Publications

assessing the groundwater quality at a saudi arabian agricultural site and the occurrence of opportunistic pathogens on irrigated food produce.	this study examines the groundwater quality in wells situated near agricultural fields in saudi arabia. fruits (e.g., tomato and green pepper) irrigated with groundwater were also assessed for the occurrence of opportunistic pathogens to determine if food safety was compromised by the groundwater. the amount of total nitrogen in most of the groundwater samples exceeded the 15 mg/l permissible limit for agricultural irrigation. fecal coliforms in densities > 12 mpn/100 ml were detected in three o ...	2015	26445052
stress-induced mutagenesis.	early research on the origins and mechanisms of mutation led to the establishment of the dogma that, in the absence of external forces, spontaneous mutation rates are constant. however, recent results from a variety of experimental systems suggest that mutation rates can increase in response to selective pressures. this chapter summarizes data demonstrating that,under stressful conditions, escherichia coli and salmonella can increase the likelihood of beneficial mutations by modulating their pot ...	2012	26442828
assessing the antimicrobial activities of ocins.	the generation of a zone of inhibition on a solid substrate indicates the bioactivity of antimicrobial peptides such as bacteriocin and enterocin. the indicator strain plays a significant role in bacteriocin assays. other characteristics of bacteriocins, such as their dispersal ability and the different zymogram components, also affect bacteriocin assays. however, universal well diffusion assays for antimicrobials, irrespective of their ability to diffuse (bacteriocin and enterocin), do not exis ...	2015	26441952
the globally widespread genus sulfurimonas: versatile energy metabolisms and adaptations to redox clines.	sulfurimonas species are commonly isolated from sulfidic habitats and numerous 16s rrna sequences related to sulfurimonas species have been identified in chemically distinct environments, such as hydrothermal deep-sea vents, marine sediments, the ocean's water column, and terrestrial habitats. in some of these habitats, sulfurimonas have been demonstrated to play an important role in chemoautotrophic processes. sulfurimonas species can grow with a variety of electron donors and acceptors, which ...	2015	26441918
efficient recombinant production of prodigiosin in pseudomonas putida.	serratia marcescens and several other bacteria produce the red-colored pigment prodigiosin which possesses bioactivities as an antimicrobial, anticancer, and immunosuppressive agent. therefore, there is a great interest to produce this natural compound. efforts aiming at its biotechnological production have so far largely focused on the original producer and opportunistic human pathogen s. marcescens. here, we demonstrate efficient prodigiosin production in the heterologous host pseudomonas puti ...	2015	26441905
effect of carbon on whole-biofilm metabolic response to high doses of streptomycin.	biofilms typically exist as complex communities comprising multiple species with the ability to adapt to a variety of harsh conditions. in clinical settings, antibiotic treatments based on planktonic susceptibility tests are often ineffective against biofilm infections. using a co2 evolution measurement system we delineated the real-time metabolic response in continuous flow biofilms to streptomycin doses much greater than their planktonic susceptibilities. stable biofilms from a multispecies cu ...	2015	26441887
biochemistry and genetics of acc deaminase: a weapon to "stress ethylene" produced in plants.	1-aminocyclopropane-1-carboxylate deaminase (accd), a pyridoxal phosphate-dependent enzyme, is widespread in diverse bacterial and fungal species. owing to accd activity, certain plant associated bacteria help plant to grow under biotic and abiotic stresses by decreasing the level of "stress ethylene" which is inhibitory to plant growth. accd breaks down acc, an immediate precursor of ethylene, to ammonia and α-ketobutyrate, which can be further metabolized by bacteria for their growth. acc deam ...	2015	26441873
chassis optimization as a cornerstone for the application of synthetic biology based strategies in microbial secondary metabolism.	the increased number of bacterial genome sequencing projects has generated over the last years a large reservoir of genomic information. in silico analysis of this genomic data has renewed the interest in bacterial bioprospecting for bioactive compounds by unveiling novel biosynthetic gene clusters of unknown or uncharacterized metabolites. however, only a small fraction of those metabolites is produced under laboratory-controlled conditions; the remaining clusters represent a pool of novel meta ...	2015	26441855
crystal structure of quinone-dependent alcohol dehydrogenase from pseudogluconobacter saccharoketogenes. a versatile dehydrogenase oxidizing alcohols and carbohydrates.	the quinone-dependent alcohol dehydrogenase (pqq-adh, e.c. 1.1.5.2) from the gram-negative bacterium pseudogluconobacter saccharoketogenes ifo 14464 oxidizes primary alcohols (e.g. ethanol, butanol), secondary alcohols (monosaccharides), as well as aldehydes, polysaccharides, and cyclodextrins. the recombinant protein, expressed in pichia pastoris, was crystallized, and three-dimensional (3d) structures of the native form, with pqq and a ca(2+) ion, and of the enzyme in complex with a zn(2+) ion ...	2015	26440996
fiber-optic chemical sensors and fiber-optic bio-sensors.	this review summarizes principles and current stage of development of fiber-optic chemical sensors (focs) and biosensors (fobs). fiber optic sensor (fos) systems use the ability of optical fibers (of) to guide the light in the spectral range from ultraviolet (uv) (180 nm) up to middle infrared (ir) (10 μm) and modulation of guided light by the parameters of the surrounding environment of the of core. the introduction of of in the sensor systems has brought advantages such as measurement in flamm ...	2015	26437407
binary combination of epsilon-poly-l-lysine and isoeugenol affect progression of spoilage microbiota in fresh turkey meat, and delay onset of spoilage in pseudomonas putida challenged meat.	proliferation of microbial population on fresh poultry meat over time elicits spoilage when reaching unacceptable levels, during which process slime production, microorganism colony formation, negative organoleptic impact and meat structure change are observed. spoilage organisms in raw meat, especially gram-negative bacteria can be difficult to combat due to their cell wall composition. in this study, the natural antimicrobial agents ε-poly-l-lysine (ε-pl) and isoeugenol were tested individuall ...	2015	26433458
performance evaluation of the verigene gram-positive and gram-negative blood culture test for direct identification of bacteria and their resistance determinants from positive blood cultures in hong kong.	a multicenter study was conducted to evaluate the diagnostic performance and the time to identifcation of the verigene blood culture test, the bc-gp and bc-gn assays, to identify both gram-positive and gram-negative bacteria and their drug resistance determinants directly from positive blood cultures collected in hong kong.	2015	26431434
