PMID(sorted descending)
functional components of the bacterial czccba efflux system reduce cadmium uptake and accumulation in transgenic tobacco plants.cadmium (cd) is a toxic trace element released into the environment by industrial and agricultural practices, threatening the health of plants and contaminating the food/feed chain. biotechnology can be used to develop plant varieties with a higher capacity for cd accumulation (for use in phytoremediation programs) or a lower capacity for cd accumulation (to reduce cd levels in food and feed). here we generated transgenic tobacco plants expressing components of the pseudomonas putida czccba effl ...201727902938
methods for the isolation of genes encoding novel pha metabolism enzymes from complex microbial communities.development of different phas as alternatives to petrochemically derived plastics can be facilitated by mining metagenomic libraries for diverse pha cycle genes that might be useful for synthesis of bio-plastics. the specific phenotypes associated with mutations of the pha synthesis pathway genes in sinorhizobium meliloti and pseudomonas putida, allows the use of powerful selection and screening tools to identify complementing novel pha synthesis genes. identification of novel genes through thei ...201727900694
novel tools for the functional expression of metagenomic dna.functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. it is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. in the following chapter, we therefore describe tools and p ...201727900689
microscope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.the annotation of genomes from ngs platforms needs to be automated and fully integrated. however, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. this shortcoming limits the knowledge that can be extracted from genomes and metabolic models. launched in 2005, the microscope platform ( is an integrative resource that supports systematic and ...201627899624
microscope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.the annotation of genomes from ngs platforms needs to be automated and fully integrated. however, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. this shortcoming limits the knowledge that can be extracted from genomes and metabolic models. launched in 2005, the microscope platform ( is an integrative resource that supports systematic and ...201627899624
bacillus subtilis early colonization of arabidopsis thaliana roots involves multiple chemotaxis receptors.colonization of plant roots by bacillus subtilis is mutually beneficial to plants and bacteria. plants can secrete up to 30% of their fixed carbon via root exudates, thereby feeding the bacteria, and in return the associated b. subtilis bacteria provide the plant with many growth-promoting traits. formation of a biofilm on the root by matrix-producing b. subtilis is a well-established requirement for long-term colonization. however, we observed that cells start forming a biofilm only several hou ...201627899502
a high-throughput microtiter plate assay for the discovery of active and enantioselective amino alcohol-specific transaminases.chiral vicinal amino alcohols are important chiral building blocks and intermediates in the pharmaceutical industry. the transaminase (tam) catalyzed kinetic resolution of racemic amino alcohols provides a straightforward approach to access these important compounds. this study describes the development of a novel microtiter plate assay to screen vicinal amino alcohol-specific tams using a tetrazolium red-based colorimetric assay to monitor the rate of α-hydroxy ketone formation at 510 nm. this ...201727899283
a dna-based real-time pcr assay for robust growth quantification of the bacterial pathogen pseudomonas syringae on arabidopsis thaliana.the interaction of pseudomonas syringae with arabidopsis is one of the most commonly used systems to study various bacterial-host interrelationships. currently, most studies are based on the growth quantification of the pathogen to characterize resistance or virulence targets. however, the standard available method for determining bacterial proliferation in planta is laborious and has several limitations.201627895701
salicylic acid is involved in the basal resistance of tomato plants to citrus exocortis viroid and tomato spotted wilt virus.tomato plants expressing the nahg transgene, which prevents accumulation of endogenous salicylic acid (sa), were used to study the importance of the sa signalling pathway in basal defence against citrus exocortis viroid (cevd) or tomato spotted wilt virus (tswv). the lack of sa accumulation in the cevd- or tswv-infected nahg tomato plants led to an early and dramatic disease phenotype, as compared to that observed in the corresponding parental money maker. addition of acibenzolar-s-methyl, a ben ...201627893781
maximization of cell viability rather than biocatalyst activity improves whole-cell ω-oxyfunctionalization is a common misconception in whole-cell biocatalysis to refer to an enzyme as the biocatalyst, thereby neglecting the structural and metabolic framework provided by the cell. here, the low whole-cell biocatalyst stability, that is, the stability of specific biocatalyst activity, in a process for the terminal oxyfunctionalization of renewable fatty acid methyl esters was investigated. this reaction, which is difficult to achieve by chemical means, is catalyzed by escherichia coli featuring the ...201727883174
whole-genome sequences of two manganese(ii)-oxidizing bacteria, bosea sp. strain biwako-01 and alphaproteobacterium strain u9-1i.this report describes the whole-genome sequences of two mn(ii)-oxidizing bacteria, filamentous mn oxide microparticle-forming bosea sp. strain biwako-01 and alphaproteobacterium strain u9-1i.201627881541
bacterial biosensors for measuring availability of environmental pollutants.traditionally, pollution risk assessment is based on the measurement of a pollutant's total concentration in a sample. the toxicity of a given pollutant in the environment, however, is tightly linked to its bioavailability, which may differ significantly from the total amount. physico-chemical and biological parameters strongly influence pollutant fate in terms of leaching, sequestration and biodegradation. bacterial sensorreporters, which consist of living micro-organisms genetically engineered ...200827879922
amperometric enzyme-based gas sensor for formaldehyde: impact of possible this work, cross-sensitivities and environmental influences on the sensitivityand the functionality of an enzyme-based amperometric sensor system for the directdetection of formaldehyde from the gas phase are studied. the sensor shows a linearresponse curve for formaldehyde in the tested range (0 - 15 vppm) with a sensitivity of1.9 μa/ppm and a detection limit of about 130 ppb. cross-sensitivities by environmentalgases like co₂, co, no, h₂, and vapors of organic solvents like methanol and eth ...200827879770
