bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic review and meta‐analysis of randomized trials on probiotics for hepatic encephalopathy
Authors: Holte Kathrine , Krag Aleksander , Gluud Lise Lotte 
Published: March 2012

Aim:  The objective of this systematic review and meta‐analysis was to assess the efficacy of probiotics and synbiotics in patients with hepatic encephalopathy.Methods:  Eligible trials were identified by searching electronic databases including MEDLINE, the Cochrane Library, Science Citation Index and Embase, abstract proceedings, reference lists and ongoing trial registers until 13 October 2010. We included randomized controlled trials comparing probiotics and synbiotics with no intervention, placebo or lactulose in patients with hepatic encephalopathy. The primary outcome measure was improvement in hepatic encephalopathy. Results were expressed as risk rates (RR) with confidence intervals (CI) and intertrial heterogeneity as I2.Results:  Seven trials with a total of 393 patients were analyzed. Compared to placebo or lactulose, treatment with probiotics or synbiotics significantly improved hepatic encephalopathy (RR = 1.40, 95% CI = 1.05–1.86, I2 = 5%). Probiotics decreased arterial ammonia (weighted mean difference 15.95; 95% CI = 26.72–3.28; I2 = 68%), but not venous ammonia (weighted mean difference 5.23; 95% CI = 21.77–11.30; I2 = 89%). Treatment with probiotics or synbiotics did not significantly affect the psychometric tests. Overall adverse events were reported in four trials with no difference between probiotics and placebo groups (RR = 0.32, 95% CI = 0.04–2.57; I2 = 59%). Regression analysis showed evidence of small‐study effects.Conclusion:  The present meta‐analysis suggests that probiotics may be an effective treatment of hepatic encephalopathy, though rigorous evaluation in standardized, randomized, clinical trial with clinically relevant outcomes is still needed.
Targeted gene delivery to hepatocytes with galactosylated amphiphilic cyclodextrins
Authors: McMahon Anthony , O'Neill Martin J , Gomez Eva , Donohue Ruth , Forde Damien , Darcy Raphael , O'Driscoll Caitriona M 
Published: March 2012

Abstract

Objectives
Achieving targeted delivery of gene medicines is desirable to maximise activity. Here, galactosylated amphiphilic cyclodextrins (CDs) are examined in terms of their ability to transfect asialoglycoprotein receptor-bearing HepG2 cells.

Methods
Cationic amphiphilic CDs were synthesised as well as amphiphilic CDs bearing galactose-targeting ligands with different linker lengths. Binding of galactosylated CDs to a galactose-specific lectin was examined by surface plasmon resonance. CDs were formulated with and without the helper lipid DOPE and complexed with plasmid DNA. Transfection was evaluated by luciferase assay. Intracellular trafficking was assessed by confocal microscopy.

Key findings
Binding of targeted CDs to a galactose-specific lectin was achieved. Binding decreased with linker length between the galactosyl group and the CD core. Contrary to the lectin binding results, transfection levels increased with an increase in linker length from 7 atoms to 15. Compared to non-targeted formulations, a significant increase in transfection was observed only in the presence of the helper lipid DOPE. Confocal microscopy revealed that DOPE caused a pronounced effect on cellular distribution.

Conclusions
The galactose-targeting ligand induced substantial increases in transfection over non-targeted formulations when DOPE was included, indicating the potential for targeted gene delivery using CD-based delivery systems.
Impacts of Hematite Nanoparticle Exposure on Biomechanical, Adhesive, and Surface Electrical Properties of Escherichia coli Cells
Authors: Zhang Wen , Hughes Joseph , Chen Yongsheng 
Published: March 2012

ABSTRACT

Despite a wealth of studies examining the toxicity of engineered nanomaterials, current knowledge on their cytotoxic mechanisms (particularly from a physical perspective) remains limited. In this work, we imaged and quantitatively characterized the biomechanical (hardness and elasticity), adhesive, and surface electrical properties of
Escherichia coli
cells with and without exposure to hematite nanoparticles (NPs) in an effort to advance our understanding of the cytotoxic impacts of nanomaterials. Both scanning electron microscopy (SEM) and atomic force microscopy (AFM) showed that
E. coli
cells had noticeable deformation with hematite treatment for 45 min with a statistical significance. The hematite-treated cells became significantly harder or stiffer than untreated ones, as evidenced by indentation and spring constant measurements. The average indentation of the hematite-treated
E. coli
cells was 120 nm, which is significantly lower (
P
< 0.01) than that of the untreated cells (approximately 400 nm). The spring constant of hematite-treated
E. coli
cells (0.28 ± 0.11 nN/nm) was about 20 times higher than that of untreated ones (0.01 ± 0.01 nN/nm). The zeta potential of
E. coli
cells, measured by dynamic light scattering (DLS), was shown to shift from −4 ± 2 mV to −27 ± 8 mV with progressive surface adsorption of hematite NPs, a finding which is consistent with the local surface potential measured by Kelvin probe force microscopy (KPFM). Overall, the reported findings quantitatively revealed the adverse impacts of nanomaterial exposure on physical properties of bacterial cells and should provide insight into the toxicity mechanisms of nanomaterials.
Composition and Seasonal Variation of Rhipicephalus turanicus and Rhipicephalus sanguineus Bacterial Communities
Authors: Lalzar Itai , Harrus Shimon , Mumcuoglu Kosta Y. , Gottlieb Yuval 
Published: March 2012

