Publications

effects of exogenous pyoverdines on fe availability and their impacts on mn(ii) oxidation by pseudomonas putida gb-1.	pseudomonas putida gb-1 is a mn(ii)-oxidizing bacterium that produces pyoverdine-type siderophores (pvds), which facilitate the uptake of fe(iii) but also influence mno2 formation. recently, a non-ribosomal peptide synthetase mutant that does not synthesize pvd was described. here we identified a gene encoding the pvdgb-1 (pvd produced by strain gb-1) uptake receptor (pputgb1_4082) of strain gb-1 and confirmed its function by in-frame mutagenesis. growth and other physiological responses of thes ...	2014	25009534
optimization of biomass and biokinetic constant in mazut biodegradation by indigenous bacteria bbrc10061.	optimization based on appropriate parameters can be applied to improve a process. mazut degradation as a critical issue in environment requires optimization to be efficiently done. to provide biodegradation conditions, experiments were designed on the least interactions among levels of parameters consisting of ph, tween 80, glucose, phosphorous source, nitrogen source, and time. kinetic constants and biomass were calculated based on 16 assays, designed using taguchi method, which constructed var ...	2014	25013725
perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer.	the x-ray structure of benzoylformate decarboxylase (bfdc) from pseudomonas putida atcc 12633 shows it to be a tetramer. this was believed to be typical of all thiamin diphosphate-dependent decarboxylases until recently when the structure of kdca, a branched-chain 2-keto acid decarboxylase from lactococcus lactis, showed it to be a homodimer. this lent credence to earlier unfolding experiments on pyruvate decarboxylase from saccharomyces cerevisiae that indicated that it might be active as a dim ...	2014	24956165
investigating bacterial populations in styrene-degrading biofilters by 16s rdna tag pyrosequencing.	microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. to further explore this relationship, 16s rdna tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. changes in microbial structure were observed bet ...	2014	24950754
investigating bacterial populations in styrene-degrading biofilters by 16s rdna tag pyrosequencing.	microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. to further explore this relationship, 16s rdna tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. changes in microbial structure were observed bet ...	2014	24950754
the oxygen-independent metabolism of cyclic monoterpenes in castellaniella defragrans 65phen.	the facultatively anaerobic betaproteobacterium castellaniella defragrans 65phen utilizes acyclic, monocyclic and bicyclic monoterpenes as sole carbon source under oxic as well as anoxic conditions. a biotransformation pathway of the acyclic β-myrcene required linalool dehydratase-isomerase as initial enzyme acting on the hydrocarbon. an in-frame deletion mutant did not use myrcene, but was able to grow on monocyclic monoterpenes. the genome sequence and a comparative proteome analysis together ...	2014	24952578
identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens dickeya dadantii 3937 and pectobacterium carotovorum wpp14 with supervised machine learning.	a wealth of genome sequences has provided thousands of genes of unknown function, but identification of functions for the large numbers of hypothetical genes in phytopathogens remains a challenge that impacts all research on plant-microbe interactions. decades of research on the molecular basis of pathogenesis focused on a limited number of factors associated with long-known host-microbe interaction systems, providing limited direction into this challenge. computational approaches to identify vi ...	2014	24952641
bdellovibrio bacteriovorus hd100 guards against pseudomonas tolaasii brown-blotch lesions on the surface of post-harvest agaricus bisporus supermarket mushrooms.	pseudomonas tolaasii is a problematic pathogen of cultured mushrooms, forming dark brown 'blotches' on mushroom surfaces and causing spoilage during crop growth and post-harvest . treating p. tolaasii infection is difficult, as other, commensal bacterial species such as pseudomonas putida are necessary for mushroom growth, so treatments must be relatively specific.	2014	24946855
the colrs signal transduction system responds to the excess of external zinc, iron, manganese, and cadmium.	the colrs two-component system has been shown to contribute to the membrane functionality and stress tolerance of pseudomonas putida as well as to the virulence of pseudomonas aeruginosa and plant pathogenic xanthomonas species. however, the conditions activating the colrs pathway and the signal(s) sensed by cols have remained unknown. here we aimed to analyze the role of the colrs system in metal tolerance of p. putida and to test whether cols can respond to metal excess.	2014	24946800
cloning, expression, purification, crystallization and x-ray crystallographic analysis of the (s)-3-hydroxybutyryl-coa dehydrogenase paah1 from ralstonia eutropha h16.	the (s)-3-hydroxybutyryl-coa dehydrogenase paah1 from ralstonia eutropha (repaah1) is an enzyme used in the biosynthesis of n-butanol from acetyl-coa by the reduction of acetoacetyl-coa to (s)-3-hydroxybutyryl-coa. the repaah1 protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 1.4 m ammonium sulfate, 0.1 m sodium cacodylate ph 6.0, 0.2 m sodium chloride at 295 k. x-ray diffraction data were collected to a maximum resolution of 2.6 å on a synchrotron beamli ...	2014	25005097
production of medium chain length polyhydroxyalkanoate in metabolic flux optimized pseudomonas putida.	pseudomnas putida is a natural producer of medium chain length polyhydroxyalkanoates (mcl-pha), a polymeric precursor of bioplastics. a two-fold increase of mcl-pha production via inactivation of the glucose dehydrogenase gene gcd, limiting the metabolic flux towards side products like gluconate was achieved before. here, we investigated the overproduction of enzymes catalyzing limiting steps of mcl-pha precursor formation.	2014	24948031
complete genome sequence of the p-nitrophenol-degrading bacterium pseudomonas putida dll-e4.	the first complete genome sequence of a p-nitrophenol (pnp)-degrading bacterium is reported here. pseudomonas putida dll-e4, a gram-negative bacterium isolated from methyl-parathion-polluted soil, can utilize pnp as the sole carbon and nitrogen source. p. putida dll-e4 has a 6,484,062 bp circular chromosome that contains 5,894 genes, with a g+c content of 62.46%.	2014	24948765
an operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element iceclc in pseudomonas knackmussii b13.	the integrative and conjugative element iceclc is a mobile genetic element in pseudomonas knackmussii b13, and an experimental model for a widely distributed group of elements in proteobacteria. iceclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. very little is known about the different factors that control the transfer frequency of this ice family. here we report the discovery of a three-gene operon encoded by ...	2014	24945944