enhancing poly(3-hydroxyalkanoate) production in escherichia coli by the removal of the regulatory gene arca.recombinant escherichia coli is a desirable platform for the production of many biological compounds including poly(3-hydroxyalkanoates), a class of naturally occurring biodegradable polyesters with promising biomedical and material applications. although the controlled production of desirable polymers is possible with the utilization of fatty acid feedstocks, a central challenge to this biosynthetic route is the improvement of the relatively low polymer yield, a necessary factor of decreasing t ...201627878786
draft genome sequence of a multi-metal resistant bacterium pseudomonas putida ath-43 isolated from greenwich island, antarctica. 201627877169
influence of bacterial extracellular polymeric substances on the sorption of zn on γ-alumina: a combination of ftir and exafs studies.extracellular polymeric substances (eps) isolated from bacteria, are abound of functional groups which can react with metals and consequently influence the immobilization of metals. in this study, we combined with zn k-edge extended x-ray absorption fine structure (exafs), fourier transform infrared (ftir) spectroscopy, and high-resolution transmission electron microscopy (hrtem) techniques to study the effects of eps isolated from bacillus subtilis and pseudomonas putida on zn sorption on γ-alu ...201727876416
bioavailability of cd, zn and hg in soil to nine recombinant luminescent metal sensor bacteria.a set of nine recombinant heavy metal-specific luminescent bacterial sensors belonging to gram-negative (escherichia and pseudomonas) and gram-positive (staphylococcus and bacillus) genera and containing various types of recombinant metalresponse genetic elements was characterized for heavy metal bioavailability studies. all nine strains were induced by hg and cd and five strains also by zn. as a lowest limit, the sensors were detecting 0.03 μg·l(-1) of hg, 2 μg·l(-1) of cd and 400 μg·l(-1) of z ...200827873907
biotests and biosensors for ecotoxicology of metal oxide nanoparticles: a minireview.nanotechnologies have become a significant priority worldwide. several manufactured nanoparticles - particles with one dimension less than 100 nm - are increasingly used in consumer products. at nanosize range, the properties of materials differ substantially from bulk materials of the same composition, mostly due to the increased specific surface area and reactivity, which may lead to increased bioavailability and toxicity. thus, for the assessment of sustainability of nanotechnologies, hazards ...200827873807
isolation of carbapenem-resistant pseudomonas spp. from food.pseudomonas spp. are ubiquitous in nature. carbapenem resistance in environmental isolates of members of this genus is thought to be rare but the exact resistance rate is unknown. in this study, carbapenem-resistant pseudomonas spp. were isolated from chicken and pork samples and the mechanisms underlying the carbapenem resistance in these strains were investigated. a total of 16 carbapenem-resistant pseudomonas aeruginosa, pseudomonas putida and pseudomonas otitidis isolates were recovered from ...201527873658
biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass.aromatic chemicals that contain an unsaturated ring with alternating double and single bonds find numerous applications in a wide range of industries, e.g. paper and dye manufacture, as fuel additives, electrical insulation, resins, pharmaceuticals, agrochemicals, in food, feed and cosmetics. their chemical production is based on petroleum (btx; benzene, toluene, and xylene), but they can also be obtained from plants by extraction. due to petroleum depletion, health compliance, or environmental ...201627871872
adaptive evolution of phosphorus metabolism in prochlorococcus.inorganic phosphorus is scarce in the eastern mediterranean sea, where the high-light-adapted ecotype hli of the marine picocyanobacterium prochlorococcus marinus thrives. physiological and regulatory control of phosphorus acquisition and partitioning has been observed in hli both in culture and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (plg) phenotype have not been studied. here, we reconstructed a genome-scale metabo ...201627868089
total syntheses of pancratistatin. a review. 200827867225
total syntheses of pancratistatin. a review. 200827867225
the systematic investigation of the quorum sensing system of the biocontrol strain pseudomonas chlororaphis subsp. aurantiaca pb-st2 unveils auri to be a biosynthetic origin for 3-oxo-homoserine lactones.the shoot endophytic biocontrol strain pseudomonas chlororaphis subsp. aurantiaca pb-st2 produces a wide range of exoproducts, including enzymes and antibiotics. the production of exoproducts is commonly tightly regulated. in order to get a deeper insight into the regulatory network of pb-st2, the strain was systematically investigated regarding its quorum sensing systems, both on the genetic and metabolic level. the genome analysis of pb-st2 revealed the presence of four putative acyl homoserin ...201627861617
draft genome sequence of pseudomonas mosselii gil3, isolated from catfish and antagonistic against hypervirulent aeromonas hydrophila.pseudomonas mosselii gil3 was isolated from a catfish that survived from lethal challenge with hypervirulent aeromonas hydrophila (vah). when assayed in vitro, the bacterium showed antagonism against vah. sequence analysis revealed that the genome of p. mosselii gil3 encodes numerous aromatic metabolism pathways and proteins for biosynthesis of antimicrobial compounds.201627856595
inhibited transport of graphene oxide nanoparticles in granular quartz sand coated with bacillus subtilis and pseudomonas putida biofilms.increasing production and use of graphene oxide nanoparticles (gonps) boost their wide dissemination in the subsurface environments where biofilms occur ubiquitously, representative of the physical and chemical heterogeneities. this study aimed at investigating the influence of gram-positive bacillus subtilis (bs) and gram-negative pseudomonas putida (pp) biofilms on the transport of gonps under different ionic strengths (0.1, 0.5, and 1.0 mm cacl2) at neutral ph 7.2 in water-saturated porous me ...201727855326
application of the freeze-dried bioluminescent bioreporter pseudomonas putida mt-2 kg1206 to the biomonitoring of groundwater samples from monitoring wells near gasoline leakage sites.this study examined the applicability of a freeze-dried bioluminescent bioreporter, pseudomonas putida mt-2 kg1206 (called kg1206), to the biomonitoring of groundwater samples. samples were collected from the monitoring wells of gas station tanks or old pipeline leakage sites in korea. in general, the freeze-dried strain in the presence of pure inducer chemicals showed low bioluminescence activity and a different activity order compared with that of the subcultured strain. the effects of kno3 as ...201727853856
