complications of port-a-cath® in patients with sickle cell cell exchange/transfusion is frequently used in the management of patients with medical complications related to acute severe sickle cell disease (scd). however, peripheral venous access is often difficult without central venous catheters (cvcs) in adult patients with moderate or severe scd.201122341844
production of indole acetic acid by pseudomonas sp.: effect of coinoculation with mesorhizobium sp. cicer on nodulation and plant growth of chickpea (cicer arietinum).pseudomonas isolates obtained from the rhizosphere of chickpea (cicer arietinum l.) and green gram (vigna radiata) were found to produce significant amount of indole acetic acid (iaa) when grown in a lb medium broth supplemented with l-tryptophan. seed bacterization of chickpea cultivar c235 with different pseudomonas isolates showed stunting effect on the development of root and shoot at 5 and 10 days of seedling growth except the strains mps79 and mps90 that showed stimulation of root growth, ...201123572992
engineering the substrate specificity of a thermophilic penicillin acylase from thermus thermophilus.a homologue of the escherichia coli penicillin acylase is encoded in the genomes of several thermophiles, including in different thermus thermophilus strains. although the natural substrate of this enzyme is not known, this acylase shows a marked preference for penicillin k over penicillin g. three-dimensional models were created in which the catalytic residues and the substrate binding pocket were identified. through rational redesign, residues were replaced to mimic the aromatic binding site o ...201223263966
isolation, analysis and antimicrobial activity of the acidic fractions of mastic, kurdica, mutica and cabolica gums from genus pistacia.the chemical entities of mastic, kurdica, mutica and cabolica gums from genus pistacia have been isolated and characterised by gc-mass spectrometry, high performance liquid chromatography and column chromatography. these chemical entities were screened for anti-microbial activities against nine strains of helicobacter pylori and some other gram-negative and gram-positive bacteria. the most bioactive components were structurally analysed. these components mimic steroid compounds, in particular, t ...201122980113
bio-activity of natural polymers from the genus pistacia: a validated model for their antimicrobial action.the polymers from mastic gum of pistacia lentiscose and subspecies of pistacia atlantica, (sp. kurdica, mutica and cabolica) have been isolated and characterised by gel permeation chromatography (gpc) and 13c nmr spectroscopy as cis-1,4-poly-?-myrcenes. they were screened against helicobacter pylori and other gram-negative and gram-positive bacteria to evaluate their antimicrobial action. in order to further test their hypothesised mode of action, two polymer types were synthesized: one from myr ...201122980106
a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes.for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ...201626511485
a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes.for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ...201626511485
the β-glucanase zglama from zobellia galactanivorans evolved a bent active site adapted for efficient degradation of algal laminarin.laminarinase is commonly used to describe β-1,3-glucanases widespread throughout archaea, bacteria, and several eukaryotic lineages. some β-1,3-glucanases have already been structurally and biochemically characterized, but very few from organisms that are in contact with genuine laminarin, the storage polysaccharide of brown algae. here we report the heterologous expression and subsequent biochemical and structural characterization of zglamagh16 from zobellia galactanivorans, the first gh16 lami ...201424337571
the β-glucanase zglama from zobellia galactanivorans evolved a bent active site adapted for efficient degradation of algal laminarin.laminarinase is commonly used to describe β-1,3-glucanases widespread throughout archaea, bacteria, and several eukaryotic lineages. some β-1,3-glucanases have already been structurally and biochemically characterized, but very few from organisms that are in contact with genuine laminarin, the storage polysaccharide of brown algae. here we report the heterologous expression and subsequent biochemical and structural characterization of zglamagh16 from zobellia galactanivorans, the first gh16 lami ...201424337571
highly diverse nirk genes comprise two major clades that harbour ammonium-producing denitrifiers.copper dependent nitrite reductase, nirk, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. distinct structural nirk classes and phylogenetic clades of nirk-type denitrifiers have previously been observed based on a limited set of nirk sequences, however, their environmental distribution or ecological strategies are currently unknown. in addition, environmental nirk-type denitrifiers are currently underestimated in pcr-dependent surveys due to primer coverage lim ...201626923558
tmrdb (tmrna database).maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url with mirror sites located at auburn university, auburn, alabama ( and the bioinformatics research center, aarhus, denmark ( the tmrdb collects and distributes information relevant to the study of tmrna. in trans-translation, this molecule combines propert ...200312520048
acrylyl-coenzyme a reductase, an enzyme involved in the assimilation of 3-hydroxypropionate by rhodobacter sphaeroides.the anoxygenic phototroph rhodobacter sphaeroides uses 3-hydroxypropionate as a sole carbon source for growth. previously, we showed that the gene (rsp_1434) known as acui, which encodes a protein of the medium-chain dehydrogenase/reductase (mdr) superfamily, was involved in 3-hydroxypropionate assimilation via the reductive conversion to propionyl-coenzyme a (coa). based on these results, we speculated that acui encoded acrylyl-coa reductase. in this work, we characterize the in vitro enzyme ac ...201323955006
opportunistic infections in hiv-infected patients differ strongly in frequencies and spectra between patients with low cd4+ cell counts examined postmortem and compensated patients examined antemortem irrespective of the haart era.aids-related mortality has changed dramatically with the onset of highly active antiretroviral therapy (haart), which has even allowed compensated hiv-infected patients to withdraw from secondary therapy directed against opportunistic pathogens. however, in recently autopsied hiv-infected patients, we observed that associations with a broad spectrum of pathogens remain, although detailed analyses are lacking. therefore, we focused on the possible frequency and spectrum shifts in pathogens associ ...201627611681
