bluuebunny/crossref_metadata_2025 huggingface dataset:
Ground‐Water Flow Model of Drawdown and Recovery Near an Underground Mine
Authors: Toran Laura , Bradbury Kenneth R.
Published: March 2006

The U.S. Geological Survey's modular code (McDonald and Harbaugh, 1984) was used to reconstruct past ground‐water flow paths and make predictions of future flow patterns to understand movement of sulfate‐contaminated ground water through a carbonate aquifer near an underground mine. The abandoned mine is in the zinc‐lead district near the town of Shullsburg in southwestern Wisconsin. The model predicts observed hydraulic head distributions and ground‐water discharge rates with fair accuracy. Instantaneous dewatering rates are underestimated, but long‐term rates can be estimated with the model. The persistence of a cone of depression at present and in the future allows uncontaminated water from surrounding areas to dilute the sulfate, as confirmed by chemical sampling. The model predicts radial flow will persist near the Shullsburg mines until approximately 1988.

The model represents a significant test of the ability of a ground‐water flow model to predict the impacts of underground mining on ground‐water systems. The method used required field data collected before, during, and after mining. A model calibrated to just one or two of these data sets is likely to have larger associated uncertainties.
Role of Interceptor Ditches in Limiting the Spread of Contaminants in Ground Water
Authors: Zheng C. , Bradbury K. R. , Anderson M. P.
Published: March 2006

The ground‐water pattern in the vicinity of an interceptor ditch used for agricultural drainage is simulated using flow and stream function models to explore the possibility of using interceptor ditches to control the spread of agricultural chemicals in shallow aquifers. The concept of the dividing streamline is used to quantify the effectiveness of the interceptor ditch for limiting the spread of potential contaminants. The simulation results suggest that the interceptor ditch may create an effective hydraulic barrier to the movement of agricultural contaminants in ground water, but its effectiveness is subject to seasonal changes in hydrological conditions, including the regional water‐table gradient, the distribution of recharge and discharge, and the ditch stage. A quantitative relationship between effectiveness of the ditch and these hydrological conditions is established.
“Testing” a Limestone Aquifer Using Water‐Table Response to Storm Water Discharged into Sinkholes
Authors: Michalski Andrew , Torlucci Joseph
Published: March 2006

The character and performance of karstified aquifers are often difficult to assess, casting some doubt as to the monitorability of waste management facilities located in karstic settings. In the case of a Puerto Rican aquifer presented herein, analysis of water‐table response to storm water discharged to sinkholes allowed characterization of the flow type in the aquifer, estimation of aquifer parameters, and aided in assessing the monitorability of the site.

Water‐level data from observation wells have indicated that storm water discharged into on‐site sinkholes produced fairly regular mounding patterns in the aquifer. Such patterns suggested an isotropic character and predominantly diffuse ground‐water transmission within the aquifer. An injection well analogy was used for storm‐water discharge at the sinkholes to analyze the water‐level data and estimate values of aquifer parameters.

The case presented herein demonstrates that analysis of transient water levels in response to natural stresses can provide a useful tool of hydrogeologic exploration at sites where sinkholes act as strong and variable point sources. At such sites, traditional well pumping/injection tests may be subject to excessive interference from the sources and lead to erroneous interpretations.
Biodegradation of Surfactants in Saturated Subsurface Sediments: A Field Study
Authors: Federle Thomas W. , Pastwa Gary M.
Published: March 2006

The mineralization of linear alkylbenzene sulfonate (LAS), linear alcohol ethoxylate (LAE), benzylamine, and monoalkyl and dialkyl quaternary ammonium compounds was determined as a function of depth in sediment profiles from beneath a laundromat waste‐water pond and pristine control pond. In addition, bacterial number, microbial activity, and concentrations of LAS and quaternary ammonium compounds were measured. Surfactant concentration decreased dramatically with increasing depth in the laundromat profile. Bacterial number and activity decreased with depth in both profiles; however, biomass and activity were higher in the laundromat profile. Mineralization was measured by amending samples with 14C‐labeled substrates and following the evolution of 14CO2 with time. LAS was mineralized without a lag period at all depths in the laundromat profile; its half‐life ranged from 3.2 to 16.5 days. In the control pond, it was mineralized more slowly (half‐life 5.2 to 1540 days) and only after a lag period of 2 to 40 days. LAE was also mineralized with shorter lags and more rapidly in the laundromat than in the control profile; half‐lives ranged between 2.8 to 8.6 days in the former and 3.5 to 137 days in the latter. Although monoalkyl and dialkyl quaternary ammonium compounds were not mineralized in the control profile, slow but significant mineralization of these compounds occurred in the laundromat profile. Benzylamine was rapidly degraded without a lag in both profiles. Field concentration data and the results of mineralization studies indicated that biodegradation combined with the effects of adsorption is a practical mechanism of surfactant removal in subsurface environments. In addition, adaptation resulting from exposure of microbial communities to surfactants is an important factor governing the fate of surfactants in the subsurface.
Forced‐Gradient Tracer Tests and Inferred Hydraulic Conductivity Distributions at the Mobile Site
Authors: Molz Fred J. , Güven Oktay , Melville Joel G. , Nohrstedt J. Steven , Overholtzer Jon K.
Published: March 2006

Four single‐well tracer tests and a two‐well tracer test performed in a 21‐m thick confined granular aquifer at a field site near Mobile, Alabama, are described. The data from these tests together with previously published data from a single‐well test and a two‐well test allow one to begin to develop a three‐dimensional picture of the hydraulic properties of the study aquifer. A consistent feature of all the tests is a high hydraulic conductivity zone which appears in the bottom third of the aquifer. This result is in agreement with hydraulic conductivity distributions inferred from previous aquifer thermal energy storage experiments at the same site. In some locations the new tests indicated high hydraulic conductivity zones in the upper third of the aquifer which were not detected in the previous two‐well test and single‐well tests performed at the same site but at different locations. Despite the three‐dimensional spatial variations of hydraulic conductivity indicated by these tests, it was possible to predict the major features of the tracer concentration as a function of time at the withdrawal well in the two‐well test by means of an available numerical model assuming perfect stratification at the test site and using a hydraulic conductivity distribution inferred from a single‐well test.