flavin mononucleotide (fmn)-based fluorescent protein (fbfp) as reporter for promoter screening in clostridium cellulolyticum.	conventional methods for screening promoters in anaerobic bacteria are generally based on detection of enzymatic reactions and thus usually complicated or strain specific. therefore a more efficient and universal method will be valuable. here, using cellulolytic bacteria clostridium cellulolyticum h10 as a model, we employed an oxygen-independent flavin-based fluorescent protein (fbfp) derived from pseudomonas putida as a quantitative reporter for the screening of promoter via monitoring fluores ...	2015	26427827
a novel and widespread class of ketosynthase is responsible for the head-to-head condensation of two acyl moieties in bacterial pyrone biosynthesis.	the biosynthesis of photopyrones, novel quorum sensing signals in photorhabdus, has been studied by heterologous expression of the photopyrone synthase ppys catalyzing the head-to-head condensation of two acyl moieties. the biochemical mechanism of pyrone formation has been investigated by amino acid exchange and bioinformatic analysis. additionally, the evolutionary origin of ppys has been studied by phylogenetic analyses also revealing homologous enzymes in pseudomonas sp. gm30 responsible for ...	2015	26425196
b1-metallo-β-lactamases: where do we stand?	metallo-β-lactamases (mbls) are class bβ-lactamases that hydrolyze almost all clinically-availableβ-lactam antibiotics. mbls feature the distinctive αβ/βα sandwich fold of the metallo-hydrolase/oxidoreductase superfamily and possess a shallow active-site groove containing one or two divalent zinc ions, flanked by flexible loops. according to sequence identity and zinc ion dependence, mbls are classified into three subclasses (b1, b2 and b3), of which the b1 subclass enzymes have emerged as the m ...	2016	26424398
mass spectrometric identification and toxicity assessment of degraded products of aflatoxin b1 and b2 by corymbia citriodora aqueous extracts.	this study explores the detoxification potential of corymbia citriodora plant extracts against aflatoxin b1 and b2 (afb1; 100 μg l(-1) and afb2; 50 μg l(-1)) in in vitro and in vivo assays. detoxification was qualitatively and quantitatively analyzed by tlc and hplc, respectively. the study was carried out by using different parameters of optimal temperature, ph and incubation time period. results indicated that c. citriodora leaf extract(s) more effectively degrade afb1 and afb2 i.e. 95.21% and ...	2015	26423838
molecular binding mechanism of ttgr repressor to antibiotics and antimicrobials.	a disturbing phenomenon in contemporary medicine is the prevalence of multidrug-resistant pathogenic bacteria. efflux pumps contribute strongly to this antimicrobial drug resistance, which leads to the subsequent failure of clinical treatments. the ttgr protein of pseudomonas putida is a hth-type transcriptional repressor that controls expression of the ttgabc efflux pump, which is the main contributor to resistance against several antimicrobials and toxic compounds in this microbe. one of the m ...	2015	26422008
bio-inspired electron-delivering system for reductive activation of dioxygen at metal centres towards artificial flavoenzymes.	development of artificial systems, capable of delivering electrons to metal-based catalysts for the reductive activation of dioxygen, has been proven very difficult for decades, constituting a major scientific lock for the elaboration of environmentally friendly oxidation processes. here we demonstrate that the incorporation of a flavin mononucleotide (fmn) in a water-soluble polymer, bearing a locally hydrophobic microenvironment, allows the efficient reduction of the fmn by nadh. this supramol ...	2015	26419885
lipopeptide biosurfactant viscosin enhances dispersal of pseudomonas fluorescens sbw25 biofilms.	pseudomonads produce several lipopeptide biosurfactants that have antimicrobial properties but that also facilitate surface motility and influence biofilm formation. detailed studies addressing the significance of lipopeptides for biofilm formation and architecture are rare. hence, the present study sets out to determine the specific role of the lipopeptide viscosin in pseudomonas fluorescens sbw25 biofilm formation, architecture and dispersal, and to relate visca gene expression to viscosin pro ...	2015	26419730
isolation and characterization of bacteria that use furans as the sole carbon source.	five bacterial strains were isolated from wastewater treatment facilities which were able to use furfural as the sole carbon source. based on 16s rrna phylogenetic analysis, these strains were identified as cupriavidus pinatubonensis (designated als1280), pigmentiphaga sp. (als1172), pseudomonas sp. bwdy (als1279), pseudomonas mendocina (als1131), and pseudomonas putida (als1267). in all cases, growth under oxygenated conditions on furfural was accompanied by the transient accumulation of 2-furo ...	2016	26419660
increasing antibiotic resistance in preservative-tolerant bacterial strains isolated from cosmetic products.	to ensure the microbiological quality, consumer safety and organoleptic properties of cosmetic products, manufacturers need to comply with defined standards using several preservatives and disinfectants. a drawback regarding the use of these preservatives is the possibility of generating cross-insusceptibility to other disinfectants or preservatives, as well as cross resistance to antibiotics. therefore, the objective of this study was to understand the adaptive mechanisms of enterobacter gergov ...	2015	26415667
aerobic cyanide degradation by bacterial isolates from cassava factory wastewater.	ten bacterial strains that utilize cyanide (cn) as a nitrogen source were isolated from cassava factory wastewater after enrichment in a liquid media containing sodium cyanide (1 mm) and glucose (0.2% w/v). the strains could tolerate and grow in cyanide concentrations of up to 5 mm. increased cyanide levels in the media caused an extension of lag phase in the bacterial growth indicating that they need some period of acclimatisation. the rate of cyanide removal by the strains depends on the initi ...	2015	26413045
gpo1 alkb gene expression for improvement of the degradation of diesel oil by a bacterial consortium.	to facilitate the biodegradation of diesel oil, an oil biodegradation bacterial consortium was constructed. the alkane hydroxylase (alkb) gene of pseudomonas putida gpo1 was constructed in a pcom8 expression vector, and the pcom8-gpo1 alkb plasmid was transformed into escherichia coli dh5α. the alkb protein was expressed by diesel oil induction and detected through sds-polyacrylamide gel electrophoresis. the culture of the recombinant (pcom8-gpo1 alkb/e. coli dh5α) with the oil biodegradation ba ...	2015	26413044
different ancestries of r tailocins in rhizospheric pseudomonas isolates.	bacterial genomes accommodate a variety of mobile genetic elements, including bacteriophage-related clusters that encode phage tail-like protein complexes playing a role in interactions with eukaryotic or prokaryotic cells. such tailocins are unable to replicate inside target cells due to the lack of a phage head with associated dna. a subset of tailocins mediate antagonistic activities with bacteriocin-like specificity. functional characterization of bactericidal tailocins of two pseudomonas pu ...	2015	26412856
