bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adhesion of Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum on bioactive TiO2 surfaces
Authors: Närhi Timo O. , Leminen Heidi , Haukioja Anna , Söderling Eva 
Published: January 2012

AbstractBackgroundBioactive TiO2 coatings have been found to enhance fibroblast adhesion and gingival attachment on the titanium surfaces, but no information is available whether the coatings also promote the adhesion of periodontal pathogens.AimThe purpose of this study was to investigate protein adsorption and the adhesion of Aggregatibacter actinomycetemcomitans (Aa) and Fusobacterium nucleatum (Fn) on bioactive TiO2 surfaces.Materials and methodsCommercially pure titanium discs (diameter 11.0 mm, grade 2) were coated with sol‐gel derived bioactive TiO2 coatings (MetAlive, Vivoxid, Turku, Finland) and preincubated in 1.5 ml PBS/diluted serum/diluted saliva at room temperature to mimic the clinical situation after implantation and to allow serum/saliva proteins to adhere on the substrates. Uncoated titanium discs were used as controls.ResultsSDS‐PAGE revealed similar protein profiles on bioactive and control titanium substrates. No differences were noticed in Aa or Fn adhesion between bioactive and control titanium. However, serum and saliva conditioning diminished Aa adhesion on both surfaces (p<0.001).ConclusionIt can be concluded that bioactive TiO2 coating does not promote adhesion of Aa and Fn.
The Fe(II)/α‐ketoglutarate‐dependent taurine dioxygenases from Pseudomonas putida and Escherichia coli are tetramers
Authors: Knauer Stefan H. , Hartl‐Spiegelhauer Olivia , Schwarzinger Stephan , Hänzelmann Petra , Dobbek Holger 
Published: January 2012

Fe(II)/α‐ketoglutarate‐dependent oxygenases are versatile catalysts associated with a number of different biological functions in which they use the oxidizing power of activated dioxygen to convert a variety of substrates. A mononuclear nonheme iron center is used to couple the decarboxylation of the cosubstrate α‐ketoglutarate with a two‐electron oxidation of the substrate, which is a hydroxylation in most cases. Although Fe(II)/α‐ketoglutarate‐dependent oxygenases have diverse amino acid sequences and substrate specifity, it is assumed that they share a common mechanism. One representative of this enzyme family is the Fe(II)/α‐ketoglutarate‐dependent taurine dioxygenase that catalyzes the hydroxylation of taurine yielding sulfite and aminoacetaldehyde. Its mechanism has been studied in detail becoming a model system for the whole enzyme family. However, its oligomeric state and architecture have been disputed. Here, we report the biochemical and kinetic characterization of the Fe(II)/α‐ketoglutarate‐dependent taurine dioxygenase from Pseudomonas putida KT2440 (TauDPp). We also present three crystal structures of the apo form of this enzyme. Comparisons with taurine dioxygenase from Escherichia coli (TauDEc) demonstrate that both enzymes are quite similar regarding their spectra, structure and kinetics, and only minor differences for the accumulation of intermediates during the reaction have been observed. Structural data and analytical gel filtration, as well as sedimentation velocity analytical ultracentrifugation, show that both TauDPp and TauDEc are tetramers in solution and in the crystals, which is in contrast to the earlier description of taurine dioxygenase from E. coli as a dimer.DatabaseThe atomic coordinates and structure factors have been deposited with the Brookhaven Protein Data Bank (entry 3PVJ, 3V15, 3V17)Structured digital abstract

tauDpp
and tauDpp bind by molecular sieving (View interaction)

tauDpp
and tauDpp bind by x‐ray crystallography (View interaction)

tauDEc
and tauDEc bind by molecular sieving (View interaction)
Evaluation of Toll‐like receptor and adaptor molecule polymorphisms for susceptibility to tuberculosis in a Colombian population
Authors: Sánchez D. , Lefebvre C. , Rioux J. , García L. F. , Barrera L. F. 
Published: January 2012

SummaryImmunological studies have supported the idea that innate immunity is critical for the control of Mycobacterium tuberculosis (Mtb) infection in humans. Despite the overwhelming evidence showing the critical role of Toll‐like receptors (TLRs) in the in vitro recognition of Mtb, the in vivo significance of individual TLRs has been more difficult to demonstrate consistently. We were interested in examining the role of genes of TLRs and molecules involved in their signalling cascades, and a case–control study was designed to test the association of polymorphisms of these innate immune genes with pulmonary tuberculosis (TB) in a Colombian population. In this study, we did not find an association with TLR2, TLR4, TLR9, MyD88 or MAL/TIRAP polymorphic variants. These findings suggest that those genes are not involved as risk factors for pulmonary TB in our population.
Studying Large Mammals With Imperfect Detection: Status and Habitat Preferences of Wild Cattle and Large Carnivores in Eastern Cambodia
Authors: Gray Thomas N. E. 
Published: January 2012

