bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and Characterization of Potentially Pathogenic Antimicrobial-Resistant
Escherichia coli
Strains from Chicken and Pig Farms in Spain
Authors: Cortés Pilar , Blanc Vanessa , Mora Azucena , Dahbi Ghizlane , Blanco Jesús E. , Blanco Miguel , López Cecilia , Andreu Antonia , Navarro Ferran , Alonso María Pilar , Bou Germán , Blanco Jorge , Llagostera Montserrat
Published: March 2010

To ascertain whether on animal farms there reside extended-spectrum β-lactamase (ESBL) and plasmidic class C β-lactamase-producing
Escherichia coli
isolates potentially pathogenic for humans, phylogenetic analyses, pulsed-field gel electrophoresis (PFGE) typing, serotyping, and virulence genotyping were performed for 86 isolates from poultry (57 isolates) and pig (29 isolates) farms.
E. coli
isolates from poultry farms carried genes encoding enzymes of the CTX-M-9 group as well as CMY-2, whereas those from pig farms mainly carried genes encoding CTX-M-1 enzymes. Poultry and pig isolates differed significantly in their phylogenetic group assignments, with phylogroup A predominating in pig isolates and phylogroup D predominating in avian isolates. Among the 86 farm isolates, 23 (26.7%) carried two or more virulence genes typical of extraintestinal pathogenic
E. coli
(ExPEC). Of these, 20 were isolated from poultry farms and only 3 from pig farms. Ten of the 23 isolates belonged to the classic human ExPEC serotypes O2:H6, O2:HNM, O2:H7, O15:H1, and O25:H4. Despite the high diversity of serotypes and pulsotypes detected among the 86 farm isolates, 13 PFGE clusters were identified. Four of these clusters contained isolates with two or more virulence genes, and two clusters exhibited the classic human ExPEC serotypes O2:HNM (ST10) and O2:H6 (ST115). Although O2:HNM and O2:H6 isolates of human and animal origins differed with respect to their virulence genes and PFGE pulsotypes, the O2:HNM isolates from pigs showed the same sequence type (ST10) as those from humans. The single avian O15:H1 isolate was compared with human clinical isolates of this serotype. Although all were found to belong to phylogroup D and shared the same virulence gene profile, they differed in their sequence types (ST362-avian and ST393-human) and PFGE pulsotypes. Noteworthy was the detection, for the first time, in poultry farms of the clonal groups O25b:H4-ST131-B2, producing CTX-M-9, and O25a-ST648-D, producing CTX-M-32. The virulence genes and PFGE profiles of these two groups were very similar to those of clinical human isolates. While further studies are required to determine the true zoonotic potential of these clonal groups, our results emphasize the zoonotic risk posed especially by poultry farms, but also by pig farms, as reservoirs of ESBL- and CMY-2-encoding
E. coli
.
Correlation of the Capsular Phenotype in
Propionibacterium freudenreichii
with the Level of Expression of
gtf
, a Unique Polysaccharide Synthase-Encoding Gene
Authors: Deutsch Stéphanie-Marie , Bivic Pierre Le , Hervé Christophe , Madec Marie-Noëlle , LaPointe Gisèle , Jan Gwenaël , Loir Yves Le , Falentin Hélène
Published: March 2010

Many food-grade bacteria produce exopolysaccharides (EPS) that affect the texture of fermented food products and that may be involved in probiotic properties.
Propionibacterium freudenreichii
is a Gram-positive food-grade bacterium with reported probiotic capabilities that is widely used as starter in Swiss-type cheese. In this study, 68 strains of
P. freudenreichii
were screened for the β-glucan capsular phenotype by immunoagglutination with a specific antibody and for the presence of the
gtf
gene coding for polysaccharide synthase. All strains were positive for PCR amplification with
gtf
gene-specific primers, but the presence of β-glucan capsular EPS was detected for only 35% of the strains studied. Disruption of
gtf
in
P. freudenreichii
revealed that
gtf
is a unique gene involved in β-glucan capsular EPS production in
P. freudenreichii
. The
gtf
gene was transferred into and expressed in
Lactococcus lactis
, in which it conferred an agglutination-positive phenotype. Expression of the
gtf
gene was measured by performing quantitative reverse transcription-PCR assays with RNA from four capsular and three noncapsular strains. A positive correlation was found between the β-glucan capsular phenotype and
gtf
gene expression. Sequencing of the region upstream of the
gtf
open reading frame revealed the presence of an insertion element (IS element) in this upstream region in the four strains with the β-glucan capsular phenotype. The role of the IS element in the expression of neighboring genes and its impact on interstrain variability of the
P. freudenreichii
capsule phenotype remain to be elucidated.
Functional Prokaryotic RubisCO from an Oceanic Metagenomic Library
Authors: Witte Brian , John David , Wawrik Boris , Paul John H. , Dayan David , Tabita F. Robert
Published: March 2010

