bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors responsible for the discrepancy between IL28B polymorphism prediction and the viral response to peginterferon plus ribavirin therapy in Japanese chronic hepatitis C patients
Authors: Saito Hiroaki , Ito Kiyoaki , Sugiyama Masaya , Matsui Teppei , Aoki Yoshihiko , Imamura Masatoshi , Murata Kazumoto , Masaki Naohiko , Nomura Hideyuki , Adachi Hiroshi , Hige Shuhei , Enomoto Nobuyuki , Sakamoto Naoya , Kurosaki Masayuki , Mizokami Masashi , Watanabe Sumio 
Published: March 2012

Aim:  IL28B polymorphisms serve to predict response to pegylated interferon plus ribavirin therapy (PEG IFN/RBV) in Japanese patients with chronic hepatitis C (CHC) very reliably. However, the prediction by the IL28B polymorphism contradicted the virological response to PEG IFN/RBV in some patients. Here, we aimed to investigate the factors responsible for the discrepancy between the IL28B polymorphism prediction and virological responses.Methods:  CHC patients with genotype 1b and high viral load were enrolled in this study. In a case–control study, clinical and virological factors were analyzed for 130 patients with rs8099917 TT genotype and 96 patients with rs8099917 TG or GG genotype who were matched according to sex, age, hemoglobin level and platelet count.Results:  Higher low‐density lipoprotein (LDL) cholesterol, lower γ‐glutamyltransferase and the percentage of wild‐type phenotype at amino acids 70 and 91 were significantly associated with the rs8099917 TT genotype. Multivariate analysis showed that rs8099917 TG or GG genotype, older age and lower LDL cholesterol were independently associated with the non‐virological responder (NVR) phenotype. In patients with rs8099917 TT genotype (predicted as virological responder [VR]), multivariate analysis showed that older age was independently associated with NVR. In patients with rs8099917 TG or GG genotype (predicted as NVR), multivariate analysis showed that younger age was independently associated with VR.Conclusion:  Patient age gave rise to the discrepancy between the prediction by IL28B polymorphism and the virological responses, suggesting that patients should be treated at a younger age.
Role of the Porphyromonas gingivalis extracytoplasmic function sigma factor, SigH
Authors: Yanamandra S.S. , Sarrafee S.S. , Anaya‐Bergman C. , Jones K. , Lewis J.P. 
Published: March 2012

SummaryLittle is known about the regulatory mechanisms that allow Porphyromonas gingivalis to survive in the oral cavity. Here we characterize the sigma (σ) factor SigH, one of six extracytoplasmic function (ECF) σ factors encoded in the P. gingivalis genome. Our results indicate that sigH expression is upregulated by exposure to molecular oxygen, suggesting that sigH plays a role in adaptation of P. gingivalis to oxygen. Furthermore, several genes involved in oxidative stress protection, such as sod, trx, tpx, ftn, feoB2 and the hemin uptake hmu locus, are downregulated in a mutant deficient in SigH designated as V2948. ECF σ consensus sequences were identified upstream of the transcriptional start sites of these genes, consistent with the SigH‐dependent regulation of these genes. Growth of V2948 was inhibited in the presence of 6% oxygen when compared with the wild‐type W83 strain, whereas in anaerobic conditions both strains were able to grow. In addition, reduced growth of V2948 was observed in the presence of peroxide and the thiol‐oxidizing reagent diamide when compared with the W83 strain. The SigH‐deficient strain V2948 also exhibited reduced hemin uptake, consistent with the observed reduced expression of genes involved in hemin uptake. Finally, survival of V2948 was reduced in the presence of host cells compared with the wild‐type W83 strain. Collectively, our studies demonstrate that SigH is a positive regulator of gene expression required for survival of the bacterium in the presence of oxygen and oxidative stress, hemin uptake and virulence.
Isolation of Legionella pneumophila from Pluvial Floods by Amoebal Coculture
Authors: Schalk J. A. C. , Docters van Leeuwen A. E. , Lodder W. J. , de Man H. , Euser S. , den Boer J. W. , de Roda Husman A. M. 
Published: March 2012

ABSTRACT

Viable
Legionella pneumophila
bacteria were isolated by amoebal coculture from pluvial floods after intense rainfall and from water collected at sewage treatment plants. Several isolated
L. pneumophila
strains belonged to sequence types that have been previously identified in patients.
Efficacy of Octenidine Hydrochloride for Reducing Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes on Cattle Hides
Authors: Ananda Baskaran Sangeetha , Upadhyay Abhinav , Upadhyaya Indu , Bhattaram Varunkumar , Venkitanarayanan Kumar 
Published: March 2012

