Publications

rhizobacterial volatiles and photosynthesis-related signals coordinate myb72 expression in arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses.	in arabidopsis roots, the transcription factor myb72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (isr) and plant survival under conditions of limited iron availability. previously, it was shown that myb72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and isr signaling. here, we show that volatile organic compounds (vocs) ...	2015	26307542
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
over-the-counter monocyclic non-steroidal anti-inflammatory drugs in environment-sources, risks, biodegradation.	recently, the increased use of monocyclic non-steroidal anti-inflammatory drugs has resulted in their presence in the environment. this may have potential negative effects on living organisms. the biotransformation mechanisms of monocyclic non-steroidal anti-inflammatory drugs in the human body and in other mammals occur by hydroxylation and conjugation with glycine or glucuronic acid. biotransformation/biodegradation of monocyclic non-steroidal anti-inflammatory drugs in the environment may be ...	2015	26478634
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
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
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
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
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
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
crystal structure of pnpcd, a two-subunit hydroquinone 1,2-dioxygenase, reveals a novel structural class of fe2+-dependent dioxygenases.	aerobic microorganisms have evolved a variety of pathways to degrade aromatic and heterocyclic compounds. however, only several classes of oxygenolytic fission reaction have been identified for the critical ring cleavage dioxygenases. among them, the most well studied dioxygenases proceed via catecholic intermediates, followed by noncatecholic hydroxy-substituted aromatic carboxylic acids. therefore, the recently reported hydroquinone 1,2-dioxygenases add to the diversity of ring cleavage reacti ...	2015	26304122
the chitinase c gene pschic from pseudomonas sp. and its synergistic effects on larvicidal activity.	pseudomonas sp. strain txg6-1, a chitinolytic gram-negative bacterium, was isolated from a vegetable field in taixing city, jiangsu province, china. in this study, a pseudomonas chitinase c gene (pschic) was isolated from the chromosomal dna of this bacterium using a pair of specific primers. the pschic gene consisted of an open reading frame of 1443 nucleotides and encoded 480 amino acid residues with a calculated molecular mass of 51.66 kda. the deduced pschic amino acid sequence lacked a sign ...	2015	26500441
antimicrobial resistance of pseudomonas spp. isolated from wastewater and wastewater-impacted marine coastal zone.	in this study, species distribution and antimicrobial susceptibility of cultivated pseudomonas spp. were studied in influent (inf), effluent (eff), and marine outfall (mout) of wastewater treatment plant (wwtp). the susceptibility was tested against 8 antimicrobial classes, active against pseudomonas spp.: aminoglycosides, carbapenems, broad-spectrum cephalosporins from the 3rd and 4th generation, extended-spectrum penicillins, as well as their combination with the β-lactamase inhibitors, monoba ...	2015	26286796
identification of the mcpa and mcpm genes, encoding methyl-accepting proteins involved in amino acid and l-malate chemotaxis, and involvement of mcpm-mediated chemotaxis in plant infection by ralstonia pseudosolanacearum (formerly ralstonia solanacearum phylotypes i and iii).	sequence analysis has revealed the presence of 22 putative methyl-accepting chemotaxis protein (mcp) genes in the ralstonia pseudosolanacearum gmi1000 genome. pcr analysis and dna sequencing showed that the highly motile r. pseudosolanacearum strain ps29 possesses homologs of all 22 r. pseudosolanacearum gmi1000 mcp genes. we constructed a complete collection of single mcp gene deletion mutants of r. pseudosolanacearum ps29 by unmarked gene deletion. screening of the mutant collection revealed t ...	2015	26276117
bacterial rotary export atpases are allosterically regulated by the nucleotide second messenger cyclic-di-gmp.	the widespread second messenger molecule cyclic di-gmp (cdg) regulates the transition from motile and virulent lifestyles to sessile, biofilm-forming ones in a wide range of bacteria. many pathogenic and commensal bacterial-host interactions are known to be controlled by cdg signaling. although the biochemistry of cyclic dinucleotide metabolism is well understood, much remains to be discovered about the downstream signaling pathways that induce bacterial responses upon cdg binding. as part of ou ...	2015	26265469
vibrio cholerae csra regulates toxr levels in response to amino acids and is essential for virulence.	toxr is a major virulence gene regulator in vibrio cholerae. although constitutively expressed under many laboratory conditions, our previous work demonstrated that the level of toxr increases significantly when cells are grown in the presence of the 4 amino acids asparagine, arginine, glutamate, and serine (nres). we show here that the increase in toxr production in response to nres requires the var/csr global regulatory circuit. the vars/vara two-component system controls the amount of active ...	2015	26242626
development of two real-time multiplex pcr assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infections.	the frequent lack of a positive and timely microbiological diagnosis in patients with lower respiratory tract infection (lrti) is an important obstacle to antimicrobial stewardship. patients are typically prescribed broad-spectrum empirical antibiotics while microbiology results are awaited, but, because these are often slow, negative, or inconclusive, de-escalation to narrow-spectrum agents rarely occurs in clinical practice. the aim of this study was to develop and evaluate two multiplex real- ...	2015	25980353