Culture-independent studies have indicated that there is significant diversity in the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) enzymes used by marine, freshwater, and terrestrial autotrophic bacteria. Surprisingly, little is known about the catalytic properties of many environmentally significant RubisCO enzymes. Because one of the goals of RubisCO research is to somehow modify or select for RubisCO molecules with improved kinetic properties, a facile means to isolate functional and novel RubisCO molecules directly from the environment was developed. In this report, we describe the first example of functional RubisCO proteins obtained from genes cloned and characterized from metagenomic libraries derived from DNA isolated from environmental samples. Two form IA marine RubisCO genes were cloned, and each gene supported both photoheterotrophic and photoautotrophic growth of a RubisCO deletion strain of
Rhodobacter capsulatus
, strain SBI/II
−
, indicating that catalytically active recombinant RubisCO was synthesized. The catalytic properties of the metagenomic RubisCO molecules were further characterized. These experiments demonstrated the feasibility of studying the functional diversity and enzymatic properties of RubisCO enzymes without first cultivating the host organisms. Further, this “proof of concept” experiment opens the way for development of a simple functional screen to examine the properties of diverse RubisCO genes isolated from any environment, and subsequent further bioselection may be possible if the growth conditions of complemented
R. capsulatus
strain SBI/II
−
are varied.
Accuracy and Sensitivity of Commercial PCR-Based Methods for Detection of
Salmonella enterica
in Feed
Authors: Koyuncu Sevinc , Andersson M. Gunnar , Häggblom Per
Published: March 2010

The present study compared the performance of commercial PCR-based
Salmonella enterica
detection methods (BAX System Q7, the iQ-Check
Salmonella
II kit, and the TaqMan
Salmonella enterica
detection kit) with culture-based methods (modified semisolid Rappaport-Vassiliadis [MSRV] and NMKL71) in spiked and naturally contaminated samples of feed mill scrapings (FMS), palm kernel meal (PKM), pelleted feed (PF), rape seed meal (RSM), soybean meal (SM), and wheat grain (WG). When results from the various feeds were compared, the number of
Salmonella enterica
CFU/25 g required to produce a positive were as follows: PKM > FMS = WG > RSM = SM = PF. These data are similar to those developed in earlier studies with culture-based
Salmonella
detection methods. PCR-based methods were performed similarly to culture-based methods, with respect to sensitivity and specificity. However, many PCR positives could not be confirmed by
Salmonella
isolation and for that reason the evaluated methods were found to be suitable only when rapid results were paramount. Nevertheless, PCR-based methods cannot presently replace culture-based methods when typing information is required for tracing studies or epidemiological investigations. The observed difference in detection levels is a potential problem when prevalence data are compared as well as when feed ingredients are tested for conformance with microbiological criteria. This paper also presents a statistical model that describes the detection probability when different levels (CFU) of
Salmonella
contamination are present in feed materials.
Evaluation of
Mycoplasma
Inactivation during Production of Biologics: Egg-Based Viral Vaccines as a Model
Authors: David Selwyn A. Wilson , Volokhov Dmitriy V. , Ye Zhiping , Chizhikov Vladimir
Published: March 2010

Although mycoplasmas are generally considered to be harmless commensals, some mycoplasma species are able to cause infections in pediatric, geriatric, or immunocompromised patients. Thus, accidental contamination of biologics with mycoplasmas represents a potential risk for the health of individuals who receive cell-derived biological and pharmaceutical products. To assess the efficiency of inactivation of mycoplasmas by the agents used in the manufacture of egg-derived influenza vaccines, we carried out a series of experiments aimed at monitoring the viability of mycoplasmas spiked into both chicken allantoic fluid and protein-rich microbiological media and then treated with beta-propiolactone, formalin, cetyltrimethylammonium bromide, Triton X-100, and sodium deoxycholate, which are agents that are commonly used for virus inactivation and disruption of viral particles during influenza vaccine production. Twenty-two mycoplasma species (with one to four strains of each species) were exposed to these inactivating agents at different concentrations. The most efficient inactivation of the mycoplasmas evaluated was observed with either 0.5% Triton X-100 or 0.5% sodium deoxycholate. Cetyltrimethylammonium bromide at concentrations of ≥0.08% was also able to rapidly inactivate (in less than 30 min) all mycoplasmas tested. In contrast, negligible reductions in mycoplasma titers were observed with 0.0125 to 0.025% formaldehyde. However, increasing the concentration of formaldehyde to 0.1 to 0.2% improved the mycoplasmacidal effect. Incubation of mycoplasmas with 0.1% beta-propiolactone for 1 to 24 h had a marked mycoplasmacidal effect. A comparison of the mycoplasma inactivation profiles showed that strains of selected species (
M
ycoplasma synoviae
,
M
ycoplasma gallisepticum
,
M
ycoplasma orale
,
M
ycoplasma pneumoniae
, and
A
choleplasma laidlawii
) represent a set of strains that can be utilized to validate the effectiveness of mycoplasma clearance obtained by inactivation and viral purification processes used for the manufacture of an inactivated egg-based vaccine.
Distinct Patterns of Picocyanobacterial Communities in Winter and Summer in the Chesapeake Bay
Authors: Cai Haiyuan , Wang Kui , Huang Sijun , Jiao Nianzhi , Chen Feng
Published: March 2010

In the Chesapeake Bay, picocyanobacteria were usually 100-fold less abundant in winter than in summer. However, little is known about how picocyanobacterial populations shift between winter and summer in the bay. This is due mainly to undetectable winter picocyanobacterial populations in bacterial 16S rRNA clone libraries. In this study, the winter and summer picocyanobacterial populations in the bay were detected using picocyanobacterium-specific primers and were compared based on the analysis of rRNA internal transcribed spacer sequences. Temperature was found to be the dominant environmental factor controlling picocyanobacterial populations in the Chesapeake Bay. In the summer, marine cluster BSynechococcusdominated the upper bay, while a unique cluster, CB1 (marine cluster A [MC-A]Synechococcus), made up the vast majority in the middle and lower bay. In the winter, the picocyanobacteria shifted to completely different populations. Subclades CB6 and CB7, which belong to MC-ASynechococcusandCyanobium, respectively, made up the entire winter picocyanobacterial populations in the bay. Interestingly, the winter members in subclade CB6 clustered closely withSynechococcusCC9311, a coastal strain known to have a greater capacity to sense and respond to changing environments than oceanic strains.
Differential Regulation by Heat Stress of Novel Cytochrome P450 Genes from the Dinoflagellate Symbionts of Reef-Building Corals
Authors: Rosic Nedeljka N. , Pernice Mathieu , Dunn Simon , Dove Sophie , Hoegh-Guldberg Ove
Published: March 2010

