Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| 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 |
| 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 |
| 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 |
| biosafety test for plant growth-promoting bacteria: proposed environmental and human safety index (ehsi) protocol. | plant growth-promoting bacteria (pgpb) colonize plants and enhance their growth by different mechanisms. some of these microorganisms may represent a potential threat to human, animal or plant health; however, their use might be approved in parts of europe if they have been recommended as plant growth enhancers. the current regulatory framework has resulted in a fragmented, contradictory system, and there is an urgent need to establish harmonized protocols for the predictability, efficiency, con ... | 2015 | 26779168 |
| biosafety test for plant growth-promoting bacteria: proposed environmental and human safety index (ehsi) protocol. | plant growth-promoting bacteria (pgpb) colonize plants and enhance their growth by different mechanisms. some of these microorganisms may represent a potential threat to human, animal or plant health; however, their use might be approved in parts of europe if they have been recommended as plant growth enhancers. the current regulatory framework has resulted in a fragmented, contradictory system, and there is an urgent need to establish harmonized protocols for the predictability, efficiency, con ... | 2015 | 26779168 |
| maldi-tof mass spectrometry: a powerful tool for clinical microbiology at hôpital principal de dakar, senegal (west africa). | our team in europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (maldi-tof) mass spectrometry (ms). to evaluate the utility of maldi-tof ms in tropical africa in collaboration with local teams, we installed an apparatus in the hôpital principal de dakar (senegal), performed routine identification of isolates, and confirmed or completed their identification in france. in the case of discordance or a la ... | 2015 | 26716681 |
| multicenter evaluation of the bruker maldi biotyper ca system for the identification of clinical aerobic gram-negative bacterial isolates. | the prompt and accurate identification of bacterial pathogens is fundamental to patient health and outcome. recent advances in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof ms) have revolutionized bacterial identification in the clinical laboratory, but uniform incorporation of this technology in the u.s. market has been delayed by a lack of fda-cleared systems. in this study, we conducted a multicenter evaluation of the maldi biotyper ca (mbt-ca) system ... | 2015 | 26529504 |
| potential roles for microbial endophytes in herbicide tolerance in plants. | herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. a growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. the current evidence for herbicide tolerance be ... | 2015 | 26350619 |
| potential roles for microbial endophytes in herbicide tolerance in plants. | herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. a growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. the current evidence for herbicide tolerance be ... | 2015 | 26350619 |
| determinants of bacteriological outcomes in exacerbations of chronic obstructive pulmonary disease. | changes in sputum microbiology following antibiotic treatment of acute exacerbations of chronic obstructive pulmonary disease (aecopd), including patterns of bacteriological relapse and superinfection are not well understood. sputum microbiology at exacerbation is not routinely performed, but pathogen presence and species are determinants of outcomes. therefore, we determined whether baseline clinical factors could predict the presence of bacterial pathogens at exacerbation. bacterial eradicatio ... | 2015 | 26370552 |
| determinants of bacteriological outcomes in exacerbations of chronic obstructive pulmonary disease. | changes in sputum microbiology following antibiotic treatment of acute exacerbations of chronic obstructive pulmonary disease (aecopd), including patterns of bacteriological relapse and superinfection are not well understood. sputum microbiology at exacerbation is not routinely performed, but pathogen presence and species are determinants of outcomes. therefore, we determined whether baseline clinical factors could predict the presence of bacterial pathogens at exacerbation. bacterial eradicatio ... | 2015 | 26370552 |