immobilization of microbes for bioremediation of crude oil polluted environments: a mini review.	petroleum hydrocarbons are the most common environmental pollutants in the world and oil spills pose a great hazard to terrestrial and marine ecosystems. oil pollution may arise either accidentally or operationally whenever oil is produced, transported, stored and processed or used at sea or on land. oil spills are a major menace to the environment as they severely damage the surrounding ecosystems. to improve the survival and retention of the bioremediation agents in the contaminated sites, bac ...	2015	26668662
is the efficacy of biological control against plant diseases likely to be more durable than that of chemical pesticides?	the durability of a control method for plant protection is defined as the persistence of its efficacy in space and time. it depends on (i) the selection pressure exerted by it on populations of plant pathogens and (ii) on the capacity of these pathogens to adapt to the control method. erosion of effectiveness of conventional plant protection methods has been widely studied in the past. for example, apparition of resistance to chemical pesticides in plant pathogens or pests has been extensively d ...	2015	26284088
functional characterization of the mannitol promoter of pseudomonas fluorescens dsm 50106 and its application for a mannitol-inducible expression system for pseudomonas putida kt2440.	a new pbbr1mcs-2-derived vector containing the pseudomonas fluorescens dsm10506 mannitol promoter pmtle and mtlr encoding its arac/xyls type transcriptional activator was constructed and optimized for low basal expression. mannitol, arabitol, and glucitol-inducible gene expression was demonstrated with pseudomonas putida and egfp as reporter gene. the new vector was applied for functional characterization of pmtle. identification of the dna binding site of mtlr was achieved by in vivo egfp measu ...	2015	26207762
plant growth promotion induced by phosphate solubilizing endophytic pseudomonas isolates.	the use of plant growth promoting bacterial inoculants as live microbial biofertilizers provides a promising alternative to chemical fertilizers and pesticides. inorganic phosphate solubilization is one of the major mechanisms of plant growth promotion by plant associated bacteria. this involves bacteria releasing organic acids into the soil which solubilize the phosphate complexes converting them into ortho-phosphate which is available for plant up-take and utilization. the study presented here ...	2015	26257721
unearthing the genomes of plant-beneficial pseudomonas model strains wcs358, wcs374 and wcs417.	plant growth-promoting rhizobacteria (pgpr) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (isr). in the past 30 years, the pseudomonas spp. pgpr strains wcs358, wcs374 and wcs417 of the willie commelin scholten (wcs) collection have been studied in detail in pioneering papers on the molecular basis of pgpr-me ...	2015	26198432
identification of a chemoreceptor for c2 and c3 carboxylic acids.	chemoreceptors are at the beginnings of chemosensory signaling cascades that mediate chemotaxis. most bacterial chemoreceptors are functionally unannotated and are characterized by a diversity in the structure of their ligand binding domains (lbds). the data available indicate that there are two major chemoreceptor families at the functional level, namely, those that respond to amino acids or to krebs cycle intermediates. since pseudomonads show chemotaxis to many different compounds and possess ...	2015	26048936
genes associated with desiccation and osmotic stress in listeria monocytogenes as revealed by insertional mutagenesis.	listeria monocytogenes is a foodborne pathogen whose survival in food processing environments may be associated with its tolerance to desiccation. to probe the molecular mechanisms used by this bacterium to adapt to desiccation stress, a transposon library of 11,700 l. monocytogenes mutants was screened, using a microplate assay, for strains displaying increased or decreased desiccation survival (43% relative humidity, 15°c) in tryptic soy broth (tsb). the desiccation phenotypes of selected muta ...	2015	26025900
biodegradation of polychlorinated biphenyls (pcbs) by the novel identified cyanobacterium anabaena pd-1.	polychlorinated biphenyls (pcbs), a class of hazardous pollutants, are difficult to dissipate in the natural environment. in this study, a cyanobacterial strain anabaena pd-1 showed good resistance against pcb congeners. compared to a control group, chlorophyll a content decreased 3.7% and 11.7% when anabaena pd-1 was exposed to 2 and 5 mg/l pcbs for 7 d. this cyanobacterial strain was capable of decomposing pcb congeners which was conclusively proved by determination of chloride ion concentrati ...	2015	26177203
activation of pathogenesis-related genes by the rhizobacterium, bacillus sp. js, which induces systemic resistance in tobacco plants.	plant growth promoting rhizobacteria (pgpr) are known to confer disease resistance to plants. bacillus sp. js demonstrated antifungal activities against five fungal pathogens in in vitro assays. to verify whether the volatiles of bacillus sp. js confer disease resistance, tobacco leaves pre-treated with the volatiles were damaged by the fungal pathogen, rhizoctonia solani and oomycete phytophthora nicotianae. pre-treated tobacco leaves had smaller lesion than the control plant leaves. in pathoge ...	2015	26060440
impact of plant domestication on rhizosphere microbiome assembly and functions.	the rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. domestication of plant species has substantially contributed to human civilization, but also cause ...	2015	26085172
impact of plant domestication on rhizosphere microbiome assembly and functions.	the rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. domestication of plant species has substantially contributed to human civilization, but also cause ...	2015	26085172
rapidec carba np test for rapid detection of carbapenemase producers.	performances of the rapidec carba np test (biomérieux) were evaluated for detection of all types of carbapenemases in enterobacteriaceae, acinetobacter baumannii, and pseudomonas aeruginosa. in less than 2 h after sample preparation, it showed a sensitivity and specificity of 96%. this ready-to-use test is well adapted to the daily need for detection of carbapenemase producers in any laboratory worldwide.	2015	26085619