Exposure to heat stress has been recognized as one of the major factors leading to the breakdown of the coral-alga symbiosis and coral bleaching. Here, we describe the presence of three new cytochrome P450 (
CYP
) genes from the reef-building coral endosymbiont
Symbiodinium
(type C3) and changes in their expression during exposure to severe and moderate heat stress conditions. Sequence analysis of the
CYP
C-terminal region and two conserved domains, the “PERF” and “heme-binding” domains, confirmed the separate identities of the
CYP
genes analyzed. In order to explore the effects of different heat stress scenarios, samples of the scleractinian coral
Acropora millepora
were exposed to elevated temperatures incrementally over an 18-h period (rapid thermal stress) and over a 120-h period (gradual thermal stress). After 18 h of gradual heating and incubation at 26°C, the
Symbiodinium CYP
mRNA pool was approximately 30% larger, while a further 6°C increase to a temperature above the average sea temperature (29°C after 72 h) resulted in a 2- to 4-fold increase in
CYP
expression. Both rapid heat stress and gradual heat stress at 32°C resulted in 50% to 90% decreases in
CYP
gene transcript abundance. Consequently, the initial upregulation of expression of
CYP
genes at moderately elevated temperatures (26°C and 29°C) was followed by a decrease in expression under the greater thermal stress conditions at 32°C. These findings indicate that in the coral-alga symbiosis under heat stress conditions there is production of chemical stressors and/or transcriptional factors that regulate the expression of genes, such as the genes encoding cytochrome P450 monooxygenases, that are involved in the first line of an organism's chemical defense.
Cloning and Biochemical Characterization of a Novel Carbendazim (Methyl-1
H
-Benzimidazol-2-ylcarbamate)-Hydrolyzing Esterase from the Newly Isolated
Nocardioides
sp. Strain SG-4G and Its Potential for Use in Enzymatic Bioremediation
Authors: Pandey Gunjan , Dorrian Susan J. , Russell Robyn J. , Brearley Clint , Kotsonis Steven , Oakeshott John G.
Published: March 2010

A highly efficient carbendazim (methyl-1
H
-benzimidazol-2-ylcarbamate, or MBC)-mineralizing bacterium was isolated from enrichment cultures originating from MBC-contaminated soil samples. This bacterium,
Nocardioides
sp. strain SG-4G, hydrolyzed MBC to 2-aminobenzimidazole, which in turn was converted to the previously unknown metabolite 2-hydroxybenzimidazole. The initial steps of this novel metabolic pathway were confirmed by growth and enzyme assays and liquid chromatography-mass spectrometry (LC-MS) studies. The enzyme responsible for carrying out the first step was purified and subjected to N-terminal and internal peptide sequencing. The cognate gene, named
mheI
(for MBC-hydrolyzing enzyme), was cloned using a reverse genetics approach. The MheI enzyme was found to be a serine hydrolase of 242 amino acid residues. Its nearest known relative is an uncharacterized hypothetical protein with only 40% amino acid identity to it. Codon optimized
mheI
was heterologously expressed in
Escherichia coli
, and the His-tagged enzyme was purified and biochemically characterized. The enzyme has a

K
m

and
k
cat
of 6.1 μM and 170 min
−1
, respectively, for MBC. Radiation-killed, freeze-dried SG-4G cells showed strong and stable MBC detoxification activity suitable for use in enzymatic bioremediation applications.
Phylogenetic Approach to the Variability of the Microsporidian
Enterocytozoon bieneusi
and Its Implications for Inter- and Intrahost Transmission
Authors: Henriques-Gil Nuno , Haro María , Izquierdo Fernando , Fenoy Soledad , del Águila Carmen
Published: March 2010

Enterocytozoon bieneusi
is a microsporidian parasite that infects many vertebrate animals, including humans. The rDNA internal transcribed spacer (ITS) shows a hypervariable sequence; however, so far no clear information has been inferred about strain evolution in this species. We reviewed all the sequences described and performed a phylogenetic study. Four groups of sequences strongly differentiated from each other were detected, although most of the isolates (94%) corresponded to group I. The highly diverse sequences of this group were analyzed using median-joining networks. The host species (humans, pets, swine, cattle, birds, and wild animals) and the continents of origin of the isolates were considered. Central haplotypes in the network were obtained from very diverse hosts and geographical origins. The results show that although
E. bieneusi
has a broad host specificity, transmission is not completely free: some strains were able to circulate within a given host species and were only occasionally transmitted to another host. Additionally, while not relevant for swine or cattle hosts, geography seems to be a relevant factor for human infection by
E. bieneusi
.
Five-Year Cohort Study of
Nosema
spp. in Germany: Does Climate Shape Virulence and Assertiveness of
Nosema ceranae
?
Authors: Gisder Sebastian , Hedtke Kati , Möckel Nadine , Frielitz Marie-Charlotte , Linde Andreas , Genersch Elke
Published: March 2010

