bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Calcining Temperature on Photocatalytic Activity of Fe‐Doped Sulfated Titania
Authors: Yang Ying , Tian Congxue 
Published: April 2012

AbstractUsing industrial titanyl sulfate as a raw material, Fe‐doped sulfated titania (FST) photocatalysts were prepared by using the one‐step thermal hydrolysis method and characterized using XRD, SEM, TGA–DSC, FTIR, UV–Vis DRS and N2 adsorption–desorption techniques. The effects of calcining temperature on the structure of the titania were investigated. The photocatalytic activity of the FST was evaluated using the photodegradation of methylene blue and photooxidation of phenol in aqueous solutions under UV and visible light irradiation, respectively. The results evinced that Ti4+ is substituted by Fe3+ in titania lattice and forms impurity level within the band gap of titania, which consequently induces the visible light absorption and visible‐light‐driven photocatalytic activity. The synergistic effects of Fe‐doping and sulfation are beneficial to the efficient separation of the photogenerated carriers and also improve the quantum efficiency of photocatalysis. In addition, Brönsted acidity arisen from the strong inductive effect of sulfate is also conducive to enhancing the photocatalytic performance of FST. However, when the calcining temperature is higher than 800°C, sulfur species and surface hydroxyl groups decompose and desorb from FST and the specific surface area decreases sharply. Moreover, severe sintering and rutile phase formation occur simultaneously. All these are detrimental to photocatalytic activity of FST.
Gene expression changes in melanoma metastases in response to high‐dose chemotherapy during isolated limb perfusion
Authors: Wouters Jasper , Stas Marguerite , Govaere Olivier , Van den Eynde Kathleen , Vankelecom Hugo , van den Oord Joost J. 
Published: April 2012

SummaryDespite recent advances in melanoma therapy, disseminated melanoma still lacks effective treatment, and recurrence of the tumor frequently occurs, even after high‐dose chemotherapy. The mechanisms responsible for this chemoresistance or for the formation of new relapses remain poorly understood. Using a human ‘model’, in which the isolated limb is perfused with high doses of the chemotherapeutic melphalan (ILP), we identified a five‐gene set (ATF3, CYR61, IER5, IL6, and PTGS2) of stress‐induced genes that was consistently upregulated after ILP in all in‐transit metastatic melanoma samples as well as in three melphalan‐treated melanoma cell lines. Early post‐ILP relapses retained these elevated expressions, whereas the expression of these genes returned to their original levels in late post‐ILP recurrences. In addition, we identified upregulation of these genes in the A375 cell line’s side population (SP) and melanospheres, established methods to enrich for candidate cancer stem cells (CSCs), which are considered chemoresistant and tumorigenic, and thus proposed to be responsible for tumor relapse. Our data identify an immediate and short‐term upregulation of early stress‐responsive genes that are potentially linked to chemoresistance and CSCs.
Molecular Identification and Characterization of a New Type of Bovine Enterovirus
Authors: Shaukat Shahzad , Angez Mehar , Alam Muhammad Masroor , Sharif Salmaan , Khurshid Adnan , Malik Farzana , Rana Muhammad Suleman , Mahmood Tariq , Zaidi Syed Sohail Zahoor 
Published: April 2012

ABSTRACTBovine enteroviruses belong to the familyPicornaviridae. Little is known about their pathogenic potential; however, they cause asymptomatic infections in cattle and are excreted in feces. In the present study, viruses isolated from environmental samples were sequenced. According to phylogenetic analyses and standard picornavirus nomenclature, these isolates constitute a new type of bovine enterovirus serogroup A.
Production of a Novel Quercetin Glycoside through Metabolic Engineering of Escherichia coli
Authors: Yoon Jeong-A , Kim Bong-Gyu , Lee Woo Ju , Lim Yoongho , Chong Youhoon , Ahn Joong-Hoon 
Published: April 2012

