bluuebunny/crossref_metadata_2025_split huggingface dataset:
Composition of the Surface Proteome ofAnaplasma marginaleand Its Role in Protective Immunity Induced by Outer Membrane Immunization
Authors: Noh Susan M. , Brayton Kelly A. , Brown Wendy C. , Norimine Junzo , Munske Gerhard R. , Davitt Christine M. , Palmer Guy H. 
Published: March 2008

ABSTRACTSurface proteins of tick-borne, intracellular bacterial pathogens mediate functions essential for invasion and colonization. Consequently, the surface proteome of these organisms is specifically relevant from two biological perspectives, induction of protective immunity in the mammalian host and understanding the transition from the mammalian host to the tick vector. In this study, the surface proteome ofAnaplasma marginale, a tick-transmitted bacterial pathogen, was targeted by using surface-specific cross-linking to form intermolecular bonds between adjacent proteins. Liquid chromatography and tandem mass spectroscopy were then employed to characterize the specific protein composition of the resulting complexes. The surface complexes ofA. marginaleisolated from erythrocytes of the mammalian host were composed of multiple membrane proteins, most of which belong to a protein family, pfam01617, which is conserved among bacteria in the genusAnaplasmaand the closely related genusEhrlichia. In contrast, the surface proteome ofA. marginaleisolated from tick cells was much less complex and contained a novel protein, AM778, not identified within the surface proteome of organisms from the mammalian host. Immunization using the cross-linked surface complex induced protection against high-level bacteremia and anemia uponA. marginalechallenge of cattle and effectively recapitulated the protection induced by immunization with whole outer membranes. These results indicate that a surface protein subset of the outer membrane is capable of inducing protective immunity and serves to direct vaccine development. Furthermore, the data support that remodeling of the surface proteome accompanies the transition between mammalian and arthropod hosts and identify novel targets for blocking transmission.
Pseudomonas aeruginosa
Induces Membrane Blebs in Epithelial Cells, Which Are Utilized as a Niche for Intracellular Replication and Motility
Authors: Angus Annette A. , Lee Amanda Ackerman , Augustin Danielle K. , Lee Ellen J. , Evans David J. , Fleiszig Suzanne M. J. 
Published: March 2008

ABSTRACT

Pseudomonas aeruginosa
is known to invade epithelial cells during infection and in vitro. However, little is known of bacterial or epithelial factors modulating
P. aeruginosa
intracellular survival or replication after invasion, except that it requires a complete lipopolysaccharide core. In this study, real-time video microscopy revealed that invasive
P. aeruginosa
isolates induced the formation of membrane blebs in multiple epithelial cell types and that these were then exploited for intracellular replication and rapid real-time motility. Further studies revealed that the type three secretion system (T3SS) of
P. aeruginosa
was required for blebbing. Mutants lacking either the entire T3SS or specific T3SS components were instead localized to intracellular perinuclear vacuoles. Most T3SS mutants that trafficked to perinuclear vacuoles gradually lost intracellular viability, and vacuoles containing those bacteria were labeled by the late endosomal marker lysosome-associated marker protein 3 (LAMP-3). Interestingly, mutants deficient only in the T3SS translocon structure survived and replicated within the vacuoles that did not label with LAMP-3. Taken together, these data suggest two novel roles of the
P. aeruginosa
T3SS in enabling bacterial intracellular survival: translocon-dependent formation of membrane blebs, which form a host cell niche for bacterial growth and motility, and effector-dependent bacterial survival and replication within intracellular perinuclear vacuoles.
Leishmania majorInfection Activates NF-κB and Interferon Regulatory Factors 1 and 8 in Human Dendritic Cells
Authors: Jayakumar Asha , Donovan Michael J. , Tripathi Vinita , Ramalho-Ortigao Marcelo , McDowell Mary Ann 
Published: March 2008