bacteria in crude oil survived autoclaving and stimulated differentially by exogenous bacteria.autoclaving of crude oil is often used to evaluate the hydrocarbon-degrading abilities of bacteria. this may be potentially useful for bioaugmentation and microbial enhanced oil recovery (meor). however, it is not entirely clear if "endogenous" bacteria (e.g., spores) in/on crude oil survive the autoclaving process, or influence subsequent evaluation of the hydrocarbon-degradation abilities of the "exogenous" bacterial strains. to test this, we inoculated autoclaved crude oil medium with six exo ...201223028421
functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ...201324062736
a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ...201020141328
functional metagenomics of spacecraft assembly cleanrooms: presence of virulence factors associated with human pathogens.strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. we wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. three geographically distinct cleanrooms were sampled during the ...201627667984
characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates.microorganisms are used in large-scale heap or tank aeration processes for the commercial extraction of a variety of metals from their ores or concentrates. these include copper, cobalt, gold and, in the past, uranium. the metal solubilization processes are considered to be largely chemical with the microorganisms providing the chemicals and the space (exopolysaccharide layer) where the mineral dissolution reactions occur. temperatures at which these processes are carried out can vary from ambie ...200515877814
conserved amino acid sequence features in the alpha subunits of mofe, vfe, and fefe nitrogenases.this study examines the structural features and phylogeny of the alpha subunits of 69 full-length nifd (mofe subunit), vnfd (vfe subunit), and anfd (fefe subunit) sequences.200919578539
biotechnological tools for environmental sustainability: prospects and challenges for environments in nigeria-a standard review.the environment is a very important component necessary for the existence of both man and other biotic organisms. the degree of sustainability of the physical environment is an index of the survival and well-being of the entire components in it. additionally, it is not sufficient to try disposing toxic/deleterious substances with any known method. the best method of sustaining the environment is such that returns back all the components (wastes) in a recyclable way so that the waste becomes usef ...201222611499
functional promiscuity of homologues of the bacterial arsa atpases.the arsa atpase of e. coli plays an essential role in arsenic detoxification. published evidence implicates arsa in the energization of as(iii) efflux via the formation of an oxyanion-translocating complex with arsb. in addition, eukaryotic arsa homologues have several recognized functions unrelated to arsenic resistance. by aligning arsa homologues, constructing phylogenetic trees, examining arsa encoding operons, and estimating the probable coevolution of these homologues with putative transpo ...201020981284
nitrous oxide formation in the colne estuary, england: the central role of nitrite.nitrate and nitrite concentrations in the water and nitrous oxide and nitrite fluxes across the sediment-water interface were measured monthly in the river colne estuary, england, from december 1996 to march 1998. water column concentrations of n(2)o in the colne were supersaturated with respect to air, indicating that the estuary was a source of n(2)o for the atmosphere. at the freshwater end of the estuary, nitrous oxide effluxes from the sediment were closely correlated with the nitrite conce ...200211872474
quantification of 16s rrnas in complex bacterial communities by multiple competitive reverse transcription-pcr in temperature gradient gel electrophoresis fingerprints.a novel approach was developed to quantify rrna sequences in complex bacterial communities. the main bacterial 16s rrnas in drentse a grassland soils (the netherlands) were amplified by reverse transcription (rt)-pcr with bacterium-specific primers and were separated by temperature gradient gel electrophoresis (tgge). the primer pair used (primers u968-gc and l1401) was found to amplify with the same efficiency 16s rrnas from bacterial cultures containing different taxa and cloned 16s ribosomal ...19989797325
nitric oxide reductase (norb) genes from pure cultures and environmental samples.a pcr-based approach was developed to recover nitric oxide (no) reductase (norb) genes as a functional marker gene for denitrifying bacteria. norb database sequences grouped in two very distinct branches. one encodes the quinol-oxidizing single-subunit class (qnorb), while the other class is a cytochrome bc-type complex (cnorb). the latter oxidizes cytochrome c, and the gene is localized adjacent to norc. while both norb types occur in denitrifying strains, the qnorb type was also found in a var ...200312788753
quantification of natural populations of gluconacetobacter diazotrophicus and herbaspirillum spp. in sugar cane (saccharum spp.) using differente polyclonal antibodies.the species gluconacetobacter diazotrophicus, herbaspirillum seropedicae and h. rubrisubalbicans are endophytic n2-fixing [diazotrophic] bacteria which colonise not only roots, but also the aerial tissue of sugar cane. however, the technique most commonly used to quantify the populations of these microbes in plants is by culturing serial dilutions of macerates of plant tissues in n free semi-solid media which are only semi-selective for the species/genera [the most probable number (mpn) techniqu ...200924031435
actinobacterial nitrate reducers and proteobacterial denitrifiers are abundant in n2o-metabolizing palsa peat.palsa peats are characterized by elevated, circular frost heaves (peat soil on top of a permanently frozen ice lens) and are strong to moderate sources or even temporary sinks for the greenhouse gas nitrous oxide (n(2)o). palsa peats are predicted to react sensitively to global warming. the acidic palsa peat skalluvaara (approximate ph 4.4) is located in the discontinuous permafrost zone in northwestern finnish lapland. in situ n(2)o fluxes were spatially variable, ranging from 0.01 to -0.02 μmo ...201222660709