| iron is a signal for stenotrophomonas maltophilia biofilm formation, oxidative stress response, omps expression, and virulence. | stenotrophomonas maltophilia is an emerging nosocomial pathogen. in many bacteria iron availability regulates, through the fur system, not only iron homeostasis but also virulence. the aim of this work was to assess the role of iron on s. maltophilia biofilm formation, eps production, oxidative stress response, omps regulation, quorum sensing (qs), and virulence. studies were done on k279a and its isogenic fur mutant f60 cultured in the presence or absence of dipyridyl. this is the first report ... | 2015 | 26388863 |
| γ-resorcylate catabolic-pathway genes in the soil actinomycete rhodococcus jostii rha1. | the rhodococcus jostii rha1 gene cluster required for γ-resorcylate (gra) catabolism was characterized. the cluster includes tsda, tsdb, tsdc, tsdd, tsdr, tsdt, and tsdx, which encode gra decarboxylase, resorcinol 4-hydroxylase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, an iclr-type regulator, a major facilitator superfamily transporter, and a putative hydrolase, respectively. the tsda gene conferred gra decarboxylase activity on escherichia coli. purified tsdb oxidized nadh in the ... | 2015 | 26319878 |
| bacterial degradation of monocyclic aromatic amines. | aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. these compounds have been considered highly toxic to human beings due to their carcinogenic nature. three groups of aromatic amines have been recognized: monocyclic, polycyclic, and heterocyclic aromatic amines. bacterial degradation of several monocyclic aromatic amines has been studied in a variety of bacteria, which utiliz ... | 2015 | 26347719 |
| evaluation of aerial microbial pollutants in al-haram al-nabawi during pilgrimage of 2013. | al-madinah al-munawwarah is the second holiest site in islam. the possibility of new emerging microbes is valid due to the increased number of pilgrims. the objectives of the current study were to estimate the numbers of fungi and bacteria inside and outside al-haram al-nabawi and to find whether new bacterial and fungal species have emerged compared to previous studies. air samples were collected twice a day from 12 spots and four directions during the pilgrim year of 2013 for four consecutive ... | 2015 | 28053593 |
| evaluation of aerial microbial pollutants in al-haram al-nabawi during pilgrimage of 2013. | al-madinah al-munawwarah is the second holiest site in islam. the possibility of new emerging microbes is valid due to the increased number of pilgrims. the objectives of the current study were to estimate the numbers of fungi and bacteria inside and outside al-haram al-nabawi and to find whether new bacterial and fungal species have emerged compared to previous studies. air samples were collected twice a day from 12 spots and four directions during the pilgrim year of 2013 for four consecutive ... | 2015 | 28053593 |
| salix purpurea stimulates the expression of specific bacterial xenobiotic degradation genes in a soil contaminated with hydrocarbons. | the objectives of this study were to uncover salix purpurea-microbe xenobiotic degradation systems that could be harnessed in rhizoremediation, and to identify microorganisms that are likely involved in these partnerships. to do so, we tested s. purpurea's ability to stimulate the expression of 10 marker microbial oxygenase genes in a soil contaminated with hydrocarbons. in what appeared to be a detoxification rhizosphere effect, transcripts encoding for alkane 1-monooxygenases, cytochrome p450 ... | 2015 | 26161539 |
| aerobic cyanide degradation by bacterial isolates from cassava factory wastewater. | ten bacterial strains that utilize cyanide (cn) as a nitrogen source were isolated from cassava factory wastewater after enrichment in a liquid media containing sodium cyanide (1 mm) and glucose (0.2% w/v). the strains could tolerate and grow in cyanide concentrations of up to 5 mm. increased cyanide levels in the media caused an extension of lag phase in the bacterial growth indicating that they need some period of acclimatisation. the rate of cyanide removal by the strains depends on the initi ... | 2015 | 26413045 |
| cyanobacteria: photoautotrophic microbial factories for the sustainable synthesis of industrial products. | cyanobacteria are widely distributed gram-negative bacteria with a long evolutionary history and the only prokaryotes that perform plant-like oxygenic photosynthesis. cyanobacteria possess several advantages as hosts for biotechnological applications, including simple growth requirements, ease of genetic manipulation, and attractive platforms for carbon neutral production process. the use of photosynthetic cyanobacteria to directly convert carbon dioxide to biofuels is an emerging area of intere ... | 2015 | 26199945 |