Nosema ceranae
and
Nosema apis
are two fungal pathogens belonging to the phylum Microsporidia and infecting the European honeybee,
Apis mellifera
. Recent studies have suggested that
N. ceranae
is more virulent than
N. apis
both at the individual insect level and at the colony level. Severe colony losses could be attributed to
N. ceranae
infections, and an unusual form of nosemosis is caused by this pathogen. In the present study, data from a 5-year cohort study of the prevalence of
Nosema
spp. in Germany, involving about 220 honeybee colonies and a total of 1,997 samples collected from these colonies each spring and autumn and analyzed via species-specific PCR-restriction fragment length polymorphism (RFLP), are described. Statistical analysis of the data revealed no relation between colony mortality and detectable levels of infection with
N. ceranae
or
N. apis
. In addition,
N. apis
is still more prevalent than
N. ceranae
in the cohort of the German bee population that was analyzed. A possible explanation for these findings could be the marked decrease in spore germination that was observed after even a short exposure to low temperatures (+4°C) for
N. ceranae
only. Reduced or inhibited
N. ceranae
spore germination at low temperatures should hamper the infectivity and spread of this pathogen in climatic regions characterized by a rather cold winter season.
Selection of Bifidobacteria Based on Adhesion and Anti-Inflammatory Capacity
In Vitro
for Amelioration of Murine Colitis
Authors: Preising Julia , Philippe David , Gleinser Marita , Wei Hua , Blum Stephanie , Eikmanns Bernhard J. , Niess Jan-Hendrik , Riedel Christian U.
Published: March 2010

Adhesion and anti-inflammatory properties of eight strains of bifidobacteria were tested using the intestinal epithelial cell lines Caco-2, T84, and HT29. Two strains were selected for further assessment of their anti-inflammatory capacity in two murine models of colitis.
In vivo
results confirmed the high anti-inflammatory capacity of a
Bifidobacterium bifidum
strain.
Polo-Like Kinase Guides Cytokinesis in Trypanosoma brucei through an Indirect Means
Authors: Li Zhi , Umeyama Takashi , Li Ziyin , Wang Ching C.
Published: March 2010

Polo-like kinase in
Trypanosoma brucei
(TbPLK) is confined to the flagellum attachment zone (FAZ) and regulates only cytokinetic initiation. However, it apparently diffuses into the cytoplasm before the
trans
-localization of chromosomal passenger complex (CPC) from the midzone of central spindle to FAZ, which is known to be required for initiating cytokinesis. Synchronized
T. brucei
procyclic cells treated with a TbPLK inhibitor, GW843682X (GW), in late S phase were found to go through a full cell cycle at a normal pace before being arrested at cytokinetic initiation in the second cycle. However, synchronized cells treated with GW in G
1
phase were arrested at cytokinetic initiation within the first cell cycle, suggesting that inhibition of TbPLK at its emergence blocks cytokinesis within the same cell cycle. To rule out potential off-target effects from GW, TbPLK RNA interference (RNAi) was induced to deplete TbPLK, and the progression of synchronized cells from late S phase was also found to be arrested at cytokinetic initiation within the first cell cycle. Apparently, TbPLK has accomplished its role in guiding cytokinesis before the late S phase, presumably by phosphorylating a certain substrate(s) during S phase, which may play a critical role in initiating the subsequent cytokinesis.
Plasmodium falciparum PF10_0164 (ETRAMP10.3) Is an Essential Parasitophorous Vacuole and Exported Protein in Blood Stages
Authors: MacKellar Drew C. , O'Neill Matthew T. , Aly Ahmed S. I. , Sacci John B. , Cowman Alan F. , Kappe Stefan H. I.
Published: March 2010

Upregulated in infectious sporozoites gene 4 (
UIS4
) encodes a parasitophorous vacuole membrane protein expressed in the sporozoite and liver stages of rodent malaria parasites. Parasites that lack
UIS4
arrest in early liver-stage development, and vaccination of mice with
uis4
−
sporozoites confers sterile protection against challenge with infectious sporozoites. Currently, it remains unclear whether an ortholog of
UIS4
is carried in the human malaria parasite
Plasmodium falciparum
, although the gene
PF10_0164
has been identified as a candidate ortholog for
UIS4
on the basis of synteny and structural similarity of the encoded protein. We show that PF10_0164 is expressed in sporozoites and blood stages of
P. falciparum
, where it localizes to the parasitophorous vacuole, and is also exported to the host erythrocyte.
PF10_0164
is refractory to disruption in asexual blood stages. Functional complementation was tested in
Plasmodium yoelii
by replacing the endogenous copy of
UIS4
with
PF10_0164
. PF10_0164 localized to the parasitophorous vacuole membrane of liver stages, but transgenic parasites did not complete liver-stage development in mice. We conclude that PF10_0164 is a parasitophorous vacuole protein that is essential in asexual blood stages and that does not complement
P. yoelii
UIS4, and it is thus likely not a functional ortholog of UIS4.
Molecular Characterization of the Interaction ofBorrelia parkeriandBorrelia turicataewith Human Complement Regulators
Authors: Schott Melanie , Grosskinsky Sonja , Brenner Christiane , Kraiczy Peter , Wallich Reinhard
Published: March 2010

