bluuebunny/crossref_metadata_2025 huggingface dataset:
A Vector Library for Silencing Central Carbon Metabolism Genes with Antisense RNAs in Escherichia coli
Authors: Nakashima Nobutaka , Ohno Satoshi , Yoshikawa Katsunori , Shimizu Hiroshi , Tamura Tomohiro
Published: November 2013

We describe here the construction of a series of 71 vectors to silence central carbon metabolism genes in
Escherichia coli
. The vectors inducibly express antisense RNAs called paired-terminus antisense RNAs, which have a higher silencing efficacy than ordinary antisense RNAs. By measuring mRNA amounts, measuring activities of target proteins, or observing specific phenotypes, it was confirmed that all the vectors were able to silence the expression of target genes efficiently. Using this vector set, each of the central carbon metabolism genes was silenced individually, and the accumulation of metabolites was investigated. We were able to obtain accurate information on ways to increase the production of pyruvate, an industrially valuable compound, from the silencing results. Furthermore, the experimental results of pyruvate accumulation were compared to
in silico
predictions, and both sets of results were consistent. Compared to the gene disruption approach, the silencing approach has an advantage in that any
E. coli
strain can be used and multiple gene silencing is easily possible in any combination.
Vibrio vulnificus Bacteriophage SSP002 as a Possible Biocontrol Agent
Authors: Lee Hyun Sung , Choi Slae , Shin Hakdong , Lee Ju-Hoon , Choi Sang Ho
Published: November 2013

A novel
Vibrio vulnificus
-infecting bacteriophage, SSP002, belonging to the
Siphoviridae
family, was isolated from the coastal area of the Yellow Sea of South Korea. Host range analysis revealed that the growth inhibition of phage SSP002 is relatively specific to
V. vulnificus
strains from both clinical and environmental samples. In addition, a one-step growth curve analysis and a bacteriophage stability test revealed a latent period of 65 min, a burst size of 23 ± 2 PFU, as well as broad temperature (20°C to 60°C) and pH stability (pH 3 to 12) ranges. A Tn
5
random transposon mutation of
V. vulnificus
and partial DNA sequencing of the inserted Tn
5
regions revealed that the
flhA
,
flhB
,
fliF
, and
fleQ
mutants are resistant to SSP002 phage infection, suggesting that the flagellum may be the host receptor for infection. The subsequent construction of specific gene-inactivated mutants (
flhA
,
flhB
,
fliF
, and
fleQ
) and complementation experiments substantiated this. Previously, the genome of phage SSP002 was completely sequenced and analyzed. Comparative genomic analysis of phage SSP002 and
Vibrio parahaemolyticus
phage vB_VpaS_MAR10 showed differences among their tail-related genes, supporting different host ranges at the species level, even though their genome sequences are highly similar. An additional mouse survival test showed that the administration of phage SSP002 at a multiplicity of infection of 1,000 significantly protects mice from infection by
V. vulnificus
for up to 2 months, suggesting that this phage may be a good candidate for the development of biocontrol agents against
V. vulnificus
infection.
Use of Bacteroidales Microbial Source Tracking To Monitor Fecal Contamination in Fresh Produce Production
Authors: Ravaliya Kruti , Gentry-Shields Jennifer , Garcia Santos , Heredia Norma , Fabiszewski de Aceituno Anna , Bartz Faith E. , Leon Juan S. , Jaykus Lee-Ann
Published: November 2013

In recent decades, fresh and minimally processed produce items have been associated with an increasing proportion of food-borne illnesses. Most pathogens associated with fresh produce are enteric (fecal) in origin, and contamination can occur anywhere along the farm-to-fork chain. Microbial source tracking (MST) is a tool developed in the environmental microbiology field to identify and quantify the dominant source(s) of fecal contamination. This study investigated the utility of an MST method based on
Bacteroidales
16S rRNA gene sequences as a means of identifying potential fecal contamination, and its source, in the fresh produce production environment. The method was applied to rinses of fresh produce, source and irrigation waters, and harvester hand rinses collected over the course of 1 year from nine farms (growing tomatoes, jalapeño peppers, and cantaloupe) in Northern Mexico. Of 174 samples, 39% were positive for a universal
Bacteroidales
marker (AllBac), including 66% of samples from cantaloupe farms (3.6 log
10
genome equivalence copies [GEC]/100 ml), 31% of samples from tomato farms (1.7 log
10
GEC/100 ml), and 18% of samples from jalapeño farms (1.5 log
10
GEC/100 ml). Of 68 AllBac-positive samples, 46% were positive for one of three human-specific markers, and none were positive for a bovine-specific marker. There was no statistically significant correlation between
Bacteroidales
and generic
Escherichia coli
across all samples. This study provides evidence that
Bacteroidales
markers may serve as alternative indicators for fecal contamination in fresh produce production, allowing for determination of both general contamination and that derived from the human host.
PhaM Is the Physiological Activator of Poly(3-Hydroxybutyrate) (PHB) Synthase (PhaC1) in Ralstonia eutropha
Authors: Pfeiffer Daniel , Jendrossek Dieter
Published: November 2013