effects of nacl concentration on anode microbes in microbial fuel cells.	understanding of how operational parameters affect the composition of exoelectrogenic microbes is an important step in the development of efficient microbial fuel cells (mfcs). in the present study, single-chamber mfcs were inoculated with rice paddy-field soil and continuously supplied with an acetate medium containing different concentrations of nacl (0-1.8 m). polarization analyses showed that power output increased as the nacl concentration increased to 0.1 m, while it was markedly diminishe ...	2015	26061773
draft genome sequence of the bacterium pseudomonas putida cbb5, which can utilize caffeine as a sole carbon and nitrogen source.	pseudomonas putida cbb5 was isolated from soil by enriching for growth on caffeine (1,3,7-trimethylxanthine). the draft genome of this strain is 6.9 mb, with 5,941 predicted coding sequences. it includes the previously studied alx gene cluster encoding alkylxanthine n-demethylase enzymes and other genes that enable the degradation of purine alkaloids.	2015	26067973
catalytic and hydrodynamic properties of styrene monooxygenases from rhodococcus opacus 1cp are modulated by cofactor binding.	styrene monooxygenases (smos) are flavoenzymes catalyzing the epoxidation of styrene into styrene oxide. smos are composed of a monooxygenase (stya) and a reductase (styb). the latter delivers reduced fad to stya on the expense of nadh. we identified rhodococcus opacus 1cp as the first microorganism to possess three different stya isoforms occurring in two systems stya1/stya2b and stya/styb, respectively. the hydrodynamic properties of stya isozymes were found to be modulated by the binding of t ...	2015	26054733
new metabolic pathway for degradation of 2-nitrobenzoate by arthrobacter sp. spg.	arthrobacter sp. spg utilized 2-nitrobenzoate as its sole source of carbon and energy and degraded it with accumulation of stoichiometric amounts of nitrite ions. salicylate and catechol were detected as metabolites of the 2-nitrobenzoate degradation using high performance liquid chromatography and gas chromatography-mass spectrometry. enzyme activities for 2-nitrobenzoate-2-monooxygenase, salicylate hydroxylase, and catechol-1,2-dioxygenase were detected in the crude extracts of the 2-nitrobenz ...	2015	26082768
pseudomonas putida and pseudomonas fluorescens species group recovery from human homes varies seasonally and by environment.	by shedding light on variation in time as well as in space, long-term biogeographic studies can help us define organisms' distribution patterns and understand their underlying drivers. here we examine distributions of pseudomonas in and around 15 human homes, focusing on the p. putida and p. fluorescens species groups. we describe recovery from 10,941 samples collected during up to 8 visits per home, occurring on average 2.6 times per year. we collected a mean of 141 samples per visit, from site ...	2015	26023929
bactericidal compounds controlling growth of the plant pathogen pseudomonas syringae pv. actinidiae, which forms biofilms composed of a novel exopolysaccharide.	pseudomonas syringae pv. actinidiae is the major cause of bacterial canker and is a severe threat to kiwifruit production worldwide. many aspects of the disease caused by p. syringae pv. actinidiae, such as the pathogenicity-relevant formation of a biofilm composed of extracellular polymeric substances (epss), are still unknown. here, a highly virulent strain of p. syringae pv. actinidiae, nz v-13, was studied with respect to biofilm formation and architecture using a flow cell system combined w ...	2015	25841017
carbapenemase producing bacteria in the food supply escaping detection.	carbapenem antimicrobials are critically important to human health and they are often the only remaining effective antibiotics for treating serious infections. resistance to these drugs mediated by acquired carbapenemase enzymes is increasingly encountered in gram-negative bacteria and is considered a public health emergency. animal origin food products are recognized as a potential source of resistant organisms, although carbapenem resistance has only recently been reported. in western countrie ...	2015	25966303
draft genome sequence of se(iv)-reducing bacterium pseudomonas migulae es3-33.	pseudomonas migulae es3-33 is a gram-negative strain that strongly reduces se(iv) and was isolated from a selenium mining area in enshi, southwest china. here we present the draft genome of this strain containing potential genes involved in selenite reduction and a large number of genes encoding resistances to copper and antibiotics.	2015	25953191
occurrence of multidrug resistant extended spectrum beta-lactamase-producing bacteria on iceberg lettuce retailed for human consumption.	antibiotic resistance in bacteria is a global problem exacerbated by the dissemination of resistant bacteria via uncooked food, such as green leafy vegetables. new strains of bacteria are emerging on a daily basis with novel expanded antibiotic resistance profiles. in this pilot study, we examined the occurrence of antibiotic resistant bacteria against five classes of antibiotics on iceberg lettuce retailed in local convenience stores in rochester, michigan. in this study, 138 morphologically di ...	2015	26064922
mutational analyses of glucose dehydrogenase and glucose-6-phosphate dehydrogenase genes in pseudomonas fluorescens reveal their effects on growth and alginate production.	the biosynthesis of alginate has been studied extensively due to the importance of this polymer in medicine and industry. alginate is synthesized from fructose-6-phosphate and thus competes with the central carbon metabolism for this metabolite. the alginate-producing bacterium pseudomonas fluorescens relies on the entner-doudoroff and pentose phosphate pathways for glucose metabolism, and these pathways are also important for the metabolism of fructose and glycerol. in the present study, the im ...	2015	25746989