two-step production of phenylpyruvic acid from l-phenylalanine by growing and resting cells of engineered escherichia coli: process optimization and kinetics modeling.phenylpyruvic acid (ppa) is widely used in the pharmaceutical, food, and chemical industries. here, a two-step bioconversion process, involving growing and resting cells, was established to produce ppa from l-phenylalanine using the engineered escherichia coli constructed previously. first, the biotransformation conditions for growing cells were optimized (l-phenylalanine concentration 20.0 g·l-1, temperature 35°c) and a two-stage temperature control strategy (keep 20°c for 12 h and increase the ...201627851793
a broad mercury resistant strain of pseudomonas putida secretes pyoverdine under limited iron conditions and high mercury concentrations.the pseudomonas putida fb1, known as a broad-spectrum mercury resistant strain, becomes yellow-green due to the secretion of pyoverdine (pvds) under limited iron conditions and high mercury concentrations. different modified nelson's media were obtained by adding mercury, iron, and the complexing agent nitrilotriacetic acid to demonstrate that the strain produces only the highest concentrations of pvds due to the induction with 25 µm hg(2+). an amount of 250 mg pvds was purified from the superna ...201627848043
mutation of the streptococcus gordonii thiol-disulfide oxidoreductase sdba leads to enhanced biofilm formation mediated by the ciarh two-component signaling system.streptococcus gordonii is a commensal inhabitant of human oral biofilms. previously, we identified an enzyme called sdba that played an important role in biofilm formation by s. gordonii. sdba is thiol-disulfide oxidoreductase that catalyzes disulfide bonds in secreted proteins. surprisingly, inactivation of sdba results in enhanced biofilm formation. in this study we investigated the basis for biofilm formation by the δsdba mutant. the results revealed that biofilm formation was mediated by the ...201627846284
production of selenium nanoparticles in pseudomonas putida kt2440.selenium (se) is an essential element for the cell that has multiple applications in medicine and technology; microorganisms play an important role in se transformations in the environment. here we report the previously unidentified ability of the soil bacterium pseudomonas putida kt2440 to synthesize nanoparticles of elemental selenium (nano-se) from selenite. our results show that p. putida is able to reduce selenite aerobically, but not selenate, to nano-se. kinetic analysis indicates that, i ...201627845437
transcriptional responses of the bacterium burkholderia terrae bs001 to the fungal host lyophyllum sp. strain karsten under soil-mimicking this study, the mycosphere isolate burkholderia terrae bs001 was confronted with the soil fungus lyophyllum sp. strain karsten on soil extract agar plates in order to examine its transcriptional responses over time. at the initial stages of the experiment (t1-day 3; t2-day 5), contact between both partner organisms was absent, whereas in the final stage (t3-day 8), the two populations made intimate physical contact. overall, a strong modulation of the strain bs001 gene expression patterns was ...201627844108
transcriptional responses of the bacterium burkholderia terrae bs001 to the fungal host lyophyllum sp. strain karsten under soil-mimicking this study, the mycosphere isolate burkholderia terrae bs001 was confronted with the soil fungus lyophyllum sp. strain karsten on soil extract agar plates in order to examine its transcriptional responses over time. at the initial stages of the experiment (t1-day 3; t2-day 5), contact between both partner organisms was absent, whereas in the final stage (t3-day 8), the two populations made intimate physical contact. overall, a strong modulation of the strain bs001 gene expression patterns was ...201627844108
biofilm removal using carbon dioxide aerosols without nitrogen purge.biofilms can cause serious concerns in many applications. not only can they cause economic losses, but they can also present a public health hazard. therefore, it is highly desirable to remove biofilms from surfaces. many studies on co2 aerosol cleaning have employed nitrogen purges to increase biofilm removal efficiency by reducing the moisture condensation generated during the cleaning. however, in this study, periodic jets of co2 aerosols without nitrogen purges were used to remove pseudomona ...201627842343
development of a simplified purification method for a novel formaldehyde dismutase variant from pseudomonas putida j3.formaldehyde dismutase (fdm) is a very interesting enzyme, due to the fact that it comprises an internal cofactor regeneration mechanism. the fdm, therefore, is able to catalyze redox reactions independent of exogenous cofactor addition, rendering the enzyme powerful for industrial applications. currently, only one enzyme of this type has been characterized enzymatically. furthermore, only one additional dna-sequence with high homology to fdm has been published. in this work, we identified a new ...201727836796
influence of ph on dynamics of microbial enhanced oil recovery processes using biosurfactant producing pseudomonas putida: mathematical modelling and numerical present work, the influence of reservoir ph conditions on dynamics of microbial enhanced oil recovery (meor) processes using pseudomonas putida was analysed numerically from the developed mathematical model for meor processes. further, a new strategy to improve the meor performance has also been proposed. it is concluded from present study that by reversing the reservoir ph from highly acidic to low alkaline condition (ph 5-8), flow and mobility of displaced oil, displacement efficiency, and ...201727836230
coconut lethal yellowing diseases: a phytoplasma threat to palms of global economic and social significance.the recent discovery of bogia coconut syndrome in papua new guinea (png) is the first report of a lethal yellowing disease (lyd) in oceania. numerous outbreaks of lyds of coconut have been recorded in the caribbean and africa since the late nineteenth century and have caused the death of millions of palms across several continents during the twentieth century. despite the severity of economic losses, it was only in the 1970s that the causes of lyds were identified as phytoplasmas, a group of ins ...201627833616
synergistic nisin-polymyxin combinations for the control of pseudomonas biofilm formation.the emergence and dissemination of multi-drug resistant pathogens is a global concern. moreover, even greater levels of resistance are conferred on bacteria when in the form of biofilms (i.e., complex, sessile communities of bacteria embedded in an organic polymer matrix). for decades, antimicrobial peptides have been hailed as a potential solution to the paucity of novel antibiotics, either as natural inhibitors that can be used alone or in formulations with synergistically acting antibiotics. ...201627833601
