bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of a Bacteriophage on the Population Dynamics of Toxic Dinoflagellates by Lysis of Algicidal Bacteria
Authors: Cai Wenwei , Wang Hui , Tian Yun , Chen Feng , Zheng Tianling 
Published: September 2011

ABSTRACTA lytic phage (øZCW1) was isolated from an algicidal bacteriumPseudoalteromonassp. strain SP48 that specifically kills the toxic dinoflagellateAlexandrium tamarense. We demonstrated that øZCW1 could trigger the growth ofA. tamarenseby inhibiting the growth of algicidal bacterium SP48. In contrast, the growth ofA. tamarensewas suppressed when cocultured with either SP48 or the øZCW1-resistant mutant of SP48. This study provides the first evidence of the indirect impact of bacteriophage on bloom-forming microalgae via phage lysis of alga-killing bacteria.
Active Autotrophic Ammonia-Oxidizing Bacteria in Biofilm Enrichments from Simulated Creek Ecosystems at Two Ammonium Concentrations Respond to Temperature Manipulation
Authors: Avrahami Sharon , Jia Zhongjun , Neufeld Josh D. , Murrell J. Colin , Conrad Ralf , Küsel Kirsten 
Published: September 2011

ABSTRACT

The first step of nitrification, the oxidation of ammonia to nitrite, is important for reducing eutrophication in freshwater environments when coupled with anammox (anaerobic ammonium oxidation) or denitrification. We analyzed active formerly biofilm-associated aerobic ammonia-oxidizing communities originating from Ammerbach (AS) and Leutra South (LS) stream water (683 ± 550 [mean ± standard deviation] and 16 ± 7 μM NH
4
+
, respectively) that were developed in a flow-channel experiment and incubated under three temperature regimens. By stable-isotope probing using
13
CO
2
, we found that members of the
Bacteria
and not
Archaea
were the functionally dominant autotrophic ammonia oxidizers at all temperatures under relatively high ammonium loads. The copy numbers of bacterial
amoA
genes in
13
C-labeled DNA were lower at 30°C than at 13°C in both stream enrichment cultures. However, the community composition of the ammonia-oxidizing bacteria (AOB) in the
13
C-labeled DNA responded differently to temperature manipulation at two ammonium concentrations. In LS enrichments incubated at the
in situ
temperature (13°C),
Nitrosomonas oligotropha
-like sequences were retrieved with sequences from
Nitrosospira
AmoA cluster 4, while the proportion of
Nitrosospira
sequences increased at higher temperatures. In AS enrichments incubated at 13°C and 20°C, AmoA cluster 4 sequences were dominant;
Nitrosomonas nitrosa
-like sequences dominated at 30°C. Biofilm-associated AOB communities were affected differentially by temperature at two relatively high ammonium concentrations, implicating them in a potential role in governing contaminated freshwater AOB distributions.
Fine-Scale Distribution Patterns of Synechococcus Ecological Diversity in Microbial Mats of Mushroom Spring, Yellowstone National Park
Authors: Becraft Eric D. , Cohan Frederick M. , Kühl Michael , Jensen Sheila I. , Ward David M. 
Published: September 2011

ABSTRACT

Past analyses of sequence diversity in high-resolution protein-encoding genes have identified putative ecological species of unicellular cyanobacteria in the genus
Synechococcus
, which are specialized to 60°C but not 65°C in Mushroom Spring microbial mats. Because these studies were limited to only two habitats, we studied the distribution of
Synechococcus
sequence variants at 1°C intervals along the effluent flow channel and at 80-μm vertical-depth intervals throughout the upper photic layer of the microbial mat. Diversity at the
psaA
locus, which encodes a photosynthetic reaction center protein (PsaA), was sampled by PCR amplification, cloning, and sequencing methods at 60, 63, and 65°C sites. The evolutionary simulation programs Ecotype Simulation and AdaptML were used to identify putative ecologically distinct populations (ecotypes). Ecotype Simulation predicted a higher number of putative ecotypes in cases where habitat variation was limited, while AdaptML predicted a higher number of ecologically distinct phylogenetic clades in cases where habitat variation was high. Denaturing gradient gel electrophoresis was used to track the distribution of dominant sequence variants of ecotype populations relative to temperature variation and to O
2
, pH, and spectral irradiance variation, as measured using microsensors. Different distributions along effluent channel flow and vertical gradients, where temperature, light, and O
2
concentrations are known to vary, confirmed the ecological distinctness of putative ecotypes.
The Lcn972 Bacteriocin-Encoding Plasmid pBL1 Impairs Cellobiose Metabolism in Lactococcus lactis
Authors: Campelo Ana B. , Gaspar Paula , Roces Clara , Rodríguez Ana , Kok Jan , Kuipers Oscar P. , Neves Ana Rute , Martínez Beatriz 
Published: September 2011