characterization of a nitrilase and a nitrile hydratase from pseudomonas sp. strain uw4 that converts indole-3-acetonitrile to indole-3-acetic acid.indole-3-acetic acid (iaa) is a fundamental phytohormone with the ability to control many aspects of plant growth and development. pseudomonas sp. strain uw4 is a rhizospheric plant growth-promoting bacterium that produces and secretes iaa. while several putative iaa biosynthetic genes have been reported in this bacterium, the pathways leading to the production of iaa in strain uw4 are unclear. here, the presence of the indole-3-acetamide (iam) and indole-3-acetaldoxime/indole-3-acetonitrile (ia ...201424837382
copper active sites in biology. 201424588098
distribution in microbial genomes of genes similar to loda and goxa which encode a novel family of quinoproteins with amino acid oxidase activity.l-amino acid oxidases (laos) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. the generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. they are involved in processes such as biofilm development and microbial competition. laos are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine. the marine ba ...201525886995
mortality in captive baboons (papio spp.): a-23-year study.we report the causes of mortality for 4350 captive baboons that died or were euthanized due to natural causes during a 23 year period at the southwest national primate research center.201424483852
extraction of total nucleic acids from bacterial isolates using the biomérieux nuclisens easymag total nucleic acid extractor.the biomerieux nuclisens easymag total nucleic acid extractor was evaluated for use on bacterial isolates in the clinical microbiology laboratory. forty eight isolates were extracted, yielding quantifiable amounts of dna for all isolates. the easymag is appropriate for dna extraction from bacterial isolates and will be incorporated in the clinical laboratory.201627658494
a new lab developed real time pcr assay for direct detection of c. difficle from stool sample without dna extraction.clostridium difficile is a major cause of nosocomial antibiotic-associated infectious diarrhea and pseudomembranous colitis. detection of c. difficile by anaerobic bacterial culture and/or cytotoxicity assays has been largely replaced by rapid enzyme immunoassays (eia). however, due to the lack of sensitivity of stool eia, we developed a multiplex real-time pcr assay targeting the c. difficile toxin genes tcdb. stool samples from hospitalized pediatric patients suspected of having c. difficile-a ...201627829823
aminoglycoside modifying enzymes.aminoglycosides have been an essential component of the armamentarium in the treatment of life-threatening infections. unfortunately, their efficacy has been reduced by the surge and dissemination of resistance. in some cases the levels of resistance reached the point that rendered them virtually useless. among many known mechanisms of resistance to aminoglycosides, enzymatic modification is the most prevalent in the clinical setting. aminoglycoside modifying enzymes catalyze the modification at ...201020833577
performances of the vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid identification of bacteria in routine clinical microbiology.rapid and cost-effective matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms)-based systems will replace conventional phenotypic methods for routine identification of bacteria. we report here the first evaluation of the new maldi-tof ms-based vitek ms system in a large clinical microbiology laboratory. this system uses an original spectrum classifier algorithm and a specific database designed for the identification of clinically relevant species. we have te ...201222593596
application of smartgene idns software to partial 16s rrna gene sequences for a diverse group of bacteria in a clinical laboratory.laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. with the emergence of 16s rrna gene sequencing as an identification tool, we evaluated the usefulness of smartgene idns, a 16s rrna sequence database and software program for microbial identification. identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the smartgene and mic ...200617050811
comparison of bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to bd phoenix automated microbiology system for identification of gram-negative bacilli.we compared the bd phoenix automated microbiology system to the bruker biotyper (version 2.0) matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry (ms) system for identification of gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. the bd phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. the bruker biotyper correctly identified 408 (93%) and 360 (82 ...201121209160
the tetr family of regulators.the most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a dna-binding domain. among the >20 classes of one-component systems, the tetr family of regulators (tfrs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. however, tfrs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and ma ...201324006471
metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. 201424758379
beneficial effects of spices in food preservation and safety.spices have been used since ancient times. although they have been employed mainly as flavoring and coloring agents, their role in food safety and preservation have also been studied in vitro and in vivo. spices have exhibited numerous health benefits in preventing and treating a wide variety of diseases such as cancer, aging, metabolic, neurological, cardiovascular, and inflammatory diseases. the present review aims to provide a comprehensive summary of the most relevant and recent findings on ...201627708620
unusual non-fluorescent broad spectrum siderophore activity (sid egyii) by pseudomonas aeruginosa strain egyii dsm 101801 and a new insight towards simple siderophore bioassay.present study highlights an unusual non-fluorescent hydroxamate broad spectrum siderophore (sid egyii) activity from pseudomonas aeruginosa strain egyii dsm 101801, a soil bacterial isolate, along with simple low cost effective siderophore bioassay. detection of sid egyii activity qualitatively was proved by masking this activity against erwinia amylovora strain egy1 dsm 101800, an indicator strain, in well-cut diffusion assay containing 100 µm fecl3. sid egyii activity was expressed quantitativ ...201627015845
molecular diagnosis of actinomadura madurae infection by 16s rrna deep dna sequencing can be used to catalog individual organisms within complex, polymicrobial specimens. here, we utilized deep sequencing of 16s rrna to implicate actinomadura madurae as the cause of mycetoma in a diabetic patient when culture and conventional molecular methods were overwhelmed by overgrowth of other organisms.201324108607
virulence functions of autotransporter proteins. 200111179284
