Publications

a comparison of the sorption reactivity of bacteriogenic and mycogenic mn oxide nanoparticles.	biogenic mno2 minerals affect metal fate and transport in natural and engineered systems by strongly sorbing metals ions. the ability to produce mno2 is widely dispersed in the microbial tree of life, leading to potential differences in the minerals produced by different organisms. in this study, we compare the structure and reactivity of biogenic mn oxides produced by the biofilm-forming bacterium pseudomonas putida gb-1 and the white-rot fungus coprinellus sp. the rate of mn(ii) oxidation, and ...	2015	25668070
cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from serratia sp.	the chrt gene encodes a chromate reductase enzyme which catalyzes the reduction of cr(vi). the chromate reductase is also known as flavin mononucleotide (fmn) reductase (fmn_red). the aim of the present study was to clone the full-length chrt dna from serratia sp. cqmus2 and analyze the deduced amino acid sequence and three-dimensional structure. the putative chrt gene fragment of serratia sp. cqmus2 was isolated by polymerase chain reaction (pcr), according to the known fmn_red gene sequence fr ...	2014	25667630
cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from serratia sp.	the chrt gene encodes a chromate reductase enzyme which catalyzes the reduction of cr(vi). the chromate reductase is also known as flavin mononucleotide (fmn) reductase (fmn_red). the aim of the present study was to clone the full-length chrt dna from serratia sp. cqmus2 and analyze the deduced amino acid sequence and three-dimensional structure. the putative chrt gene fragment of serratia sp. cqmus2 was isolated by polymerase chain reaction (pcr), according to the known fmn_red gene sequence fr ...	2014	25667630
interstrain interactions between bacteria isolated from vacuum-packaged refrigerated beef.	the formation of bacterial spoilage communities in food is influenced by both extrinsic and intrinsic environmental factors. although many reports describe how these factors affect bacterial growth, much less is known about interactions among bacteria, which may influence community structure. this study investigated interactions among representative species of bacteria isolated from vacuum-packaged (vp) beef. thirty-nine effectors and 20 target isolates were selected, representing 10 bacterial g ...	2015	25662972
the phasin phaf controls bacterial shape and size in a network-forming strain of pseudomonas putida.	pseudomonas putida n, a poly-3-hydroxyalkonate (pha)-producing bacterium, showing ampicillin resistance, is an unusual strain. in the presence of this antibiotic, it grows as giant cells (25-50μm) forming complex networks inter-connected by micro-tubular structures. the transformation of this bacterium with a plasmid containing the gene phaf, which encodes a phasin involved in the molecular architecture of the pha-granules, (i) restores the wild-type phenotype by reducing both bacterial size and ...	2015	25661838
collagen-like proteins (clpa, clpb, clpc, and clpd) are required for biofilm formation and adhesion to plant roots by bacillus amyloliquefaciens fzb42.	the genes of collagen-like proteins (clps) have been identified in a broad range of bacteria, including some human pathogens. they are important for biofilm formation and bacterial adhesion to host cells in some human pathogenic bacteria, including several bacillus spp. strains. interestingly, some bacterial clp-encoding genes (clps) have also been found in non-human pathogenic strains such as b. cereus and b. amyloliquefaciens, which are types of plant-growth promoting rhizobacteria (pgpr). in ...	2015	25658640
draft genome sequence of acinetobacter oleivorans pf1, a diesel-degrading and plant-growth-promoting endophytic strain isolated from poplar trees growing on a diesel-contaminated plume.	we report the 3.7-mb draft genome of acinetobacter oleivorans strain pf1, a hydrocarbonoclastic gram-negative bacterium in the class gammaproteobacteria, isolated from poplar trees growing on a diesel-contaminated plume at the ford motor company site in genk, belgium. strain pf1 is a potent plant-growth promoter, useful for diesel fuel phytoremediation applications.	2015	25657268
tetrahydroisoquinolines affect the whole-cell phenotype of mycobacterium tuberculosis by inhibiting the atp-dependent mure ligase.	(s)-leucoxine, isolated from the colombian lauraceae tree rhodostemonodaphne crenaticupula madriñan, was found to inhibit the growth of mycobacterium tuberculosis h37rv. a biomimetic approach for the chemical synthesis of a wide array of 1-substituted tetrahydroisoquinolines was undertaken with the aim of elucidating a common pharmacophore for these compounds with novel mode(s) of anti-tb action.	2015	25656411
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
transferable antibiotic resistance plasmids from biogas plant digestates often belong to the incp-1ε subgroup.	manure is known to contain residues of antibiotics administered to farm animals as well as bacteria carrying antibiotic resistance genes (args). these genes are often located on mobile genetic elements. in biogas plants (bgps), organic substrates such as manure and plant material are mixed and fermented in order to provide energy, and resulting digestates are used for soil fertilization. the fate of plasmid carrying bacteria from manure during the fermentation process is unknown. the present stu ...	2014	25653641
transferable antibiotic resistance plasmids from biogas plant digestates often belong to the incp-1ε subgroup.	manure is known to contain residues of antibiotics administered to farm animals as well as bacteria carrying antibiotic resistance genes (args). these genes are often located on mobile genetic elements. in biogas plants (bgps), organic substrates such as manure and plant material are mixed and fermented in order to provide energy, and resulting digestates are used for soil fertilization. the fate of plasmid carrying bacteria from manure during the fermentation process is unknown. the present stu ...	2014	25653641
dysbiosis of the gut microbiota in disease.	there is growing evidence that dysbiosis of the gut microbiota is associated with the pathogenesis of both intestinal and extra-intestinal disorders. intestinal disorders include inflammatory bowel disease, irritable bowel syndrome (ibs), and coeliac disease, while extra-intestinal disorders include allergy, asthma, metabolic syndrome, cardiovascular disease, and obesity.	2015	25651997
ccer and akgr regulate central carbon and energy metabolism in alphaproteobacteria.	many pathways of carbon and energy metabolism are conserved across the phylogeny, but the networks that regulate their expression or activity often vary considerably among organisms. in this work, we show that two previously uncharacterized transcription factors (tfs) are direct regulators of genes encoding enzymes of central carbon and energy metabolism in the alphaproteobacterium rhodobacter sphaeroides. the laci family member ccer (rsp_1663) directly represses genes encoding enzymes in the en ...	2015	25650399