genome-wide analysis of sphingomonas wittichii rw1 behaviour during inoculation and growth in contaminated sand.	the efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (that is, bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. here we present a comprehensive analysis of genome-wide gene expression of the bacterium sphingomonas wittichii rw1 in contaminated non-ste ...	2014	24936762
genome-wide analysis of sphingomonas wittichii rw1 behaviour during inoculation and growth in contaminated sand.	the efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (that is, bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. here we present a comprehensive analysis of genome-wide gene expression of the bacterium sphingomonas wittichii rw1 in contaminated non-ste ...	2014	24936762
nucleophilic 1,4-additions for natural product discovery.	natural products remain an important source of drug candidates, but the difficulties inherent to traditional isolation, coupled with unacceptably high rates of compound rediscovery, limit the pace of natural product detection. here we describe a reactivity-based screening method to rapidly identify exported bacterial metabolites that contain dehydrated amino acids (i.e., carbonyl- or imine-activated alkenes), a common motif in several classes of natural products. our strategy entails the use of ...	2014	24937678
selective allylic hydroxylation of acyclic terpenoids by cyp154e1 from thermobifida fusca yx.	allylic alcohols are valuable precursors in the synthesis of pharmaceutical intermediates, agrochemicals and natural products. regioselective oxidation of parental alkenes is a challenging task for chemical catalysts and requires several steps including protection and deprotection. many cytochrome p450 enzymes are known to catalyse selective allylic hydroxylation under mild conditions. here, we describe cyp154e1 from thermobifida fusca yx that enables this type of oxidation. several acyclic terp ...	2014	24991288
assessment of bacterial bph gene in amazonian dark earth and their adjacent soils.	amazonian anthrosols are known to harbour distinct and highly diverse microbial communities. as most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. to gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, ...	2014	24927167
metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia.	mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. the characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicat ...	2014	24955113
butanol tolerance regulated by a two-component response regulator slr1037 in photosynthetic synechocystis sp. pcc 6803.	butanol production directly from co2 in photosynthetic cyanobacteria is restricted by the high toxicity of butanol to the hosts. in previous studies, we have found that a few two-component signal transduction systems (tcstss) were differentially regulated in synechocystis sp. pcc 6803 after butanol treatment.	2014	24932218
characterization of the xiamenmycin biosynthesis gene cluster in streptomyces xiamenensis 318.	xiamenmycin (1) is a prenylated benzopyran derivative with anti-fibrotic activity. to investigate the genetic basis of xiamenmycin biosynthesis, we performed genome mining in the xiamenmycin-producing streptomyces xiamenensis wild-type strain 318 to identify a candidate gene cluster. the complete gene cluster, consisting of five genes, was confirmed by a series of gene inactivations and heterologous expression. based on bioinformatics analyses of each gene and feeding experiments, we found that ...	2014	24919072
colony morphology and transcriptome profiling of pseudomonas putida kt2440 and its mutants deficient in alginate or all eps synthesis under controlled matric potentials.	pseudomonas putida is a versatile bacterial species adapted to soil and its fluctuations. like many other species living in soil, p. putida often faces water limitation. alginate, an exopolysaccharide (eps) produced by p. putida, is known to create hydrated environments and alleviate the effect of water limitation. in addition to alginate, p. putida is capable of producing cellulose (bcs), putida exopolysaccharide a (pea), and putida exopolysaccharide b (peb). however, unlike alginate, not much ...	2014	24912454
emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds.	marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. the unique physiochemical properties of the marine environment (such as ph, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. these facts have resulted in the production of bioactive substances with different pro ...	2014	24918453
cultivation to improve in vivo solubility of overexpressed arginine deiminases in escherichia coli and the enzyme characteristics.	overexpression of foreign genes in escherichia coli cells is an efficient means to obtain recombinant proteins. the technique is, however, often hampered by misfolding, degradation, aggregation and formation in inclusion bodies of products.	2014	24908259
exploring the electron transfer pathway in the oxidation of avermectin by cyp107z13 in streptomyces ahygroscopicus zb01.	streptomyces ahygroscopicus zb01 can effectively oxidize 4″-oh of avermectin to form 4″-oxo-avermectin. cyp107z13 is responsible for this site-specific oxidation in zb01. in the present study, we explored the electron transfer pathway in oxidation of avermectin by cyp107z13 in zb01. a putative [3fe-4s] ferredoxin gene fd68 and two possible nadh-dependent ferredoxin reductase genes fdr18 and fdr28 were cloned from the genomic dna of zb01. fd68 gene disruption mutants showed no catalytic activity ...	2014	24905717
steroid conversion with cyp106a2 - production of pharmaceutically interesting dhea metabolites.	steroids are lipophilic compounds with a gonane skeleton and play an important role in higher organisms. due to different functionalizations - mainly hydroxylations - at the steroid molecule, they vary highly in their mode of action. the pharmaceutical industry is, therefore, interested in hydroxysteroids as therapeutic agents. the insertion of hydroxyl groups into a steroid core, however, is hardly accomplishable by classical chemical means; that is because microbial steroid hydroxylations are ...	2014	24903845
simultaneous heterotrophic nitrification and aerobic denitrification by chryseobacterium sp. r31 isolated from abattoir wastewater.	a heterotrophic carbon utilizing microbe (r31) capable of simultaneous nitrification and denitrification (snd) was isolated from wastewater of an indian slaughterhouse. from an initial cod value of 583.0 mg/l, 95.54% was removed whilst, from a starting nh4 (+)-n concentration of 55.7 mg/l, 95.87% was removed after 48 h contact. the concentrations of the intermediates hydroxylamine, nitrite, and nitrate were low, thus ensuring nitrogen removal. aerobic denitrification occurring during ammonium re ...	2014	24991552
ada response - a strategy for repair of alkylated dna in bacteria.	alkylating agents are widespread in the environment and also occur endogenously. they can be cytotoxic or mutagenic to the cells introducing alkylated bases to dna or rna. all organisms have evolved multiple dna repair mechanisms to counteract the effects of dna alkylation: the most cytotoxic lesion, n(3)-methyladenine (3mea), is excised by alka glycosylase initiating base excision repair (ber); toxic n(1)-methyladenine (1mea) and n(3)-methylcytosine (3mec), induced in dna and rna, are removed b ...	2014	24810496