type v protein secretion pathway: the autotransporter story.gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. to overcome this barrier, bacteria have developed several systems for protein secretion. the type v secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type vc or at-2 family of proteins. since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the adv ...200415590781
surface display of proteins by gram-negative bacterial autotransporters.expressing proteins of interest as fusions to proteins of the bacterial envelope is a powerful technique with many biotechnological and medical applications. autotransporters have recently emerged as a good tool for bacterial surface display. these proteins are composed of an n-terminal signal peptide, followed by a passenger domain and a translocator domain that mediates the outer membrane translocation of the passenger. the natural passenger domain of autotransporters can be replaced by hetero ...200616787545
ability of the microscan rapid gram-negative id type 3 panel to identify nonenteric glucose-fermenting and nonfermenting gram-negative bacilli.the microscan rapid neg id3 panel is designed for the identification of enterobacteriaceae and nonenteric glucose-fermenting and nonfermenting gram-negative bacilli. we evaluated this panel for its ability to identify gram-negative non-enterobacteriaceae bacteria. a total of 134 strains, representing 26 genera and 42 species, were taken from storage at -70(o)c, passaged three times before testing, and inoculated into the panels according to the manufacturer's directions before being inserted int ...200212354875
microbial community structure elucidates performance of glyceria maxima plant microbial fuel cell.the plant microbial fuel cell (pmfc) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a pmfc. this paper characterises the anode-rhizosphere bacterial community of a glyceria maxima (reed mannagrass) pmfc. electrochemically active bacteria (eab) were ...201222361855
organotin compounds in surface sediments of the southern baltic coastal zone: a study on the main factors for their accumulation and degradation.sediment samples were collected in the gulf of gdańsk, and the vistula and szczecin lagoons-all located in the coastal zone of the southern baltic sea-just after the total ban on using harmful organotins in antifouling paints on ships came into force, to assess their butyltin and phenyltin contamination extent. altogether, 26 sampling stations were chosen to account for different potential exposure to organotin pollution and environmental conditions: from shallow and well-oxygenated waters, ship ...201324026206
organotin compounds in surface sediments of the southern baltic coastal zone: a study on the main factors for their accumulation and degradation.sediment samples were collected in the gulf of gdańsk, and the vistula and szczecin lagoons-all located in the coastal zone of the southern baltic sea-just after the total ban on using harmful organotins in antifouling paints on ships came into force, to assess their butyltin and phenyltin contamination extent. altogether, 26 sampling stations were chosen to account for different potential exposure to organotin pollution and environmental conditions: from shallow and well-oxygenated waters, ship ...201324026206
implementation of a zebrafish health program in a research facility: a 4-year retrospective the past two decades, zebrafish (danio rerio)-based research has contributed to significant scientific advances. still, husbandry and health programs did not evolve at the same pace, as evidenced by the absence of general guidelines. health monitoring is essential to animal welfare, to permit animal exchanges across facilities, to contribute to robust experimental results, and for data reproducibility. in this study, we report a health program implemented in a zebrafish research facility to p ...201627186875
approach to analyze the diversity of myxobacteria in soil by semi-nested pcr-denaturing gradient gel electrophoresis (dgge) based on taxon-specific gene.the genotypic diversity of insoluble macromolecules degraded myxobacteria, provided an opportunity to discover new bacterial resources and find new ecological functions. in this study, we developed a semi-nested-pcr-denaturing gradient gel electrophoresis (dgge) strategy to determine the presence and genotypic diversity of myxobacteria in soil. after two rounds of pcr with myxobacteria-specific primers, an 194 bp fragment of mgla, a key gene involved in gliding motility, suitable for dgge was ob ...201425280065
comparison of methods for quantification of cytochrome cd(1)-denitrifying bacteria in environmental marine samples.two pcr primer sets were developed for the detection and quantification of cytochrome cd(1)-denitrifying bacteria in environmental marine samples. the specificity and sensitivity of these primers were tested. both primer sets were suitable for detection, but only one set, cd3f-cd4r, was suitable for the quantification and enumeration of the functional community using most-probable-number pcr and competitive pcr techniques. quantification of cytochrome cd(1) denitrifiers taken from marine sedimen ...200010742243
diversity of nitrite reductase (nirk and nirs) gene fragments in forested upland and wetland soils.the genetic heterogeneity of nitrite reductase gene (nirk and nirs) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirk gene fragments could be amplified from both soils, whereas nirs gene fragments could be amplified only from the marsh soil. pcr products were cloned and screened by restriction fragment length polymorphism (rflp), and representative fragments were sequenced. the diversity of nirk clones was lower than the dive ...200211916709
nitrous oxide reductase (nosz) gene fragments differ between native and cultivated michigan soils.the effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosz) fragments from denitrifying prokaryotes in native and cultivated soil was explored. thirty-six soil cores were composited from each of the two soil management conditions. nosz gene fragments were amplified from triplicate samples, and pcr products were cloned and screened by restriction fragment length polymorphism (rflp). the total nosz rflp profiles increased in similarity with soil sa ...200414711656
designing a functional type 2 copper center that has nitrite reductase activity within α-helical coiled of the ultimate objectives of de novo protein design is to realize systems capable of catalyzing redox reactions on substrates. this goal is challenging as redox-active proteins require design considerations for both the reduced and oxidized states of the protein. in this paper, we describe the spectroscopic characterization and catalytic activity of a de novo designed metallopeptide cu(i/ii)(tril23h)(3)(+/2+), where cu(i/ii) is embeded in α-helical coiled coils, as a model for the cu(t2) ce ...201223236170
