Publications

engineering protocells: prospects for self-assembly and nanoscale production-lines.	the increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic "organisms" with a myriad of possible capabilities. the prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. until now, artificial cell technology has been largely restricted to the modification and metabolic eng ...	2015	25815781
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
a duplex pcr assay for the detection of ralstonia solanacearum phylotype ii strains in musa spp.	banana wilt outbreaks that are attributable to moko disease-causing strains of the pathogen ralstonia solanacearum (rs) remain a social and economic burden for both multinational corporations and subsistence farmers. all known moko strains belong to the phylotype ii lineage, which has been previously recognized for its broad genetic basis. moko strains are paraphyletic and are distributed among seven related but distinct phylogenetic clusters (sequevars) that are potentially major threats to mus ...	2015	25811378
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
genome-wide investigation of the genes involved in nicotine metabolism in pseudomonas putida j5 by tn5 transposon mutagenesis.	pseudomonas putida j5 is an efficient nicotine-degrading bacterial strain isolated from the tobacco rhizosphere. we successfully performed a comprehensive whole-genome analysis of nicotine metabolism-associated genes by tn5 transposon mutagenesis in p. putida j5. a total of 18 mutants with unique insertions screened from 16,324 tn5-transformants failed to use nicotine as the sole carbon source. flanking sequences of the tn5 transposon were cloned with a shotgun method from all of the nicotine-gr ...	2015	25808517
mammalian synthetic biology: emerging medical applications.	in this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. we start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. a comprehensive list of on-off switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. subsequently, boolean logic gates, synthetic mammalian oscillators and toggle ...	2015	25808341
iaa producing enterobacter sp. i-3 as a potent bio-herbicide candidate for weed control: a special reference with lettuce growth inhibition.	development of bio-herbicides is an emerging method to weed management in agricultural field. very few studies were conducted on identification of microbial bio-herbicides to weed control. the present study was aimed to isolate and identify the effective bio-herbicide potential bacterium from soil and assess their role on plant growth inhibition. three-hundred and one rhizobacteria were isolated from agriculture field soil samples collected from various parts of republic of korea. two bacterial ...	2015	25805908
the intracellular scots pine shoot symbiont methylobacterium extorquens dsm13060 aggregates around the host nucleus and encodes eukaryote-like proteins.	endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. while endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells, methylobacterium extorquens strain dsm13060 is a facultatively intracellular symbiont of the meristematic cells of scots pine (pinus sylvestris l.) shoot tips. the bacterium promotes host growth and development without the production of known plant growth-st ...	2015	25805725
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
bacterial cell surface properties: role of loosely bound extracellular polymeric substances (lb-eps).	this study investigated the effect of loosely bound extracellular polymeric substances (lb-eps) on the comprehensive surface properties of four bacteria (bacillus subtilis, streptococcus suis, escherichia coli and pseudomonas putida). the removal of lb-eps from bacterial surfaces by high-speed centrifugation (12,000×g) was confirmed by sem images. viability tests showed that the percentages of viable cells ranged from 95.9% to 98.0%, and no significant difference was found after treatment (p>0.0 ...	2015	25805151
[comparison of phenotypic methods for the detection of beta-lactamases mbl in strains from the enterobacteriaceae family and non-fermentative bacilli isolated from clinical specimens].	bacterial resistance is growing because of treatment a broad spectrum antibio- tics. gram-negative pathogens which producing carbapenemase are a one of major problem in many hospitals. rapid detection those strains provide an early inhibition of infection and control the expansion of microorganisms. the aim of work was to characterize the frequency of appearance mbls in specific groups of gram-negative bacilli which are resistant or intermediate to at least one of carbapenems.	2014	25804071
genetic analysis of plant endophytic pseudomonas putida bp25 and chemo-profiling of its antimicrobial volatile organic compounds.	black pepper associated bacterium bp25 was isolated from root endosphere of apparently healthy cultivar panniyur-5 that protected black pepper against phytophthora capsici and radopholus similis - the major production constraints. the bacterium was characterized and mechanisms of its antagonistic action against major pathogens are elucidated. the polyphasic phenotypic analysis revealed its identity as pseudomonas putida. multi locus sequence typing revealed that the bacterium shared gene sequenc ...	2015	25801973
an integrated view of redox and catalytic properties of b-type ppdyp from pseudomonas putida met94 and its distal variants.	ppdyp from pseudomonas putida met94 is an extremely versatile b-type dye-decolourising peroxidase (dyp) capable of efficient oxidation of a wide range of anthraquinonic and azo dyes, phenolic substrates, the non-phenolic veratryl alcohol and even manganese and ferrous ions. in reaction with h2o2 it forms a stable compound i at a rate of (1.4±0.3)×10(6)m(-1)s(-1), comparable to those of classical peroxidases and other dyps. we provide the first report of standard redox potential (e(0')) of the co ...	2015	25797439
continuous ozonation treatment of ofloxacin: transformation products, water matrix effect and aquatic toxicity.	the continuous ozonation of the antibiotic ofloxacin (ofx) has been performed using a synthetic water matrix and in a sewage treatment plant (stp) effluent. the aim was to study the effect of the water matrix on the ozonation with particular emphasis on the aquatic toxicity of treated water. ofx was completely removed in both water matrices, although the amount of ozone consumed for its depletion was strongly matrix-dependent. the extent of mineralization was limited and a number of intermediate ...	2015	25796038
