bluuebunny/crossref_metadata_2025 huggingface dataset:
ELEVATED CARBON DIOXIDE DIFFERENTIALLY ALTERS THE PHOTOPHYSIOLOGY OF THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE) AND EMILIANIA HUXLEYI (HAPTOPHYTA)1
Authors: McCarthy Avery , Rogers Susan P. , Duffy Stephen J. , Campbell Douglas A.
Published: April 2012

Increasing anthropogenic carbon dioxide is causing changes to ocean chemistry, which will continue in a predictable manner. Dissolution of additional atmospheric carbon dioxide leads to increased concentrations of dissolved carbon dioxide and bicarbonate and decreased pH in ocean water. The concomitant effects on phytoplankton ecophysiology, leading potentially to changes in community structure, are now a focus of concern. Therefore, we grew the coccolithophore Emiliania huxleyi (Lohmann) W. W. Hay et H. Mohler and the diatom strains Thalassiosira pseudonana (Hust.) Hasle et Heimdal CCMP 1014 and T. pseudonana CCMP 1335 under low light in turbidostat photobioreactors bubbled with air containing 390 ppmv or 750 ppmv CO2. Increased pCO2 led to increased growth rates in all three strains. In addition, protein levels of RUBISCO increased in the coastal strains of both species, showing a larger capacity for CO2 assimilation at 750 ppmv CO2. With increased pCO2, both T. pseudonana strains displayed an increased susceptibility to PSII photoinactivation and, to compensate, an augmented capacity for PSII repair. Consequently, the cost of maintaining PSII function for the diatoms increased at increased pCO2. In E. huxleyi, PSII photoinactivation and the counter‐acting repair, while both intrinsically larger than in T. pseudonana, did not change between the current and high‐pCO2 treatments. The content of the photosynthetic electron transport intermediary cytochrome b6/f complex increased significantly in the diatoms under elevated pCO2, suggesting changes in electron transport function.
CYTOLOGICAL AND PHYLOGENETIC DIVERSITY IN FRESHWATER ESOPTRODINIUM/BERNARDINIUM SPECIES (DINOPHYCEAE)1
Authors: Fawcett Ryan C. , Parrow Matthew W.
Published: April 2012

The genera Esoptrodinium Javornický and Bernardinium Chodat comprise freshwater, athecate dinoflagellates with an incomplete cingulum but differing reports regarding cingulum orientation and the presence of chloroplasts and an eyespot. To examine this reported diversity, six isolates were collected from different freshwater ponds and brought into clonal culture. The isolates were examined using LM to determine major cytological differences, and rDNA sequences were compared to determine relatedness and overall phylogenetic position within the dinoflagellates. All isolates were athecate with a left‐oriented cingulum that did not fully encircle the cell, corresponding to the current taxonomic concept of Esoptrodinium. However, consistent cytological differences were observed among clonal isolates. Most isolates exhibited unambiguous pale green chloroplasts and a distinct bright‐red eyespot located at the base of the longitudinal flagellum. However, one isolate had cryptic chloroplasts that were difficult to observe using LM, and another had an eyespot that was so reduced as to be almost undetectable. Another isolate lacked visible chloroplasts but did possess the characteristic eyespot. Nuclear rDNA phylogenies strongly supported a monophyletic Esoptrodinium clade containing all isolates from this study together with a previous sequence from Portugal, within the Tovelliaceae. Esoptrodinium subclades were largely correlated with cytological differences, and the data suggested that independent chloroplast and eyespot reduction and/or loss may have occurred within this taxon. Overall, the isolates encompassed the majority of cytological diversity reported in previous observations of Bernardinium/Esoptrodinium in field samples. Systematic issues with the current taxonomic distinction between Bernardinium and Esoptrodinium are discussed.
Drug‐Induced Blood Consumption: The Impact of Adverse Drug Reactions on Demand for Blood Components in German Departments of Internal Medicine
Authors: Rottenkolber Dominik , Schmiedl Sven , Rottenkolber Marietta , Thuermann Petra A. , Hasford Joerg
Published: April 2012