The apparent success of the model prediction presented here, as well as the success of a similar numerical simulation of the previous two‐well test reported earlier, seem to support the conclusion that the study aquifer has an approximately stratified flow field at the test site. These field test results provide further evidence that reliable predictions of solute transport in a real aquifer will depend on a sufficiently detailed knowledged of the major features of the three‐dimensional advection pattern in the aquifer. Based on this study and previous studies, it appears that a healthy mixture of viewpoints and techniques (geologic, hydrologic, geophysical, etc.) will be necessary to characterize the transport properties of natural ground‐water systems.
Dimensionless Time‐Drawdown Plots of Late Aquifer Test Data
Authors: Şen Zekâi
Published: March 2006

The Jacob straight‐line method is concerned with the late time Theis type curve. The Jacob method gives a straight line on semilogarithmic paper. In practice, the Jacob straight line is taken for granted by ground‐water hydrologists, hydrogeologists, and engineers, and applied almost universally. Not every straight line on semilogarithmic paper, however, warrants the application of the Jacob method. The Jacob straight‐line method has physical restrictions (in addition to the mathematical requirements of having the dimensionless time factor, u, less than 0.01) which are ignored. Therefore, determination of the storage coefficient and transmissivity from the semilogarithmic plot of data yields either over or underestimations.

The objective of this paper is to show that the slope of the straight line on semilogarithmic paper can provide useful quantitative information for the proper application of the Jacob method. Differences in the slopes of the theoretical and field lines implies various physical circumstances. In practice, the Jacob method must be used with great care. The physical construction of the aquifer and flow conditions must be considered.
Molecular Mechanism of the Constitutive Activation of the L250Q Human Melanocortin‐4 Receptor Polymorphism‡
Authors: Proneth Bettina , Xiang Zhimin , Pogozheva Irina D. , Litherland Sally A. , Gorbatyuk Oleg S. , Shaw Amanda M. , Millard William J. , Mosberg Henry I. , Haskell‐Luevano Carrie
Published: March 2006

The Melanocortin‐4 Receptor is a G‐protein coupled receptor that has been physiologically linked to participate in the regulation of energy homeostasis. The Melanocortin‐4 Receptor is stimulated by endogenous melanocortin agonists derived from the pro‐opiomelanocortin gene transcript and antagonized by the endogenous antagonist agouti‐related protein. Central administration of melanocortin agonists has been demonstrated to decrease food intake and conversely, treatment with antagonists resulted in increased food intake. Deletion of the Melanocortin‐4 Receptor gene from the mouse genome results in an obese and hyperphagic phenotype. Polymorphisms of the human Melanocortin‐4‐Receptor have been found in severely obese individuals, suggesting that Melanocortin‐4 Receptor malfunction might be involved in human obesity and obesity‐associated diabetes. Herein, we have performed experiments to understand the molecular mechanisms associated with the L250Q human Melanocortin‐4‐Receptor polymorphism discovered in an extremely obese woman. This L250Q human Melanocortin‐4‐Receptor has been pharmacologically characterized to result in a constitutively active receptor. The fact that a constitutively active human Melanocortin‐4‐Receptor mutation was found in an obese person is a physiologic contradiction, as chronic activation of the human Melanocortin‐4‐Receptor and subsequently high cyclic adenosine monophosphate levels should theoretically result in a normal or lean phenotype. In this study, we demonstrated that agouti‐related protein acts as an inverse agonist at this constitutively active receptor, and we propose a mechanism by which agouti‐related protein might contribute to the obese phenotype in the L250Q patient. In addition, using receptor mutagenesis, pharmacology, and computer modeling approaches, we investigated the molecular mechanism by which modification of the L250 residue results in constitutive activation of the human Melanocortin‐4‐Receptor.
Molecular Analyses of the Interaction ofBorrelia hermsiiFhbA with the Complement Regulatory Proteins Factor H and Factor H-Like Protein 1
Authors: Hovis Kelley M. , Jones Janice P. , Sadlon Tania , Raval Gauri , Gordon David L. , Marconi Richard T.
Published: March 2006

Borrelia hermsii, the primary etiological agent of tick-borne relapsing fever in North America, binds the complement regulatory protein factor H (FH) as a means of evading opsonophagocytosis and the alternative complement pathway. The ability of FH-binding protein A (FhbA) to bind FH-like protein 1 (FHL-1) has not been assessed previously. In this study, using a whole-cell absorption assay, we demonstrated thatB. hermsiiabsorbs both FH and FHL-1 from human serum. Consistent with this, affinity ligand binding immunoblot analyses revealed that FH constructs spanning short consensus repeats 1 to 7 and 16 to 20 bind to FhbA. To investigate the molecular basis of the interaction of FhbA with FH/FHL-1, recombinant FhbA truncated proteins were generated and tested for FH/FHL-1 binding. Binding required determinants located in both the N- and C-terminal domains of FhbA, suggesting that long-range intramolecular interactions are involved in the formation and presentation of the FH/FHL-1-binding pocket. To identify specific FhbA residues involved in binding, random mutagenesis was performed. These analyses identified a loop region of FhbA that may serve as a contact point for FH/FHL-1. The data presented here expand our understanding of the pathogenic mechanisms of the relapsing fever spirochetes and of the molecular nature of the interaction between FH/FHL-1 and FhbA.
Active Cytotoxic Necrotizing Factor 1 Associated with Outer Membrane Vesicles from UropathogenicEscherichia coli
Authors: Kouokam J. Clavin , Wai Sun Nyunt , Fällman Maria , Dobrindt Ulrich , Hacker Jörg , Uhlin Bernt Eric
Published: March 2006