ABSTRACTMost flavonoids exist as sugar conjugates. Naturally occurring flavonoid sugar conjugates include glucose, galactose, glucuronide, rhamnose, xylose, and arabinose. These flavonoid glycosides have diverse physiological activities, depending on the type of sugar attached. To synthesize an unnatural flavonoid glycoside,Actinobacillus actinomycetemcomitansgenetll(encoding dTDP-6-deoxy-l-lyxo-4-hexulose reductase, which converts the endogenous nucleotide sugar dTDP-4-dehydro-6-deoxy-l-mannose to dTDP-6-deoxytalose) was introduced intoEscherichia coli. In addition, nucleotide-sugar dependent glycosyltransferases (UGTs) were screened to find a UGT that could use dTDP-6-deoxytalose. Supplementation of this engineered strain ofE. coliwith quercetin resulted in the production of quercetin-3-O-(6-deoxytalose). To increase the production of quercetin 3-O-(6-deoxytalose) by increasing the supplement of dTDP-6-deoxytalose inE. coli, we engineered nucleotide biosynthetic genes ofE. coli, such asgalU(UTP-glucose 1-phosphate uridyltransferase),rffA(dTDP-4-oxo-6-deoxy-d-glucose transaminase), and/orrfbD(dTDP-4-dehydrorahmnose reductase). The engineeredE. colistrain produced approximately 98 mg of quercetin 3-O-(6-deoxytalose)/liter, which is 7-fold more than that produced by the wild-type strain, and the by-products, quercetin 3-O-glucose and quercetin 3-O-rhamnose, were also significantly reduced.
Genetic Complementation of the Obligate Marine Actinobacterium Salinispora tropica with the Large Mechanosensitive Channel Gene
mscL
Rescues Cells from Osmotic Downshock
Authors: Bucarey Sergio A. , Penn Kevin , Paul Lauren , Fenical William , Jensen Paul R. 
Published: April 2012

ABSTRACT

Marine actinomycetes in the genus
Salinispora
fail to grow when seawater is replaced with deionized (DI) water in complex growth media. While bioinformatic analyses have led to the identification of a number of candidate marine adaptation genes, there is currently no experimental evidence to support the genetic basis for the osmotic requirements associated with this taxon. One hypothesis is that the lineage-specific loss of
mscL
is responsible for the failure of strains to grow in media prepared with DI water. The
mscL
gene encodes a conserved transmembrane protein that reduces turgor pressure under conditions of acute osmotic downshock. In the present study, the
mscL
gene from a
Micromonospora
strain capable of growth on media prepared with DI water was transformed into
S. tropica
strain CNB-440. The single-copy, chromosomal genetic complementation yielded a recombinant
Salinispora mscL
+
strain that demonstrated an increased capacity to survive osmotic downshock. The enhanced survival of the
S. tropica
transformant provides experimental evidence that the loss of
mscL
is associated with the failure of
Salinispora
spp. to grow in low-osmotic-strength media.
Novel Genes Involved in Pseudomonas fluorescens Pf0-1 Motility and Biofilm Formation
Authors: Mastropaolo Matthew D. , Silby Mark W. , Nicoll Julie S. , Levy Stuart B. 
Published: April 2012

ABSTRACT

AdnA in
Pseudomonas fluorescens
, an ortholog of FleQ in
P. aeruginosa
, regulates both motility and flagellum-mediated attachment to various surfaces. A whole-genome microarray determined the AdnA transcriptome by comparing the gene expression pattern of wild-type Pf0-1 to that of Pf0-2x (
adnA
deletion mutant) in broth culture. In the absence of AdnA, expression of 92 genes was decreased, while 11 genes showed increased expression. Analysis of 16 of these genes fused to
lacZ
confirmed the microarray results. Several genes were further evaluated for their role in motility and biofilm formation. Two genes, Pfl01_1508 and Pfl01_1517, affected motility and had different effects on biofilm formation in Pf0-1. These two genes are predicted to specify proteins similar to the glycosyl transferases FgtA1 and FgtA2, which have been shown to be involved in virulence and motility in
P. syringae
. Three other genes, Pfl01_1516, Pfl01_1572, and Pfl01_1573, not previously associated with motility and biofilm formation in
Pseudomonas
had similar effects on biofilm formation in Pf0-1. Deletion of each of these genes led to different motility defects. Our data revealed an additional level of complexity in the control of flagellum function beyond the core genes known to be required and may yield insights into processes important for environmental persistence of
P. fluorescens
Pf0-1.
Genome-Based Cluster Deletion Reveals an Endocrocin Biosynthetic Pathway in Aspergillus fumigatus
Authors: Lim Fang Yun , Hou Yanpeng , Chen Yiming , Oh Jee-Hwan , Lee Inhyung , Bugni Tim S. , Keller Nancy P. 
Published: April 2012