determination of zinc, cadmium and lead bioavailability in contaminated soils at the single-cell level by a combination of whole-cell biosensors and flow cytometry.	zinc, lead and cadmium are metallic trace elements (mtes) that are widespread in the environment and tend to accumulate in soils because of their low mobility and non-degradability. the purpose of this work is to evaluate the applicability of biosensors as tools able to provide data about the bioavailability of such mtes in contaminated soils. here, we tested the genetically-engineered strain escherichia coli pp(znta)gfp as a biosensor applicable to the detection of zinc, lead and cadmium by the ...	2015	25894939
pseudomonas fluorescens pirates both ferrioxamine and ferricoelichelin siderophores from streptomyces ambofaciens.	iron is essential in many biological processes. however, its bioavailability is reduced in aerobic environments, such as soil. to overcome this limitation, microorganisms have developed different strategies, such as iron chelation by siderophores. some bacteria have even gained the ability to detect and utilize xenosiderophores, i.e., siderophores produced by other organisms. we illustrate an example of such an interaction between two soil bacteria, pseudomonas fluorescens strain bbc6r8 and stre ...	2015	25724953
above-belowground interactions govern the course and impact of biological invasions.	introduction of exotic organisms that subsequently become invasive is considered a serious threat to global biodiversity, and both scientists and nature-conservationists attempt to find explanations and means to meet this challenge. this requires a thorough analysis of the invasion phenomenon in an evolutionary and ecological context; in the case of invasive plants, we must have a major focus on above-belowground interactions. thus, we discuss different theories that have been proposed to explai ...	2015	25854693
a high-throughput screening assay for distinguishing nitrile hydratases from nitrilases.	a modified colorimetric high-throughput screen based on ph changes combined with an amidase inhibitor capable of distinguishing between nitrilases and nitrile hydratases. this enzymatic screening is based on a binary response and is suitable for the first step of hierarchical screening projects.	2015	26221095
inhibition of cell differentiation in bacillus subtilis by pseudomonas protegens.	interspecies interactions have been described for numerous bacterial systems, leading to the identification of chemical compounds that impact bacterial physiology and differentiation for processes such as biofilm formation. here, we identified soil microbes that inhibit biofilm formation and sporulation in the common soil bacterium bacillus subtilis. we did so by creating a reporter strain that fluoresces when the transcription of a biofilm-specific gene is repressed. using this reporter in a co ...	2015	25825426
dimeric c-di-gmp is required for post-translational regulation of alginate production in pseudomonas aeruginosa.	pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. among the proteins required for alginate production, alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-gmp) binding activity post-translationally regulates alginate secretion. in this study, we repo ...	2015	25817996
identification of nasal colonization with β-lactamase-producing enterobacteriaceae in patients, health care workers and students in madagascar.	this study assesses the nasal occurrence of β-lactamase-producing enterobacteriaceae both in patients in a hospital department of infectious diseases at admission and in healthy madagascan students and health care workers. nasal swabs from 681 students, 824 health care workers, and 169 patients were obtained in antananarivo, madagascar, and transferred to germany. screening for β-lactamase (esbl, ampc) producing enterobacteriaceae was performed by cultural and molecular approaches, comprising br ...	2015	25908994
interstrain interactions between bacteria isolated from vacuum-packaged refrigerated beef.	the formation of bacterial spoilage communities in food is influenced by both extrinsic and intrinsic environmental factors. although many reports describe how these factors affect bacterial growth, much less is known about interactions among bacteria, which may influence community structure. this study investigated interactions among representative species of bacteria isolated from vacuum-packaged (vp) beef. thirty-nine effectors and 20 target isolates were selected, representing 10 bacterial g ...	2015	25662972
characterization of the xylella fastidiosa pd1671 gene encoding degenerate c-di-gmp ggdef/eal domains, and its role in the development of pierce's disease.	xylella fastidiosa is an important phytopathogenic bacterium that causes many serious plant diseases including pierce's disease of grapevines. x. fastidiosa is thought to induce disease by colonizing and clogging xylem vessels through the formation of cell aggregates and bacterial biofilms. here we examine the role in x. fastidiosa virulence of an uncharacterized gene, pd1671, annotated as a two-component response regulator with potential ggdef and eal domains. ggdef domains are found in c-di-gm ...	2015	25811864
draft genome sequence of the polychlorinated biphenyl-degrading bacterium pseudomonas putida kf703 (nbrc 110666) isolated from biphenyl-contaminated soil.	pseudomonas putida kf703 (nbrc 110666) utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (pcbs). here, we report the draft genome sequence of the kf703 strain, which provides insight into the molecular mechanisms of adaptation to an environment polluted by aromatic compounds.	2015	25792060
type iii secretion system and virulence markers highlight similarities and differences between human- and plant-associated pseudomonads related to pseudomonas fluorescens and p. putida.	pseudomonas fluorescens is commonly considered a saprophytic rhizobacterium devoid of pathogenic potential. nevertheless, the recurrent isolation of strains from clinical human cases could indicate the emergence of novel strains originating from the rhizosphere reservoir, which could be particularly resistant to the immune system and clinical treatment. the importance of type three secretion systems (t3sss) in the related pseudomonas aeruginosa nosocomial species and the occurrence of this secre ...	2015	25636837