the salmonella enterica serovar typhi leuo global regulator forms tetramers: residues involved in oligomerization, dna binding, and transcriptional regulation.	leuo is a lysr-type transcriptional regulator (lttr) that has been described to be a global regulator in escherichia coli and salmonella enterica, since it positively and negatively regulates the expression of genes involved in multiple biological processes. leuo is comprised of an n-terminal dna-binding domain (dbd) with a winged helix-turn-helix (whth) motif and of a long linker helix (lh) involved in dimerization that connects the dbd with the c-terminal effector-binding domain (ebd) or regul ...	2014	24659766
blocking peptidoglycan recycling in pseudomonas aeruginosa attenuates intrinsic resistance to fosfomycin.	gram-negative bacteria recycle as much as half of their cell wall per generation. here we show that interference with cell wall recycling in pseudomonas aeruginosa strains results in four- to eight-fold increased susceptibility to the antibiotic fosfomycin, pushing the minimal inhibitory concentration for strains pa14 and pa01 to therapeutically appropriate values of 2-4 and 8-16 mg/l, respectively. a newly discovered metabolic pathway that connects cell wall recycling with peptidoglycan de novo ...	2014	24819062
evaluation of zosteric acid for mitigating biofilm formation of pseudomonas putida isolated from a membrane bioreactor system.	this study provides data to define an efficient biocide-free strategy based on zosteric acid to counteract biofilm formation on the membranes of submerged bioreactor system plants. 16s rrna gene phylogenetic analysis showed that gammaproteobacteria was the prevalent taxa on fouled membranes of an italian wastewater plant. pseudomonas was the prevalent genus among the cultivable membrane-fouler bacteria and pseudomonas putida was selected as the target microorganism to test the efficacy of the an ...	2014	24879523
structure of the acinetobacter baumannii dithiol oxidase dsba bound to elongation factor ef-tu reveals a novel protein interaction site.	the multidrug resistant bacterium acinetobacter baumannii is a significant cause of nosocomial infection. biofilm formation, that requires both disulfide bond forming and chaperone-usher pathways, is a major virulence trait in this bacterium. our biochemical characterizations show that the periplasmic a. baumannii dsba (abdsba) enzyme has an oxidizing redox potential and dithiol oxidase activity. we found an unexpected non-covalent interaction between abdsba and the highly conserved prokaryotic ...	2014	24860094
genome features of pseudomonas putida ls46, a novel polyhydroxyalkanoate producer and its comparison with other p. putida strains.	a novel strain of pseudomonas putida ls46 was isolated from wastewater on the basis of its ability to synthesize medium chain-length polyhydroxyalkanoates (mcl-phas). p.putida ls46 was differentiated from other p.putida strains on the basis of cpn60 (ut). the complete genome of p.putida ls46 was sequenced and annotated. its chromosome is 5,86,2556 bp in size with gc ratio of 61.69. it is encoding 5316 genes, including 7 rrna genes and 76 trna genes. nucleotide sequence data of the complete p. pu ...	2014	25401060
proposed carrier lipid-binding site of undecaprenyl pyrophosphate phosphatase from escherichia coli.	undecaprenyl pyrophosphate phosphatase (uppp), an integral membrane protein, catalyzes the dephosphorylation of undecaprenyl pyrophosphate to undecaprenyl phosphate, which is an essential carrier lipid in the bacterial cell wall synthesis. sequence alignment reveals two consensus regions, containing glutamate-rich (e/q)xxxe plus pgxsrsxxt motifs and a histidine residue, specific to the bacterial uppp enzymes. the predicted topological model suggests that both of these regions are localized near ...	2014	24855653
screening of metagenomic and genomic libraries reveals three classes of bacterial enzymes that overcome the toxicity of acrylate.	acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-coa. previous work identified an acrylyl-coa reductase, encoded by the gene acui, as being important for conferring on bacteria the ability to grow in the presence of acrylate. however, some bac ...	2014	24848004
complete sequencing of novosphingobium sp. pp1y reveals a biotechnologically meaningful metabolic pattern.	novosphingobium sp. strain pp1y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. it exploits the aromatic fraction of fuel oils as a carbon and energy source. pp1y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. here, we report the complete functional annotation of the whole novosphingobium genome.	2014	24884518
diverse alkane hydroxylase genes in microorganisms and environments.	alkb and cyp153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. hundreds of diverse alkb and cyp153 genes including many novel ones were found in bacterial genomes, whereas none were found ...	2014	24829093
undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads.	there is a significant need for new antibiotics due to the rise in drug resistance. drugs such as methicillin and vancomycin target bacterial cell wall biosynthesis, but methicillin-resistant staphylococcus aureus (mrsa) and vancomycin-resistant enterococci (vre) have now arisen and are of major concern. inhibitors acting on new targets in cell wall biosynthesis are thus of particular interest since they might also restore sensitivity to existing drugs, and the cis-prenyl transferase undecapreny ...	2014	24827744
molecular evolution and functional characterisation of an ancient phenylalanine ammonia-lyase gene (nnpal1) from nelumbo nucifera: novel insight into the evolution of the pal family in angiosperms.	phenylalanine ammonia-lyase (pal; e.c.4.3.1.5) is a key enzyme of the phenylpropanoid pathway in plant development, and it catalyses the deamination of phenylalanine to trans-cinnamic acid, leading to the production of secondary metabolites. this enzyme has been identified in many organisms, ranging from prokaryotes to higher plants. because nelumbo nucifera is a basal dicot rich in many secondary metabolites, it is a suitable candidate for research on the phenylpropanoid pathway.	2014	24884360
pyoverdine synthesis by the mn(ii)-oxidizing bacterium pseudomonas putida gb-1.	when iron-starved, the mn(ii)-oxidizing bacteria pseudomonas putida strains gb-1 and mnb1 produce pyoverdines (pvdgb-1 and pvdmnb1), siderophores that both influence iron uptake and inhibit manganese(ii) oxidation by these strains. to explore the properties and genetics of a pvd that can affect manganese oxidation, lc-ms/ms, and various siderotyping techniques were used to identify the peptides of pvdgb-1 and pvdmnb1 as being (for both pvds): chromophore-asp-lys-ohasp-ser-gly-athr-lys-cohorn, re ...	2014	24847318