In North America, tick-borne relapsing fever is caused by the speciesBorrelia hermsii,B. parkeri, andB. turicatae, which are transmitted to humans through the bite of the respective infected tick vectors. Here we describe the identification and functional characterization of a surface lipoprotein ofB. parkeri, designated BpcA, that binds the human complement regulators factor H and factor H-related protein 1 and, simultaneously, the host protease plasminogen. In contrast, the homologousB. turicataeprotein failed to bind human factor H and factor H-related protein 1 but retained its plasminogen binding capacity. Factor H bound to BpcA maintains its regulatory capacity to control C3b deposition and C3 convertase activity. Ectopic expression of BpcA in a serum-sensitiveB. burgdorferistrain protects transformed cells from complement-mediated killing. Furthermore, bound plasminogen/plasmin endowsB. parkeriandB. turicataewith the potential to degrade extracellular matrix components. These findings expand our understanding of the putative recent evolutionary separation ofBorrelia parkeriandBorrelia turicatae, provide evidence thatB. parkeridiffers fromB. turicataein its ability to resist complement attack, and may help in understanding the pathological processes underlying tick-borne relapsing fever.
Identification of the Targets of Cross-Reactive Antibodies Induced byStreptococcus pneumoniaeColonization
Authors: Roche Aoife M. , Weiser Jeffrey N.
Published: March 2010

Much of the efficacy of current pneumococcal conjugate vaccines lies in their ability to decrease carriage of vaccine serotypes in the population. Novel and more-broadly acting vaccines would also need to target carriage in order to be as effective. We have previously shown that model murine carriage ofStreptococcus pneumoniaecan elicit antibody-dependent immunity and can protect against a virulent heterologous challenge strain. This study set out to identifyS. pneumoniaesurface antigens that may elicit cross-reactive antibodies following colonization. Western blot analysis using sera from colonized mice identified the previously characterized immunogens pneumococcal surface protein A (PspA), putative proteinase maturation protein A (PpmA), and pneumococcal surface adhesin A (PsaA) as such antigens. Using flow cytometry, PspA was found to be the major target of surface-bound cross-reactive IgG in sera from TIGR4Δcps-colonized mice, with a modest contribution from PpmA and none from PsaA. In human sera, however, only mutants lacking PpmA were shown to have reduced binding of surface IgG compared to wild-type strains, suggesting that prior exposure toS. pneumoniaein humans may induce PpmA antibodies. We also investigated if cross-reactive antibodies induced by these antigens may be cross-protective against carriage. Despite the immunogenicity of PspA, PpmA, and PsaA, mice were still protected following colonization with mutants lacking these antigens, suggesting they are not necessary for cross-protection induced by carriage. Our findings suggest that a whole-organism approach may be needed to broadly diminish carriage.
Chlamydia muridarumT-Cell Antigens Formulated with the Adjuvant DDA/TDB Induce Immunity against Infection That Correlates with a High Frequency of Gamma Interferon (IFN-γ)/Tumor Necrosis Factor Alpha and IFN-γ/Interleukin-17 Double-Positive CD4+T Cells
Authors: Yu Hong , Jiang Xiaozhou , Shen Caixia , Karunakaran Karuna P. , Jiang Janina , Rosin Nicole L. , Brunham Robert C.
Published: March 2010

Major impediments to developing aChlamydiavaccine lie in identifying immunologically relevant T-cell antigens and delivery in a manner to stimulate protective immunity. Using an immunoproteomic approach, we previously identified three immunodominantChlamydiaT-cell antigens (PmpG-1, PmpE/F-2, and RplF). Because RplF has high homology to a human ortholog, it may not be suitable for human vaccine development. Therefore, in this study, we evaluated protection againstChlamydiainfection in the genital tract in C57BL/6 mice immunized withChlamydia-specific membrane proteins PmpG-1, PmpE/F-2, and major outer membrane protein (MOMP; as a reference) or a combination of them formulated with one of three adjuvants, CpG oligodeoxynucleotide (CpG-ODN), AbISCO-100 (AbISCO), or DDA/TDB (dimethyldioctadecylammonium bromide/d-(+)-trehalose 6,6′-dibehenate). The results show that immunization with the CpG-ODN formulation failed to provide protection againstChlamydiainfection; the AbISCO formulation conferred moderate protection, and the DDA/TDB formulation showed the highest degree of protective efficacy. The combination of PmpG-1, PmpE/F-2, and MOMP proteins formulated with DDA/TDB exhibited the greatest degree of protection among all vaccine groups studied. Moreover, this vaccine combination also engendered significant protection in BALB/c mice, which have a different major histocompatibility complex (MHC) background. We measured cell-mediated immune cytokine responses in mice immunized with PmpG-1 mixed with each of the three adjuvants. The results demonstrate that mice immunized with the DDA/TDB formulation induced the strongest gamma interferon (IFN-γ) and interleukin-17 (IL-17) responses, characterized by the highest frequency of IFN-γ/tumor necrosis factor alpha (TNF-α) and IFN-γ/IL-17 double-positive CD4+T cells. In conclusion, aChlamydiavaccine based on the recombinant proteins PmpG-1, PmpE/F-2, and MOMP delivered in a DDA/TDB adjuvant conferred protection against infection that correlated with IFN-γ/TNF-α and IFN-γ/IL-17 double-positive CD4+T cells.
Inflammatory changes in the aneurysm wall: a review
Authors: Tulamo Riikka , Frösen Juhana , Hernesniemi Juha , Niemelä Mika
Published: March 2010

