bluuebunny/crossref_metadata_2025_split huggingface dataset:
Archaeal Populations in Hypersaline Sediments Underlying Orange Microbial Mats in the Napoli Mud Volcano
Authors: Lazar Cassandre Sara , L'Haridon Stéphane , Pignet Patricia , Toffin Laurent 
Published: February 2011

ABSTRACT

Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the “active” archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (
mcrA
) genes were affiliated with the anaerobic methanotrophic
Archaea
(ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic
Methanococcoides
in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano.
d
-2,3-Butanediol Production Due to Heterologous Expression of an Acetoin Reductase in Clostridium acetobutylicum
Authors: Siemerink Marco A. J. , Kuit Wouter , López Contreras Ana M. , Eggink Gerrit , van der Oost John , Kengen Servé W. M. 
Published: February 2011

ABSTRACT

Acetoin reductase (ACR) catalyzes the conversion of acetoin to 2,3-butanediol. Under certain conditions,
Clostridium acetobutylicum
ATCC 824 (and strains derived from it) generates both
d
- and
l
-stereoisomers of acetoin, but because of the absence of an ACR enzyme, it does not produce 2,3-butanediol. A gene encoding ACR from
Clostridium beijerinckii
NCIMB 8052 was functionally expressed in
C. acetobutylicum
under the control of two strong promoters, the constitutive
thl
promoter and the late exponential
adc
promoter. Both ACR-overproducing strains were grown in batch cultures, during which 89 to 90% of the natively produced acetoin was converted to 20 to 22 mM
d
-2,3-butanediol. The addition of a racemic mixture of acetoin led to the production of both
d
-2,3-butanediol and
meso
-2,3-butanediol. A metabolic network that is in agreement with the experimental data is proposed. Native 2,3-butanediol production is a first step toward a potential homofermentative 2-butanol-producing strain of
C. acetobutylicum
.
Acid Stress-Mediated Metabolic Shift in Lactobacillus sanfranciscensis LSCE1
Authors: Serrazanetti Diana I. , Ndagijimana Maurice , Sado-Kamdem Sylvain L. , Corsetti Aldo , Vogel Rudi F. , Ehrmann Matthias , Guerzoni M. Elisabetta 
Published: February 2011

ABSTRACT

Lactobacillus sanfranciscensis
LSCE1 was selected as a target organism originating from recurrently refreshed sourdough to study the metabolic rerouting associated with the acid stress exposure during sourdough fermentation. In particular, the acid stress induced a metabolic shift toward overproduction of 3-methylbutanoic and 2-methylbutanoic acids accompanied by reduced sugar consumption and primary carbohydrate metabolite production. The fate of labeled leucine, the role of different nutrients and precursors, and the expression of the genes involved in branched-chain amino acid (BCAA) catabolism were evaluated at pH 3.6 and 5.8. The novel application of the program XCMS to the solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) data allowed accurate separation and quantification of 2-methylbutanoic and 3-methylbutanoic acids, generally reported as a cumulative datum. The metabolites coming from BCAA catabolism increased up to seven times under acid stress. The gene expression analysis confirmed that some genes associated with BCAA catabolism were overexpressed under acid conditions. The experiment with labeled leucine showed that 2-methylbutanoic acid originated also from leucine. While the overproduction of 3-methylbutanoic acid under acid stress can be attributed to the need to maintain redox balance, the rationale for the production of 2-methylbutanoic acid from leucine can be found in a newly proposed biosynthesis pathway leading to 2-methylbutanoic acid and 3 mol of ATP per mol of leucine. Leucine catabolism to 3-methylbutanoic and 2-methylbutanoic acids suggests that the switch from sugar to amino acid catabolism supports growth in
L. sanfranciscensis
in restricted environments such as sourdough characterized by acid stress and recurrent carbon starvation.
Genomic Potential of Marinobacter aquaeolei, a Biogeochemical “Opportunitroph”
Authors: Singer Esther , Webb Eric A. , Nelson William C. , Heidelberg John F. , Ivanova Natalia , Pati Amrita , Edwards Katrina J. 
Published: February 2011