microbial tyrosinases: promising enzymes for pharmaceutical, food bioprocessing, and environmental industry.	tyrosinase is a natural enzyme and is often purified to only a low degree and it is involved in a variety of functions which mainly catalyse the o-hydroxylation of monophenols into their corresponding o-diphenols and the oxidation of o-diphenols to o-quinones using molecular oxygen, which then polymerizes to form brown or black pigments. the synthesis of o-diphenols is a potentially valuable catalytic ability and thus tyrosinase has attracted a lot of attention with respect to industrial applica ...	2014	24895537
chromosome segregation proteins of vibrio cholerae as transcription regulators.	abstract bacterial para and parb proteins are best known for their contribution to plasmid and chromosome segregation, but they may also contribute to other cell functions. in segregation, para interacts with parb, which binds to pars centromere-analogous sites. in transcription, plasmid par proteins can serve as repressors by specifically binding to their own promoters and, additionally, in the case of parb, by spreading from a pars site to nearby promoters. here, we have asked whether chromoso ...	2014	24803519
detection of silver nanoparticles inside marine diatom thalassiosira pseudonana by electron microscopy and focused ion beam.	in the following article an electron/ion microscopy study will be presented which investigates the uptake of silver nanoparticles (agnps) by the marine diatom thalassiosira pseudonana, a primary producer aquatic species. this organism has a characteristic silica exoskeleton that may represent a barrier for the uptake of some chemical pollutants, including nanoparticles (nps), but that presents a technical challenge when attempting to use electron-microscopy (em) methods to study np uptake. here ...	2014	24797958
polar localization of escherichia coli chemoreceptors requires an intact tol-pal complex.	subcellular biomolecular localization is critical for the metabolic and structural properties of the cell. the functional implications of the spatiotemporal distribution of protein complexes during the bacterial cell cycle have long been acknowledged; however, the molecular mechanisms for generating and maintaining their dynamic localization in bacteria are not completely understood. here we demonstrate that the trans-envelope tol-pal complex, a widely conserved component of the cell envelope of ...	2014	24720726
using unnatural amino acids to probe the energetics of oxyanion hole hydrogen bonds in the ketosteroid isomerase active site.	hydrogen bonds are ubiquitous in enzyme active sites, providing binding interactions and stabilizing charge rearrangements on substrate groups over the course of a reaction. but understanding the origin and magnitude of their catalytic contributions relative to hydrogen bonds made in aqueous solution remains difficult, in part because of complexities encountered in energetic interpretation of traditional site-directed mutagenesis experiments. it has been proposed for ketosteroid isomerase and ot ...	2014	24787954
an uncultivated nitrate-reducing member of the genus herminiimonas degrades toluene.	stable isotope probing (sip) is a cultivation-free methodology that provides information about the identity of microorganisms participating in assimilatory processes in complex communities. in this study, a herminiimonas-related bacterium was identified as the dominant member of a denitrifying microcosm fed [(13)c]toluene. the genome of the uncultivated toluene-degrading bacterium was obtained by applying pyrosequencing to the heavy dna fraction. the draft genome comprised ~3.8 mb, in 131 assemb ...	2014	24632261
maldi-tof identification of the human gut microbiome in people with and without diarrhea in senegal.	in africa, there are several problems with the specific identification of bacteria. recently, maldi-tof mass spectrometry has become a powerful tool for the routine microbial identification in many clinical laboratories.	2014	24784934
gastrointestinal pathology in juvenile and adult cftr-knockout ferrets.	cystic fibrosis (cf) is a multiorgan disease caused by loss of a functional cystic fibrosis transmembrane conductance regulator (cftr) chloride channel in many epithelia of the body. here we report the pathology observed in the gastrointestinal organs of juvenile to adult cftr-knockout ferrets. cf gastrointestinal manifestations included gastric ulceration, intestinal bacterial overgrowth with villous atrophy, and rectal prolapse. metagenomic phylogenetic analysis of fecal microbiota by deep seq ...	2014	24637292
novel metabolic features in acinetobacter baylyi adp1 revealed by a multiomics approach.	expansive knowledge of bacterial metabolism has been gained from genome sequencing output, but the high proportion of genes lacking a proper functional annotation in a given genome still impedes the accurate prediction of the metabolism of a cell. to access to a more global view of the functioning of the soil bacterium acinetobacter baylyi adp1, we adopted a multi 'omics' approach. application of rna-seq transcriptomics and lc/ms-based metabolomics, along with the systematic phenotyping of the c ...	2014	25374488
social behavior and decision making in bacterial conjugation.	bacteria frequently acquire novel genes by horizontal gene transfer (hgt). hgt through the process of bacterial conjugation is highly efficient and depends on the presence of conjugative plasmids (cps) or integrated conjugative elements (ices) that provide the necessary genes for dna transmission. this review focuses on recent advancements in our understanding of ssdna transfer systems and regulatory networks ensuring timely and spatially controlled dna transfer (tra) gene expression. as will be ...	2014	24809026
unmasking the measles-like parchment discoloration: molecular and microanalytical approach.	many ancient parchments are defaced by red or purple maculae associated with localized destruction of collagen fibres. although the main characteristics of this damage were present in most of the manuscripts analysed by many authors, no common microbial or fungal denominator has been found so far, and little or no correspondence between the microbial or fungal species isolated from materials could be addressed. in this study, culture-independent molecular methods and scanning electron microscopy ...	2014	24684276
unmasking the measles-like parchment discoloration: molecular and microanalytical approach.	many ancient parchments are defaced by red or purple maculae associated with localized destruction of collagen fibres. although the main characteristics of this damage were present in most of the manuscripts analysed by many authors, no common microbial or fungal denominator has been found so far, and little or no correspondence between the microbial or fungal species isolated from materials could be addressed. in this study, culture-independent molecular methods and scanning electron microscopy ...	2014	24684276
integration of bioinformatics to biodegradation.	bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. the present review describes development of various bioinformatics tools that may be applied in the field of biodegradation. several databases, including the university of minnesota biocatalysis/biodegradation database (um-bbd), a database of biodegradative oxygenases (oxdbase), biodegradation network-molecular biology database (bionemo) metacyc, and biocyc have been developed to enable ...	2014	24808763