competition between burkholderia pseudomallei and b. thailandensis.	burkholderia pseudomallei is a gram-negative bacterium that causes melioidosis, an often fatal disease in tropical countries. burkholderia thailandensis is a non-virulent but closely related species. both species are soil saprophytes but are almost never isolated together.	2015	25879538
lipopeptide biosynthesis in pseudomonas fluorescens is regulated by the protease complex clpap.	lipopeptides (lp) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities. in pseudomonas and other bacterial genera, lp biosynthesis is governed by large multimodular nonribosomal peptide synthetases (nrps). to date, relatively little is known about the regulatory genetic network of lp biosynthesis.	2015	25885431
genetic characterization of caffeine degradation by bacteria and its potential applications.	the ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. extensive research into this subject has revealed two distinct pathways, n-demethylation and c-8 oxidation, for bacterial caffeine degradation. however, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. this review article discusses the recent discoveries of the genes responsible for both n-demethylation and c-8 oxidation. all of ...	2015	25678373
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
a vector system for abc transporter-mediated secretion and purification of recombinant proteins in pseudomonas species.	pseudomonas fluorescens is an efficient platform for recombinant protein production. p. fluorescens has an abc transporter secreting endogenous thermostable lipase (tlia) and protease, which can be exploited to transport recombinant proteins across the cell membrane. in this study, the expression vector pdart was constructed by inserting tlidef, genes encoding the abc transporter, along with the construct of the lipase abc transporter recognition domain (lard), into pdsk519, a widely used shuttl ...	2015	25548043
research into acetone removal from air by biofiltration using a biofilter with straight structure plates.	the biological air treatment method is based on the biological destruction of organic compounds using certain cultures of microorganisms. this method is simple and may be applied in many branches of industry. the main element of biological air treatment devices is a filter charge. tests were carried out using a new-generation laboratory air purifier with a plate structure. this purifier is called biofilter. the biofilter has a special system for packing material humidification which does not req ...	2015	26019659
draft genome sequences of pseudomonas fluorescens strains pa4c2 and pa3g8 and pseudomonas putida pa14h7, three biocontrol bacteria against dickeya phytopathogens.	pseudomonas fluorescens strains pa4c2 and pa3g8 and pseudomonas putida strain pa14h7 were isolated from potato rhizosphere and show an ability to inhibit the growth of dickeya phytopathogens. here, we report their draft genome sequences, which provide a basis for understanding the molecular mechanisms involved in antibiosis against dickeya.	2015	25635023
comparative genomic analysis and phenazine production of pseudomonas chlororaphis, a plant growth-promoting rhizobacterium.	pseudomonas chlororaphis ht66, a plant growth-promoting rhizobacterium that produces phenazine-1-carboxamide with high yield, was compared with three genomic sequenced p. chlororaphis strains, gp72, 30-84 and o6. the genome sizes of four strains vary from 6.66 to 7.30 mb. comparisons of predicted coding sequences indicated 4833 conserved genes in 5869-6455 protein-encoding genes. phylogenetic analysis showed that the four strains are closely related to each other. its competitive colonization in ...	2015	26484173
functional amyloids keep quorum-sensing molecules in check.	the mechanism by which extracellular metabolites, including redox mediators and quorum-sensing signaling molecules, traffic through the extracellular matrix of biofilms is poorly explored. we hypothesize that functional amyloids, abundant in natural biofilms and possessing hydrophobic domains, retain these metabolites. using surface plasmon resonance, we demonstrate that the quorum-sensing (qs) molecules, 2-heptyl-3-hydroxy-4(1h)-quinolone and n-(3-oxododecanoyl)-l-homoserine lactone, and the re ...	2015	25586180
choosing a suitable method for the identification of replication origins in microbial genomes.	as the replication of genomic dna is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. making sense of dna replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. thus, clearly comprehending the positions and sequences of replicat ...	2015	26483774
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 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
structural and mechanistic insights into the pseudomonas fluorescens 2-nitrobenzoate 2-nitroreductase nbaa.	the bacterial 2-nitroreductase nbaa is the primary enzyme initiating the degradation of 2-nitrobenzoate (2-nba), and its activity is controlled by posttranslational modifications. to date, the structure of nbaa remains to be elucidated. in this study, the crystal structure of a cys194ala nbaa mutant was determined to a 1.7-å resolution. the substrate analog 2-nba methyl ester was used to decipher the substrate binding site by inhibition of the wild-type nbaa protein. tandem mass spectrometry sho ...	2015	26025888
metabolism of β-valine via a coa-dependent ammonia lyase pathway.	pseudomonas species strain sbv1 can rapidly grow on medium containing β-valine as a sole nitrogen source. the tertiary amine feature of β-valine prevents direct deamination reactions catalyzed by aminotransferases, amino acid dehydrogenases, and amino acid oxidases. however, lyase- or aminomutase-mediated conversions would be possible. to identify enzymes involved in the degradation of β-valine, a pssbv1 gene library was prepared and used to complement the β-valine growth deficiency of a closely ...	2015	26004802