ABSTRACT

The genus of
Marinobacter
is one of the most ubiquitous in the global oceans and assumed to significantly impact various biogeochemical cycles. The genome structure and content of
Marinobacter aquaeolei
VT8 was analyzed and compared with those from other organisms with diverse adaptive strategies. Here, we report the many “opportunitrophic” genetic characteristics and strategies that
M. aquaeolei
has adopted to promote survival under various environmental conditions. Genome analysis revealed its metabolic potential to utilize oxygen and nitrate as terminal electron acceptors, iron as an electron donor, and urea, phosphonate, and various hydrocarbons as alternative N, P, and C sources, respectively. Miscellaneous sensory and defense mechanisms, apparently acquired via horizontal gene transfer, are involved in the perception of environmental fluctuations and antibiotic, phage, toxin, and heavy metal resistance, enabling survival under adverse conditions, such as oil-polluted water. Multiple putative integrases, transposases, and plasmids appear to have introduced additional metabolic potential, such as phosphonate degradation. The genomic potential of
M. aquaeolei
and its similarity to other opportunitrophs are consistent with its cosmopolitan occurrence in diverse environments and highly variable lifestyles.
Biofilm Formation by and Thermal Niche and Virulence Characteristics of Escherichia spp
Authors: Ingle Danielle J. , Clermont Olivier , Skurnik David , Denamur Erick , Walk Seth T. , Gordon David M. 
Published: February 2011

ABSTRACT

In order to better understand the ecological and virulence characteristics of the various clades of
Escherichia
,
in vitro
and
in vivo
experiments were undertaken. Members of the recently described cryptic clades of
Escherichia
(clades III, IV, and V) were found to have an enhanced ability to form biofilms compared to strains of
Escherichia coli
,
E. fergusonii
, or
E. albertii
. Members of the cryptic clades were also able to replicate at a lower temperature (5°C versus 11°C) than strains of the named species of
Escherichia
. Neither a strain's maximal growth rate nor its optimal temperature for growth varied with respect to the strain's phylogenetic affiliation.
Escherichia
strains not belonging to the species
E. coli
were positive for a mix of traits thought to enhance a strain's ability to cause either intestinal or extraintestinal disease. However, no non-
E. coli
Escherichia
strain was virulent in a mouse model of extraintestinal infection. The frequency of resistance to antibiotics was low, and none of the strains tested harbored class 1, 2, or 3 integrons. The results of these experiments support the hypothesis that members of the cryptic
Escherichia
clades may be better able to persist in the external environment compared to
E. coli
,
E. fergusonii
, or
E. albertii
, isolates.
Influence of Temperature and Backslopping Time on the Microbiota of a Type I Propagated Laboratory Wheat Sourdough Fermentation
Authors: Vrancken Gino , Rimaux Tom , Weckx Stefan , Leroy Frédéric , De Vuyst Luc 
Published: February 2011

ABSTRACTSourdough fermentation is a cereal fermentation that is characterized by the formation of stable yeast/lactic acid bacteria (LAB) associations. It is a unique process among food fermentations in that the LAB that mostly dominate these fermentations are heterofermentative. In the present study, four wheat sourdough fermentations were carried out under different conditions of temperature and backslopping time to determine their effect on the composition of the microbiota of the final sourdoughs. A substantial effect of temperature was observed. A fermentation with 10 backsloppings (once every 24 h) at 23°C resulted in a microbiota composed ofLeuconostoc citreumas the dominant species, whereas fermentations at 30 and 37°C with backslopping every 24 h resulted in ecosystems dominated byLactobacillus fermentum. Longer backslopping times (every 48 h at 30°C) resulted in a combination ofLactobacillus fermentumandLactobacillus plantarum. Residual maltose remained present in all fermentations, except those with longer backslopping times, and ornithine was found in almost all fermentations, indicating enhanced sourdough-typical LAB activity. The sourdough-typical speciesLactobacillus sanfranciscensiswas not found. Finally, a nonflour origin for this species was hypothesized.
Screening for Antimicrobial Resistance Genes and Virulence Factors via Genome Sequencing
Authors: Bennedsen Mads , Stuer-Lauridsen Birgitte , Danielsen Morten , Johansen Eric 
Published: February 2011