antimicrobial activity of pantothenol against staphylococci possessing a prokaryotic type ii pantothenate kinase.	pantothenol is a provitamin of pantothenic acid (vitamin b5) that is widely used in healthcare and cosmetic products. this analog of pantothenate has been shown to markedly inhibit the phosphorylation activity of the prokaryotic type ii pantothenate kinase of staphylococcus aureus, which catalyzes the first step of the coenzyme a biosynthetic pathway. since type ii enzymes are found exclusively in staphylococci, pantothenol suppresses the growth of s. aureus, s. epidermidis, and s. saprophyticus ...	2014	24759689
isolation and characterization of broad spectrum coaggregating bacteria from different water systems for potential use in bioaugmentation.	the bridging bacteria with broad-spectrum coaggregation ability play an important role during multispecies-biofilm development. in this study, through a visual and semi-quantitative assay, twenty-two bacterial strains with aggregation ability were obtained from 8 different water environments, and these strains were assigned to 7 genera according to their 16s rdna and they were aeromonas, bacillus, comamonas, exiguobacterium, pseudomonas, shewanella and comamonas. furthermore, all possible 231 pa ...	2014	24736645
mp3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data.	the identification of virulent proteins in any de-novo sequenced genome is useful in estimating its pathogenic ability and understanding the mechanism of pathogenesis. similarly, the identification of such proteins could be valuable in comparing the metagenome of healthy and diseased individuals and estimating the proportion of pathogenic species. however, the common challenge in both the above tasks is the identification of virulent proteins since a significant proportion of genomic and metagen ...	2014	24736651
gammaproteobacterial diazotrophs and nifh gene expression in surface waters of the south pacific ocean.	in addition to the cyanobacterial n2-fixers (diazotrophs), there is a high nifh gene diversity of non-cyanobacterial groups present in marine environments, yet quantitative information about these groups is scarce. n2 fixation potential (nifh gene expression), diversity and distributions of the uncultivated diazotroph phylotype γ-24774a11, a putative gammaproteobacterium, were investigated in the western south pacific ocean. γ-24774a11 gene copies correlated positively with diazotrophic cyanobac ...	2014	24722632
nitrile as activating group in the asymmetric bioreduction of β-cyanoacrylic acids catalyzed by ene-reductases.	asymmetric bioreduction of an (e)-β-cyano-2,4-dienoic acid derivative by ene-reductases allowed a shortened access to a precursor of pregabalin [(s)-3-(aminomethyl)-5-methylhexanoic acid] possessing the desired configuration in up to 94% conversion and >99% ee. deuterium labelling studies showed that the nitrile moiety was the preferred activating/anchor group in the active site of the enzyme over the carboxylic acid or the corresponding methyl ester.	2014	26190962
production of polypeptide antibiotic from streptomyces parvulus and its antibacterial activity.	a highly potent secondary metabolite producing actinomycetes strain is isolated from marine soil sediments of visakhapatnam sea coast, bay of bengal. over all ten strains are isolated from the collected soil sediments. among the ten actinomycetes strains the broad spectrum strain rspsn2 was selected for molecular characterization, antibiotic production and its purification. the nucleotide sequence of the 1 rrna gene (1261 base pairs) of the most potent strain evidenced a 96% similarity with stre ...	2014	24948949
prophage induction and differential reca and umudab transcriptome regulation in the dna damage responses of acinetobacter baumannii and acinetobacter baylyi.	the sos response to dna damage that induces up to 10% of the prokaryotic genome requires reca action to relieve lexa transcriptional repression. in acinetobacter species, which lack lexa, the error-prone polymerase accessory umudab is instead required for ddrr induction after dna damage, suggesting it might be a lexa analog. rna-seq experiments defined the dna damage transcriptome (mitomycin c-induced) of wild type, reca and umudab mutant strains of both a. baylyi adp1 and a. baumannii atcc 1797 ...	2014	24709747
analysis of biodegradation performance of furfural and 5-hydroxymethylfurfural by amorphotheca resinae zn1.	furfural and 5-hydroxymethylfurfural (hmf) are the degradation products of lignocellulose during pretreatment operations and significantly inhibit the consequent enzymatic hydrolysis and fermentation processes. the biodetoxification fungus amorphotheca resinae zn1 had demonstrated its excellent capacity on degrading lignocellulose derived inhibitors and helped the fermentation processes to achieve high yield of ethanol and biochemicals. analysis of the biological degradation performance of furfu ...	2014	24708699
fructose 1-phosphate is the one and only physiological effector of the cra (frur) regulator of pseudomonas putida.	fructose-1-phosphate (f1p) is the preferred effector of the catabolite repressor/activator (cra) protein of the soil bacterium pseudomonas putida but its ability to bind other metabolic intermediates in vivo is unclear. the cra protein of this microorganism (cra(pp)) was submitted to mobility shift assays with target dna sequences (the pfrub promoter) and candidate effectors fructose-1,6-bisphosphate (fbp), glucose 6-phosphate (g6p), and fructose-6-phosphate (f6p). 1 mm f1p was sufficient to rel ...	2014	24918052
glass-forming property of hydroxyectoine is the cause of its superior function as a desiccation protectant.	we were able to demonstrate that hydroxyectoine, in contrast to ectoine, is a good glass-forming compound. fourier transform infrared and spin label electron spin resonance studies of dry ectoine and hydroxyectoine have shown that the superior glass-forming properties of hydroxyectoine result from stronger intermolecular h-bonds with the oh group of hydroxyectoine. spin probe experiments have also shown that better molecular immobilization in dry hydroxyectoine provides better redox stability of ...	2014	24772110
isolation, bioactivity, and production of ortho-hydroxydaidzein and ortho-hydroxygenistein.	daidzein and genistein are two major components of soy isoflavones. they exist abundantly in plants and possess multiple bioactivities. in contrast, ortho-hydroxydaidzein (ohd) and ortho-hydroxygenistein (ohg), including 6-hydroxydaidzein (6-ohd), 8-hydroxydaidzein (8-ohd), 3'-hydroxydaidzein (3'-ohd), 6-hydroxygenistein (6-ohg), 8-hydroxygenistein (8-ohg), and 3'-hydroxygenistein (3'-ohg), are rarely found in plants. instead, they are usually isolated from fermented soybean foods or microbial f ...	2014	24705463