ABSTRACT

Endocrocin is a simple anthraquinone frequently identified in extracts of numerous fungi. Several biosynthetic schemes for endocrocin synthesis have been hypothesized, but to date, no dedicated secondary metabolite gene cluster that produces this polyketide as its major metabolite has been identified. Here we describe our biosynthetic and regulatory characterization of the endocrocin gene cluster in
Aspergillus fumigatus
. This is the first report of this anthraquinone in this species. The biosynthetic genes required for endocrocin production are regulated by the global regulator of secondary metabolism, LaeA, and encode an iterative nonreducing polyketide synthase (
encA
), a physically discrete metallo-β-lactamase type thioesterase (
encB
), and a monooxygenase (
encC
). Interestingly, the deletion of a gene immediately adjacent to
encC
, termed
encD
and encoding a putative 2-oxoglutarate-Fe(II) type oxidoreductase, resulted in higher levels of endocrocin production than in the wild-type strain, whereas overexpression of
encD
eliminated endocrocin accumulation. We found that overexpression of the
encA
transcript resulted in higher transcript levels of
encA-D
and higher production of endocrocin. We discuss a model of the
enc
cluster as one evolutionary origin of fungal anthraquinones derived from a nonreducing polyketide synthase and a discrete metallo-β-lactamase-type thioesterase.
A Positive Correlation between Bacterial Autoaggregation and Biofilm Formation in Native Sinorhizobium meliloti Isolates from Argentina
Authors: Sorroche Fernando G. , Spesia Mariana B. , Zorreguieta Ángeles , Giordano Walter 
Published: April 2012

ABSTRACT

Sinorhizobium meliloti
is a symbiotic nitrogen-fixing bacterium that elicits nodule formation on roots of alfalfa plants.
S. meliloti
produces two exopolysaccharides (EPSs), termed EPS I and EPS II, that are both able to promote symbiosis. EPS I and EPS II are secreted in two major fractions that reflect differing degrees of subunit polymerization, designated high- and low-molecular-weight fractions. We reported previously that EPSs are crucial for autoaggregation and biofilm formation in
S. meliloti
reference strains and isogenic mutants. However, the previous observations were obtained by use of “domesticated” laboratory strains, with mutations resulting from successive passages under unnatural conditions, as has been documented for reference strain Rm1021. In the present study, we analyzed the autoaggregation and biofilm formation abilities of native
S. meliloti
strains isolated from root nodules of alfalfa plants grown in four regions of Argentina. 16S rRNA gene analysis of all the native isolates revealed a high degree of identity with reference
S. meliloti
strains. PCR analysis of the
expR
gene of all the isolates showed that, as in the case of reference strain Rm8530, this gene is not interrupted by an insertion sequence (IS) element. A positive correlation was found between autoaggregation and biofilm formation abilities in these rhizobia, indicating that both processes depend on the same physical adhesive forces. Extracellular complementation experiments using mutants of the native strains showed that autoaggregation was dependent on EPS II production. Our results indicate that a functional EPS II synthetic pathway and its proper regulation are essential for cell-cell interactions and surface attachment of
S. meliloti
.
Simple Absolute Quantification Method Correcting for Quantitative PCR Efficiency Variations for Microbial Community Samples
Authors: Brankatschk Robert , Bodenhausen Natacha , Zeyer Josef , Bürgmann Helmut 
Published: April 2012

ABSTRACT

Real-time quantitative PCR (qPCR) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. Currently, the standard-curve (SC) method of absolute quantification is widely employed for these kinds of analysis. However, the SC method assumes that the amplification efficiency (
E
) is the same for both the standard and the sample target template. We analyzed 19 bacterial strains and nine environmental samples in qPCR assays, targeting the
nifH
and 16S rRNA genes. The
E
values of the qPCRs differed significantly, depending on the template. This has major implications for the quantification. If the sample and standard differ in their
E
values, quantification errors of up to orders of magnitude are possible. To address this problem, we propose and test the one-point calibration (OPC) method for absolute quantification. The OPC method corrects for differences in
E
and was derived from the ΔΔ

