bluuebunny/crossref_metadata_2025_split huggingface dataset:
Obstructive sleep apnea as a risk factor for silent cerebral infarction
Authors: Cho Eo Rin , Kim Hyun , Seo Hyung Suk , Suh Sooyeon , Lee Seung Ku , Shin Chol 
Published: February 2013

SummaryPrevious studies have suggested that obstructive sleep apnea (OSA) may be a risk factor for stroke. In this study, we assessed that OSA is an independent risk factor of silent cerebral infarction (SCI) in the general population, and in a non‐obese population. This study recruited a total of 746 participants (252 men and 494 women) aged 50–79 years as part of the Korean Genome and Epidemiology Study (KoGES); they underwent polysomnography, brain magnetic resonance imaging and health screening examinations. SCI was assessed by subtypes and brain regions, and lacunar infarction represented lesions <15 mm in size in the penetrating arteries. Moderate–severe OSA was determined by apnea–hypopnea index ≥15. The results indicated that 12.06% had moderate–severe OSA, 7.64% of participants had SCI and 4.96% had lacunar infarction. Moderate–severe OSA was associated positively with SCI [odds ratio (OR): 2.44, 95% confidence interval (CI): 1.03–5.80] and lacunar infarction (OR: 3.48, 95% CI: 1.31–9.23) in the age ≥65‐year group compared with those with non‐OSA. Additionally, in the basal ganglia, OSA was associated with an increase in the odds for SCI and lacunar infarction in all age groups, and especially in the ≥65‐year age group. In the non‐obese participants, OSA was also associated positively with SCI in the ≥65‐year age group, lacunar infarction in all age groups, and especially in the ≥65‐year age group. There was also a positive association with the basal ganglia. Moderate–severe OSA was associated positively with SCI and lacunar infarction in elderly participants. Treatment of OSA may reduce new first‐time cerebrovascular events and recurrences.
The effects of Porphyromonas gingivalis on the cell cycle progression of human gingival epithelial cells
Authors: Pan C , Xu X , Tan L , Lin L , Pan Y 
Published: February 2013

ObjectivePorphyromonas gingivalis is a major pathogen in the development and progression of periodontal disease. The interactions or cross‐talk between bacteria and gingival epithelial cells drive bacteria to manipulate the cell cycle to favor bacterial survival and virulence expression within the host. This study aims to dissect the effects of P. gingivalis on the cell cycle in human gingival epithelial cells.Materials and MethodsWe established a model of P. gingivalis invading IHGE cells. The cell cycle distribution of human gingival epithelial cells was analyzed by flow cytometry. Cyclin D and cyclin E mRNA and protein were detected by real‐time PCR and Western blot, respectively.ResultsPorphyromonas gingivalis‐induced facilitation of cell growth was correlated with the acceleration of G1 phase of cell cycle. Cyclin D1 mRNA levels were significantly upregulated from 6 to 12 h after infection. Cyclin E protein and mRNA levels were elevated at 10 and 12 h after invasion.ConclusionsWe confirmed that P. gingivalis significantly enhances IHGE cell proliferation by promoting the G1/S transition, involving the up‐regulation of cyclin D and cyclin E.
Symbiotic Characterization of Vibrio fischeri ES114 Mutants That Display Enhanced Luminescence in Culture
Authors: Lyell Noreen L. , Stabb Eric V. 
Published: February 2013

ABSTRACT

Vibrio fischeri
ES114 is a bioluminescent symbiont of the squid
Euprymna scolopes
. Like most isolates from
E. scolopes
, ES114 produces only dim luminescence outside the host, even in dense cultures. We previously identified mutants with brighter luminescence, and here we report their symbiotic phenotypes, providing insights into the host environment.
Survival, Sublethal Injury, and Recovery of Environmental
Burkholderia pseudomallei
in Soil Subjected to Desiccation
Authors: Larsen Eloise , Smith James J. , Norton Robert , Corkeron Maree 
Published: February 2013