Therapy for adverse drug reactions (ADRs) often results in the application of blood components. This study aims to assess the demand for blood components and the resulting economic burden (hospital perspective) in German hospitals induced by ADRs leading to admissions to departments of internal medicine. In this prospective study, ADRs leading to hospitalization were surveyed in four regional pharmacovigilance centres in Germany during the years 2000–2007. ADRs assessed as ‘possible’, ‘likely’ or ‘very likely’ were included. Market prices for blood components and hospitalization data were determined by desktop research. A probabilistic sensitivity analysis was performed. A total of 6099 patients were admitted to internal medicine departments because of an outpatient ADR of whom 1165 patients (19.1%; mean age, 73.0 ± 13.0 years) required treatment with blood components owing to major bleeding events. Overall consumption was 4185 erythrocyte concentrates (EC), 426 fresh frozen plasma (FFP) and 48 thrombocyte (TC) units. On the basis of statistical hospital data, we estimated a nationwide demand of approximately 132,020 EC, 13,440 FFP and 1515 TC units, resulting in total costs of €12.66 million per year for all German hospitals. Some 19.2% of all ADR cases were assessed as preventable. Theoretically, a nationwide decreased demand for blood components and a savings potential of €2.43 million per year could be achieved by preventing ADRs in Germany. Blood components are used in one‐fifth (mainly gastrointestinal bleeding) of all ADRs, leading to hospitalizations in internal medicine departments. Both blood demand and hospital procurement costs can be significantly lowered by preventing ADRs.
Effects of Calcining Temperature on Photocatalytic Activity of Fe‐Doped Sulfated Titania
Authors: Yang Ying , Tian Congxue
Published: April 2012

Using 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

Despite 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

Bovine 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

Most 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

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

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

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

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

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

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

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

Leishmania, 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

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

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.
Fructose Degradation in the Haloarchaeon Haloferax volcanii Involves a Bacterial Type Phosphoenolpyruvate-Dependent Phosphotransferase System, Fructose-1-Phosphate Kinase, and Class II Fructose-1,6-Bisphosphate Aldolase
Authors: Pickl Andreas , Johnsen Ulrike , Schönheit Peter
Published: April 2012

The halophilic archaeon
Haloferax volcanii
utilizes fructose as a sole carbon and energy source. Genes and enzymes involved in fructose uptake and degradation were identified by transcriptional analyses, deletion mutant experiments, and enzyme characterization. During growth on fructose, the gene cluster HVO_1495 to HVO_1499, encoding homologs of the five bacterial phosphotransferase system (PTS) components enzyme IIB (EIIB), enzyme I (EI), histidine protein (HPr), EIIA, and EIIC, was highly upregulated as a cotranscript. The in-frame deletion of HVO_1499, designated
ptfC
(
ptf
stands for
p
hospho
t
ransferase system for
f
ructose) and encoding the putative fructose-specific membrane component EIIC, resulted in a loss of growth on fructose, which could be recovered by complementation in
trans
. Transcripts of HVO_1500 (
pfkB
) and HVO_1494 (
fba
), encoding putative fructose-1-phosphate kinase (1-PFK) and fructose-1,6-bisphosphate aldolase (FBA), respectively, as well as 1-PFK and FBA activities were specifically upregulated in fructose-grown cells.
pfkB
and
fba
knockout mutants did not grow on fructose, whereas growth on glucose was not inhibited, indicating the functional involvement of both enzymes in fructose catabolism. Recombinant 1-PFK and FBA obtained after homologous overexpression were characterized as having kinetic properties indicative of functional 1-PFK and a class II type FBA. From these data, we conclude that fructose uptake in
H. volcanii
involves a fructose-specific PTS generating fructose-1-phosphate, which is further converted via fructose-1,6-bisphosphate to triose phosphates by 1-PFK and FBA. This is the first report of the functional involvement of a bacterial-like PTS and of class II FBA in the sugar metabolism of archaea.
Characterization of SSR42, a Novel Virulence Factor Regulatory RNA That Contributes to the Pathogenesis of a Staphylococcus aureus USA300 Representative
Authors: Morrison John M. , Miller Eric W. , Benson Meredith A. , Alonzo Francis , Yoong Pauline , Torres Victor J. , Hinrichs Steven H. , Dunman Paul M.
Published: April 2012

Staphylococcus aureus
is a major human pathogen that is capable of producing an expansive repertoire of cell surface-associated and extracellular virulence factors. Herein we describe an
S. aureus
regulatory RNA, SSR42, which modulates the expression of approximately 80 mRNA species, including several virulence factors, in
S. aureus
strains UAMS-1 and USA300 (LAC) during stationary-phase growth. Mutagenesis studies revealed that SSR42 codes for an 891-nucleotide RNA molecule and that the molecule's regulatory effects are mediated by the full-length transcript. Western blotting and functional assays indicated that the regulatory effects of SSR42 correlate with biologically significant changes in corresponding protein abundances. Further, in
S. aureus
strain LAC, SSR42 is required for wild-type levels of erythrocyte lysis, resistance to human polymorphonuclear leukocyte killing, and pathogenesis in a murine model of skin and soft tissue infection. Taken together, our results indicate that SSR42 is a novel
S. aureus
regulatory RNA molecule that contributes to the organism's ability to cause disease.
Interventions in sports settings to reduce alcohol consumption and alcohol-related harm: a systematic review protocol
Authors: Kingsland Melanie , Wiggers John , Wolfenden Luke
Published: April 2012