C
T

method with correction for
E
, which is commonly used for relative quantification in gene expression studies. The SC and OPC methods were compared by quantifying artificial template mixtures from
Geobacter sulfurreducens
(DSM 12127) and
Nostoc commune
(Culture Collection of Algae and Protozoa [CCAP] 1453/33), which differ in their
E
values. While the SC method deviated from the expected
nifH
gene copy number by 3- to 5-fold, the OPC method quantified the template mixtures with high accuracy. Moreover, analyzing environmental samples, we show that even small differences in
E
between the standard and the sample can cause significant differences between the copy numbers calculated by the SC and the OPC methods.
Development and Evaluation of a Quantitative PCR Assay Targeting Sandhill Crane (Grus canadensis) Fecal Pollution
Authors: Ryu Hodon , Lu Jingrang , Vogel Jason , Elk Michael , Chávez-Ramírez Felipe , Ashbolt Nicholas , Santo Domingo Jorge 
Published: April 2012

ABSTRACT

While the microbial water quality in the Platte River is seasonally impacted by excreta from migrating cranes, there are no methods available to study crane fecal contamination. Here we characterized microbial populations in crane feces using phylogenetic analysis of 16S rRNA gene fecal clone libraries. Using these sequences, a novel crane quantitative PCR (Crane1) assay was developed, and its applicability as a microbial source tracking (MST) assay was evaluated by determining its host specificity and detection ability in environmental waters. Bacteria from crane excreta were dominated by bacilli and proteobacteria, with a notable paucity of sequences homologous to
Bacteroidetes
and
Clostridia
. The Crane1 marker targeted a dominant clade of unclassified
Lactobacillales
sequences closely related to
Catellicoccus marimammalium
. The host distribution of the Crane1 marker was relatively high, being positive for 69% (66/96) of the crane excreta samples tested. The assay also showed high host specificity, with 95% of the nontarget fecal samples (i.e.,
n
= 553; 20 different free-range hosts) being negative. Of the presumed crane-impacted water samples (
n
= 16), 88% were positive for the Crane1 assay, whereas none of the water samples not impacted by cranes were positive (
n
= 165). Bayesian statistical models of the Crane1 MST marker demonstrated high confidence in detecting true-positive signals and a low probability of false-negative signals from environmental water samples. Altogether, these data suggest that the newly developed marker could be used in environmental monitoring studies to study crane fecal pollution dynamics.
Biofilm Roughness Determines Cryptosporidium parvum Retention in Environmental Biofilms
Authors: Wolyniak DiCesare E. A. , Hargreaves B. R. , Jellison K. L. 
Published: April 2012

ABSTRACT

The genus
Cryptosporidium
is a group of waterborne protozoan parasites that have been implicated in significant outbreaks of gastrointestinal infections throughout the world. Biofilms trap these pathogens and can contaminate water supplies through subsequent release. Biofilm microbial assemblages were collected seasonally from three streams in eastern Pennsylvania and used to grow biofilms in laboratory microcosms. Daily oocyst counts in the influx and efflux flow allowed the calculation of daily oocyst retention in the biofilm. Following the removal of oocysts from the influx water, oocyst attachment to the biofilm declined to an equilibrium state within 5 days that was sustained for at least 25 days. Varying the oocyst loading rate for the system showed that biofilm retention could be saturated, suggesting that discrete binding sites determined the maximum number of oocysts retained. Oocyst retention varied seasonally but was consistent across all three sites; however, seasonal oocyst retention was not consistent across years at the same site. No correlation between oocyst attachment and any measured water quality parameter was found. However, oocyst retention was strongly correlated with biofilm surface roughness and roughness varied among seasons and across years. We hypothesize that biofilm roughness and oocyst retention are dependent on environmentally driven changes in the biofilm community rather than directly on water quality conditions. It is important to understand oocyst transport dynamics to reduce risks of human infection. Better understanding of factors controlling biofilm retention of oocysts should improve our understanding of oocyst transport at different scales.
Overexpression of S4D Mutant of Leishmania donovani ADF/Cofilin Impairs Flagellum Assembly by Affecting Actin Dynamics
Authors: Kumar Gaurav , Srivastava Rashmi , Mitra Kalyan , Sahasrabuddhe Amogh A. , Gupta Chhitar M. 
Published: April 2012