Poly(3-hydroxybutyrate) (PHB) synthase (PhaC1) is the key enzyme of PHB synthesis in
Ralstonia eutropha
and other PHB-accumulating bacteria and catalyzes the polymerization of 3-hydroxybutyryl-CoA to PHB. Activity assays of
R. eutropha
PHB synthase are characterized by the presence of lag phases and by low specific activity. It is assumed that the lag phase is caused by the time necessary to convert the inactive PhaC1 monomer into the active dimeric form by an unknown priming process. The lag phase can be reduced by addition of nonionic detergents such as hecameg [6-
O
-(
N
-heptyl-carbamoyl)-methyl-α-
d
-glucopyranoside], which apparently accelerates the formation of PhaC1 dimers. We identified the PHB granule-associated protein (PGAP) PhaM as the natural primer (activator) of PHB synthase activity. PhaM was recently discovered as a novel type of PGAP with multiple functions in PHB metabolism. Addition of PhaM to PHB synthase assays resulted in immediate polymerization of 3HB coenzyme A with high specific activity and without a significant lag phase. The effect of PhaM on (i) PhaC1 activity, (ii) oligomerization of PhaC1, (iii) complex formation with PhaC1, and (iv) PHB granule formation
in vitro
and
in vivo
was shown by cross-linking experiments of purified proteins (PhaM, PhaC1) with glutardialdehyde, by size exclusion chromatography, and by fluorescence microscopic detection of
de novo
-synthesized PHB granules.
Newly Cultured Bacteria with Broad Diversity Isolated from Eight-Week Continuous Culture Enrichments of Cow Feces on Complex Polysaccharides
Authors: Ziemer Cherie J.
Published: November 2013

One of the functions of the mammalian large intestinal microbiota is the fermentation of plant cell wall components. In ruminant animals, the majority of their nutrients are obtained via pregastric fermentation; however, up to 20% can be recovered from microbial fermentation in the large intestine. Eight-week continuous culture enrichments of cattle feces with cellulose and xylan-pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented:
Firmicutes
(51.9%),
Bacteroidetes
(30.9%),
Proteobacteria
(11.1%),
Actinobacteria
(3.5%),
Synergistetes
(1.5%), and
Fusobacteria
(1.1%). The majority of bacterial isolates had <98.5% identity to cultured bacteria with sequences in the Ribosomal Database Project and thus represent new species and/or genera. Within the
Firmicutes
isolates, most were classified in the families
Lachnospiraceae
,
Ruminococcaceae
,
Erysipelotrichaceae
, and
Clostridiaceae
I. The majority of the
Bacteroidetes
were most closely related to
Bacteroides thetaiotaomicron
,
B. ovatus
, and
B. xylanisolvens
and members of the
Porphyromonadaceae
family. Many of the
Firmicutes
and
Bacteroidetes
isolates were related to species demonstrated to possess enzymes which ferment plant cell wall components; the others were hypothesized to cross-feed these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 98% of the isolates not represented as previously cultured, there are new opportunities to study the genomic and metabolic capacities of these members of the complex intestinal microbiota.
Phenotypic Effect of “Candidatus Rickettsiella viridis,” a Facultative Symbiont of the Pea Aphid (Acyrthosiphon pisum), and Its Interaction with a Coexisting Symbiont
Authors: Tsuchida Tsutomu , Koga Ryuichi , Fujiwara Akiko , Fukatsu Takema
Published: November 2013

A gammaproteobacterial facultative symbiont of the genus
Rickettsiella
was recently identified in the pea aphid,
Acyrthosiphon pisum
. Infection with this symbiont altered the color of the aphid body from red to green, potentially affecting the host's ecological characteristics, such as attractiveness to different natural enemies. In European populations of
A. pisum
, the majority of
Rickettsiella
-infected aphids also harbor another facultative symbiont, of the genus
Hamiltonella
. We investigated this
Rickettsiella
symbiont for its interactions with the coinfecting
Hamiltonella
symbiont, its phenotypic effects on
A. pisum
with and without
Hamiltonella
coinfection, and its infection prevalence in
A. pisum
populations. Histological analyses revealed that coinfecting
Rickettsiella
and
Hamiltonella
exhibited overlapping localizations in secondary bacteriocytes, sheath cells, and hemolymph, while
Rickettsiella
-specific localization was found in oenocytes.
Rickettsiella
infections consistently altered hosts' body color from red to green, where the greenish hue was affected by both host and symbiont genotypes.
Rickettsiella
-
Hamiltonella
coinfections also changed red aphids to green; this greenish hue tended to be enhanced by
Hamiltonella
coinfection. With different host genotypes,
Rickettsiella
infection exhibited either weakly beneficial or nearly neutral effects on host fitness, whereas
Hamiltonella
infection and
Rickettsiella
-
Hamiltonella
coinfection had negative effects. Despite considerable frequencies of
Rickettsiella
infection in European and North American
A. pisum
populations, no
Rickettsiella
infection was detected among 1,093 insects collected from 14 sites in Japan. On the basis of these results, we discuss possible mechanisms for the interaction of
Rickettsiella
with other facultative symbionts, their effects on their hosts' phenotypes, and their persistence in natural host populations. We propose the designation “
Candidatus
Rickettsiella viridis” for the symbiont.
Polycyclic Aromatic Hydrocarbon Degradation of Phytoplankton-Associated Arenibacter spp. and Description of Arenibacter algicola sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium
Authors: Gutierrez Tony , Rhodes Glenn , Mishamandani Sara , Berry David , Whitman William B. , Nichols Peter D. , Semple Kirk T. , Aitken Michael D.
Published: November 2013