ABSTRACT

pBL1 is a
Lactococcus lactis
theta-replicating 10.9-kbp plasmid that encodes the synthetic machinery of the bacteriocin Lcn972. In this work, the transcriptomes of exponentially growing
L. lactis
strains with and without pBL1 were compared. A discrete response was observed, with a total of 10 genes showing significantly changed expression. Upregulation of the lactococcal oligopeptide uptake (
opp
) system was observed, which was likely linked to a higher nitrogen demand required for Lcn972 biosynthesis. Strikingly,
celB
, coding for the membrane porter IIC of the cellobiose phosphoenolpyruvate-dependent phosphotransferase system (PTS), and the upstream gene
llmg0186
were downregulated. Growth profiles for
L. lactis
strains MG1363, MG1363/pBL1, and MG1363 Δ
celB
grown in chemically defined medium (CDM) containing cellobiose confirmed slower growth of MG1363/pBL1 and MG1363 Δ
celB
, while no differences were observed with growth on glucose. The presence of pBL1 shifted the fermentation products toward a mixed acid profile and promoted substantial changes in intracellular pool sizes for glycolytic intermediates in cells growing on cellobiose as determined by high-pressure liquid chromatography (HPLC) and nuclear magnetic resonance (NMR). Overall, these data support the genetic evidence of a constriction in cellobiose uptake. Notably, several cell wall precursors accumulated, while other UDP-activated sugar pools were lower, which could reflect rerouting of precursors toward the production of structural or storage polysaccharides. Moreover, cells growing slowly on cellobiose and those lacking
celB
were more tolerant to Lcn972 than cellobiose-adapted cells. Thus, downregulation of
celB
could help to build up a response against the antimicrobial activity of Lcn972, enhancing self-immunity of the producer cells.
Expression of Biomass-Degrading Enzymes Is a Major Event during Conidium Development in Trichoderma reesei
Authors: Metz Benjamin , Seidl-Seiboth Verena , Haarmann Thomas , Kopchinskiy Alexeij , Lorenz Patrick , Seiboth Bernhard , Kubicek Christian P. 
Published: September 2011

ABSTRACT

The conidium plays a critical role in the life cycle of many filamentous fungi, being the primary means for survival under unfavorable conditions. To investigate the transcriptional changes taking place during the transition from growing hyphae to conidia in
Trichoderma reesei
, microarray experiments were performed. A total of 900 distinct genes were classified as differentially expressed, relative to their expression at time zero of conidiation, at least at one of the time points analyzed. The main functional categories (FunCat) overrepresented among the upregulated genes were those involving solute transport, metabolism, transcriptional regulation, secondary metabolite synthesis, lipases, proteases, and, particularly, cellulases and hemicellulases. Categories overrepresented among the downregulated genes were especially those associated with ribosomal and mitochondrial functions. The upregulation of cellulase and hemicellulase genes was dependent on the function of the positive transcriptional regulator XYR1, but XYR1 exerted no influence on conidiation itself. At least 20% of the significantly regulated genes were nonrandomly distributed within the
T. reesei
genome, suggesting an epigenetic component in the regulation of conidiation. The significant upregulation of cellulases and hemicellulases during this process, and thus cellulase and hemicellulase content in the spores of
T. reesei
, contributes to the hypothesis that the ability to hydrolyze plant biomass is a major trait of this fungus enabling it to break dormancy and reinitiate vegetative growth after a period of facing unfavorable conditions.
Protein Phosphatase Pph3 and Its Regulatory Subunit Psy2 Regulate Rad53 Dephosphorylation and Cell Morphogenesis during Recovery from DNA Damage in Candida albicans
Authors: Sun Ling Ling , Li Wan Jie , Wang Hai Tao , Chen Jie , Deng Ping , Wang Yue , Sang Jian Li 
Published: September 2011