expression, and molecular and enzymatic characterization of cu-containing nitrite reductase from a marine ammonia-oxidizing gammaproteobacterium, nitrosococcus oceani.ammonia-oxidizing bacteria (aob) remove intracellular nitrite to prevent its toxicity by a nitrifier denitrification pathway involving two denitrifying enzymes, nitrite reductase and nitric oxide reductase. here, a cu-containing nitrite reductase from nitrosococcus oceani strain ns58, a gammaproteobacterial marine aob, was expressed in escherichia coli and purified to homogeneity. sequence homology analysis indicated that the nitrite reductase from n. oceani was phylogenetically closer to its co ...201222641151
zinc-substituted pseudoazurin solved by s/zn-sad phasing.the copper(ii) centre of the blue copper protein pseudoazurin from alcaligenes faecalis has been substituted by zinc(ii) via denaturing the protein, chelation and removal of copper and refolding the apoprotein, followed by the addition of an aqueous solution of zncl2. vapour-diffusion experiments produced colourless hexagonal crystals (space group p65), which when cryocooled had unit-cell parameters a=b=49.01, c=98.08 å. diffraction data collected at 100 k using a copper sealed tube were phased ...201525615962
cloning and expression analysis of genes encoding lytic endopeptidases l1 and l5 from lysobacter sp. strain xl1.lytic enzymes are the group of hydrolases that break down structural polymers of the cell walls of various microorganisms. in this work, we determined the nucleotide sequences of the lysobacter sp. strain xl1 alpa and alpb genes, which code for, respectively, secreted lytic endopeptidases l1 (alpa) and l5 (alpb). in silico analysis of their amino acid sequences showed these endopeptidases to be homologous proteins synthesized as precursors similar in structural organization: the mature enzyme se ...201222865082
biotechnology of cold-active proteases.the bulk of earth's biosphere is cold (<5 °c) and inhabited by psychrophiles. biocatalysts from psychrophilic organisms (psychrozymes) have attracted attention because of their application in the ongoing efforts to decrease energy consumption. proteinases as a class represent the largest category of industrial enzymes. there has been an emphasis on employing cold-active proteases in detergents because this allows laundry operations at ambient temperatures. proteases have been used in environment ...201324832807
bacterial and archaeal α-amylases: diversity and amelioration of the desirable characteristics for industrial applications.industrial enzyme market has been projected to reach us$ 6.2 billion by 2020. major reasons for continuous rise in the global sales of microbial enzymes are because of increase in the demand for consumer goods and biofuels. among major industrial enzymes that find applications in baking, alcohol, detergent, and textile industries are α-amylases. these are produced by a variety of microbes, which randomly cleave α-1,4-glycosidic linkages in starch leading to the formation of limit dextrins. α-amy ...201627516755
a survey of orphan enzyme activities.using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an enzyme commission number. here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. the survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases ...200717623104
brucella β 1,2 cyclic glucan is an activator of human and mouse dendritic cells.bacterial cyclic glucans are glucose polymers that concentrate within the periplasm of alpha-proteobacteria. these molecules are necessary to maintain the homeostasis of the cell envelope by contributing to the osmolarity of gram negative bacteria. here, we demonstrate that brucella β 1,2 cyclic glucans are potent activators of human and mouse dendritic cells. dendritic cells activation by brucella β 1,2 cyclic glucans requires tlr4, myd88 and trif, but not cd14. the brucella cyclic glucans show ...201223166489
in vitro activities of bal9141, a novel broad-spectrum pyrrolidinone cephalosporin, against gram-negative nonfermenters.the activities of bal9141 (formerly ro 63-9141), a novel pyrrolidinone-3-ylidenemethyl cephalosporin, against 244 strains of gram-negative nonfermenters were evaluated. the overall mic at which 50% of isolates are inhibited (mic50) and the overall mic90 were 2 and 64 microg/ml, respectively, which are similar to those of imipenem, lower than those of the other cephalosporins tested, amoxicillin, and the ticarcillin-clavulanic acid combination, and much higher than those of ciprofloxacin. bal9141 ...200211850276
biochemical and susceptibility tests useful for identification of nonfermenting gram-negative rods.six hundred nineteen strains of nonfermenting gram-negative rods were tested for alkaline phosphatase, benzyl-arginine arylamidase, pyrrolidonyl arylamidase, ethylene glycol acidification, and susceptibility to desferrioxamine and colistin. the results were highly discriminant. therefore, the proposed tests may be helpful for the identification of this group of organisms.200211880447
evaluation of the new vitek 2 card for identification of clinically relevant gram-negative rods.the vitek 2 card for gram-negative bacteria (biomérieux,marcy-l'etoile, france) has been redesigned to improve the identification of fermenting and nonfermenting bacilli. forty-seven biochemical tests, including 19 enzymatic tests, are present in the new card and interpreted in a kinetic mode. final identification results are available within 10 h. the database allows the identification of 159 different taxa. six hundred fifty-five gram-negative rods (gnr; 511 fermenters and 144 nonfermenters), ...200415364991
quantitative determination of free-dna uptake in river bacteria at the single-cell level by in situ rolling-circle amplification.detection of plasmid dna uptake in river bacteria at the single-cell level was carried out by rolling-circle amplification (rca). uptake of a plasmid containing the green fluorescent protein gene (gfp) by indigenous bacteria from two rivers in osaka, japan, was monitored for 506 h using this in situ gene amplification technique with optimized cell permeabilization conditions. plasmid uptake determined by in situ rca was compared to direct counts of cells expressing gfp under fluorescence microsc ...200616957252