elimination of persistent emerging micropollutants in a suspended-bed photocatalytic reactor: influence of operating conditions and combination with aerobic biological treatment.a larger, lab-scale photocatalytic suspended-bed reactor using tio2 sol-gel-coated expanded clay granules as a bed material was evaluated for oxidative removal of the persistent pharmaceuticals doxycycline, prednisolone, amoxicillin, and sulfamethizole, as well as their mixture, in ppm concentrations. the photocatalytic degradation potential of drug molecules increases as their adsorption affinity increases towards tio2-containing coatings. the performance of the photocatalytic reactor in the re ...201627830220
development and evaluation of an experimental protocol for 3-d visualization and characterization of the structure of bacterial biofilms in porous media using laboratory x-ray tomography.the development of a reliable model allowing accurate predictions of biofilm growth in porous media relies on a good knowledge of the temporal evolution of biofilm structure within the porous network. since little is known about the real 3-d structure of biofilms in porous media, this work was aimed at developing a new experimental protocol to visualize the 3-d microstructure of the inside of a porous medium using laboratory x-ray microtomography. a reliable and reproducible methodology is propo ...201627827532
novel culturing techniques select for heterotrophs and hydrocarbon degraders in a subantarctic soil.the soil substrate membrane system (ssms) is a novel micro-culturing technique targeted at terrestrial soil systems. we applied the ssms to pristine and diesel fuel spiked polar soils, along with traditional solid media culturing and culture independent 454 tag pyrosequencing to elucidate the effects of diesel fuel on the soil community. the ssms enriched for up to 76% of the total soil diversity within high diesel fuel concentration soils, in contrast to only 26% of the total diversity for the ...201627827405
occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in shandong province, p.r. china.soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. an enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. in the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation.201627821056
isolation and characteristics of sulfentrazone-degrading bacteria.this study aimed to isolate and characterize bacteria able to use sulfentrazone in the commercial formulation as their sole carbon source. the isolation of the potential sulfentrazone-degrading bacteria was made from soil samples with a recent history of herbicide application and from isolates identified through rdna sequencing. subsequently, we assessed the growth of the isolates and their sulfentrazone degradation ability using high-performance liquid chromatography. twenty-six potential sulfe ...201727820678
bacterial genome engineering and synthetic biology: combating pathogens.the emergence and prevalence of multidrug resistant (mdr) pathogenic bacteria poses a serious threat to human and animal health globally. nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of mdr pathogenic bacteria. according to recent reports by the world health organization (who) and centers for disease control and prevention (cdc), there is an unprecedented increase in th ...201627814687
occurrence and antimicrobial susceptibility of enteric rods and pseudomonads isolated from the dental prostheses determine the occurrence and the in vitro antimicrobial susceptibility of enteric rods and pseudomonads from the denture biofilm of 52 subjects at the center for dental specialties of sobral/ ceara, brazil.201627812616
draft genome sequences of four achromobacter ruhlandii strains isolated from cystic fibrosis patients.achromobacter species are being increasingly isolated from the respiratory tract of cystic fibrosis patients. recent reports indicate that achromobacter ruhlandii is a potential human pathogen in cystic fibrosis-related infections. here we report the draft genome of four a. ruhlandii strains isolated from cystic fibrosis patients in brazil. this report describes a. ruhlandii as a potential opportunistic pathogen in cystic fibrosis and provides a framework to for additional enquires into potentia ...201627812598
identification of klebsiella pneumoniae carbapenemase-producing klebsiella oxytoca in clinical isolates in tehran hospitals, iran by chromogenic medium and molecular methods.production of carbapenemase, especially klebsiella pneumoniae carbapenemases (kpc), is one of the antibiotic resistance mechanisms of enterobacteriaceae such as klebsiella oxytoca. this study aimed to investigate and identify kpc-producing k. oxytoca isolates using molecular and phenotypic methods.201627812488
lapf and its regulation by fis affect the cell surface hydrophobicity of pseudomonas putida.the ability of bacteria to regulate cell surface hydrophobicity is important for the adaptation to different environmental conditions. the hydrophobicity of cell surface can be determined by several factors, including outer membrane and surface proteins. in this study, we report that an adhesin lapf influences cell surface hydrophobicity of pseudomonas putida. cells lacking lapf are less hydrophobic than wild-type cells in stationary growth phase. moreover, the overexpression of the global regul ...201627812186
the genome of the toluene-degrading pseudomonas veronii strain 1ydbtex2 and its differential gene expression in contaminated sand.the natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (btex) may be accelerated by inoculation of specific biodegraders (bioaugmentation). bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. in order to better understand the adaptive response of cells during a transition to con ...201627812150
mycelia as a focal point for horizontal gene transfer among soil bacteria.horizontal gene transfer (hgt) is a main mechanism of bacterial evolution endowing bacteria with new genetic traits. the transfer of mobile genetic elements such as plasmids (conjugation) requires the close proximity of cells. hgt between genetically distinct bacteria largely depends on cell movement in water films, which are typically discontinuous in natural systems like soil. using laboratory microcosms, a bacterial reporter system and flow cytometry, we here investigated if and to which degr ...201627811990
ecological risk assessment of pharmaceuticals in the receiving environment of pharmaceutical wastewater in pakistan.the pharmaceutical industry of pakistan is growing with an annual growth rate of 10%. besides this growth, this industry is not complying with environmental standards, and discharging its effluent into domestic wastewater network. only limited information is available about the occurrence of pharmaceutical compounds (pcs) in the environmental matrices of pakistan that has motivated us to aim at the occurrence and ecological risk assessment of 11 pcs of different therapeutic classes in the wastew ...201727810578
flhf is required for swarming motility and full pathogenicity of bacillus cereus.besides sporulation, bacillus cereus can undergo a differentiation process in which short swimmer cells become elongated and hyperflagellated swarmer cells that favor migration of the bacterial community on a surface. the functionally enigmatic flagellar protein flhf, which is the third paralog of the signal recognition particle (srp) gtpases ffh and ftsy, is required for swarming in many bacteria. previous data showed that flhf is involved in the control of the number and positioning of flagell ...201627807433