a dye-decolorizing peroxidase from bacillus subtilis exhibiting substrate-dependent optimum temperature for dyes and β-ether lignin dimer.	in the biorefinery using lignocellulosic biomass as feedstock, pretreatment to breakdown or loosen lignin is important step and various approaches have been conducted. for biological pretreatment, we screened bacillus subtilis kctc2023 as a potential lignin-degrading bacterium based on veratryl alcohol (va) oxidation test and the putative heme-containing dye-decolorizing peroxidase was found in the genome of b. subtilis kctc2023. the peroxidase from b. subtilis kctc2023 (bsdyp) was capable of ox ...	2015	25650125
synergic role of the two ars operons in arsenic tolerance in pseudomonas putida kt2440.	the chromosome of pseudomonas putida kt2440 carries two clusters of genes, denoted ars1 and ars2, that are annotated as putative arsenic resistance operons. in this work, we present evidence that both operons encode functional arsenic-response regulatory genes as well as arsenic extrusion systems that confer resistance to both arsenite [as(iii)] and arsenate [as(v)]. transcriptional fusions of p(ars1) and p(ars2) to lacz revealed that expression of both operons was induced by arsenite and arsena ...	2014	25646541
effects of even and odd number fatty acids cofeeding on pha production and composition in pseudomonas putida bet001 isolated from palm oil mill effluent.	the biosynthesis of medium-chain-length poly-3-hydroxyalkanoates by pseudomonas putida bet001 cultivated on mixed carbon sources was investigated. the mixed carbon sources consisted of heptanoic acid (ha) and oleic acid (oa). a relatively low pha content at 1.2% (w/w) and 11.4% (w/w) was obtained when ha or oa was used as the sole carbon source. when these fatty acids were supplied as a mixture, pha content increased threefold. interestingly, the mixture-derived pha composed of both odd and even ...	2016	25643814
feasibility study of an alkaline-based chemical treatment for the purification of polyhydroxybutyrate produced by a mixed enriched culture.	this study focused on investigating the feasibility of purifying polyhydroxybutyrate (phb) from mixed culture biomass by alkaline-based chemical treatment. the phb-containing biomass was enriched on acetate under non-sterile conditions. alkaline treatment (0.2 m naoh) together with surfactant sds (0.2 w/v% sds) could reach 99% purity, with more than 90% recovery. the lost phb could be mostly attributed to phb hydrolysis during the alkaline treatment. phb hydrolysis could be moderated by increasi ...	2015	25642402
integrated engineering of β-oxidation reversal and ω-oxidation pathways for the synthesis of medium chain ω-functionalized carboxylic acids.	an engineered reversal of the β-oxidation cycle was exploited to demonstrate its utility for the synthesis of medium chain (6-10-carbons) ω-hydroxyacids and dicarboxylic acids from glycerol as the only carbon source. a redesigned β-oxidation reversal facilitated the production of medium chain carboxylic acids, which were converted to ω-hydroxyacids and dicarboxylic acids by the action of an engineered ω-oxidation pathway. the selection of a key thiolase (bktb) and thioesterase (ydii) in combinat ...	2015	25638687
type iii secretion system and virulence markers highlight similarities and differences between human- and plant-associated pseudomonads related to pseudomonas fluorescens and p. putida.	pseudomonas fluorescens is commonly considered a saprophytic rhizobacterium devoid of pathogenic potential. nevertheless, the recurrent isolation of strains from clinical human cases could indicate the emergence of novel strains originating from the rhizosphere reservoir, which could be particularly resistant to the immune system and clinical treatment. the importance of type three secretion systems (t3sss) in the related pseudomonas aeruginosa nosocomial species and the occurrence of this secre ...	2015	25636837
enzyme fusion for whole-cell biotransformation of long-chain sec-alcohols into esters.	enzyme fusion was investigated as a strategy to improve productivity of a two-step whole-cell biocatalysis. the biotransformation of long-chain sec-alcohols into esters by an alcohol dehydrogenase (adh) and baeyer-villiger monooxygenases (bvmos) was used as the model reaction. the recombinant escherichia coli, expressing the fusion enzymes between the adh of micrococcus luteus nctc2665 and the bvmo of pseudomonas putida kt2440 or rhodococcus jostii rha1, showed significantly greater bioconversio ...	2015	25636834
insights into methyltransferase specificity and bioactivity of derivatives of the antibiotic plantazolicin.	peptide antibiotics represent a class of conformationally constrained natural products of growing pharmaceutical interest. plantazolicin (pzn) is a linear, polyheterocyclic natural product with highly selective and potent activity against the anthrax-causing bacterium, bacillus anthracis. the bioactivity of pzn is contingent on dimethylation of its n-terminal arg residue by an s-adenosylmethionine-dependent methyltransferase. here, we explore the substrate tolerances of two homologous pzn methyl ...	2015	25635336
draft genome sequences of pseudomonas fluorescens strains pa4c2 and pa3g8 and pseudomonas putida pa14h7, three biocontrol bacteria against dickeya phytopathogens.	pseudomonas fluorescens strains pa4c2 and pa3g8 and pseudomonas putida strain pa14h7 were isolated from potato rhizosphere and show an ability to inhibit the growth of dickeya phytopathogens. here, we report their draft genome sequences, which provide a basis for understanding the molecular mechanisms involved in antibiosis against dickeya.	2015	25635023
heterologous production of curcuminoids.	curcuminoids, components of the rhizome of turmeric, show several beneficial biological activities, including anticarcinogenic, antioxidant, anti-inflammatory, and antitumor activities. despite their numerous pharmaceutically important properties, the low natural abundance of curcuminoids represents a major drawback for their use as therapeutic agents. therefore, they represent attractive targets for heterologous production and metabolic engineering. the understanding of biosynthesis of curcumin ...	2015	25631288
effects of lb broth, naphthalene concentration, and acetone on the naphthalene degradation activities by pseudomonas putida g7.	luria-bertani broth and acetone were usually used in naphthalene degradation experiments as nutrient and solvent. however, their effect on the degradation was seldom mentioned. in this work, we investigated the effect of lb, naphthalene concentration, and acetone on the degradation of naphthalene by pseudomonas putida g7, which is useful for the degradation of naphthalene on future field remediation. by adding lb, the naphthalene degradation efficiencies and naphthalene dioxygenase were both dec ...	2015	25630128
metabolite profiling reveals abiotic stress tolerance in tn5 mutant of pseudomonas putida.	pseudomonas is an efficient plant growth-promoting rhizobacteria (pgpr); however, intolerance to drought and high temperature limit its application in agriculture as a bioinoculant. transposon 5 (tn5) mutagenesis was used to generate a stress tolerant mutant from a pgpr pseudomonas putida nbri1108 isolated from chickpea rhizosphere. a mutant nbri1108t, selected after screening of nearly 10,000 transconjugants, exhibited significant tolerance towards high temperature and drought. southern hybridi ...	2015	25629312
