bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen Source-Dependent Capsule Induction in Human-Pathogenic Cryptococcus Species
Authors: Frazzitta Aubrey E. , Vora Haily , Price Michael S. , Tenor Jennifer L. , Betancourt-Quiroz Marisol , Toffaletti Dena L. , Cheng Nan , Perfect John R. 
Published: August 2013

ABSTRACT

Cryptococcus neoformans
and
C. gattii
cause meningoencephalitis and are an increasing human health threat. These pathogenic
Cryptococcus
species are neurotropic and persist in the cerebrospinal fluid (CSF) of the mammalian host during infection. In order to survive in the host, pathogenic fungi must procure nutrients, such as carbon and nitrogen, from the CSF. To enhance our understanding of nutrient acquisition during central nervous system infection by
Cryptococcus
species, we examined the utilization of nitrogen sources available in CSF. We screened for the growth and capsule production of 817 global environmental and clinical isolates on various sources of nitrogen. Both environmental and clinical strains grew robustly on uric acid, Casamino Acids, creatinine, and asparagine as sole nitrogen sources. Urea induced the greatest magnitude of capsule induction. This induction was greater in
Cryptococcus gattii
than in
C. neoformans
. We confirmed the ability of nonpreferred nitrogen sources to increase capsule production in pathogenic species of
Cryptococcus
. Since urea is metabolized to ammonia and CO
2
(a known signal for capsule induction), we examined urea metabolism mutants for their transcriptional response to urea regarding capsule production. The transcriptional profile of
C. neoformans
under urea-supplemented conditions revealed both similar and unique responses to other capsule-inducing conditions, including both intra- and extracellular urea utilization. As one of the most abundant nitrogen sources in the CSF, the ability of
Cryptococcus
to import urea and induce capsule production may substantially aid this yeast's survival and propagation in the host.
The Function of the Na
+
-Driven Flagellum of Vibrio cholerae Is Determined by Osmolality and pH
Authors: Halang Petra , Leptihn Sebastian , Meier Thomas , Vorburger Thomas , Steuber Julia 
Published: August 2013

ABSTRACT

Vibrio cholerae
is motile by its polar flagellum, which is driven by a Na
+
-conducting motor. The stators of the motor, composed of four PomA and two PomB subunits, provide access for Na
+
to the torque-generating unit of the motor. To characterize the Na
+
pathway formed by the PomAB complex, we studied the influence of chloride salts (chaotropic, Na
+
, and K
+
) and pH on the motility of
V. cholerae
. Motility decreased at elevated pH but increased if a chaotropic chloride salt was added, which rules out a direct Na
+
and H
+
competition in the process of binding to the conserved PomB D23 residue. Cells expressing the PomB S26A/T or D42N variants lost motility at low Na
+
concentrations but regained motility in the presence of 170 mM chloride. Both PomA and PomB were modified by
N
,
N
′-dicyclohexylcarbodiimide (DCCD), indicating the presence of protonated carboxyl groups in the hydrophobic regions of the two proteins. Na
+
did not protect PomA and PomB from this modification. Our study shows that both osmolality and pH have an influence on the function of the flagellum from
V. cholerae
. We propose that D23, S26, and D42 of PomB are part of an ion-conducting pathway formed by the PomAB stator complex.
Roles of HynAB and Ech, the Only Two Hydrogenases Found in the Model Sulfate Reducer
Desulfovibrio gigas
Authors: Morais-Silva Fabio O. , Santos Catia I. , Rodrigues Rute , Pereira Inês A. C. , Rodrigues-Pousada Claudina 
Published: August 2013