ABSTRACT

The efficacy of octenidine hydrochloride (OH; 0.025, 0.15, and 0.25%) for inactivating
Escherichia coli
O157:H7,
Salmonella
spp., and
Listeria monocytogenes
on cattle hides was investigated at 23°C in the presence and absence of bovine feces. All tested concentrations of OH were effective in decreasing more than 5.0 log CFU of bacteria/cm
2
in 5 min (
P
< 0.01). The results suggest that OH could be used to decontaminate cattle hides; however, further studies under commercial settings are necessary to validate these results.
High-Throughput Sequence-Based Analysis of the Intestinal Microbiota of Weanling Pigs Fed Genetically Modified MON810 Maize Expressing Bacillus thuringiensis Cry1Ab (Bt Maize) for 31 Days
Authors: Buzoianu Stefan G. , Walsh Maria C. , Rea Mary C. , O'Sullivan Orla , Cotter Paul D. , Ross R. Paul , Gardiner Gillian E. , Lawlor Peadar G. 
Published: March 2012

ABSTRACT

The objective of this study was to investigate if feeding genetically modified (GM) MON810 maize expressing the
Bacillus thuringiensis
insecticidal protein (Bt maize) had any effects on the porcine intestinal microbiota. Eighteen pigs were weaned at ∼28 days and, following a 6-day acclimatization period, were assigned to diets containing either GM (Bt MON810) maize or non-GM isogenic parent line maize for 31 days (
n
= 9/treatment). Effects on the porcine intestinal microbiota were assessed through culture-dependent and -independent approaches. Fecal, cecal, and ileal counts of total anaerobes,
Enterobacteriaceae
, and
Lactobacillus
were not significantly different between pigs fed the isogenic or Bt maize-based diets. Furthermore, high-throughput 16S rRNA gene sequencing revealed few differences in the compositions of the cecal microbiotas. The only differences were that pigs fed the Bt maize diet had higher cecal abundance of
Enterococcaceae
(0.06 versus 0%;
P
< 0.05),
Erysipelotrichaceae
(1.28 versus 1.17%;
P
< 0.05), and
Bifidobacterium
(0.04 versus 0%;
P
< 0.05) and lower abundance of
Blautia
(0.23 versus 0.40%;
P
< 0.05) than pigs fed the isogenic maize diet. A lower enzyme-resistant starch content in the Bt maize, which is most likely a result of normal variation and not due to the genetic modification, may account for some of the differences observed within the cecal microbiotas. These results indicate that Bt maize is well tolerated by the porcine intestinal microbiota and provide additional data for safety assessment of Bt maize. Furthermore, these data can potentially be extrapolated to humans, considering the suitability of pigs as a human model.
Biofilm Growth and Near-Infrared Radiation-Driven Photosynthesis of the Chlorophyll
d
-Containing Cyanobacterium Acaryochloris marina
Authors: Behrendt Lars , Schrameyer Verena , Qvortrup Klaus , Lundin Luisa , Sørensen Søren J. , Larkum Anthony W. D. , Kühl Michael 
Published: March 2012

ABSTRACT

The cyanobacterium
Acaryochloris marina
is the only known phototroph harboring chlorophyll (Chl)
d
. It is easy to cultivate it in a planktonic growth mode, and
A. marina
cultures have been subject to detailed biochemical and biophysical characterization. In natural situations,
A. marina
is mainly found associated with surfaces, but this growth mode has not been studied yet. Here, we show that the
A. marina
type strain MBIC11017 inoculated into alginate beads forms dense biofilm-like cell clusters, as in natural
A. marina
biofilms, characterized by strong O
2
concentration gradients that change with irradiance. Biofilm growth under both visible radiation (VIS, 400 to 700 nm) and near-infrared radiation (NIR, ∼700 to 730 nm) yielded maximal cell-specific growth rates of 0.38 per day and 0.64 per day, respectively. The population doubling times were 1.09 and 1.82 days for NIR and visible light, respectively. The photosynthesis versus irradiance curves showed saturation at a photon irradiance of
E