comparison of traditional phenotypic identification methods with partial 5' 16s rrna gene sequencing for species-level identification of nonfermenting gram-negative bacilli.correct identification of nonfermenting gram-negative bacilli (nfb) is crucial for patient management. we compared phenotypic identifications of 96 clinical nfb isolates with identifications obtained by 5' 16s rrna gene sequencing. sequencing identified 88 isolates (91.7%) with >99% similarity to a sequence from the assigned species; 61.5% of sequencing results were concordant with phenotypic results, indicating the usability of sequencing to identify nfb.201020164273
evaluation of the bruker biotyper and vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for identification of nonfermenting gram-negative bacilli isolated from cultures from cystic fibrosis patients.the bruker biotyper and vitek ms matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry (ms) instruments were evaluated for the identification of nonfermenting gram-negative bacilli (nfgnb) by a blinded comparison to conventional biochemical or molecular methods. two hundred nfgnb that were recovered from cultures from cystic fibrosis patients in the university of iowa health care (uihc) microbiology laboratory between 1 january 2006 and 31 october 2010 were sen ...201222495566
performances and reliability of bruker microflex lt and vitek ms maldi-tof mass spectrometry systems for the identification of clinical clinical microbiology laboratories, routine microbial identification is mostly performed using culture based methodologies requiring 24 to 72 hours from culturing to identification. matrix assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) technology has been established as a cost effective, reliable, and faster alternative identification platform. in this study, we evaluated the reliability of the two available maldi-tof ms systems for their routine clinical ...201526793718
aerobic bacterial flora of biotic and abiotic compartments of a hyperendemic zoonotic cutaneous leishmaniasis (zcl) focus.identification of the microflora of the sand fly gut and the environmental distribution of these bacteria are important components for paratransgenic control of leishmania transmission by sand flies.201525630498
biochemical and molecular mechanisms of plant-microbe-metal interactions: relevance for phytoremediation.plants and microbes coexist or compete for survival and their cohesive interactions play a vital role in adapting to metalliferous environments, and can thus be explored to improve microbe-assisted phytoremediation. plant root exudates are useful nutrient and energy sources for soil microorganisms, with whom they establish intricate communication systems. some beneficial bacteria and fungi, acting as plant growth promoting microorganisms (pgpms), may alleviate metal phytotoxicity and stimulate p ...201627446148
in vitro activities of ertapenem (mk-0826) against clinical bacterial isolates from 11 north american medical centers.this study compared the in vitro activities of the new long-half-life carbapenem ertapenem (also known as mk-0826 and l-749,345) with those of imipenem, amoxicillin-clavulanate, and ciprofloxacin against 5,558 recent clinical isolates from 11 north american medical centers. we confirmed the greater activity of ertapenem than of imipenem against the enterobacteriaceae and the greater activity of imipenem against pseudomonads and gram-positive bacteria.200111353653
bacteria that travel: the quality of aircraft water.the travelling population is increasing globally year on year. international tourist arrival figures reached 1087 million in 2013 and 1133 million in 2014; of which 53% and 54% respectively accounted for air transport. the water on board aircraft is sourced from surface or ground water; piped to a central filling point and distributed to each aircraft by water service vehicles at the home base or at the destination airport. the purpose of this study was to ascertain the microbial, chemical (ph; ...201526529000
detection of extended spectrum beta-lactamases resistance genes among bacteria isolated from selected drinking water distribution channels in southwestern nigeria.extended spectrum beta-lactamases (esbl) provide high level resistance to beta-lactam antibiotics among bacteria. in this study, previously described multidrug resistant bacteria from raw, treated, and municipal taps of dwds from selected dams in southwestern nigeria were assessed for the presence of esbl resistance genes which include bla tem, bla shv, and bla ctx by pcr amplification. a total of 164 bacteria spread across treated (33), raw (66), and municipal taps (68), belonging to α-proteoba ...201627563674
a prospective study of the causes of febrile illness requiring hospitalization in children in cambodia.febrile illnesses are pre-eminent contributors to morbidity and mortality among children in south-east asia but the causes are poorly understood. we determined the causes of fever in children hospitalised in siem reap province, cambodia.201323593267
propionate oxidation by and methanol inhibition of anaerobic ammonium-oxidizing bacteria.anaerobic ammonium oxidation (anammox) is a recently discovered microbial pathway and a cost-effective way to remove ammonium from wastewater. anammox bacteria have been described as obligate chemolithoautotrophs. however, many chemolithoautotrophs (i.e., nitrifiers) can use organic compounds as a supplementary carbon source. in this study, the effect of organic compounds on anammox bacteria was investigated. it was shown that alcohols inhibited anammox bacteria, while organic acids were convert ...200515691967
metabolic profiles and genetic diversity of denitrifying communities in activated sludge after addition of methanol or ethanol.external carbon sources can enhance denitrification rates and thus improve nitrogen removal in wastewater treatment plants. the effects of adding methanol and ethanol on the genetic and metabolic diversity of denitrifying communities in activated sludge were compared using a pilot-scale plant with two parallel lines. a full-scale plant receiving the same municipal wastewater, but without external carbon source addition, was the reference. metabolic profiles obtained from potential denitrificatio ...200616885297
skew-laplace and cell-size distribution in microbial axenic cultures: statistical assessment and biological interpretation.we report a skew-laplace statistical analysis of both flow cytometry scatters and cell size from microbial strains primarily grown in batch cultures, others in chemostat cultures and bacterial aquatic populations. cytometry scatters best fit the skew-laplace distribution while cell size as assessed by an electronic particle analyzer exhibited a moderate fitting. unlike the cultures, the aquatic bacterial communities clearly do not fit to a skew-laplace distribution. due to its versatile nature, ...201020592754