comparison of local features from two spanish hospitals reveals common and specific traits at multiple levels of the molecular epidemiology of metallo-β-lactamase-producing pseudomonas spp.	twenty-seven well-characterized metallo-β-lactamase (mbl)-producing pseudomonas strains from two distantly located hospitals were analyzed. the results revealed specific features defining the multilevel epidemiology of strains from each hospital in terms of species, clonality, predominance of high-risk clones, composition/diversity of integrons, and linkages of tn402-related structures. therefore, despite the global trends driving the epidemiology of mbl-producing pseudomonas spp., the presence ...	2014	24492368
cyclic-amp and bacterial cyclic-amp receptor proteins revisited: adaptation for different ecological niches.	escherichia coli cyclic-amp receptor protein (crp) represents one of the paradigms of bacterial gene regulation. yet despite decades of intensive study, new information continues to emerge that prompts reassessment of this classic regulatory system. moreover, in recent years crps from several other bacterial species have been characterized, allowing the general applicability of the crp paradigm to be tested. here the properties of the e. coli, mycobacterium tuberculosis and pseudomonas putida cr ...	2014	24509484
bloodstream infections caused by pseudomonas spp.: how to detect carbapenemase producers directly from blood cultures.	the carba np test has been evaluated to detect carbapenemase-producing pseudomonas spp. directly from blood cultures. this rapid and cost-effective test permits an early identification of carbapenemase-producing pseudomonas spp. directly from blood cultures with excellent sensitivity and specificity. results may be useful in particular for guiding the first-line therapy and epidemiological purposes.	2014	24501031
life history analysis of integrative and conjugative element activation in growing microcolonies of pseudomonas.	integrative and conjugative elements (ice) are in some ways parasitic mobile dna that propagate vertically through replication with the bacterial host chromosome but at low frequencies can excise and invade new recipient cells through conjugation and reintegration (horizontal propagation). the factors that contribute to successful horizontal propagation are not very well understood. here, we study the influence of host cell life history on the initiation of transfer of a model ice named iceclc i ...	2014	24464463
characterization of an allylic/benzyl alcohol dehydrogenase from yokenella sp. strain wzy002, an organism potentially useful for the synthesis of α,β-unsaturated alcohols from allylic aldehydes and ketones.	a novel whole-cell biocatalyst with high allylic alcohol-oxidizing activities was screened and identified as yokenella sp. wzy002, which chemoselectively reduced the c=o bond of allylic aldehydes/ketones to the corresponding α,β-unsaturated alcohols at 30°c and ph 8.0. the strain also had the capacity of stereoselectively reducing aromatic ketones to (s)-enantioselective alcohols. the enzyme responsible for the predominant allylic/benzyl alcohol dehydrogenase activity was purified to homogeneity ...	2014	24509923
enzyme architecture: on the importance of being in a protein cage.	substrate binding occludes water from the active sites of many enzymes. there is a correlation between the burden to enzymatic catalysis of deprotonation of carbon acids and the substrate immobilization at solvent-occluded active sites for ketosteroid isomerase (ksi--small burden, substrate pka=13), triosephosphate isomerase (tim, substrate pka≈18) and diaminopimelate epimerase (dap epimerase, large burden, substrate pka≈29) catalyzed reaction. ksi binds substrates at a surface cleft, tim binds ...	2014	24699188
complete genome sequence of the radiation-resistant bacterium rubrobacter radiotolerans rsps-4.	rubrobacter radiotolerans strain rsps-4 is a slightly thermophilic member of the phylum "actinobacteria" isolated from a hot spring in são pedro do sul, portugal. this aerobic and halotolerant bacterium is also extremely resistant to gamma and uv radiation, which are the main reasons for the interest in sequencing its genome. here, we present the complete genome sequence of strain rsps-4 as well as its assembly and annotation. we also compare the gene sequence of this organism with that of the t ...	2014	25197483
bacillus thuringiensis subsp. israelensis and its dipteran-specific toxins.	bacillus thuringiensis subsp. israelensis (bti) is the first bacillus thuringiensis to be found and used as an effective biological control agent against larvae of many mosquito and black fly species around the world. its larvicidal activity resides in four major (of 134, 128, 72 and 27 kda) and at least two minor (of 78 and 29 kda) polypeptides encoded respectively by cry4aa, cry4ba, cry11aa, cyt1aa, cry10aa and cyt2ba, all mapped on the 128 kb plasmid known as pbtoxis. these six δ-endotoxins f ...	2014	24686769
force field independent metal parameters using a nonbonded dummy model.	the cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. in this work we refine existing literature parameters for octahedrally coordinated mn(2+), zn(2+), mg(2+), and ca(2+), as well as providing new parameters for ni(2+), co(2+), and fe(2+). in all the cases, we are able to reproduce both m(2+)-o distances and experimental solvation free energies, which has not bee ...	2014	24670003
cloning, expression, purification, crystallization and x-ray crystallographic analysis of (s)-3-hydroxybutyryl-coa dehydrogenase from clostridium butyricum.	(s)-3-hydroxybutyryl-coa dehydrogenase from clostridium butyricum (cbhbd) is an enzyme that catalyzes the second step in the biosynthesis of n-butanol from acetyl-coa by the reduction of acetoacetyl-coa to 3-hydroxybutyryl-coa. the cbhbd protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 2 m ammonium sulfate, 0.1 m caps ph 10.5, 0.2 m lithium sulfate at 295 k. x-ray diffraction data were collected to a maximum resolution of 2.3 å on a synchrotron beamline. ...	2014	24699745
outbreak of pseudomonas oryzihabitans pseudobacteremia related to contaminated equipment in an emergency room of a tertiary hospital in korea.	pseudomonas oryzihabitans is frequently found in various sites within hospital settings, including sink drains and respiratory therapy equipment. although it rarely causes human infections, p. oryzihabitans has recently been considered a potential nosocomial pathogen, especially in immunocompromised hosts. we report our experience of an outbreak of p. oryzihabitans pseudobacteremia, presumably due to faulty aseptic preparation of a saline gauze canister.	2014	24693469
diagnosis of carrion's disease by direct blood pcr in thin blood smear negative samples.	bartonella bacilliformis is the etiologic agent of carrion's disease. this disease has two well established phases, the most relevant being the so called oroya fever, in which b. bacilliformis infect the erythrocytes resulting in severe anemia and transient immunosuppression, with a high lethality in the absence of adequate antibiotic treatment. the presence of b. bacilliformis was studied in 113 blood samples suspected of carrion's disease based on clinical criteria, despite the absence of a po ...	2014	24651298