ABSTRACT

Sulfate-reducing bacteria are characterized by a high number of hydrogenases, which have been proposed to contribute to the overall energy metabolism of the cell, but exactly in what role is not clear.
Desulfovibrio
spp. can produce or consume H
2
when growing on organic or inorganic substrates in the presence or absence of sulfate. Because of the presence of only two hydrogenases encoded in its genome, the periplasmic HynAB and cytoplasmic Ech hydrogenases,
Desulfovibrio gigas
is an excellent model organism for investigation of the specific function of each of these enzymes during growth. In this study, we analyzed the physiological response to the deletion of the genes that encode the two hydrogenases in
D. gigas
, through the generation of Δ
echBC
and Δ
hynAB
single mutant strains. These strains were analyzed for the ability to grow on different substrates, such as lactate, pyruvate, and hydrogen, under respiratory and fermentative conditions. Furthermore, the expression of both hydrogenase genes in the three strains studied was assessed through quantitative reverse transcription-PCR. The results demonstrate that neither hydrogenase is essential for growth on lactate-sulfate, indicating that hydrogen cycling is not indispensable. In addition, the periplasmic HynAB enzyme has a bifunctional activity and is required for growth on H
2
or by fermentation of pyruvate. Therefore, this enzyme seems to play a dominant role in
D. gigas
hydrogen metabolism.
Flexibility of Syntrophic Enzyme Systems in Desulfovibrio Species Ensures Their Adaptation Capability to Environmental Changes
Authors: Meyer Birte , Kuehl Jennifer V. , Deutschbauer Adam M. , Arkin Adam P. , Stahl David A. 
Published: August 2013

ABSTRACT

The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as
Desulfovibrio
. To evaluate the metabolic flexibility of syntrophic
Desulfovibrio
to adapt to naturally fluctuating methanogenic environments, we studied
Desulfovibrio alaskensis
strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners,
Methanococcus maripaludis
and
Methanospirillum hungatei
, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome
c
3
) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC
red
and Fd
red
, relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains
Desulfovibrio
in naturally fluctuating methanogenic environments.
Complementation of the F
o
c
Subunit of Escherichia coli with That of Streptococcus mutans and Properties of the Hybrid F
o
F
1
ATP Synthase
Authors: Araki Makoto , Hoshi Kazuya , Fujiwara Masasuke , Sasaki Yuka , Yonezawa Hideo , Senpuku Hidenobu , Iwamoto-Kihara Atsuko , Maeda Masatomo 
Published: August 2013

ABSTRACT

The
c
subunit of
Streptococcus mutans
ATP synthase (F
o
F
1
) is functionally exchangeable with that of
Escherichia coli
, since
E. coli
with a hybrid F
o
F
1
is able to grow on minimum succinate medium through oxidative phosphorylation.
E. coli
F
1
bound to the hybrid F
o
with the
S. mutans
c
subunit showed N,N′-dicyclohexylcarbodiimide-sensitive ATPase activity similar to that of
E. coli
F
o
F
1
. Thus, the
S. mutans
c
subunit assembled into a functional F
o
together with the
E. coli
a
and
b
subunits, forming a normal F
1
binding site. Although the H
+
pathway should be functional, as was suggested by the growth on minimum succinate medium, ATP-driven H
+
transport could not be detected with inverted membrane vesicles
in vitro
. This observation is partly explained by the presence of an acidic residue (Glu-20) in the first transmembrane helix of the
S. mutans
c
subunit, since the site-directed mutant carrying Gln-20 partly recovered the ATP-driven H
+
transport. Since
S. mutans
is recognized to be a primary etiological agent of human dental caries and is one cause of bacterial endocarditis, our system that expresses hybrid F
o
with the
S. mutans
c
subunit would be helpful to find antibiotics and chemicals specifically directed to
S. mutans
.
Measurements of mRNA Degradation in Borrelia burgdorferi
Authors: Archambault Linda , Borchert J. Simmons , Bergeron Jennifer , Snow Santina , Schlax Paula Jean 
Published: August 2013

ABSTRACT

The importance of gene regulation in the enzootic cycle of
Borrelia burgdorferi
, the spirochete that causes Lyme disease, is well established.
B. burgdorferi
regulates gene expression in response to changes in environmental stimuli associated with changing hosts. In this study, we monitored mRNA decay in
B. burgdorferi
following transcriptional arrest with actinomycin D. The time-dependent decay of transcripts encoding RNA polymerase subunits (
rpoA
and
rpoS
), ribosomal proteins (
rpsD
,
rpsK
,
rpsM
,
rplQ
, and
rpsO
), a nuclease (
pnp
), outer surface lipoproteins (
ospA
and
ospC
), and a flagellar protein (
flaB
) have different profiles and indicate half-lives ranging from approximately 1 min to more than 45 min in cells cultured at 35°C. Our results provide a first step in characterizing mRNA decay in
B. burgdorferi
and in investigating its role in gene expression and regulation.
Library Screen Identifies Enterococcus faecalis CcpA, the Catabolite Control Protein A, as an Effector of Ace, a Collagen Adhesion Protein Linked to Virulence
Authors: Gao Peng , Pinkston Kenneth L. , Bourgogne Agathe , Cruz Melissa R. , Garsin Danielle A. , Murray Barbara E. , Harvey Barrett R. 
Published: August 2013