ABSTRACT

The ability of the pathogenic fungus
Candida albicans
to switch cellular morphologies is important for infection and virulence. Recent studies have revealed that
C. albicans
yeast cells can switch to filamentous growth under genotoxic stress in a manner dependent on the DNA replication/damage checkpoint. Here, we have investigated the functions of Pph3 (orf19.4378) and Psy2 (orf19.3685), whose orthologues in
Saccharomyces cerevisiae
mediate the dephosphorylation of the DNA damage checkpoint kinase Rad53 and the histone variant H2AX during recovery from DNA damage. Deleting
PPH3
or
PSY2
causes hypersensitivity to DNA-damaging agents, including cisplatin, methylmethane sulfonate (MMS), and UV light. In addition,
pph3
Δ and
psy2
Δ cells exhibit strong filamentous growth under genotoxic stress. Flow cytometry analysis shows that the mutant cells have lost the ability to adapt to genotoxic stress and remain arrested even after the stress is withdrawn. Furthermore, we show that Pph3 and Psy2 are required for the dephosphorylation of Rad53, but not H2AX, during DNA damage recovery. Taken together, these results show that
C. albicans
Pph3 and Psy2 have important roles in mediating genotoxin-induced filamentous growth and regulating Rad53 dephosphorylation.
RAS/Cyclic AMP and Transcription Factor Msn2 Regulate Mating and Mating-Type Switching in the Yeast Kluyveromyces lactis
Authors: Barsoum E. , Rajaei N. , Åström S. U. 
Published: September 2011

ABSTRACT

In response to harsh environmental conditions, ascomycetes produce stress-resistant spores to promote survival. As sporulation requires a diploid DNA content, species with a haploid lifestyle, such as
Kluyveromyces lactis
, first induce mating in response to stress. In
K. lactis
, mating and mating-type switching are induced by the DNA-binding protein Mts1. Mts1 expression is known to be upregulated by nutrient limitation, but the mechanism is unknown. We show that a
ras2
mutation results in a hyperswitching phenotype. In contrast, strains lacking the phosphodiesterase Pde2 had lower switching rates compared to that of the wild type (WT). As Ras2 promotes cyclic AMP (cAMP) production and Pde2 degrades cAMP, these data suggest that low cAMP levels induce switching. Because the
MTS1
regulatory region contains several Msn2 binding sites and Msn2 is a transcription factor that is activated by low cAMP levels, we investigated if Msn2 regulates
MTS1
transcription. Consistently with this idea, an
msn2
mutant strain displayed lower switching rates than the WT strain. The transcription of
MTS1
is highly induced in the
ras2
mutant strain. In contrast, an
msn2 ras2
double mutant strain displays WT levels of the
MTS1
transcript, showing that Msn2 is a critical inducer of
MTS1
transcription. Strains lacking Msn2 and Pde2 also exhibit mating defects that can be complemented by the ectopic expression of Mts1. Finally, we show that
MTS1
is subjected to negative autoregulation, presumably adding robustness to the mating and switching responses. We suggest a model in which Ras2/cAMP/Msn2 mediates the stress-induced mating and mating-type switching responses in
K. lactis
.
Zap1 Control of Cell-Cell Signaling in Candida albicans Biofilms
Authors: Ganguly Shantanu , Bishop Andrew C. , Xu Wenjie , Ghosh Suman , Nickerson Kenneth W. , Lanni Frederick , Patton-Vogt Jana , Mitchell Aaron P. 
Published: September 2011

ABSTRACT

Biofilms of
Candida albicans
include both yeast cells and hyphae. Prior studies indicated that a
zap1
Δ/Δ mutant, defective in zinc regulator Zap1, has increased accumulation of yeast cells in biofilms. This altered yeast-hypha balance may arise from internal regulatory alterations or from an effect on the production of diffusible quorum-sensing (QS) molecules. Here, we develop biosensor reporter strains that express yeast-specific
YWP1-RFP
or hypha-specific
HWP1-RFP
, along with a constitutive
TDH3-GFP
normalization standard. Seeding these biosensor strains into biofilms allows a biological activity assay of the surrounding biofilm milieu. A
zap1
Δ/Δ biofilm induces the yeast-specific
YWP1-RFP
reporter in a wild-type biosensor strain, as determined by both quantitative reverse transcription-PCR (qRT-PCR) gene expression measurements and confocal microscopy. Remediation of the
zap1
Δ/Δ zinc uptake defect through zinc transporter gene
ZRT2
overexpression reverses induction of the yeast-specific
YWP1-RFP
reporter. Gas chromatography-mass spectrometry (GC-MS) measurements of known organic QS molecules show that the
zap1
Δ/Δ mutant accumulates significantly less farnesol than wild-type or complemented strains and that
ZRT2
overexpression does not affect farnesol accumulation. Farnesol is a well-characterized inhibitor of hypha formation; hence, a reduction in farnesol levels in
zap1
Δ/Δ biofilms is unexpected. Our findings argue that a Zap1- and zinc-dependent signal affects the yeast-hypha balance and that it is operative in the low-farnesol environment of the
zap1
Δ/Δ biofilm. In addition, our results indicate that Zap1 is a positive regulator of farnesol accumulation.
Adjusting the Spokes of the Flagellar Motor with the DNA-Binding Protein H-NS
Authors: Paul Koushik , Carlquist William C. , Blair David F. 
Published: September 2011