hierarchy of carbon source utilization in soil bacteria: hegemonic preference for benzoate in complex aromatic compound mixtures degraded by cupriavidus pinatubonensis strain jmp134.	cupriavidus pinatubonensis jmp134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. however, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. we carried out a systematic study on the substrate preference of c. pinatubonensis jmp134 g ...	2015	25795675
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
the challenge of efflux-mediated antibiotic resistance in gram-negative bacteria.	the global emergence of multidrug-resistant gram-negative bacteria is a growing threat to antibiotic therapy. the chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. multidrug pumps, particularly those represented by the clinically relevant acrab-tolc and mex pumps of the resistance-nodulation-division (rnd) superfamily, not only mediate intrinsic and acquired mult ...	2015	25788514
carnitine in bacterial physiology and metabolism.	carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. in bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized thr ...	2015	25787873
identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution.	proline racemase (pror) is a member of the pyridoxal 5'-phosphate-independent racemase family, and is involved in the stickland reaction (fermentation) in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic trypanosoma. hydroxyproline epimerase (hype), which is in the same protein family as pror, catalyzes the first step of the trans-4-hydroxy-l-proline metabolism of bacteria. their substrate specificities were previously considered to ...	2015	25786142
proteomics as the final step in the functional metagenomics study of antimicrobial resistance.	the majority of clinically applied antimicrobial agents are derived from natural products generated by soil microorganisms and therefore resistance is likely to be ubiquitous in such environments. this is supported by the fact that numerous clinically important resistance mechanisms are encoded within the genomes of such bacteria. advances in genomic sequencing have enabled the in silico identification of putative resistance genes present in these microorganisms. however, it is not sufficient to ...	2015	25784907
interdomain hydrophobic interactions modulate the thermostability of microbial esterases from the hormone-sensitive lipase family.	microbial hormone-sensitive lipases (hsls) contain a cap domain and a catalytic domain. however, it remains unclear how the cap domain interacts with the catalytic domain to maintain the stability of microbial hsls. here, we isolated an hsl esterase, e40, from a marine sedimental metagenomic library. e40 exhibited the maximal activity at 45 °c and was quite thermolabile, with a half-life of only 2 min at 40 °c, which may be an adaptation of e40 to the permanently cold sediment environment. the s ...	2015	25771540
relationship between heat-labile enterotoxin secretion capacity and virulence in wild type porcine-origin enterotoxigenic escherichia coli strains.	heat-labile enterotoxin (lt) is an important virulence factor secreted by some strains of enterotoxigenic escherichia coli (etec). the prototypic human-origin strain h10407 secretes lt via a type ii secretion system (t2ss). we sought to determine the relationship between the capacity to secrete lt and virulence in porcine-origin wild type (wt) etec strains. sixteen wt etec strains isolated from cases of severe diarrheal disease were analyzed by gm1ganglioside enzyme-linked immunosorbent assay to ...	2015	25768732
crystal structure of the n-acetylmuramic acid α-1-phosphate (murnac-α1-p) uridylyltransferase muru, a minimal sugar nucleotidyltransferase and potential drug target enzyme in gram-negative pathogens.	the n-acetylmuramic acid α-1-phosphate (murnac-α1-p) uridylyltransferase muru catalyzes the synthesis of uridine diphosphate (udp)-murnac, a crucial precursor of the bacterial peptidoglycan cell wall. muru is part of a recently identified cell wall recycling pathway in gram-negative bacteria that bypasses the general de novo biosynthesis of udp-murnac and contributes to high intrinsic resistance to the antibiotic fosfomycin, which targets udp-murnac de novo biosynthesis. to provide insights into ...	2015	25767118
5-methyl phenazine-1-carboxylic acid: a novel bioactive metabolite by a rhizosphere soil bacterium that exhibits potent antimicrobial and anticancer activities.	a new rhizosphere soil bacterium that exhibits antimicrobial potential against human pathogens was isolated. on the basis of 16s ribosomal rna nucleotide sequence homology and subsequent phylogenetic tree analysis, the strain puw5 was identified as pseudomonas putida. a bioactive metabolite was extracted and purified using silica gel column chromatography and preparative hplc. characterization of metabolite was done by employing fourier transform infrared spectroscopy (ftir), nuclear magnetic re ...	2015	25765238
bacterial motion in narrow capillaries.	motile bacteria often have to pass through small tortuous pores in soil or tissue of higher organisms. however, their motion in this prevalent type of niche is not fully understood. here, we modeled it with narrow glass capillaries and identified a critical radius (rc) for bacterial motion. near the surface of capillaries narrower than that, the swimming trajectories are helices. in larger capillaries, they swim in distorted circles. under non-slip condition, the peritrichous escherichia coli sw ...	2014	25764548
bacterial motion in narrow capillaries.	motile bacteria often have to pass through small tortuous pores in soil or tissue of higher organisms. however, their motion in this prevalent type of niche is not fully understood. here, we modeled it with narrow glass capillaries and identified a critical radius (rc) for bacterial motion. near the surface of capillaries narrower than that, the swimming trajectories are helices. in larger capillaries, they swim in distorted circles. under non-slip condition, the peritrichous escherichia coli sw ...	2014	25764548
beyond iron: non-classical biological functions of bacterial siderophores.	bacteria secrete small molecules known as siderophores to acquire iron from their surroundings. for over 60 years, investigations into the bioinorganic chemistry of these molecules, including fundamental coordination chemistry studies, have provided insight into the crucial role that siderophores play in bacterial iron homeostasis. the importance of understanding the fundamental chemistry underlying bacterial life has been highlighted evermore in recent years because of the emergence of antibiot ...	2015	25764171
