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hydrogenosome-localization of arginine deiminase in trichomonas vaginalis.the arginine dihydrolase (adh) pathway has an analogous function to the urea cycle in mitochondria-containing cells, by removing nitrogen from amino acids and generating atp. subcellular localization of the adh pathway enzymes in trichomonas vaginalis revealed that arginine deiminase (adi) localizes to the hydrogenosome, a mitochondrion-like organelle of anaerobic protists. however the other enzymes of the adh pathway, ornithine carbamyltransferase and carbamate kinase localize to the cytosol. t ...201021074581
clinical and antimicrobial efficacy of nitradine ™-based disinfecting cleaning tablets in complete denture wearers.this study evaluated the efficacy of nitradine ™-based disinfecting cleaning tablets for complete denture, in terms of denture biofilm removal and antimicrobial action.201021308285
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
whole-cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls.whole-cell microbial biosensors are one of the newest molecular tools used in environmental monitoring. such biosensors are constructed through fusing a reporter gene such as lux, gfp or lacz, to a responsive promoter. there have been many reports of the applications of biosensors, particularly their use in assaying pollutant toxicity and bioavailability. this paper reviews the basic concepts behind the construction of whole-cell microbial biosensors for pollutant monitoring, and describes the a ...201022205873
assessment of formate dehydrogenase stress stability in vivo using inactivation by hydrogen peroxide.kinetic studies on hydrogen peroxide-induced inactivation of mutant formate dehydrogenase from pseudomonas sp. 101 (psefdh cys255ala) suggest a simple bimolecular mechanism for enzyme reaction with the inactivation agent. in the excess of hydrogen peroxide, the decrease in enzyme activity follows first-order kinetics. therefore, the first-order effective inactivation kinetic constants determined for various fdh forms at a constant h(2)o(2) concentration can be used as a quantitative measure of t ...201022649634
degradation of h-acid by free and immobilized cells of alcaligenes latus.alcaligenes latus, isolated from industrial effluent, was able to grow in mineral salts medium with 50 ppm (0.15 mm) of h-acid as a sole source of carbon. immobilization of alcaligenes latus in ca-alginate and polyurethane foam resulted in cells embedded in the matrices. when free cells and immobilized cells were used for biodegradation studies at concentration ranging from 100 ppm (0.3 mm) to 500 ppm (1.15 mm) degradation rate was enhanced with immobilized cells. cells immobilized in polyuretha ...201024031573
rhamnolipid biosurfactants as new players in animal and plant defense against microbes.rhamnolipids are known as very efficient biosurfactant molecules. they are used in a wide range of industrial applications including food, cosmetics, pharmaceutical formulations and bioremediation of pollutants. the present review provides an overview of the effect of rhamnolipids in animal and plant defense responses. we describe the current knowledge on the stimulation of plant and animal immunity by these molecules, as well as on their direct antimicrobial properties. given their ecological a ...201021614194
macrocyclic histone deacetylase inhibitors.histone deacetylase inhibitors (hdaci) are an emerging class of novel anti-cancer drugs that cause growth arrest, differentiation, and apoptosis of tumor cells. in addition, they have shown promise as anti-parasitic, anti-neurodegenerative, anti-rheumatologic and immunosuppressant agents. to date, several structurally distinct small molecule hdaci have been reported including aryl hydroxamates, benzamides, short-chain fatty acids, electrophilic ketones, and macrocyclic peptides. macrocyclic hdac ...201020536416
risk factors and prevention of late-onset sepsis in premature infants.late-onset sepsis in premature infants is a major cause of morbidity, mortality, and increased medical costs. risk factors include low birth weight, low gestational age, previous antimicrobial exposure, poor hand hygiene, and central venous catheters. methods studied to prevent late-onset sepsis include early feedings, immune globulin administration, prophylactic antimicrobial administration, and improved hand hygiene. in this review, we will outline the risk factors for development of late-onse ...201020116186
hydroxylated metabolites of 4-monochlorobiphenyl and its metabolic pathway in whole poplar plants.4-monochlorobiphenyl (cb3), mainly an airborne pollutant, undergoes rapid biotransformation to produce hydroxylated metabolites (oh-cb3s). however, up to now, hydroxylation of cb3 has not been studied in living organisms. in order to explore the formation of hydroxylated metabolites of cb3 in whole plants, poplars (populus deltoides x nigra, dn34) were exposed to cb3 for 10 days. poplars are a model plant with complete genomic sequence, and they are widely used in phytoremediation. results showe ...201020402517
enzymatic determination of diglyceride using an iridium nano-particle based single use, disposable biosensor.a single use, disposable iridium-nano particle contained biosensor had been developed for the determination of diglyceride (dg). in this study hydrogen peroxide, formed through the enzymatic breakdown of dg via lipase, glycerol kinase and glycerol 3-phosphate oxidase, was electrochemically oxidized at an applied potential of +0.5 v versus the ag/agcl reference electrode. the oxidation current was then used to quantify the diglyceride concentration. optimum enzyme concentrations and the surfactan ...201022219685