new weapons to fight old enemies: novel strategies for the (bio)control of bacterial biofilms in the food industry.biofilms are microbial communities characterized by their adhesion to solid surfaces and the production of a matrix of exopolymeric substances, consisting of polysaccharides, proteins, dna and lipids, which surround the microorganisms lending structural integrity and a unique biochemical profile to the biofilm. biofilm formation enhances the ability of the producer/s to persist in a given environment. pathogenic and spoilage bacterial species capable of forming biofilms are a significant problem ...201627803696
partial least squares with structured output for modelling the metabolomics data obtained from complex experimental designs: a study into the y-block coding.partial least squares (pls) is one of the most commonly used supervised modelling approaches for analysing multivariate metabolomics data. pls is typically employed as either a regression model (pls-r) or a classification model (pls-da). however, in metabolomics studies it is common to investigate multiple, potentially interacting, factors simultaneously following a specific experimental design. such data often cannot be considered as a "pure" regression or a classification problem. nevertheless ...201627801817
novel conopeptides of largely unexplored indo pacific conus sp.cone snails are predatory creatures using venom as a weapon for prey capture and defense. since this venom is neurotoxic, the venom gland is considered as an enormous collection of pharmacologically interesting compounds having a broad spectrum of targets. as such, cone snail peptides represent an interesting treasure for drug development. here, we report five novel peptides isolated from the venom of conus longurionis, conus asiaticus and conus australis. lo6/7a and lo6/7b were retrieved from c ...201627801785
preliminary investigation on the use of allyi isothiocyanate to increase the shelf-life of gilthead sea bream (sparus aurata) fillets.the aim of this work is to evaluate the activity of allyl isothiocyanate (aitc) against fish spoilage bacteria (specific spoilage organisms; ssos) as well as its possible use in gilthead sea bream (sparus aurata) fillets to extend their shelf-life. in this regard, in vitro tests are carried out in order to evaluate the inhibitory activity of aitc and its vapours on several strains of ssos. the aitc effect on the shelf-life of sea bream fillets was made by putting them in plastic trays hermetical ...201527800402
evolutionary switches between two serine codon sets are driven by selection.serine is the only amino acid that is encoded by two disjoint codon sets so that a tandem substitution of two nucleotides is required to switch between the two sets. previously published evidence suggests that, for the most evolutionarily conserved serines, the codon set switch occurs by simultaneous substitution of two nucleotides. here we report a genome-wide reconstruction of the evolution of serine codons in triplets of closely related species from diverse prokaryotes and eukaryotes. the res ...201627799560
responses of pseudomonas putida to zinc excess determined at the proteome level: pathways dependent and independent of colrs.zinc is an important micronutrient for bacteria, but its excess is toxic. recently, the colrs two-component system was shown to detect and respond to zinc excess and to contribute to zinc tolerance of pseudomonas putida. here, we applied a label-free whole-cell proteome analysis to compare the zinc-induced responses of p. putida and colr knockout. we identified dozens of proteins that responded to zinc in a colr-independent manner, among others, known metal efflux systems czccba1, czccba2, cada2 ...201627797207
molecular and spectroscopic characterization of aspergillus flavipes and pseudomonas putida l-methionine γ-lyase in vitro.pseudomonas putida l-methionine γ-lyase (ppmgl) has been recognized as an efficient anticancer agent, however, its antigenicity and stability remain as critical challenges for its clinical use. from our studies, aspergillus flavipes l-methionine γ-lyase (afmgl) displayed more affordable biochemical properties than ppmgl. thus, the objective of this work was to comparatively assess the functional properties of afmgl and ppmgl via stability of their internal aldimine linkage, tautomerism of pyrido ...201627796875
exported epoxide hydrolases modulate erythrocyte vasoactive lipids during plasmodium falciparum infection.erythrocytes are reservoirs of important epoxide-containing lipid signaling molecules, including epoxyeicosatrienoic acids (eets). eets function as vasodilators and anti-inflammatory modulators in the bloodstream. bioactive eets are hydrolyzed to less active diols (dihydroxyeicosatrienoic acids) by epoxide hydrolases (ehs). the malaria parasite plasmodium falciparum infects host red blood cells (rbcs) and exports hundreds of proteins into the rbc compartment. in this study, we show that two para ...201627795395
biochemical and genetic bases of indole-3-acetic acid (auxin phytohormone) degradation by the plant-growth-promoting rhizobacterium paraburkholderia phytofirmans psjn.several bacteria use the plant hormone indole-3-acetic acid (iaa) as a sole carbon and energy source. a cluster of genes (named iac) encoding iaa degradation has been reported in pseudomonas putida 1290, but the functions of these genes are not completely understood. the plant-growth-promoting rhizobacterium paraburkholderia phytofirmans psjn harbors iac gene homologues in its genome, but with a different gene organization and context than those of p. putida 1290. the iac gene functions enable p ...201727795307
draft genome sequence of a pseudomonas sp. strain carrying blaimp-25 and blavim-2 carbapenemase genes from hospital sewage.pseudomonas strain wchp16 recovered from hospital sewage in west china hospital, chengdu, china was found to carry two carbapenemase genes blaimp-25 and blavim-2 here, we report its 5.7-mb draft genome sequence, comprising 141 contigs and an average 59.53% g+c content. the genome contained 5,504 coding sequences and 67 trna genes.201627795238
heavy metal pollution from gold mines: environmental effects and bacterial strategies for resistance.mining activities can lead to the generation of large quantities of heavy metal laden wastes which are released in an uncontrolled manner, causing widespread contamination of the ecosystem. though some heavy metals classified as essential are important for normal life physiological processes, higher concentrations above stipulated levels have deleterious effects on human health and biota. bacteria able to withstand high concentrations of these heavy metals are found in the environment as a resul ...201627792205
