baltic seawater, indicating the constant production of nodularin by
Nodularia
. This qPCR method for the
ndaF
gene can be used for detailed studies of
Nodularia
blooms and their formation.
ndaF
gene copies and nodularin were detected mostly in the surface water but also in deeper water layers (down to 30 m). Toxic
Nodularia
blooms are not only horizontally but also vertically widely distributed, and thus, the Baltic fauna is extensively exposed to nodularin.
Developmental Regulation of an Adhesin Gene during Cellular Morphogenesis in the Fungal Pathogen
Candida albicans
Authors: Argimón Silvia , Wishart Jill A. , Leng Roger , Macaskill Susan , Mavor Abigail , Alexandris Thomas , Nicholls Susan , Knight Andrew W. , Enjalbert Brice , Walmsley Richard , Odds Frank C. , Gow Neil A. R. , Brown Alistair J. P. 
Published: February 2007

ABSTRACT

Candida albicans
expresses specific virulence traits that promote disease establishment and progression. These traits include morphological transitions between yeast and hyphal growth forms that are thought to contribute to dissemination and invasion and cell surface adhesins that promote attachment to the host. Here, we describe the regulation of the adhesin gene
ALS3
, which is expressed specifically during hyphal development in
C. albicans
. Using a combination of reporter constructs and regulatory mutants, we show that this regulation is mediated by multiple factors at the transcriptional level. The analysis of
ALS3
promoter deletions revealed that this promoter contains two activation regions: one is essential for activation during hyphal development, while the second increases the amplitude of this activation. Further deletion analyses using the
Renilla reniformis
luciferase reporter delineate the essential activation region between positions −471 and −321 of the promoter. Further 5′ or 3′ deletions block activation.
ALS3
transcription is repressed mainly by Nrg1 and Tup1, but Rfg1 contributes to this repression. Efg1, Tec1, and Bcr1 are essential for the transcriptional activation of
ALS3
, with Tec1 mediating its effects indirectly through Bcr1 rather than through the putative Tec1 sites in the
ALS3
promoter.
ALS3
transcription is not affected by Cph2, but Cph1 contributes to full
ALS3
activation. The data suggest that multiple morphogenetic signaling pathways operate through the promoter of this adhesin gene to mediate its developmental regulation in this major fungal pathogen.
Streptococcus gordoniiHsa Environmentally Constrains Competitive Binding byStreptococcus sanguinisto Saliva-Coated Hydroxyapatite
Authors: Nobbs Angela H. , Zhang Yongshu , Khammanivong Ali , Herzberg Mark C. 
Published: February 2007

ABSTRACTCompetition between pioneer colonizing bacteria may determine polymicrobial succession during dental plaque development, but the ecological constraints are poorly understood. For example, moreStreptococcus sanguinisthanStreptococcus gordoniiorganisms are consistently isolated from the same intraoral sites, yetS. gordoniifails to be excluded and survives as a species over time. To explain this observation, we hypothesized thatS. gordoniicould compete withS. sanguinisto adhere to saliva-coated hydroxyapatite (sHA), an in vitro model of the tooth surface. Both species bound similarly to sHA, yet 10- to 50-fold excessS. gordoniiDL1 reduced binding ofS. sanguinisSK36 by 85 to >95%.S. sanguinis, by contrast, did not significantly compete withS. gordoniito adhere.S. gordoniicompeted withS. sanguinismore effectively than other species of oral streptococci and depended upon the salivary film on HA. Next, putativeS. gordoniiadhesins were analyzed for contributions to interspecies competitive binding. Like wild-typeS. gordonii, isogenic mutants with mutations in antigen I/II polypeptides (sspAB), amylase-binding proteins (abpAB), and Csh adhesins (cshAB) competed effectively againstS. sanguinis. By contrast, anhsa-deficient mutant ofS. gordoniishowed significantly reduced binding and competitive capabilities, while these properties were restored in anhsa-complemented strain. Thus, Hsa confers a selective advantage toS. gordoniioverS. sanguinisin competitive binding to sHA. Hsa expression may, therefore, serve as an environmental constraint againstS. sanguinis, enablingS. gordoniito persist within the oral cavity, despite the greater natural prevalence ofS. sanguinisin plaque and saliva.
Species-Specific Functioning of the
Pseudomonas
XcpQ Secretin: Role for the C-Terminal Homology Domain and Lipopolysaccharide
Authors: Bitter Wilbert , van Boxtel Ria , Groeneweg Mathijs , Carballo Patricia Sánchez , Zähringer Ulrich , Tommassen Jan , Koster Margot 
Published: February 2007