Pyrosequencing of the bacterial community associated with a cosmopolitan marine diatom during enrichment with crude oil revealed several
Arenibacter
phylotypes, of which one (OTU-202) had become significantly enriched by the oil. Since members of the genus
Arenibacter
have not been previously shown to degrade hydrocarbons, we attempted to isolate a representative strain of this genus in order to directly investigate its hydrocarbon-degrading potential. Based on 16S rRNA sequencing, one isolate (designated strain TG409
T
) exhibited >99% sequence identity to three type strains of this genus. On the basis of phenotypic and genotypic characteristics, strain TG409
T
represents a novel species in the genus
Arenibacter
, for which the name
Arenibacter algicola
sp. nov. is proposed. We reveal for the first time that polycyclic aromatic hydrocarbon (PAH) degradation is a shared phenotype among members of this genus, indicating that it could be used as a taxonomic marker for this genus. Kinetic data for PAH mineralization rates showed that naphthalene was preferred to phenanthrene, and its mineralization was significantly enhanced in the presence of glass wool (a surrogate for diatom cell surfaces). During enrichment on hydrocarbons, strain TG409
T
emulsified
n
-tetradecane and crude oil, and cells were found to be preferentially attached to oil droplets, indicating an ability by the strain to express cell surface amphiphilic substances (biosurfactants or bioemulsifiers) as a possible strategy to increase the bioavailability of hydrocarbons. This work adds to our growing knowledge on the diversity of bacterial genera in the ocean contributing to the degradation of oil contaminants and of hydrocarbon-degrading bacteria found living in association with marine eukaryotic phytoplankton.
Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type
Authors: Carberry CIara A. , Waters Sinead M. , Kenny David A. , Creevey Christopher J.
Published: November 2013

Methane is an undesirable end product of rumen fermentative activity because of associated environmental impacts and reduced host feed efficiency. Our study characterized the rumen microbial methanogenic community in beef cattle divergently selected for phenotypic residual feed intake (RFI) while offered a high-forage (HF) diet followed by a low-forage (LF) diet. Rumen fluid was collected from 14 high-RFI (HRFI) and 14 low-RFI (LRFI) animals at the end of both dietary periods. 16S rRNA gene clone libraries were used, and methanogen-specific tag-encoded pyrosequencing was carried out on the samples. We found that
Methanobrevibacter
spp. are the dominant methanogens in the rumen, with
Methanobrevibacter smithii
being the most abundant species. Differences in the abundance of
Methanobrevibacter smithii
and
Methanosphaera stadtmanae
genotypes were detected in the rumen of animals offered the LF compared to the HF diet while the abundance of
Methanobrevibacter smithii
genotypes was different between HRFI and LRFI animals irrespective of diet. Our results demonstrate that while a core group of methanogen operational taxonomic units (OTUs) exist across diet and phenotype, significant differences were observed in the distribution of genotypes within those OTUs. These changes in genotype abundance may contribute to the observed differences in methane emissions between efficient and inefficient animals.
Substrate Promiscuity: AglB, the Archaeal Oligosaccharyltransferase, Can Process a Variety of Lipid-Linked Glycans
Authors: Cohen-Rosenzweig Chen , Guan Ziqiang , Shaanan Boaz , Eichler Jerry
Published: November 2013

Across evolution, N-glycosylation involves oligosaccharyltransferases that transfer lipid-linked glycans to selected Asn residues of target proteins. While these enzymes catalyze similar reactions in each domain, differences exist in terms of the chemical composition, length and degree of phosphorylation of the lipid glycan carrier, the sugar linking the glycan to the lipid carrier, and the composition and structure of the transferred glycan. To gain insight into how oligosaccharyltransferases cope with such substrate diversity, the present study analyzed the archaeal oligosaccharyltransferase AglB from four haloarchaeal species. Accordingly, it was shown that despite processing distinct lipid-linked glycans in their native hosts, AglB from
Haloarcula marismortui
,
Halobacterium salinarum
, and
Haloferax mediterranei
could readily replace their counterpart from
Haloferax volcanii
when introduced into
Hfx. volcanii
cells deleted of
aglB
. As the four enzymes show significant sequence and apparently structural homology, it appears that the functional similarity of the four AglB proteins reflects the relaxed substrate specificity of these enzymes. Such demonstration of AglB substrate promiscuity is important not only for better understanding of N-glycosylation in
Archaea
and elsewhere but also for efforts aimed at transforming
Hfx. volcanii
into a glycoengineering platform.
Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions
Authors: Javidpour Pouya , Pereira Jose H. , Goh Ee-Been , McAndrew Ryan P. , Ma Suzanne M. , Friedland Gregory D. , Keasling Jay D. , Chhabra Swapnil R. , Adams Paul D. , Beller Harry R.
Published: November 2013