AbstractStudying large mammal species in tropical forests is a conservation challenge with species’ behavior and ecology often increasing the probability of non‐detection during surveys. Consequently, knowledge of the distribution, status, and natural history of many large mammal species in Southeast Asia is limited. I developed occupancy models from camera‐trapping data, thereby accounting for imperfect detection at sampling sites, to clarify the status and habitat requirements of four globally threatened or near threatened large mammals (banteng Bos javanicus, gaur Bos gaurus, dhole Cuon alpinus, and leopard Panthera pardus) in Mondulkiri Protected Forest, eastern Cambodia. Camera traps were operational for >3500 trap nights with 202 photographic encounters of the four study species. Model averaged occupancy estimates were between 5 percent (leopard) and 140 percent (gaur) higher than naive estimates (i.e., proportion of camera‐trap sites species recorded from) thus highlighting the importance of accounting for detectability during conservation surveys. I recommend the use of an occupancy framework when using camera‐trap data to study the status, ecology, and habitat preferences of poorly known and elusive species. The results highlight the importance of mixed deciduous and semi‐evergreen forest for wild cattle in eastern Cambodia and I emphasize that these habitats must be considered in conservation planning across the Lower Mekong Dry Forest Ecoregion.
Lysosomal Signaling Enhances Mitochondria‐Mediated Photodynamic Therapy in A431 Cancer Cells: Role of Iron
Authors: Saggu Shalini , Hung Hsin‐I , Quiogue Geraldine , Lemasters John J. , Nieminen Anna‐Liisa 
Published: January 2012

AbstractIn photodynamic therapy (PDT), light activates a photosensitizer added to a tissue, resulting in singlet oxygen formation and cell death. The photosensitizer phthalocyanine 4 (Pc 4) localizes primarily to mitochondrial membranes in cancer cells, resulting in mitochondria‐mediated cell death. The aim of this study was to determine how lysosomes contribute to PDT‐induced cell killing by mitochondria‐targeted photosensitizers such as Pc 4. We monitored cell killing of A431 cells after Pc 4‐PDT in the presence and absence of bafilomycin, an inhibitor of the vacuolar proton pump of lysosomes and endosomes. Bafilomycin was not toxic by itself, but greatly enhanced Pc 4‐PDT‐induced cell killing. To investigate whether iron loading of lysosomes affects bafilomycin‐induced killing, cells were incubated with ammonium ferric citrate (30 μm) for 30 h prior to PDT. Ammonium ferric citrate enhanced Pc 4 plus bafilomycin‐induced cell killing without having toxicity by itself. Iron chelators (desferrioxamine and starch‐desferrioxamine) and the inhibitor of the mitochondrial calcium (and ferrous iron) uniporter, Ru360, protected against Pc 4 plus bafilomycin toxicity. These results support the conclusion that chelatable iron stored in the lysosomes enhances the efficacy of bafilomycin‐mediated PDT and that lysosomal disruption augments PDT with Pc 4.
Catalytic dechlorination of diclofenac by biogenic palladium in a microbial electrolysis cell
Authors: Gusseme Bart De , Soetaert Maarten , Hennebel Tom , Vanhaecke Lynn , Boon Nico , Verstraete Willy 
Published: January 2012

SummaryDiclofenac is one of the most commonly detected pharmaceuticals in wastewater treatment plant (WWTP) effluents and the receiving water bodies. In this study, biogenic Pd nanoparticles (‘bio‐Pd’) were successfully applied in a microbial electrolysis cell (MEC) for the catalytic reduction of diclofenac. Hydrogen gas was produced in the cathodic compartment, and consumed as a hydrogen donor by the bio‐Pd on the graphite electrodes. In this way, complete dechlorination of 1 mg diclofenac l−1 was achieved during batch recirculation experiments, whereas no significant removal was observed in the absence of the biocatalyst. The complete dechlorination of diclofenac was demonstrated by the concomitant production of 2‐anilinophenylacetate (APA). Through the addition of −0.8 V to the circuit, continuous and complete removal of diclofenac was achieved in synthetic medium at a minimal HRT of 2 h. Continuous treatment of hospital WWTP effluent containing 1.28 µg diclofenac l−1 resulted in a lower removal efficiency of 57%, which can probably be attributed to the affinity of other environmental constituents for the bio‐Pd catalyst. Nevertheless, reductive catalysis coupled to sustainable hydrogen production in a MEC offers potential to lower the release of micropollutants from point‐sources such as hospital WWTPs.
Metabolic Engineering of Clostridium acetobutylicum ATCC 824 for Isopropanol-Butanol-Ethanol Fermentation
Authors: Lee Joungmin , Jang Yu-Sin , Choi Sung Jun , Im Jung Ae , Song Hyohak , Cho Jung Hee , Seung Do Young , Papoutsakis E. Terry , Bennett George N. , Lee Sang Yup 
Published: December 2011