aquatic toxicity and biodegradability of a surfactant produced by bacillus subtilis this work, the environmental compatibility of a biosurfactant produced by a bacillus subtilis strain isolated from the soil of a brazilian mangrove was investigated. the biosurfactant, identified as surfactin, is able to reduce surface tension (st) to 31.5 ± 0.1 mn m(-1) and exhibits a lowcritical micelle concentration (cmc) value (0.015 ± 0.003 g l(-1)). the highest crude biosurfactant concentration (224.3 ± 1.9 mg l(-1)) was reached at 72 h of fermentation. acute toxicity tests, carried out ...201727791474
production of encapsulated creatinase using yeast spores.yeast spores can be used as a carrier to produce enzyme capsules. in the present study, this technique was applied to a diagnostic enzyme named creatinase. we found that a secretory form of pseudomonas putida creatinase could be entrapped in the spore wall, and such spores were used as creatinase capsules. the activity of the encapsulated creatinase was largely improved by mild spore wall defective mutations, such as dit1 or osw2 deletions. the advantages of this method include the following: en ...201627791465
inhibition of xanthomonas fragariae, causative agent of angular leaf spot of strawberry, through iron commercial production settings, few options exist to prevent or treat angular leaf spot (als) of strawberry, a disease of economic importance and caused by the bacterial pathogen xanthomonas fragariae. in the process of isolating and identifying x. fragariae bacteria from symptomatic plants, we observed growth inhibition of x. fragariae by bacterial isolates from the same leaf macerates. identified as species of pseudomonas and rhizobium, these isolates were confirmed to suppress growth of x. ...201627790193
the bacterial enhancer-dependent rna polymerase.transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. one class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the rna polymerase down into a state unable to melt out promoter dna for transcription initiation. promoter dna opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bebps ...201627789741
draft genome sequence of the marine rhodobacteraceae strain o3.65, cultivated from oil-polluted seawater of the deepwater horizon oil spill.the marine alphaproteobacterium strain o3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the deepwater horizon (dwh) oil spill and belongs to the ubiquitous, diverse and ecological relevant roseobacter group within the rhodobacteraceae. here, we present a preliminary set of physiological features of strain o3.65 and a description and annotation of its draft genome sequence. based on our data we suggest potential ecological roles of th ...201627777651
effect of crc and hfq proteins on the transcription, processing, and stability of the pseudomonas putida crcz pseudomonas putida, the hfq and crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mrnas that bear specific target motifs and inhibiting their translation. the effect of these two proteins is antagonized by the crcz and crcy small rnas (srnas), the levels of which vary greatly according to growth conditions. the crcz and crcy genes are transcribed from promoters pcrcz and pcrcy, respectively, a process that relies on the cbrb tr ...201627777366
biofilm as a production platform for heterologous production of rhamnolipids by the non-pathogenic strain pseudomonas putida kt2440.although a transition toward sustainable production of chemicals is needed, the physiochemical properties of certain biochemicals such as biosurfactants make them challenging to produce in conventional bioreactor systems. alternative production platforms such as surface-attached biofilm populations could potentially overcome these challenges. rhamnolipids are a group of biosurfactants highly relevant for industrial applications. however, they are mainly produced by the opportunistic pathogen pse ...201627776509
depth and well type related to groundwater microbiological contamination.use of groundwater from private wells in households has increased considerably, owing to a better cost/benefit ratio than that of water provided by local utilities for a fee. however, this water is usually untreated, which makes it a vehicle for diseases. thus, monitoring this water is necessary to ensure its integrity and quality. we aimed to evaluate the physical, chemical, and microbiological parameters of untreated groundwater drawn from different types of wells, and the antimicrobial suscep ...201627775681
effect of rhamnolipid solubilization on hexadecane bioavailability: enhancement or reduction?in this study, liquid culture systems containing rhamnolipid-solubilized, separate-phase, and multi-state hexadecane as the carbon source were employed for examining the effect of rhamnolipid solubilization on the bioavailability of hexadecane. experimental results showed that the uptake of rhamnolipid-solubilized hexadecane by pseudomonas aeruginosa atcc 9027, a rhamnolipid producing strain, was enhanced compared to the uptake of mass hexadecane as a separate phase, indicating rhamnolipid solub ...201727773441
characterization of a novel blaimp gene, blaimp-58, using whole genome sequencing in a pseudomonas putida isolate detected in denmark.a multidrug-resistant strain of pseudomonas putida was isolated from the urine of a 65-year-old women hospitalized for serious clinical conditions. using whole genome sequencing a novel blaimp gene, blaimp-58 was discovered and characterized.201727771209
global transcriptional response of solvent-sensitive and solvent-tolerant pseudomonas putida strains exposed to toluene.pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. pan-genome analysis has revealed that 30% of genes belong to the core-genome of pseudomonas. accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. for the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic di ...201727768818
recombineering and i-scei-mediated pseudomonas putida kt2440 scarless gene deletion.pseudomonas putida kt2440 is a saprophytic, generally recognized as safe microorganism that plays important roles in the biodegradation and production of value-added chemicals. chromosomal gene deletion of p. putida kt2440 usually involves time-consuming gene coning, conjugal transfer and counterselection. recently, we developed a p. putida kt2440 markerless gene deletion method based on recombineering and cre/loxp site-specific recombination. pcr-based λ red recombineering circumvents the tedio ...201627765807
bacterial selection for biological control of plant disease: criterion determination and validation.this study aimed to evaluate the biocontrol potential of bacteria isolated from different plant species and soils. the production of compounds related to phytopathogen biocontrol and/or promotion of plant growth in bacterial isolates was evaluated by measuring the production of antimicrobial compounds (ammonia and antibiosis) and hydrolytic enzymes (amylases, lipases, proteases, and chitinases) and phosphate solubilization. of the 1219 bacterial isolates, 92% produced one or more of the eight co ...201627765523