immobilization of escherichia coli cells expressing 4-oxalocrotonate tautomerase for improved biotransformation of β-nitrostyrene.	the enzyme 4-oxalocrotonate tautomerase (4-ot) encoded by the xylh gene is a part of the degradation pathway of aromatic compounds in pseudomonas putida mt-2. 4-ot was described to catalyze michael-type addition of acetaldehyde to β-nitrostyrene, and the whole cell system based on recombinantly expressed 4-ot has been developed previously. in this study biocatalytic process based on escherichia coli whole cells expressing 4-ot was significantly improved using immobilization and ex situ product r ...	2015	26410191
biodegradation of the organic disulfide 4,4'-dithiodibutyric acid by rhodococcus spp.	four rhodococcus spp. exhibited the ability to use 4,4'-dithiodibutyric acid (dtdb) as a sole carbon source for growth. the most important step for the production of a novel polythioester (pte) using dtdb as a precursor substrate is the initial cleavage of dtdb. thus, identification of the enzyme responsible for this step was mandatory. because rhodococcus erythropolis strain mi2 serves as a model organism for elucidation of the biodegradation of dtdb, it was used to identify the genes encoding ...	2015	26407888
molybdenum-containing nicotine hydroxylase genes in a nicotine degradation pathway that is a variant of the pyridine and pyrrolidine pathways.	ochrobactrum sp. strain sjy1 utilizes nicotine as a sole source of carbon, nitrogen, and energy via a variant of the pyridine and pyrrolidine pathways (the vpp pathway). several strains and genes involved in the vpp pathway have recently been reported; however, the first catalyzing step for enzymatic turnover of nicotine is still unclear. in this study, a nicotine hydroxylase for the initial hydroxylation step of nicotine degradation was identified and characterized. the nicotine hydroxylase (vp ...	2015	26407884
formation of polyphosphate by polyphosphate kinases and its relationship to poly(3-hydroxybutyrate) accumulation in ralstonia eutropha strain h16.	a protein (phax) that interacted with poly(3-hydroxybutyrate) (phb) depolymerase phaza1 and with phb granule-associated phasin protein phap2 was identified by two-hybrid analysis. deletion of phax resulted in an increase in the level of polyphosphate (polyp) granule formation and in impairment of phb utilization in nutrient broth-gluconate cultures. a procedure for enrichment of polyp granules from cell extracts was developed. twenty-seven proteins that were absent in other cell fractions were i ...	2015	26407880
the cababc operon essential for biofilm and rugose colony development in vibrio vulnificus.	a transcriptome analysis identified vibrio vulnificus cababc genes which were preferentially expressed in biofilms. the cababc genes were transcribed as a single operon. the caba gene was induced by elevated 3',5'-cyclic diguanylic acid (c-di-gmp) and encoded a calcium-binding protein caba. comparison of the biofilms produced by the caba mutant and its parent strain jn111 in microtiter plates using crystal-violet staining demonstrated that caba contributed to biofilm formation in a calcium-depen ...	2015	26406498
diversity of alkane hydroxylase genes on the rhizoplane of grasses planted in petroleum-contaminated soils.	the study investigated the diversity and genotypic features of alkane hydroxylase genes on rhizoplanes of grasses planted in artificial petroleum-contaminated soils to acquire new insights into the bacterial communities responsible for petroleum degradation in phytoremediation. four types of grass (cynodon dactylon, two phenotypes of zoysia japonica, and z. matrella) were used. the concentrations of total petroleum hydrocarbon effectively decreased in the grass-planted systems compared with the ...	2015	26405645
an engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system.	biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. auxotrophy for a substance not found in the natural environment is an ideal biological containment. here, we constructed an escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-l-tyrosine. this synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme ...	2015	26401457
recent advances and opportunities in synthetic logic gates engineering in living cells.	recently, a number of synthetic biologic gates including and, or, nor, not, xor and nand have been engineered and characterized in a wide range of hosts. the hope in the emerging synthetic biology community is to construct an inventory of well-characterized parts and install distinct gene and circuit behaviours that are externally controllable. though the field is still growing and major successes are yet to emerge, the payoffs are predicted to be significant. in this review, we highlight specif ...	2014	26396651
c-type cytochrome assembly is a key target of copper toxicity within the bacterial periplasm.	in the absence of a tight control of copper entrance into cells, bacteria have evolved different systems to control copper concentration within the cytoplasm and the periplasm. central to these systems, the cu(+) atpase copa plays a major role in copper tolerance and translocates copper from the cytoplasm to the periplasm. the fate of copper in the periplasm varies among species. copper can be sequestered, oxidized, or released outside the cells. here we describe the identification of copi, a pe ...	2015	26396241
h2-driven biotransformation of n-octane to 1-octanol by a recombinant pseudomonas putida strain co-synthesizing an o2-tolerant hydrogenase and a p450 monooxygenase.	an in vivo biotransformation system is presented that affords the hydroxylation of n-octane to 1-octanol on the basis of nadh-dependent cyp153a monooxygenase and nad(+)-reducing hydrogenase heterologously synthesized in a bacterial host. the hydrogenase sustains h2-driven nadh cofactor regeneration even in the presence of o2, the co-substrate of monooxygenase.	2015	26394141
an integrated insight into the response of sedimentary microbial communities to heavy metal contamination.	response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. to explore the microbial response to heavy metal contamination (e.g., cr, mn, zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16s rrna gene amplicons and a functional gene microarray. analysis of 16s rrna sequences revealed that the composition an ...	2015	26391875
redox-switch regulatory mechanism of thiolase from clostridium acetobutylicum.	thiolase is the first enzyme catalysing the condensation of two acetyl-coenzyme a (coa) molecules to form acetoacetyl-coa in a dedicated pathway towards the biosynthesis of n-butanol, an important solvent and biofuel. here we elucidate the crystal structure of clostridium acetobutylicum thiolase (cathl) in its reduced/oxidized states. cathl, unlike those from other aerobic bacteria such as escherichia coli and zoogloea ramegera, is regulated by the redox-switch modulation through reversible disu ...	2015	26391388
culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation.	oil sands surface mining for bitumen results in the formation of oil sands process water (ospw), containing acutely toxic naphthenic acids (nas). potential exists for ospw toxicity to be mitigated by aerobic degradation of the nas by microorganisms indigenous to the oil sands tailings ponds, the success of which is dependent on the methods used to exploit the metabolisms of the environmental microbial community. having hypothesized that the xenobiotic tolerant biofilm mode-of-life may represent ...	2015	26388865
iron is a signal for stenotrophomonas maltophilia biofilm formation, oxidative stress response, omps expression, and virulence.	stenotrophomonas maltophilia is an emerging nosocomial pathogen. in many bacteria iron availability regulates, through the fur system, not only iron homeostasis but also virulence. the aim of this work was to assess the role of iron on s. maltophilia biofilm formation, eps production, oxidative stress response, omps regulation, quorum sensing (qs), and virulence. studies were done on k279a and its isogenic fur mutant f60 cultured in the presence or absence of dipyridyl. this is the first report ...	2015	26388863
the influence of environmental conditions on kinetics of arsenite oxidation by manganese-oxides.	manganese-oxides are one of the most important minerals in soil due to their widespread distribution and high reactivity. despite their invaluable role in cycling many redox sensitive elements, numerous unknowns remain about the reactivity of different manganese-oxide minerals under varying conditions in natural systems. by altering temperature, ph, and concentration of arsenite we were able to determine how manganese-oxide reactivity changes with simulated environmental conditions. the interact ...	2015	26388696
phylogenetic and kinetic characterization of a suite of dehydrogenases from a newly isolated bacterium, strain sg61-1l, that catalyze the turnover of guaiacylglycerol-β-guaiacyl ether stereoisomers.	lignin is a complex aromatic polymer found in plant cell walls that makes up 15 to 40% of plant biomass. the degradation of lignin substructures by bacteria is of emerging interest because it could provide renewable alternative feedstocks and intermediates for chemical manufacturing industries. we have isolated a bacterium, strain sg61-1l, that rapidly degrades all of the stereoisomers of one lignin substructure, guaiacylglycerol-β-guaiacyl ether (gge), which contains a key β-o-4 linkage found i ...	2015	26386069
metabolic pathway involved in 2-methyl-6-ethylaniline degradation by sphingobium sp. strain mea3-1 and cloning of the novel flavin-dependent monooxygenase system meaba.	2-methyl-6-ethylaniline (mea) is the main microbial degradation intermediate of the chloroacetanilide herbicides acetochlor and metolachlor. sphingobium sp. strain mea3-1 can utilize mea and various alkyl-substituted aniline and phenol compounds as sole carbon and energy sources for growth. we isolated the mutant strain mea3-1mut, which converts mea only to 2-methyl-6-ethyl-hydroquinone (mehq) and 2-methyl-6-ethyl-benzoquinone (mebq). mea may be oxidized by the p450 monooxygenase system to 4-hyd ...	2015	26386060
contribution of the distal pocket residue to the acyl-chain-length specificity of (r)-specific enoyl-coenzyme a hydratases from pseudomonas spp.	(r)-specific enoyl-coenzyme a (enoyl-coa) hydratases (phajs) are capable of supplying monomers from fatty acid β-oxidation to polyhydroxyalkanoate (pha) biosynthesis. phaj1pp from pseudomonas putida showed broader substrate specificity than did phaj1pa from pseudomonas aeruginosa, despite sharing 67% amino acid sequence identity. in this study, the substrate specificity characteristics of two pseudomonas phaj1 enzymes were investigated by site-directed mutagenesis, chimeragenesis, x-ray crystall ...	2015	26386053
pbar, an iclr family transcriptional activator for the regulation of the 3-phenoxybenzoate 1',2'-dioxygenase gene cluster in sphingobium wenxiniae jz-1t.	the 3-phenoxybenzoate (3-pba) 1',2'-dioxygenase gene cluster (pbaa1a2b cluster), which is responsible for catalyzing 3-phenoxybenzoate to 3-hydroxybenzoate and catechol, is inducibly expressed in sphingobium wenxiniae strain jz-1(t) by its substrate 3-pba. in this study, we identified a transcriptional activator of the pbaa1a2b cluster, pbar, using a dna affinity approach. pbar is a 253-amino-acid protein with a molecular mass of 28,000 da. pbar belongs to the iclr family of transcriptional regu ...	2015	26386050
empirical antibiotic therapy for pneumonia in intensive care units: a multicentre, retrospective analysis of potentially pathogenic microorganisms identified by endotracheal aspirates cultures.	the purpose of this investigation was to explore the presumed relationship between the days of hospitalisation and microorganisms identified by endotracheal aspirate cultures in relation to adequate empirical treatment strategies of pneumonia in the intensive care unit (icu). all potentially pathogenic microorganisms identified by (surveillance) cultures of endotracheal aspirates obtained in the icus of two dutch teaching hospitals in 2007 and 2012 were retrospectively collected and analysed. an ...	2015	26385348
characterization of flavin-containing opine dehydrogenase from bacteria.	opines, in particular nopaline and octopine, are specific compounds found in crown gall tumor tissues induced by infections with agrobacterium species, and are synthesized by well-studied nad(p)h-dependent dehydrogenases (synthases), which catalyze the reductive condensation of α-ketoglutarate or pyruvate with l-arginine. the corresponding genes are transferred into plant cells via a tumor-inducing (ti) plasmid. in addition to the reverse oxidative reaction(s), the genes noxb-noxa and ooxb-ooxa ...	2015	26382958
complete genome sequence of the phenanthrene-degrading soil bacterium delftia acidovorans cs1-4.	polycyclic aromatic hydrocarbons (pah) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of pah-contaminated soil. delftia acidovorans cs1-4 (formerly delftia sp. cs1-4) was isolated by using phenanthrene as the sole carbon source from pah contaminated soil in wisconsin. its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of pah. three genomic libraries were constructed and sequenced: an illu ...	2015	26380642
2-hydroxy acids in plant metabolism.	glycolate, malate, lactate, and 2-hydroxyglutarate are important 2-hydroxy acids (2ha) in plant metabolism. most of them can be found as d- and l-stereoisomers. these 2ha play an integral role in plant primary metabolism, where they are involved in fundamental pathways such as photorespiration, tricarboxylic acid cycle, glyoxylate cycle, methylglyoxal pathway, and lysine catabolism. recent molecular studies in arabidopsis thaliana have helped elucidate the participation of these 2ha in in plant ...	2015	26380567
extracellular vesicles: role in inflammatory responses and potential uses in vaccination in cancer and infectious diseases.	almost all cells and organisms release membrane structures containing proteins, lipids, and nucleic acids called extracellular vesicles (evs), which have a wide range of functions concerning intercellular communication and signaling events. recently, the characterization and understanding of their biological role have become a main research area due to their potential role in vaccination, as biomarkers antigens, early diagnostic tools, and therapeutic applications. here, we will overview the rec ...	2015	26380326