deinococcus as new chassis for industrial biotechnology: biology, physiology and tools.	deinococcus spp are among the most radiation-resistant micro-organisms that have been discovered. they show remarkable resistance to a range of damage caused by ionizing radiation, desiccation, uv radiation and oxidizing agents. traditionally, escherichia coli and saccharomyces cerevisiae have been the two platforms of choice for engineering micro-organisms for biotechnological applications, because they are well understood and easy to work with. however, in recent years, researchers have begun ...	2015	25809882
characterization of chromosomal and megaplasmid partitioning loci in thermus thermophilus hb27.	in low-copy-number plasmids, the partitioning loci (par) act to ensure proper plasmid segregation and copy number maintenance in the daughter cells. in many bacterial species, par gene homologues are encoded on the chromosome, but their function is much less understood. in the two-replicon, polyploid genome of the hyperthermophilic bacterium thermus thermophilus, both the chromosome and the megaplasmid encode par gene homologues (parabc and parabm, respectively). the mode of partitioning of the ...	2015	25909452
challenges and opportunities for customizing polyhydroxyalkanoates.	polyhydroxyalkanoates (phas) as an alternative to synthetic plastics have been gaining increasing attention. being natural in their origin, phas are completely biodegradable and eco-friendly. however, consistent efforts to exploit this biopolymer over the last few decades have not been able to pull phas out of their nascent stage, inspite of being the favorite of the commercial world. the major limitations are: (1) the high production cost, which is due to the high cost of the feed and (2) poor ...	2015	26063933
supramolecular protein assembly supports immobilization of a cytochrome p450 monooxygenase system as water-insoluble gel.	diverse applications of the versatile bacterial cytochrome p450 enzymes (p450s) are hampered by their requirement for the auxiliary proteins, ferredoxin reductases and ferredoxins, that transfer electrons to p450s. notably, this limits the use of p450s as immobilized enzymes for industrial purposes. herein, we demonstrate the immobilization of a bacterial p450 and its redox protein partners by supramolecular complex formation using a self-assembled heterotrimeric protein. employment of homodimer ...	2015	25733255
hydrazidase, a novel amidase signature enzyme that hydrolyzes acylhydrazides.	the degradation mechanisms of natural and artificial hydrazides have been elucidated. here we screened and isolated bacteria that utilize the acylhydrazide 4-hydroxybenzoic acid 1-phenylethylidene hydrazide (hbph) from soils. physiological and phylogenetic studies identified one bacterium as microbacterium sp. strain hm58-2, from which we purified intracellular hydrazidase, cloned its gene, and prepared recombinant hydrazidase using an escherichia coli expression system. the microbacterium sp. h ...	2015	25583978
efflux pump-deficient mutants as a platform to search for microbes that produce antibiotics.	pseudomonas putida dot-t1e-18 is a strain deficient in the major antibiotic efflux pump (ttgabc) that exhibits an overall increased susceptibility to a wide range of drugs when compared with the wild-type strain. we used this strain as a platform to search for microbes able to produce antibiotics that inhibit growth. a collection of 2400 isolates from soil, sediments and water was generated and a drop assay developed to identify, via growth inhibition halos, strains that prevent the growth of do ...	2015	26059350
microbial community in high arsenic shallow groundwater aquifers in hetao basin of inner mongolia, china.	a survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in hetao basin, inner mongolia, using the 454 pyrosequencing approach. a total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (otus). groundwater and sediment samples were divided into low and high arse ...	2015	25970606
pan-genome dynamics of pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite.	phylogenetic heterogeneity across pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. here, we sequenced a stress tolerant genotype i.e. pseudomonas sp. strain rl isolated from a hexachlorocyclohexane (hch) contaminated pond (45 mg of total hch g(-1) sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to p. stutzeri, p. mendoc ...	2015	25898829
nitrogen removal from micro-polluted reservoir water by indigenous aerobic denitrifiers.	treatment of micro-polluted source water is receiving increasing attention because of environmental awareness on a global level. we isolated and identified aerobic denitrifying bacteria zoogloea sp. n299, acinetobacter sp. g107, and acinetobacter sp. 81y and used these to remediate samples of their native source water. we first domesticated the isolated strains in the source water, and the 48-h nitrate removal rates of strains n299, g107, and 81y reached 33.69%, 28.28%, and 22.86%, respectively, ...	2015	25867475
draft genome sequence of pseudomonas toyotomiensis kf710, a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil.	pseudomonas toyotomiensis kf710 utilizes biphenyl and degrades polychlorinated biphenyls (pcbs). here, we report the genome sequence of the kf710 strain, consisting of 5,596,721 bp with 5,155 coding sequences. the biphenyl catabolic genes were almost identical to those of pseudomonas pseudoalcaligenes kf707, one of the most well-characterized biphenyl-utilizing strains.	2015	25838482
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
chemotaxis and degradation of organophosphate compound by a novel moderately thermo-halo tolerant pseudomonas sp. strain bur11: evidence for possible existence of two pathways for degradation.	an organophosphate (op) degrading chemotactic bacterial strain bur11 isolated from an agricultural field was identified as a member of pseudomonas genus on the basis of its 16s rrna gene sequence. the strain could utilize parathion, chlorpyrifos and their major hydrolytic intermediates as sole source of carbon for its growth and exhibited positive chemotactic response towards most of them. optimum concentration of parathion for its growth was recorded to be 200 ppm and 62% of which was degraded ...	2015	26587344