structural basis for nitrous oxide generation by bacterial nitric oxide reductases.the crystal structure of the bacterial nitric oxide reductase (cnor) from pseudomonas aeruginosa is reported. its overall structure is similar to those of the main subunit of aerobic and micro-aerobic cytochrome oxidases (coxs), in agreement with the hypothesis that all these enzymes are members of the haem-copper oxidase superfamily. however, substantial structural differences between cnor and cox are observed in the catalytic centre and the delivery pathway of the catalytic protons, which shou ...201222451105
structural changes caused by radiation-induced reduction and radiolysis: the effect of x-ray absorbed dose in a fungal multicopper oxidase.x-ray radiation induces two main effects at metal centres contained in protein crystals: radiation-induced reduction and radiolysis and a resulting decrease in metal occupancy. in blue multicopper oxidases (bmcos), the geometry of the active centres and the metal-to-ligand distances change depending on the oxidation states of the cu atoms, suggesting that these alterations are catalytically relevant to the binding, activation and reduction of o(2). in this work, the x-ray-determined three-dimens ...201222525754
marinobacter hydrocarbonoclasticus ny-4, a novel denitrifying, moderately halophilic marine bacterium.the isolation and characterization of a novel halophilic denitrifying marine bacterium is described. the halophilic bacterium, designated as ny-4, was isolated from soil in yancheng city, china, and identified as marinobacter hydrocarbonoclasticus by 16s rrna gene sequence phylogenetic analysis. this organism can grow in nacl concentrations ranging from 20 to 120 g/l. optimum growth occurs at 80 g/l nacl and ph 8.0. the organism can grow on a broad range of carbon sources and demonstrated effici ...201325538872
paracoccus denitrificans pd1222 utilizes hypotaurine via transamination followed by spontaneous desulfination to yield acetaldehyde and, finally, acetate for growth.hypotaurine (ht; 2-aminoethane-sulfinate) is known to be utilized by bacteria as a sole source of carbon, nitrogen, and energy for growth, as is taurine (2-aminoethane-sulfonate); however, the corresponding ht degradation pathway has remained undefined. genome-sequenced paracoccus denitrificans pd1222 utilized ht (and taurine) quantitatively for heterotrophic growth and released the ht sulfur as sulfite (and sulfate) and ht nitrogen as ammonium. enzyme assays with cell extracts suggested that an ...201323603744
mechanisms for control of biological electron transfer reactions.electron transfer (et) through and between proteins is a fundamental biological process. the rates and mechanisms of these et reactions are controlled by the proteins in which the redox centers that donate and accept electrons reside. the protein influences the magnitudes of the et parameters, the electronic coupling and reorganization energy that are associated with the et reaction. the protein can regulate the rates of the et reaction by requiring reaction steps to optimize the system for et, ...201425085775
the mononuclear molybdenum enzymes. 201424467397
evaluation of pcr-generated chimeras, mutations, and heteroduplexes with 16s rrna gene-based evaluate pcr-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16s ribosomal dna (rdna)-based cloning approach, a model community of four species was constructed from alpha, beta, and gamma subdivisions of the division proteobacteria as well as gram-positive bacterium, all of which could be distinguished by hhai restriction digestion patterns. the overall pcr artifacts were significantly different among the three taq dna polymerases examined: 20% for z-taq, with the ...200111157258
synthesis, production, and biotechnological applications of exopolysaccharides and polyhydroxyalkanoates by archaea.extreme environments, generally characterized by atypical temperatures, ph, pressure, salinity, toxicity, and radiation levels, are inhabited by various microorganisms specifically adapted to these particular conditions, called extremophiles. among these, the microorganisms belonging to the archaea domain are of significant biotechnological importance as their biopolymers possess unique properties that offer insights into their biology and evolution. particular attention has been devoted to two ...201122007151
human interleukin-2 and hen egg white lysozyme: screening for bacteriolytic activity against various bacterial cells.the bacteriolytic activity of interleukin-2 and hen egg white lysozyme against 34 different species of microorganisms has been studied. it was found that 6 species of microorganisms are lysed in the presence of interleukin-2. all interleukin-2-sensitive microorganisms belong either to the enterobacteriaceae, bacillaceae, or the lactobacillaceae family. it was also found that 12 species of microorganisms are lysed in the presence of lysozyme, and 16 species of microorganisms are lysed in the pres ...201627099789
diversity surveys and evolutionary relationships of aoxb genes in aerobic arsenite-oxidizing bacteria.a new primer set was designed to specifically amplify ca. 1,100 bp of aoxb genes encoding the as(iii) oxidase catalytic subunit from taxonomically diverse aerobic as(iii)-oxidizing bacteria. comparative analysis of aoxb protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. aoxb phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16s rrna phylogeny. alphaproteobacteria-, betaproteo ...200818502920
unsuspected diversity of arsenite-oxidizing bacteria as revealed by widespread distribution of the aoxb gene in this study, new strains were isolated from an environment with elevated arsenic levels, sainte-marie-aux-mines (france), and the diversity of aoxb genes encoding the arsenite oxidase large subunit was investigated. the distribution of bacterial aoxb genes is wider than what was previously thought. aoxb subfamilies characterized by specific signatures were identified. an exhaustive analysis of aoxb sequences from this study and from public databases shows that horizontal gene transfer has like ...201121571879
functional expression of a penicillin acylase from the extreme thermophile thermus thermophilus hb27 in escherichia coli.penicillin acylases (pacs) are enzymes of industrial relevance in the manufacture of β-lactam antibiotics. development of a pac with a longer half-life under the reaction conditions used is essential for the improvement of the operational stability of the process. a gene encoding a homologue to escherichia coli pac was found in the genome of the thermophilic bacterium thermus thermophilus (tth) hb27. because of the nature of this pac and its complex maturation that is crucial to reach its functi ...201222876915