Introduction

Alcohol consumption is a primary cause of physical, psychological and social harm to both the user and others. At both the professional and non-professional level, sports players and fans report consuming alcohol at greater levels than people not involved in sports. Limited systematic reviews have been conducted assessing interventions targeting alcohol consumption behaviour and related harms in the sporting context.

Methods and analysis

The review aims to determine if interventions implemented in the sport setting decrease alcohol consumption and related harms. Participants may include all persons regardless of age or other characteristics. Studies will be included which have implemented interventions within the sport setting and have either measured: alcohol consumption, excessive alcohol consumption or intoxication or alcohol-related injury or violence. Randomised controlled trials, staggered enrolment trials, stepped-wedged trials, quasi-randomised trials, quasi-experimental trials and natural experiments will be included. Studies without a parallel comparison group will be excluded. Data will be sourced from a range of electronic databases and sources of grey literature. Two authors will independently screen all titles and abstracts of papers identified through the search strategy. Two authors will independently examine the full text of all remaining papers to determine eligibility. Two authors will independently extract data from eligible studies and independently assess risk of bias by assessing the adequacy of study characteristics. Where studies are sufficiently homogeneous, trial results will be synthesised using a fixed-effects meta-analysis. Standardised mean differences will be used for continuous outcomes and RRs will be used for binary outcomes.

Dissemination

The findings of this study will be disseminated widely through mechanisms including peer-reviewed publications and conference presentations.
THE ENERGY-MOMENTUM TENSOR ON LOW DIMENSIONAL Spinc MANIFOLDS
Authors: HABIB GEORGES , NAKAD ROGER
Published: April 2012

On a compact surface endowed with any Spinc structure, we give a formula involving the Energy-Momentum tensor in terms of geometric quantities. A new proof of a Bär-type inequality for the eigenvalues of the Dirac operator is given. The round sphere 𝕊2 with its canonical Spinc structure satisfies the limiting case. Finally, we give a spinorial characterization of immersed surfaces in 𝕊2 × ℝ by solutions of the generalized Killing spinor equation associated with the induced Spinc structure on 𝕊2 × ℝ.
Reservoir potential of sands formed in glaciomarine environments: an analogue study based on Cenozoic examples from McMurdo Sound, Antarctica
Authors: Fielding Christopher R. , Blackstone Brian A. , Frank Tracy D. , Gui Zi
Published: April 2012

This paper provides documentation of unexpectedly high-reservoir-quality glaciomarine sands found in the Cenozoic succession beneath McMurdo Sound, Antarctica, as an analogue study for evaluations of hydrocarbon prospectivity in basins elsewhere. The Oligocene to Lower Miocene succession of the Victoria Land Basin, an extant portion of the West Antarctic Rift System, comprises diamictites, mudrocks and sandstones with minor conglomerates. These lithologies are arranged in repetitive stacking patterns (cycles), interpreted to record repeated advance and retreat of glaciers into and out of the basin, with attendant eustatic and isostatic effects. Phases of ice retreat within the cycles comprise an array of mudrocks, sandy mudrocks and sandstones, deposited mainly during relative sea-level highstands. Clean, well-sorted, unconsolidated and porous sands <25 m thick from such intervals, which are interpreted to be mainly deltaic in origin, were encountered. Some of these sands, which have visible porosity as high as 41%, flowed into the well bore together with significant volumes of cold formation water. Diagenetic modification of sands in these intervals is minimal, which can be attributed to the low-temperature nature of the subsurface environment. Accordingly, glaciomarine sands in near-field glaciogenic successions should be considered as potential reservoir facies in prospectivity assessments.
3D seismic analysis of buried tunnel valleys in the Central North Sea: tunnel valley fill sedimentary architecture
Authors: Stewart M. , Lonergan L. , Hampson G.
Published: April 2012