Major efforts in bioenergy research have focused on producing fuels that can directly replace petroleum-derived gasoline and diesel fuel through metabolic engineering of microbial fatty acid biosynthetic pathways. Typically, growth and pathway induction are conducted under aerobic conditions, but for operational efficiency in an industrial context, anaerobic culture conditions would be preferred to obviate the need to maintain specific dissolved oxygen concentrations and to maximize the proportion of reducing equivalents directed to biofuel biosynthesis rather than ATP production. A major concern with fermentative growth conditions is elevated NADH levels, which can adversely affect cell physiology. The purpose of this study was to identify homologs of
Escherichia coli
FabG, an essential reductase involved in fatty acid biosynthesis, that display a higher preference for NADH than for NADPH as a cofactor. Four potential NADH-dependent FabG variants were identified through bioinformatic analyses supported by crystallographic structure determination (1.3- to 2.0-Å resolution).
In vitro
assays of cofactor (NADH/NADPH) preference in the four variants showed up to ∼35-fold preference for NADH, which was observed with the
Cupriavidus taiwanensis
FabG variant. In addition, FabG homologs were overexpressed in fatty acid- and methyl ketone-overproducing
E. coli
host strains under anaerobic conditions, and the
C. taiwanensis
variant led to a 60% higher free fatty acid titer and 75% higher methyl ketone titer relative to the titers of the control strains. With further engineering, this work could serve as a starting point for establishing a microbial host strain for production of fatty acid-derived biofuels (e.g., methyl ketones) under anaerobic conditions.
Improved Short-Sequence-Repeat Genotyping of Mycobacterium avium subsp. paratuberculosis by Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Ahlstrom Christina , Barkema Herman W. , De Buck Jeroen
Published: November 2013

Accurate sequence analysis of mononucleotide repeat regions is difficult, complicating the use of short sequence repeats (SSRs) as a tool for bacterial strain discrimination. Although multiple SSR loci in the genome of
Mycobacterium avium
subsp.
paratuberculosis
allow genotyping of
M. avium
subsp.
paratuberculosis
isolates with high discriminatory power, further characterization of the most discriminatory loci is limited due to inherent difficulties in sequencing mononucleotide repeats. Here, a method was evaluated using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as an alternative to Sanger sequencing to further differentiate the dominant mycobacterial interspersed repetitive-unit (MIRU)–variable-number tandem-repeat (VNTR)
M. avium
subsp.
paratuberculosis
type (
n
= 37) in Canadian dairy herds by targeting a highly discriminatory mononucleotide SSR locus. First, PCR-amplified DNA was digested with two restriction enzymes to yield a sufficiently small fragment containing the SSR locus. Second, MALDI-TOF MS was performed to identify the mass, and thus repeat length, of the target. Sufficiently intense, discriminating spectra were obtained to determine repeat lengths up to 15, an improvement over the limit of 11 using traditional sequencing techniques. Comparison to synthetic oligonucleotides and Sanger sequencing results confirmed a valid and reproducible assay that increased discrimination of the dominant
M. avium
subsp.
paratuberculosis
MIRU-VNTR type. Thus, MALDI-TOF MS was a reliable, fast, and automatable technique to accurately resolve
M. avium
subsp.
paratuberculosis
genotypes based on SSRs.
Type IV Pilus Biogenesis, Twitching Motility, and DNA Uptake in Thermus thermophilus: Discrete Roles of Antagonistic ATPases PilF, PilT1, and PilT2
Authors: Salzer Ralf , Joos Friederike , Averhoff Beate
Published: November 2013

Natural transformation has a large impact on lateral gene flow and has contributed significantly to the ecological diversification and adaptation of bacterial species.
Thermus thermophilus
HB27 has emerged as the leading model organism for studies of DNA transporters in thermophilic bacteria. Recently, we identified a zinc-binding polymerization nucleoside triphosphatase (NTPase), PilF, which is essential for the transport of DNA through the outer membrane. Here, we present genetic evidence that PilF is also essential for the biogenesis of pili. One of the most challenging questions was whether
T. thermophilus
has any depolymerization NTPase acting as a counterplayer of PilF. We identified two depolymerization NTPases, PilT1 (TTC1621) and PilT2 (TTC1415), both of which are required for type IV pilus (T4P)-mediated twitching motility and adhesion but dispensable for natural transformation. This suggests that T4P dynamics are not required for natural transformation. The latter finding is consistent with our suggestion that in
T. thermophilus
, T4P and natural transformation are linked but distinct systems.
Diversity in Robustness of Lactococcus lactis Strains during Heat Stress, Oxidative Stress, and Spray Drying Stress
Authors: Dijkstra Annereinou R. , Setyawati Meily C. , Bayjanov Jumamurat R. , Alkema Wynand , van Hijum Sacha A. F. T. , Bron Peter A. , Hugenholtz Jeroen
Published: November 2013

In this study we tested 39
Lactococcus lactis
strains isolated from diverse habitats for their robustness under heat and oxidative stress, demonstrating high diversity in survival (up to 4 log units). Strains with an
L. lactis
subsp.
lactis
phenotype generally displayed more-robust phenotypes than strains with an
L. lactis
subsp.
cremoris
phenotype, whereas the habitat from which the strains had been isolated did not appear to influence stress survival. Comparison of the stress survival phenotypes with already available comparative genomic data sets revealed that the absence or presence of specific genes, including genes encoding a GntR family transcriptional regulator, a manganese ABC transporter permease, a cellobiose phosphotransferase system (PTS) component, the FtsY protein, and hypothetical proteins, was associated with heat or oxidative stress survival. Finally, 14 selected strains also displayed diversity in survival after spray drying, ranging from 20% survival for the most robust strains, which appears acceptable for industrial application, to 0.1% survival for the least-tolerant strains. The high and low levels of survival upon spray drying correlated clearly with the combined robustness under heat and oxidative stress. These results demonstrate the relevance of screening culture collections for robustness under heat and oxidative stress on top of the typical screening for acidifying and flavor-forming properties.
Distinct Roles of a Mitogen-Activated Protein Kinase in Cytokinesis between Different Life Cycle Forms of Trypanosoma brucei
Authors: Wei Ying , Li Ziyin
Published: November 2013