ABSTRACT

The
Enterococcus faecalis
cell wall-anchored protein Ace is an important virulence factor involved in cell adhesion and infection. Expression of Ace on the cell surface is affected by many factors, including stage of growth, culture temperature, and environmental components, such as serum, urine, and collagen. However, the mechanisms that regulate or modulate Ace display are not well understood. With interest in identifying genes associated with Ace expression, we utilized a whole-cell enzyme-linked immunosorbent assay (ELISA)-based screening method to identify mutants from a transposon insertion mutant library which exhibited distinct Ace surface expression profiles. We identified a
ccpA
insertion mutant which showed significantly decreased levels of Ace surface expression at early growth phase versus those of wild-type OG1RF. Confirmation of the observation was achieved through flow cytometry and complementation analysis. Compared to the wild type, the
E. faecalis ccpA
mutant had an impaired ability to adhere to collagen when grown to early exponential phase, consistent with the lack of Ace expression in the early growth phase. As a key component of carbon catabolite regulation, CcpA has been previously reported to play a critical role in regulating expression of proteins involved in
E. faecalis
carbohydrate uptake and utilization. Our discovery is the first to associate CcpA with the production of a major
E. faecalis
virulence factor, providing new insights into the regulation of
E. faecalis
pathogenesis.
MacA, a Periplasmic Membrane Fusion Protein of the Macrolide Transporter MacAB-TolC, Binds Lipopolysaccharide Core Specifically and with High Affinity
Authors: Lu Shuo , Zgurskaya Helen I. 
Published: August 2013

ABSTRACT

The
Escherichia coli
MacAB-TolC transporter has been implicated in efflux of macrolide antibiotics and secretion of enterotoxin STII. In this study, we found that purified MacA, a periplasmic membrane fusion protein, contains one tightly bound rough core lipopolysaccharide (R-LPS) molecule per MacA molecule. R-LPS was bound specifically to MacA protein with affinity exceeding that of polymyxin B. Sequence analyses showed that MacA contains two high-density clusters of positively charged amino acid residues located in the cytoplasmic N-terminal domain and the periplasmic C-terminal domain. Substitutions in the C-terminal cluster reducing the positive-charge density completely abolished binding of R-LPS. At the same time, these substitutions significantly reduced the functionality of MacA in the protection of
E. coli
against macrolides
in vivo
and in the
in vitro
MacB ATPase stimulation assays. Taken together, our results suggest that R-LPS or a similar glycolipid is a physiological substrate of MacAB-TolC.
Pasteurella multocida Heddleston Serovar 3 and 4 Strains Share a Common Lipopolysaccharide Biosynthesis Locus but Display both Inter- and Intrastrain Lipopolysaccharide Heterogeneity
Authors: Harper Marina , St. Michael Frank , John Marietta , Vinogradov Evgeny , Steen Jennifer A. , van Dorsten Lieke , Steen Jason A. , Turni Conny , Blackall Patrick J. , Adler Ben , Cox Andrew D. , Boyce John D. 
Published: August 2013

ABSTRACT

Pasteurella multocida
is a Gram-negative multispecies pathogen and the causative agent of fowl cholera, a serious disease of poultry which can present in both acute and chronic forms. The major outer membrane component lipopolysaccharide (LPS) is both an important virulence factor and a major immunogen. Our previous studies determined the LPS structures expressed by different
P. multocida
strains and revealed that a number of strains belonging to different serovars contain the same LPS biosynthesis locus but express different LPS structures due to mutations within glycosyltransferase genes. In this study, we report the full LPS structure of the serovar 4 type strain, P1662, and reveal that it shares the same LPS outer core biosynthesis locus, L3, with the serovar 3 strains P1059 and Pm70. Using directed mutagenesis, the role of each glycosyltransferase gene in LPS outer core assembly was determined. LPS structural analysis of 23 Australian field isolates that contain the L3 locus revealed that at least six different LPS outer core structures can be produced as a result of mutations within the LPS glycosyltransferase genes. Moreover, some field isolates produce multiple but related LPS glycoforms simultaneously, and three LPS outer core structures are remarkably similar to the globo series of vertebrate glycosphingolipids. Our in-depth analysis showing the genetics and full range of
P. multocida
lipopolysaccharide structures will facilitate the improvement of typing systems and the prediction of the protective efficacy of vaccines.
Transposon Mutagenesis Identified Chromosomal and Plasmid Genes Essential for Adaptation of the Marine Bacterium Dinoroseobacter shibae to Anaerobic Conditions
Authors: Ebert Matthias , Laaß Sebastian , Burghartz Melanie , Petersen Jörn , Koßmehl Sebastian , Wöhlbrand Lars , Rabus Ralf , Wittmann Christoph , Tielen Petra , Jahn Dieter 
Published: August 2013