ABSTRACTThe salient feature of dendritic cells (DC) is the initiation of appropriate adaptive immune responses by discriminating between pathogens. Using a prototypic model of intracellular infection, we previously showed thatLeishmania majorparasites prime human DC for efficient interleukin-12 (IL-12) secretion.L. majorinfection is associated with self-limiting cutaneous disease and powerful immunity. In stark contrast, the causative agent of visceral leishmaniasis,Leishmania donovani, does not prime human DC for IL-12 production. Here, we report that DC priming byL. majorinfection results in the early activation of NF-κB transcription factors and the up-regulation and nuclear translocation of interferon regulatory factor 1 (IRF-1) and IRF-8. The inhibition of NF-κB activation by the pretreatment of DC with caffeic acid phenethyl ester blocksL. major-induced IRF-1 and IRF-8 activation and IL-12 expression. We further demonstrate that IRF-1 and IRF-8 obtained fromL. major-infected human DC specifically bind to their consensus binding sites on theIL-12p35promoter, indicating thatL. majorinfection either directly stimulates a signaling cascade or induces an autocrine pathway that activates IRF-1 and IRF-8, ultimately resulting inIL-12transcription.
A Novel Sensor Kinase-Response Regulator Hybrid Controls Biofilm Formation and Type VI Secretion System Activity in
Burkholderia cenocepacia
Authors: Aubert Daniel F. , Flannagan Ronald S. , Valvano Miguel A. 
Published: March 2008

ABSTRACT

Burkholderia cenocepacia
is an important opportunistic pathogen causing serious chronic infections in patients with cystic fibrosis (CF). Adaptation of
B. cenocepacia
to the CF airways may play an important role in the persistence of the infection. We have identified a sensor kinase-response regulator (BCAM0379) named AtsR in
B. cenocepacia
K56-2 that shares 19% amino acid identity with RetS from
Pseudomonas aeruginosa
.
atsR
inactivation led to increased biofilm production and a hyperadherent phenotype in both abiotic surfaces and lung epithelial cells. Also, the
atsR
mutant overexpressed and hypersecreted an Hcp-like protein known to be specifically secreted by the type VI secretion system (T6SS) in other gram-negative bacteria. Amoeba plaque assays demonstrated that the
atsR
mutant was more resistant to
Dictyostelium
predation than the wild-type strain and that this phenomenon was T6SS dependent. Macrophage infection assays also demonstrated that the
atsR
mutant induces the formation of actin-mediated protrusions from macrophages that require a functional Hcp-like protein, suggesting that the T6SS is involved in actin rearrangements. Three
B. cenocepacia
transposon mutants that were found in a previous study to be impaired for survival in chronic lung infection model were mapped to the T6SS gene cluster, indicating that the T6SS is required for infection in vivo. Together, our data show that AtsR is involved in the regulation of genes required for virulence in
B. cenocepacia
K56-2, including genes encoding a T6SS.
Population Diversity and Dynamics of
Streptococcus mitis
,
Streptococcus oralis
, and
Streptococcus infantis
in the Upper Respiratory Tracts of Adults, Determined by a Nonculture Strategy
Authors: Bek-Thomsen Malene , Tettelin Hervé , Hance Ioana , Nelson Karen E. , Kilian Mogens 
Published: March 2008

ABSTRACT

We reinvestigated the clonal diversity and dynamics of
Streptococcus mitis
and two other abundant members of the commensal microbiota of the upper respiratory tract,
Streptococcus oralis
and
Streptococcus infantis
, to obtain information about the origin of frequently emerging clones in this habitat. A culture-independent method was used, based on cloning and sequencing of PCR amplicons of the housekeeping gene
gdh
, which shows remarkable, yet species-specific, genetic polymorphism. Samples were collected from all potential ecological niches in the oral cavity and pharynx of two adults on two occasions separated by 2 years. Based on analysis of close to 10,000 sequences, significant diversity was observed in populations of all three species. Fluctuations in the relative proportions of individual clones and species were observed over time. While a few clones dominated, the proportions of most clones were very small. The results show that the frequent turnover of
S. mitis
,
S. oralis
, and
S. infantis
clones observed by cultivation can be explained by fluctuations in the relative proportions of clones, most of which are below the level of detection by the traditional culture technique, possibly combined with loss and acquisition from contacts. These findings provide a platform for understanding the mechanisms that govern the balance within the complex microbiota at mucosal sites and between the microbiota and the mucosal immune system of the host.
Modulation of the Bovine Trophoblastic Innate Immune Response byBrucella abortus
Authors: Carvalho Neta Alcina V. , Stynen Ana P. R. , Paixão Tatiane A. , Miranda Karina L. , Silva Fabiana L. , Roux Christelle M. , Tsolis Renée M. , Everts Robin E. , Lewin Harris A. , Adams L. Garry , Carvalho Alex F. , Lage Andrey P. , Santos Renato L. 
Published: March 2008