ABSTRACT

Secretins are oligomeric proteins that mediate the export of macromolecules across the bacterial outer membrane. The members of the secretin superfamily possess a C-terminal homology domain that is important for oligomerization and channel formation, while their N-terminal halves are thought to be involved in system-specific interactions. The XcpQ secretin of
Pseudomonas
spp. is a component of the type II secretion pathway. XcpQ from
Pseudomonas alcaligenes
is not able to functionally replace the secretin of the closely related species
Pseudomonas aeruginosa.
By analysis of chimeric XcpQ proteins, a region important for species-specific functioning was mapped between amino acid residues 344 and 478 in the C-terminal homology domain. Two chromosomal suppressor mutations were obtained that resulted in the proper functioning in
P. aeruginosa
of
P. alcaligenes
XcpQ and inactive hybrids. These mutations caused a defect in the synthesis of the lipopolysaccharide (LPS) outer core region. Subsequent analysis of different LPS mutants showed that changes in the outer core and not the loss of O antigen caused the suppressor phenotype. High concentrations of divalent cations in the growth medium also allowed
P. alcaligenes
XcpQ and inactive hybrids to function properly in
P. aeruginosa
. Since divalent cations are known to affect the structure of LPS, this observation supports the hypothesis that LPS has a role in the functioning of secretins.
A Phosphoenolpyruvate-Dependent Phosphotransferase System Is the Principal Maltose Transporter in
Streptococcus mutans
Authors: Webb Alexander J. , Homer Karen A. , Hosie Arthur H. F. 
Published: February 2007

ABSTRACT

We report that a phosphoenolpyruvate-dependent phosphotransferase system, MalT, is the principal maltose transporter for
Streptococcus mutans.
MalT also contributes to maltotriose uptake. Since maltose and maltodextrins are products of starch degradation found in saliva, the ability to take up and ferment these carbohydrates may contribute to dental caries.
Performance of the Translational Apparatus Varies with the Ecological Strategies of Bacteria
Authors: Dethlefsen Les , Schmidt Thomas M. 
Published: February 2007

ABSTRACT
Protein synthesis is the predominant activity of growing bacteria; the protein synthesis system accounts for more than one-half the cell's dry mass and consumes most of the cell's energy during rapid growth. Translation has been studied extensively using model organisms, and the translational apparatus is qualitatively similar in terms of structure and function across all known forms of life. However, little is known about variation between organisms in translational performance. Using measurements of macromolecular content in a phylogenetically diverse collection of bacteria with contrasting ecological strategies, we found that the translational power (the rate of protein synthesis normalized to the mass of the protein synthesis system) is three- to fourfold higher among bacteria that respond rapidly to nutrient availability than among bacteria that respond slowly. An analysis of codon use in completely sequenced bacterial genomes confirmed that the selective forces acting on translation vary with the ecological strategy. We propose that differences in translational power result from ecologically based variation among microbes in the relative importance of two competing benefits: reducing the biomass invested in the protein synthesis system and reducing the energetic expense of protein synthesis.
Intermolecular Forces and Enthalpies in the Adhesion of
Streptococcus mutans
and an Antigen I/II-Deficient Mutant to Laminin Films
Authors: Busscher Henk J. , van de Belt-Gritter Betsy , Dijkstra Rene J. B. , Norde Willem , Petersen Fernanda C. , Scheie Anne A. , van der Mei Henny C. 
Published: February 2007