Cytotoxic necrotizing factor type 1 (CNF1) is one of the virulence factors produced by uropathogenicEscherichia coli(UPEC). How this toxin is translocated from the bacterial cytoplasm to the surrounding environment is not well understood. Our data suggest that CNF1 may be regarded as a secreted protein, since it could be detected in culture supernatants. Furthermore, we found that CNF1 was tightly associated to outer membrane vesicles, suggesting that such vesicles play a role in the secretion of this protein. Interestingly, vesicle samples containing CNF1 could exert the effects known for this protein on HeLa cell cultures, showing that CNF1 is transported by vesicles in its active form. Taken together, our results strongly suggest that outer membrane vesicles could be a means for the bacteria to deliver CNF1 to the environment and to the infected tissue. In addition, our results indicate that the histone-like nucleoid structuring protein H-NS has a role in the downregulation of CNF1 production and that it affects the outer membrane vesicle release in UPEC strain J96.
Contribution of NK, NK T, γδ T, and αβ T Cells to the Gamma Interferon Response Required for Liver Protection againstTrypanosoma cruzi
Authors: Sardinha Luiz Roberto , Elias Rosa Maria , Mosca Tainá , Bastos Karina R. B. , Marinho Cláudio R. F. , D'Império Lima Maria Regina , Álvarez José M.
Published: March 2006

In the present work, we show that intracellularTrypanosoma cruziis rarely found in the livers of acutely infected mice, but inflammation is commonly observed. The presence of numerous intrahepatic amastigotes in infected gamma interferon (IFN-γ)-deficient mice corroborates the notion that the liver is protected by an efficient local immunity. The contribution of different cell populations was suggested by data showing that CD4- and CD8-deficient mice were able to restrain liver parasite growth. Therefore, we have characterized the liver-infiltrating lymphocytes and determined the sources of IFN-γ during acuteT. cruziinfection. We observed that natural killer (NK) cells increased by day 7, while T and B cells increased by day 14. Among CD3+cells, CD4+, CD8+, and CD4−CD8−cell populations were greatly expanded. A large fraction of CD3+cells were positive for PanNK, a β1 integrin expressed by NK and NK T cells. However, these lymphocytes were not classic NK T cells because they did not express NK1.1 and showed no preferential usage of Vβ8. Otherwise, liver NK T (CD3+NK1.1+) cells were not increased in acutely infected mice. The majority of PanNK+CD4+and PanNK+CD8+cells expressed T-cell receptor αβ (TCRαβ), whereas PanNK+CD4−CD8−cells were positive for TCRγδ. In fact, γδ T cells showed the most remarkable increase (40- to 100-fold) among liver lymphocytes. Most importantly, intracellular analysis revealed high levels of IFN-γ production at day 7 by NK cells and at day 14 by CD4+, CD8+, and CD4−CD8−TCRγδ+cells. We concluded that NK cells are a precocious source of IFN-γ in the livers of acutely infected mice, and, as the disease progresses, conventional CD4+and CD8+T cells and γδ T cells, but not classic NK-T cells, may provide the IFN-γ required for liver protection againstT. cruzi.
Exposure of Lymphocytes to High Doses of
Actinobacillus actinomycetemcomitans
Cytolethal Distending Toxin Induces Rapid Onset of Apoptosis-Mediated DNA Fragmentation
Authors: Shenker Bruce J. , Demuth Donald R. , Zekavat Ali
Published: March 2006

We have shown previously that treatment of human lymphocytes with the
Actinobacillus actinomycetemcomitans
cytolethal distending toxin (Cdt) results in dose-dependent G
2
arrest, followed 24 h later by apoptotic cell death. Here we demonstrated that for Jurkat cells exposed to high concentrations of Cdt (>0.2 ng/ml) there was a dose-dependent increase in the level of S-phase cells and a concomitant decrease in the level of G
2
cells. Fluorescence-activated cell sorter analysis demonstrated that the S-phase cells did not incorporate BrdU and likely represented cells that arrested in G
2
and underwent significant DNA fragmentation. Analysis of the kinetics of the appearance of both S-phase cells and apoptotic cells supported this interpretation. Cells exposed to low doses of toxin exhibited G
2
arrest at 24 h, but at 48 and 72 h there were also decreases in the level of G
2
cells and concomitant increases in the levels of S, G
0
/G
1
, and sub-G
0
cells; these changes were paralleled by increased numbers of apoptotic cells. Cells exposed to high doses of toxin exhibited these changes 24 to 48 h earlier. We also examined the relationship between G
2
arrest, DNA fragmentation, and activation of the apoptotic cascade. We employed two inhibitors of apoptosis, overexpression of Bcl-2 and the caspase-3 inhibitor zvad. Both inhibitors blocked Cdt-induced apoptosis, Cdt-induced DNA fragmentation, and phosphorylation of the histone H2AX. However, the cells retained the ability to undergo G
2
arrest in the presence of the toxin. Thus, it appears that high doses of Cdt induce rapid onset of DNA degradation resulting from activation of the apoptotic cascade.
Mapping of a Domain Required for Protein-Protein Interactions and Inhibitory Activity of a
Helicobacter pylori
Dominant-Negative VacA Mutant Protein
Authors: Torres Victor J. , McClain Mark S. , Cover Timothy L.
Published: March 2006