ABSTRACT

Environmental
Burkholderia pseudomallei
isolated from sandy soil at Castle Hill, Townsville, in the dry tropic region of Queensland, Australia, was inoculated into sterile-soil laboratory microcosms subjected to variable soil moisture. Survival and sublethal injury of the
B. pseudomallei
strain were monitored by recovery using culture-based methods. Soil extraction buffer yielded higher recoveries as an extraction agent than sterile distilled water.
B. pseudomallei
was not recoverable when inoculated into desiccated soil but remained recoverable from moist soil subjected to 91 days' desiccation and showed a growth response to increased soil moisture over at least 113 days. Results indicate that endemic dry tropic soil may act as a reservoir during the dry season, with an increase in cell number and potential for mobilization from soil into water in the wet season.
Streptomyces lividans Blasticidin S Deaminase and Its Application in Engineering a Blasticidin S-Producing Strain for Ease of Genetic Manipulation
Authors: Li Li , Wu Jun , Deng Zixin , Zabriskie T. Mark , He Xinyi 
Published: February 2013

ABSTRACT

Blasticidin S is a peptidyl nucleoside antibiotic produced by
Streptomyces griseochromogenes
that exhibits strong fungicidal activity. To circumvent an effective DNA uptake barrier system in the native producer and investigate its biosynthesis
in vivo
, the blasticidin S biosynthetic gene cluster (
bls
) was engrafted to the chromosome of
Streptomyces lividans
. However, the resulting mutant, LL2, produced the inactive deaminohydroxyblasticidin S instead of blasticidin S. Subsequently, a blasticidin S deaminase (SLBSD, for
S. lividans
blasticidin S deaminase) was identified in
S. lividans
and shown to govern this
in vivo
conversion. Purified SLBSD was found to be capable of transforming blasticidin S to deaminohydroxyblasticidin S
in vitro
. It also catalyzed deamination of the cytosine moiety of cytosylglucuronic acid, an intermediate in blasticidin S biosynthesis. Disruption of the SLBSD gene in
S. lividans
LL2 led to successful production of active blasticidin S in the resultant mutant,
S. lividans
WJ2. To demonstrate the easy manipulation of the blasticidin S biosynthetic gene cluster,
blsE
,
blsF
, and
blsL
, encoding a predicted radical
S
-adenosylmethionine (SAM) protein, an unknown protein, and a guanidino methyltransferase, were individually inactivated to access their role in blasticidin S biosynthesis.
Combined Fluxomics and Transcriptomics Analysis of Glucose Catabolism via a Partially Cyclic Pentose Phosphate Pathway in Gluconobacter oxydans 621H
Authors: Hanke Tanja , Nï¿½h Katharina , Noack Stephan , Polen Tino , Bringer Stephanie , Sahm Hermann , Wiechert Wolfgang , Bott Michael 
Published: February 2013

ABSTRACT

In this study, the distribution and regulation of periplasmic and cytoplasmic carbon fluxes in
Gluconobacter oxydans
621H with glucose were studied by
13
C-based metabolic flux analysis (
13
C-MFA) in combination with transcriptomics and enzyme assays. For
13
C-MFA, cells were cultivated with specifically
13
C-labeled glucose, and intracellular metabolites were analyzed for their labeling pattern by liquid chromatography-mass spectrometry (LC-MS). In growth phase I, 90% of the glucose was oxidized periplasmically to gluconate and partially further oxidized to 2-ketogluconate. Of the glucose taken up by the cells, 9% was phosphorylated to glucose 6-phosphate, whereas 91% was oxidized by cytoplasmic glucose dehydrogenase to gluconate. Additional gluconate was taken up into the cells by transport. Of the cytoplasmic gluconate, 70% was oxidized to 5-ketogluconate and 30% was phosphorylated to 6-phosphogluconate. In growth phase II, 87% of gluconate was oxidized to 2-ketogluconate in the periplasm and 13% was taken up by the cells and almost completely converted to 6-phosphogluconate. Since
G. oxydans
lacks phosphofructokinase, glucose 6-phosphate can be metabolized only via the oxidative pentose phosphate pathway (PPP) or the Entner-Doudoroff pathway (EDP).
13
C-MFA showed that 6-phosphogluconate is catabolized primarily via the oxidative PPP in both phases I and II (62% and 93%) and demonstrated a cyclic carbon flux through the oxidative PPP. The transcriptome comparison revealed an increased expression of PPP genes in growth phase II, which was supported by enzyme activity measurements and correlated with the increased PPP flux in phase II. Moreover, genes possibly related to a general stress response displayed increased expression in growth phase II.
A Defined, Glucose-Limited Mineral Medium for the Cultivation of Listeria spp
Authors: Schneebeli Rudolf , Egli Thomas 
Published: February 2013