isolation of extracellular polymeric substances from biofilms of the thermoacidophilic archaeon sulfolobus acidocaldarius.	extracellular polymeric substances (eps) are the major structural and functional components of microbial biofilms. the aim of this study was to establish a method for eps isolation from biofilms of the thermoacidophilic archaeon, sulfolobus acidocaldarius, as a basis for eps analysis. biofilms of s. acidocaldarius were cultivated on the surface of gellan gum-solidified brock medium at 78°c for 4 days. five eps extraction methods were compared, including shaking of biofilm suspensions in phosphat ...	2015	26380258
analysis of the pathogenic potential of nosocomial pseudomonas putida strains.	pseudomonas putida strains are ubiquitous in soil and water but have also been reported as opportunistic human pathogens capable of causing nosocomial infections. in this study we describe the multilocus sequence typing of four p. putida strains (hb13667, hb8234, hb4184, and hb3267) isolated from in-patients at the besançon hospital (france). the four isolates (in particular hb3267) were resistant to a number of antibiotics. the pathogenicity and virulence potential of the strains was tested ex ...	2015	26379646
acinetobacter baumannii virulence is mediated by the concerted action of three phospholipases d.	acinetobacter baumannii causes a broad range of opportunistic infections in humans. its success as an emerging pathogen is due to a combination of increasing antibiotic resistance, environmental persistence and adaptation to the human host. to date very little is known about the molecular basis of the latter. here we demonstrate that a. baumannii can use phosphatidylcholine, an integral part of human cell membranes, as sole carbon and energy source. we report on the identification of three phosp ...	2015	26379240
impact of nanoscale zero valent iron on bacteria is growth phase dependent.	the toxic effect of nanoscale zero valent iron (nzvi) particles on bacteria from different growth phases was studied. four bacterial strains namely escherichia coli strains jm109 and bw25113, and pseudomonas putida strains kt2440 and f1 were experimented. the growth curves of these strains were determined. bacterial cells were harvested based on the predetermined time points, and exposed to nzvi. cell viability was determined by the plate count method. bacterial cells in lag and stationary phase ...	2016	26378872
directed evolution of the escherichia coli camp receptor protein at the camp pocket.	the escherichia coli camp receptor protein (crp) requires camp binding to undergo a conformational change for dna binding and transcriptional regulation. two crp residues, thr(127) and ser(128), are known to play important roles in camp binding through hydrogen bonding and in the camp-induced conformational change, but the connection between the two is not completely clear. here, we simultaneously randomized the codons for these two residues and selected crp mutants displaying high crp activity ...	2015	26378231
the sociality of bioremediation: hijacking the social lives of microbial populations to clean up heavy metal contamination.		2015	26377978
bypasses in intracellular glucose metabolism in iron-limited pseudomonas putida.	decreased biomass growth in iron (fe)-limited pseudomonas is generally attributed to downregulated expression of fe-requiring proteins accompanied by an increase in siderophore biosynthesis. here, we applied a stable isotope-assisted metabolomics approach to explore the underlying carbon metabolism in glucose-grown pseudomonas putida kt2440. compared to fe-replete cells, fe-limited cells exhibited a sixfold reduction in growth rate but the glucose uptake rate was only halved, implying an imbalan ...	2015	26377487
bypasses in intracellular glucose metabolism in iron-limited pseudomonas putida.	decreased biomass growth in iron (fe)-limited pseudomonas is generally attributed to downregulated expression of fe-requiring proteins accompanied by an increase in siderophore biosynthesis. here, we applied a stable isotope-assisted metabolomics approach to explore the underlying carbon metabolism in glucose-grown pseudomonas putida kt2440. compared to fe-replete cells, fe-limited cells exhibited a sixfold reduction in growth rate but the glucose uptake rate was only halved, implying an imbalan ...	2015	26377487
spontaneous phenotypic suppression of gaca-defective vibrio fischeri is achieved via mutation of csra and ihfa.	symbiosis defective gaca-mutant derivatives of vibrio fischeri are growth impaired thereby creating a selective advantage for growth-enhanced spontaneous suppressors. suppressors were isolated and characterized for effects of the mutations on gaca-mutant defects of growth, siderophore activity and luminescence. the mutations were identified by targeted and whole genome sequencing.	2015	26376921
exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in streptomyces.	there is a great demand for precisely quantitating the expression of genes of interest in synthetic and systems biotechnology as new and fascinating insights into the genetics of streptomycetes have come to light. here, we developed, for the first time to our knowledge, a quantitative method based on flow cytometry and a superfolder green fluorescent protein (sfgfp) at single-cell resolution in streptomyces. single cells of filamentous bacteria were obtained by releasing the protoplasts from the ...	2015	26374838
high-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of pseudomonas putida mt-2.	pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the tol plasmid pww0 along with other chromosomally encoded activities. tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. all xyl sequences were transcribed in response to aromatic substrates and the 3'-ter ...	2016	26373670
the rna chaperone hfq enables the environmental stress tolerance super-phenotype of pseudomonas putida.	the natural physiological regime of the soil bacterium pseudomonas putida involves incessant exposure to endogenous metabolic conflicts and environmental physicochemical insults. yet, the role of assisted small rna-mrna pairing in the stress tolerance super-phenotype that is the trademark of this bacterium has not been accredited. we have thoroughly explored the physiological consequences -in particular those related to exogenous stress - of deleting the hfq gene of p. putida, which encodes the ...	2016	26373442
ecology of anti-biofilm agents ii: bacteriophage exploitation and biocontrol of biofilm bacteria.	bacteriophages are the viruses of bacteria. in the guise of phage therapy they have been used for decades to successfully treat what are probable biofilm-containing chronic bacterial infections. more recently, phage treatment or biocontrol of biofilm bacteria has been brought back to the laboratory for more rigorous assessment as well as towards the use of phages to combat environmental biofilms, ones other than those directly associated with bacterial infections. considered in a companion artic ...	2015	26371011