accumulation of high-value lipids in single-cell microorganisms: a mechanistic approach and future perspectives.	in recent years attention has been focused on the utilization of microorganisms as alternatives for industrial and nutritional applications. considerable research has been devoted to techniques for growth, extraction, and purification of high-value lipids for their use as biofuels and biosurfactants as well as high-value metabolites for nutrition and health. these successes argue that the elucidation of the mechanisms underlying the microbial biosynthesis of such molecules, which are far from be ...	2014	24628496
responses to elevated c-di-gmp levels in mutualistic and pathogenic plant-interacting bacteria.	despite a recent burst of research, knowledge on c-di-gmp signaling pathways remains largely fragmentary and molecular mechanisms of regulation and even c-di-gmp targets are yet unknown for most bacteria. besides genomics or bioinformatics, accompanying alternative approaches are necessary to reveal c-di-gmp regulation in bacteria with complex lifestyles. we have approached this study by artificially altering the c-di-gmp economy of diverse pathogenic and mutualistic plant-interacting bacteria a ...	2014	24626229
effects of different compost amendments on the abundance and composition of alkb harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons.	alkane degrading microorganisms play an important role for the bioremediation of petrogenic contaminated environments. in this study, we investigated the effects of compost addition on the abundance and diversity of bacteria harboring the alkane monooxygenase gene (alkb) in an oil-contaminated soil originated from an industrial zone in celje, slovenia (technosol). soil without any amendments (control soil) and soil amended with two composts differing in their maturation stage and nutrient availa ...	2014	24659987
structural basis for bacterial quorum sensing-mediated oxalogenesis.	the burkholderia species utilize acetyl-coa and oxaloacetate, substrates for citrate synthase in the tca cycle, to produce oxalic acid in response to bacterial cell to cell communication, called quorum sensing. quorum sensing-mediated oxalogenesis via a sequential reaction by obca and obcb counteracts the population-collapsing alkaline ph of the stationary growth phase. thus, the oxalic acid produced plays an essential role as an excreted public good for survival of the group. here, we report st ...	2014	24616091
expanding ester biosynthesis in escherichia coli.	to expand the capabilities of whole-cell biocatalysis, we have engineered escherichia coli to produce various esters. the alcohol o-acyltransferase (atf) class of enzyme uses acyl-coa units for ester formation. the release of free coa upon esterification with an alcohol provides the free energy to facilitate ester formation. the diversity of coa molecules found in nature in combination with various alcohol biosynthetic pathways allows for the biosynthesis of a multitude of esters. small to mediu ...	2014	24609358
functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in sphingobium sp. pnb.	sphingobium sp. pnb, like other sphingomonads, has multiple ring-hydroxylating oxygenase (rho) genes. three different fosmid clones have been sequenced to identify the putative genes responsible for the degradation of various aromatics in this bacterial strain. comparison of the map of the catabolic genes with that of different sphingomonads revealed a similar arrangement of gene clusters that harbors seven sets of rho terminal components and a sole set of electron transport (et) proteins. the p ...	2014	24918041
bactericidal and bacteriostatic antibiotics and the fenton reaction.	in gammaproteobacteria ros are not exclusively responsible for the activity of bactericidal compounds. future research is required to determine whether the high-valence feo2+ formed in the presence of bactericidal compounds enhances killing in addition to the direct inhibition of cell-wall assembly, protein synthesis or interference with dna metabolism.	2014	24602244
experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site.	the positioning of catalytic groups within proteins plays an important role in enzyme catalysis, and here we investigate the positioning of the general base in the enzyme ketosteroid isomerase (ksi). the oxygen atoms of asp38, the general base in ksi, were previously shown to be involved in anion-aromatic interactions with two neighboring phe residues. here we ask whether those interactions are sufficient, within the overall protein architecture, to position asp38 for catalysis or whether the si ...	2014	24597914
ethylene-forming enzyme and bioethylene production.	worldwide, ethylene is the most produced organic compound. it serves as a building block for a wide variety of plastics, textiles, and chemicals, and a process has been developed for its conversion into liquid transportation fuels. currently, commercial ethylene production involves steam cracking of fossil fuels, and is the highest co2-emitting process in the chemical industry. therefore, there is great interest in developing technology for ethylene production from renewable resources including ...	2014	24589138
comparative study of hydroalcoholic extracts of momordica charantia l. against foodborne pathogens.	the antimicrobial effect of 24 different hydroalcoholic extracts (100, 75, 50 and 25% methanol and water) obtained from four parts (leaf+stem (aerial), peel, pulp and seed) of momordica charantia l. were investigated against five gram-positive, six gram-negative and four fungal strains. the extraction was done by individual cold percolation method using hexane, different hydroalcoholic solvent (100, 75, 50 and 25% methanol) and water. the antimicrobial activity was done by agar well diffusion as ...	2014	24843188
coffee husk composting: an investigation of the process using molecular and non-molecular tools.	various parameters were measured during a 90-day composting process of coffee husk with cow dung (pile 1), with fruit/vegetable wastes (pile 2) and coffee husk alone (pile 3). samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. c/n ratios of piles 1 and 2 decreased significantly over the 90 days. the highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (piles 1 and 2) indicated microbial succession wi ...	2014	24369846
the complete nucleotide sequence of the carbapenem resistance-conferring conjugative plasmid pld209 from a pseudomonas putida clinical strain reveals a chimeric design formed by modules derived from both environmental and clinical bacteria.	the complete sequence of the carbapenem-resistance-conferring conjugative plasmid pld209 from a pseudomonas putida clinical strain is presented. pld209 is formed by 3 well-defined regions: an adaptability module encompassing a tn402-like class 1 integron of clinical origin containing blavim-2 and aaca4 gene cassettes, partitioning and transfer modules, and a replication module derived from plasmids of environmental bacteria. pld209 is thus a mosaic of modules originating in both the clinical and ...	2014	24395220