a novel arabinose-inducible genetic operation system developed for clostridium cellulolyticum.	clostridium cellulolyticum and other cellulolytic clostridium strains are natural producers of lignocellulosic biofuels and chemicals via the consolidated bioprocessing (cbp) route, and systems metabolic engineering is indispensable to meet the cost-efficient demands of industry. several genetic tools have been developed for clostridium strains, and an efficient and stringent inducible genetic operation system is still required for the precise regulation of the target gene function.	2015	25763107
further characterization of o-nitrobenzaldehyde degrading bacterium pseudomonas sp. onba-17 and deduction on its metabolic pathway.	a previously reported o-nitrobenzaldehyde (onba) degrading bacterium pseudomonas sp. onba-17 was further identified and characterized. based on results of dna base composition and dna-dna hybridization, the strain was identified as p. putida. its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. higher removal rate was achieved under shaking conditions. all tested onba with different initial concentrations could be completely degraded within 5 d. in addi ...	2014	25763034
further characterization of o-nitrobenzaldehyde degrading bacterium pseudomonas sp. onba-17 and deduction on its metabolic pathway.	a previously reported o-nitrobenzaldehyde (onba) degrading bacterium pseudomonas sp. onba-17 was further identified and characterized. based on results of dna base composition and dna-dna hybridization, the strain was identified as p. putida. its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. higher removal rate was achieved under shaking conditions. all tested onba with different initial concentrations could be completely degraded within 5 d. in addi ...	2014	25763034
screening and optimization of low-cost medium for pseudomonas putida rs-198 culture using rsm.	the plant growth-promoting rhizobacterial strain pseudomonas putida rs-198 was isolated from salinized soils from xinjiang province. we optimized the composition of the low-cost medium of p. putida rs-198 based on its bacterial concentration, as well as its phosphate-dissolving and indole acetic acid (iaa)-producing capabilities using the response surface methodology (rsm), and a mathematical model was developed to show the effect of each medium component and its interactions on phosphate dissol ...	2014	25763026
screening and optimization of low-cost medium for pseudomonas putida rs-198 culture using rsm.	the plant growth-promoting rhizobacterial strain pseudomonas putida rs-198 was isolated from salinized soils from xinjiang province. we optimized the composition of the low-cost medium of p. putida rs-198 based on its bacterial concentration, as well as its phosphate-dissolving and indole acetic acid (iaa)-producing capabilities using the response surface methodology (rsm), and a mathematical model was developed to show the effect of each medium component and its interactions on phosphate dissol ...	2014	25763026
pgprs and nitrogen-fixing legumes: a perfect team for efficient cd phytoremediation?	cadmium (cd) is a toxic, biologically non-essential and highly mobile metal that has become an increasingly important environmental hazard to both wildlife and humans. in contrast to conventional remediation technologies, phytoremediation based on legume-rhizobia symbiosis has emerged as an inexpensive decontamination alternative which also revitalize contaminated soils due to the role of legumes in nitrogen cycling. in recent years, there is a growing interest in understanding symbiotic legume- ...	2015	25763004
a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria.	luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ...	2015	25759807
resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms.	decomposition of organic matter is an important ecosystem process governed in part by bacteria. the process of decomposition is expected to benefit from interspecific bacterial interactions such as resource partitioning and facilitation. however, the relative importance of resource niche breadth (metabolic diversity) and resource niche overlap (functional redundancy) on decomposition and the temporal stability of ecosystem processes received little scientific attention. therefore, this study aim ...	2015	25759686
construction of a novel phenol synthetic pathway in escherichia coli through 4-hydroxybenzoate decarboxylation.	phenol is a bulk chemical with lots of applications in the chemical industry. fermentative production of phenol had been realized in both pseudomonas putida and escherichia coli by recruiting tyrosine phenol-lyase (tpl). the tpl pathway needs tyrosine as the direct precursor for phenol production. in this work, a novel phenol synthetic pathway was created in e. coli by recruiting 4-hydroxybenzoate decarboxylase, which can convert 4-hydroxybenzoate to phenol and carbon dioxide. activating 3-deoxy ...	2015	25758959
next generation sequencing analysis reveals that the ribonucleases rnase ii, rnase r and pnpase affect bacterial motility and biofilm formation in e. coli.	the rna steady-state levels in the cell are a balance between synthesis and degradation rates. although transcription is important, rna processing and turnover are also key factors in the regulation of gene expression. in escherichia coli there are three main exoribonucleases (rnase ii, rnase r and pnpase) involved in rna degradation. although there are many studies about these exoribonucleases not much is known about their global effect in the transcriptome.	2015	25757888
effect of silver nanoparticles on pseudomonas putida biofilms at different stages of maturity.	this study determined the effect of silver nanoparticles (agnps) on pseudomonas putida kt2440 biofilms at different stages of maturity. three biofilm stages (1-3, representing early to late stages of development) were identified from bacterial adenosine triphosphate (atp) activity under static (96-well plate) and dynamic conditions (center for disease control and prevention biofilm reactor). extracellular polymeric substance (eps) levels, measured using crystal violet and total carbohydrate assa ...	2015	25756827
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
complete genome sequence of solvent-tolerant pseudomonas putida s12 including megaplasmid ptts12.	pseudomonas putida s12 is a solvent-tolerant gamma-proteobacterium with an extensive track record for production of industrially relevant chemicals. here we report the annotated complete genome sequence of this organism, including the megaplasmid ptts12 which encodes many of the unique features of the s12 strain.	2015	25746905