ABSTRACT

A 16S rRNA gene approach, including 454 pyrosequencing and quantitative PCR (qPCR), was used to describe the bacterial community in
Rhipicephalus turanicus
and to evaluate the dynamics of key bacterial tenants of adult ticks during the active questing season. The bacterial community structure of
Rh. turanicus
was characterized by high dominance of
Coxiella
and
Rickettsia
and extremely low taxonomic diversity. Parallel diagnostic PCR further revealed a novel
Coxiella
species which was present and numerically dominant in all individual ticks tested (
n
= 187).
Coxiella
sp. densities were significantly higher in female versus male ticks and were overall stable throughout the questing season. In addition, we revealed the presence of the novel
Coxiella
sp. in
Rh. sanguineus
adult ticks, eggs, and hatched larvae, indicating its vertical transmission. The presence of both spotted fever group
Rickettsia
spp. (SFGR) and non-SFGR was verified in the various individual ticks. The prevalence and density of
Rickettsia
spp. were very low compared to those of
Coxiella
sp. Furthermore,
Rickettsia
sp. densities were similar in males and females and significantly declined toward the end of the questing season. No correlation was found between
Coxiella
sp. and
Rickettsia
sp. densities. These results suggest different control mechanisms in the tick over its different bacterial populations and point to an obligatory and facultative association between the two tick species and
Coxiella
sp. and
Rickettsia
spp., respectively.
Contact-Free Inactivation of Candida albicans Biofilms by Cold Atmospheric Air Plasma
Authors: Maisch Tim , Shimizu Tetsuji , Isbary Georg , Heinlin Julia , Karrer Sigrid , Klämpfl Tobias G. , Li Yang-Fang , Morfill Gregor , Zimmermann Julia L. 
Published: March 2012

ABSTRACT

Candida albicans
is one of the main species able to form a biofilm on almost any surface, causing both skin and superficial mucosal infections. The worldwide increase in antifungal resistance has led to a decrease in the efficacy of standard therapies, prolonging treatment time and increasing health care costs. Therefore, the aim of this work was to demonstrate the applicability of atmospheric plasma at room temperature for inactivating
C. albicans
growing in biofilms without thermally damaging heat-sensitive materials. This so-called cold atmospheric plasma is produced by applying high voltage to accelerate electrons, which ionize the surrounding air, leading to the production of charged particles, reactive species, and photons. A newly developed plasma device was used, which exhibits a large plasma-generating surface area of 9 by 13 cm (117 cm
2
). Different time points were selected to achieve an optimum inactivation efficacy range of ≥3 log
10
to 5 log
10
reduction in CFU per milliliter, and the results were compared with those of 70% ethanol. The results obtained show that contact-free antifungal inactivation of
Candida
biofilms by cold atmospheric plasma is a promising tool for disinfection of surfaces (and items) in both health care settings and the food industry, where ethanol disinfection should be avoided.
Selected Antimicrobial Essential Oils Eradicate Pseudomonas spp. and Staphylococcus aureus Biofilms
Authors: Kavanaugh Nicole L. , Ribbeck Katharina 
Published: March 2012

ABSTRACT
Biofilms are difficult to eliminate with standard antimicrobial treatments due to their high antibiotic resistance relative to free-living cells. Here, we show that selected antimicrobial essential oils can eradicate bacteria within biofilms with higher efficiency than certain important antibiotics, making them interesting candidates for the treatment of biofilms.
Role of Aspergillus niger
acrA
in Arsenic Resistance and Its Use as the Basis for an Arsenic Biosensor
Authors: Choe Se-In , Gravelat Fabrice N. , Al Abdallah Qusai , Lee Mark J. , Gibbs Bernard F. , Sheppard Donald C. 
Published: March 2012