biocatalyst development by directed evolution.biocatalysis has emerged as a great addition to traditional chemical processes for production of bulk chemicals and pharmaceuticals. to overcome the limitations of naturally occurring enzymes, directed evolution has become the most important tool for improving critical traits of biocatalysts such as thermostability, activity, selectivity, and tolerance towards organic solvents for industrial applications. recent advances in mutant library creation and high-throughput screening have greatly facil ...201222310212
thermus oshimai jl-2 and t. thermophilus jl-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.the complete genomes of thermus oshimai jl-2 and t. thermophilus jl-18 each consist of a circular chromosome, 2.07 mb and 1.9 mb, respectively, and two plasmids ranging from 0.27 mb to 57.2 kb. comparison of the t. thermophilus jl-18 chromosome with those from other strains of t. thermophilus revealed a high degree of synteny, whereas the megaplasmids from the same strains were highly plastic. the t. oshimai jl-2 chromosome and megaplasmids shared little or no synteny with other sequenced thermu ...201324019992
microbial oxidation of arsenite in a subarctic environment: diversity of arsenite oxidase genes and identification of a psychrotolerant arsenite oxidiser.arsenic is toxic to most living cells. the two soluble inorganic forms of arsenic are arsenite (+3) and arsenate (+5), with arsenite the more toxic. prokaryotic metabolism of arsenic has been reported in both thermal and moderate environments and has been shown to be involved in the redox cycling of arsenic. no arsenic metabolism (either dissimilatory arsenate reduction or arsenite oxidation) has ever been reported in cold environments (i.e. < 10 degrees c).201020673331
biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation.lindane, the gamma-isomer of hexachlorocyclohexane (hch), is a potent insecticide. purified lindane or unpurified mixtures of this and alpha-, beta-, and delta-isomers of hch were widely used as commercial insecticides in the last half of the 20th century. large dumps of unused hch isomers now constitute a major hazard because of their long residence times in soil and high nontarget toxicities. the major pathway for the aerobic degradation of hch isomers in soil is the lin pathway, and variants ...201020197499
in silico analysis of bacterial arsenic islands reveals remarkable synteny and functional relatedness between arsenate and order to construct a more universal model for understanding the genetic requirements for bacterial asiii oxidation, an in silico examination of the available sequences in the genbank was assessed and revealed 21 conserved 5-71 kb arsenic islands within phylogenetically diverse bacterial genomes. the arsenic islands included the asiii oxidase structural genes aioba, ars operons (e.g., arsrcb) which code for arsenic resistance, and pho, pst, and phn genes known to be part of the classical phosp ...201324312089
phylogenetic analysis of tmrna genes within a bacterial subgroup reveals a specific structural signature.bacterial tmrna mediates a trans-translation reaction, which permits the recycling of stalled ribosomes and probably also contributes to the regulated expression of a subset of genes. its action results in the addition of a small number of c-terminal amino acids to protein whose synthesis had stalled and these constitute a proteolytic recognition tag for the degradation of these incompletely synthesized proteins. previous work has identified pseudoknots and stem-loops that are widely conserved i ...200111266563
detection and enumeration of aromatic oxygenase genes by multiplex and real-time pcr.our abilities to detect and enumerate pollutant-biodegrading microorganisms in the environment are rapidly advancing with the development of molecular genetic techniques. techniques based on multiplex and real-time pcr amplification of aromatic oxygenase genes were developed to detect and quantify aromatic catabolic pathways, respectively. pcr primer sets were identified for the large subunits of aromatic oxygenases from alignments of known gene sequences and tested with genetically well-charact ...200312788736
a new classification system for bacterial rieske non-heme iron aromatic ring-hydroxylating oxygenases.rieske non-heme iron aromatic ring-hydroxylating oxygenases (rhos) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many rhos have been discovered, which do not belong to any group in the previous classification. here, we present a scheme for classification of rhos reflecting new sequence information and interactio ...200818387195
high interlaboratory reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry-based species identification of nonfermenting bacteria.matrix-assisted laser desorption ionization-time of flight mass spectrometry has emerged as a rapid, cost-effective alternative for bacterial species identification. identifying 60 blind-coded nonfermenting bacteria samples, this international study (using eight laboratories) achieved 98.75% interlaboratory reproducibility. only 6 of the 480 samples were misidentified due to interchanges (4 samples) or contamination (1 sample) or not identified because of insufficient signal intensity (1 sample) ...200919776231
the phn island: a new genomic island encoding catabolism of polynuclear aromatic hydrocarbons.bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (pah), which are widespread environmental pollutants. at least six genotypes of pah degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (rhd) that initiates bacterial pah metabolism. a given rhd genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (hgt) is an important process for dissemination of pah-degrading genes. but, mechanisms of hgt for mos ...201222493593
the use of fluorogenic substrates to measure fungal presence and activity in soil.our objective was to determine if 4-methylumbelliferyl-labelled enzyme substrates could be used to detect and quantify specific components of chitinase and cellulase activities as specific indicators of the presence and activity of fungal biomass. the fluorogenic substrates 4-methylumbelliferyl (muf) n-acetyl-beta-d-glucosaminide and muf beta-d-lactoside were used for the detection and quantification of beta-n-acetylglucosaminidase (ec (nagase) and endo 1,4-beta-glucanase (ec ...19989464399
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