efficacy of ph elevation as a bactericidal strategy for treating ballast water of freight carriers.	treatment of ship ballast water with sodium hydroxide (naoh) is one method currently being developed to minimize the risk to introduce aquatic invasive species. the bactericidal capability of sodium hydroxide was determined for 148 bacterial strains from ballast water collected in 2009 and 2010 from the m/v indiana harbor, a bulk-freight carrier plying the laurentian great lakes, usa. primary culture of bacteria was done using brain heart infusion agar and a developmental medium. strains were ch ...	2015	26257948
biotechnological production of 1,2,4-butanetriol: an efficient process to synthesize energetic material precursor from renewable biomass.	1,2,4-butanetriol (bt) is a valuable chemical with extensive applications in many different fields. the traditional chemical routes to synthesize bt suffer from many drawbacks, e.g., harsh reaction conditions, multiple steps and poor selectivity, limiting its industrial production. in this study, an engineered escherichia coli strain was constructed to produce bt from xylose, which is a major component of the lignocellulosic biomass. through the coexpression of a xylose dehydrogenase (ccxylb) an ...	2015	26670289
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
structural and biochemical characterization of the francisella tularensis pathogenicity regulator, macrophage locus protein a (mgla).	francisella tularensis is one of the most infectious bacteria known and is the etiologic agent of tularemia. francisella virulence arises from a 33 kilobase (kb) pathogenicity island (fpi) that is regulated by the macrophage locus protein a (mgla) and the stringent starvation protein a (sspa). these proteins interact with both rna polymerase (rnap) and the pathogenicity island gene regulator (pigr) to activate fpi transcription. however, the molecular mechanisms involved are not well understood. ...	2015	26121147
identification of novel mycobacterium tuberculosis cd4 t-cell antigens via high throughput proteome screening.	elicitation of cd4 ifn-gamma t cell responses to mycobacterium tuberculosis (mtb) is a rational vaccine strategy to prevent clinical tuberculosis. diagnosis of mtb infection is based on t-cell immune memory to mtb antigens. the mtb proteome contains over four thousand open reading frames (orfs). we conducted a pilot antigen identification study using 164 mtb proteins and mtb-specific t-cells expanded in vitro from 12 persons with latent mtb infection. enrichment of mtb-reactive t-cells from pbmc ...	2015	25857935
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
adaptation of the autotrophic acetogen sporomusa ovata to methanol accelerates the conversion of co2 to organic products.	acetogens are efficient microbial catalysts for bioprocesses converting c1 compounds into organic products. here, an adaptive laboratory evolution approach was implemented to adapt sporomusa ovata for faster autotrophic metabolism and co2 conversion to organic chemicals. s. ovata was first adapted to grow quicker autotrophically with methanol, a toxic c1 compound, as the sole substrate. better growth on different concentrations of methanol and with h2-co2 indicated the adapted strain had a more ...	2015	26530351
biocatalytic production of trehalose from maltose by using whole cells of permeabilized recombinant escherichia coli.	trehalose is a non-reducing disaccharide, which can protect proteins, lipid membranes, and cells from desiccation, refrigeration, dehydration, and other harsh environments. trehalose can be produced by different pathways and trehalose synthase pathway is a convenient, practical, and low-cost pathway for the industrial production of trehalose. in this study, 3 candidate tres genes were screened from genomic databases of pseudomonas and expressed in escherichia coli. one of them from p. stutzeri a ...	2015	26462117
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
selection and evaluation of reference genes for reverse transcription-quantitative pcr expression studies in a thermophilic bacterium grown under different culture conditions.	the phylum deinococcus-thermus is a deeply-branching lineage of bacteria widely recognized as one of the most extremophilic. members of the thermus genus are of major interest due to both their bioremediation and biotechnology potentials. however, the molecular mechanisms associated with these key metabolic pathways remain unknown. reverse-transcription quantitative pcr (rt-qpcr) is a high-throughput means of studying the expression of a large suite of genes over time and under different conditi ...	2015	26115538
nonphotosynthetic pigments as potential biosignatures.	previous work on possible surface reflectance biosignatures for earth-like planets has typically focused on analogues to spectral features produced by photosynthetic organisms on earth, such as the vegetation red edge. although oxygenic photosynthesis, facilitated by pigments evolved to capture photons, is the dominant metabolism on our planet, pigmentation has evolved for multiple purposes to adapt organisms to their environment. we present an interdisciplinary study of the diversity and detect ...	2015	25941875
bioremediation of polyaromatic hydrocarbons (pahs) using rhizosphere technology.	the remediation of polluted sites has become a priority for society because of increase in quality of life standards and the awareness of environmental issues. over the past few decades there has been avid interest in developing in situ strategies for remediation of environmental contaminants, because of the high economic cost of physicochemical strategies, the biological tools for remediation of these persistent pollutants is the better option. major foci have been considered on persistent orga ...	2015	26221084
complete genome sequence analysis of two pseudomonas plecoglossicida phages, potential therapeutic agents.	pseudomonas plecoglossicida is a lethal pathogen of ayu (plecoglossus altivelis) in japan and is responsible for substantial economic costs to ayu culture. previously, we demonstrated the efficacy of phage therapy against p. plecoglossicida infection using two lytic phages (pppw-3 and pppw-4) (s. c. park, i. shimamura, m. fukunaga, k. mori, and t. nakai, appl environ microbiol 66:1416-1422, 2000, http://dx.doi.org/10.1128/aem.66.4.1416-1422.2000; s. c. park and t. nakai, dis aquat org 53:33-39, ...	2015	25416766