ABSTRACT

Second-generation genome sequencing and alignment of the resulting reads to
in silico
genomes containing antimicrobial resistance and virulence factor genes were used to screen for undesirable genes in 28 strains which could be used in human nutrition. No virulence factor genes were detected, while several isolates contained antimicrobial resistance genes.
Activity and Diversity of Methanotrophic Bacteria at Methane Seeps in Eastern Lake Constance Sediments
Authors: Deutzmann Jörg S. , Wörner Susanne , Schink Bernhard 
Published: February 2011

ABSTRACT

The activity and community structure of aerobic methanotrophic communities were investigated at methane seeps (pockmarks) in the littoral and profundal zones of an oligotrophic freshwater lake (Lake Constance, Germany). Measurements of potential methane oxidation rates showed that sediments inside littoral pockmarks are hot spots of methane oxidation. Potential methane oxidation rates at littoral pockmark sites exceeded the rates of the surrounding sediment by 2 orders of magnitude. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the
pmoA
gene revealed major differences in the methanotrophic community composition between littoral pockmarks and the surrounding sediments. Clone library analysis confirmed that one distinct
Methylobacter
-related group dominates the community at littoral pockmarks. In profundal sediments, the differences between pockmarks and surrounding sediments were found to be less pronounced.
Evolution of Mating within the Candida parapsilosis Species Group
Authors: Sai Sixiang , Holland Linda M. , McGee Conor F. , Lynch Denise B. , Butler Geraldine 
Published: February 2011

ABSTRACT

Candida orthopsilosis
and
Candida metapsilosis
are closely related to
Candida parapsilosis
, a major cause of infection in premature neonates. Mating has not been observed in these species. We show that ∼190 isolates of
C. parapsilosis
contain only an
MTL
a
idiomorph at the mating-type-like locus. Here, we describe the isolation and characterization of the
MTL
loci from
C. orthopsilosis
and
C. metapsilosis
. Among 16
C. orthopsilosis
isolates, 9 were homozygous for
MTL
a
, 5 were homozygous for
MTL
α, and 2 were
MTL
a
/α heterozygotes. The
C. orthopsilosis
isolates belonged to two divergent groups, as characterized by restriction patterns at
MTL
, which probably represent subspecies. We sequenced both idiomorphs from each group and showed that they are 95% identical and that the regulatory genes are intact. In contrast, 18 isolates of
C. metapsilosis
contain only
MTL
α idiomorphs. Our results suggest that the role of
MTL
in determining cell type is being eroded in the
C. parapsilosis
species complex. The population structure of
C. orthopsilosis
indicates that mating may occur. However, expression of genes in the mating signal transduction pathway does not respond to exposure to alpha factor.
C. parapsilosis
is also nonresponsive, even when the GTPase-activating protein gene
SST2
is deleted. In addition, splicing of introns in
MTL
a
1
and
MTL
a
2
is defective in
C. orthopsilosis
. Mating is not detected. The alpha factor peptide, which is the same sequence in
C. parapsilosis
,
C. orthopsilosis
, and
C. metapsilosis
, can induce a mating response in
Candida albicans
. It is therefore likely either that mating of
C. orthopsilosis
takes place under certain unidentified conditions or that the mating pathway has been adapted for other functions, such as cross-species communication.
Degeneration in Codon Usage within the Region of Suppressed Recombination in the Mating-Type Chromosomes of Neurospora tetrasperma
Authors: Whittle C. A. , Sun Y. , Johannesson H. 
Published: February 2011

ABSTRACT

The origin and early evolution of sex chromosomes are currently poorly understood. The
Neurospora tetrasperma
mating-type (
mat
) chromosomes have recently emerged as a model system for the study of early sex chromosome evolution, since they contain a young (<6 million years ago [Mya]), large (>6.6-Mb) region of suppressed recombination. Here we examined preferred-codon usage in 290 genes (121,831 codon positions) in order to test for early signs of genomic degeneration in
N. tetrasperma
mat
chromosomes. We report several key findings about codon usage in the region of recombination suppression, including the following: (i) this region has been subjected to marked and largely independent degeneration among gene alleles; (ii) the level of degeneration is magnified over longer periods of recombination suppression; and (iii) both
mat a
and
mat A
chromosomes have been subjected to deterioration. The frequency of shifts from preferred codons to nonpreferred codons is greater for shorter genes than for longer genes, suggesting that short genes play an especially significant role in early sex chromosome evolution. Furthermore, we show that these degenerative changes in codon usage are best explained by altered selection efficiency in the recombinationally suppressed region. These findings demonstrate that the fungus
N. tetrasperma
provides an effective system for the study of degenerative genomic changes in young regions of recombination suppression in sex-regulating chromosomes.
The Gα Subunit Signals through the Ste50 Protein during the Mating Pheromone Response in the Yeast Kluyveromyces lactis
Authors: Sánchez-Paredes Edith , Kawasaki Laura , Ongay-Larios Laura , Coria Roberto 
Published: February 2011