ABSTRACTClostridium acetobutylicumnaturally produces acetone as well as butanol and ethanol. Since acetone cannot be used as a biofuel, its production needs to be minimized or suppressed by cell or bioreactor engineering. Thus, there have been attempts to disrupt or inactivate the acetone formation pathway. Here we present another approach, namely, converting acetone to isopropanol by metabolic engineering. Since isopropanol can be used as a fuel additive, the mixture of isopropanol, butanol, and ethanol (IBE) produced by engineeredC. acetobutylicumcan be directly used as a biofuel. IBE production is achieved by the expression of a primary/secondary alcohol dehydrogenase gene fromClostridium beijerinckiiNRRL B-593 (i.e.,adhB-593) inC. acetobutylicumATCC 824. To increase the total alcohol titer, a synthetic acetone operon (actoperon;adc-ctfA-ctfB) was constructed and expressed to increase the flux toward isopropanol formation. When this engineering strategy was applied to the PJC4BK strain lacking in thebukgene (encoding butyrate kinase), a significantly higher titer and yield of IBE could be achieved. The resulting PJC4BK(pIPA3-Cm2) strain produced 20.4 g/liter of total alcohol. Fermentation could be prolonged byin situremoval of solvents by gas stripping, and 35.6 g/liter of the IBE mixture could be produced in 45 h.
Time-Dependent Profiles of Transcripts Encoding Lignocellulose-Modifying Enzymes of the White Rot Fungus Phanerochaete carnosa Grown on Multiple Wood Substrates
Authors: MacDonald Jacqueline , Master Emma R. 
Published: December 2011

ABSTRACT

The abundances of nine transcripts predicted to encode lignocellulose-modifying enzymes were measured over the course of
Phanerochaete carnosa
cultivation on four wood species. Profiles were consistent with sequential decay; transcripts encoding lignin-degrading peroxidases featured a significant substrate-dependent response. The chitin synthase gene was identified as the optimal internal reference gene for transcript quantification.
Wolbachia Strain wAlbB Enhances Infection by the Rodent Malaria Parasite Plasmodium berghei in Anopheles gambiae Mosquitoes
Authors: Hughes Grant L. , Vega-Rodriguez Joel , Xue Ping , Rasgon Jason L. 
Published: December 2011

ABSTRACT

Wolbachia
, a common bacterial endosymbiont of insects, has been shown to protect its hosts against a wide range of pathogens. However, not all strains exert a protective effect on their host. Here we assess the effects of two divergent
Wolbachia
strains, wAlbB from
Aedes albopictus
and wMelPop from
Drosophila melanogaster
, on the vector competence of
Anopheles gambiae
challenged with
Plasmodium berghei
. We show that the wAlbB strain significantly increases
P. berghei
oocyst levels in the mosquito midgut while wMelPop modestly suppresses oocyst levels. The wAlbB strain is avirulent to mosquitoes while wMelPop is moderately virulent to mosquitoes pre-blood meal and highly virulent after mosquitoes have fed on mice. These various effects on
P. berghei
levels suggest that
Wolbachia
strains differ in their interactions with the host and/or pathogen, and these differences could be used to dissect the molecular mechanisms that cause interference of pathogen development in mosquitoes.
Characteristics of the Freshwater Cyanobacterium Microcystis aeruginosa Grown in Iron-Limited Continuous Culture
Authors: Dang T. C. , Fujii M. , Rose A. L. , Bligh M. , Waite T. D. 
Published: December 2011