systematic profiling of indole-3-acetic acid biosynthesis in bacteria using lc-ms/ms.	indole-3-acetic acid (iaa) is produced from tryptophan through five synthesis pathways. a comprehensive method for the quantification of iaa and biosynthesis-related intermediates in a culture medium was developed. sample preparation was simple with protein precipitation. the analytes were separated on a superficially porous c18 silica column and detected by electrospray ionization-tandem mass spectrometry in the positive ion multiple reaction monitoring mode. the limit of detection was 0.05 μm, ...	2015	25746752
engineering sugar utilization and microbial tolerance toward lignocellulose conversion.	production of fuels and chemicals through a fermentation-based manufacturing process that uses renewable feedstock such as lignocellulosic biomass is a desirable alternative to petrochemicals. although it is still in its infancy, synthetic biology offers great potential to overcome the challenges associated with lignocellulose conversion. in this review, we will summarize the identification and optimization of synthetic biological parts used to enhance the utilization of lignocellulose-derived s ...	2015	25741507
promotion of arsenic phytoextraction efficiency in the fern pteris vittata by the inoculation of as-resistant bacteria: a soil bioremediation perspective.	a greenhouse pot experiment was carried out to evaluate the efficiency of arsenic phytoextraction by the fern pteris vittata growing in arsenic-contaminated soil, with or without the addition of selected rhizobacteria isolated from the polluted site. the bacterial strains were selected for arsenic resistance, the ability to reduce arsenate to arsenite, and the ability to promote plant growth. p. vittata plants were cultivated for 4 months in a contaminated substrate consisting of arsenopyrite ci ...	2015	25741356
impact of alkyl polyglucosides surfactant lutensol gd 70 on modification of bacterial cell surface properties.	alkyl polyglucosides, due to their low toxicity and environmental compatibility, could be used in biodegradation of hydrophobic compounds. in this study, the influence of lutensol gd 70 on the cell hydrophobicity and zeta potential was measured. the particle size distribution and surfactant biodegradation were also investigated. microbacterium sp. strain e19, pseudomonas stutzeri strain 9, and the same strain cultivated in stress conditions were used in studies. adding surfactant to the diesel o ...	2015	25741049
bioconversion of styrene to poly(hydroxyalkanoate) (pha) by the new bacterial strain pseudomonas putida nbus12.	styrene is a toxic pollutant commonly found in waste effluents from plastic processing industries. we herein identified and characterized microorganisms for bioconversion of the organic eco-pollutant styrene into a valuable biopolymer medium-chain-length poly(hydroxyalkanoate) (mcl-pha). twelve newly-isolated styrene-degrading pseudomonads were obtained and partial phac genes were detected by pcr in these isolates. these isolates assimilated styrene to produce mcl-pha, forming pha contents betwe ...	2015	25740622
bacterial-biota dynamics of eight bryophyte species from different ecosystems.	despite the importance of bryophyte-associated microorganisms in various ecological aspects including their crucial roles in the soil-enrichment of organic mass and n2 fixation, nonetheless, little is known about the microbial diversity of the bryophyte phyllospheres (epi-/endophytes). to get insights into bacterial community structures and their dynamics on the bryophyte habitats in different ecosystems and their potential biological roles, we utilized the 16s rrna gene pcr-dgge and subsequent ...	2014	25737654
bacterial-biota dynamics of eight bryophyte species from different ecosystems.	despite the importance of bryophyte-associated microorganisms in various ecological aspects including their crucial roles in the soil-enrichment of organic mass and n2 fixation, nonetheless, little is known about the microbial diversity of the bryophyte phyllospheres (epi-/endophytes). to get insights into bacterial community structures and their dynamics on the bryophyte habitats in different ecosystems and their potential biological roles, we utilized the 16s rrna gene pcr-dgge and subsequent ...	2014	25737654
soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation.	salinity is one of the most brutal environmental factors limiting the productivity of crop plants because most of the crop plants are sensitive to salinity caused by high concentrations of salts in the soil, and the area of land affected by it is increasing day by day. for all important crops, average yields are only a fraction - somewhere between 20% and 50% of record yields; these losses are mostly due to drought and high soil salinity, environmental conditions which will worsen in many region ...	2014	25737642
soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation.	salinity is one of the most brutal environmental factors limiting the productivity of crop plants because most of the crop plants are sensitive to salinity caused by high concentrations of salts in the soil, and the area of land affected by it is increasing day by day. for all important crops, average yields are only a fraction - somewhere between 20% and 50% of record yields; these losses are mostly due to drought and high soil salinity, environmental conditions which will worsen in many region ...	2014	25737642
impact of dissolved organic matter on bacterial tactic motility, attachment, and transport.	bacterial dispersal is a key driver of the ecology of microbial contaminant degradation in soils. this work investigated the role of dissolved organic matter (dom) in the motility, attachment, and transport of the soil bacterium pseudomonas putida g7 in saturated porous media. the study is based on the hypothesis that dom quality is critical to triggering tactic motility and, consequently, affects bacterial transport and dispersal. sunflower root exudates, humic acids (ha), and the synthetic ole ...	2015	25734420
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
a reusable immobilization matrix for the biodegradation of phenol at 5000 mg/l.	bacteria-mediated degradation of toxins has been reported as a practical technique for the innocuous removal of toxic organic compounds from water. specifically, immobilized and pre-acclimatized pseudomonas putida has been shown to clear low levels of contaminants (less than 2000 mg/l) from wastewater, wherein the bacteria consumes toxic aromatic compounds as the only source of carbon and energy. here we report the preparation of a high-capacity composite adsorbent as an immobilization matrix fo ...	2015	25733015
biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyalkanoates) by recombinant escherichia coli from glucose.	the polyhydroxyalkanoate (pha) copolymers consisting of short-chain-length (scl) and medium-chain-length (mcl) monomers have various properties ranging from stiff to flexible depending on the molar fraction of the monomer compositions. it has been reported that phag, which is first known as a (r)-3-hydroxyacyl-acyl carrier protein (acp)-coa transferase, actually functions as a 3-hydroxyacyl-acp thioesterase, and the product of pp0763 gene from pseudomonas putida kt2440 has a (r)-3-hydroxyacyl (3 ...	2015	25732207
arsh is an organoarsenical oxidase that confers resistance to trivalent forms of the herbicide monosodium methylarsenate and the poultry growth promoter roxarsone.	environmental organoarsenicals are produced by microorganisms and are introduced anthropogenically as herbicides and antimicrobial growth promoters for poultry and swine. nearly every prokaryote has an ars (arsenic resistance) operon, and some have an arsh gene encoding an atypical flavodoxin. the role of arsh in arsenic resistance has been unclear. here we demonstrate that arsh is an organoarsenical oxidase that detoxifies trivalent methylated and aromatic arsenicals by oxidation to pentavalent ...	2015	25732202
engineering biological approaches for detection of toxic compounds: a new microbial biosensor based on the pseudomonas putida ttgr repressor.	environmental contamination by toxic organic compounds and antimicrobials is one of the causes for the recent surge of multidrug-resistant pathogenic bacteria. monitoring contamination is therefore the first step in containment of antimicrobial resistance and requires the development of simple, sensitive, and quantitative tools that detect a broad spectrum of toxic compounds. in this study, we have engineered a new microbial biosensor based on the ttgr-regulated promoter that controls expression ...	2015	25731724
the quest for a practical synthesis of morphine alkaloids and their derivatives by chemoenzymatic methods.	we became interested in approaches to morphine in the early 1990s following our immersion into the new program on the enzymatic dihydroxylation of aromatics. larry kwart, a former classmate of one of us at rice university, who worked with our group at virginia tech in the mid-1980s, introduced to us the use of blocked mutants of pseudomonas putida (pp39d) for the production of arene-cis-dihydrodiols. larry had gained expertise in microbiology from a postdoctoral stay with david gibson, who disco ...	2015	25730681
third generation cephalosporin resistant enterobacteriaceae and multidrug resistant gram-negative bacteria causing bacteremia in febrile neutropenia adult cancer patients in lebanon, broad spectrum antibiotics use as a major risk factor, and correlation with poor prognosis.	bacteremia remains a major cause of life-threatening complications in patients receiving anticancer chemotherapy. the spectrum and susceptibility profiles of causative microorganisms differ with time and place. data from lebanon are scarce. we aim at evaluating the epidemiology of bacteremia in cancer patients in a university hospital in lebanon, emphasizing antibiotic resistance and risk factors of multi-drug resistant organism (mdro)-associated bacteremia.	2015	25729741
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
gene mdpc plays a regulatory role in the methyl-tert-butyl ether degradation pathway of methylibium petroleiphilum strain pm1.	among the few bacteria known to utilize methyl tert-butyl ether (mtbe) as a sole carbon source, methylibium petroleiphilum pm1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its mtbe degradation pathway is limited. we investigated the role of a putative transcriptional activator gene, mdpc, in the induction of mtbe-degradation genes mdpa (encoding mtbe monooxygenase) and mdpj (encoding tert-butyl alcohol hydroxylase) of strain pm1 in a g ...	2015	25724531
diabetic foot gangrene patient with multi-drug resistant pseudomonas putida infection in karawaci district, indonesia.	pseudomonas putida is a rod-shaped, non fermenting gram-negative organism frequently found in the environment that utilizes aerobic metabolism, previously thought to be of low pathogenicity. it had been reported as cause of skin and soft tissue infection, especially in immunocompromised patients. a female green grocer, 51 year-old came to internal medicine out-patient clinic with gangrene and osteomyelitis on her 1(st), 2(nd) and 3(rd) digit and wound on the sole of the right foot since 1 month ...	2015	25722620
comparative genome analysis reveals the molecular basis of nicotine degradation and survival capacities of arthrobacter.	arthrobacter is one of the most prevalent genera of nicotine-degrading bacteria; however, studies of nicotine degradation in arthrobacter species remain at the plasmid level (plasmid pao1). here, we report the bioinformatic analysis of a nicotine-degrading arthrobacter aurescens m2012083, and show that the moeb and moga genes that are essential for nicotine degradation in arthrobacter are absent from plasmid pao1. homologues of all the nicotine degradation-related genes of plasmid pao1 were foun ...	2015	25721465
an event-driven approach for studying gene block evolution in bacteria.	gene blocks are genes co-located on the chromosome. in many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. the conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. an open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. these models, however, are not generally applicable to ...	2015	25717195
structural studies on laz, a promiscuous anticancer neisserial protein.	azurin and laz (lipidated azurin) are 2 bacterial proteins with anticancer, anti-viral and anti-parasitic activities. azurin, isolated from the bacterium pseudomonas aeruginosa, termed paz, demonstrates anticancer activity against a range of cancers but not against brain tumors. in contrast, laz is produced by members of gonococci/meningococci, including neisseria meningitides which can cross the blood-brain barrier to infect brain meninges. it has been previously reported that laz has an additi ...	2015	25714335