root inoculation with pseudomonas putida kt2440 induces transcriptional and metabolic changes and systemic resistance in maize plants.	pseudomonas putida kt2440 (kt2440) rhizobacteria colonize a wide range of plants. they have been extensively studied for their capacity to adhere to maize seeds, to tolerate toxic secondary metabolites produced by maize roots and to be attracted by maize roots. however, the response of maize plants to kt2440 colonization has not been investigated yet. maize roots were inoculated with kt2440 and the local (roots) and systemic (leaves) early plant responses were investigated. the colonization beha ...	2014	25628626
root inoculation with pseudomonas putida kt2440 induces transcriptional and metabolic changes and systemic resistance in maize plants.	pseudomonas putida kt2440 (kt2440) rhizobacteria colonize a wide range of plants. they have been extensively studied for their capacity to adhere to maize seeds, to tolerate toxic secondary metabolites produced by maize roots and to be attracted by maize roots. however, the response of maize plants to kt2440 colonization has not been investigated yet. maize roots were inoculated with kt2440 and the local (roots) and systemic (leaves) early plant responses were investigated. the colonization beha ...	2014	25628626
a genomic region involved in the formation of adhesin fibers in bacillus cereus biofilms.	bacillus cereus is a bacterial pathogen that is responsible for many recurrent disease outbreaks due to food contamination. spores and biofilms are considered the most important reservoirs of b. cereus in contaminated fresh vegetables and fruits. biofilms are bacterial communities that are difficult to eradicate from biotic and abiotic surfaces because of their stable and extremely strong extracellular matrix. these extracellular matrixes contain exopolysaccharides, proteins, extracellular dna, ...	2014	25628606
a genomic region involved in the formation of adhesin fibers in bacillus cereus biofilms.	bacillus cereus is a bacterial pathogen that is responsible for many recurrent disease outbreaks due to food contamination. spores and biofilms are considered the most important reservoirs of b. cereus in contaminated fresh vegetables and fruits. biofilms are bacterial communities that are difficult to eradicate from biotic and abiotic surfaces because of their stable and extremely strong extracellular matrix. these extracellular matrixes contain exopolysaccharides, proteins, extracellular dna, ...	2014	25628606
a moonlighting metabolic protein influences repair at dna double-stranded breaks.	catalytically active proteins with divergent dual functions are often described as 'moonlighting'. in this work we characterize a new, chromatin-based function of lys20, a moonlighting protein that is well known for its role in metabolism. lys20 was initially described as homocitrate synthase (hcs), the first enzyme in the lysine biosynthetic pathway in yeast. its nuclear localization led to the discovery of a key role for lys20 in dna damage repair through its interaction with the myst family h ...	2015	25628362
prediction of distal residue participation in enzyme catalysis.	a scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. scores are based on the partial order optimum likelihood (pool) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. predictions of distal residue participation in catalysis are compared with experimental ...	2015	25627867
toxic effect of environmentally relevant concentration of silver nanoparticles on environmentally beneficial bacterium pseudomonas putida.	silver nanoparticles (ag nps) are being increasingly used in many consumer products owing to their excellent antimicrobial properties. the continuous use of ag nps in consumer products will lead to environmental release. the present study evaluated the toxic effects and the possible underlying mechanism of ag nps on pseudomonas putida. ag np exposure inhibited growth of the cells. increased lipid peroxidation occurred coincident with suppression of the antioxidant defense system. ag np exposure ...	2015	25627470
the loss of function of phac1 is a survival mechanism that counteracts the stress caused by the overproduction of poly-3-hydroxyalkanoates in pseudomonas putidaδfadba.	the poly-3-hydroxylkanoate (pha)-overproducing mutant pseudomonas putida u δfadba (ppδfadba) lacks the genes encoding the main β-oxidation pathway (fadba). this strain accumulates enormous amounts of bioplastics when cultured in chemically defined media containing pha precursors (different n-alkanoic or n-aryl-alkanoic acids) and an additional carbon source. in medium containing glucose or 4-hydroxy-phenylacetate, the mutant does not accumulate phas and grows just as the wild type (p. putida u). ...	2015	25627209
the lipid-modifying multiple peptide resistance factor is an oligomer consisting of distinct interacting synthase and flippase subunits.	phospholipids are synthesized at the inner leaflet of the bacterial cytoplasmic membrane but have to be translocated to the outer leaflet to maintain membrane lipid bilayer composition and structure. even though phospholipid flippases have been proposed to exist in bacteria, only one such protein, mprf, has been described. mprf is a large integral membrane protein found in several prokaryotic phyla, whose c terminus modifies phosphatidylglycerol (pg), the most common bacterial phospholipid, with ...	2015	25626904
functional characterization of a vanillin dehydrogenase in corynebacterium glutamicum.	vanillin dehydrogenase (vdh) is a crucial enzyme involved in the degradation of lignin-derived aromatic compounds. herein, the vdh from corynebacterium glutamicum was characterized. the relative molecular mass (mr) determined by sds-page was ~51 kda, whereas the apparent native mr values revealed by gel filtration chromatography were 49.5, 92.3, 159.0 and 199.2 kda, indicating the presence of dimeric, trimeric and tetrameric forms. moreover, the enzyme showed its highest level of activity toward ...	2015	25622822
aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin.	lignin represents an untapped feedstock for the production of fuels and chemicals, but its intrinsic heterogeneity makes lignin valorization a significant challenge. in nature, many aerobic organisms degrade lignin-derived aromatic molecules through conserved central intermediates including catechol and protocatechuate. harnessing this microbial approach offers potential for lignin upgrading in modern biorefineries, but significant technical development is needed to achieve this end. catechol an ...	2015	25617773
development of eukaryotic zoospores within polycyclic aromatic hydrocarbon (pah)-polluted environments: a set of behaviors that are relevant for bioremediation.	in this study, we assessed the development (formation, taxis and settlement) of eukaryotic zoospores under different regimes of exposure to polycyclic aromatic hydrocarbons (pahs), which imitated environmental scenarios of pollution and bioremediation. with this aim, we used an oomycete, pythium aphanidermatum, as a source of zoospores and two pah-degrading bacteria (mycobacterium gilvum vm552 and pseudomonas putida g7). the oomycete and both bacteria were not antagonistic, and zoospore formatio ...	2015	25617701
large-scale 13c flux profiling reveals conservation of the entner-doudoroff pathway as a glycolytic strategy among marine bacteria that use glucose.	marine bacteria form one of the largest living surfaces on earth, and their metabolic activity is of fundamental importance for global nutrient cycling. here, we explored the largely unknown intracellular pathways in 25 microbes representing different classes of marine bacteria that use glucose: alphaproteobacteria, gammaproteobacteria, and flavobacteriia of the bacteriodetes phylum. we used (13)c isotope experiments to infer metabolic fluxes through their carbon core pathways. notably, 90% of a ...	2015	25616803