k

(saturating irradiance) >250 μmol photons m
−2
s
−1
for blue light but no clear saturation at 365 μmol photons m
−2
s
−1
for NIR. The maximal gross photosynthesis rates in the aggregates were ∼1,272 μmol O
2
mg Chl
d
−1
h
−1
(NIR) and ∼1,128 μmol O
2
mg Chl
d
−1
h
−1
(VIS). The photosynthetic efficiency (α) values were higher in NIR-irradiated cells [(268 ± 0.29) × 10
−6
m
2
mg Chl
d
−1
(mean ± standard deviation)] than under blue light [(231 ± 0.22) × 10
−6
m
2
mg Chl
d
−1
].
A. marina
is well adapted to a biofilm growth mode under both visible and NIR irradiance and under O
2
conditions ranging from anoxia to hyperoxia, explaining its presence in natural niches with similar environmental conditions.
Diversity of Integron- and Culture-Associated Antibiotic Resistance Genes in Freshwater Floc
Authors: Drudge Christopher N. , Elliott Amy V. C. , Plach Janina M. , Ejim Linda J. , Wright Gerard D. , Droppo Ian G. , Warren Lesley A. 
Published: March 2012

ABSTRACT
Clinically important antibiotic resistance genes were detected in culturable bacteria and class 1 integron gene cassettes recovered from suspended floc, a significant aquatic repository for microorganisms and trace elements, across freshwater systems variably impacted by anthropogenic activities. Antibiotic resistance gene cassettes in floc total community DNA differed appreciably in number and type from genes detected in bacteria cultured from floc. The number of floc antibiotic resistance gene cassette types detected across sites was positively correlated with total (the sum of Ag, As, Cu, and Pb) trace element concentrations in aqueous solution and in a component of floc readily accessible to bacteria. In particular, concentrations of Cu and Pb in the floc component were positively correlated with floc resistance gene cassette diversity. Collectively, these results identify suspended floc as an important reservoir, distinct from bulk water and bed sediment, for antibiotic resistance in aquatic environments ranging from heavily impacted urban sites to remote areas of nature reserves and indicate that trace elements, particularly Cu and Pb, are geochemical markers of resistance diversity in this environmental reservoir. The increase in contamination of global water supplies suggests that aquatic environments will become an even more important reservoir of clinically important antibiotic resistance in the future.
Transcriptional and Enzymatic Profiling of Pleurotus ostreatus Laccase Genes in Submerged and Solid-State Fermentation Cultures
Authors: Castanera Raúl , Pérez Gúmer , Omarini Alejandra , Alfaro Manuel , Pisabarro Antonio G. , Faraco Vincenza , Amore Antonella , Ramírez Lucía 
Published: March 2012

ABSTRACT

The genome of the white rot basidiomycete
Pleurotus ostreatus
includes 12 phenol oxidase (laccase) genes. In this study, we examined their expression profiles in different fungal strains under different culture conditions (submerged and solid cultures) and in the presence of a wheat straw extract, which was used as an inducer of the laccase gene family. We used a reverse transcription-quantitative PCR (RT-qPCR)-based approach and focused on determining the reaction parameters (in particular, the reference gene set for the normalization and reaction efficiency determinations) used to achieve an accurate estimation of the relative gene expression values. The results suggested that (i) laccase gene transcription is upregulated in the induced submerged fermentation (iSmF) cultures but downregulated in the solid fermentation (SSF) cultures, (ii) the
Lacc2
and
Lacc10
genes are the main sources of laccase activity in the iSmF cultures upon induction with water-soluble wheat straw extracts, and (iii) an additional, as-yet-uncharacterized activity (Unk1) is specifically induced in SSF cultures that complements the activity of Lacc2 and Lacc10. Moreover, both the enzymatic laccase activities and the
Lacc
gene family transcription profiles greatly differ between closely related strains. These differences can be targeted for biotechnological breeding programs for enzyme production in submerged fermentation reactors.
Stringent Response Regulation of Biofilm Formation in Vibrio cholerae
Authors: He Huajun , Cooper Jennifer N. , Mishra Arunima , Raskin David M. 
Published: March 2012