| infectious diseases linked to cross-contamination of flexible endoscopes. | flexible endoscopes are widely used to examine, diagnose, and treat medical disorders. while the risk of endoscopy-related transmission of infection is estimated to be very low, more health care-associated infections are related to contaminated endoscopes than to any other medical device. flexible endoscopes can get highly contaminated with microorganisms, secretions and blood during use. the narrow lumens and multiple internal channels make the cleaning of flexible endoscopes a complex and diff ... | 2015 | 26355428 |
| laboratory diagnosis of melioidosis: past, present and future. | melioidosis is an emerging, potentially fatal disease caused by burkholderia pseudomallei, which requires prolonged antibiotic treatment to prevent disease relapse. however, difficulties in laboratory diagnosis of melioidosis may delay treatment and affect disease outcomes. isolation of b. pseudomallei from clinical specimens has been improved with the use of selective media. however, even with positive cultures, identification of b. pseudomallei can be difficult in clinical microbiology laborat ... | 2015 | 25908634 |
| structural and kinetic characterization of recombinant 2-hydroxymuconate semialdehyde dehydrogenase from pseudomonas putida g7. | the first enzyme in the oxalocrotonate branch of the naphthalene-degradation lower pathway in pseudomonas putida g7 is nahi, a 2-hydroxymuconate semialdehyde dehydrogenase which converts 2-hydroxymuconate semialdehyde to 2-hydroxymuconate in the presence of nad(+). nahi is in family 8 (aldh8) of the nad(p)(+)-dependent aldehyde dehydrogenase superfamily. in this work, we report the cloning, expression, purification and preliminary structural and kinetic characterization of the recombinant nahi. ... | 2015 | 26032336 |
| stenotrophomonas maltophilia responds to exogenous ahl signals through the luxr solo smor (smlt1839). | quorum sensing (qs) mediated by acyl homoserine lactone (ahl) molecules are probably the most widespread and studied among gram-negative bacteria. canonical ahl systems are composed by a synthase (luxi family) and a regulator element (luxr family), whose genes are usually adjacent in the genome. however, incomplete ahl-qs machinery lacking the synthase luxi is frequently observed in proteobacteria, and the regulator element is then referred as luxr solo. it has been shown that certain luxr solos ... | 2015 | 26029670 |
| 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 |
| metabolic engineering of corynebacterium glutamicum for methanol metabolism. | methanol is already an important carbon feedstock in the chemical industry, but it has found only limited application in biotechnological production processes. this can be mostly attributed to the inability of most microbial platform organisms to utilize methanol as a carbon and energy source. with the aim to turn methanol into a suitable feedstock for microbial production processes, we engineered the industrially important but nonmethylotrophic bacterium corynebacterium glutamicum toward the ut ... | 2015 | 25595770 |
| 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 |
| functional characterization of a vanillin dehydrogenase in corynebacterium glutamicum. | vanillin dehydrogenase (vdh) is a crucial enzyme involved in the degradation of lignin-derived aromatic compounds. herein, the vdh from corynebacterium glutamicum was characterized. the relative molecular mass (mr) determined by sds-page was ~51 kda, whereas the apparent native mr values revealed by gel filtration chromatography were 49.5, 92.3, 159.0 and 199.2 kda, indicating the presence of dimeric, trimeric and tetrameric forms. moreover, the enzyme showed its highest level of activity toward ... | 2015 | 25622822 |
| 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 |
| 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 |
| pseudomonas sp. lz-q continuously degrades phenanthrene under hypersaline and hyperalkaline condition in a membrane bioreactor system. | 2015 | 27340693 | |
| pseudomonas sp. lz-q continuously degrades phenanthrene under hypersaline and hyperalkaline condition in a membrane bioreactor system. | 2015 | 27340693 | |
| identification of a new marine bacterial strain sd8 and optimization of its culture conditions for producing alkaline protease. | while much attention has been given to marine microorganisms for production of enzymes, which in general are relatively more stable and active compared to those from plants and animals, studies on alkaline protease production from marine microorganisms have been very limited. in the present study, the alkaline protease producing marine bacterial strain sd8 isolated from sea muds in the geziwo qinhuangdao sea area of china was characterized and its optimal culture conditions were investigated. st ... | 2015 | 26716833 |