ABSTRACT

Anaerobic growth and survival are integral parts of the life cycle of many marine bacteria. To identify genes essential for the anoxic life of
Dinoroseobacter shibae
, a transposon library was screened for strains impaired in anaerobic denitrifying growth. Transposon insertions in 35 chromosomal and 18 plasmid genes were detected. The essential contribution of plasmid genes to anaerobic growth was confirmed with plasmid-cured
D. shibae
strains. A combined transcriptome and proteome approach identified oxygen tension-regulated genes. Transposon insertion sites of a total of 1,527 mutants without an anaerobic growth phenotype were determined to identify anaerobically induced but not essential genes. A surprisingly small overlap of only three genes (
napA
,
phaA
, and the Na
+
/P
i
antiporter gene Dshi_0543) between anaerobically essential and induced genes was found. Interestingly, transposon mutations in genes involved in dissimilatory and assimilatory nitrate reduction (
napA
,
nasA
) and corresponding cofactor biosynthesis (genomic
moaB
,
moeB
, and
dsbC
and plasmid-carried
dsbD
and
ccmH
) were found to cause anaerobic growth defects. In contrast, mutation of anaerobically induced genes encoding proteins required for the later denitrification steps (
nirS
,
nirJ
,
nosD
), dimethyl sulfoxide reduction (
dmsA1
), and fermentation (
pdhB1
,
arcA
,
aceE
,
pta
,
acs
) did not result in decreased anaerobic growth under the conditions tested. Additional essential components (ferredoxin,
cccA
) of the anaerobic electron transfer chain and central metabolism (
pdhB
) were identified. Another surprise was the importance of sodium gradient-dependent membrane processes and genomic rearrangements via viruses, transposons, and insertion sequence elements for anaerobic growth. These processes and the observed contributions of cell envelope restructuring (
lysM
,
mipA
,
fadK
), C4-dicarboxylate transport (
dctM1
,
dctM3
), and protease functions to anaerobic growth require further investigation to unravel the novel underlying adaptation strategies.
Breast milk and cognitive development—the role of confounders: a systematic review
Authors: Walfisch Asnat , Sermer Corey , Cressman Alex , Koren Gideon 
Published: August 2013

ObjectivesThe association between breastfeeding and child cognitive development is conflicted by studies reporting positive and null effects. This relationship may be confounded by factors associated with breastfeeding, specifically maternal socioeconomic class and IQ.DesignSystematic review of the literature.Setting and participantsAny prospective or retrospective study, in any language, evaluating the association between breastfeeding and cognitive development using a validated method in healthy term infants, children or adults, was included.Primary and secondary outcome measuresExtracted data included the study design, target population and sample size, breastfeeding exposure, cognitive development assessment tool used and participants’ age, summary of the results prior to, and following, adjustment for confounders, and all confounders adjusted for. Study quality was assessed as well.Results84 studies met our inclusion criteria (34 rated as high quality, 26 moderate and 24 low quality). Critical assessment of accepted studies revealed the following associations: 21 null, 28 positive, 18 null after adjusting for confounders and 17 positive—diminished after adjusting for confounders. Directionality of effect did not correlate with study quality; however, studies showing a decreased effect after multivariate analysis were of superior quality compared with other study groupings (14/17 high quality, 82%). Further, studies that showed null or diminished effect after multivariate analysis corrected for significantly more confounders (7.7±3.4) as compared with those that found no change following adjustment (5.6±4.5, p=0.04). The majority of included studies were carried out during childhood (75%) and set in high-income countries (85.5%).ConclusionsMuch of the reported effect of breastfeeding on child neurodevelopment is due to confounding. It is unlikely that additional work will change the current synthesis. Future studies should attempt to rigorously control for all important confounders. Alternatively, study designs using sibling cohorts discordant for breastfeeding may yield more robust conclusions.
Impact of the economic crisis on children's health in Catalonia: a before–after approach
Authors: Rajmil Luis , Medina-Bustos Antonia , Fernández de Sanmamed María-José , Mompart-Penina Anna 
Published: August 2013