bacterial selection for biological control of plant disease: criterion determination and validation.this study aimed to evaluate the biocontrol potential of bacteria isolated from different plant species and soils. the production of compounds related to phytopathogen biocontrol and/or promotion of plant growth in bacterial isolates was evaluated by measuring the production of antimicrobial compounds (ammonia and antibiosis) and hydrolytic enzymes (amylases, lipases, proteases, and chitinases) and phosphate solubilization. of the 1219 bacterial isolates, 92% produced one or more of the eight co ...201627765523
determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering.protein function often depends on global, collective internal motions. however, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. we demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. with this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrom ...201627757419
label-free, rapid and quantitative phenotyping of stress response in e. coli via ramanome.rapid profiling of stress-response at single-cell resolution yet in a label-free, non-disruptive and mechanism-specific manner can lead to many new applications. we propose a single-cell-level biochemical fingerprinting approach named "ramanome", which is the collection of single-cell raman spectra (scrs) from a number of cells randomly selected from an isogenic population at a given time and condition, to rapidly and quantitatively detect and characterize stress responses of cellular population ...201627756907
an apple fruit fermentation (aff) treatment improves the composition of the rhizosphere microbial community and growth of strawberry (fragaria × ananassa duch 'benihoppe') seedlings.plant growth can be promoted by the application of apple fruit fermentation (aff), despite unclear of the underlying mechanisms, the effects involved in aff on rhizosphere microorganisms have been hypothesized. we investigated the consequences of applying aff alone or in combination with bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of denaturing gradient gel electrophoresis (dgge) and 16s rdna were performed to determine aff effects on rhizosphere. moreove ...201627755580
flavin-dependent redox transfers by the two-component diketocamphane monooxygenases of camphor-grown pseudomonas putida ncimb 10007.the progressive titres of key monooxygenases and their requisite native donors of reducing power were used to assess the relative contribution of various camphor plasmid (cam plasmid)- and chromosome-coded activities to biodegradation of (rac)-camphor at successive stages throughout growth of pseudomonas putida ncimb 10007 on the bicylic monoterpenoid. a number of different flavin reductases (frs) have the potential to supply reduced flavin mononucleotide to both 2,5- and 3,6-diketocamphane mono ...201627754389
screening through the plicable promoter toolbox enhances protein production in escherichia coli.escherichia coli is a common host for recombinant protein production in which production titers are highly dependent on the employed expression system. promoters are thereby a key element to control gene expression levels. in this study, a novel plicable promoter toolbox was developed which enables in a single cloning step and after a screening experiment to identify out of ten iptg-inducible promoters (t7, a3, lpp, tac, pac, sp6, lac, npr, trc and syn) the most suitable one for high level prote ...201627753230
matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity.sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. however, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. in the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity a ...201627749924
antibiotic resistance of diverse bacteria from aquaculture in borneo.the administration of antimicrobials in aquaculture provides a selective pressure creating a reservoir of multiple resistant bacteria in the cultured fish and shrimps as well as the aquaculture environment. the objective of this study was to determine the extent of antibiotic resistance in aquaculture products and aquaculture's surrounding environment in sarawak, malaysian borneo. ninety-four identified bacterial isolates constituted of 17 genera were isolated from sediment, water, and cultured ...201627746817
harnessing host-vector microbiome for sustainable plant disease management of phloem-limited bacteria.plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as candidatus (ca.) phytoplasma species and several species of ca. liberibacter. recent studies on plant-microbe and plant-insect interactions of these pathogens have demonstrated that ...201627746788
plant drought tolerance enhancement by trehalose production of desiccation-tolerant microorganisms.a collection of desiccation-tolerant xeroprotectant-producing microorganisms was screened for their ability to protect plants against drought, and their role as plant growth-promoting rhizobacteria was investigated in two different crops (tomato and pepper). the most commonly described biochemical mechanisms for plant protection against drought by microorganisms including the production of phytohormones, antioxidants and xeroprotectants were analyzed. in particular, the degree of plant protectio ...201627746776
host range of the conjugative transfer system of incp-9 naphthalene-catabolic plasmid nah7 and characterization of its orit region and relaxase.nah7 and pww0 from gammaproteobacterial pseudomonas putida strains are incp-9 conjugative plasmids that carry the genes for degradation of naphthalene and toluene, respectively. although such genes on these plasmids are well-characterized, experimental investigation of their conjugation systems remains at a primitive level. to clarify these conjugation systems, in this study, we investigated the nah7-encoded conjugation system by (i) analyzing the origin of its conjugative transfer (orit)-contai ...201727742684
structural basis for the transcriptional repressor nicr2 in nicotine degradation from pseudomonas.nicotine is an environmental toxicant in tobacco wastes, imposing severe hazards for the health of human and other mammalians. nicr2, a tetr-like repressor from pseudomonas putida s16, plays a critical role in regulating nicotine degradation. here, we determined the crystal structures of nicr2 and its complex with the inducer 6-hydroxy-3-succinoyl-pyridine (hsp). the n-terminal domain of nicr2 contains a conserved helix-turn-helix (hth) dna-binding motif, while the c-terminal domain contains a c ...201727741553
investigation into the mode of phosphate activation in the 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase from pseudomonas putida f1.the 4-hydroxy-4-methyl-2-oxoglutarate (hmg)/4-carboxy-4-hydroxy-2-oxoadipate (cha) aldolase is the last enzyme of both the gallate and protocatechuate 4,5-cleavage pathways which links aromatic catabolism to central cellular metabolism. the enzyme is a class ii, divalent metal dependent, aldolase which is activated in the presence of inorganic phosphate (pi), increasing its turnover rate >10-fold. this phosphate activation is unique for a class ii aldolase. the aldolase pyruvate methyl proton ex ...201627741265