ABSTRACT

Yeast mating signal transduction pathways require a heterotrimeric G protein composed of Gα, Gβ, and Gγ subunits connected to a mitogen-activated protein kinase (MAPK) module. While in
Saccharomyces cerevisiae
elimination of Gα induces constitutive activation of the mating pathway, in
Kluyveromyces lactis
it produces partial sterility, which indicates that
K. lactis
Gα (KlGα) is required to positively activate mating. We use physical interaction experiments to determine that KlGα interacts with the adaptor protein KlSte50p. The Ras association (RA) domain of KlSte50p favored interaction with the GDP-bound KlGα subunit, and when the KlGα protein is constitutively activated, the interaction drops significantly. Additionally, KlSte50p strongly associates with the MAPK kinase kinase (MAPKKK) KlSte11p through its sterile alpha motif (SAM) domain. Genetic experiments placed KlSte50p downstream of the G protein α subunit, indicating that KlGα may stimulate the mating pathway via KlSte50p. Fusion of KlSte50p to the KlGβ subunit partially eliminated the requirement of KlGα for mating, indicating that one contribution of KlGα to the mating pathway is to facilitate plasma membrane anchoring of KlSte50p.
Sch9 Kinase Integrates Hypoxia and CO
2
Sensing To Suppress Hyphal Morphogenesis in Candida albicans
Authors: Stichternoth Catrin , Fraund Alida , Setiadi Eleonora , Giasson Luc , Vecchiarelli Anna , Ernst Joachim F. 
Published: February 2011

ABSTRACT

The yeast-hypha transition is an important virulence trait of
Candida albicans
. We report that the AGC kinase Sch9 prevents hypha formation specifically under hypoxia at high CO
2
levels.
sch9
mutants showed no major defects in growth and stress resistance but a striking hyperfilamentous phenotype under hypoxia (<10% O
2
), although only in the presence of elevated CO
2
levels (>1%) and at temperatures of <37°C during surface growth. The
sch9
hyperfilamentous phenotype was independent of Rim15 kinase and was recreated by inhibition of Tor1 kinase by rapamycin or caffeine in a wild-type strain, suggesting that Sch9 suppression requires Tor1. Caffeine inhibition also revealed that both protein kinase A isoforms, as well as transcription factors Czf1 and Ace2, are required to generate the
sch9
mutant phenotype. Transcriptomal analyses showed that Sch9 regulates most genes solely under hypoxia and in the presence of elevated CO
2
. In this environment, Sch9 downregulates genes encoding cell wall proteins and nutrient transporters, while under normoxia Sch9 and Tor1 coregulate a minor fraction of Sch9-regulated genes, e.g., by inducing glycolytic genes. Other than in
Saccharomyces cerevisiae
, both
sch9
and
rim15
mutants showed decreased chronological aging under normoxia but not under hypoxia, indicating significant rewiring of the Tor1-Sch9-Rim15 pathway in
C. albicans
. The results stress the importance of environmental conditions on Sch9 function and establish a novel response circuitry to both hypoxia and CO
2
in
C. albicans
, which suppresses hypha formation but also allows efficient nutrient uptake, metabolism, and virulence.
Organic Hydroperoxide Resistance Protein and Ergothioneine Compensate for Loss of Mycothiol in Mycobacterium smegmatis Mutants
Authors: Ta Philong , Buchmeier Nancy , Newton Gerald L. , Rawat Mamta , Fahey Robert C. 
Published: February 2011