ObjectivesTo analyse changes in the family living conditions of children in Catalonia between 2006 and the 2010–2012 period, and to study associations between these changes and health outcomes.DesignA before–after analysis of two cross-sectional surveys.SettingPopulation younger than 15 years of age from Catalonia, Spain.ParticipantsRepresentative samples of children in the 2006 Catalan Health Survey (ESCA), baseline, before the crisis; n=2200) and the first four waves of ESCA 2010–2012 (after start of the crisis, n=1967).Main outcome measuresOverweight/obesity, health behaviour, mental health and health-related quality of life (HRQOL). Logistic regression and multiple linear regression models were used to analyse the influence of changes in family conditions on outcome measures, including interaction terms to describe the potential influence of the study period on the results.ResultsThe percentage of unemployed families rose from 9.1% (2006) to 20.6% (2010–2012), with inequalities by level of education. Overweight/obesity increased from 18.4% (95% CI 16.5% to 20.4%) to 26.9% (24.6% to 29.2%) in 2010–2012, and inequalities related to maternal education and employment status persisted. Eating habits have improved in 2010–2012 in disadvantaged families (ie, junk food consumption improved in families with a maternal primary education level; beta (B)=2.85; 0.83 to 4.88, for the survey interaction by primary education level). An improvement in HRQOL was found in the second survey (B=6.07; 4.15 to 7.99), although children whose mothers had a primary education showed poorer HRQOL scores in this survey than in 2006 (B=−4.14; −7.17 to −1.12).ConclusionsAlthough some health-related behaviour improved during the study period, childhood obesity increased and inequalities in HRQOL appeared. Policy measures that fight against these inequalities should be urgently implemented to avoid their negative impact on the health of future generations of Catalans.
Graft-related disease progression in dura mater graft-associated Creutzfeldt-Jakob disease: a cross-sectional study
Authors: Sakai Kenji , Hamaguchi Tsuyoshi , Noguchi-Shinohara Moeko , Nozaki Ichiro , Takumi Ichiro , Sanjo Nobuo , Nakamura Yosikazu , Kitamoto Tetsuyuki , Saito Nobuhito , Mizusawa Hidehiro , Yamada Masahito 
Published: August 2013

ObjectivesDetails of abnormal prion protein (PrPSc) propagation in the human central nervous system (CNS) are unclear. To assess the spread of PrPScthrough the human CNS, we evaluated dura mater graft-associated Creutzfeldt-Jakob disease (dCJD) cases focusing on sites of grafting and dCJD pathological subtypes.DesignA cross-sectional study.Settingnationwide surveillance data of human prion diseases in Japan over the past 12 years were applied for the study.ParticipantsClinical data were obtained from 84 dCJD patients.Outcome measuresThe clinical courses in cases of dCJD were analysed according to the grafting sites (supratentorial and infratentorial groups) and the pathological subtypes (non-plaque and plaque types).ResultsOf the 84 cases of dCJD in this study, 36 (43%) were included in the supratentorial group and 39 (46%) were included in the infratentorial group. As initial manifestations, vertigo (p=0.007) and diplopia (p=0.041) were significantly more frequent in the infratentorial group than in the supratentorial group. During their clinical course, cerebellar signs appeared more frequently in the infratentorial group than in the supratentorial group (p=0.024). In the non-plaque type cases (n=53), the infratentorial group developed vertigo more frequently than the supratentorial group (p=0.017); moreover, cerebellar signs appeared more frequently in the infratentorial group (p=0.014). However, there was no significant difference between groups in the plaque type (n=18).ConclusionsThe high frequency of clinical manifestations related to brain stem and cerebellar dysfunction in the non-plaque type dCJD with infratentorial grafting suggests that PrPSccommonly shows direct propagation into the CNS from contaminated dura mater grafts.