ABSTRACTBrucellosis is still a widespread zoonotic disease. Very little is known about the interaction betweenBrucella abortusand trophoblastic cells, which is essential for better understanding the pathogenesis of theBrucella-induced placentitis and abortion, a key event for transmission of the disease. The goal of this study was to evaluate the profile of gene expression by bovine trophoblastic cells during infection withB. abortus. Explants of chorioallantoic membranes were inoculated withB. abortusstrain 2308. Microarray analysis was performed at 4 h after infection, and expression of cytokines and chemokines by trophoblastic cells was assessed by real-time reverse transcription-PCR at 6 and 12 h after inoculation. In addition, cytokine and chemokine expression in placentomes from experimentally infected cows was evaluated. Expression of proinflammatory genes by trophoblastic cells was suppressed at 4 h after inoculation, whereas a significant upregulation of CXC chemokines, namely, CXCL6 (GCP-2) and CXCL8 (interleukin 8), was observed at 12 but not at 6 h after inoculation. Placentomes of experimentally infected cows had a similar profile of chemokine expression, with upregulation of CXCL6 and CXCL8. Our data indicate thatB. abortusmodulates the innate immune response by trophoblastic cells, suppressing the expression of proinflammatory mediators during the early stages of infection that is followed by a delayed and mild expression of proinflammatory chemokines, which is similar to the profile of chemokine expression in the placentomes of experimentally infected cows. This trophoblastic response is likely to contribute to the pathogenesis ofB. abortus-induced placentitis.
Role of RppA in the Regulation of Polymyxin B Susceptibility, Swarming, and Virulence Factor Expression in
Proteus mirabilis
Authors: Wang Won-Bo , Chen I-Chun , Jiang Sin-Sien , Chen Hui-Ru , Hsu Chia-Yu , Hsueh Po-Ren , Hsu Wei-Bin , Liaw Shwu-Jen 
Published: March 2008

ABSTRACT

Proteus mirabilis
, a human pathogen that frequently causes urinary tract infections, is intrinsically highly resistant to cationic antimicrobial peptides, such as polymyxin B (PB). To explore the mechanisms underlying
P. mirabilis
resistance to PB, a mutant which displayed increased (>160-fold) sensitivity to PB was identified by transposon mutagenesis. This mutant was found to have Tn
5
inserted into a novel gene,
rppA
. Sequence analysis indicated that
rppA
may encode a response regulator of the two-component system and is located upstream of the
rppB
gene, which may encode a membrane sensor kinase. An
rppA
knockout mutant of
P. mirabilis
had an altered lipopolysaccharide (LPS) profile. The LPS purified from the
rppA
knockout mutant could bind more PB than the LPS purified from the wild type. These properties of the
rppA
knockout mutant may contribute to its PB-sensitive phenotype. The
rppA
knockout mutant exhibited greater swarming motility and cytotoxic activity and expressed higher levels of flagellin and hemolysin than the wild type, suggesting that RppA negatively regulates swarming, hemolysin expression, and cytotoxic activity in
P. mirabilis
. PB could modulate LPS synthesis and modification, swarming, hemolysin expression, and cytotoxic activity in
P. mirabilis
through an RppA-dependent pathway, suggesting that PB could serve as a signal to regulate RppA activity. Finally, we demonstrated that the expression of
rppA
was up-regulated by a low concentration of PB and down-regulated by a high concentration of Mg
2+
. Together, these data highlight the essential role of RppA in regulating PB susceptibility and virulence functions in
P. mirabilis
.
Limited Role for Iron Regulation in
Coxiella burnetii
Pathogenesis
Authors: Briggs Heather L. , Pul Nicolein , Seshadri Rekha , Wilson Mary J. , Tersteeg Claudia , Russell-Lodrigue Kasi E. , Andoh Masako , Bäumler Andreas J. , Samuel James E. 
Published: March 2008