| degradation of benzene by pseudomonas veronii 1ydbtex2 and 1yb2 is catalyzed by enzymes encoded in distinct catabolism gene clusters. | pseudomonas veronii 1ydbtex2, a benzene and toluene degrader, and pseudomonas veronii 1yb2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. these strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydrox ... | 2015 | 26475106 |
| degradation of benzene by pseudomonas veronii 1ydbtex2 and 1yb2 is catalyzed by enzymes encoded in distinct catabolism gene clusters. | pseudomonas veronii 1ydbtex2, a benzene and toluene degrader, and pseudomonas veronii 1yb2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. these strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydrox ... | 2015 | 26475106 |
| diversity of pseudomonas genomes, including populus-associated isolates, as revealed by comparative genome analysis. | the pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. their diversity influences the phylogenetic diversity and heterogeneity of these communities. on the basis of average amino acid identity, comparative genome analysis of >1,000 pseudomonas genomes, including 21 pseudomonas strains isolated from the roots of native populus deltoides (eastern cottonwood) trees resu ... | 2015 | 26519390 |
| diversity of pseudomonas genomes, including populus-associated isolates, as revealed by comparative genome analysis. | the pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. their diversity influences the phylogenetic diversity and heterogeneity of these communities. on the basis of average amino acid identity, comparative genome analysis of >1,000 pseudomonas genomes, including 21 pseudomonas strains isolated from the roots of native populus deltoides (eastern cottonwood) trees resu ... | 2015 | 26519390 |
| biocontrol of the potato blackleg and soft rot diseases caused by dickeya dianthicola. | development of protection tools targeting dickeya species is an important issue in the potato production. here, we present the identification and the characterization of novel biocontrol agents. successive screenings of 10,000 bacterial isolates led us to retain 58 strains that exhibited growth inhibition properties against several dickeya sp. and/or pectobacterium sp. pathogens. most of them belonged to the pseudomonas and bacillus genera. in vitro assays revealed a fitness decrease of the test ... | 2015 | 26497457 |
| biocontrol of the potato blackleg and soft rot diseases caused by dickeya dianthicola. | development of protection tools targeting dickeya species is an important issue in the potato production. here, we present the identification and the characterization of novel biocontrol agents. successive screenings of 10,000 bacterial isolates led us to retain 58 strains that exhibited growth inhibition properties against several dickeya sp. and/or pectobacterium sp. pathogens. most of them belonged to the pseudomonas and bacillus genera. in vitro assays revealed a fitness decrease of the test ... | 2015 | 26497457 |
| iron oxide nanoparticle-mediated hyperthermia stimulates dispersal in bacterial biofilms and enhances antibiotic efficacy. | the dispersal phase that completes the biofilm lifecycle is of particular interest for its potential to remove recalcitrant, antimicrobial tolerant biofilm infections. here we found that temperature is a cue for biofilm dispersal and a rise by 5 °c or more can induce the detachment of pseudomonas aeruginosa biofilms. temperature upshifts were found to decrease biofilm biomass and increase the number of viable freely suspended cells. the dispersal response appeared to involve the secondary messen ... | 2015 | 26681339 |
| year-long metagenomic study of river microbiomes across land use and water quality. | select bacteria, such as escherichia coli or coliforms, have been widely used as sentinels of low water quality; however, there are concerns regarding their predictive accuracy for the protection of human and environmental health. to develop improved monitoring systems, a greater understanding of bacterial community structure, function, and variability across time is required in the context of different pollution types, such as agricultural and urban contamination. here, we present a year-long s ... | 2015 | 26733955 |
| fleq dna binding consensus sequence revealed by studies of fleq-dependent regulation of biofilm gene expression in pseudomonas aeruginosa. | the transcription factor fleq from pseudomonas aeruginosa derepresses expression of genes involved in biofilm formation when intracellular levels of the second messenger cyclic diguanosine monophosphate (c-di-gmp) are high. fleq also activates transcription of flagellar genes, and the expression of these genes is highest at low intracellular c-di-gmp. fleq thus plays a central role in mediating the transition between planktonic and biofilm lifestyles of p. aeruginosa. previous work showed that f ... | 2015 | 26483521 |