production of lycopene in the non-carotenoid-producing yeast yarrowia lipolytica.	the codon-optimized genes crtb and crti of pantoea ananatis were expressed in yarrowia lipolytica under the control of the tef1 promoter of y. lipolytica. additionally, the rate-limiting genes for isoprenoid biosynthesis in y. lipolytica, ggs1 and hmg1, were overexpressed to increase the production of lycopene. all of the genes were also expressed in a y. lipolytica strain with pox1 to pox6 and gut2 deleted, which led to an increase in the size of lipid bodies and a further increase in lycopene ...	2014	24375130
bioremediation of p-nitrophenol by pseudomonas putida 1274 strain.	p-nitrophenol (pnp) occurs as contaminants of industrial effluents and it is the most important environmental pollutant and causes significant health and environmental risks, because it is toxic to many living organisms. nevertheless, the information regarding pnp degradation pathways and their enzymes remain limited.	2014	24581307
functional characterization of a stys sensor kinase reveals distinct domains associated with intracellular and extracellular sensing of styrene in p. putida ca-3.	bacterial two-component systems (tcss) are of vital importance in the translation of rapidly changing environmental conditions into appropriate cellular regulatory responses enabling adaptation, growth, and survival. the diverse range of environmental signals that tcss can process, coupled with discrete modular domains within tcs proteins, offers considerable potential for the rational design of bio-sensor and/or bio-reporter strains. in this study we functionally characterize the multi-domain s ...	2014	24637704
new hydrocarbon degradation pathways in the microbial metagenome from brazilian petroleum reservoirs.	current knowledge of the microbial diversity and metabolic pathways involved in hydrocarbon degradation in petroleum reservoirs is still limited, mostly due to the difficulty in recovering the complex community from such an extreme environment. metagenomics is a valuable tool to investigate the genetic and functional diversity of previously uncultured microorganisms in natural environments. using a function-driven metagenomic approach, we investigated the metabolic abilities of microbial communi ...	2014	24587220
hydrogen peroxide-independent production of α-alkenes by oletje p450 fatty acid decarboxylase.	cytochrome p450 oletje from jeotgalicoccus sp. atcc 8456, a new member of the cyp152 peroxygenase family, was recently found to catalyze the unusual decarboxylation of long-chain fatty acids to form α-alkenes using h2o2 as the sole electron and oxygen donor. because aliphatic α-alkenes are important chemicals that can be used as biofuels to replace fossil fuels, or for making lubricants, polymers and detergents, studies on oletje fatty acid decarboxylase are significant and may lead to commercia ...	2014	24565055
production and characterization of protein encapsulated silver nanoparticles by marine isolate streptomyces parvulus ssnp11.	production of protein encapsulated silver nanoparticles (agnps) assisted by marine actinomycetes strain has been investigated. the selective isolate was identified as streptomyces parvulus ssnp11 based on chemotaxonomic and 16s rrna analysis. maximum agnps production was observed within 24 h incubation time. the produced agnps are spherical in shape with monodispersive and crystalline in nature. the particle size distribution ranges from 1.66 to 11.68 nm with a mean size of 2.1 nm. the biosynthe ...	2014	24891741
functional metagenomics for the investigation of antibiotic resistance.	antibiotic resistance is a major threat to human health and well-being. to effectively combat this problem we need to understand the range of different resistance genes that allow bacteria to resist antibiotics. to do this the whole microbiota needs to be investigated. as most bacteria cannot be cultivated in the laboratory, the reservoir of antibiotic resistance genes in the non-cultivatable majority remains relatively unexplored. currently the only way to study antibiotic resistance in these o ...	2014	24556726
alleviation of salt stress by enterobacter sp. ej01 in tomato and arabidopsis is accompanied by up-regulation of conserved salinity responsive factors in plants.	microbiota in the niches of the rhizosphere zones can affect plant growth and responses to environmental stress conditions via mutualistic interactions with host plants. specifically, some beneficial bacteria, collectively referred to as plant growth promoting rhizobacteria (pgprs), increase plant biomass and innate immunity potential. here, we report that enterobacter sp. ej01, a bacterium isolated from sea china pink (dianthus japonicus thunb) in reclaimed land of gyehwa-do in korea, improved ...	2014	24598995
physical, chemical, and biological methods for the removal of arsenic compounds.	arsenic is a toxic metalloid which is widely distributed in nature. it is normally present as arsenate under oxic conditions while arsenite is predominant under reducing condition. the major discharges of arsenic in the environment are mainly due to natural sources such as aquifers and anthropogenic sources. it is known that arsenite salts are more toxic than arsenate as it binds with vicinal thiols in pyruvate dehydrogenase while arsenate inhibits the oxidative phosphorylation process. the comm ...	2014	24696853
assessment of ms/ms search algorithms with parent-protein profiling.	peptide mass spectrometry relies crucially on algorithms that match peptides to spectra. we describe a method to evaluate the accuracy of these algorithms based on the masses of parent proteins before trypsin endoprotease digestion. measurement of conformance to parent proteins provides a score for comparison of the performances of different algorithms as well as alternative parameter settings for a given algorithm. tracking of conformance scores for spectrum matches to proteins with progressive ...	2014	24533481
isolation and characterization of a nitrile-hydrolysing bacterium isoptericola variabilis rgt01.	a nitrile-hydrolysing bacterium, identified as isoptericola variabilis rgt01, was isolated from industrial effluent through enrichment culture technique using acrylonitrile as the carbon source. whole cells of this microorganism exhibited a broad range of nitrile-hydrolysing activity as they hydrolysed five aliphatic nitriles (acetonitrile, acrylonitrile, propionitrile, butyronitrile and valeronitrile), two aromatic nitriles (benzonitrile and m-tolunitrile) and two arylacetonitriles (4-methoxyph ...	2014	25320428
a thermodynamic theory of microbial growth.	our ability to model the growth of microbes only relies on empirical laws, fundamentally restricting our understanding and predictive capacity in many environmental systems. in particular, the link between energy balances and growth dynamics is still not understood. here we demonstrate a microbial growth equation relying on an explicit theoretical ground sustained by boltzmann statistics, thus establishing a relationship between microbial growth rate and available energy. the validity of our equ ...	2014	24522260