Mitogen-activated protein kinase (MAPK) modules are evolutionarily conserved signaling cascades that function in response to the environment and play crucial roles in intracellular signal transduction in eukaryotes. The involvement of a MAP kinase in regulating cytokinesis in yeast, animals, and plants has been reported, but the requirement for a MAP kinase for cytokinesis in the early-branching protozoa is not documented. Here, we show that a MAP kinase homolog (TbMAPK6) from
Trypanosoma brucei
plays distinct roles in cytokinesis in two life cycle forms of
T. brucei
. TbMAPK6 is distributed throughout the cytosol in the procyclic form but is localized in both the cytosol and the nucleus in the bloodstream form. RNA interference (RNAi) of TbMAPK6 results in moderate growth inhibition in the procyclic form but severe growth defects and rapid cell death in the bloodstream form. Moreover, TbMAPK6 appears to be implicated in furrow ingression and cytokinesis completion in the procyclic form but is essential for cytokinesis initiation in the bloodstream form. Despite the distinct defects in cytokinesis in the two forms, RNAi of TbMAPK6 also caused defective basal body duplication/segregation in a small cell population in both life cycle forms. Altogether, our results demonstrate the involvement of the TbMAPK6-mediated pathway in regulating cytokinesis in trypanosomes and suggest distinct roles of TbMAPK6 in cytokinesis between different life cycle stages of
T. brucei
.
Percutaneous treatment of symptomatic aneurysmal bone cyst of L5 by percutaneous injection of osteoconductive material (Cerament)
Authors: Guarnieri Gianluigi , Vassallo Pasquale , Muto Massimo , Muto Mario
Published: November 2013

We present a case report of a 33-year-old woman with back pain for several months which was resistant to medical treatment. Thoracolumbar MRI and multidetector CT showed an aneurysmal bone cyst intersecting the body and pedicles of L5. Minimally invasive treatment was performed with percutaneous injection of osteoconductive cement (Cerament) to induce sclerosis and bone remodeling of the bone cyst lesion with an analgesic effect. Before treatment, spinal angiography was performed to exclude arterial afferents. No bone biopsy was done. Under general anesthesia and fluoroscopic guidance, a first vertebroplasty was performed by a bilateral transpedicular approach using the osteoconductive cement followed 2 months later by a second treatment with CT-fluoro-guided direct injection of Cerament. No complications occurred during the procedure. At 4 and 6 months follow-up the MRI/CT showed sclerotic bone remodeling of the walls of the aneurysmal cyst with clinical improvement.
Numerical modelling of desiccation cracking in a restrained ring test
Authors: Amarisiri Aruna , Shannon Benjamin , Kodikara Jayantha
Published: November 2013

Tensile cracking due to desiccation and fracture properties are of great importance in clay liners, earth dam engineering, waste contaminant systems, and mine tailings. This paper presents restrained shrinkage test results and analyses of consolidated desiccating soil, and compares results with numerical analyses using the computer program Universal Distinct Element Code (UDEC). The cohesive crack method was used as it is more appropriate than linear elastic fracture mechanics for soil cracking at high moisture contents with the likely presence of plasticity during fracture. The variation of the radial stresses on the inner ring with water content was used to model mode I cracking and gather fracture properties of the propagating crack. The model was validated on kaolin clay tested under restrained ring shrinkage and was compared with various test results and results from the literature. The test could be a valuable tool in determining fracture properties during desiccation.
Adapting Hazus for seismic risk assessment in Canada
Authors: Nastev Miroslav
Published: November 2013

Although earthquakes have been recognised as major natural hazards with the potential to cause loss of life, property damage, and social and economic disruption in Canada, most risk and emergency managers still lack the necessary tools and guidance to adequately undertake rigorous risk assessments. Recently, Natural Resources Canada (NRCan) has adopted Hazus, a standardized best-practice methodology developed by the US Federal Emergency Management Agency (FEMA) for estimating potential losses from common natural hazards, such as earthquakes, floods, and hurricanes. Hazus combines science, engineering knowledge, and mathematical modelling with geographic information systems technology to estimate physical damage and economic and social losses. Besides the ground shaking, the earthquake model considers landslide, liquefaction, and fault rupture susceptibilities. Depending on the severity of the resulting transient ground motion and permanent ground deformation, five potential damage states (none, slight, moderate, extensive, complete) are employed to estimate the amount of structural damage and consequent economic and social losses. This note reports some of the typical features of the recently adapted Hazus earthquake model, with an emphasis on the considerations of earthquake-induced hazards, and overviews the ongoing activities and potential challenges in implementing this model in Canada.
Nonlinear cyclic behavior of laterally loaded pile in cohesive soil
Authors: Heidari Mehdi , Jahanandish Mojtaba , El Naggar Hesham , Ghahramani Arsalan
Published: November 2013