the three bacterial lines of defense against antimicrobial agents.	antimicrobial agents target a range of extra- and/or intracellular loci from cytoplasmic wall to membrane, intracellular enzymes and genetic materials. meanwhile, many resistance mechanisms employed by bacteria to counter antimicrobial agents have been found and reported in the past decades. based on their spatially distinct sites of action and distribution of location, antimicrobial resistance mechanisms of bacteria were categorized into three groups, coined the three lines of bacterial defense ...	2015	26370986
determinants of bacteriological outcomes in exacerbations of chronic obstructive pulmonary disease.	changes in sputum microbiology following antibiotic treatment of acute exacerbations of chronic obstructive pulmonary disease (aecopd), including patterns of bacteriological relapse and superinfection are not well understood. sputum microbiology at exacerbation is not routinely performed, but pathogen presence and species are determinants of outcomes. therefore, we determined whether baseline clinical factors could predict the presence of bacterial pathogens at exacerbation. bacterial eradicatio ...	2015	26370552
determinants of bacteriological outcomes in exacerbations of chronic obstructive pulmonary disease.	changes in sputum microbiology following antibiotic treatment of acute exacerbations of chronic obstructive pulmonary disease (aecopd), including patterns of bacteriological relapse and superinfection are not well understood. sputum microbiology at exacerbation is not routinely performed, but pathogen presence and species are determinants of outcomes. therefore, we determined whether baseline clinical factors could predict the presence of bacterial pathogens at exacerbation. bacterial eradicatio ...	2015	26370552
mutations in rna polymerase bridge helix and switch regions affect active-site networks and transcript-assisted hydrolysis.	in bacterial rna polymerase (rnap), the bridge helix and switch regions form an intricate network with the catalytic active centre and the main channel. these interactions are important for catalysis, hydrolysis and clamp domain movement. by targeting conserved residues in escherichia coli rnap, we are able to show that functions of these regions are differentially required during σ(70)-dependent and the contrasting σ(54)-dependent transcription activations and thus potentially underlie the key ...	2015	26365052
efflux systems in bacteria and their metabolic engineering applications.	the production of valuable chemicals from metabolically engineered microbes can be limited by excretion from the cell. efflux is often overlooked as a bottleneck in metabolic pathways, despite its impact on alleviating feedback inhibition and product toxicity. in the past, it has been assumed that endogenous efflux pumps and membrane porins can accommodate product efflux rates; however, there are an increasing number of examples wherein overexpressing efflux systems is required to improve metabo ...	2015	26363557
membrane-associated glucose-methanol-choline oxidoreductase family enzymes phcc and phcd are essential for enantioselective catabolism of dehydrodiconiferyl alcohol.	sphingobium sp. strain syk-6 is able to degrade various lignin-derived biaryls, including a phenylcoumaran-type compound, dehydrodiconiferyl alcohol (dca). in syk-6 cells, the alcohol group of the b-ring side chain of dca is initially oxidized to the carboxyl group to generate 3-(2-(4-hydroxy-3-methoxyphenyl)-3-(hydroxymethyl)-7-methoxy-2,3-dihydrobenzofuran-5-yl) acrylic acid (dca-c). next, the alcohol group of the a-ring side chain of dca-c is oxidized to the carboxyl group, and then the resul ...	2015	26362985
metabolic engineering of a novel muconic acid biosynthesis pathway via 4-hydroxybenzoic acid in escherichia coli.	cis,cis-muconic acid (ma) is a commercially important raw material used in pharmaceuticals, functional resins, and agrochemicals. ma is also a potential platform chemical for the production of adipic acid (aa), terephthalic acid, caprolactam, and 1,6-hexanediol. a strain of escherichia coli k-12, bw25113, was genetically modified, and a novel nonnative metabolic pathway was introduced for the synthesis of ma from glucose. the proposed pathway converted chorismate from the aromatic amino acid pat ...	2015	26362984
synergistic effect of pseudomonas putida and bacillus amyloliquefaciens ameliorates drought stress in chickpea (cicer arietinum l.).	two plant growth promoting rhizobacteria (pgpr) pseudomonas putida nbrira and bacillus amyloliquefaciens nbrisn13 with ability to tolerate abiotic stress along with multiple pgp traits like acc deaminase activity, minerals solubilisation, hormones production, biofilm formation, siderophore activity were evaluated for their synergistic effect to ameliorate drought stress in chickpea. earlier we have reported both the strains individually for their pgp attributes and stress amelioration in host pl ...	2015	26362119
synergistic effect of pseudomonas putida and bacillus amyloliquefaciens ameliorates drought stress in chickpea (cicer arietinum l.).	two plant growth promoting rhizobacteria (pgpr) pseudomonas putida nbrira and bacillus amyloliquefaciens nbrisn13 with ability to tolerate abiotic stress along with multiple pgp traits like acc deaminase activity, minerals solubilisation, hormones production, biofilm formation, siderophore activity were evaluated for their synergistic effect to ameliorate drought stress in chickpea. earlier we have reported both the strains individually for their pgp attributes and stress amelioration in host pl ...	2015	26362119
identification of a chemoreceptor that specifically mediates chemotaxis toward metabolizable purine derivatives.	chemotaxis is an essential mechanism that enables bacteria to move toward favorable ecological niches. escherichia coli, the historical model organism for studying chemotaxis, has five well-studied chemoreceptors. however, many bacteria with different lifestyle have more chemoreceptors, most of unknown function. using a high throughput screening approach, we identified a chemoreceptor from pseudomonas putida kt2440, named mcph, which specifically recognizes purine and its derivatives, adenine, g ...	2016	26355499
infectious diseases linked to cross-contamination of flexible endoscopes.	flexible endoscopes are widely used to examine, diagnose, and treat medical disorders. while the risk of endoscopy-related transmission of infection is estimated to be very low, more health care-associated infections are related to contaminated endoscopes than to any other medical device. flexible endoscopes can get highly contaminated with microorganisms, secretions and blood during use. the narrow lumens and multiple internal channels make the cleaning of flexible endoscopes a complex and diff ...	2015	26355428
application of internal standard method in recombinant luminescent bacteria test.	mercury and its organic compounds have been of severe concern worldwide due to their damage to the ecosystem and human health. the development of effective and affordable technology to monitor and signal the presence of bioavailable mercury is an urgent need. the mer gene is a mercury-responsive resistant gene, and a mercury-sensing recombinant luminescent bacterium using the mer gene was constructed in this study. the mer operon from marine pseudomonas putida strain sp1 was amplified and fused ...	2015	26354701
