bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical applicability of dOFM devices for dermal sampling
Authors: Bodenlenz M. , Aigner B. , Dragatin C. , Liebenberger L. , Zahiragic S. , Höfferer C. , Birngruber T. , Priedl J. , Feichtner F. , Schaupp L. , Korsatko S. , Ratzer M. , Magnes C. , Pieber T. R. , Sinner F. 
Published: April 2013

BackgroundSampling the dermal interstitial fluid (ISF) allows the pharmacokinetics and pharmacodynamics of dermatological drugs to be studied directly at their site of action.Dermal open‐flow microperfusion (dOFM) is a recently developed technique that can provide minimally invasive, continuous, membrane‐free (thus unfiltered) access to the dermal ISF. Herein, we evaluate the clinical applicability and reliability of novel wearable dOFM devices in a clinical setting.MethodsPhysicians inserted 141 membrane‐free dOFM probes into the dermis of 17 healthy and psoriatic volunteers and sampled dermal ISF for 25 h by using wearable push‐pull pumps. The tolerability, applicability, reproducibility, and reliability of multiple insertions and 25 h continuous sampling was assessed by pain scoring, physician feedback, ultrasound probe depth measurements, and 25 h‐drift and variability of the sodium relative recovery.ResultsInsertion pain was moderate and decreased with each additional probe. Probe insertion was precise, although slightly deeper in lesional skin. The wearable push‐pull pump enabled uninterrupted ISF sampling over 25 h with low variability. The relative recovery was drift‐free and highly reproducible.ConclusiondOFM sampling devices are tolerable and reliable for prolonged continuous dermal sampling in a multiprobe clinical setting. These devices should enable the study of a wide range of drugs and their biomarkers in the skin.
Comparison of Genotypes and Antibiotic Resistances of Campylobacter jejuni and Campylobacter coli on Chicken Retail Meat and at Slaughter
Authors: Kittl Sonja , Korczak Bożena M. , Niederer Lilian , Baumgartner Andreas , Buettner Sabina , Overesch Gudrun , Kuhnert Peter 
Published: April 2013

ABSTRACT

Multilocus sequence typing (MLST) and antibiotic resistance patterns of
Campylobacter jejuni
and
Campylobacter coli
from retail chicken meat showed high overlap with isolates collected at slaughterhouses, indicating little selection along the production chain. They also showed significant common sequence types with human clinical isolates, revealing chicken meat as a likely source for human infection.
Living Side by Side with a Virus: Characterization of Two Novel Plasmids from Thermococcus prieurii, a Host for the Spindle-Shaped Virus TPV1
Authors: Gorlas Aurore , Krupovic Mart , Forterre Patrick , Geslin Claire 
Published: April 2013

ABSTRACT

Microbial cells often serve as an evolutionary battlefield for different types of mobile genetic elements, such as viruses and plasmids. Here, we describe the isolation and characterization of two new archaeal plasmids which share the host with the spindle-shaped
Thermococcus prieurii
virus 1 (TPV1). The two plasmids, pTP1 and pTP2, were isolated from the hyperthermophilic archaeon
Thermococcus prieurii
(phylum
Euryarchaeota
), a resident of a deep-sea hydrothermal vent located at the East Pacific Rise at 2,700-m depth (7ï¿½25′24 S, 107ï¿½47′66 W). pTP1 (3.1 kb) and pTP2 (2.0 kb) are among the smallest known plasmids of hyperthermophilic archaea, and both are predicted to replicate via the rolling-circle mechanism. The two plasmids and the virus TPV1 do not have a single gene in common and stably propagate in infected cells without any apparent antagonistic effect on each other. The compatibility of the three genetic elements and the high copy number of pTP1 and pTP2 plasmids (50 copies/cell) might be useful for developing new genetic tools for studying hyperthermophilic euryarchaea and their viruses.
Functional Screening of a Metagenomic Library Reveals Operons Responsible for Enhanced Intestinal Colonization by Gut Commensal Microbes
Authors: Yoon Mi Young , Lee Kang-Mu , Yoon Yujin , Go Junhyeok , Park Yongjin , Cho Yong-Joon , Tannock Gerald W. , Yoon Sang Sun 
Published: April 2013