Pile foundations may be subjected to lateral dynamic loads due to different hazards, such as impact of ships on bridge piers or jetties during berthing, wave and wind actions on offshore structures, and seismic wave motion on different buildings. The beam on nonlinear Winkler foundation (BNWF) approach is widely employed for predicting the response of piles under lateral loading because of its simplicity and practical accuracy. p–y curves are employed to represent the nonlinear soil reactions within the framework of the BNWF approach. However, they are empirically obtained from limited full-scale field tests and are not unique, accounting only for the pile width and not its mechanical properties. On the other hand, the strain wedge (SW) method allows the assessment of three-dimensional (3-D) soil–pile interaction of laterally loaded piles by incorporating soil continuity and pile properties as well as soil properties. In this study, the nonlinear p–y curves generated by the SW model are implemented as the backbone curve of developed BNWF model to effectively account for different response features of the pile–soil system. These features include the soil and pile nonlinear behavior, cyclic degradation of soil stiffness and strength, formation of soil–pile gap, and radiation damping. Two case studies of cyclic lateral load tests for single piles are investigated to examine the effects of soil degradation and gap formation on the response of laterally loaded piles embedded in cohesive soil. The developed model is shown to be capable of representing different soil–pile interaction features observed in experiments. The predictions of the developed BNWF model are in good agreement with experimental results. Finally, a comprehensive parametric study is performed to compare the predictions of the SWM-based model of the pile response under cyclic loading with that obtained from the conventional p–y curve–based model for different pile cross-section configurations, mechanical properties (strength and stiffness), and soil strength–stiffness.
Large-strain elastic viscoplastic consolidation analysis of very soft clay layers with vertical drains under preloading
Authors: Hu Ya-Yuan , Zhou Wan-Huan , Cai Yuan-Qiang
Published: November 2013

A very soft clay layer is highly compressible and exhibits significant creep under loading. The classical linearly elastic constitutive relationship and small-strain assumption are not suitable for the consolidation analysis of very soft clays. This paper presents a new large-strain consolidation model that incorporates the Yin–Graham elastic viscoplastic (EVP) constitutive equation for use in studying the consolidation of very soft clay layers with vertical drains under preloading. First, the large-strain fluid continuity equation and the EVP constitutive equation are incorporated into a quadratic differential equation of pore-water pressure and its integral terms. Second, the alternating-direction implicit (ADI) method and virtual node method are adopted to obtain the finite difference solution. A computer program named “BSSDS” is developed for large-strain EVP consolidation analysis of clay layers with vertical drains, taking into account the complicated in situ conditions, such as resistance of vertical drains, smear effects, variation of permeability with void ratio, and multilayered soils. Third, the new large-strain numerical method is applied to the consolidation modeling of very soft clay layers with vertical drains under preloading at a site that is part of the Hong Kong – Shenzhen Western Corridor Link Project. It is found that the foundation settlements of the new large-strain EVP consolidation model have good agreement with the measured data. Finally, three different consolidation models are used to calculate the average degree of consolidation and settlements of the clay layers. The analysis shows that it is essential to consider both large-strain compression and creep effects in the analysis of very soft clay layers with vertical drains under loading.
The radial–azimuthal instability of accretion disk with anomalous viscosity
Authors: Chen Yue Qi , Jiang Wei Qun
Published: November 2013

The stability of the accretion disk is solved by numerical simulations when the radial and azimuthal perturbations are considered, where we adopt the anomalous viscosity model, which is close to real accretion disks. The results are discussed in the inner, intermediate, and outer regions of the accretion disk, respectively. With the increase of viscosity, α, the thermal mode and the viscous mode, as well as the acoustic modes, become more unstable in the disk dominated by radiation pressure (inner region). The instability is also influenced by the azimuthal perturbation wavenumber, n. With the increase of n, the thermal mode becomes more unstable, while the in-mode and out-mode become more stable no matter if the disk is dominated by radiation pressure or by gas pressure (intermediate and outer regions). There are many differences between our results and others’ results, especially in the inner region of the disk, when the anomalous viscosity is considered.
Condition-dependent sex difference in nestling House Wren (Troglodytes aedon) response to phytohaemagglutinin injection
Authors: Thompson C.F. , Sakaluk S.K. , Masters B.S. , Johnson B.G.P. , Vogel L.A. , Forsman A.M. , Johnson L.S.
Published: November 2013

Adult male and female birds typically respond differently to immunological challenges, but whether this difference is present in altricial nestlings is not well-documented. Furthermore, the timing of the development of different axes of the immune system might vary in nestlings and also be affected by differences in condition and health state. We tested for sex-related differences in the immune response of nestling House Wrens (Troglodytes aedon Vieillot, 1809) to the injection of phytohaemagglutinin (PHA) and in the bacteria-killing capacity of their plasma. Based on prior work, we predicted that if there were sex-related differences in immune responsiveness, they would most likely occur when the sexes differed in some measure of condition or health state. Female nestlings had a stronger response to the injection of PHA than males in the one of three breeding seasons in which the condition of nestling females exceeded that of males, suggesting that the response to PHA injection is condition-dependent rather than sex-dependent. The sexes, however, did not differ in bactericidal activity, suggesting that different axes of the immune system may not be affected to the same degree by differences in sex or in condition.
An improved sampling method of complex network
Authors: Gao Qi , Ding Xintong , Pan Feng , Li Weixing
Published: November 2013