The
Helicobacter pylori
VacA toxin is an 88-kDa secreted protein that causes multiple alterations in mammalian cells and is considered an important virulence factor in the pathogenesis of peptic ulcer disease and gastric cancer. We have shown previously that a VacA mutant protein lacking amino acids 6 to 27 (Δ6-27p88 VacA) is able to inhibit many activities of wild-type VacA in a dominant-negative manner. Analysis of a panel of C-terminally truncated Δ6-27p88 VacA proteins indicated that a fragment containing amino acids 1 to 478 (Δ6-27p48) exhibited a dominant-negative phenotype similar to that of the full-length Δ6-27p88 VacA protein. In contrast, a shorter VacA fragment lacking amino acids 6 to 27 (Δ6-27p33) did not exhibit detectable inhibitory activity. The Δ6-27p48 protein physically interacted with wild-type p88 VacA, whereas the Δ6-27p33 protein did not. Mutational analysis indicated that amino acids 351 to 360 are required for VacA protein-protein interactions and for dominant-negative inhibitory activity. The C-terminal portion (p55 domain) of wild-type p88 VacA could complement either Δ6-27p33 or Δ(6-27/351-360)p48, reconstituting dominant-negative inhibitory activity. Collectively, our data provide strong evidence that the inhibitory properties of dominant-negative VacA mutant proteins are dependent on interactions between the mutant VacA proteins and wild-type VacA, and they allow mapping of a domain involved in the formation of oligomeric VacA complexes.
An IncI1 Plasmid Contributes to the Adherence of the Atypical EnteroaggregativeEscherichia coliStrain C1096 to Cultured Cells and Abiotic Surfaces
Authors: Dudley Edward G. , Abe Cecilia , Ghigo Jean-Marc , Latour-Lambert Patricia , Hormazabal Juan Carlos , Nataro James P.
Published: March 2006

EnteroaggregativeEscherichia coli(EAEC) is defined by a characteristic “stacked-brick” aggregative adherence (AA) pattern to cultured cells. In well-studied EAEC prototype strains (called typical EAEC strains), the AA phenotype requires aggregative adherence fimbriae (AAFs). However, previous studies suggest that known AAF alleles are not found in all EAEC strains. To define mechanisms contributing to adherence in an atypical strain, we studied EAEC strain C1096. AnE. coliK12 derivative carrying two plasmids, designated pSERB1 and pSERB2, from C1096 adhered to cell lines and exhibited an AA pattern. Nucleotide sequence analysis of pSERB1 indicated that it is related to plasmids of the IncI1 incompatibility group. These plasmids encode genes involved in pilus-mediated conjugal transfer, as well aspilL-V, which encodes a second pilus of the type IV family. Insertional inactivation of the gene predicted to encode the major type IV pilin subunit (pilS) reduced conjugal transfer of the plasmid by 4 orders of magnitude. Adherence of the mutant strain to polystyrene and to HT29 cells was reduced by approximately 21% and 75%, respectively. In a continuous-flow microfermentor, thepilSinactivation reduced mature biofilm formation on a glass slide by approximately 50%. In addition, the simultaneous presence of both pSERB1 and pSERB2 plasmids promotedpilS-independent biofilm formation. We conclude that the IncI1 plasmid of EAEC C1096 encodes a type IV pilus that contributes to plasmid conjugation, epithelial cell adherence, and adherence to abiotic surfaces. We also observe that AA can be mediated by factors distinct from AAF adhesins.
MyD88 Deficiency Enhances Acquisition and Transmission of
Borrelia burgdorferi
by
Ixodes scapularis
Ticks
Authors: Bockenstedt Linda K. , Liu Nengyin , Schwartz Ira , Fish Durland
Published: March 2006

Borrelia burgdorferi
strains exhibit various degrees of infectivity and pathogenicity in mammals, which may be due to their relative ability to evade initial host immunity. Innate immune cells recognize
B. burgdorferi
by Toll-like receptors (TLRs) that use the intracellular molecule MyD88 to mediate effector functions. To determine whether impaired TLR signaling enhances
Ixodes scapularis
acquisition of
B. burgdorferi
, we fed nymphs on wild-type (WT) and MyD88
−/−
mice previously infected with two clinical isolates of
B. burgdorferi
, BL206, a high-virulence strain, and B348, an attenuated strain. Seventy-three percent of the nymphs that fed on BL206-infected WT mice and 40% of the nymphs that fed on B348-infected WT mice acquired
B. burgdorferi
, whereas 100% of the nymphs that fed on MyD88
−/−
mice became infected, irrespective of
B. burgdorferi
strain. Ticks that acquired infection after feeding on MyD88
−/−
mice harbored more spirochetes than those that fed on WT mice, as assessed by quantitative PCR for
B. burgdorferi
DNA. Vector transmission of BL206 and B348 was also enhanced when MyD88
−/−
mice were the blood meal hosts, with the mean pathogen burden at the skin inoculation site significantly higher than levels in WT mice. These results show that the absence of MyD88 facilitates passage of both low- and high-infectivity
B. burgdorferi
strains between the tick vector and the mammal and enhances the infectivity of a low-infectivity
B. burgdorferi
strain.
Correlation between Eosinophils and Protection against Reinfection withSchistosoma mansoniand the Effect of Human Immunodeficiency Virus Type 1 Coinfection in Humans
Authors: Ganley-Leal Lisa M. , Mwinzi Pauline N. , Cetre-Sossah Catherine B. , Andove Julius , Hightower Allen W. , Karanja Diana M. S. , Colley Daniel G. , Secor W. Evan
Published: March 2006