Fourteen overlapping 3D seismic reflection data sets, originally acquired by the oil and gas industry, were used to image and investigate complex networks of buried tunnel valleys in the UK sector of the Central North Sea. More than 180 individual tunnel valleys were observed and mapped to horizontal resolutions of 12–50 m and vertical resolutions of 8–10 m. The results presented here identify three recurring seismic facies that locally define stratigraphic organization from base to top of the buried tunnel valley fills: (i) high-amplitude disrupted units, (ii) a unit containing gently dipping disrupted reflections or transparent facies and (iii) well-layered continuous reflections. A comparison to similar works in the region is used to infer tunnel valley infill during changing depositional conditions from high-energy subglacial meltwater to quiet glaciolacustrine or glaciomarine environments.
Upregulation of anticoagulant proteins, protein S and tissue factor pathway inhibitor, in the mouse myocardium with cardio-specific TNF-α overexpression
Authors: Higuchi Yoshihiro , Kubota Toru , Koyanagi Masamichi , Maeda Toyoki , Feldman Arthur M. , Makino Naoki
Published: April 2012

Heart failure (HF) has been recognized as a hypercoagulable state. However, the natural anticoagulation systems in the failing heart have not been studied. Recent experimental and clinical data have indicated that not only the thrombomodulin (TM)/protein C (PC) pathway but also the protein S (PS)/tissue factor pathway inhibitor (TFPI) system function as potent natural anticoagulants. To investigate the balance between procoagulant and anticoagulant activities in the failing heart, we measured the cardiac expression of tissue factor (TF), type 1 plasminogen activator inhibitor (PAI-1), TM, PC, PS, and TFPI by RT-PCR and/or Western blot analysis in male transgenic (TG) mice with heart-specific overexpression of TNF-α. Both procoagulant (TF and PAI-1) and anticoagulant (PS and TFPI) factors were upregulated in the myocardium of 24-wk-old TG (end-stage HF) but not in that of 4-wk-old TG (early decompensated HF) compared with the wild-type mice. Both factors were also upregulated in the infarcted myocardium at 3 days after coronary ligation in the wild-type mice. The expression of TM was downregulated in the TG heart, and PC was not detected in the hearts. The transcript levels of PS orphan receptors, Mer and Tyro3, but not Axl, were significantly upregulated in the TG heart. Double immunohistochemical staining revealed that myocardial infiltrating CD3-positive T cells may produce PS in the TG myocardium. In conclusion, the PS/TFPI was upregulated in the myocardium of a different etiological model of HF, thus suggesting a role for the PS/TFPI system in the protection of the failing heart under both inflammatory and hypercoagulable states.
Olfactory ferric and ferrous iron absorption in iron-deficient rats
Authors: Ruvin Kumara V. M. , Wessling-Resnick Marianne
Published: April 2012

The absorption of metals from the nasal cavity to the blood and the brain initiates an important route of occupational exposures leading to health risks. Divalent metal transporter-1 (DMT1) plays a significant role in the absorption of intranasally instilled manganese, but whether iron uptake would be mediated by the same pathway is unknown. In iron-deficient rats, blood59Fe levels after intranasal administration of the radioisotope in the ferrous form were significantly higher than those observed for iron-sufficient control rats. Similar results were obtained when ferric iron was instilled intranasally, and blood levels of59Fe were even greater in the iron-deficient rats compared with the amount of ferrous iron absorbed. Experiments with Belgrade ( b/b) rats showed that DMT1 deficiency limited ferric iron uptake from the nasal cavity to the blood compared with +/b controls matched for iron deficiency. These results indicate that olfactory uptake of ferric iron by iron-deficient rats involves DMT1. Western blot experiments confirmed that DMT1 levels are significantly higher in iron-deficient rats compared with iron-sufficient controls in olfactory tissue. Thus the molecular mechanism of olfactory iron absorption is regulated by body iron status and involves DMT1.
A Miniaturized Ligand Binding Assay for EGFR
Authors: Schwenk Jochen M. , Poetz Oliver , Zeillinger Robert , Joos Thomas O.
Published: April 2012

In order to study receptor abundance and its function in solutions or in homogenates from clinical specimen, methods such as sandwich or radioimmunoassays are most commonly employed. For the determination of epidermal growth factor receptor (EGFR), we describe the development of a miniaturized bead-based ligand binding assay using its ligand EGF as immobilized capture reagent. This assay was used to analyze lysates from cell lines, and the ligand-bound EGFR was detected using an EGFR-specific antibody combined with a fluorescence-based reporter system. In a proof-of concept study with lysates from breast biopsies, the assay allowed to classify breast cancer samples in accordance to clinically the relevant EGFR cut-off level. The study suggests that such a ligand binding receptor assay could become an integral part of protein profiling procedures to provide additional information about receptor functionality in addition to its abundance.
Periodic Loop Solutions and Their Limit Forms for the Kudryashov‐Sinelshchikov Equation
Authors: He Bin , Meng Qing , Zhang Jinhua , Long Yao
Published: April 2012