ABSTRACT

Members of the genus
Listeria
are fastidious bacteria with respect to their nutritional requirements, and several minimal media described in the literature fail to support growth of all
Listeria
spp. Furthermore, strict limitation by a single nutrient, e.g., the carbon source, has not been demonstrated for any of the published minimal media. This is an important prerequisite for defined studies of growth and physiology, including “omics.” Based on a theoretical analysis of previously published mineral media for
Listeria
, an improved, well-balanced growth medium was designed. It supports the growth, not only of all tested
Listeria monocytogenes
strains, but of all other
Listeria
species, with the exception of
L. ivanovii
. The growth performance of
L. monocytogenes
strain Scott A was tested in the newly designed medium; glucose served as the only carbon and energy source for growth, whereas neither the supplied amino acids nor the buffering and complexing components (MOPS [morpholinepropanesulfonic acid] and EDTA) supported growth. Omission of amino acids, trace elements, or vitamins, alone or in combination, resulted in considerably reduced biomass yields. Furthermore, we monitored the specific growth rates of various
Listeria
strains cultivated in the designed mineral medium and compared them to growth in complex medium (brain heart infusion broth [BHI]). The novel mineral medium was optimized for the commonly used strain
L. monocytogenes
Scott A to achieve optimum cell yields and maximum specific growth rates. This mineral medium is the first published synthetic medium for
Listeria
that has been shown to be strictly carbon (glucose) limited.
Genetic Determinants for Cadmium and Arsenic Resistance among Listeria monocytogenes Serotype 4b Isolates from Sporadic Human Listeriosis Patients
Authors: Lee Sangmi , Rakic-Martinez M. , Graves L. M. , Ward T. J. , Siletzky R. M. , Kathariou S. 
Published: February 2013

ABSTRACT

In
Listeria monocytogenes
serotype 4b isolates from sporadic listeriosis, heavy metal resistance was primarily encountered in certain clonal groups (ECI, ECII, and ECIa). All arsenic-resistant isolates harbored the arsenic resistance cassette previously identified in pLI100; ECIa harbored additional arsenic resistance genes and a novel cadmium resistance determinant in a conserved chromosomal locus.
High Diversity of Magnetotactic Deltaproteobacteria in a Freshwater Niche
Authors: Wang Yinzhao , Lin Wei , Li Jinhua , Pan Yongxin 
Published: February 2013

ABSTRACT

Knowledge of the diversity of magnetotactic bacteria in natural environments is crucial for understanding their contribution to various biological and geological processes. Here we report a high diversity of magnetotactic bacteria in a freshwater site. Ten out of 18 operational taxonomic units (OTUs) were affiliated with the
Deltaproteobacteria
. Some rod-shaped bacteria simultaneously synthesized greigite and magnetite magnetosomes.
Transcriptomic and Genetic Analysis of Direct Interspecies Electron Transfer
Authors: Shrestha Pravin Malla , Rotaru Amelia-Elena , Summers Zarath M. , Shrestha Minita , Liu Fanghua , Lovley Derek R. 
Published: February 2013

ABSTRACT

The possibility that metatranscriptomic analysis could distinguish between direct interspecies electron transfer (DIET) and H
2
interspecies transfer (HIT) in anaerobic communities was investigated by comparing gene transcript abundance in cocultures in which
Geobacter sulfurreducens
was the electron-accepting partner for either
Geobacter metallireducens
, which performs DIET, or
Pelobacter carbinolicus
, which relies on HIT. Transcript abundance for
G. sulfurreducens
uptake hydrogenase genes was 7-fold lower in cocultures with
G. metallireducens
than in cocultures with
P. carbinolicus
, consistent with DIET and HIT, respectively, in the two cocultures. Transcript abundance for the pilus-associated cytochrome OmcS, which is essential for DIET but not for HIT, was 240-fold higher in the cocultures with
G. metallireducens
than in cocultures with
P. carbinolicus
. The pilin gene
pilA
was moderately expressed despite a mutation that might be expected to repress
pilA
expression. Lower transcript abundance for
G. sulfurreducens
genes associated with acetate metabolism in the cocultures with
P. carbinolicus
was consistent with the repression of these genes by H
2
during HIT. Genes for the biogenesis of pili and flagella and several
c
-type cytochrome genes were among the most highly expressed in
G. metallireducens
. Mutant strains that lacked the ability to produce pili, flagella, or the outer surface
c
-type cytochrome encoded by Gmet_2896 were not able to form cocultures with
G. sulfurreducens
. These results demonstrate that there are unique gene expression patterns that distinguish DIET from HIT and suggest that metatranscriptomics may be a promising route to investigate interspecies electron transfer pathways in more-complex environments.
Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities
Authors: Bokulich Nicholas A. , Mills David A. 
Published: February 2013