ABSTRACT

Arsenic contamination of groundwater sources is a major issue worldwide, since exposure to high levels of arsenic has been linked to a variety of health problems. Effective methods of detection are thus greatly needed as preventive measures. In an effort to develop a fungal biosensor for arsenic, we first identified seven putative arsenic metabolism and transport genes in
Aspergillus niger
, a widely used industrial organism that is generally regarded as safe (GRAS). Among the genes tested for RNA expression in response to arsenate,
acrA
, encoding a putative plasma membrane arsenite efflux pump, displayed an over 200-fold increase in gene expression in response to arsenate. We characterized the function of this
A. niger
protein in arsenic efflux by gene knockout and confirmed that AcrA was located at the cell membrane using an enhanced green fluorescent protein (eGFP) fusion construct. Based on our observations, we developed a putative biosensor strain containing a construct of the native promoter of
acrA
fused with
egfp
. We analyzed the fluorescence of this biosensor strain in the presence of arsenic using confocal microscopy and spectrofluorimetry. The biosensor strain reliably detected both arsenite and arsenate in the range of 1.8 to 180 μg/liter, which encompasses the threshold concentrations for drinking water set by the World Health Organization (10 and 50 μg/liter).
Efficient Production of Polymyxin in the Surrogate Host Bacillus subtilis by Introducing a Foreign
ectB
Gene and Disrupting the
abrB
Gene
Authors: Park Soo-Young , Choi Soo-Keun , Kim Jihoon , Oh Tae-Kwang , Park Seung-Hwan 
Published: March 2012

ABSTRACT

In our previous study,
Bacillus subtilis
strain BSK3S, containing a polymyxin biosynthetic gene cluster from
Paenibacillus polymyxa
, could produce polymyxin only in the presence of exogenously added
l
-2,4-diaminobutyric acid (Dab). The dependence of polymyxin production on exogenous Dab was removed by introducing an
ectB
gene encoding the diaminobutyrate synthase of
P. polymyxa
into BSK3S (resulting in strain BSK4). We found, by observing the complete inhibition of polymyxin synthesis when the
spo0A
gene was knocked out (strain BSK4-0A), that Spo0A is indispensable for the production of polymyxin. Interestingly, the
abrB-spo0A
double-knockout mutant, BSK4-0A-rB, and the single
abrB
mutant, BSK4-rB, showed 1.7- and 2.3-fold increases, respectively, in polymyxin production over that of BSK4. These results coincided with the transcription levels of
pmxA
in the strains observed by quantitative real-time PCR (qRT-PCR). The AbrB protein was shown to bind directly to the upstream region of
pmxA
, indicating that AbrB directly inhibits the transcription of polymyxin biosynthetic genes. The BSK4-rB strain, producing high levels of polymyxin, will be useful for the development and production of novel polymyxin derivatives.
Soil Fungal Cellobiohydrolase I Gene (
cbhI
) Composition and Expression in a Loblolly Pine Plantation under Conditions of Elevated Atmospheric CO
2
and Nitrogen Fertilization
Authors: Weber Carolyn F. , Balasch Monica Moya , Gossage Zachary , Porras-Alfaro Andrea , Kuske Cheryl R. 
Published: March 2012

ABSTRACT

The simultaneous increase of atmospheric CO
2
and nitrogen (N) deposition to terrestrial ecosystems is predicted to alter plant productivity and, consequently, to change the amount and quality of above- and belowground carbon entering forest soils. It is not known how such changes will impact the composition and function of soil fungal communities that play a key role in degrading complex carbon. We sequenced the fungal cellobiohydrolase I gene (
cbhI
) from soil DNA and cDNA to compare the richness and composition of resident and expressed
cbhI
genes at a U.S. Department of Energy free air-carbon dioxide enrichment (FACE) site (NC), which had been exposed to elevated atmospheric CO
2
and/or N fertilization treatment for several years. Our results provide evidence that the richness and composition of the cellulolytic fungi surveyed in this study were distinct in the DNA- and cDNA-based gene surveys and were dominated by Basidiomycota that have low or no representation in public databases. The surveys did not detect differences in richness or phylum-level composition of
cbhI
-containing, cellulolytic fungi that correlated with elevated CO
2
or N fertilization at the time of sampling.
Biofilms Reduce Solar Disinfection of Cryptosporidium parvum Oocysts
Authors: Wolyniak DiCesare E. A. , Hargreaves B. R. , Jellison K. L. 
Published: March 2012