ABSTRACT

A continuous culturing system (chemostat) made of metal-free materials was successfully developed and used to maintain Fe-limited cultures of
Microcystis aeruginosa
PCC7806 at nanomolar iron (Fe) concentrations (20 to 50 nM total Fe). EDTA was used to maintain Fe in solution, with bioavailable Fe controlled by absorption of light by the ferric EDTA complex and resultant reduction of Fe(III) to Fe(II). A kinetic model describing Fe transformations and biological uptake was applied to determine the biologically available form of Fe (i.e., unchelated ferrous iron) that is produced by photoreductive dissociation of the ferric EDTA complex. Prediction by chemostat theory modified to account for the light-mediated formation of bioavailable Fe rather than total Fe was in good agreement with growth characteristics of
M. aeruginosa
under Fe limitation. The cellular Fe quota increased with increasing dilution rates in a manner consistent with the Droop theory. Short-term Fe uptake assays using cells maintained at steady state indicated that
M. aeruginosa
cells vary their maximum Fe uptake rate (ρ
max
) depending on the degree of Fe stress. The rate of Fe uptake was lower for cells grown under conditions of lower Fe availability (i.e., lower dilution rate), suggesting that cells in the continuous cultures adjusted to Fe limitation by decreasing ρ
max
while maintaining a constant affinity for Fe.
Role for Rhizobium rhizogenes K84 Cell Envelope Polysaccharides in Surface Interactions
Authors: Abarca-Grau Ana M. , Burbank Lindsey P. , de Paz Héctor D. , Crespo-Rivas Juan C. , Marco-Noales Ester , López María M. , Vinardell Jose M. , von Bodman Susanne B. , Penyalver Ramón 
Published: December 2011

ABSTRACT

Rhizobium rhizogenes
strain K84 is a commercial biocontrol agent used worldwide to control crown gall disease. The organism binds tightly to polypropylene substrate and efficiently colonizes root surfaces as complex, multilayered biofilms. A genetic screen identified two mutants in which these surface interactions were affected. One of these mutants failed to attach and form biofilms on the abiotic surface although, interestingly, it exhibited normal biofilm formation on the biological root tip surface. This mutant is disrupted in a
wcbD
ortholog gene, which is part of a large locus predicted to encode functions for the biosynthesis and export of a group II capsular polysaccharide (CPS). Expression of a functional copy of
wcbD
in the mutant background restored the ability of the bacteria to attach and form normal biofilms on the abiotic surface. The second identified mutant attached and formed visibly denser biofilms on both abiotic and root tip surfaces. This mutant is disrupted in the
rkpK
gene, which is predicted to encode a UDP-glucose 6-dehydrogenase required for O-antigen lipopolysaccharide (LPS) and K-antigen capsular polysaccharide (KPS) biosynthesis in rhizobia. The
rkpK
mutant from strain K84 was deficient in O-antigen synthesis and exclusively produced rough LPS. We also show that strain K84 does not synthesize the KPS typical of some other rhizobia strains. In addition, we identified a putative type II CPS, distinct from KPS, that mediates cell-surface interactions, and we show that O antigen of strain K84 is necessary for normal cell-cell interactions in the biofilms.
Enhanced Microbial Utilization of Recalcitrant Cellulose by an
Ex Vivo
Cellulosome-Microbe Complex
Authors: You Chun , Zhang Xiao-Zhou , Sathitsuksanoh Noppadon , Lynd Lee R. , Zhang Y.-H. Percival 
Published: December 2011

ABSTRACT

A cellulosome-microbe complex was assembled
ex vivo
on the surface of
Bacillus subtilis
displaying a miniscaffoldin that can bind with three dockerin-containing cellulase components: the endoglucanase Cel5, the processive endoglucanase Cel9, and the cellobiohydrolase Cel48. The hydrolysis performances of the synthetic cellulosome bound to living cells, the synthetic cellulosome, a noncomplexed cellulase mixture with the same catalytic components, and a commercial fungal enzyme mixture were investigated on low-accessibility recalcitrant Avicel and high-accessibility regenerated amorphous cellulose (RAC). The cell-bound cellulosome exhibited 4.5- and 2.3-fold-higher hydrolysis ability than cell-free cellulosome on Avicel and RAC, respectively. The cellulosome-microbe synergy was not completely explained by the removal of hydrolysis products from the bulk fermentation broth by free-living cells and appeared to be due to substrate channeling of long-chain hydrolysis products assimilated by the adjacent cells located in the boundary layer. Our results implied that long-chain hydrolysis products in the boundary layer may inhibit cellulosome activity to a greater extent than the short-chain products in bulk phase. The findings that cell-bound cellulosome expedited the microbial cellulose utilization rate by 2.3- to 4.5-fold would help in the development of better consolidated bioprocessing microorganisms (e.g.,
B. subtilis
) that can hydrolyze recalcitrant cellulose rapidly at low secretory cellulase levels.
Improvement of Modified Charcoal-Cefoperazone-Deoxycholate Agar by Supplementation with a High Concentration of Polymyxin B for Detection of Campylobacter jejuni and C. coli in Chicken Carcass Rinses
Authors: Chon Jung-Whan , Hyeon Ji-Yeon , Yim Jin-Hyuk , Kim Jong-Hyun , Song Kwang-Young , Seo Kun-Ho 
Published: December 2011