Sampling subnet is an important topic of complex network research. Sampling methods influence the structure and characteristics of subnet. Random multiple snowball with Cohen (RMSC) process sampling which combines the advantages of random sampling and snowball sampling is proposed in this paper. It has the ability to explore global information and discover the local structure at the same time. The experiments indicate that this novel sampling method could keep the similarity between sampling subnet and original network on degree distribution, connectivity rate and average shortest path. This method is applicable to the situation where the prior knowledge about degree distribution of original network is not sufficient.
Synchronization induced by disorder of phase directions
Authors: Xia Yingjie , Zhou Yinzuo
Published: November 2013

We study the influence of randomly distributed phase directions of external force in an array of coupled pendula, instead of studying the influence of continuous phase. We find that with the increase of the absolute value of the phase, the chaotic behaviors of the coupled arrays may be controlled and different synchronized patterns can be induced. These results demonstrate that by introducing the randomness of the phase directions, rather than the continuous value of the phase, it can lead to a synchronization in nonlinear systems. This finding may provide a new insight for understanding the mechanism of disorder induced synchronization.
Large eddy simulation of shock train in a convergent–divergent nozzle
Authors: Mousavi Seyed Mahmood , Roohi Ehsan
Published: November 2013

This paper discusses the suitability of the Large Eddy Simulation (LES) turbulence modeling for the accurate simulation of the shock train phenomena in a convergent-divergent nozzle. To this aim, we selected an experimentally tested geometry and performed LES simulation for the same geometry. The structure and pressure recovery inside the shock train in the nozzle captured by LES model are compared with the experimental data, analytical expressions and numerical solutions obtained using various alternative turbulence models, including k–ε RNG, k–ω SST, and Reynolds stress model (RSM). Comparing with the experimental data, we observed that the LES solution not only predicts the "locations of the first shock" precisely, but also its results are quite accurate before and after the shock train. After validating the LES solution, we investigate the effects of the inlet total pressure on the shock train starting point and length. The effects of changes in the back pressure, nozzle inlet angle (NIA) and wall temperature on the behavior of the shock train are investigated by details.
Moderate deviation for parameter estimator in the stochastic parabolic equations with additive fractional Brownian motion
Authors: Hui Jiang
Published: November 2013

In this paper, we study the asymptotic behaviors of parameter estimator in a diagonalizable stochastic evolution equation driven by additive fractional Brownian motion with Hurst parameter H ∈ [½, 1). The moderate deviation for this estimator can be obtained.
A STUDY ON PERFORMANCE OF AIR-TO-AIR HEXAGONAL PLASTIC PLATE HEAT EXCHANGER
Authors: CUI QING , OH MYUNG-DO
Published: November 2013

In this research, 3D analysis model of air-to-air hexagonal plastic plate heat exchanger (HX) is developed numerically and compared with the available experiment. The heat transfer performances with polypropylene (PP) and aluminum (Al) indicate that PP HX can transfer heat as good as Al under this HX application. On the basis of this model, the crest length, the crest pitch and the inlet and outlet chamfer size are designed as three key parameters to improve the heat transfer performances of HX.
Contractile protein expression is upregulated by reactive oxygen species in aorta of Goto-Kakizaki rat
Authors: Chettimada Sukrutha , Ata Hirotaka , Rawat Dhwajbahadur K. , Gulati Salil , Kahn Andrea G. , Edwards John G. , Gupte Sachin A.
Published: November 2013

Although it is known that blood vessels undergo remodeling in type 2 diabetes (T2D), the signaling pathways that underlie the structural and functional changes seen in diabetic arteries remain unclear. Our objective was to determine whether the remodeling in type 2 diabetic Goto-Kakizaki (GK) rats is evoked by elevated reactive oxygen species (ROS). Our results show that aortas from GK rats produced greater force ( P < 0.05) in response to stimulation with KCl and U46619 than aortas from Wistar rats. Associated with these changes, aortic expression of contractile proteins (measured as an index of remodeling) and the microRNA (miR-145), which act to upregulate transcription of contractile protein genes, was twofold higher ( P < 0.05) in GK than Wistar (age-matched control) rats, and there was a corresponding increase in ROS and decrease in nitric oxide signaling. Oral administration of the antioxidant Tempol (1 mmol/l) to Wistar and GK rats reduced ( P < 0.05) myocardin and calponin expression. Tempol (1 mmol/l) decreased expression of miR-145 in Wistar and GK rat aorta. To elucidate the mechanism through which ROS increases miR-145, we measured their levels in freshly isolated aorta and cultured aortic smooth muscle cells incubated for 12 h in the presence of H2O2 (300 μmol/l). H2O2 increased expression of miR-145, and there were corresponding nuclear increases in myocardin, a miR-145 target protein. Intriguingly, H2O2-induced expression of miR-145 was decreased by U0126 (10 μmol/l), a MEK1/2 inhibitor, and myocardin was decreased by anti-miR-145 (50 nmol/l) and U0126 (10 μmol/l). Our novel findings demonstrate that ROS evokes vascular wall remodeling and dysfunction by enhancing expression of contractile proteins in T2D.
Individual differences in cardiac and vascular components of the pressor response to isometric handgrip exercise in humans
Authors: Watanabe Kazuhito , Ichinose Masashi , Tahara Rei , Nishiyasu Takeshi
Published: November 2013