Longitudinal investigations of an adult male population of Kenyan car washers who have heavy and quantifiable occupational exposure toSchistosoma mansonicercariae revealed that some individuals develop resistance to reinfection while others remain highly susceptible. We sought to characterize immune correlates associated with host protection in this population. Previous studies have demonstrated an association of peripheral eosinophilia with resistance to reinfection with schistosomes. Thus, we investigated the relationship between the percentage of circulating eosinophils and the effect of human immunodeficiency virus type 1 (HIV-1) coinfection on the susceptibility of the car washers to reinfection with schistosomes. Elevated percentages of circulating eosinophils were associated with resistance to reinfection byS. mansoniin HIV-1-seronegative persons. In the HIV-1-seropositive cohort, low CD4+-T-cell counts were associated with a less intense eosinophilia. Moreover, eosinophils from the car washers expressed high levels of FcεRI β chain, a molecule important in immunoglobulin E (IgE)-mediated immunity. Levels of FcεRI β chain expression correlated with serum levels of total and antigen-specific IgE for HIV-1-negative car washers, but this was not the case for individuals coinfected with HIV-1. Overall, these data further implicate eosinophils as having a potential role in development of protective immunity against schistosomes and suggest that changes associated with HIV-1 coinfection increase susceptibility to reinfection.
Immunization with theHaemophilus ducreyiHemoglobin Receptor HgbA Protects against Infection in the Swine Model of Chancroid
Authors: Afonina Galyna , Leduc Isabelle , Nepluev Igor , Jeter Chrystina , Routh Patty , Almond Glen , Orndorff Paul E. , Hobbs Marcia , Elkins Christopher
Published: March 2006

The etiologic agent of chancroid isHaemophilus ducreyi. To fulfill its obligate requirement for heme,H. ducreyiuses two TonB-dependent receptors: the hemoglobin receptor (HgbA) and a receptor for free heme (TdhA). Expression of HgbA is necessary forH. ducreyito survive and initiate disease in a human model of chancroid. In this study, we used a swine model ofH. ducreyiinfection to demonstrate that an experimental HgbA vaccine efficiently prevents chancroid, as determined by several parameters. Histological sections of immunized animals lacked typical microscopic features of chancroid. All inoculated sites from mock-immunized pigs yielded viableH. ducreyicells, whereas no viableH. ducreyicells were recovered from inoculated sites of HgbA-immunized pigs. Antibodies from sera of HgbA-immunized animals bound to and initiated antibody-dependent bactericidal activity against homologousH. ducreyistrain 35000HP and heterologous strain CIP542 ATCC; however, an isogenichgbAmutant of 35000HP was not killed, proving specificity. Anti-HgbA immunoglobulin G blocked hemoglobin binding to the HgbA receptor, suggesting a novel mechanism of protection through the limitation of heme/iron acquisition byH. ducreyi. Such a vaccine strategy might be applied to other bacterial pathogens with strict heme/iron requirements. Taken together, these data suggest continuing the development of an HgbA subunit vaccine to prevent chancroid.
Cloning, Expression, and Characterization of Fimbrial Operon F9 from Enterohemorrhagic
Escherichia coli
O157:H7
Authors: Low Alison S. , Dziva Francis , Torres Alfredo G. , Martinez Jessenya L. , Rosser Tracy , Naylor Stuart , Spears Kevin , Holden Nicola , Mahajan Arvind , Findlay John , Sales Jill , Smith David G. E. , Low J. Christopher , Stevens Mark P. , Gally David L.
Published: March 2006

Recent transposon mutagenesis studies with two enterohemorrhagic
Escherichia coli
(EHEC) strains, a sero- type O26:H- strain and a serotype O157:H7 strain, led to identification of a putative fimbrial operon that promotes colonization of young calves (1 to 2 weeks old). The distribution of the gene encoding the major fimbrial subunit present in O-island 61 of EHEC O157:H7 in a characterized set of 78 diarrheagenic
E. coli
strains was determined, and this gene was found in 87.2% of the strains and is therefore not an EHEC-specific region. The cluster was amplified by long-range PCR and cloned into the inducible expression vector pBAD18. Induced expression in
E. coli
K-12 led to production of fimbriae, as demonstrated by transmission electron microscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. The fimbriae were purified, and sera to the purified major subunit were raised and used to demonstrate expression from wild-type
E. coli
O157:H7 strains. Induced expression of the fimbriae, designated F9 fimbriae, was used to characterize binding to bovine epithelial cells, bovine gastrointestinal tissue explants, and extracellular matrix components. The fimbriae promoted increases in the levels of
E. coli
K-12 binding only to bovine epithelial cells. In contrast, induced expression of F9 fimbriae in
E. coli
O157:H7 significantly reduced adherence of the bacteria to bovine gastrointestinal explant tissue. This may have been due to physical hindrance of type III secretion-dependent attachment. The main F9 subunit gene was deleted in
E. coli
O157:H7, and the resulting mutant was compared with the wild-type strain for colonization in weaned cattle. While the shedding levels of the mutant were reduced, the animals were still colonized at the terminal rectum, indicating that the adhesin is not responsible for the rectal tropism observed but may contribute to colonization at other sites, as demonstrated previously with very young animals.
Immunization Enhances Inflammation and Tissue Destruction in Response toPorphyromonas gingivalis
Authors: Leone Cataldo W. , Bokhadhoor Haneen , Kuo David , Desta Tesfahun , Yang Julia , Siqueira Michelle F. , Amar Salomon , Graves Dana T.
Published: March 2006