ABSTRACT

Modified charcoal-cefoperazone-deoxycholate agar (mCCDA) was improved by supplementation with a high concentration of polymyxin B. The ability of the supplemented medium to isolate
Campylobacter jejuni
and
C. coli
from chicken carcass rinses was compared to that of Campy-Cefex agar and mCCDA. Modification of mCCDA with increased polymyxin B yielded a significantly (
P
< 0.05) higher isolation rate and greater selectivity than those achieved using Campy-Cefex agar and mCCDA.
Development of a Markerless Gene Replacement System for Acidithiobacillus ferrooxidans and Construction of a
pfkB
Mutant
Authors: Wang Huiyan , Liu Xiangmei , Liu Shuangshuang , Yu Yangyang , Lin Jianqun , Lin Jianqiang , Pang Xin , Zhao Jian 
Published: December 2011

ABSTRACT

The extremely acidophilic, chemolithoautotrophic
Acidithiobacillus ferrooxidans
is an important bioleaching bacterium of great value in the metallurgical industry and environmental protection. In this report, a mutagenesis system based on the homing endonuclease I-SceI was developed to produce targeted, unmarked gene deletions in the strain
A. ferrooxidans
ATCC 23270. A targeted phosphofructokinase (PFK) gene (
pfkB
) mutant of
A. ferrooxidans
ATCC 23270 was constructed by homologous recombination and identified by PCR with specific primers as well as Southern blot analysis. This potential
pfkB
gene (AFE_1807) was also characterized by expression in PFK-deficient
Escherichia coli
cells, and heteroexpression of the PFKB protein demonstrated that it had functional PFK activity, though it was significantly lower (about 800-fold) than that of phosphofructokinase-2 (PFK-B) expressed by the
pfkB
gene from
E. coli
K-12. The function of the potential PFKB protein in
A. ferrooxidans
was demonstrated by comparing the properties of the
pfkB
mutant with those of the wild type. The
pfkB
mutant strain displayed a relatively reduced growth capacity in S
0
medium (0.5% [wt/vol] elemental sulfur in 9K basal salts solution adjusted to pH 3.0 with H
2
SO
4
), but the mutation did not completely prevent
A. ferrooxidans
from assimilating exogenous glucose. The transcriptional analysis of some related genes in central carbohydrate metabolism in the wild-type and mutant strains with or without supplementation of glucose was carried out by quantitative reverse transcription-PCR. This report suggests that the markerless mutagenesis strategy could serve as a model for functional studies of other genes of interest from
A. ferrooxidans
and multiple mutations could be made in a single
A. ferrooxidans
strain.
Production of Indole-3-Acetic Acid via the Indole-3-Acetamide Pathway in the Plant-Beneficial Bacterium Pseudomonas chlororaphis O6 Is Inhibited by ZnO Nanoparticles but Enhanced by CuO Nanoparticles
Authors: Dimkpa Christian O. , Zeng Jia , McLean Joan E. , Britt David W. , Zhan Jixun , Anderson Anne J. 
Published: December 2011

ABSTRACT

The beneficial bacterium
Pseudomonas chlororaphis
O6 produces indole-3-acetic acid (IAA), a plant growth regulator. However, the pathway involved in IAA production in this bacterium has not been reported. In this paper we describe the involvement of the indole-3-acetamide (IAM) pathway in IAA production in
P. chlororaphis
O6 and the effects of CuO and ZnO nanoparticles (NPs). Sublethal levels of CuO and ZnO NPs differentially affected the levels of IAA secreted in medium containing tryptophan as the precursor. After 15 h of growth, CuO NP-exposed cells had metabolized more tryptophan than the control and ZnO NP-challenged cells. The CuO NP-treated cells produced higher IAA levels than control cultures lacking NPs. In contrast, ZnO NPs inhibited IAA production. Mixing of CuO and ZnO NPs resulted in an intermediate level of IAA production relative to the levels in the separate CuO and ZnO NP treatments. The effect of CuO NPs on IAA levels could be duplicated by ions at the concentrations released from the NPs. However, ion release did not account for the inhibition caused by the ZnO NPs. The mechanism underlying changes in IAA levels cannot be accounted for by effects on transcript accumulation from genes encoding a tryptophan permease or the IAM hydrolase in 15-h cultures. These findings raise the issue of whether sublethal doses of NPs would modify the beneficial effects of association between plants and bacteria.