ABSTRACT

In gram-negative bacteria, iron acquisition proteins are commonly regulated by Fur (
f
erric
u
ptake
r
egulator), which binds iron-regulated promoters (the Fur box). We hypothesized that
Coxiella burnetii
requires iron and employs an iron-regulatory system and used various approaches to define a Fur regulon. Cloned
C. burnetii fur
complemented an
Escherichia coli fur
deletion mutant. A ferrous iron transporter gene (CBU1766), a putative iron binding protein-encoding gene (CBU0970), and a cation efflux pump gene (CBU1362) were identified by genome annotation and using a Fur titration assay. Bioinformatically predicted Fur box-containing promoters were tested for transcriptional control by iron. Five genes demonstrated at least a twofold induction with minimal iron. Putatively regulated genes were evaluated in a two-plasmid regulator/promoter heterologous expression system. These data suggested a very limited Fur-regulated system in
C. burnetii
. In an in vitro tissue culture model, a significant increase in bacterial growth was observed with infected cells treated with deferoxamine in comparison to growth under iron-replete conditions. In an iron-overloaded animal model in vivo, the level of bacterial growth detected in the iron-injected animals was significantly decreased in comparison to growth in control animals. In a low-iron-diet animal model, a significant increase in splenomegaly was observed, but no significant change in bacterial growth was identified. The small number of predicted iron acquisition systems, few Fur-regulated genes, and enhanced replication under a decreased iron level predict a requirement of a low level of iron for survival, perhaps to avoid creation of additional reactive oxygen radicals.
Sex ratio, flowering and fruit set in dioecious Rubus chamaemorus (Rosaceae) in Labrador
Authors: Karst Amanda L. , Antos Joseph A. , Allen Geraldine A. 
Published: March 2008

Rubus chamaemorus L. is a dioecious clonal herb with highly variable fruit production. Our overall objective was to determine how fruit production (and the reproductive stages leading to fruit) for R. chamaemorus varied with habitat and population (especially sex ratio) characteristics at scales from 1 m2 quadrats to whole populations in southeastern Labrador, Canada. During the climatically favourable year studied, reproductive variables were only weakly correlated with habitat characteristics. Strongly biased sex ratios were found at scales of 1–10 m. Male-dominated quadrats exhibited a significantly higher proportion of flowering ramets than did female-dominated quadrats. Female-biased sex ratios of flowering ramets and large distances between male and female flowers were correlated with decreased seed set. We found no differences in microhabitats of males and females. Although the biased local sex ratios could limit sexual reproduction, the high fruit set we measured clearly indicates that populations are able to produce abundant fruit during favourable years in this unpredictable environment.
Development of the K-stiffness method for geosynthetic reinforced soil walls constructed with c-ϕ soils
Authors: Miyata Yoshihisa , Bathurst Richard J. 
Published: March 2008

In this paper the K-stiffness method is extended to the case of c-ϕ soils using data obtained from a total of nine new case studies – six from Japan and three from the USA. A common feature in this new data set is that the walls were all constructed with a vertical face using backfill soils with a range of fines content. The walls varied widely with respect to facing type. This new data set together with previously published data for vertical walls is now used to isolate the effect of soil cohesion on reinforcement loads within the framework of the original K-stiffness method. The new data set is used to calibrate a modified K-stiffness method equation that includes a cohesion influence factor. The modified K-stiffness method is demonstrated to quantitatively improve the estimate of the magnitude and distribution of reinforcement loads for internal stability design of vertical-faced geosynthetic reinforced soil walls with c-ϕ soil backfills when compared to the current American Association of State Highway and Transportation Officials simplified method.
Modelling evaporation of paste tailings from the Bulyanhulu mine
Authors: Simms Paul , Grabinsky Murray , Zhan Guosheng 
Published: March 2008