Rupture of a saccular intracranial artery aneurysm (IA) causes subarachnoid hemorrhage, a significant cause of stroke and death. The current treatment options, endovascular coiling and clipping, are invasive and somewhat risky. Since only some IAs rupture, those IAs at risk for rupture should be identified. However, to improve the imaging of rupture-prone IAs and improve IA treatment, IA wall pathobiology requires more thorough knowledge. Chronic inflammation has become understood as an important phenomenon in IA wall pathobiology, featuring inflammatory cell infiltration as well as proliferative and fibrotic remodulatory responses. We review the literature on what is known about inflammation in the IA wall and also review the probable mechanisms of how inflammation would result in the degenerative changes that ultimately lead to IA wall rupture. We also discuss current options in imaging inflammation and how knowledge of inflammation in IA walls may improve IA treatment.
Geochemical factors controlling the accumulation and dispersal of heavy metals in the Bay of Fundy sediments
Authors: Loring D. H.
Published: March 2010

Total Zn, Cu, Pb, Co, Ni, Cr, V, Hg, Be, As, Ba, and Se concentrations vary regionally and in response to textural variations of the sediments of the Bay of Fundy. They are, except for local anomalies, at or near natural levels in relation to their source rocks and other unpolluted marine sediments.Chemical partition indicates that small but significant amounts (1–27%) of the total element concentrations are potentially available to the biota. Potential bioavailable metals are derived from natural and industrial sources and are held in the sediments by fine grained organic material (Hg, Pb), hydrous iron oxides (Cr, V, Co, Pb), ion exchange positions (Zn), and calcareous components (Cu, Zn, Ba).Of the total metal content, however, 73–99% is not readily available to the biota but held in various sulphide (Zn, Cu, Pb, As, Se), oxide (Cr, Ni, Co, V), and silicate minerals (Cr, V, Co, Ni). The host minerals have accumulated at the same rates as other detrital material except for particles of zinc oxide that have been derived from industrial sources adjacent to the Bay of Fundy. The accumulations of fine grained host minerals are the main control on the abundance and distribution of Hg, Be, Zn, Pb, and As in the sediments whereas the dispersal of the ferromagnesian silicates and various oxide minerals, rather than the grain size of their hosts, accounts for dispersal of Cr, V, Co, and Ni in the sediments. These factors together with the present depositional pattern of the particles account for the accumulation and relative enrichment of most metals along with other fine grained materials in the "Quoddy region" of the bay. Local anomalies of detrital minerals related to bedrock exposures also account for high concentrations of Cr, V, and Ni in the vicinity of Grand Manan Island and along the Nova Scotian coast. Relatively high metal concentrations also occur near a dredge dispersal site off St. John Harbour and may reflect the initial impact of anthropogenic inputs on the natural levels of metals in the Fundy sediments.
Interpretation of lead isotope data from zinc–lead mineralization in the northern part of the western Canadian Cordillera
Authors: Morrow D. W. , Cumming G. L.
Published: March 2010

Lead isotope data, from a group of seven zinc–lead deposits in Devonian carbonate strata of northeastern British Columbia, have very radiogenic and variable compositions and form a series of parallel linear arrays on Pb/Pb diagrams. These arrays are entirely separate from the less radiogenic and much less variable lead compositions of the Devonian shale-hosted zinc–lead deposits in the laterally adjacent Paleozoic basinal sequence, which themselves define steeply dipping linear trends. Both of these types of arrays reflect multistage histories during the evolution of Pb compositions. One stage may have been a period of residence of Pb in uranium-rich Paleozoic shale, which caused the development of the radiogenic leads that were emplaced later in the carbonate-hosted zinc–lead deposits.Unlike the Devonian carbonate-hosted deposits the "Silver-rich vein" group of deposits is homogeneous in Pb isotope composition. This contrast in the isotopic homogeneity between deposits may reflect differences in the mechanisms by which these deposits formed.
An assessment of the age and tectonic setting of volcanics near the base of the Windermere Supergroup in northeastern Washington: implications for latest Proterozoic – earliest Cambrian continental separation
Authors: Devlin William J. , Bond Gerard C. , Brueckner Hannes K.
Published: March 2010

Mafic metavolcanics of the Huckleberry Formation in northeastern Washington occur near the base of the Windermere Supergroup, a sequence of immature clastic rocks thought to have been deposited during a rift event associated with the establishment of the early Paleozoic miogeocline of the North American Cordillera. Previously reported K–Ar data from the Huckleberry volcanics yielded a wide scatter of ages, with a preferred age of extrusion of between 827 and 918 Ma, in apparent agreement with the Late Proterozoic (800–900 Ma) age assigned to this rift event based on geologic relations and ages from the youngest rocks unconformably underlying the Windermere Supergroup. Quantitative subsidence analyses that have been recently applied to the post-rift strata of the miogeocline yield ages for the final phases of rifting, which led directly to continental separation and the onset of sea-floor spreading, of 555–600 Ma. A significant problem arises between the older ages for rifting and the younger ages for breakup, since it implies that a rift phase preceding breakup could have spanned more than 200 Ma.This paper presents new geochemical and isotopic data from the same exposures of Huckleberry volcanics analyzed by K–Ar techniques in an attempt to assess their tectonic setting and age of extrusion. Major- and trace-element compositions are found to be consistent with the rift setting previously interpreted for the Windermere Supergroup. Isotopic analyses, although inconclusive with respect to the true age of the Huckleberry volcanics, indicate that the Rb–Sr system has been disturbed subsequent to extrusion of the volcanics, and therefore the K–Ar ages should be considered suspect. Isotopic data that are beginning to emerge from the northern Canadian Cordillera indicate that the Windermere Supergroup may in fact be younger, in closer agreement with the ages for breakup indicated by the subsidence analyses.
Faunal distributions across the Ordovician–Silurian boundary, Anticosti Island and Percé, Québec, Canada
Authors: Lespérance Pierre J.
Published: March 2010