interaction of piriformospora indica with azotobacter chroococcum.	microbial communities in rhizosphere interact with each other and form a basis of a cumulative impact on plant growth. rhizospheric microorganisms like piriformospora indica and azotobacter chroococcum are well known for their beneficial interaction with plants. these features make p. indica/a. chroococcum co-inoculation of crops most promising with respect to sustainable agriculture and to understanding the transitions in the evolution of rhizospheric microbiome. here, we investigated interacti ...	2015	26350628
potential roles for microbial endophytes in herbicide tolerance in plants.	herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. a growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. the current evidence for herbicide tolerance be ...	2015	26350619
potential roles for microbial endophytes in herbicide tolerance in plants.	herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. a growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. the current evidence for herbicide tolerance be ...	2015	26350619
pseudomonas putida kt2440 strain metabolizes glucose through a cycle formed by enzymes of the entner-doudoroff, embden-meyerhof-parnas, and pentose phosphate pathways.	the soil bacterium pseudomonas putida kt2440 lacks a functional embden-meyerhof-parnas (emp) pathway, and glycolysis is known to proceed almost exclusively through the entner-doudoroff (ed) route. to investigate the raison d'être of this metabolic arrangement, the distribution of periplasmic and cytoplasmic carbon fluxes was studied in glucose cultures of this bacterium by using (13)c-labeled substrates, combined with quantitative physiology experiments, metabolite quantification, and in vitro e ...	2015	26350459
benzoic acid-inducible gene expression in mycobacteria.	conditional expression is a powerful tool to investigate the role of bacterial genes. here, we adapt the pseudomonas putida-derived positively regulated xyls/pm expression system to control inducible gene expression in mycobacterium smegmatis and mycobacterium tuberculosis, the causative agent of human tuberculosis. by making simple changes to a gram-negative broad-host-range xyls/pm-regulated gene expression vector, we prove that it is possible to adapt this well-studied expression system to no ...	2015	26348349
toxicity of synthetic herbicides containing 2,4-d and mcpa moieties towards pseudomonas putida mt-2 and its response at the level of membrane fatty acid composition.	one of the attempts to create more effective herbicidal compounds includes the use of ionic liquids. herbicidal ionic liquids have more effective biological activity, they are less volatile, more thermally stable, and exhibit superior efficiency in comparison to typically employed herbicides, allowing the reduction of the herbicide dose applied per hectare. however, studies on the environmental toxicity of this group of compounds are very rarely available. environmental toxicity is an important ...	2016	26347932
production of cinnamic and p-hydroxycinnamic acids in engineered microbes.	the aromatic compounds cinnamic and p-hydroxycinnamic acids (phcas) are phenylpropanoids having applications as precursors for the synthesis of thermoplastics, flavoring, cosmetic, and health products. these two aromatic acids can be obtained by chemical synthesis or extraction from plant tissues. however, both manufacturing processes have shortcomings, such as the generation of toxic subproducts or a low concentration in plant material. alternative production methods are being developed to enab ...	2015	26347861
isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail achatina fulica.	the enzymatic hydrolysis of cellulose by cellulases is one of the major limiting steps in the conversion of lignocellulosic biomass to yield bioethanol. to overcome this hindrance, significant efforts are underway to identify novel cellulases. the snail achatina fulica is a gastropod with high cellulolytic activity, mainly due to the abundance of glycoside hydrolases produced by both the animal and its resident microbiota. in this study, we partially assessed the cellulolytic aerobic bacterial d ...	2015	26347735
intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens.	a community-based sessile life style is the normal mode of growth and survival for many bacterial species. under such conditions, cell-to-cell interactions are inevitable and ultimately lead to the establishment of dense, complex and highly structured biofilm populations encapsulated in a self-produced extracellular matrix and capable of coordinated and collective behavior. remarkably, in food processing environments, a variety of different bacteria may attach to surfaces, survive, grow, and for ...	2015	26347727
bacterial degradation of monocyclic aromatic amines.	aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. these compounds have been considered highly toxic to human beings due to their carcinogenic nature. three groups of aromatic amines have been recognized: monocyclic, polycyclic, and heterocyclic aromatic amines. bacterial degradation of several monocyclic aromatic amines has been studied in a variety of bacteria, which utiliz ...	2015	26347719
transcriptional analysis of amorphotheca resinae zn1 on biological degradation of furfural and 5-hydroxymethylfurfural derived from lignocellulose pretreatment.	furfural and 5-hydroxymethylfurfural (hmf) are the two major inhibitor compounds generated from lignocellulose pretreatment, especially for dilute acid, steam explosion, neutral hot water pretreatment methods. the two inhibitors severely inhibit the cell growth and metabolism of fermenting strains in the consequent bioconversion step. the biodetoxification strain amorphotheca resinae zn1 has demonstrated its extraordinary capacity of fast and complete degradation of furfural and hmf into corresp ...	2015	26346604
strategies for the use of bacteriocins in gram-negative bacteria: relevance in food microbiology.	bacteriocins are ribosomally synthesized peptides that have bacteriostatic or bactericidal effects on other bacteria. the use of bacteriocins has emerged as an important strategy to increase food security and to minimize the incidence of foodborne diseases, due to its minimal impact on the nutritional and sensory properties of food products. gram-negative bacteria are naturally resistant to the action of bacteriocins produced by gram-positive bacteria, which are widely explored in foods. however ...	2015	26344957
the landscape of intertwined associations in homooligomeric proteins.	we present an overview of the full repertoire of intertwined associations in homooligomeric proteins. this overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers ...	2015	26340815
draft genome sequence of pseudomonas putida jlr11, a facultative anaerobic 2,4,6-trinitrotoluene biotransforming bacterium.	we report the draft genome sequence of pseudomonas putida jlr11, a facultative anaerobic bacterium that has been studied in detail for its capacity to use the explosive 2,4,6-trinitrotoluene (tnt) as a nitrogen source. the sequence confirms the mechanisms used by this versatile strain to reduce and assimilate nitrogen from tnt.	2015	26337875
analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial bacillus amyloliquefaciens sqr9.	the plant growth-promoting rhizobacteria (pgpr) strain bacillus amyloliquefaciens sqr9, isolated from the cucumber rhizosphere, protects the host plant from pathogen invasion and promotes plant growth through efficient root colonization. the phytohormone indole-3-acetic acid (iaa) has been suggested to contribute to the plant-growth-promoting effect of bacillus strains. the possible iaa synthetic pathways in b. amyloliquefaciens sqr9 were investigated in this study, using a combination of chemic ...	2015	26337367
understanding of real alternative redox partner of streptomyces peucetius doxa: prediction and validation using in silico and in vitro analyses.	streptomyces peucetius atcc27952 contains the cytochrome p450 monoxygenase doxa that is responsible for the hydroxylation of daunorubicin into doxorubicin. although s. peucetius atcc27952 contains several potential redox partners, the most suitable endogenous electron-transport system is still unclear; therefore, we conducted a study of potential redox partners using accelrys discovery studio 3.5. recombinant doxa along with its redox partners from s. peucetius fdx1, fdr2, and fdx3, and the puti ...	2015	26334717
synthetic fatty acids prevent plasmid-mediated horizontal gene transfer.	bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic resistance genes among human pathogens. antibiotic resistance spread could be halted or diminished by molecules that interfere with the conjugation process. in this work, synthetic 2-alkynoic fatty acids were identified as a novel class of conjugation inhibitors. their chemical properties were investigated by using the prototype 2-hexadecynoic acid and its derivatives. essential featu ...	2015	26330514
recombinant antibody production evolves into multiple options aimed at yielding reagents suitable for application-specific needs.	antibodies have been a pillar of basic research, while their relevance in clinical diagnostics and therapy is constantly growing. consequently, the production of both conventional and fragment antibodies constantly faces more demanding challenges for the improvement of their quantity and quality. the answer to such an increasing need has been the development of a wide array of formats and alternative production platforms. this review offers a critical comparison and evaluation of the different o ...	2015	26330219
multifaceted roles of extracellular dna in bacterial physiology.	in textbooks, dna is generally defined as the universal storage material for genetic information in all branches of life. beyond this important intracellular role, dna can also be present outside of living cells and is an abundant biopolymer in aquatic and terrestrial ecosystems. the origin of extracellular dna in such ecological niches is diverse: it can be actively secreted or released by prokaryotic and eukaryotic cells by means of autolysis, apoptosis, necrosis, bacterial secretion systems o ...	2015	26328805
multifaceted roles of extracellular dna in bacterial physiology.	in textbooks, dna is generally defined as the universal storage material for genetic information in all branches of life. beyond this important intracellular role, dna can also be present outside of living cells and is an abundant biopolymer in aquatic and terrestrial ecosystems. the origin of extracellular dna in such ecological niches is diverse: it can be actively secreted or released by prokaryotic and eukaryotic cells by means of autolysis, apoptosis, necrosis, bacterial secretion systems o ...	2015	26328805
molecular characterization of selected multidrug resistant pseudomonas from water distribution systems in southwestern nigeria.	persistence of antibiotic resistant bacteria, including multidrug resistant (mdr) pseudomonads, is an important environmental health problem associated with drinking water distribution systems (dwds) worldwide. there is paucity of data on the molecular characteristics of antibiotic resistance genes and their mode of transfer among pseudomonads from dwds located in resource-challenged areas such as southwestern nigeria.	2015	26328550
insect's intestinal organ for symbiont sorting.	symbiosis has significantly contributed to organismal adaptation and diversification. for establishment and maintenance of such host-symbiont associations, host organisms must have evolved mechanisms for selective incorporation, accommodation, and maintenance of their specific microbial partners. here we report the discovery of a previously unrecognized type of animal organ for symbiont sorting. in the bean bug riptortus pedestris, the posterior midgut is morphologically differentiated for harbo ...	2015	26324935
combined endophytic inoculants enhance nickel phytoextraction from serpentine soil in the hyperaccumulator noccaea caerulescens.	this study assesses the effects of specific bacterial endophytes on the phytoextraction capacity of the ni-hyperaccumulator noccaea caerulescens, spontaneously growing in a serpentine soil environment. five metal-tolerant endophytes had already been selected for their high ni tolerance (6 mm) and plant growth promoting ability. here we demonstrate that individual bacterial inoculation is ineffective in enhancing ni translocation and growth of n. caerulescens in serpentine soil, except for specif ...	2015	26322074
innovative biological approaches for monitoring and improving water quality.	water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. contaminants can be identified and quantified in situ using microbial whole-cell biosenso ...	2015	26322034
γ-resorcylate catabolic-pathway genes in the soil actinomycete rhodococcus jostii rha1.	the rhodococcus jostii rha1 gene cluster required for γ-resorcylate (gra) catabolism was characterized. the cluster includes tsda, tsdb, tsdc, tsdd, tsdr, tsdt, and tsdx, which encode gra decarboxylase, resorcinol 4-hydroxylase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, an iclr-type regulator, a major facilitator superfamily transporter, and a putative hydrolase, respectively. the tsda gene conferred gra decarboxylase activity on escherichia coli. purified tsdb oxidized nadh in the ...	2015	26319878
yjeh is a novel exporter of l-methionine and branched-chain amino acids in escherichia coli.	amino acid efflux transport systems have important physiological functions and play vital roles in the fermentative production of amino acids. however, no methionine exporter has yet been identified in escherichia coli. in this study, we identified a novel amino acid exporter, yjeh, in e. coli. the yjeh overexpression strain exhibited high tolerance to the structural analogues of l-methionine and branched-chain amino acids, decreased intracellular amino acid levels, and enhanced export rates in ...	2015	26319875
analysis of preference for carbon source utilization among three strains of aromatic compounds degrading pseudomonas.	soil isolates pseudomonas putida csv86, pseudomonas aeruginosa pp4 and pseudomonas sp. c5pp degrade naphthalene, phthalate isomers and carbaryl, respectively. strain csv86 displayed a diauxic growth pattern on phenylpropanoid compounds (veratraldehyde, ferulic acid, vanillin or vanillic acid) plus glucose with a distinct second lag-phase. the glucose concentration in the medium remained constant with higher cell respiration rates on aromatics and maximum protocatechuate 3,4-dioxygenase activity ...	2015	26316546