ABSTRACT
The H-NS protein of bacteria is a global regulator that stimulates transcription of flagellar genes and that also acts directly to modulate flagellar motor function. H-NS is known to bind FliG, a protein of the rotor that interacts with the stator and is directly involved in rotation of the motor. Here, we find that H-NS, well known for its ability to organize DNA, acts in the flagellar motor to organize protein subunits in the rotor. It binds to a middle domain of FliG that bridges the core parts of the rotor and parts nearer the edge that interact with the stator. In the absence of H-NS the organization of FliG subunits is disrupted, whereas overexpression of H-NS enhances FliG organization as monitored by targeted disulfide cross-linking, alters the disposition of a helix joining the middle and C-terminal domains of FliG, and enhances motor performance under conditions requiring a strengthened rotor-stator interface. The H-NS homolog StpA was also shown to bind FliG and to act similarly, though less effectively, in organizing FliG. The motility-enhancing effects of H-NS contrast with those of the recently characterized motility inhibitor YcgR. The present findings provide an integrated, structurally grounded framework for understanding the roughly opposing effects of these motility regulators.
Mutations in Genes
patA
and
patL
of Anabaena sp. Strain PCC 7120 Result in Similar Phenotypes, and the Proteins Encoded by Those Genes May Interact
Authors: Liu Jinjie , Wolk C. Peter 
Published: September 2011

ABSTRACT

PatA resembles a response regulator protein with a defective DNA-binding domain, and PatL (All3305) is a pentapeptide repeat protein. A yeast two-hybrid library identified PatL as a protein with which PatA may interact. Heterocysts of
patA
and
patL Anabaena
sp. form nearly exclusively terminally in long filaments, further linking the genes.
The Opportunistic Pathogen Serratia marcescens Utilizes Type VI Secretion To Target Bacterial Competitors
Authors: Murdoch Sarah L. , Trunk Katharina , English Grant , Fritsch Maximilian J. , Pourkarimi Ehsan , Coulthurst Sarah J. 
Published: September 2011

ABSTRACT

The type VI secretion system (T6SS) is the most recently described and least understood of the protein secretion systems of Gram-negative bacteria. It is widely distributed and has been implicated in the virulence of various pathogens, but its mechanism and exact mode of action remain to be defined. Additionally there have been several very recent reports that some T6SSs can target bacteria rather than eukaryotic cells.
Serratia marcescens
is an opportunistic enteric pathogen, a class of bacteria responsible for a significant proportion of hospital-acquired infections. We describe the identification of a functional T6SS in
S. marcescens
strain Db10, the first report of type VI secretion by an opportunist enteric bacterium. The T6SS of
S. marcescens
Db10 is active, with secretion of Hcp to the culture medium readily detected, and is expressed constitutively under normal growth conditions from a large transcriptional unit. Expression of the T6SS genes did not appear to be dependent on the integrity of the T6SS. The
S. marcescens
Db10 T6SS is not required for virulence in three nonmammalian virulence models. It does, however, exhibit dramatic antibacterial killing activity against several other bacterial species and is required for
S. marcescens
to persist in a mixed culture with another opportunist pathogen,
Enterobacter cloacae
. Importantly, this antibacterial killing activity is highly strain specific, with the
S. marcescens
Db10 T6SS being highly effective against another strain of
S. marcescens
with a very similar and active T6SS. We conclude that type VI secretion plays a crucial role in the competitiveness, and thus indirectly the virulence, of
S. marcescens
and other opportunistic bacterial pathogens.
Genetic Analysis of
SCO2997
, Encoding a TagF Homologue, Indicates a Role for Wall Teichoic Acids in Sporulation of Streptomyces coelicolor A3(2)
Authors: Kleinschnitz Eva-Maria , Latus Annette , Sigle Steffen , Maldener Iris , Wohlleben Wolfgang , Muth Günther 
Published: September 2011