The disappearances of typical Ordovician taxa are staggered within the strata of member 7 of the Ellis Bay Formation and immediately above on Anticosti Island. The appearances of typical Silurian taxa on Anticosti Island are also staggered, but range from member 7 into the typical Becscie Formation. The Hirnantia brachiopod fauna and the Mucronaspis trilobite fauna of the Percé area are younger than the base of the Gamachian and are of the persculptus Zone. An ordered succession of appearances on Anticosti Island and the Oslo region is demonstrated: the lower boundary of the Oulodus? nathani conodont Zone, then the brachiopods Zygospiraella and Stricklandia, and then the trilobite Acernaspis. The acuminatus Zone within the Anticosti Island and Percé sequences cannot be recognized as such; its lower boundary is, however, drawn on the basis of the first appearance of Acernaspis, in accordance with what is known of the first occurrence of this trilobite in Europe and Asia. The Anticosti Island and Percé area sequences are taken to represent continuous uninterrupted deposition without strong palaeoecological control on the evolving faunas in either place; each taxonomic unit evolved at its own rate.
Evidence for magma heterogeneity in the White River Ash (Yukon Territory)
Authors: Downes Hilary
Published: March 2010

Two Recent Plinian eruptions in the Wrangell Mountains (southeast Alaska) gave rise to two distinct ash-fall deposits that are collectively known as the White River Ash and cover much of the Yukon Territory, northwest Canada. Analysis of the pumiceous glass indicates that the magma chamber was compositionally inhomogeneous prior to each eruption. No compositional stratigraphy has been detected in the deposits, indicating either thorough mixing in the eruption cloud or thorough reworking after deposition. Thus each individual sample of ash represents a large part of the magma chamber, whereas larger pumice fragments are more homogeneous. Variations in temperature, 950–990 and 995–1030 °C, respectively, for the older and younger eruptions, and −log fo2 values, 9.3–8.3 and 8.3–7.7, derived from the Fe–Ti oxides, support the conclusion that the magma chamber was inhomogeneous.
A COSMOLOGICAL MODEL WITH FERMIONIC FIELD AND GAUSS–BONNET TERM
Authors: RAKHI R. , VIJAYAGOVINDAN G. V. , INDULEKHA K. , ABRAHAM NOBLE P.
Published: March 2010

In this work, a cosmological model inspired by string theory with Gauss–Bonnet term coupled to the fermionic field is taken into consideration. The self-interaction potential is considered as a combination of the scalar and pseudoscalar invariants. Here the cosmological contribution of the coupling of Gauss–Bonnet term with a non-Dirac fermionic field — characterized by an interaction term[Formula: see text] — is investigated. It is observed that the new type of coupling plays a significant role in the accelerating behavior of the universe. Specifically, in addition to the late time acceleration for the universe, [Formula: see text] produces an early decelerating behavior. The behavior of the equation-of-state parameter (w) is such that it guarantees the stability of the theory.
POST-ANNEALING EFFECTS ON THE STRUCTURAL, OPTICAL AND ELECTRICAL PROPERTIES OF ITO FILMS STUDIED BY SPECTROSCOPIC ELLIPSOMETRY
Authors: INRITSAPONG Y. , CHINDAUDOM P. , NUNTAWONG N. , PATTHANASETTHAKUL V. , HORPHATHUM M. , EIAMCHAI P. , POKAIPISIT A. , LIMSUWAN P.
Published: March 2010

ITO thin films were coated on unheated glass and Si -wafer (100) substrates by ion-assisted evaporation. The effects of post annealing, in vacuum at 250°C and 350°C for 1 h, on the structural, optical and electrical properties were studied. The structure was characterized by X-ray diffraction (XRD). The surface morphology of the films was investigated by atomic force microscopy (AFM). The optical properties were evaluated by spectrophotometer and spectroscopic ellipsometry (SE). The resistivity was measured by the four-point probes method. It was found that the increase of post-annealing temperature would improve the film crystallinity and electrical properties. The preferred orientation of ITO thin film after annealing is (222). The resistivity of the as-deposited film is found to be 5.52 × 10-4 Ωcm and decreases to 2.11 × 10-4 Ωcm after annealing at 350°C. The AFM image reveals that the surface roughness decreases with increasing annealing temperature. The uniqueness test based on SE analysis data has been applied for ITO modeling. This modeling indicates that the film microstructure consists of three layers including the higher-index ITO layer, the effective medium approximation (EMA) layer to represent a slightly lower optical index, and the surface roughness layer on top. The EMA thickness and its relative composition decrease with increasing annealing temperature. The extinction coefficient in the IR region increases whereas the refractive index decreases with increasing annealing temperature.
HOLOGRAPHIC DARK ENERGY FROM A MODIFIED GBIG SCENARIO
Authors: NOZARI KOUROSH , RASHIDI NARGES
Published: March 2010

We construct a holographic dark energy model in a braneworld setup where gravity is induced on the brane embedded in a bulk with the Gauss–Bonnet curvature term. We include possible modifications of the induced gravity and its coupling with a canonical scalar field on the brane. Through a perturbational approach to calculating the effective gravitation constant on the brane, we examine the outcome of this model as a candidate for holographic dark energy.
CHROMOSOMES AS INTERDEPENDENT ACCOUNTING UNITS: THE ASSIGNED ORIENTATION OFC. ELEGANSCHROMOSOMES MINIMIZES THE TOTAL W-BASE CHARGAFF DIFFERENCE
Authors: FORSDYKE DONALD R. , ZHANG CHIYU , WEI JI-FU
Published: March 2010