ABSTRACT

The antigen I/II family of surface proteins is expressed by most oral streptococci, including
Streptococcus mutans
, and mediates specific adhesion to, among other things, salivary films and extracellular matrix proteins. In this study we showed that antigen I/II-deficient
S. mutans
isogenic mutant IB03987 was nearly unable to adhere to laminin films under flow conditions due to a lack of specific interactions (0.8 × 10
6
and 1.1 × 10
6
cells cm
−2
at pH 5.8 and 6.8, respectively) compared with parent strain LT11 (21.8 × 10
6
and 26.1 × 10
6
cells cm
−2
). The adhesion of both the parent and mutant strains was slightly greater at pH 6.8 than at pH 5.8. In addition, atomic force microscopy (AFM) experiments demonstrated that the parent strain experienced less repulsion when it approached a laminin film than the mutant experienced. Upon retraction, combined specific and nonspecific adhesion forces were stronger for the parent strain (up to −5.0 and −4.9 nN at pH 5.8 and 6.8, respectively) than for the mutant (up to −1.5 and −2.1 nN), which was able to interact only through nonspecific interactions. Enthalpy was released upon adsorption of laminin to the surface of the parent strain but not upon adsorption of laminin to the surface of IB03987. A comparison of the adhesion forces in AFM with the adhesion forces reported for specific ligand-receptor complexes resulted in the conclusion that the number of antigen I/II binding sites for laminin on
S. mutans
LT11 is on the order of 6 × 10
4
sites per organism and that the sites are probably arranged along exterior surface structures, as visualized here by immunoelectron microscopy.
σ
B
Regulates IS
256
-Mediated
Staphylococcus aureus
Biofilm Phenotypic Variation
Authors: Valle Jaione , Vergara-Irigaray Marta , Merino Nekane , Penadés José R. , Lasa Iñigo 
Published: February 2007

ABSTRACT

Biofilm formation in
Staphylococcus aureus
is subject to phase variation, and biofilm-negative derivatives emerge sporadically from a biofilm-positive bacterial population. To date, the only known mechanism for generating biofilm phenotypic variation in staphylococci is the reversible insertion/excision of IS
256
in biofilm-essential genes. In this study, we present evidence suggesting that the absence of the σ
B
transcription factor dramatically increases the rate of switching to the biofilm-negative phenotype in the clinical isolate
S. aureus
15981, under both steady-state and flow conditions. The phenotypic switching correlates with a dramatic increase in the number of IS
256
copies in the chromosomes of biofilm-negative variants, as well as with an augmented IS
256
insertion frequency into the
icaC
and the
sarA
genes. IS
256
-mediated biofilm switching is reversible, and biofilm-positive variants could emerge from biofilm-negative σ
B
mutants. Analysis of the chromosomal insertion frequency using a recombinant IS
256
element tagged with an erythromycin marker showed an almost three-times-higher transposition frequency in a Δσ
B
strain. However, regulation of IS
256
activity by σ
B
appears to be indirect, since transposase transcription is not affected in the absence of σ
B
and IS
256
activity is inhibited to wild-type levels in a Δσ
B
strain under NaCl stress. Overall, our results identify a new role for σ
B
as a negative regulator of insertion sequence transposition and support the idea that deregulation of IS
256
activity abrogates biofilm formation capacity in
S. aureus
.
Role of the PDZ Domains in
Escherichia coli
DegP Protein
Authors: Iwanczyk Jack , Damjanovic Daniela , Kooistra Joel , Leong Vivian , Jomaa Ahmad , Ghirlando Rodolfo , Ortega Joaquin 
Published: February 2007

ABSTRACT

PDZ domains are modular protein interaction domains that are present in metazoans and bacteria. These domains possess unique structural features that allow them to interact with the C-terminal residues of their ligands. The
Escherichia coli
essential periplasmic protein DegP contains two PDZ domains attached to the C-terminal end of the protease domain. In this study we examined the role of each PDZ domain in the protease and chaperone activities of this protein. Specifically, DegP mutants with either one or both PDZ domains deleted were generated and tested to determine their protease and chaperone activities, as well as their abilities to sequester unfolded substrates. We found that the PDZ domains in DegP have different roles; the PDZ1 domain is essential for protease activity and is responsible for recognizing and sequestering unfolded substrates through C-terminal tags, whereas the PDZ2 domain is mostly involved in maintaining the hexameric cage of DegP. Interestingly, neither of the PDZ domains was required for the chaperone activity of DegP. In addition, we found that the loops connecting the protease domain to PDZ1 and connecting PDZ1 to PDZ2 are also essential for the protease activity of the hexameric DegP protein. New insights into the roles of the PDZ domains in the structure and function of DegP are provided. These results imply that DegP recognizes substrate molecules targeted for degradation and substrate molecules targeted for refolding in different manners and suggest that the substrate recognition mechanisms may play a role in the protease-chaperone switch, dictating whether the substrate is degraded or refolded.