It is well established that host-bacterium interactions play a critical role in the initiation and progression of periodontal diseases. By the use of inhibitors, it has been shown that mediators associated with the innate immune response significantly contribute to the disease process. Less is known regarding the role of the acquired immune response. To investigate mechanisms by which the acquired immune response toPorphyromonas gingivaliscould affect connective tissue, we used a well-documented calvarial model to study host-bacterium interactions. Injection ofP. gingivalisstimulated gamma interferon, interleukin 6, macrophage inflammatory protein 2, and monocyte chemoattractant protein 1 expression as determined by real-time PCR. Prior immunization againstP. gingivalissignificantly enhanced the mRNA levels of these cytokines and chemokines. Similarly, immunization significantly increased and prolonged the formation of a polymorphonuclear leukocyte and mononuclear cell infiltrate (P< 0.05). In addition, the area of connective tissue destruction, osteoclastogenesis, bone loss, mRNA expression of proapoptotic genes, and degree of fibroblast apoptosis were increased in immunized mice (P< 0.05). These results indicate that activation of the acquired immunity byP. gingivalisincreases the inflammatory and destructive responses which occur in part through up-regulating the innate immune response and enhancing osteoclastogenesis and fibroblast apoptosis.
The Host Defense Peptide Beta-Defensin 1 Confers Protection againstBordetella pertussisin Newborn Piglets
Authors: Elahi Shokrollah , Buchanan Rachelle M. , Attah-Poku Sam , Townsend Hugh G. G. , Babiuk Lorne A. , Gerdts Volker
Published: March 2006

Innate immunity plays an important role in protection against respiratory infections in humans and animals. Host defense peptides such as beta-defensins represent major components of innate immunity. We recently developed a novel porcine model of pertussis, an important respiratory disease of young children and infants worldwide. Here, we investigated the role of porcine beta-defensin 1 (pBD-1), a porcine defensin homologue of human beta-defensin 2, in conferring protection against respiratory infection withBordetella pertussis. In this model, newborn piglets were fully susceptible to infection and developed severe bronchopneumonia. In contrast, piglets older than 4 weeks of age were protected against infection withB. pertussis. Protection was associated with the expression of pBD-1 in the upper respiratory tract. In fact, pBD-1 expression was developmentally regulated, and the absence of pBD-1 was thought to contribute to the increased susceptibility of newborn piglets to infection withB. pertussis. Bronchoalveolar lavage specimens collected from older animals as well as chemically synthesized pBD-1 displayed strong antimicrobial activity againstB. pertussisin vitro. Furthermore, in vivo treatment of newborn piglets with only 500 μg pBD-1 at the time of challenge conferred protection against infection withB. pertussis. Interestingly, pBD-1 displayed no bactericidal activity in vitro againstBordetella bronchiseptica, a closely related natural pathogen of pigs. Our results demonstrate that host defense peptides play an important role in protection against pertussis and are essential in modulating innate immune responses against respiratory infections.
Monoclonal Antibody Detection of CD46 Clustering beneath
Neisseria gonorrhoeae
Microcolonies
Authors: Weyand Nathan J. , Lee Shaun W. , Higashi Dustin L. , Cawley Daniel , Yoshihara Paul , So Magdalene
Published: March 2006

CD46 (membrane cofactor protein), a complement-regulatory protein that participates in innate and acquired immunity, also serves as a receptor for viral and bacterial pathogens. CD46 isoforms terminate in one of two cytoplasmic tails, Cyt1 or Cyt2, which differ in signaling and trafficking properties. Dissecting the functions of the two cytoplasmic tails in these cellular processes has been hampered by the absence of specific reagents. Here we report the construction of Cyt1- and Cyt2-specific monoclonal antibodies (MAbs). These MAbs recognize unique epitopes within the tails and can be used for immunofluorescence microscopy, immunoblotting, and immunoprecipitation. Studies of
Neisseria gonorrhoeae
-infected cells with the CD46 tail MAbs demonstrate the differential recruitment of Cyt1 and Cyt2 to the cortical plaque.
MyD88 Innate Immune Function in a Zebrafish Embryo Infection Model
Authors: van der Sar Astrid M. , Stockhammer Oliver W. , van der Laan Carina , Spaink Herman P. , Bitter Wilbert , Meijer Annemarie H.
Published: March 2006

Innate immunity signaling mechanisms during vertebrate embryogenesis are largely unknown. To study Toll-like receptor (TLR) signaling function in the zebrafish embryo model, we designed an experimental setup for antisense morpholino knockdown under conditions of bacterial infection. Clearance of
Salmonella enterica
serovar Typhimurium Ra bacteria was significantly impaired after knockdown of myeloid differentiation factor 88 (MyD88), a common adaptor protein in TLR and interleukin-1 receptor signaling. Thereby, we demonstrate for the first time that the innate immune response of the developing embryo involves MyD88-dependent signaling, which further establishes the zebrafish embryo as a model for the study of vertebrate innate immunity.
Active Immunization against
Pneumocystis carinii
with a Recombinant
P. carinii
Antigen
Authors: Wells Jesse , Haidaris Constantine G. , Wright Terry W. , Gigliotti Francis
Published: March 2006