DNAs of individual chromosomes violate, albeit perhaps by only one in a thousand bases, Chargaff's second parity rule, which is that Chargaff's first parity rule for duplex DNA (A = T, G = C) applies, to a close approximation, to single stranded DNA. If the "top" strand of one chromosome has A > T and the "top" strand of another has T > A, can they complement to approach even parity (A = T)? Assignment of orientation to the six chromosomes of Caenorhabditis elegans is said to have been arbitrary and, of 26(= 64) possible combinations of top (T) and bottom (B) strands, the GenBank orientation (designated "TTTTTT") is but one. Yet, for the W bases (A and T) the chromosomes in the GenBank orientation complement to reduce the Chargaff difference (A–T) to only 200 bases (i.e. only one in 323,658 bases does not have a potential Watson-Crick pairing partner). This suggests that the assignment was not arbitrary. However, the GenBank orientation for the S bases (G and C) allows an approach to even parity less well than many other orientations, the best of which is BBBBTT (indicating a disparity between the GenBank orientations of the first four autosomes and those of chromosomes V and X). Although only the euchromatic regions of Drosophila melanogaster chromosomes have been sequenced, there are orientations that allow an approach to even parity. We conclude that, with respect to their Chargaff differences, the chromosomes of C. elegans have the potential to engage in interdependent base accounting. Since this might also apply to D. melanogaster, even when heterochromatin-associated DNA rich in tandem repeats (microsatellite DNA) is excluded, then heterochromatic DNA might not normally participate in the hypothetical accounting process.
NONLINEAR NON-EQUILIBRIUM PATTERN FORMATION IN A SPATIAL AQUATIC SYSTEM: EFFECT OF FISH PREDATION
Authors: UPADHYAY RANJIT KUMAR , THAKUR N. K. , DUBEY B.
Published: March 2010

An attempt has been made to introduce the mathematical modeling of nonlinear non-equilibrium spatio-temporal pattern formation in a minimal model of a spatial aquatic system. A hybrid model of the spatio-temporally continuous phytoplankton-zooplankton system with Holling type IV predator response but discrete agents like fish dynamics has been presented. The model has been investigated for plankton patch formation, which is known from natural plankton populations. Fish predation has a significant role in the temporal evolution of spatial pattern of phytoplankton-zooplankton system, which suggests that unstable diffusive system can be made stable by increasing the rate of fish predation and diffusivity constant to sufficiently large values.
FLEXIBILITY AND MOBILITY IN MESOPHILIC AND THERMOPHILIC HOMOLOGOUS PROTEINS FROM MOLECULAR DYNAMICS AND FOLDUNFOLD METHOD
Authors: MAMONOVA TATYANA B. , GLYAKINA ANNA V. , KURNIKOVA MARIA G. , GALZITSKAYA OXANA V.
Published: March 2010

To function properly protein molecules require both flexibility and rigidity, therefore fast and accurate prediction of protein rigidity/flexibility is one of the important problems in protein science. In this work we used two theoretical approaches to determine flexible regions in four homologous pairs of proteins from thermophilic and mesophilic organisms. Protein pairs chosen in this study were selected to represent four typical folding classes. Our first approach, FoldUnfold, uses amino acid sequence and statistical information on the density of contacts of amino acids in tertiary structures of known globular proteins. The main advantages of such knowledge-based methodology are its computational speed and ability to make predictions in the absence of three-dimensional (3D) structure of a protein. The second approach uses a graph theory-based rigid cluster decomposition termed FIRST, applied together with Molecular Dynamics (MD) simulations of proteins with known structure. While MD simulations are time-consuming, they are the most direct way of studying physical properties of proteins, including their rigidity/flexibility. Flexible regions predicted by both methods in this work were in good agreement with each other. We also showed that high mobility of a site is not necessarily indicative of its high flexibility and vice versa. In our simulations thermophile proteins were less flexible than their mesophilic homologues. Longer flexible loops were found in mesophilic proteins of all classes.
ON INTER-STOREY DRIFT LIMITATION OF STEEL–CONCRETE HYBRID STRUCTURES FOR TALL BUILDINGS
Authors: LI G. Q. , DING X. , CHEN S. W.
Published: March 2010

The inter-storey drift limitation is an important index for the structural design of tall buildings. The inter-storey drift limitation of steel-hybrid structures for tall buildings is studied in this paper. It is found that it is more reasonable to divide the inter-storey drift of steel–concrete hybrid structures into harmless part and harmful part. It is meaningful to limit the harmful drift for preventing the crack of concrete walls in hybrid structures. A formula to calculate the allowable harmful inter-storey drift with no cracks of concrete walls is deduced for hybrid structures for tall buildings. The effectiveness of the formula is verified through the FEM analysis of a typical tall building hybrid structure.
FinFET-based power simulator for interconnection networks
Authors: Lee Chun-Yi , Jha Niraj K.
Published: March 2010

Double-gate FETs, specifically FinFETs, are emerging as promising substitutes for bulk CMOS at the 32nm technology node and beyond because of the various obstacles to scaling faced by CMOS, such as short-channel effects, leakage power, and process variations. Another trend in chip multiprocessor design is incorporation of sophisticated on-chip interconnection networks. However, such networks are significant power-consumers. In this article, we address these two trends by presenting a power simulator for FinFET-based on-chip interconnection networks. It estimates both dynamic and leakage power. We present results for various FinFET design styles and temperatures (since leakage power changes drastically with temperature), and show that one FinFET design style may be much superior to another from the power consumption point of view.