development of a growth-dependent selection system for identification of l-threonine aldolases.	threonine aldolases (tas) are useful enzymes for the synthesis of β-hydroxy-α-amino acids due to their capability to catalyze asymmetric aldol reactions. starting from two prochiral compounds, an aldehyde and glycine, two chiral stereocenters were formed in a single step via c-c bond formation. owing to poor diastereoselectivity and low activity, the enzymatic synthesis of β-hydroxy-α-amino acids by tas is still a challenge. for identification of new tas, a growth-dependent selection system in p ...	2015	25616526
detoxification of the veterinary antibiotic chloramphenicol using electron beam irradiation.	electron beam irradiation has shown potential as an alternative process for the treatment of industrial effluents that contain toxic organic chemicals. this study investigated the effectiveness of electron beam in degrading chloramphenicol (cap) in aqueous solution. the degradation efficiency was 32.4% at 1 kgy, 86.9% at 5 kgy, and 100% at 10 kgy. the total organic carbon (toc) of cap in aqueous solution declined 4.6% at 1 kgy, 12.1% at 5 kgy, and 17.1% at 10 kgy of irradiation with electron bea ...	2015	25616384
detection of tetracycline resistance genes in bacteria isolated from fish farms using polymerase chain reaction.	five common tetracycline resistance genes tet(a), tet(b), tet(m), tet(o) and tet(s) were studied by polymerase chain reaction in 100 bacteria isolated from iranian fish farms. in the antibiogram test most of the bacteria were either intermediately or completely resistant to tetracycline. nine isolates out of 46 aeromonas spp. contained either tet(a/m/s) resistant genes as follows: tet(a) in a. veronii/sobria (n = 1), a. media (n = 2), a. aquariorum (n = 1), and a. veronii (n = 3); tet(m) in one ...	2014	25610578
oric-encoded instructions for the initiation of bacterial chromosome replication.	replication of the bacterial chromosome initiates at a single origin of replication that is called oric. this occurs via the concerted action of numerous proteins, including dnaa, which acts as an initiator. the origin sequences vary across species, but all bacterial orics contain the information necessary to guide assembly of the dnaa protein complex at oric, triggering the unwinding of dna and the beginning of replication. the requisite information is encoded in the unique arrangement of speci ...	2014	25610430
oric-encoded instructions for the initiation of bacterial chromosome replication.	replication of the bacterial chromosome initiates at a single origin of replication that is called oric. this occurs via the concerted action of numerous proteins, including dnaa, which acts as an initiator. the origin sequences vary across species, but all bacterial orics contain the information necessary to guide assembly of the dnaa protein complex at oric, triggering the unwinding of dna and the beginning of replication. the requisite information is encoded in the unique arrangement of speci ...	2014	25610430
structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso peptide from an understudied halophilic actinomycete.	natural products are the most historically significant source of compounds for drug development. however, unacceptably high rates of compound rediscovery associated with large-scale screening of common microbial producers have resulted in the abandonment of many natural product drug discovery efforts, despite the increasing prevalence of clinically problematic antibiotic resistance. screening of underexplored taxa represents one strategy to avoid rediscovery. herein we report the discovery, isol ...	2015	25601074
metabolic engineering of corynebacterium glutamicum for methanol metabolism.	methanol is already an important carbon feedstock in the chemical industry, but it has found only limited application in biotechnological production processes. this can be mostly attributed to the inability of most microbial platform organisms to utilize methanol as a carbon and energy source. with the aim to turn methanol into a suitable feedstock for microbial production processes, we engineered the industrially important but nonmethylotrophic bacterium corynebacterium glutamicum toward the ut ...	2015	25595770
rhizosphere microbial community composition affects cadmium and zinc uptake by the metal-hyperaccumulating plant arabidopsis halleri.	the remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. we compared t ...	2015	25595759
effect of plant growth-promoting rhizobacteria inoculation on cadmium (cd) uptake by eruca sativa.	microbe-assisted phyto-remediation approach is widely applied and appropriate choice to reduce the environmental risk of heavy metals originated from contaminated soils. the present study was designed to screen out the nested belongings of eruca sativa plants and pseudomonas putida (atcc 39213) at varying cadmium (cd) levels and their potential to deal with cd uptake from soils. we carried out pot trial experiment by examining the soil containing e. sativa seedlings either treated with p. putida ...	2015	25592913
quorum sensing triggers the stochastic escape of individual cells from pseudomonas putida biofilms.	the term 'quorum sensing' (qs) is generally used to describe the phenomenon that bacteria release and perceive signal molecules to coordinate cooperative behaviour in response to their population size. qs-based communication has therefore been considered a social trait. here we show that qs signals (n-acyl-homoserine lactones, ahls) are stochastically produced in young biofilms of pseudomonas putida and act mainly as self-regulatory signals rather than inducing neighbouring cells. we demonstrate ...	2015	25592773
production of cinnamic and p-hydroxycinnamic acid from sugar mixtures with engineered escherichia coli.	the aromatic compounds cinnamic acid (ca) and p-hydroxycinnamic acid (phca) are used as flavoring agents as well as precursors of chemicals. these compounds are present in plants at low concentrations, therefore, complex purification processes are usually required to extract the product. an alternative production method for these aromatic acids is based on the use of microbial strains modified by metabolic engineering. these biotechnological processes are usually based on the use of simple sugar ...	2015	25592545
oxidative stress protection by polyphosphate--new roles for an old player.	inorganic polyphosphate is a universally conserved biopolymer whose association with oxidative stress resistance has been documented in many species, but whose mode of action has been poorly understood. here we review the recent discovery that polyphosphate functions as a protein-protective chaperone, examine the mechanisms by which polyphosphate-metal ion interactions reduce oxidative stress, and summarize polyphosphate's roles in regulating general stress response pathways. given the simple ch ...	2015	25589044