ABSTRACT

Biofilm formation is a key factor in
Vibrio cholerae
environmental survival and host colonization. Production of biofilm enables
V. cholerae
to survive and persist in aquatic environments and aids in the passage through the gastric acid barrier to allow access to the small intestine. The genes involved in biofilm formation are regulated by the transcriptional activators
vpsR
and
vpsT
, which are in turn transcriptionally regulated by a number of environmental signals. In this study, the role of the stringent response in biofilm formation was examined.
V. cholerae
mutants deficient in stringent response had a reduced ability to form biofilms, although they were not completely deficient in biofilm formation. There are three (p)ppGpp synthases in
V. cholerae
: RelA, SpoT, and RelV. All three synthases were necessary for
vpsR
transcription, with RelV showing the strongest effect. RelA was the only synthase that was necessary for
vpsT
expression. Stringent response regulation of
vpsR
and
vpsT
was shown to partially occur through
rpoS
. Biofilm formation in
V. cholerae
is controlled by a complex regulatory apparatus, with negative regulators of biofilm gene expression, such as quorum sensing, and positive regulators of biofilm genes, including stringent response, interacting to ensure that biofilm formation is coordinated with the environment.
Analysis of the CtrA Pathway in Magnetospirillum Reveals an Ancestral Role in Motility in Alphaproteobacteria
Authors: Greene Shannon E. , Brilli Matteo , Biondi Emanuele G. , Komeili Arash 
Published: March 2012

ABSTRACT

Developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and posttranslational levels. Key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. In this work, we probed the role of the CtrA regulatory network, conserved throughout the
Alphaproteobacteria
, in the magnetotactic bacterium
Magnetospirillum magneticum
strain AMB-1, which possesses unique intracellular organization and compartmentalization. While we have shown that CtrA in AMB-1 is not essential for viability, it is required for motility, and its putative phosphorylation state dictates the ability of CtrA to activate the flagellar biosynthesis gene cascade. Gene expression analysis of strains expressing active and inactive CtrA alleles points to the composition of the extended CtrA regulon, including both direct and indirect targets. These results, combined with a bioinformatic study of the AMB-1 genome, enabled the prediction of an AMB-1-specific CtrA binding site. Further, phylogenetic studies comparing CtrA sequences from alphaproteobacteria in which the role of CtrA has been experimentally examined reveal an ancestral role of CtrA in the regulation of motility and suggest that its essential functions in other alphaproteobacteria were acquired subsequently.
Characterization of the Two-Component Monooxygenase System AlnT/AlnH Reveals Early Timing of Quinone Formation in Alnumycin Biosynthesis
Authors: Grocholski Thadée , Oja Terhi , Humphrey Laurence , Mäntsälä Pekka , Niemi Jarmo , Metsä-Ketelä Mikko 
Published: March 2012

ABSTRACT

Alnumycin A is an aromatic polyketide with a strong resemblance to related benzoisochromanequinone (BIQ) antibiotics, such as the model antibiotic actinorhodin. One intriguing difference between these metabolites is that the positions of the benzene and quinone rings are reversed in alnumycin A in comparison to the BIQ polyketides. In this paper we demonstrate that inactivation of either the monooxygenase
alnT
gene or the flavin reductase
alnH
gene results in the accumulation of a novel nonquinoid metabolite, thalnumycin A (ThA), in the culture medium. Additionally, two other previously characterized metabolites, K1115 A and 1,6-dihydroxy-8-propylanthraquinone (DHPA), were identified, which had oxidized into quinones putatively nonenzymatically at the incorrect position in the central ring. None of the compounds isolated contained correctly formed pyran rings, which suggests that on the alnumycin pathway quinone biosynthesis occurs prior to third ring cyclization. The regiochemistry of the two-component monooxygenase system AlnT/AlnH was finally confirmed
in vitro
by using ThA, FMN, and NADH in enzymatic synthesis, where the reaction product, thalnumycin B (ThB), was verified to contain the expected
p
-hydroquinone structure in the lateral ring.
Environment-Mediated Accumulation of Diacyl Lipoproteins over Their Triacyl Counterparts in Staphylococcus aureus
Authors: Kurokawa Kenji , Kim Min-Su , Ichikawa Rie , Ryu Kyoung-Hwa , Dohmae Naoshi , Nakayama Hiroshi , Lee Bok Luel 
Published: March 2012