ABSTRACT

Evidence suggests that gut microbes colonize the mammalian intestine through propagation as an adhesive microbial community. A bacterial artificial chromosome (BAC) library of murine bowel microbiota DNA in the surrogate host
Escherichia coli
DH10B was screened for enhanced adherence capability. Two out of 5,472 DH10B clones, 10G6 and 25G1, exhibited enhanced capabilities to adhere to inanimate surfaces in functional screens. DNA segments inserted into the 10G6 and 25G1 clones were 52 and 41 kb and included 47 and 41 protein-coding open reading frames (ORFs), respectively. DNA sequence alignments, tetranucleotide frequency, and codon usage analysis strongly suggest that these two DNA fragments are derived from species belonging to the genus
Bacteroides
. Consistent with this finding, a large portion of the predicted gene products were highly homologous to those of
Bacteroides
spp. Transposon mutagenesis and subsequent experiments that involved heterologous expression identified two operons associated with enhanced adherence.
E. coli
strains transformed with the 10a or 25b operon adhered to the surface of intestinal epithelium and colonized the mouse intestine more vigorously than did the control strain. This study has revealed the genetic determinants of unknown commensals (probably resembling
Bacteroides
species) that enhance the ability of the bacteria to colonize the murine bowel.
Butyrate-Producing Bacteria, Including Mucin Degraders, from the Swine Intestinal Tract
Authors: Levine Uri Y. , Looft Torey , Allen Heather K. , Stanton Thad B. 
Published: April 2013

ABSTRACT

To identify bacteria with potential for influencing gut health, 980 anaerobes were cultured from the swine intestinal tract and analyzed for butyrate production. Fifteen isolates in the order
Clostridiales
produced butyrate and had butyryl coenzyme A (CoA):acetate CoA transferase activity. Three of the isolates grew on mucin, suggesting an intimate association with host intestinal mucosa.
Taxonomy and Distribution of Phenazine-Producing Pseudomonas spp. in the Dryland Agroecosystem of the Inland Pacific Northwest, United States
Authors: Parejko James A. , Mavrodi Dmitri V. , Mavrodi Olga V. , Weller David M. , Thomashow Linda S. 
Published: April 2013

ABSTRACTWe investigated the taxonomic placement of phenazine-producing fluorescentPseudomonasspp. in the Inland Pacific Northwest region of the United States. Five distinct species were identified, two of which were provisionally considered to be new. Agroclimatic zone and soil silt content affected the species diversity across the region.
Changes in the Rumen Epimural Bacterial Diversity of Beef Cattle as Affected by Diet and Induced Ruminal Acidosis
Authors: Petri R. M. , Schwaiger T. , Penner G. B. , Beauchemin K. A. , Forster R. J. , McKinnon J. J. , McAllister T. A. 
Published: April 2013

ABSTRACT

Little is known about the nature of the rumen epithelial adherent (epimural) microbiome in cattle fed different diets. Using denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and pyrosequencing of the V3 hypervariable coding region of 16S rRNA, epimural bacterial communities of 8 cattle were profiled during the transition from a forage to a high-concentrate diet, during acidosis, and after recovery. A total of 153,621 high-quality gene sequences were obtained, with populations exhibiting less taxonomic variability among individuals than across diets. The bacterial community composition exhibited clustering (
P
< 0.03) by diet, with only 14 genera, representing >1% of the rumen epimural population, differing (
P
≤ 0.05) among diets. During acidosis, levels of
Atopobium
,
Desulfocurvus
,
Fervidicola
,
Lactobacillus
, and
Olsenella
increased, while during the recovery,
Desulfocurvus
,
Lactobacillus
, and
Olsenella
reverted to levels similar to those with the high-grain diet and
Sharpea
and
Succinivibrio
reverted to levels similar to those with the forage diet. The relative abundances of bacterial populations changed during diet transition for all qPCR targets except
Streptococcus
spp. Less than 5% of total operational taxonomic units (OTUs) identified exhibited significant variability across diets. Based on DGGE, the community structures of epithelial populations differed (
P
≤ 0.10); segregation was most prominent for the mixed forage diet versus the grain, acidotic challenge, and recovery diets.
Atopobium
, cc142,
Lactobacillus
,
Olsenella
, RC39,
Sharpea
,
Solobacterium
,
Succiniclasticum
, and
Syntrophococcus
were particularly prevalent during acidosis. Determining the metabolic roles of these key genera in the rumens of cattle fed high-grain diets could define a clinical microbial profile associated with ruminal acidosis.
Mitochondrial Two-Component Signaling Systems in Candida albicans
Authors: Mavrianos John , Berkow Elizabeth L. , Desai Chirayu , Pandey Alok , Batish Mona , Rabadi Marissa J. , Barker Katherine S. , Pain Debkumar , Rogers P. David , Eugenin Eliseo A. , Chauhan Neeraj 
Published: April 2013