extraordinary solute-stress tolerance contributes to the environmental tenacity of mycobacteria.	mycobacteria are associated with a number of well-characterized diseases, yet we know little about their stress biology in natural ecosystems. this study focuses on the isolation and characterization of strains from yellowstone national park (ynp) and glacier national park (gnp; usa), the majority of those identified were mycobacterium parascrofulaceum, mycobacterium avium (ynp) or mycobacterium gordonae (gnp). generally, their windows for growth spanned a temperature range of > 60 °c; selected ...	2015	26059202
nicotine-degrading microorganisms and their potential applications.	nicotine-degrading microorganisms (ndms) are a special microbial group which can use nicotine as the sole carbon and nitrogen source for growth. since the 1950s, the bioconversion of nicotine by microbes has received increasing attention, and several ndms have been identified, such as arthrobacter nicotinovorans, microsporum gypseum, pellicularia filamentosa jts-208, and pseudomonas sp. 41. in recent years, increasing numbers of ndms have been isolated and identified from tobacco plantation soil ...	2015	25805341
vanadium removal from ld converter slag using bacteria and fungi.	removal of vanadium from linz-donawits (ld) converter slag was investigated by means of three different species of microbial systems: acidithiobacillus thiooxidans (autotrophic bacteria), pseudomonas putida (heterotrophic bacteria) and aspergillus niger (fungi). the bioleaching process was carried out in both one-step and two-step process and the leaching efficiencies in both cases were compared. formation of inorganic and organic acids during the leaching process caused mobilization of vanadium ...	2015	25697901
pyrosequencing analysis of microbial community and food-borne bacteria on restaurant cutting boards collected in seri kembangan, malaysia, and their correlation with grades of food premises.	this study adopts the pyrosequencing technique to identify bacteria present on 26 kitchen cutting boards collected from different grades of food premises around seri kembangan, a city in malaysia. pyrosequencing generated 452,401 of total reads of otus with an average of 1.4×10(7) bacterial cells/cm(2). proteobacteria, firmicutes and bacteroides were identified as the most abundant phyla in the samples. taxonomic richness was generally high with >1000 operational taxonomic units (otus) observed ...	2015	25679309
contribution of arbuscular mycorrhizal fungi and/or bacteria to enhancing plant drought tolerance under natural soil conditions: effectiveness of autochthonous or allochthonous strains.	autochthonous microorganisms [a consortium of arbuscular-mycorrhizal (am) fungi and bacillus thuringiensis (bt)] were assayed and compared to rhizophagus intraradices (ri), bacillus megaterium (bm) or pseudomonas putida (psp) and non-inoculation on trifolium repens in a natural arid soil under drought conditions. the autochthonous bacteria bt and the allochthonous bacteria psp increased nutrients and the relative water content and decreased stomatal conductance, electrolyte leakage, proline and ...	2015	25462971
efficacy of lactoferricin b in controlling ready-to-eat vegetable spoilage caused by pseudomonas spp.	the microbial content of plant tissues has been reported to cause the spoilage of ca. 30% of chlorine-disinfected fresh vegetables during cold storage. the aim of this work was to evaluate the efficacy of antimicrobial peptides in controlling microbial vegetable spoilage under cold storage conditions. a total of 48 bacterial isolates were collected from ready-to-eat (rte) vegetables and identified as belonging to acinetobacter calcoaceticus, aeromonas media, pseudomonas cichorii, pseudomonas flu ...	2015	26453993
[oil biodegradation by microbial-plant associations].	the degradation of petroleum hydrocarbons by plant-microbial associations, as well as the peculiarities of the interaction between microorganisms in consortium and the associated plants, have been studied. it was shown that degrader microorganisms that are part of the consortium rhodococcus erythropolis s26, acinetobacter baumannii 1 b, acinetobacter baumannii 7, and pseudomonas putida f701 were effective in the degradation of oil and were good colonizers of plant roots (barley). the efficiency ...	2015	26027354
lucy: a versatile new fluorescent reporter protein.	we report on the discovery, isolation, and use of a novel yellow fluorescent protein. lucigen yellow (lucy) binds one fad molecule within its core, thus shielding it from water and maintaining its structure so that fluorescence is 10-fold higher than freely soluble fad. lucy displays excitation and emission spectra characteristic of fad, with 3 excitation peaks at 276 nm, 377 nm, and 460 nm and a single emission peak at 530 nm. these excitation and emission maxima provide the large stokes shift ...	2015	25906065
sequencing of plasmids pambl1 and pambl2 from pseudomonas aeruginosa reveals a blavim-1 amplification causing high-level carbapenem resistance.	carbapenemases are a major concern for the treatment of infectious diseases caused by gram-negative bacteria. although plasmids are responsible for the spread of resistance genes among these pathogens, there is limited information on the nature of the mobile genetic elements carrying carbapenemases in pseudomonas aeruginosa.	2015	26209313
development of a growth-dependent selection system for identification of l-threonine aldolases.	threonine aldolases (tas) are useful enzymes for the synthesis of β-hydroxy-α-amino acids due to their capability to catalyze asymmetric aldol reactions. starting from two prochiral compounds, an aldehyde and glycine, two chiral stereocenters were formed in a single step via c-c bond formation. owing to poor diastereoselectivity and low activity, the enzymatic synthesis of β-hydroxy-α-amino acids by tas is still a challenge. for identification of new tas, a growth-dependent selection system in p ...	2015	25616526
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