favored and disfavored pathways of protein crosslinking by glucose: glucose lysine dimer (glucold) and crossline versus glucosepane.we describe the isolation and molecular characterization of a novel glucose-lysine dimer crosslink 1,3-bis-(5-amino-5-carboxypentyl)-4-(1',2',3',4'-tetrahydroxybutyl)-3h-imidazolium salt, named glucold. glucold was easily formed from the amadori product (fructose-lysine). however, when bsa was incubated with 100 mm glucose for 25 days, the levels of the lysine-lysine glucose crosslinks glucold and crossline were only 21 and <1 pmol/mg, respectively, compared to 611 pmol/mg protein for the lysine ...201020607325
favored and disfavored pathways of protein crosslinking by glucose: glucose lysine dimer (glucold) and crossline versus glucosepane.we describe the isolation and molecular characterization of a novel glucose-lysine dimer crosslink 1,3-bis-(5-amino-5-carboxypentyl)-4-(1',2',3',4'-tetrahydroxybutyl)-3h-imidazolium salt, named glucold. glucold was easily formed from the amadori product (fructose-lysine). however, when bsa was incubated with 100 mm glucose for 25 days, the levels of the lysine-lysine glucose crosslinks glucold and crossline were only 21 and <1 pmol/mg, respectively, compared to 611 pmol/mg protein for the lysine ...201020607325
single turnover kinetics of tryptophan hydroxylase: evidence for a new intermediate in the reaction of the aromatic amino acid hydroxylases.tryptophan hydroxylase (trph) uses a non-heme mononuclear iron center to catalyze the tetrahydropterin-dependent hydroxylation of tryptophan to 5-hydroxytryptophan. the reactions of the trph.fe(ii), trph.fe(ii).tryptophan, trph.fe(ii).6meph(4).tryptophan, and trph.fe(ii).6meph(4).phenylalanine complexes with o(2) were monitored by stopped-flow absorbance spectroscopy and rapid quench methods. the second-order rate constant for the oxidation of trph.fe(ii) has a value of 104 m(-1) s(-1) irrespect ...201020687613
screen-printed carbon electrodes modified by rhodium dioxide and glucose dehydrogenase.the described glucose biosensor is based on a screen-printed carbon electrode (spce) modified by rhodium dioxide, which functions as a mediator. the electrode is further modified by the enzyme glucose dehydrogenase, which is immobilized on the electrode's surface through electropolymerization with m-phenylenediamine. the enzyme biosensor was optimized and tested in model glucose samples. the biosensor showed a linear range of 500-5000 mg l(-1) of glucose with a detection limit of 210 mg l(-1) (e ...201021528113
screen-printed carbon electrodes modified by rhodium dioxide and glucose dehydrogenase.the described glucose biosensor is based on a screen-printed carbon electrode (spce) modified by rhodium dioxide, which functions as a mediator. the electrode is further modified by the enzyme glucose dehydrogenase, which is immobilized on the electrode's surface through electropolymerization with m-phenylenediamine. the enzyme biosensor was optimized and tested in model glucose samples. the biosensor showed a linear range of 500-5000 mg l(-1) of glucose with a detection limit of 210 mg l(-1) (e ...201021528113
species sorting and neutral processes are both important during the initial assembly of bacterial communities.many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. on the other hand, there are other studies that could show that bacterial communities are neutrally assembled. in this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of ...201121270841
nad (+) -dependent formate dehydrogenase from plants.nad(+)-dependent formate dehydrogenase (fdh, ec 1.2.1.2) widely occurs in nature. fdh consists of two identical subunits and contains neither prosthetic groups nor metal ions. this type of fdh was found in different microorganisms (including pathogenic ones), such as bacteria, yeasts, fungi, and plants. as opposed to microbiological fdhs functioning in cytoplasm, plant fdhs localize in mitochondria. formate dehydrogenase activity was first discovered as early as in 1921 in plant; however, until ...201122649703
new stability indicating rp-hplc method for the estimation of cefpirome sulphate in bulk and pharmaceutical dosage forms.a simple stability indicating reversed-phase hplc method was developed and subsequently validated for estimation of cefpirome sulphate (cps) present in pharmaceutical dosage forms. the proposed rp-hplc method utilizes a lichrocart-lichrosphere100, c18 rp column (250 mm × 4mm × 5 μm) in an isocratic separation mode with mobile phase consisting of methanol and water in the proportion of 50:50 % (v/v), at a flow rate 1ml/min, and the effluent was monitored at 270 nm. the retention time of cps was 2 ...201122145113
radiosynthesis of antitumor spliceosome modulators.a set of novel antitumor agents (the sudemycins) has recently been described that are analogs of the natural product fr901464. we report the radiosynthesis of two of these antitumor drug lead compounds, using a three step procedure: (1) ester hydrolysis, (2) lindlar's catalyst/tritium gas to give a (s,z)-4-acetoxypent-2-enoic acid derivative, and finally (3) amide bond formation. these labeled analogs are useful in developing a better understanding of the pharmacological properties of this new c ...201121531567
donor site morbidity following harvest of split-thickness skin grafts in south eastern nigeria.split-thickness skin grafting is a very common procedure. few documentation of its complications exist in the literatures especially in our sub-region where excessive scarring is a major issue.201127182501