The Kudryashov‐Sinelshchikov equation is studied by using the bifurcation method of dynamical systems and the method of phase portraits analysis. We show that the limit forms of periodic loop solutions contain loop soliton solutions, smooth periodic wave solutions, and periodic cusp wave solutions. Also, some new exact travelling wave solutions are presented through some special phase orbits.
Efficient Sunlight-Induced Methylene Blue Removal over One-Dimensional Mesoporous Monoclinic BiVO4Nanorods
Authors: Hou Linrui , Yang Long , Li Jiaoyang , Tan Jie , Yuan Changzhou
Published: April 2012

Sunlight-driven mesoporous BiVO4nanorods with monoclinic structure have been successfully synthesizedviaa simple hydrothermal method. The as-prepared one-dimensional BiVO4nanorods exhibited high specific surface area due to their unique mesoporous structure. The mesoporous BiVO4nanorods possessed strong photoabsorption properties in the visible light region as well as the ultravisible region, and the band gap was estimated to beca.2.18 eV. The photocatalytic activities were evaluated by decolorization of methylene blue under sunlight irradiation. Photocatalytic tests demonstrated that the decolorization rate of as-prepared mesoporous BiVO4nanorods was even up to 98.8% in 180 min, much better than that prepared by solid-state reaction (23.1%) and the commercial TiO2(Degussa P25) (14.2%) under the same conditions, due to their higher specific surface area and appropriate band gap. Moreover, the unique BiVO4nanorods exhibit high stability after five photocatalytic degradation recycles.
High-Energy Passive Mode-Locking of Fiber Lasers
Authors: Ding Edwin , Renninger William H. , Wise Frank W. , Grelu Philippe , Shlizerman Eli , Kutz J. Nathan
Published: April 2012

Mode-locking refers to the generation of ultrashort optical pulses in laser systems. A comprehensive study of achieving high-energy pulses in a ring cavity fiber laser that is passively mode-locked by a series of waveplates and a polarizer is presented in this paper. Specifically, it is shown that the multipulsing instability can be circumvented in favor of bifurcating to higher-energy single pulses by appropriately adjusting the group velocity dispersion in the fiber and the waveplate/polarizer settings in the saturable absorber. The findings may be used as practical guidelines for designing high-power lasers since the theoretical model relates directly to the experimental settings.
Tin Content Determination in Canned Fruits and Vegetables by Hydride Generation Inductively Coupled Plasma Optical Emission Spectrometry
Authors: Rončević Sanda , Benutić Anica , Nemet Ivan , Gabelica Buga
Published: April 2012

Tin content in samples of canned fruits and vegetables was determined by hydride generation inductively coupled plasma atomic emission spectrometry (HG-ICP-OES), and it was compared with results obtained by standard method of flame atomic absorption spectrometry (AAS). Selected tin emission lines intensity was measured in prepared samples after addition of tartaric acid and followed by hydride generation with sodium borohydride solution. The most favorable line at 189.991 nm showed the best detection limit (1.9 μg L−1) and limit of quantification (6.4 μg kg−1). Good linearity and sensitivity were established from time resolved analysis and calibration tests. Analytical accuracy of 98–102% was obtained by recovery study of spiked samples. Method of standard addition was applied for tin determination in samples from fully protected tinplate. Tin presence at low-concentration range was successfully determined. It was shown that tenth times less concentrations of Sn were present in protected cans than in nonprotected or partially protected tinplate.
The Many Faces of Mitochondrial Autophagy: Making Sense of Contrasting Observations in Recent Research
Authors: May Alexander I. , Devenish Rodney J. , Prescott Mark
Published: April 2012

Research into the selective autophagic degradation of mitochondria—mitophagy—has intensified in recent years, yielding significant insights into the function, mechanism, and regulation of this process in the eukaryotic cell. However, while some molecular players in budding yeast, such as Atg32p, Uth1p, and Aup1p, have been identified, studies further interrogating the mechanistic and regulatory features of mitophagy have yielded inconsistent and sometimes conflicting results. In this review, we focus on the current understanding of mitophagy mechanism, induction, and regulation in yeast, and suggest that differences in experimental conditions used in the various studies of mitophagy may contribute to the observed discrepancies. Consideration and understanding of these differences may help place the mechanism and regulation of mitophagy in context, and further indicate the intricate role that this essential process plays in the life and death of eukaryotic cells.