the crystal structure of the versatile cytochrome p450 enzyme cyp109b1 from bacillus subtilis.	the crystal structure of the versatile cyp109b1 enzyme from bacillus subtilis has been solved at 1.8 å resolution. this is the first structure of an enzyme from this cyp family, whose members are prevalent across diverse species of bacteria. in the crystal structure the enzyme has an open conformation with an access channel leading from the heme to the surface. the substrate-free structure reveals the location of the key residues in the active site that are responsible for binding the substrate ...	2015	25587700
opening study on the development of a new biosensor for metal toxicity based on pseudomonas fluorescens pyoverdine.	to date, different kinds of biosensing elements have been used effectively for environmental monitoring. microbial cells seem to be well-suited for this task: they are cheap, adaptable to variable field conditions and give a measurable response to a broad number of chemicals. among different pollutants, heavy metals are still a major problem for the environment. a reasonable starting point for the selection of a biorecognition element to develop a biosensor for metals could be that of a microorg ...	2013	25586414
functional amyloids keep quorum-sensing molecules in check.	the mechanism by which extracellular metabolites, including redox mediators and quorum-sensing signaling molecules, traffic through the extracellular matrix of biofilms is poorly explored. we hypothesize that functional amyloids, abundant in natural biofilms and possessing hydrophobic domains, retain these metabolites. using surface plasmon resonance, we demonstrate that the quorum-sensing (qs) molecules, 2-heptyl-3-hydroxy-4(1h)-quinolone and n-(3-oxododecanoyl)-l-homoserine lactone, and the re ...	2015	25586180
personal care product preservatives: risk assessment and mixture toxicities with an industrial wastewater.	the aquatic toxicity of eight preservatives frequently used in personal care products (pcps) (iodopropynyl butylcarbamate, bronopol, diazolidinyl urea, benzalkonium chloride, zinc pyrithione, propylparaben, triclosan and a mixture of methylchloroisothiazolinone and methylisothiazolinone) was assessed by means of two different approaches: a battery of bioassays composed of single species tests of bacteria (vibrio fischeri and pseudomonas putida) and protozoa (tetrahymena thermophila), and a whole ...	2015	25585550
hydrazidase, a novel amidase signature enzyme that hydrolyzes acylhydrazides.	the degradation mechanisms of natural and artificial hydrazides have been elucidated. here we screened and isolated bacteria that utilize the acylhydrazide 4-hydroxybenzoic acid 1-phenylethylidene hydrazide (hbph) from soils. physiological and phylogenetic studies identified one bacterium as microbacterium sp. strain hm58-2, from which we purified intracellular hydrazidase, cloned its gene, and prepared recombinant hydrazidase using an escherichia coli expression system. the microbacterium sp. h ...	2015	25583978
integration of chemotaxis, transport and catabolism in pseudomonas putida and identification of the aromatic acid chemoreceptor pcay.	aromatic and hydroaromatic compounds that are metabolized through the β-ketoadipate catabolic pathway serve as chemoattractants for pseudomonas putida f1. a screen of p. putida f1 mutants, each lacking one of the genes encoding the 18 putative methyl-accepting chemotaxis proteins (mcps), revealed that pcay encodes the mcp required for metabolism-independent chemotaxis to vanillate, vanillin, 4-hydroxybenzoate, benzoate, protocatechuate, quinate, shikimate, as well as 10 substituted benzoates tha ...	2015	25582673
differential transcriptional response to antibiotics by pseudomonas putida dot-t1e.	multi-drug resistant bacteria are a major threat to humanity, especially because the current battery of known antibiotics is not sufficient to combat infections produced by these microbes. therefore, the study of how current antibiotics act and how bacteria defend themselves against antibiotics is of critical importance. pseudomonas putida dot-t1e exhibits an impressive array of rnd efflux pumps, which confer this microorganism high resistance to organic solvents and antibiotics that would kill ...	2015	25581266
the role of biocatalysis in the asymmetric synthesis of alkaloids.	alkaloids are not only one of the most intensively studied classes of natural products, their wide spectrum of pharmacological activities also makes them indispensable drug ingredients in both traditional and modern medicine. among the methods for their production, biotechnological approaches are gaining importance, and biocatalysis has emerged as an essential tool in this context. a number of chemo-enzymatic strategies for alkaloid synthesis have been developed over the years, in which the biot ...	2013	25580241
isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using pseudomonas putida strains as hosts.	metagenomes contain the dna from many microorganisms, both culturable and non-culturable, and are a potential resource of novel genes. in this study, a 5.2-gb metagenomic dna library was constructed from a soil sample (artificially polluted with four aromatic compounds, i.e., biphenyl, phenanthrene, carbazole, and 3-chlorobenzoate) in escherichia coli by using a broad-host-range cosmid vector. the resultant library was introduced into naphthalene-degrading pseudomonas putida-derived strains havi ...	2015	25573469
production of fatty acid-derived valuable chemicals in synthetic microbes.	fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. metabolic engineering of microorganisms has provided a platform for effective production of these valuable b ...	2014	25566540
the role of bacteria and mycorrhiza in plant sulfur supply.	plant growth is highly dependent on bacteria, saprophytic, and mycorrhizal fungi which facilitate the cycling and mobilization of nutrients. over 95% of the sulfur (s) in soil is present in an organic form. sulfate-esters and sulfonates, the major forms of organo-s in soils, arise through deposition of biological material and are transformed through subsequent humification. fungi and bacteria release s from sulfate-esters using sulfatases, however, release of s from sulfonates is catalyzed by a ...	2014	25566295
novel assay to measure the plasmid mobilizing potential of mixed microbial communities.	mobilizable plasmids lack necessary genes for complete conjugation and are therefore non-self-transmissible. instead, they rely on the conjugation system of conjugal plasmids to be horizontally transferred to new recipients. while community permissiveness, the fraction of a mixed microbial community that can receive self-transmissible conjugal plasmids, has been studied, the intrinsic ability of a community to mobilize plasmids that lack conjugation systems is unexplored. here, we present a nove ...	2014	25566238
microbial interactions and the ecology and evolution of hawaiian drosophilidae.	adaptive radiations are characterized by an increased rate of speciation and expanded range of habitats and ecological niches exploited by those species. the hawaiian drosophilidae is a classic adaptive radiation; a single ancestral species colonized hawaii approximately 25 million years ago and gave rise to two monophyletic lineages, the hawaiian drosophila and the genus scaptomyza. the hawaiian drosophila are largely saprophagous and rely on approximately 40 endemic plant families and their as ...	2014	25566196