Mice immunized with recombinant mouse
Pneumocystis carinii
antigen A12-thiredoxin fusion protein developed an antibody response that recognized
P. carinii
antigens, as determined by Western blotting and immunofluorescence analysis. Compared to mice immunized with thioredoxin alone, mice immunized with A12-thioredoxin had significantly reduced lung
P. carinii
burdens after CD4
+
T-cell depletion and challenge with
P. carinii
.
Human Neutrophil Calprotectin Reduces the Susceptibility ofBorrelia burgdorferito Penicillin
Authors: Montgomery Ruth R. , Schreck Kimberly , Wang Xiaomei , Malawista Stephen E.
Published: March 2006

Borrelia burgdorferi, the spirochetal agent of Lyme disease, is susceptible to killing by a variety of polymorphonuclear leukocyte (PMN) components. Some are most effective against metabolically activeB. burgdorferi. The abundant PMN cytoplasmic protein calprotectin, elevated 10- to 100-fold in inflammation, inhibits the growth of spirochetes through chelation of the essential cation, Zn. Since the action of some therapeutic antibiotics depends on bacterial division, we investigated the antibiotic sensitivities of spirochetes in calprotectin. In physiologic calprotectin,B. burgdorferiis not eliminated by therapeutic doses of penicillin G; in contrast, doxycycline is effective. Calprotectin may modify the clearance of spirochetes at sites of inflammation.
Adaptive Immunity-Dependent Intestinal Hypermotility Contributes to Host Defense againstGiardiaspp
Authors: Andersen Yolanda S. , Gillin Frances D. , Eckmann Lars
Published: March 2006

Humans infected withGiardiaexhibit intestinal hypermotility, but the underlying mechanisms and functional significance are uncertain. Here we show in murine models of giardiasis that small-intestinal hypermotility occurs in a delayed fashion relative to peak parasite burden, is dependent on adaptive immune defenses, and contributes to giardial clearance.
Chlamydiae Modulate Gamma Interferon, Interleukin-1β, and Tumor Necrosis Factor Alpha Receptor Expression in HeLa Cells
Authors: Shirey Kari Ann , Carlin Joseph M.
Published: March 2006

Chlamydia psittaciwas found to modulate receptor expression for the cytokine receptors that are involved in the synergistic induction of indoleamine dioxygenase in epithelial cells. Increases in receptor expression were seen even with inactivatedChlamydia, suggesting that chlamydial antigens and not products of infection are important for up-regulating cytokine receptor expression.
VisceralLeishmania donovaniInfection in Interleukin-13−/−Mice
Authors: Murray Henry W. , Tsai Christine W. , Liu Jianguo , Ma Xiaojing
Published: March 2006

Leishmania donovani-infected interleukin-13−/−BALB/c mice showed impaired initial gamma interferon secretion and incomplete granuloma assembly at parasitized liver foci. Nonetheless, control of early parasite replication, resolution of liver infection, and responsiveness to antileishmanial chemotherapy were intact. By itself, interleukin-13 does not appear to materially influence acquired resistance in this intracellular infection.
Temporal Distribution and Parasite Load Kinetics in Blood and Tissues during
Neospora caninum
Infection in Mice
Authors: Collantes-Fernández Esther , López-Pérez Inmaculada , Álvarez-García Gema , Ortega-Mora Luis M.
Published: March 2006

The kinetics of
Neospora caninum
loads in mice inoculated with NC-Liv or NC-1 isolates were studied. The acute phase was characterized by parasitemia and the detection of parasite DNA in several organs, whereas during the chronic phase, the parasite was detected mainly in the brain. Mice infected with NC-Liv developed clinical signs, showing higher brain parasite burdens than NC-1-infected mice.
Mutation of Phosphotransacetylase but Not Isocitrate Lyase Reduces the Virulence of
Salmonella enterica
Serovar Typhimurium in Mice
Authors: Kim Yang Re , Brinsmade Shaun R. , Yang Zheng , Escalante-Semerena Jorge , Fierer Joshua
Published: March 2006

A phosphotransacetylase (
pta
) mutant of
Salmonella enterica
serovar Typhimurium was attenuated in mice but survived normally in macrophages. Complementation of the
pta
mutation in
trans
restored virulence. An isocitrate lyase (
aceA
) mutant was virulent, so the inability to use acetate as a sole carbon source does not explain the phenotype.
CATEGORIZATION OF CONTINUOUS NUMERIC PERCEPTS BY MODIFIED FUZZY ART WITH Q-LEARNING
Authors: UEDA HIROAKI , KIMOTO HIDEAKI , NARAKI TAKESHI , TAKAHASHI KENICHI , MIYAHARA TETSUHIRO
Published: March 2006

We propose a new method to categorize continuous numeric percepts for Q-learning, where percept vectors are classified into categories on the basis of fuzzy ART and Q-learning uses categories as states to acquire rules for agent behavior. For efficient learning, we modify fuzzy ART to reduce the number of categories without deteriorating the efficiency of reinforcement learning. In our modification, a vigilance parameter is defined for each category in order to control the size of a category and it is updated during learning. The method to update a vigilance parameter is based on category integration, which contributes to reducing the number of categories. Here, we define the similarity for any category pair to judge whether category integration should be performed or not. When two categories are integrated into a new category, a vigilance parameter for the category is calculated and categories used for integration are discarded, so that the number of categories is reduced without restricting the number of categories. Experimental results show that Q-learning with modified fuzzy ART acquires good rules for agent behavior more efficiently than Q-learning with ordinary fuzzy ART, although the number of categories generated by modified fuzzy ART is much less than that generated by ordinary one.
A NEW UNIFORM NEURON MODEL OF GENERALIZED LOGIC OPERATORS BASED ON [a,b]
Authors: MAO MING-YI , CHEN ZHI-CHENG , HE HUA-CAN
Published: March 2006