molecular dynamics investigation of the substrate binding mechanism in carboxylesterase.	a recombinant carboxylesterase, cloned from pseudomonas putida and designated as rppe, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2'-chlorophenyl)acetate (rac-aco-cpa) with excellent (s)-enantioselectivity. semirational design of the enzyme showed that the w187h variant could increase the activity by ∼100-fold compared to the wild type (wt) enzyme. in this study, we performed all-atom molecular dynamics (md) simulations of both apo-rppe and rppe in complex with (s)-aco-cp ...	2015	25711934
the crc/crcz-crcy global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in pseudomonas putida.	in metabolically versatile bacteria, carbon catabolite repression (ccr) facilitates the preferential assimilation of the most efficient carbon sources, improving growth rates and fitness. in pseudomonas putida, the crc and hfq proteins and the crcz and crcy small rnas, which are believed to antagonize crc/hfq, are key players in ccr. unlike that seen in other bacterial species, succinate and glucose elicit weak ccr in this bacterium. in the present work, metabolic, transcriptomic and constraint- ...	2015	25711694
genes involved in nutrient competition by pseudomonas putida jbc17 to suppress green mold in postharvest satsuma mandarin.	understanding the mechanisms underlying biocontrol activity in biocontrol agents is indispensable to implement biological control. however, the understanding of specific mechanisms for nutrient competition in nutrient limited environments is still limited. this study was performed to control green mold of postharvest satsuma mandarin (mandarin) using pseudomonas putida jbc17 (jbc17), and identify the genes involved in nutrient competition. treatment with jbc17 on wounded mandarin fruits at a con ...	2015	25707389
natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools.	genetically encoded optical tools have revolutionized modern biology by allowing detection and control of biological processes with exceptional spatiotemporal precision and sensitivity. natural photoreceptors provide researchers with a vast source of molecular templates for engineering of fluorescent proteins, biosensors, and optogenetic tools. here, we give a brief overview of natural photoreceptors and their mechanisms of action. we then discuss fluorescent proteins and biosensors developed fr ...	2015	25706899
assessing the antimicrobial activity of polyisoprene based surfaces.	there has been an intense research effort in the last decades in the field of biofouling prevention as it concerns many aspects of everyday life and causes problems to devices, the environment, and human health. many different antifouling and antimicrobial materials have been developed to struggle against bacteria and other micro- and macro-organism attachment to different surfaces. however the "miracle solution" has still to be found. the research presented here concerns the synthesis of bio-ba ...	2015	25706513
arbekacin treatment of a patient infected with a pseudomonas putida producing a metallo-beta-lactamase.	treatment of infections caused by multidrug-resistant pseudomonas species is difficult because few antibiotics active against such organisms are available. arbekacin, a relatively new aminoglycoside, is effective against pseudomonas spp. in vitro. however, no clinical report on arbekacin treatment of a human infection with a multidrug-resistant pseudomonas has appeared to date. we encountered a case of pneumonia caused by a pseudomonas strain producing a metallo-beta-lactamase; the patient was s ...	2013	25705398
colonization of lettuce rhizosphere and roots by tagged streptomyces.	beneficial microorganisms are increasingly used in agriculture, but their efficacy often fails due to limited knowledge of their interactions with plants and other microorganisms present in rhizosphere. we studied spatio-temporal colonization dynamics of lettuce roots and rhizosphere by genetically modified streptomyces spp. five streptomyces strains, strongly inhibiting in vitro the major soil-borne pathogen of horticultural crops, sclerotinia sclerotiorum, were transformed with pij8641 plasmid ...	2015	25705206
hormetic effect of ionic liquid 1-ethyl-3-methylimidazolium acetate on bacteria.	the biological effect of ionic liquids (ils) is one of the highly debated topics as they are being contemplated for various industrial applications. 1-ethyl-3-methylimidazolium acetate ([emim][ac]) showed remarkable hormesis on anaerobic clostridium sp. and aerobic pseudomonas putida. bacterial growth was stimulated at up to 2.5 g l(-1) and inhibited at >2.5 g l(-1) of [emim][ac]. the growth of clostridium sp. and p. putida were higher by 0.4 and 4-fold respectively, in the presence of 0.5 g l(- ...	2015	25703901
engineering towards nitroreductase functionality in ene-reductase scaffolds.	nitroreductases (nrs) and ene-reductases (ers) both utilize flavin mononucleotide cofactors but catalyze distinct reactions. nrs reduce nitroaromatics, whereas ers reduce unsaturated c=c double bonds, and these functionalities are known to somewhat overlap. recent studies on the er xenobiotic reductase a (xena) from pseudomonas putida demonstrated the possibility of increasing nr activity with active site modifications. structural comparison between nrs and ers led us to hypothesize that active ...	2015	25703443
dephosphorylated npr is involved in an envelope stress response of escherichia coli.	besides the canonical phosphoenolpyruvate-dependent phosphotransferase system (pts) for carbohydrate transport, most proteobacteria possess the so-called nitrogen pts (pts(ntr)) that transfers a phosphate group from phosphoenolpyruvate (pep) over enzyme i(ntr) (ei(ntr)) and npr to enzyme iia(ntr) (eiia(ntr)). the pts(ntr) lacks membrane-bound components and functions exclusively in a regulatory capacity. while eiia(ntr) has been implicated in a variety of cellular processes such as potassium hom ...	2015	25701731
rhizobia and their bio-partners as novel drivers for functional remediation in contaminated soils.	environmental pollutants have received considerable attention due to their serious effects on human health. there are physical, chemical, and biological means to remediate pollution; among them, bioremediation has become increasingly popular. the nitrogen-fixing rhizobia are widely distributed in the soil and root ecosystems and can increase legume growth and production by supplying nitrogen, resulting in the reduced need for fertilizer applications. rhizobia also possess the biochemical and eco ...	2015	25699064
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