ABSTRACT

Solar radiation reduces
Cryptosporidium
infectivity. Biofilms grown from stream microbial assemblages inoculated with oocysts were exposed to solar radiation. The infectivity of oocysts attached at the biofilm surface and oocysts suspended in water was about half that of oocysts attached at the base of a 32-μm biofilm.
Analysis of the Conformation and Function of the Plasmodium falciparum Merozoite Proteins MTRAP and PTRAMP
Authors: Uchime Onyinyechukwu , Herrera Raul , Reiter Karine , Kotova Svetlana , Shimp Richard L. , Miura Kazutoyo , Jones Dominique , Lebowitz Jacob , Ambroggio Xavier , Hurt Darrell E. , Jin Albert J. , Long Carole , Miller Louis H. , Narum David L. 
Published: March 2012

ABSTRACT

Thrombospondin repeat (TSR)-like domains are structures involved with cell adhesion.
Plasmodium falciparum
proteins containing TSR domains play crucial roles in parasite development. In particular, the preerythrocytic
P. falciparum
circumsporozoite protein is involved in hepatocyte invasion. The importance of these domains in two other malaria proteins, the merozoite-specific thrombospondin-related anonymous protein (MTRAP) and the thrombospondin-related apical membrane protein (PTRAMP), were assessed using near-full-length recombinant proteins composed of the extracellular domains produced in
Escherichia coli
. MTRAP is thought to be released from invasive organelles identified as micronemes during merozoite invasion to mediate motility and host cell invasion through an interaction with aldolase, an actin binding protein involved in the moving junction. PTRAMP function remains unknown. In this study, the conformation of recombinant MTRAP (rMTRAP) appeared to be a highly extended protein (2 nm by 33 nm, width by length, respectively), whereas rPTRAMP had a less extended structure. Using an erythrocyte binding assay, rMTRAP but not rPTRAMP bound human erythrocytes; rMTRAP binding was mediated through the TSR domain. MTRAP- and in general PTRAMP-specific antibodies failed to inhibit
P. falciparum
development
in vitro
. Altogether, MTRAP is a highly extended bifunctional protein that binds to an erythrocyte receptor and the merozoite motor.
Functional Analysis of Sequence Motifs Involved in the Polyadenylation of Trichomonas vaginalis mRNAs
Authors: Fuentes Vanessa , Barrera Guadalupe , Sánchez Joaquín , Hernández Roberto , López-Villaseñor Imelda 
Published: March 2012

ABSTRACT

Synthesis of functional mRNA in eukaryotes involves processing of precursor transcripts, including the addition of a poly(A) tail at the 3′ end. A multiprotein complex recognizes a polyadenylation signal, generally the hexanucleotide AAUAAA in metazoans, to direct processing of the pre-mRNA. Based on sequence analysis of several cDNAs, we have previously suggested that the UAAA tetranucleotide (which may include the UAA translation stop codon) could be the polyadenylation signal in
Trichomonas vaginalis
, a parasitic protozoon that causes human trichomoniasis. This proposal is analyzed here with the aid of a transient-expression system of a reporter gene (
cat
flanked by
T. vaginalis
actin noncoding sequences). When cells were transfected with a plasmid bearing the original 3′ untranslated region (UTR) sequence containing the UAAA motif, the resulting
cat
mRNA was polyadenylated similarly to the endogenous actin mRNA. Base changes in the UAAA sequence produced alterations to the polyadenylation site of the reporter mRNAs, while nucleotide substitutions at either side of UAAA did not. Furthermore, relocation of the UAAA motif redirected the processing and polyadenylation of the reporter mRNA. In addition, a pre-mRNA cleavage site for polyadenylation was defined. Interaction of
T. vaginalis
proteins with the UAAA motif was shown by electrophoretic mobility shift assays. Based on our findings, we provide evidence that in
T. vaginalis
the UAAA tetranucleotide has a role equivalent to that of the metazoan consensus AAUAAA polyadenylation signal.
The Structure of Mlc Titration Factor A (MtfA/YeeI) Reveals a Prototypical Zinc Metallopeptidase Related to Anthrax Lethal Factor
Authors: Xu Qingping , Göhler Anna-Katharina , Kosfeld Anne , Carlton Dennis , Chiu Hsiu-Ju , Klock Heath E. , Knuth Mark W. , Miller Mitchell D. , Elsliger Marc-André , Deacon Ashley M. , Godzik Adam , Lesley Scott A. , Jahreis Knut , Wilson Ian A. 
Published: March 2012