We tested the hypotheses that, in humans, changes in cardiac output (CO) and total peripheral vascular resistance (TPR) occurring in response to isometric handgrip exercise vary considerably among individuals and that those individual differences are related to differences in muscle metaboreflex and arterial baroreflex function. Thirty-nine healthy subjects performed a 1-min isometric handgrip exercise at 50% of maximal voluntary contraction. This was followed by a 4-min postexercise muscle ischemia (PEMI) period to selectively maintain activation of the muscle metaboreflex. All subjects showed increases in arterial pressure during exercise. Interindividual coefficients of variation (CVs) for the changes in CO and TPR between rest and exercise periods (CO: 95.1% and TPR: 87.8%) were more than twofold greater than CVs for changes in mean arterial pressure (39.7%). There was a negative correlation between CO and TPR responses during exercise ( r = −0.751, P < 0.01), but these CO and TPR responses correlated positively with the corresponding responses during PEMI ( r = 0.568 and 0.512, respectively, P < 0.01). The CO response during exercise did not correlate with PEMI-induced changes in an index of cardiac parasympathetic tone and cardiac baroreflex sensitivity. These findings demonstrate that the changes in CO and TPR that occur in response to isometric handgrip exercise vary considerably among individuals and that the two responses have an inverse relationship. They also suggest that individual differences in components of the pressor response are attributable in part to variations in muscle metaboreflex-mediated cardioaccelerator and vasoconstrictor responses.
Protective effects of histamine on Gq-mediated relaxation in regenerated endothelium
Authors: Chan Calvin K. , Liao Song Yan , Zhang Yue Lin , Xu Aimin , Tse Hung Fat , Vanhoutte Paul M.
Published: November 2013

In the porcine coronary artery, regenerated endothelium is dysfunctional as regards the responses to endothelium-dependent agonists. The current study aimed to determine the possible involvement of histamine in such dysfunction. Pigs were treated chronically with pyrilamine (H1receptor inhibitor, 2 mg·kg−1·day−1) with part of their coronary endothelium and allowed to regenerate for 28 days after balloon denudation. The results showed a reduction in relaxation to bradykinin (Gqprotein dependent) only in the pyrilamine-treated group (area under the curve, 269.7 ± 13.4 vs. 142.0 ± 31.0, native endothelium vs. regenerated endothelium) but not in the control group (253.0 ± 22.1 vs. 231.9 ± 29.5, native endothelium vs. regenerated endothelium). The differences in the relaxation to serotonin (Giprotein dependent) between native and regenerated endothelium were not affected by the pyrilamine treatment (control group, 106.3 ± 17.0 vs. 55.61 ± 12.7; and pyrilamine group, 106.0 ± 8.20 vs. 49.30 ± 6.31, native endothelium vs. regenerated endothelium). These findings indicate that during regeneration of the endothelium, the activation of H1receptors by endogenous histamine may be required to maintain the endothelium-dependent Gqprotein-mediated relaxation to bradykinin, suggesting a beneficial role of the monoamine in the process of endothelial regeneration.
Experimental model of transthoracic, vascular-targeted, photodynamically induced myocardial infarction
Authors: Chrastina Adrian , Pokreisz Peter , Schnitzer Jan E.
Published: November 2013

We describe a novel model of myocardial infarction (MI) in rats induced by percutaneous transthoracic low-energy laser-targeted photodynamic irradiation. The procedure does not require thoracotomy and represents a minimally invasive alternative to existing surgical models. Target cardiac area to be photodynamically irradiated was triangulated from the thoracic X-ray scans. The acute phase of MI was histopathologically characterized by the presence of extensive vascular occlusion, hemorrhage, loss of transversal striations, neutrophilic infiltration, and necrotic changes of cardiomyocytes. Consequently, damaged myocardium was replaced with fibrovascular and granulation tissue. The fibrotic scar in the infarcted area was detected by computer tomography imaging. Cardiac troponin I (cTnI), a specific marker of myocardial injury, was significantly elevated at 6 h (41 ± 6 ng/ml, n = 4, P < 0.05 vs. baseline) and returned to baseline after 72 h. Triphenyltetrazolium chloride staining revealed transmural anterolateral infarcts targeting 25 ± 3% of the left ventricle at day 1 with a decrease to 20 ± 3% at day 40 ( n = 6 for each group, P < 0.01 vs. day 1). Electrocardiography (ECG) showed significant ST-segment elevation in the acute phase with subsequent development of a pathological Q wave and premature ventricular contractions in the chronic phase of MI. Vectorcardiogram analysis of spatiotemporal electrical signal transduction revealed changes in inscription direction, QRS loop morphology, and redistribution in quadrant areas. The photodynamically induced MI in n = 51 rats was associated with 12% total mortality. Histological findings, ECG abnormalities, and elevated cTnI levels confirmed the photosensitizer-dependent induction of MI after laser irradiation. This novel rodent model of MI might provide a platform to evaluate new diagnostic or therapeutic interventions.