carbon-limited fed-batch production of medium-chain-length polyhydroxyalkanoates by a phaz-knockout strain of pseudomonas putida kt2440.	a medium-chain-length poly-3-hydroxyalkanote (mcl-pha) depolymerase knockout mutant of pseudomonas putida kt2440 was produced by double homologous recombination. a carbon-limited shake-flask study confirmed that depolymerase activity was eliminated. lysis of both mutant and wild-type strains occurred under these conditions. in carbon-limited, fed-batch culture, the yield of unsaturated monomers from unsaturated substrate averaged only 0.62 mol mol(-1) for the phaz minus strain compared to 0.72 m ...	2015	25563970
comparison of biomass detachment from biofilms of two different pseudomonas spp. under constant shear conditions.	in the context of biofilm development, detachment is of practical importance when placed in a biofilm management perspective. the objective of the present study was to examine biofilm structure and biofilm detachment under controlled conditions for two distinct microorganisms grown under constant shear conditions. detached biofilm biomass was regularly collected and analysed over the course of 72 h biofilm growth by pseudomonas putida and pseudomonas fluorescens cells, and biofilm structural dev ...	2015	25563340
toxicity of fungal-generated silver nanoparticles to soil-inhabiting pseudomonas putida kt2440, a rhizospheric bacterium responsible for plant protection and bioremediation.	silver nanoparticles have attracted considerable attention due to their beneficial properties. but toxicity issues associated with them are also rising. the reports in the past suggested health hazards of silver nanoparticles at the cellular, molecular, or whole organismal level in eukaryotes. whereas, there is also need to examine the exposure effects of silver nanoparticle to the microbes, which are beneficial to humans as well as environment. the available literature suggests the harmful effe ...	2015	25562807
widening functional boundaries of the σ(54) promoter pu of pseudomonas putida by defeating extant physiological constraints.	the extant layout of the σ(54) promoter pu, harboured by the catabolic tol plasmid, pww0, of pseudomonas putida is one of the most complex instances of endogenous and exogenous signal integration known in the prokaryotic domain. in this regulatory system, all signal inputs are eventually translated into occupation of the promoter sequence by either of two necessary components: the m-xylene responsive transcriptional factor xylr and the σ(54) containing form of rna polymerase. modelling of these ...	2015	25560994
a holistic view of polyhydroxyalkanoate metabolism in pseudomonas putida.	polyhydroxyalkanoate (pha) metabolism has been traditionally considered as a futile cycle involved in carbon and energy storage. the use of cutting-edge technologies linked to systems biology has improved our understanding of the interaction between bacterial physiology, pha metabolism and other cell functions in model bacteria such as pseudomonas putida kt2440. pha granules or carbonosomes are supramolecular complexes of biopolyester and proteins that are essential for granule segregation durin ...	2016	25556983
detection and characterization of a bacteriocin, putadicin t01, produced by pseudomonas putida isolated from hot spring water.	pseudomonas strains isolated from hot spring water were tested for bacteriocin-like substance (bls) production using a target panel of closely related microorganisms and other gram-positive and gram-negative bacteria. molecular identification was carried out through specific pcr and 16s rna sequence analysis. isolates were identified as brevundimonas diminuta and pseudomonas putida, the latter exhibited antimicrobial activity. pseudomonas putida strains produce an inhibitory substance against ot ...	2015	25556393
effect of trace metals and electron shuttle on simultaneous reduction of reactive black-5 azo dye and hexavalent chromium in liquid medium by pseudomonas sp.	this study demonstrates the role of electron shuttles and trace metals in the biotransformation of azo dye reactive black-5 and hexavalent chromium (crvi) that are released simultaneously in tannery effluent. previously isolated bacterial strain pseudomonas putida ki was used for the simultaneous reduction of the dye (100 mg l(-1)) and crvi (2 mg l(-1)) in a mineral salts medium (msm). among various trace metals, only cu(ii) had a stimulating effect on the bacterial-mediated reduction process. a ...	2015	25556007
identification of new metabolites of bacterial transformation of indole by gas chromatography-mass spectrometry and high performance liquid chromatography.	arthrobacter sp. spg transformed indole completely in the presence of an additional carbon source. high performance liquid chromatography and gas chromatography-mass spectrometry detected indole-3-acetic acid, indole-3-glyoxylic acid, and indole-3-aldehyde as biotransformation products. this is the first report of the formation of indole-3-acetic acid, indole-3-glyoxylic acid, and indole-3-aldehyde from indole by any bacterium.	2014	25548566
cj1386, an atypical hemin-binding protein, mediates hemin trafficking to kata in campylobacter jejuni.	catalase enzymes detoxify h2o2 by the dismutation of h2o2 into o2 and h2o through the use of hemin cofactors. while the structure and biochemical properties of catalase enzymes have been well characterized over many decades of research, it remained unclear how catalases acquire hemin. we have previously reported that cj1386 is essential for ensuring proper hemin content in campylobacter jejuni catalase (kata) (a. flint, y. q. sun, and a. stintzi, j bacteriol 194: 334-345, 2012). in this report, ...	2014	25548249
cj1386, an atypical hemin-binding protein, mediates hemin trafficking to kata in campylobacter jejuni.	catalase enzymes detoxify h2o2 by the dismutation of h2o2 into o2 and h2o through the use of hemin cofactors. while the structure and biochemical properties of catalase enzymes have been well characterized over many decades of research, it remained unclear how catalases acquire hemin. we have previously reported that cj1386 is essential for ensuring proper hemin content in campylobacter jejuni catalase (kata) (a. flint, y. q. sun, and a. stintzi, j bacteriol 194: 334-345, 2012). in this report, ...	2014	25548249
comparative proteome analysis reveals four novel polyhydroxybutyrate (phb) granule-associated proteins in ralstonia eutropha h16.	identification of proteins that were present in a polyhydroxybutyrate (phb) granule fraction isolated from ralstonia eutropha but absent in the soluble, membrane, and membrane-associated fractions revealed the presence of only 12 polypeptides with phb-specific locations plus 4 previously known phb-associated proteins with multiple locations. none of the previously postulated phb depolymerase isoenzymes (phaza2 to phaza5, phazd1, and phazd2) and none of the two known 3-hydroxybutyrate oligomer hy ...	2015	25548058
the bacillus cereus group is an excellent reservoir of novel lanthipeptides.	lantibiotics are ribosomally synthesized peptides that contain multiple posttranslational modifications. research on lantibiotics has increased recently, mainly due to their broad-spectrum antimicrobial activity, especially against some clinical gram-positive pathogens. many reports about various bacteriocins in the bacillus cereus group have been published, but few were about lantibiotics. in this study, we identified 101 putative lanthipeptide gene clusters from 77 out of 223 strains of this g ...	2015	25548056