ABSTRACT

Two-component signal transduction pathways are one of the primary means by which microorganisms respond to environmental signals. These signaling cascades originated in prokaryotes and were inherited by eukaryotes via endosymbiotic lateral gene transfer from ancestral cyanobacteria. We report here that the nuclear genome of the pathogenic fungus
Candida albicans
contains elements of a two-component signaling pathway that seem to be targeted to the mitochondria. The
C. albicans
two-component response regulator protein Srr1 (
s
tress
r
esponse
r
egulator 1) contains a mitochondrial targeting sequence at the N terminus, and fluorescence microscopy reveals mitochondrial localization of green fluorescent protein-tagged Srr1. Moreover, phylogenetic analysis indicates that
C. albicans
Srr1 is more closely related to histidine kinases and response regulators found in marine bacteria than are other two-component proteins present in the fungi. These data suggest conservation of this protein during the evolutionary transition from endosymbiont to a subcellular organelle. We used microarray analysis to determine whether the phenotypes observed with a
srr1Δ/Δ
mutant could be correlated with gene transcriptional changes. The expression of mitochondrial genes was altered in the
srr1Δ/Δ
null mutant in comparison to their expression in the wild type. Furthermore, apoptosis increased significantly in the
srr1Δ/Δ
mutant strain compared to the level of apoptosis in the wild type, suggesting the activation of a mitochondrion-dependent apoptotic cell death pathway in the
srr1Δ/Δ
mutant. Collectively, this study shows for the first time that a lower eukaryote like
C. albicans
possesses a two-component response regulator protein that has survived in mitochondria and regulates a subset of genes whose functions are associated with the oxidative stress response and programmed cell death (apoptosis).
Poly(ADP-Ribose) Polymerase Is a Substrate Recognized by Two Metacaspases of Podospora anserina
Authors: Strobel Ingmar , Osiewacz Heinz D. 
Published: April 2013

ABSTRACTThe two metacaspases MCA1 and MCA2 of the fungal aging model organismPodospora anserina(PaMCA1 and PaMCA2, respectively) have previously been demonstrated to be involved in the control of programmed cell death (PCD) and life span. In order to identify specific pathways and components which are controlled by the activity of these enzymes, we set out to characterize them further. Heterologous overexpression inEscherichia coliof the two metacaspase genes resulted in the production of proteins which aggregate and form inclusion bodies from which the active protein has been recovered via refolding in appropriate buffers. The renaturated proteins are characterized by an arginine-specific activity and are active in caspase-like self-maturation leading to the generation of characteristic small protein fragments. Both activities are dependent on the presence of calcium. Incubation of the two metacaspases with recombinant poly(ADP-ribose) polymerase (PARP), a known substrate of mammalian caspases, led to the identification of PARP as a substrate of the twoP. anserinaproteases. Using double mutants in whichP. anserina Parp(PaParp) is overexpressed andPaMca1is either overexpressed or deleted, we provide evidence forin vivodegradation of PaPARP by PaMCA1. These results support the idea that the substrate profiles of caspases and metacaspases are at least partially overlapping. Moreover, they link PCD and DNA maintenance in the complex network of molecular pathways involved in aging and life span control.
Regulation of Copper Toxicity by Candida albicans
GPA2
Authors: Schwartz Jennifer A. , Olarte Karen T. , Michalek Jamie L. , Jandu Gurjinder S. , Michel Sarah L. J. , Bruno Vincent M. 
Published: April 2013

ABSTRACT

Copper is an essential nutrient that is toxic to cells when present in excess. The fungal pathogen
Candida albicans
employs several mechanisms to survive in the presence of excess copper, but the molecular pathways that govern these responses are not completely understood. We report that deletion of
GPA2
, which specifies a G-protein α subunit, confers increased resistance to excess copper and propose that the increased resistance is due to a combination of decreased copper uptake and an increase in copper chelation by metallothioneins. This is supported by our observations that a
gpa2
Δ/Δ mutant has reduced expression of the copper uptake genes,
CTR1
and
FRE7
, and a marked decrease in copper accumulation following exposure to high copper levels. Furthermore, deletion of
GPA2
results in an increased expression of the copper metallothionein gene,
CRD2
. Gpa2p functions upstream in the cyclic AMP (cAMP)-protein kinase A (PKA) pathway to govern hyphal morphogenesis. The copper resistance phenotype of the
gpa2
Δ/Δ mutant can be reversed by artificially increasing the intracellular concentration of cAMP. These results provide evidence for a novel role of the PKA pathway in regulation of copper homeostasis. Furthermore, the connection between the PKA pathway and copper homeostasis appears to be conserved in the pathogen
Cryptococcus neoformans
but not in the nonpathogenic
Saccharomyces cerevisiae
.
One Single Basic Amino Acid at the ω-1 or ω-2 Site Is a Signal That Retains Glycosylphosphatidylinositol-Anchored Protein in the Plasma Membrane of Aspergillus fumigatus
Authors: Ouyang Haomiao , Chen Xiaomin , Lü Yang , Wilson Iain B. H. , Tang Guomin , Wang Aoquan , Jin Cheng 
Published: April 2013