ABSTRACT

Ultra-high-throughput sequencing (HTS) of fungal communities has been restricted by short read lengths and primer amplification bias, slowing the adoption of newer sequencing technologies to fungal community profiling. To address these issues, we evaluated the performance of several common internal transcribed spacer (ITS) primers and designed a novel primer set and work flow for simultaneous quantification and species-level interrogation of fungal consortia. Primer comparison and validation were predicted
in silico
and by sequencing a “mock community” of mixed yeast species to explore the challenges of amplicon length and amplification bias for reconstructing defined yeast community structures. The amplicon size and distribution of this primer set are smaller than for all preexisting ITS primer sets, maximizing sequencing coverage of hypervariable ITS domains by very-short-amplicon, high-throughput sequencing platforms. This feature also enables the optional integration of quantitative PCR (qPCR) directly into the HTS preparatory work flow by substituting qPCR with these primers for standard PCR, yielding quantification of individual community members. The complete work flow described here, utilizing any of the qualified primer sets evaluated, can rapidly profile mixed fungal communities and capably reconstructed well-characterized beer and wine fermentation fungal communities.
Taxis of Pseudomonas putida F1 toward Phenylacetic Acid Is Mediated by the Energy Taxis Receptor Aer2
Authors: Luu Rita A. , Schneider Benjamin J. , Ho Christie C. , Nesteryuk Vasyl , Ngwesse Stacy E. , Liu Xianxian , Parales Juanito V. , Ditty Jayna L. , Parales Rebecca E. 
Published: February 2013

ABSTRACT

The phenylacetic acid (PAA) degradation pathway is a widely distributed funneling pathway for the catabolism of aromatic compounds, including the environmental pollutants styrene and ethylbenzene. However, bacterial chemotaxis to PAA has not been studied. The chemotactic strain
Pseudomonas putida
F1 has the ability to utilize PAA as a sole carbon and energy source. We identified a putative PAA degradation gene cluster (
paa
) in
P. putida
F1 and demonstrated that PAA serves as a chemoattractant. The chemotactic response was induced during growth with PAA and was dependent on PAA metabolism. A functional
cheA
gene was required for the response, indicating that PAA is sensed through the conserved chemotaxis signal transduction system. A
P. putida
F1 mutant lacking the energy taxis receptor Aer2 was deficient in PAA taxis, indicating that Aer2 is responsible for mediating the response to PAA. The requirement for metabolism and the role of Aer2 in the response indicate that
P. putida
F1 uses energy taxis to detect PAA. We also revealed that PAA is an attractant for
Escherichia coli
; however, a mutant lacking a functional Aer energy receptor had a wild-type response to PAA in swim plate assays, suggesting that PAA is detected through a different mechanism in
E. coli
. The role of Aer2 as an energy taxis receptor provides the potential to sense a broad range of aromatic growth substrates as chemoattractants. Since chemotaxis has been shown to enhance the biodegradation of toxic pollutants, the ability to sense PAA gradients may have implications for the bioremediation of aromatic hydrocarbons that are degraded via the PAA pathway.
Sigma Factor RpoS Controls Alkylresorcinol Synthesis through ArpR, a LysR-Type Regulatory Protein, during Encystment of Azotobacter vinelandii
Authors: Romero Yanet , Moreno Soledad , Guzmán Josefina , Espín Guadalupe , Segura Daniel 
Published: February 2013