cpxr activates mexab-oprm efflux pump expression and enhances antibiotic resistance in both laboratory and clinical nalb-type isolates of pseudomonas aeruginosa.resistance-nodulation-division (rnd) efflux pumps are responsible for multidrug resistance in pseudomonas aeruginosa. in this study, we demonstrate that cpxr, previously identified as a regulator of the cell envelope stress response in escherichia coli, is directly involved in activation of expression of rnd efflux pump mexab-oprm in p. aeruginosa. a conserved cpxr binding site was identified upstream of the mexa promoter in all genome-sequenced p. aeruginosa strains. cpxr is required to enhance ...201627736975
identification of comamonas testosteroni as an androgen degrader in sewage.numerous studies have reported the masculinization of freshwater wildlife exposed to androgens in polluted rivers. microbial degradation is a crucial mechanism for eliminating steroid hormones from contaminated ecosystems. the aerobic degradation of testosterone was observed in various bacterial isolates. however, the ecophysiological relevance of androgen-degrading microorganisms in the environment is unclear. here, we investigated the biochemical mechanisms and corresponding microorganisms of ...201627734937
comprehensive genomic and phenotypic metal resistance profile of pseudomonas putida strain s13.1.2 isolated from a vineyard soil.trace metals are required in many cellular processes in bacteria but also induce toxic effects to cells when present in excess. as such, various forms of adaptive responses towards extracellular trace metal ions are essential for the survival and fitness of bacteria in their environment. a soil pseudomonas putida, strain s13.1.2 has been isolated from french vineyard soil samples, and shown to confer resistance to copper ions. further investigation revealed a high capacity to tolerate elevated c ...201627730570
molecular detection of acanthamoeba spp., naegleria fowleri and vermamoeba (hartmannella) vermiformis as vectors for legionella spp. in untreated and solar pasteurized harvested rainwater.legionella spp. employ multiple strategies to adapt to stressful environments including the proliferation in protective biofilms and the ability to form associations with free-living amoeba (fla). the aim of the current study was to identify legionella spp., acanthamoeba spp., vermamoeba (hartmannella) vermiformis and naegleria fowleri that persist in a harvested rainwater and solar pasteurization treatment system.201627724947
triclosan in water, implications for human and environmental health.triclosan (tcs) is a broad spectrum antibacterial agent present as an active ingredient in some personal care products such as soaps, toothpastes and sterilizers. it is an endocrine disrupting compound and its increasing presence in water resources as well as in biosolid-amended soils used in farming, its potential for bioaccumulation in fatty tissues and toxicity in aquatic organisms are a cause for concern to human and environmental health. tcs has also been detected in blood, breast milk, uri ...201627722057
highly efficient and stable novel nanobiohybrid catalyst to avert 3,4-dihydroxybenzoic acid pollutant in water.the present study reported for the first time covalent immobilization of protocatechuate 3,4-dioxygenase (3,4-pod) onto functionalized multi-walled carbon nanotubes (f-mwcnt) for degrading the toxic 3,4-dihydroxybenzoic acid (3,4-dhba) pollutant in water. the f-mwcnts had a maximum 3,4-pod loading of 1060 μg/mg. immobilized 3,4 pod had 44% of relative structural changes to its free configurations. nevertheless, >90% of relative activity and about 50% of catalytic efficiency were retained to the ...201627721429
robust at-line quantification of poly(3-hydroxyalkanoate) biosynthesis by flow cytometry using a bodipy 493/503-syto 62 double-staining.poly(3-hydroxyalkanoates) (phas) are bio-based and biodegradable polyesters which have been considered as a promising alternative to petrol-based plastics. their bacterial production is a dynamic process in which intracellular polymerization and depolymerization are closely linked and depend on the availability of carbon substrates and other nutrients. these dynamics require a fast and quantitative method to determine the optimal harvest-time of pha containing cells or to adjust carbon supply. i ...201627720900
metabolic engineering of corynebacterium glutamicum for enhanced production of 5-aminovaleric acid.5-aminovaleric acid (5ava) is an important five-carbon platform chemical that can be used for the synthesis of polymers and other chemicals of industrial interest. enzymatic conversion of l-lysine to 5ava has been achieved by employing lysine 2-monooxygenase encoded by the davb gene and 5-aminovaleramidase encoded by the dava gene. additionally, a recombinant escherichia coli strain expressing the davb and dava genes has been developed for bioconversion of l-lysine to 5ava. to use glucose and xy ...201627717386
identification and validation of novel small proteins in pseudomonas putida.small proteins of 50 amino acids or less have been understudied due to difficulties that impede their annotation and detection. in order to obtain information on small open reading frames (sorfs) in pseudomonas putida, bioinformatic and proteomic approaches were used to identify putative sorfs in the well-characterized strain kt2440. a plasmid-based system was established for sorf validation, enabling expression of c-terminal sequential peptide affinity tagged variants and their detection via pr ...201627717237
toxicity evaluation of selected ammonium-based ionic liquid forms with mcpp and dicamba moieties on pseudomonas putida.combination of the hydrophilic herbicidal anion with hydrophobic, antimicrobial ammonium cation allows to obtain compounds in ionic liquid form with better properties then conventional herbicides. both cation and anion can be modified by selection of herbicide and the length of alkyl chains in cation structure. however the knowledge of their potential toxic effects are still limited. furthermore, the relation between hydrophobicity associated with the length of alkyl chains and toxicity for ioni ...201727716584
characterization of four new distinct ω-transaminases from pseudomonas putida nbrc 14164 for kinetic resolution of racemic amines and amino alcohols.four uncharacterized ω-transaminases (ωtas) from pseudomonas putida nbrc 14164 have been identified and cloned from the pool of fully sequenced genomes. the genes were functionally expressed in escherichia coli bl21, and the enzymes were purified and characterized. four tas showed highly (s)-selective ωta activity and converted (s)-α-methylbenzylamine and pyruvate to acetophenone and l-ala. the maximum activity of cloned enzymes was in the ph range of 8.0-8.5 (pp36420), 8.5-9.5 (pp21050), 9.0-9. ...201727714638
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