ABSTRACT

Although the plasma membrane is the terminal destination for glycosylphosphatidylinositol (GPI) proteins in higher eukaryotes, cell wall-attached GPI proteins (GPI-CWPs) are found in many fungal species. In yeast, some of the
cis
-requirements directing localization of GPI proteins to the plasma membrane or cell wall are now understood. However, it remains to be determined how
Aspergillus fumigatus
, an opportunistic fungal pathogen, signals, and sorts GPI proteins to either the plasma membrane or the cell wall. In this study, chimeric green fluorescent proteins (GFPs) were constructed as fusions with putative C-terminal GPI signal sequences from
A. fumigatus
Mp1p, Gel1p, and Ecm33p, as well as site-directed mutations thereof. By analyzing cellular localization of chimeric GFPs using Western blotting, electron microscopy, and fluorescence microscopy, we showed that, in contrast to yeast, a single Lys residue at the ω-1 or ω-2 site alone could retain GPI-anchored GFP in the plasma membrane. Although the signal for cell wall distribution has not been identified yet, it appeared that the threonine/serine-rich region at the C-terminal half of
Af
Mp1 was not required for cell wall distribution. Based on our results, the
cis
-requirements directing localization of GPI proteins in
A. fumigatus
are different from those in yeast.
Polyphosphate Deficiency in Mycobacterium tuberculosis Is Associated with Enhanced Drug Susceptibility and Impaired Growth in Guinea Pigs
Authors: Singh Ramandeep , Singh Mamta , Arora Garima , Kumar Santosh , Tiwari Prabhakar , Kidwai Saqib 
Published: April 2013

ABSTRACT

Inorganic polyphosphate (polyP), a linear polymer of hundreds of phosphate residues linked by ATP-like phosphoanhydride bonds, is found in all organisms and performs a wide variety of functions. This study shows that polyP accumulation occurs in
Mycobacterium tuberculosis
upon exposure to various stress conditions.
M. tuberculosis
possesses a single homolog of
ppk-1
, and we have disrupted
ppk-1
in the
M. tuberculosis
genome by allelic replacement. The mutant strain exhibited negligible levels of intracellular polyP, decreased expression of
sigF
and
phoP
, and reduced growth in the stationary phase and displayed a survival defect in response to nitrosative stress and in THP-1 macrophages compared to the wild-type strain. We report that reduction in polyP levels is associated with increased susceptibility of
M. tuberculosis
to certain TB drugs and impairs its ability to cause disease in guinea pigs. These results suggest that polyP contributes to persistence of
M. tuberculosis
in vitro
and plays an important role in the physiology of bacteria residing within guinea pigs.
Nonnative Disulfide Bond Formation Activates the σ
32
-Dependent Heat Shock Response in Escherichia coli
Authors: Müller Alexandra , Hoffmann Jörg H. , Meyer Helmut E. , Narberhaus Franz , Jakob Ursula , Leichert Lars I. 
Published: April 2013