ABSTRACT

Azotobacter vinelandii
is a bacterium which undergoes a differentiation process leading to the formation of metabolically dormant cysts. During the encystment process,
A. vinelandii
produces alkylresorcinol lipids (ARs) that replace the membrane phospholipids and are also components of the layers covering the cyst. The synthesis of ARs in
A. vinelandii
has been shown to occur by the activity of enzymes encoded by the
arsABCD
operon, which is expressed only during the differentiation process. Also, the production of ARs has been shown to be dependent on the stationary-phase sigma factor RpoS, which is also implicated in the control of the synthesis of other cyst components (i.e., alginate and poly-β-hydroxybutyrate). In this study, we identified ArpR, a LysR-type transcriptional regulator expressed only during encystment that positively regulates
arsABCD
transcription. We show that this activation is dependent on acetoacetyl-coenzyme A (acetoacetyl-CoA), which might provide a metabolic signal for encystment. We also show that RpoS regulates
arsABCD
expression through the control of
arpR
transcription.
Mating Pair Formation Homologue TraG Is a Variable Membrane Protein Essential for Contact-Independent Type IV Secretion of Chromosomal DNA by Neisseria gonorrhoeae
Authors: Kohler Petra L. , Chan Yolande A. , Hackett Kathleen T. , Turner Nicholas , Hamilton Holly L. , Cloud-Hansen Karen A. , Dillard Joseph P. 
Published: February 2013

ABSTRACT

Neisseria gonorrhoeae
uses a type IV secretion system (T4SS) to secrete chromosomal DNA into the surrounding milieu. The DNA is effective in transforming gonococci in the population, and this mechanism of DNA donation may contribute to the high degree of genetic diversity in this species. Similar to other F-like T4SSs, the gonococcal T4SS requires a putative membrane protein, TraG, for DNA transfer. In F-plasmid and related systems, the homologous protein acts in pilus production, mating pair stabilization, and entry exclusion. We characterized the localization, membrane topology, and variation of TraG in
N. gonorrhoeae
. TraG was found to be an inner-membrane protein with one large periplasmic region and one large cytoplasmic region. Each gonococcal strain carried one of three different alleles of
traG
. Strains that carried the smallest allele of
traG
were found to lack the peptidoglycanase gene
atlA
but carried a peptidoglycan endopeptidase gene in place of
atlA
. The purified endopeptidase degraded gonococcal peptidoglycan
in vitro
, cutting the peptide cross-links. Although the other two
traG
alleles functioned for DNA secretion in strain MS11, the smallest
traG
did not support DNA secretion. Despite the requirement for a mating pair stabilization homologue, static coculture transformation experiments demonstrated that DNA transfer was nuclease sensitive and required active uptake by the recipient, thus demonstrating that transfer occurred by transformation and not conjugation. Together, these results demonstrate the TraG acts in a process of DNA export not specific to conjugation and that different forms of TraG affect what substrates can be transported.
Ultrastructural Analysis of the Rugose Cell Envelope of a Member of the Pasteurellaceae Family
Authors: Azari Fereshteh , Nyland Lori , Yu Chunxiao , Radermacher Michael , Mintz Keith P. , Ruiz Teresa 
Published: February 2013

ABSTRACT

Bacterial membranes serve as selective environmental barriers and contain determinants required for bacterial colonization and survival. Cell envelopes of Gram-negative bacteria consist of an outer and an inner membrane separated by a periplasmic space. Most Gram-negative bacteria display a smooth outer surface (e.g.,
Enterobacteriaceae
), whereas members of the
Pasteurellaceae
and
Moraxellaceae
families show convoluted surfaces.
Aggregatibacter actinomycetemcomitans
, an oral pathogen representative of the
Pasteurellaceae
family, displays a convoluted membrane morphology. This phenotype is associated with the presence of morphogenesis protein C (MorC). Inactivation of the
morC
gene results in a smooth membrane appearance when visualized by two-dimensional (2D) electron microscopy. In this study, 3D electron microscopy and atomic force microscopy of whole-mount bacterial preparations as well as 3D electron microscopy of ultrathin sections of high-pressure frozen and freeze-substituted specimens were used to characterize the membranes of both wild-type and
morC
mutant strains of
A. actinomycetemcomitans
. Our results show that the mutant strain contains fewer convolutions than the wild-type bacterium, which exhibits a higher curvature of the outer membrane and a periplasmic space with 2-fold larger volume/area ratio than the mutant bacterium. The inner membrane of both strains has a smooth appearance and shows connections with the outer membrane, as revealed by visualization and segmentation of 3D tomograms. The present studies and the availability of genetically modified organisms with altered outer membrane morphology make
A. actinomycetemcomitans
a model organism for examining membrane remodeling and its implications in antibiotic resistance and virulence in the
Pasteurellaceae
and
Moraxellaceae
bacterial families.