| fleq dna binding consensus sequence revealed by studies of fleq-dependent regulation of biofilm gene expression in pseudomonas aeruginosa. | the transcription factor fleq from pseudomonas aeruginosa derepresses expression of genes involved in biofilm formation when intracellular levels of the second messenger cyclic diguanosine monophosphate (c-di-gmp) are high. fleq also activates transcription of flagellar genes, and the expression of these genes is highest at low intracellular c-di-gmp. fleq thus plays a central role in mediating the transition between planktonic and biofilm lifestyles of p. aeruginosa. previous work showed that f ... | 2015 | 26483521 |
| diversity of cyclic di-gmp-binding proteins and mechanisms. | cyclic di-gmp (c-di-gmp) synthetases and hydrolases (ggdef, eal, and hd-gyp domains) can be readily identified in bacterial genome sequences by using standard bioinformatic tools. in contrast, identification of c-di-gmp receptors remains a difficult task, and the current list of experimentally characterized c-di-gmp-binding proteins is likely incomplete. several classes of c-di-gmp-binding proteins have been structurally characterized; for some others, the binding sites have been identified; and ... | 2015 | 26055114 |
| diversity of cyclic di-gmp-binding proteins and mechanisms. | cyclic di-gmp (c-di-gmp) synthetases and hydrolases (ggdef, eal, and hd-gyp domains) can be readily identified in bacterial genome sequences by using standard bioinformatic tools. in contrast, identification of c-di-gmp receptors remains a difficult task, and the current list of experimentally characterized c-di-gmp-binding proteins is likely incomplete. several classes of c-di-gmp-binding proteins have been structurally characterized; for some others, the binding sites have been identified; and ... | 2015 | 26055114 |
| lipopeptide biosurfactant viscosin enhances dispersal of pseudomonas fluorescens sbw25 biofilms. | pseudomonads produce several lipopeptide biosurfactants that have antimicrobial properties but that also facilitate surface motility and influence biofilm formation. detailed studies addressing the significance of lipopeptides for biofilm formation and architecture are rare. hence, the present study sets out to determine the specific role of the lipopeptide viscosin in pseudomonas fluorescens sbw25 biofilm formation, architecture and dispersal, and to relate visca gene expression to viscosin pro ... | 2015 | 26419730 |
| persistence of nasal colonization with human pathogenic bacteria and associated antimicrobial resistance in the german general population. | the nares represent an important bacterial reservoir for endogenous infections. this study aimed to assess the prevalence of nasal colonization by different important pathogens, the associated antimicrobial susceptibility and risk factors. we performed a prospective cohort study among 1878 nonhospitalized volunteers recruited from the general population in germany. participants provided nasal swabs at three time points (each separated by 4-6 months). staphylococcus aureus, enterobacteriaceae and ... | 2015 | 26862431 |
| persistence of nasal colonization with human pathogenic bacteria and associated antimicrobial resistance in the german general population. | the nares represent an important bacterial reservoir for endogenous infections. this study aimed to assess the prevalence of nasal colonization by different important pathogens, the associated antimicrobial susceptibility and risk factors. we performed a prospective cohort study among 1878 nonhospitalized volunteers recruited from the general population in germany. participants provided nasal swabs at three time points (each separated by 4-6 months). staphylococcus aureus, enterobacteriaceae and ... | 2015 | 26862431 |
| bacterial colonies in solid media and foods: a review on their growth and interactions with the micro-environment. | bacteria, either indigenous or added, are immobilized in solid foods where they grow as colonies. since the 80's, relatively few research groups have explored the implications of bacteria growing as colonies and mostly focused on pathogens in large colonies on agar/gelatine media. it is only recently that high resolution imaging techniques and biophysical characterization techniques increased the understanding of the growth of bacterial colonies, for different sizes of colonies, at the microscop ... | 2015 | 26648910 |