ABSTRACT

MtfA of
Escherichia coli
(formerly YeeI) was previously identified as a regulator of the phosphoenolpyruvate (PEP)-dependent:glucose phosphotransferase system. MtfA homolog proteins are highly conserved, especially among beta- and gammaproteobacteria. We determined the crystal structures of the full-length MtfA apoenzyme from
Klebsiella pneumoniae
and its complex with zinc (holoenzyme) at 2.2 and 1.95 Å, respectively. MtfA contains a conserved H
149
E
150
XXH
153
+E
212
+Y
205
metallopeptidase motif. The presence of zinc in the active site induces significant conformational changes in the region around Tyr205 compared to the conformation of the apoenzyme. Additionally, the zinc-bound MtfA structure is in a self-inhibitory conformation where a region that was disordered in the unliganded structure is now observed in the active site and a nonproductive state of the enzyme is formed. MtfA is related to the catalytic domain of the anthrax lethal factor and the Mop protein involved in the virulence of
Vibrio cholerae
, with conservation in both overall structure and in the residues around the active site. These results clearly provide support for MtfA as a prototypical zinc metallopeptidase (gluzincin clan).
Stress Response and Virulence Functions of the Acinetobacter baumannii NfuA Fe-S Scaffold Protein
Authors: Zimbler Daniel L. , Park Thomas M. , Arivett Brock A. , Penwell William F. , Greer Samuel M. , Woodruff Tessa M. , Tierney David L. , Actis Luis A. 
Published: March 2012

ABSTRACT

To successfully establish an infection,
Acinetobacter baumannii
must overcome the iron starvation and oxidative stress imposed by the human host. Although previous studies have shown that ATCC 19606
T
cells acquire iron via the acinetobactin-mediated siderophore system, little is known about intracellular iron metabolism and its relation to oxidative stress in this pathogen. Screening of an insertion library resulted in the isolation of the ATCC 19606
T
derivative 1644, which was unable to grow in iron-chelated media. Rescue cloning and DNA sequencing showed that the insertion inactivated a gene coding for an NfuA Fe-S cluster protein ortholog, without any effect on the expression of the acinetobactin system. The
nfuA
mutant was also more sensitive to hydrogen peroxide and cumene hydroperoxide than the parental strain. The iron chelation- and oxidative-stress-deficient responses of this mutant were corrected when complemented with either the ATCC 19606
T
parental allele or the
Escherichia coli
MG1655
nfuA
ortholog. Furthermore, electron paramagnetic resonance (EPR) and inductively coupled plasma-atomic emission spectroscopy (ICP-AES) analyses showed that the ATCC 19606
T
NfuA ortholog has iron-binding properties compatible with the formation of [Fe-S] cluster protein.
Ex vivo
and
in vivo
assays using human epithelial cells and
Galleria mellonella
, respectively, showed that NfuA is critical for bacterial growth independent of their capacity to acquire iron or the presence of excess of free iron. Taken together, these observations indicate that the
A. baumannii
NfuA ortholog plays a role in intracellular iron utilization and protection from oxidative-stress responses that this pathogen could encounter during the infection of the human host.
Transcription Activation by NtcA in the Absence of Consensus NtcA-Binding Sites in an Anabaena Heterocyst Differentiation Gene Promoter
Authors: Camargo Sergio , Valladares Ana , Flores Enrique , Herrero Antonia 
Published: March 2012

ABSTRACT

Heterocyst differentiation is orchestrated by the N control transcriptional regulator NtcA and the differentiation-specific factor HetR. In
Anabaena
sp. strain PCC 7120, the
devBCA
operon is expressed from two different promoters activated upon N stepdown. The distal
devB
promoter (transcription start point [TSP] located at position −704) represents a canonical class II NtcA-activated promoter, including a consensus NtcA-binding site centered 39.5 nucleotides upstream from the TSP. Transcription activation from a second TSP (−454) requires NtcA and is impaired in
hetR
mutants. In a wild-type background, three different DNA fragments, including both or each individual promoter, directed
gfp
expression localized mainly to proheterocysts and heterocysts. Expression was undetectable in an
ntcA
background and, for the fragment including the proximal promoter alone, also in a
hetR
background. In spite of the absence of consensus NtcA-binding sequences between the two TSPs, NtcA was shown to interact with this DNA region, and NtcA and its effector, 2-oxoglutarate, were necessary and sufficient for
in vitro
transcription from the −454 TSP. No HetR binding to the DNA or
in vitro
transcription from the proximal
devB
TSP promoted by HetR alone were detected. However, a moderate positive effect of HetR on NtcA binding to the DNA between the two
devB
TSPs was observed. The proximal
devB
promoter appears to represent a suboptimal NtcA-activated promoter for which HetR may act as a coactivator, with the physiological effect of restricting gene activation to conditions of prevalence of high NtcA and HetR levels, such as those taking place during heterocyst differentiation.