ABSTRACT

Formation of nonnative disulfide bonds in the cytoplasm, so-called disulfide stress, is an integral component of oxidative stress. Quantification of the extent of disulfide bond formation in the cytoplasm of
Escherichia coli
revealed that disulfide stress is associated with oxidative stress caused by hydrogen peroxide, paraquat, and cadmium. To separate the impact of disulfide bond formation from unrelated effects of these oxidative stressors in subsequent experiments, we worked with two complementary approaches. We triggered disulfide stress either chemically by diamide treatment of cells or genetically in a mutant strain lacking the major disulfide-reducing systems TrxB and Gor. Studying the proteomic response of
E. coli
exposed to disulfide stress, we found that intracellular disulfide bond formation is a particularly strong inducer of the heat shock response. Real-time quantitative PCR experiments showed that disulfide stress induces the heat shock response in
E. coli
σ
32
dependently. However, unlike heat shock treatment, which induces these genes transiently, transcripts of σ
32
-dependent genes accumulated over time in disulfide stress-treated cells. Analyzing the stability of σ
32
, we found that this constant induction can be attributed to an increase of the half-life of σ
32
upon disulfide stress. This is concomitant with aggregation of
E. coli
proteins treated with diamide. We conclude that oxidative stress triggers the heat shock response in
E. coli
σ
32
dependently. The component of oxidative stress responsible for the induction of heat shock genes is disulfide stress. Nonnative disulfide bond formation in the cytoplasm causes protein unfolding. This stabilizes σ
32
by preventing its DnaK- and FtsH-dependent degradation.
Features of Pro-σ
K
Important for Cleavage by SpoIVFB, an Intramembrane Metalloprotease
Authors: Zhou Ruanbao , Chen Kangming , Xiang Xianling , Gu Liping , Kroos Lee 
Published: April 2013

ABSTRACT

Intramembrane proteases regulate diverse processes by cleaving substrates within a transmembrane segment or near the membrane surface.
Bacillus subtilis
SpoIVFB is an intramembrane metalloprotease that cleaves Pro-σ
K
during sporulation. To elucidate features of Pro-σ
K
important for cleavage by SpoIVFB, coexpression of the two proteins in
Escherichia coli
was used along with cell fractionation. In the absence of SpoIVFB, a portion of the Pro-σ
K
was peripherally membrane associated. This portion was not observed in the presence of SpoIVFB, suggesting that it serves as the substrate. Deletion of Pro-σ
K
residues 2 to 8, addition of residues at its N terminus, or certain single-residue substitutions near the cleavage site impaired cleavage. Certain multiresidue substitutions near the cleavage site changed the position of cleavage, revealing preferences for a small residue preceding the cleavage site N-terminally (i.e., at the P1 position) and a hydrophobic residue at the second position following the cleavage site C-terminally (i.e., P2′). These features appear to be conserved among Pro-σ
K
orthologs. SpoIVFB did not tolerate an aromatic residue at P1 or P2′ of Pro-σ
K
. A Lys residue at P3′ of Pro-σ
K
could not be replaced with Ala unless a Lys was provided farther C-terminally (e.g., at P9′). α-Helix-destabilizing residues near the cleavage site were not crucial for SpoIVFB to cleave Pro-σ
K
. The preferences and tolerances of SpoIVFB are somewhat different from those of other intramembrane metalloproteases, perhaps reflecting differences in the interaction of the substrate with the membrane and the enzyme.
Associations between objectively measured physical activity intensity in childhood and measures of subclinical cardiovascular disease in adolescence: prospective observations from the European Youth Heart Study
Authors: Ried-Larsen Mathias , Grøntved Anders , Møller Niels Christian , Larsen Kristian Traberg , Froberg Karsten , Andersen Lars Bo 
Published: April 2013

Background and aimNo prospective studies have investigated the association between physical activity (PA) and carotid subclinical cardiovascular disease across childhood. Therefore, the primary aim was to investigate the association between PA intensity across childhood and carotid intima media thickness (cIMT) and stiffness in adolescence. Second, we included a clustered cardiovascular disease risk score as outcome.MethodsThis was a prospective study of a sample of 254 children (baseline age 8–10 years) with a 6-year follow-up. The mean exposure and the change in minutes of moderate-and-vigorous and vigorous PA intensity were measured using the Actigraph activity monitor. Subclinical cardiovascular disease was expressed as cIMT, carotid arterial stiffness and secondarily as a metabolic risk z-score including the homoeostasis model assessment score of insulin resistance, triglycerides, total cholesterol to high-density lipoprotein ratio, inverse of cardiorespiratory fitness, systolic blood pressure and the sum of four skinfolds.ResultsNo associations were observed between PA intensity variables and cIMT or carotid arterial stiffness (p>0.05). Neither change in PA intensity (moderate-and-vigorous nor vigorous) nor mean minutes of moderate-and-vigorous PA intensity was associated to the metabolic risk z-score in adolescence (p>0.05). However, a significant inverse association was observed between mean minutes of vigorous PA and the metabolic risk z-score in adolescence independent of gender and biological maturity (standard β=–0.19 p=0.007).ConclusionsA high mean exposure to, or changes in, minutes spent at higher PA intensities across childhood was not associated to cIMT or stiffness in the carotid arteries in adolescence. Our observations suggest that a high volume of vigorous PA across childhood independently associated with lower metabolic cardio vascular disease risk in adolescence.