ABSTRACT

Streptomyces coelicolor
contains two gene clusters putatively involved in wall teichoic acid biosynthesis. Inactivation of the
tagF
homologue
SCO2997
or
SCO2584
, a component of the
Streptomyces
spore wall synthesizing complex, affected sporulation. The mutant phenotypes resembled those of
mre
mutants, suggesting a function of wall teichoic acids in the differentiation of
Streptomyces
.
Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli
Authors: Marbaniang Carmelita N. , Gowrishankar J. 
Published: September 2011

ABSTRACT

Initially identified as an inhibitor of
oriC
-initiated DNA replication
in vitro
, the ArgP or IciA protein of
Escherichia coli
has subsequently been described as a nucleoid-associated protein and also as a transcriptional regulator of genes involved in DNA replication (
dnaA
and
nrdA
) and amino acid metabolism (
argO
,
dapB
, and
gdhA
[the last in
Klebsiella pneumoniae
]). ArgP mediates lysine (Lys) repression of
argO
,
dapB
, and
gdhA
in vivo
, for which two alternative mechanisms have been identified: at the
dapB
and
gdhA
regulatory regions, ArgP binding is reduced upon the addition of Lys, whereas at
argO
, RNA polymerase is trapped at the step of promoter clearance by Lys-bound ArgP. In this study, we have examined promoter-
lac
fusions in strains that were
argP
+
or Δ
argP
or that were carrying dominant
argP
mutations in order to identify several new genes that are ArgP-regulated
in vivo
, including
lysP
,
lysC
,
lysA
,
dapD
, and
asd
(in addition to
argO
,
dapB
, and
gdhA
). All were repressed upon Lys supplementation, and
in vitro
studies demonstrated that ArgP binds to the corresponding regulatory regions in a Lys-sensitive manner (with the exception of
argO
, whose binding to ArgP was Lys insensitive). Neither
dnaA
nor
nrdA
was ArgP regulated
in vivo
, although their regulatory regions exhibited low-affinity binding to ArgP. Our results suggest that ArgP is a transcriptional regulator for Lys repression of genes in
E. coli
but that it is noncanonical in that it also exhibits low-affinity binding, without apparent direct regulatory effect, to a number of additional sites in the genome.
How do centres begin the process to prevent contrast-induced acute kidney injury: a report from a new regional collaborative
Authors: Brown Jeremiah R , McCullough Peter A , Splaine Mark E , Davies Louise , Ross Cathy S , Dauerman Harold L , Robb John F , Boss Richard , Goldberg David J , Fedele Frank A , Kellett Mirle A , Phillips William J , Ver Lee Peter N , Nelson Eugene C , MacKenzie Todd A , O'Connor Gerald T , Sarnak Mark J , Malenka David J ,   for the Northern New England Cardiovascular Disease Study Group
Published: September 2011

ObjectivesThis study evaluates the variation in practice patterns associated with contrast-induced acute kidney injury (CI-AKI) and identifies clinical practices that have been associated with a reduction in CI-AKI.BackgroundCI-AKI is recognised as a complication of invasive cardiovascular procedures and is associated with cardiovascular events, prolonged hospitalisation, end-stage renal disease, and all-cause mortality. Reducing the risk of CI-AKI is a patient safety objective set by the National Quality Forum.MethodsThis study prospectively collected quantitative and qualitative data from 10 centres, which participate in the Northern New England Cardiovascular Disease Study Group PCI Registry. Quantitative data were collected from the PCI Registry. Qualitative data were obtained through clinical team meetings to map care processes related to CI-AKI and focus groups to understand attitudes towards CI-AKI prophylaxis. Fixed and random effects modelling were conducted to test the differences across centres.ResultsSignificant variation in rates of CI-AKI were found across 10 medical centres. Both fixed effects and mixed effects logistic regression demonstrated significant variability across centres, even after adjustment for baseline covariates (p<0.001 for both modelling approaches). Patterns were found in reported processes and clinical leadership that were attributable to centres with lower rates of CI-AKI. These included reducing nil by mouth (NPO) time to 4 h prior to case, and standardising volume administration protocols in combination with administering three to four high doses of N-acetylcysteine (1200 mg) for each patient.ConclusionsThese data suggest that clinical leadership and institution-focused efforts to standardise preventive practices can help reduce the incidence of CI-AKI.