transcriptional analysis of deinococcus radiodurans reveals novel small rnas that are differentially expressed under ionizing radiation.	small noncoding rnas (srnas) are posttranscriptional regulators that have been identified in multiple species and shown to play essential roles in responsive mechanisms to environmental stresses. the natural ability of specific bacteria to resist high levels of radiation has been of high interest to mechanistic studies of dna repair and biomolecular protection. deinococcus radiodurans is a model extremophile for radiation studies that can survive doses of ionizing radiation of >12,000 gy, 3,000 ...	2015	25548054
a vector system for abc transporter-mediated secretion and purification of recombinant proteins in pseudomonas species.	pseudomonas fluorescens is an efficient platform for recombinant protein production. p. fluorescens has an abc transporter secreting endogenous thermostable lipase (tlia) and protease, which can be exploited to transport recombinant proteins across the cell membrane. in this study, the expression vector pdart was constructed by inserting tlidef, genes encoding the abc transporter, along with the construct of the lipase abc transporter recognition domain (lard), into pdsk519, a widely used shuttl ...	2015	25548043
functional expression of l-lysine α-oxidase from scomber japonicus in escherichia coli for one-pot synthesis of l-pipecolic acid from dl-lysine.	l-pipecolic acid is a key component of biologically active molecules and a pharmaceutically important chiral building block. it can be stereoselectively produced from l-lysine by a two-step bioconversion involving l-lysine α-oxidase and ∆(1)-piperideine-2-carboxylae (pip2c) reductase. in this study, we focused on an l-lysine α-oxidase from scomber japonicus that was originally identified as an apoptosis-inducing protein (aip) and applied the enzyme to one-pot fermentation of l-pipecolic acid in ...	2015	25547835
effect of elevated oxygen concentration on bacteria, yeasts, and cells propagated for production of biological compounds.	the response of bacteria, yeast, and mammalian and insects cells to oxidative stress is a topic that has been studied for many years. however, in most the reported studies, the oxidative stress was caused by challenging the organisms with h2o2 and redox-cycling drugs, but not by subjecting the cells to high concentrations of molecular oxygen. in this review we summarize available information about the effect of elevated oxygen concentrations on the physiology of microorganisms and cells at vario ...	2014	25547171
pseudomonas putida fis binds to the lapf promoter in vitro and represses the expression of lapf.	the biofilm matrix of the rhizospheric bacterium pseudomonas putida consists mainly of a proteinaceous component. the two largest p. putida proteins, adhesins lapa and lapf, are involved in biofilm development but prevail in different developmental stages of the biofilm matrix. lapa is abundant in the initial stage of biofilm formation whereas lapf is found in the mature biofilm. although the transcriptional regulation of the adhesins is not exhaustively studied, some factors that can be involve ...	2014	25545773
expression levels of chaperones influence biotransformation activity of recombinant escherichia coli expressing micrococcus luteus alcohol dehydrogenase and pseudomonas putida baeyer-villiger monooxygenase.	we demonstrated for the first time that the archaeal chaperones (i.e., γ-prefoldin and thermosome) can stabilize enzyme activity in vivo. ricinoleic acid biotransformation activity of recombinant escherichia coli expressing micrococcus luteus alcohol dehydrogenase and the pseudomonas putida kt2440 baeyer-villiger monooxygenase improved significantly with co-expression of γ-prefoldin or recombinant themosome originating from the deep-sea hyperthermophile archaea methanocaldococcus jannaschii. fur ...	2015	25545273
characterization of the algc gene expression pattern in the multidrug resistant acinetobacter baumannii aiims 7 and correlation with biofilm development on abiotic surface.	relative quantification of algc gene expression was evaluated in the multidrug resistant strain acinetobacter baumannii aiims 7 biofilm (3 to 96 h, on polystyrene surface) compared to the planktonic counterparts. comparison revealed differential algc expression pattern with maximum 81.59-fold increase in biofilm cells versus 3.24-fold in planktonic cells (p < 0.05). expression levels strongly correlated with specific biofilm stages (scale of 3 to 96 h), coinciding maximum at initial surface atta ...	2014	25544957
experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.	the rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. solute binding proteins (sbps) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. we describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 sbps against a ...	2014	25540822
experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.	the rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. solute binding proteins (sbps) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. we describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 sbps against a ...	2014	25540822
a new recombineering system for photorhabdus and xenorhabdus.	precise and fluent genetic manipulation is still limited to only a few prokaryotes. ideally the highly advanced technologies available in escherichia coli could be broadly applied. our efforts to apply lambda red technology, widely termed 'recombineering', in photorhabdus and xenorhabdus yielded only limited success. consequently we explored the properties of an endogenous photorhabdus luminescens lambda red-like operon, plu2934/plu2935/plu2936. bioinformatic and functional tests indicate that p ...	2014	25539914
a new recombineering system for photorhabdus and xenorhabdus.	precise and fluent genetic manipulation is still limited to only a few prokaryotes. ideally the highly advanced technologies available in escherichia coli could be broadly applied. our efforts to apply lambda red technology, widely termed 'recombineering', in photorhabdus and xenorhabdus yielded only limited success. consequently we explored the properties of an endogenous photorhabdus luminescens lambda red-like operon, plu2934/plu2935/plu2936. bioinformatic and functional tests indicate that p ...	2014	25539914
in vitro antagonistic activity, plant growth promoting traits and phylogenetic affiliation of rhizobacteria associated with wild plants grown in arid soil.	the role of plant growth-promoting rhizobacteria (pgpr) in adaptation of plants in extreme environments is not yet completely understood. for this study native bacteria were isolated from rhizospeheric arid soils and evaluated for both growth-promoting abilities and antagonistic potential against phytopathogenic fungi and nematodes. the phylogentic affiliation of these representative isolates was also characterized. rhizobacteria associated with 11 wild plant species from the arid soil of almadi ...	2014	25538687
antimicrobial resistance in pseudomonas sp. causing infections in trauma patients: a 6 year experience from a south asian country.	drug resistance to pseudomonas sp. has spread to such a level irrespective of the type of patients, that its pattern of distribution and antibiotic resistance needs to be studied in detail, especially in trauma patients and hence the study. a 6 year study was carried out among trauma patients to see the trend and type of resistance prevalent in the apex hospital for trauma care in india among nonduplicate isolates where multidrug-resistance (mdr), cross-resistance and pan-drug resistance in pseu ...	2014	25538457