| classification and taxonomy of vegetable macergens. | macergens are bacteria capable of releasing pectic enzymes (pectolytic bacteria). these enzymatic actions result in the separation of plant tissues leading to total plant destruction. this can be attributed to soft rot diseases in vegetables. these macergens primarily belong to the genus erwinia and to a range of opportunistic pathogens namely: the xanthomonas spp., pseudomonas spp., clostridium spp., cytophaga spp., and bacillus spp. they consist of taxa that displayed considerable heterogeneit ... | 2015 | 26640465 |
| antibacterial activity of stenotrophomonas maltophilia endolysin p28 against both gram-positive and gram-negative bacteria. | maltocin p28 is a phage-tail like bacteriocin produced by stenotrophomonas maltophilia p28. the orf8 of maltocin p28 gene cluster is predicted to encode an endolysin and we name it endolysin p28. sequence analysis revealed that it contains the lysozyme_like superfamily conserved domain. endolysin p28 has the four consensus motifs as that of escherichia coli phage lambda gpr. in this study, endolysin p28 was expressed in e. coli bl21 (de3) and purified with a c-terminal oligo-histidine tag. the a ... | 2015 | 26635765 |
| oprg harnesses the dynamics of its extracellular loops to transport small amino acids across the outer membrane of pseudomonas aeruginosa. | oprg is an outer membrane protein of pseudomonas aeruginosa whose function as an antibiotic-sensitive porin has been controversial and not well defined. circumstantial evidence led to the proposal that oprg might transport hydrophobic compounds by using a lateral gate in the barrel wall thought to be lined by three conserved prolines. to test this hypothesis and to find the physiological substrates of oprg, we reconstituted the purified protein into liposomes and found it to facilitate the trans ... | 2015 | 26655471 |
| pseudomonads rule degradation of polyaromatic hydrocarbons in aerated sediment. | given that the degradation of aromatic pollutants in anaerobic environments such as sediment is generally very slow, aeration could be an efficient bioremediation option. using stable isotope probing (sip) coupled with pyrosequencing analysis of 16s rrna genes, we identified naphthalene-utilizing populations in aerated polyaromatic hydrocarbon (pah)-polluted sediment. the results showed that naphthalene was metabolized at both 10 and 20°c following oxygen delivery, with increased degradation at ... | 2015 | 26635740 |
| the extent of functional redundancy changes as species' roles shift in different environments. | assessing the ecological impacts of environmental change requires knowledge of the relationship between biodiversity and ecosystem functioning. the exact nature of this relationship can differ considerably between ecosystems, with consequences for the efficacy of species diversity as a buffer against environmental change. using a microbial model system, we show that the relationship can vary depending on environmental conditions. shapes suggesting functional redundancy in one environment can cha ... | 2015 | 26578806 |
| antimicrobial effect of malpighia punicifolia and extension of water buffalo steak shelf-life. | in the present study, a multiple approach was used to characterize malpighia punicifolia extract and to evaluate its inhibitory activity against several meat spoilage bacteria. first, volatile fraction, vitamins and phenolic compounds of the extract obtained by supercritical fluid extraction were determined by gc-ms and hplc. then, the antimicrobial action of the extract was in vitro evaluated against pseudomonas putida dsmz 291(t), pseudomonas fluorescens dsmz 50009(t), pseudomonas fragi dsmz 3 ... | 2015 | 26556435 |
| antimicrobial effect of malpighia punicifolia and extension of water buffalo steak shelf-life. | in the present study, a multiple approach was used to characterize malpighia punicifolia extract and to evaluate its inhibitory activity against several meat spoilage bacteria. first, volatile fraction, vitamins and phenolic compounds of the extract obtained by supercritical fluid extraction were determined by gc-ms and hplc. then, the antimicrobial action of the extract was in vitro evaluated against pseudomonas putida dsmz 291(t), pseudomonas fluorescens dsmz 50009(t), pseudomonas fragi dsmz 3 ... | 2015 | 26556435 |
| a putative non-canonical ras-like gtpase from p. falciparum: chemical properties and characterization of the protein. | during its development the malaria parasite p. falciparum has to adapt to various different environmental contexts. key cellular mechanisms involving g-protein coupled signal transduction chains are assumed to act at these interfaces. heterotrimeric g-proteins are absent in plasmodium. we here describe the first cloning and expression of a putative, non-canonical ras-like g protein (acronym pfg) from plasmodium. pfg reveals an open reading frame of 2736 bp encoding a protein of 912 amino acids w ... | 2015 | 26540393 |
| evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. | the field of metagenomics (study of genetic material recovered directly from an environment) has grown rapidly, with many bioinformatics analysis methods being developed. to ensure appropriate use of such methods, robust comparative evaluation of their accuracy and features is needed. for taxonomic classification of sequence reads, such evaluation should include use of clade exclusion, which better evaluates a method's accuracy when identical sequences are not present in any reference database, ... | 2015 | 26537885 |
| the metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases. | the metacyc database (metacyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. the majority of metacyc pathways are small-molecule metabolic pathways that have been experimentally determined. metacyc contains more than 2400 pathways derived from >46,000 publications, and is the largest curated collection of metabolic pathways. biocyc (biocyc.org) is a collection of 5700 organism-specific pathway/genome databases (pgdbs), each ... | 2015 | 26527732 |
| the metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases. | the metacyc database (metacyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. the majority of metacyc pathways are small-molecule metabolic pathways that have been experimentally determined. metacyc contains more than 2400 pathways derived from >46,000 publications, and is the largest curated collection of metabolic pathways. biocyc (biocyc.org) is a collection of 5700 organism-specific pathway/genome databases (pgdbs), each ... | 2015 | 26527732 |
| phylogenetic analysis based evolutionary study of 16s rrna in known pseudomonas sp. | molecular evolution analysis of 16s rrna sequences of native pseudomonas strains and different fluorescent pseudomonads were conducted on the basis of molecular evolutionary genetics analysis version 5.2 (mega5.2). topological evaluations show common origin for native strains with other known strains with available sequences at genbank database. phylogenetic affiliation of different pseudomonas sp based on 16s rrna gene shows that molecular divergence contributes to the genetic diversity of pseu ... | 2015 | 26664032 |
| biodegradation of di-n-butyl phthalate by achromobacter sp. isolated from rural domestic wastewater. | a bacterial strain w-1, isolated from rural domestic wastewater, can utilize the environmental hormone di-n-butyl phthalate (dbp) as the sole carbon and energy source. the isolated bacterium species was confirmed to belong to the genus achromobacter based on its 16s rrna gene sequence. the results of substrate utilization tests showed that the strain w-1 could utilize other common phthalates and phenol. high-performance liquid chromatography analysis revealed that the optimal conditions for dbp ... | 2015 | 26516878 |
| biodegradation kinetics and interactions of styrene and ethylbenzene as single and dual substrates for a mixed bacterial culture. | this study examined biodegradation kinetics of styrene and ethylbenzene as representatives of alkenylbenzenes and mono-alkylbenzenes, respectively. the compounds were studied independently and as binary mixtures using a series of aerobic batch degradation experiments introduced by acclimatized mix culture. initial concentration of styrene and ethylbenzene in the liquid phase vacillated from 0 to 220 mg/l. the andrew model was applied for the biodegradation of individual substrates and the estima ... | 2015 | 26483955 |
| the genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. | ribosomally synthesized and post-translationally modified peptides (ripps) are a burgeoning class of natural products with diverse activity that share a similar origin and common features in their biosynthetic pathways. the precursor peptides of these natural products are ribosomally produced, upon which a combination of modification enzymes installs diverse functional groups. this genetically encoded peptide-based strategy allows for rapid diversification of these natural products by mutation i ... | 2015 | 26462797 |
| the lapg protein plays a role in pseudomonas aeruginosa biofilm formation by controlling the presence of the cdra adhesin on the cell surface. | pseudomonas aeruginosa is a clinically relevant species involved in biofilm-based chronic infections. we provide evidence that the p. aeruginosa lapg protein functions as a periplasmic protease that can cleave the protein adhesin cdra off the cell surface, and thereby plays a role in biofilm formation and biofilm dispersal. the p. aeruginosa lapg protein is shown to be a functional homolog of the pseudomonas putida lapg protein which has previously been shown to function as a periplasmic proteas ... | 2015 | 26458733 |
| 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 |