cometabolism of methyl tert-butyl ether by a new microbial consortium ers.	the release of methyl tert-butyl-ether (mtbe) into the environment has increased the worldwide concern about the pollution of mtbe. in this paper, a microbial consortium was isolated from the soil sample near an oil station, which can degrade mtbe directly with a low biomass yield and mtbe degrading efficiency. further research has indicated that this consortium can degrade mtbe efficiently when grown on n-octane as the cometabolic substrate. the results of 16s rdna based on phylogenetic analysi ...	2015	25697553
core principles of bacterial autoinducer systems.	autoinduction (ai), the response to self-produced chemical signals, is widespread in the bacterial world. this process controls vastly different target functions, such as luminescence, nutrient acquisition, and biofilm formation, in different ways and integrates additional environmental and physiological cues. this diversity raises questions about unifying principles that underlie all ai systems. here, we suggest that such core principles exist. we argue that the general purpose of ai systems is ...	2015	25694124
inhibition of the growth of bacillus subtilis dsm10 by a newly discovered antibacterial protein from the soil metagenome.	a functional metagenomics based approach exploiting the microbiota of suppressive soils from an organic field site has succeeded in the identification of a clone with the ability to inhibit the growth of bacillus subtilis dsm10. sequencing of the fosmid identified a putative β-lactamase-like gene abgt. transposon mutagenesis of the abgt gene resulted in a loss in ability to inhibit the growth of b. subtilis dsm10. further analysis of the deduced amino acid sequence of abgt revealed moderate homo ...	2015	25692994
integrating food webs with metabolic networks: modeling contaminant degradation in marine ecosystems.		2015	25691892
single-step fermentative production of the cholesterol-lowering drug pravastatin via reprogramming of penicillium chrysogenum.	the cholesterol-lowering blockbuster drug pravastatin can be produced by stereoselective hydroxylation of the natural product compactin. we report here the metabolic reprogramming of the antibiotics producer penicillium chrysogenum toward an industrial pravastatin production process. following the successful introduction of the compactin pathway into the β-lactam-negative p. chrysogenum ds50662, a new cytochrome p450 (p450 or cyp) from amycolatopsis orientalis (cyp105as1) was isolated to catalyz ...	2015	25691737
chromosome organization and replisome dynamics in mycobacterium smegmatis.	subcellular organization of the bacterial nucleoid and spatiotemporal dynamics of dna replication and segregation have been studied intensively, but the functional link between these processes remains poorly understood. here we use quantitative time-lapse fluorescence microscopy for single-cell analysis of chromosome organization and dna replisome dynamics in mycobacterium smegmatis. we report that dna replication takes place near midcell, where, following assembly of the replisome on the replic ...	2015	25691587
a single serine residue determines selectivity to monovalent metal ions in metalloregulators of the merr family.	merr metalloregulators alleviate toxicity caused by an excess of metal ions, such as copper, zinc, mercury, lead, cadmium, silver, or gold, by triggering the expression of specific efflux or detoxification systems upon metal detection. the sensor protein binds the inducer metal ion by using two conserved cysteine residues at the c-terminal metal-binding loop (mbl). divalent metal ion sensors, such as merr and zntr, require a third cysteine residue, located at the beginning of the dimerization (α ...	2015	25691529
microbial community successional patterns in beach sands impacted by the deepwater horizon oil spill.	although petroleum hydrocarbons discharged from the deepwater horizon (dwh) blowout were shown to have a pronounced impact on indigenous microbial communities in the gulf of mexico, effects on nearshore or coastal ecosystems remain understudied. this study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the dwh oil was deposited on pensacola beach sands (fl, usa), using metagenomic and 16s rrna gene amplicon techniques. gamma- and alphaproteobac ...	2015	25689026
ligand binding specificity of rutr, a member of the tetr family of transcription regulators in escherichia coli.	rutr is a member of the large family of tetr transcriptional regulators in escherichia coli. it was originally discovered as the regulator of the rutabcdefg operon encoding a novel pathway for pyrimidine utilization, but its highest affinity target is the control region of the carab operon, encoding carbamoylphosphate synthase. unlike most other tetr-like regulators, rutr exerts both positive and negative effects on promoter activity. furthermore, rutr exhibits a very narrow ligand binding speci ...	2015	25685666
bio-preparates support the productivity of potato plants grown under desert farming conditions of north sinai: five years of field trials.	organic agriculture as well as good agricultural practices (gaps) intrigues the concern of both consumers and producers of agricultural commodities. bio-preparates of various rhizospheric microorganisms (rmos) are potential sources of biological inputs supporting plant nutrition and health. the response of open-field potatoes to the application of rmo bio-preparates, the biofertilizer "biofertile" and the bioagent "biocontrol", were experimented over 5 successive years under n-hunger of north si ...	2013	25685470
bio-preparates support the productivity of potato plants grown under desert farming conditions of north sinai: five years of field trials.	organic agriculture as well as good agricultural practices (gaps) intrigues the concern of both consumers and producers of agricultural commodities. bio-preparates of various rhizospheric microorganisms (rmos) are potential sources of biological inputs supporting plant nutrition and health. the response of open-field potatoes to the application of rmo bio-preparates, the biofertilizer "biofertile" and the bioagent "biocontrol", were experimented over 5 successive years under n-hunger of north si ...	2013	25685470
diversity of bacteria nesting the plant cover of north sinai deserts, egypt.	north sinai deserts were surveyed for the predominant plant cover and for the culturable bacteria nesting their roots and shoots. among 43 plant species reported, 13 are perennial (e.g. fagonia spp., pancratium spp.) and 30 annuals (e.g. bromus spp., erodium spp.). eleven species possessed rhizo-sheath, e.g. cyperus capitatus, panicum turgidum and trisetaria koelerioides. microbiological analyses demonstrated: the great diversity and richness of associated culturable bacteria, in particular nitr ...	2012	25685397