ABSTRACT

The
mshA
::Tn
5
mutant of
Mycobacterium smegmatis
does not produce mycothiol (MSH) and was found to markedly overproduce both ergothioneine and an ∼15-kDa protein determined to be organic hydroperoxide resistance protein (Ohr). An
mshA
(
G32D
) mutant lacking MSH overproduced ergothioneine but not Ohr. Comparison of the mutant phenotypes with those of the wild-type strain indicated the following: Ohr protects against organic hydroperoxide toxicity, whereas ergothioneine does not; an additional MSH-dependent organic hydroperoxide peroxidase exists; and elevated isoniazid resistance in the mutant is associated with both Ohr and the absence of MSH. Purified Ohr showed high activity with linoleic acid hydroperoxide, indicating lipid hydroperoxides as the likely physiologic targets. The reduction of oxidized Ohr by NADH was shown to be catalyzed by lipoamide dehydrogenase and either lipoamide or DlaT (SucB). Since free lipoamide and lipoic acid levels were shown to be undetectable in
M. smegmatis
, the bound lipoyl residues of DlaT are the likely source of the physiological dithiol reductant for Ohr. The pattern of occurrence of homologs of Ohr among bacteria suggests that the
ohr
gene has been distributed by lateral transfer. The finding of multiple Ohr homologs with various sequence identities in some bacterial genomes indicates that there may be multiple physiologic targets for Ohr proteins.
Insight into Bacterial Phosphotransferase System-Mediated Signaling by Interspecies Transplantation of a Transcriptional Regulator
Authors: Bahr Thomas , Lüttmann Denise , März Walter , Rak Bodo , Görke Boris 
Published: February 2011

ABSTRACT

The bacterial sugar:phosphotransferase system (PTS) delivers phosphoryl groups via proteins EI and HPr to the EII sugar transporters. The antitermination protein LicT controls β-glucoside utilization in
Bacillus subtilis
and belongs to a family of bacterial transcriptional regulators that are antagonistically controlled by PTS-catalyzed phosphorylations at two homologous PTS regulation domains (PRDs). LicT is inhibited by phosphorylation of PRD1, which is mediated by the β-glucoside transporter EII
Bgl
. Phosphorylation of PRD2 is catalyzed by HPr and stimulates LicT activity. Here, we report that LicT, when artificially expressed in the nonrelated bacterium
Escherichia coli
, is likewise phosphorylated at both PRDs, but the phosphoryl group donors differ. Surprisingly,
E. coli
HPr phosphorylates PRD1 rather than PRD2, while the stimulatory phosphorylation of PRD2 is carried out by the HPr homolog NPr. This demonstrates that subtle differences in the interaction surface of HPr can switch its affinities toward the PRDs. NPr transfers phosphoryl groups from EI
Ntr
to EIIA
Ntr
. Together these proteins form the paralogous PTS
Ntr
, which controls the activity of K
+
transporters in response to unknown signals. This is achieved by binding of dephosphorylated EIIA
Ntr
to other proteins. We generated LicT mutants that were controlled either negatively by HPr or positively by NPr and were suitable bio-bricks, in order to monitor or to couple gene expression to the phosphorylation states of these two proteins. With the aid of these tools, we identified the stringent starvation protein SspA as a regulator of EIIA
Ntr
phosphorylation, indicating that PTS
Ntr
represents a stress-related system in
E. coli
.
Observations of caregiver supervision of children at beaches: identification of factors associated with high supervision
Authors: Petrass Lauren A , Blitvich Jennifer D , Finch Caroline F 
Published: February 2011

ObjectiveTo identify independent factors associated with caregiver supervision levels at beaches.MethodsChildren (aged 1–14 years) engaged in beach play and their caregivers were observed at Australian beaches during September–April, 2008/09. Caregiver, child, and environmental factor data were collected and recorded on a validated observation instrument. The main outcome of interest was a continuous measure of supervision. After adjusting for potential clustering by beach/state, multivariable linear regression was used to identify independent factors associated with caregiver supervision.ResultsFour independent predictors of supervision and one interaction effect (child age by the caregiver and child position on beach) were identified. Caregivers who were supervising from a different position to where the child was playing were less likely to provide high supervision, as were older caregivers (>35 years) compared to younger caregivers (≤34 years). Compared to children playing alone, children playing with one, or two or more others were less likely to receive high supervision, and children aged 1–4 years were likely to receive higher supervision than older children.ConclusionThis study provides new knowledge about underlying factors associated with the level of caregiver supervision in beach settings. Future studies should continue to explore independent predictors of supervision so that effective programmes, which focus on caregiver supervision, can be targeted to address poor supervision practices.