removing selected steroid hormones, biocides and pharmaceuticals from water by means of biogenic manganese oxide nanoparticles in situ at ppb levels.	the oxidation of organic micro-pollutants by biogenic manganese oxide nanoparticles (biomnox) has been studied with respect to possible implementation of biomnox in wastewater treatment. for this it would be prerequisite that microbial mn(2+) oxidation and biomnox-driven pollutant removal can occur in situ, i.e. in the same reactor as the removal. here we present the in situ reactivity of biomnox produced by pseudomonas putida towards a range of micro-pollutants at environmentally relevant conce ...	2015	25532770
biodegradation of hexachlorobenzene by a constructed microbial consortium.	a consortium comprised of an engineered escherichia coli dh5α and a natural pentachlorophenol (pcp) degrader, sphingobium chlorophenolicum atcc 39723, was assembled for degradation of hexachlorobenzene (hcb), a persistent organic pollutant. the engineered e. coli strain, harbouring a gene cassette (cama (+) camb (+) camc) that encodes the f87w/y96f/l244a/v247l mutant of cytochrome p-450cam (cyp101), oxidised hcb to pcp. the resulting pcp was then further completely degraded by atcc 39723. the re ...	2015	25532745
comparison of mcl-poly(3-hydroxyalkanoates) synthesis by different pseudomonas putida strains from crude glycerol: citrate accumulates at high titer under pha-producing conditions.	achieving a sustainable society requires, among other things, the use of renewable feedstocks to replace chemicals obtained from petroleum-derived compounds. crude glycerol synthesized inexpensively as a byproduct of biodiesel production is currently considered a waste product, which can potentially be converted into value-added compounds by bacterial fermentation. this study aimed at evaluating several characterized p. putida strains to produce medium-chain-length poly(3-hydroxyalkanoates) (mcl ...	2014	25532606
a double built-in containment strategy for production of recombinant proteins in transgenic rice.	using transgenic rice as a bioreactor for mass production of pharmaceutical proteins could potentially reduce the cost of production significantly. however, a major concern over the bioreactor transgenic rice is the risk of its unintended spreading into environment and into food or feed supplies. here we report a mitigating method to prevent unwanted transgenic rice spreading by a double built-in containment strategy, which sets a selectively termination method and a visual tag technology in the ...	2014	25531447
novel reporter for identification of interference with acyl homoserine lactone and autoinducer-2 quorum sensing.	two reporter strains were established to identify novel biomolecules interfering with bacterial communication (quorum sensing [qs]). the basic design of these escherichia coli-based systems comprises a gene encoding a lethal protein fused to promoters induced in the presence of qs signal molecules. consequently, these e. coli strains are unable to grow in the presence of the respective qs signal molecules unless a nontoxic qs-interfering compound is present. the first reporter strain designed to ...	2015	25527543
evaluation of metal biouptake from the analysis of bulk metal depletion kinetics at various cell concentrations: theory and application.	bioavailability of trace metals is a key parameter for assessment of toxicity on living organisms. proper evaluation of metal bioavailability requires monitoring the various interfacial processes that control metal partitioning dynamics at the biointerface, which includes metal transport from solution to cell membrane, adsorption at the biosurface, internalization, and possible excretion. in this work, a methodology is proposed to quantitatively describe the dynamics of cd(ii) uptake by pseudomo ...	2015	25525993
plant-agrobacterium interaction mediated by ethylene and super-agrobacterium conferring efficient gene transfer.	agrobacterium tumefaciens has a unique ability to transfer genes into plant genomes. this ability has been utilized for plant genetic engineering. however, the efficiency is not sufficient for all plant species. several studies have shown that ethylene decreased the agrobacterium-mediated transformation frequency. thus, a. tumefaciens with an ability to suppress ethylene evolution would increase the efficiency of agrobacterium-mediated transformation. some studies showed that plant growth-promot ...	2014	25520733
sonication of explanted prosthesis combined with incubation in bd bactec bottles for pathogen-based diagnosis of prosthetic joint infection.	prosthetic joint infection (pji) is a rare but refractory complication of arthroplasty. accurate identification of pathogens is a key step for successful treatment of pji, which remains a challenge for clinicians and laboratory workers. we designed a combined culture method with sonication of implants and incubation in a bd bactec system to improve the effectiveness of pathogen diagnosis in pji. the aims of this study were to investigate the diagnostic accuracy of sonicate fluid cultures in the ...	2014	25520450
sonication of explanted prosthesis combined with incubation in bd bactec bottles for pathogen-based diagnosis of prosthetic joint infection.	prosthetic joint infection (pji) is a rare but refractory complication of arthroplasty. accurate identification of pathogens is a key step for successful treatment of pji, which remains a challenge for clinicians and laboratory workers. we designed a combined culture method with sonication of implants and incubation in a bd bactec system to improve the effectiveness of pathogen diagnosis in pji. the aims of this study were to investigate the diagnostic accuracy of sonicate fluid cultures in the ...	2014	25520450
photosystem ii protein33, a protein conserved in the plastid lineage, is associated with the chloroplast thylakoid membrane and provides stability to photosystem ii supercomplexes in arabidopsis.	photosystem ii (psii) is a multiprotein complex that catalyzes the light-driven water-splitting reactions of oxygenic photosynthesis. light absorption by psii leads to the production of excited states and reactive oxygen species that can cause damage to this complex. here, we describe arabidopsis (arabidopsis thaliana) at1g71500, which encodes a previously uncharacterized protein that is a psii auxiliary core protein and hence is named photosystem ii protein33 (psb33). we present evidence that p ...	2014	25511433
photosystem ii protein33, a protein conserved in the plastid lineage, is associated with the chloroplast thylakoid membrane and provides stability to photosystem ii supercomplexes in arabidopsis.	photosystem ii (psii) is a multiprotein complex that catalyzes the light-driven water-splitting reactions of oxygenic photosynthesis. light absorption by psii leads to the production of excited states and reactive oxygen species that can cause damage to this complex. here, we describe arabidopsis (arabidopsis thaliana) at1g71500, which encodes a previously uncharacterized protein that is a psii auxiliary core protein and hence is named photosystem ii protein33 (psb33). we present evidence that p ...	2014	25511433