ABSTRACTLeishmania, like other eukaryotes, contains large amounts of actin and a number of actin-related and actin binding proteins. Our earlier studies have shown that deletion of the gene corresponding toLeishmaniaactin-depolymerizing protein (ADF/cofilin) adversely affects flagellum assembly, intracellular trafficking, and cell division. To further analyze this, we have now created ADF/cofilin site-specific point mutants and then examined (i) the actin-depolymerizing, G-actin binding, and actin-bound nucleotide exchange activities of the mutant proteins and (ii) the effect of overexpression of these proteins in wild-type cells. Here we show that S4D mutant protein failed to depolymerize F-actin but weakly bound G-actin and inhibited the exchange of G-actin-bound nucleotide. We further observed that overexpression of this protein impaired flagellum assembly and consequently cell motility by severely impairing the assembly of the paraflagellar rod, without significantly affecting vesicular trafficking or cell growth. Taken together, these results indicate that dynamic actin is essentially required in assembly of the eukaryotic flagellum.
The ExbD Periplasmic Domain Contains Distinct Functional Regions for Two Stages in TonB Energization
Authors: Ollis Anne A. , Kumar Aruna , Postle Kathleen 
Published: April 2012

ABSTRACT

The TonB system of Gram-negative bacteria energizes the active transport of diverse nutrients through high-affinity TonB-gated outer membrane transporters using energy derived from the cytoplasmic membrane proton motive force. Cytoplasmic membrane proteins ExbB and ExbD harness the proton gradient to energize TonB, which directly contacts and transmits this energy to ligand-loaded transporters. In
Escherichia coli
, the periplasmic domain of ExbD appears to transition from proton motive force-independent to proton motive force-dependent interactions with TonB, catalyzing the conformational changes of TonB. A 10-residue deletion scanning analysis showed that while all regions except the extreme amino terminus of ExbD were indispensable for function, distinct roles for the amino- and carboxy-terminal regions of the ExbD periplasmic domain were evident. Like residue D25 in the ExbD transmembrane domain, periplasmic residues 42 to 61 facilitated the conformational response of ExbD to proton motive force. This region appears to be important for transmitting signals between the ExbD transmembrane domain and carboxy terminus. The carboxy terminus, encompassing periplasmic residues 62 to 141, was required for initial assembly with the periplasmic domain of TonB, a stage of interaction required for ExbD to transmit its conformational response to proton motive force to TonB. Residues 92 to 121 were important for all three interactions previously observed for formaldehyde-cross-linked ExbD: ExbD homodimers, TonB-ExbD heterodimers, and ExbD-ExbB heterodimers. The distinct requirement of this ExbD region for interaction with ExbB raised the possibility of direct interaction with the few residues of ExbB known to occupy the periplasm.
Identification of Functionally Important TonB-ExbD Periplasmic Domain Interactions
In Vivo
Authors: Ollis Anne A. , Postle Kathleen 
Published: April 2012

ABSTRACT

In Gram-negative bacteria, the cytoplasmic membrane proton-motive force energizes the active transport of TonB-dependent ligands through outer membrane TonB-gated transporters. In
Escherichia coli
, cytoplasmic membrane proteins ExbB and ExbD couple the proton-motive force to conformational changes in TonB, which are hypothesized to form the basis of energy transduction through direct contact with the transporters. While the role of ExbB is not well understood, contact between periplasmic domains of TonB and ExbD is required, with the conformational response of TonB to presence or absence of proton motive force being modulated through ExbD. A region (residues 92 to 121) within the ExbD periplasmic domain was previously identified as being important for TonB interaction. Here, the specific sites of periplasmic domain interactions between that region and the TonB carboxy terminus were identified by examining 270 combinations of 45 TonB and 6 ExbD individual cysteine substitutions for disulfide-linked heterodimer formation. ExbD residues A92C, K97C, and T109C interacted with multiple TonB substitutions in four regions of the TonB carboxy terminus. Two regions were on each side of the TonB residues known to interact with the TonB box of TonB-gated transporters, suggesting that ExbD positions TonB for correct interaction at that site. A third region contained a functionally important glycine residue, and the fourth region involved a highly conserved predicted amphipathic helix. Three ExbD substitutions, F103C, L115C, and T121C, were nonreactive with any TonB cysteine substitutions. ExbD D25, a candidate to be on a proton translocation pathway, was important to support efficient TonB-ExbD heterodimerization at these specific regions.