diversity of bacteria nesting the plant cover of north sinai deserts, egypt.	north sinai deserts were surveyed for the predominant plant cover and for the culturable bacteria nesting their roots and shoots. among 43 plant species reported, 13 are perennial (e.g. fagonia spp., pancratium spp.) and 30 annuals (e.g. bromus spp., erodium spp.). eleven species possessed rhizo-sheath, e.g. cyperus capitatus, panicum turgidum and trisetaria koelerioides. microbiological analyses demonstrated: the great diversity and richness of associated culturable bacteria, in particular nitr ...	2012	25685397
the two paralogue phon (phosphinothricin acetyl transferase) genes of pseudomonas putida encode functionally different proteins.	phosphinothricin (ppt) is a non-specific inhibitor of glutamine synthetase that has been employed as herbicide for selection of transgenic plants expressing cognate resistance genes. while the soil bacterium pseudomonas putida kt2440 has been generally considered ppt-sensitive, inspection of its genome sequence reveals the presence of two highly similar open reading frames (pp_1924 and pp_4846) encoding acetylases with a potential to cause tolerance to the herbicide. to explore this possibility, ...	2015	25684119
increasing carbapenem-resistant gram-negative bacilli and decreasing metallo-β-lactamase producers over eight years from korea.	the trends and types of carbapenemase-producing gram-negative bacilli were analyzed from clinical specimens collected between 2005 and 2012 at a korean teaching hospital. the proportions of carbapenem-resistant acinetobacter spp. increased markedly to 66%. metallo-β-lactamase producers significantly decreased and the majority shifted from the bla(vim-2) type to the bla(imp-1) type.	2015	25684011
ab initio dynamics of the cytochrome p450 hydroxylation reaction.	the iron(iv)-oxo porphyrin π-cation radical known as compound i is the primary oxidant within the cytochromes p450, allowing these enzymes to affect the substrate hydroxylation. in the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(iv) porphyrin and a substrate-centered radical. the hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. while compound i has succumbed to theoretical and spectroscopic char ...	2015	25681906
effects of three different nucleoid-associated proteins encoded on incp-7 plasmid pcar1 on host pseudomonas putida kt2440.	nucleoid-associated proteins (naps), which fold bacterial dna and influence gene transcription, are considered to be global transcriptional regulators of genes on both plasmids and the host chromosome. incompatibility p-7 group plasmid pcar1 carries genes encoding three naps: h-ns family protein pmr, ndpa-like protein pnd, and hu-like protein phu. in this study, the effects of single or double disruption of pmr, pnd, and phu were assessed in host pseudomonas putida kt2440. when pmr and pnd or pm ...	2015	25681185
arsenic methylation and volatilization by arsenite s-adenosylmethionine methyltransferase in pseudomonas alcaligenes nbrc14159.	inorganic arsenic (as) is highly toxic and ubiquitous in the environment. inorganic as can be transformed by microbial methylation, which constitutes an important part of the as biogeochemical cycle. in this study, we investigated as biotransformation by pseudomonas alcaligenes nbrc14159. p. alcaligenes was able to methylate arsenite [as(iii)] rapidly to dimethylarsenate and small amounts of trimethylarsenic oxide. an arsenite s-adenosylmethionine methyltransferase, paarsm, was identified and fu ...	2015	25681184
a first line of stress defense: small heat shock proteins and their function in protein homeostasis.	small heat shock proteins (shsps) are virtually ubiquitous molecular chaperones that can prevent the irreversible aggregation of denaturing proteins. shsps complex with a variety of non-native proteins in an atp-independent manner and, in the context of the stress response, form a first line of defense against protein aggregation in order to maintain protein homeostasis. in vertebrates, they act to maintain the clarity of the eye lens, and in humans, shsp mutations are linked to myopathies and n ...	2015	25681016
soybean (glycine max l. merr.) sprouts germinated under red light irradiation induce disease resistance against bacterial rotting disease.	specific wavelengths of light can exert various physiological changes in plants, including effects on responses to disease incidence. to determine whether specific light wavelength had effects on rotting disease caused by pseudomonas putida 229, soybean sprouts were germinated under a narrow range of wavelengths from light emitting diodes (leds), including red (650-660), far red (720-730) and blue (440-450 nm) or broad range of wavelength from daylight fluorescence bulbs. the controls were compo ...	2015	25679808
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
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
phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils.	phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. the p content in average soil is about 0.05% (w/w) but only 0.1% of the total p is available to plant because of poor solubility and its fixation in soil (illmer and schinner, soil biol biochem 27:257-263, 1995). an adequate supply of p ...	2013	25674415
homologs of the acinetobacter baumannii acei transporter represent a new family of bacterial multidrug efflux systems.	multidrug efflux systems are a major cause of resistance to antimicrobials in bacteria, including those pathogenic to humans, animals, and plants. these proteins are ubiquitous in these pathogens, and five families of bacterial multidrug efflux systems have been identified to date. by using transcriptomic and biochemical analyses, we recently identified the novel acei (acinetobacter chlorhexidine efflux) protein from acinetobacter baumannii that conferred resistance to the biocide chlorhexidine, ...	2015	25670776
in-office use of a steroid-eluting implant for maintenance of frontal ostial patency after revision sinus surgery.	achieving long-term, successful outcomes with endoscopic sinus surgery (ess) can be challenging in patients with recalcitrant chronic rhinosinusitis (crs). local complications, including scar formation and ostial stenosis, can lead to recurrent blockage and subsequent relapse. the frontal sinus is particularly vulnerable to surgical failure given its narrow outflow and inaccessibility to topical therapies. the advent of steroid-eluting sinus implants has enhanced ess outcomes, with significant r ...	2015	25668577