ABSTRACTBacterial lipoproteins are believed to exist in only one specific lipid-modified structure, such as the diacyl form or the triacyl form, in each bacterium. In the case ofStaphylococcus aureus, recent extensive matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry analysis revealed thatS. aureuslipoproteins exist in the α-aminoacylated triacyl form. Here, we discovered conditions that induce the accumulation of diacyl lipoproteins that lack α-aminoacylation inS. aureus. The accumulation of diacyl lipoproteins required a combination of conditions, including acidic pH and a post-logarithmic-growth phase. High temperatures and high salt concentrations additively accelerated the accumulation of the diacyl lipoprotein form. Following a post-logarithmic-growth phase whereS. aureusMW2 cells were grown at pH 6, SitC lipoprotein was found almost exclusively in its diacyl structure rather than in its triacyl structure. This is the first report showing that the environment mediates lipid-modified structural alterations of bacterial lipoproteins.
Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with major depressive disorder treated with antidepressants
Authors: Castro Victor M , Gallagher Patience J , Clements Caitlin C , Murphy Shawn N , Gainer Vivian S , Fava Maurizio , Weilburg Jeffrey B , Churchill Susanne E , Kohane Isaac S , Iosifescu Dan V , Smoller Jordan W , Perlis Roy H 
Published: March 2012

ObjectiveTo examine the association between exposure to newer antidepressants and risk of gastrointestinal (GI) and other bleeding complications among individuals with major depressive disorder (MDD).DesignThis study uses an incident user cohort design to compare associations between incidence of vascular/bleeding events and the relative affinity (low, moderate or high) of the antidepressant for the serotonin transporter during an exposure risk period for each patient.SettingNew England healthcare system electronic medical record database.Participants36 389 individuals with a diagnosis of MDD and monotherapy with a selective serotonin reuptake inhibitor, serotonin–norepinephrine reuptake inhibitor or other new-generation antidepressant were identified from among 3.1 million patients in a New England healthcare system.Primary and secondary outcome measuresRates of bleeding or other vascular complications, including acute liver failure, acute renal failure, asthma, breast cancer and hip fractures.Results601 GI bleeds were observed in the 21 462 subjects in the high-affinity group versus 333 among the 14 927 subjects in the lower affinity group (adjusted RR: 1.17, 95% CI 1.02 to 1.34). Similarly, 776 strokes were observed in the high-affinity group versus 434 in the lower affinity treatment group (adjusted RR: 1.18, 95% CI 1.06 to 1.32). No significant association with risk for a priori negative control outcomes, including acute liver failure, acute renal failure, asthma, breast cancer and hip fractures, was identified.ConclusionsUse of antidepressants with high affinity for the serotonin transporter may confer modestly elevated risk for GI and other bleeding complications. While multiple methodologic limitations must be considered, these results suggest that antidepressants with lower serotonin receptor affinity may be preferred in patients at greater risk for such complications.
Imaging in children presenting with acute neurological deficit: paediatric stroke mimics
Authors: Rasalkar Darshana D , Chu Winnie C W 
Published: March 2012

Abstract
Stroke mimics refer to conditions manifesting with neurologic deficits without underlying cerebrovascular diseases. Major causes in the paediatric population under this category include infections, inflammation, demyelination, neoplasm, drug related, phacomatosis, and miscellaneous disorders. These conditions and their respective imaging findings are briefly discussed here.
Anaphylaxis: current state of knowledge for the modern physician
Authors: Rutkowski Krzysztof , Dua Shelley , Nasser Shuaib 
Published: March 2012

Abstract
Anaphylaxis is a severe, potentially fatal, hypersensitivity reaction of rapid onset. It may trigger life-threatening cardiopulmonary compromise, often with skin and mucosal changes such as urticaria and angioedema. The prevalence of anaphylaxis is increasing and the number of cases of fatal anaphylaxis appears to be rising. Food, insect stings, and drugs are the most common triggers. Novel triggers are increasingly seen and include delayed anaphylaxis to red meat, food-dependent exercise-induced reactions and anaphylaxis to monoclonal antibodies. Anaphylaxis is usually IgE mediated, but other mechanisms also play a role for example direct mast cells activation. Differential diagnosis is discussed including asthma, syncope and shock; excessive endogenous histamine, food related syndromes, and some rare diagnoses. Intramuscular epinephrine is first line treatment. The role of other drugs is reviewed. Timed and serial serum tryptase measurements help to confirm the diagnosis. Long-term management is necessary to minimise the risk of recurrence and includes identification of the trigger(s), management of risk factors, education on avoidance and a formalised treatment plan with an epinephrine auto-injector if appropriate. Every patient who has experienced anaphylaxis should be referred to an allergy clinic for appropriate management. This is endorsed by many national guidelines (eg, UK NICE). Anaphylaxis is often misdiagnosed or miscoded as, for example, asthma or food allergy. Most doctors will encounter a patient with anaphylaxis in their career and should to be familiar with the clinical features, management and mechanisms of this potentially fatal condition.