The study on neural systems is very hot, especially regarding modelling of fuzzy neural networks. The neuron models have been limited in interval [0,1] before. This paper studies the logic operators and neuron models of proposition object based on [a, b]. Any interval [a, b] is called a generalized interval. Firstly, authors provide the conception of proposition object, discussed on the radix space of universal logic. Secondly, using the NTS norms theories, this paper establishes the universal logic operation models on generalized interval [a, b]. Thirdly, the paper builds up a new uniform neuron model of "Not/And/Or/Average" on generalized interval [a, b]. As an instance, authors discuss the neuron models based on standard interval [0,1], which are continuously changeable with generalized correlation coefficient "h" and generalized self-correlation coefficient "k". This work offers important theories and models for neurons reasoning, make it more flexible because of the change of h, k and [a, b], and enlarge its study domain.
PATTERN RECOGNITION OF THE TERM STRUCTURE USING INDEPENDENT COMPONENT ANALYSIS
Authors: WU EDMOND HAOCUN , YU PHILIP L. H.
Published: March 2006

Term structure is a useful curve describing some financial asset as a function of time to maturity or expiration. In this paper, we propose to use Independent Component Analysis (ICA) to model the term structure of multiple yield curves. The idea is that we first employ ICA to decompose the multivariate time series, then we suggest two ICA methods for dimension reduction and pattern recognition of the term structure. We also compare the results by using an alternative method, Principal Component Analysis (PCA). The empirical studies suggest that the proposed ICA approaches outperform PCA methods in modeling the term structure. This model can be used in financial time series analysis as well as related financial applications.
TWO-STEP SINGLE PARAMETER REGULARIZATION FISHER DISCRIMINANT METHOD FOR FACE RECOGNITION
Authors: CHEN WEN-SHENG , YUEN PONG CHI , HUANG JIAN , FANG BIN
Published: March 2006

In face recognition tasks, Fisher discriminant analysis (FDA) is one of the promising methods for dimensionality reduction and discriminant feature extraction. The objective of FDA is to find an optimal projection matrix, which maximizes the between-class-distance and simultaneously minimizes within-class-distance. The main limitation of traditional FDA is the so-called Small Sample Size (3S) problem. It induces that the within-class scatter matrix is singular and then the traditional FDA fails to perform directly for pattern classification. To overcome 3S problem, this paper proposes a novel two-step single parameter regularization Fisher discriminant (2SRFD) algorithm for face recognition. The first semi-regularized step is based on a rank lifting theorem. This step adjusts both the projection directions and their corresponding weights. Our previous three-to-one parameter regularized technique is exploited in the second stage, which just changes the weights of projection directions. It is shown that the final regularized within-class scatter matrix approaches the original within-class scatter matrix as the single parameter tends to zero. Also, our method has good computational complexity. The proposed method has been tested and evaluated with three public available databases, namely ORL, CMU PIE and FERET face databases. Comparing with existing state-of-the-art FDA-based methods in solving the S3 problem, the proposed 2SRFD approach gives the best performance.
HANDWRITING-BASED PERSONAL IDENTIFICATION
Authors: HE ZHENYU , YOU XINGE , TANG YUAN YAN , FANG BIN , DU JIANWEI
Published: March 2006

Handwriting-based personal identification, which is also called handwriting-based writer identification, is an active research topic in pattern recognition. Despite continuous effort, offline handwriting-based writer identification still remains as a challenging problem because writing features can only be extracted from the handwriting image. As a result, plenty of dynamic writing information, which is very valuable for writer identification, is unavailable for offline writer identification. In this paper, we present a novel wavelet-based Generalized Gaussian Density (GGD) method for offline writer identification. Compared with the 2-D Gabor model, which is currently widely acknowledged as a good method for offline handwriting identification, GGD method not only achieves a better identification accuracy but also greatly reduces the elapsed time on calculation in our experiments.
DOCUMENT CLUSTERING WITH PAIRWISE CONSTRAINTS
Authors: KREESURADEJ WORAPOJ , SUWANLAMAI APINYA
Published: March 2006

This paper proposes document clustering using Kohonen neural network with pairwise constraints. This algorithm works directly on textual information without mapping document into some representation that has quantitative features. The input level of the proposed neural network can directly receive a qualitative value without mapping the qualitative value into the numerical value. The proposed neural network is based on the architecture of text processing Kohonen neural network, the concepts of dissimilarity measure of symbolic objects and pairwise constrained concepts. As a result, the model can successfully assign cluster label to the objects.
A NEW TECHNIQUE FOR SELECTING FEATURES FROM PROTEIN SEQUENCES
Authors: ZHAO XING-MING , DU JI-XIANG , WANG HONG-QIANG , ZHU YUNPING , LI YIXUE
Published: March 2006

A new method for selecting features from protein sequences is proposed in this paper. First, the protein sequences are converted into fixed-dimensional feature vectors. Then, a subset of features is selected using relative entropy method and used as the inputs for Support Vector Machine (SVM). Finally, the trained SVM classifier is utilized to classify protein sequences into certain known protein families. Experimental results over proteins obtained from PIR database and GPCRs have shown that our proposed approach is really effective and efficient in selecting features from protein sequences.