Accurate predictions of drying rates are desirable to optimize surface deposition of thickened or paste tailings. A series of laboratory and field trials were implemented to study evaporation from tailings at the Bulyanhulu gold mine and were compared with numerical simulations using the unsaturated flow model SoilCover. The laboratory tests included two “large-scale” experiments on 10 cm thick layers of tailings 2 m by 1 m in plan, and a smaller column test on a 20 cm thick and 20 cm diameter sample. Data monitored during these tests included albedo, volume change, degree of cracking, matric suction, water content, and drying rate. Field data included gravimetric water contents and albedo values. The model could reasonably simulate the laboratory experiments when adjustments were made to account for self-weight consolidation and the effect of volume change on the relative permeability function. The model could simulate drying in the field for up to 3 weeks after deposition before the accumulation of gypsum and magnesium sulphate salts began to affect evaporation. Cracking and salt accumulation were observed both in the laboratory and in the field. A general model for simulating drying from paste tailings should incorporate the effects of cracking and salts.
Laboratory characterization of the spatial variability in soils by the EM-wave-based technique
Authors: Wang Yu-Hsing , Dong Xiaobo 
Published: March 2008

A slim-form, open-ended coaxial probe with an outside diameter of 2.2 mm was used in this study to take local dielectric measurements in soils. The dielectric relaxation strength of bulk water, Δκw, and the DC conductivity of the saturated sample, σmix, are jointly used to characterize the spatial variability of different specimens including glass beads, sand and mica samples, and kaolinite sediments with two different fabric associations. The pore distribution along the sample depth can be inferred from the local Δκw using mixing rules. The directional feature of the interconnected pores is captured in the tortuosity, which is derived from the measured σmix and the DC conductivity of the pore fluid σpf. In kaolinite sediments, the ratio between the sediment and the pore-fluid conductivity not only reveals the spatial variability of the sediment packing but also the relative contribution of the fluid conductivity and the surface conduction to the overall sediment conductivity.
ON THE RELATIONSHIPS BETWEEN CLUSTERING AND SPATIAL CO-LOCATION PATTERN MINING
Authors: HUANG YAN , ZHANG PUSHENG , ZHANG CHENGYANG 
Published: March 2008

The goal of spatial co-location pattern mining is to find subsets of spatial features frequently located together in spatial proximity. Example co-location patterns include services requested frequently and located together from mobile devices (e.g., PDAs and cellular phones) and symbiotic species in ecology (e.g., Nile crocodile and Egyptian plover). Spatial clustering groups similar spatial objects together. Reusing research results in clustering, e.g. algorithms and visualization techniques, by mapping co-location mining problem into a clustering problem would be very useful. However, directly clustering spatial objects from various spatial features may not yield well-defined co-location patterns. Clustering spatial objects in each layer followed by overlaying the layers of clusters may not applicable to many application domains where the spatial objects in some layers are not clustered. In this paper, we propose a new approach to the problem of mining co-location patterns using clustering techniques. First, we propose a novel framework for co-location mining using clustering techniques. We show that the proximity of two spatial features can be captured by summarizing their spatial objects embedded in a continuous space via various techniques. We define the desired properties of proximity functions compared to similarity functions in clustering. Furthermore, we summarize the properties of a list of popular spatial statistical measures as the proximity functions. Finally, we show that clustering techniques can be applied to reveal the rich structure formed by co-located spatial features. A case study on real datasets shows that our method is effective for mining co-locations from large spatial datasets.
Maximum Sustainable Yield of Marine Capture Fisheries in Developing Archipelagic States—Balancing Law, Science, Politics and Practice
Authors: Andrew Neil , Lugten Gail 
Published: March 2008

AbstractThe contemporary legal regime for marine capture fisheries is dominated by management based on maximum sustainable yield (MSY). This study examines the law, science, politics and practice of MSY in a selection of developing archipelagic states to assess whether and how MSY is being used in the management of single fish species and as part of a broader ecosystem approach to fisheries management.