wses consensus conference: guidelines for first-line management of intra-abdominal infections.intra-abdominal infections are still associated with high rate of morbidity and mortality.a multidisciplinary approach to the management of patients with intra-abdominal infections may be an important factor in the quality of care. the presence of a team of health professionals from various disciplines, working in concert, may improve efficiency, outcome, and the cost of care.a world society of emergency surgery (wses) consensus conference was held in bologna on july 2010, during the 1st congres ...201121232143
prevalence, aetiology and antibiotic resistance profiles of coagulase negative staphylococci isolated in a teaching hospital.in this paper we carried out a study about prevalence of the clinically significant coagulase negative staphylococcal (cns) isolates found in an university hospital. two hundred four cns isolates from 191 patients obtained between the period of 1998 to 2002, were studied. about 27% (52/191) of the infection cases studied were confirmed as cns-associated diseases. blood stream infection (bsi) was the most frequent cns associated-disease (25%; 13/52). the great majority of the bsi was verified in ...201124031628
escherichia coli isolated from urinary tract infections of lebanese patients between 2000 and 2009: epidemiology and profiles of resistance.the purpose of this study was to investigate the bacterial etiology of urinary tract infections in one of the busiest hospitals of lebanon and to examine the epidemiologic and microbiologic properties of escherichia coli isolated from urinary tract infections of lebanese patients over a 10-year period. methods. this retrospective study analyzed the data generated between 2000 and 2009 (10,013 gram-positive and gram-negative bacteria). bacterial identification was based on standard culture and bi ...201122295204
oxidative stress-mediated brain dehydroepiandrosterone (dhea) formation in alzheimer's disease diagnosis.neurosteroids are steroids made by brain cells independently of peripheral steroidogenic sources. the biosynthesis of most neurosteroids is mediated by proteins and enzymes similar to those identified in the steroidogenic pathway of adrenal and gonadal cells. dehydroepiandrosterone (dhea) is a major neurosteroid identified in the brain. over the years we have reported that, unlike other neurosteroids, dhea biosynthesis in rat, bovine, and human brain is mediated by an oxidative stress-mediated m ...201122654823
antiviral activity of natural products extracted from marine organisms.many epidemics have broken out over the centuries. hundreds and thousands of humans have died over a disease. available treatments for infectious diseases have always been limited. some infections are more deadly than the others, especially viral pathogens. these pathogens have continuously resisted all kinds of medical treatment, due to a need for new treatments to be developed. drugs are present in nature and are also synthesized in vitro and they help in combating diseases and restoring healt ...201123678429
neuro-intensive care of patients with acute cns infections.infections in the central nervous system (cns) are caused by a wide range of microorganisms resulting in distinct clinical syndromes including meningitis, encephalitis, and pyogenic infections, such as empyema and brain abscess. bacterial and viral infections in the cns can be rapidly fatal and can result in severe disability in survivors. appropriate identification and acute management of these infections often occurs in a critical care setting and is vital to improving outcomes in this group o ...201122102180
neuro-intensive care of patients with acute cns infections.infections in the central nervous system (cns) are caused by a wide range of microorganisms resulting in distinct clinical syndromes including meningitis, encephalitis, and pyogenic infections, such as empyema and brain abscess. bacterial and viral infections in the cns can be rapidly fatal and can result in severe disability in survivors. appropriate identification and acute management of these infections often occurs in a critical care setting and is vital to improving outcomes in this group o ...201122102180
postoperative endophthalmitis following cataract surgery in asia.postoperative endophthalmitis is a rare clinical occurrence. however, it remains one of the most serious complications following cataract surgery because of its poor prognosis. we investigated the epidemiologic trends in postoperative endophthalmitis following cataract surgery, particularly in asian populations. the incidence of postcataract endophthalmitis was generally consistent with epidemiologic data reported from caucasian populations. the most frequently occurring causative organism was c ...201124555121
coupled chemo(enzymatic) reactions in continuous flow.this review highlights the state of the art in the field of coupled chemo(enzymatic) reactions in continuous flow. three different approaches to such reaction systems are presented herein and discussed in view of their advantages and disadvantages as well as trends for their future development.201122238518
a water-damaged home and health of occupants: a case study.a family of five and pet dog who rented a water-damaged home and developed multiple health problems. the home was analyzed for species of mold and bacteria. the diagnostics included mri for chronic sinusitis with ent and sinus surgery, and neurological testing for neurocognitive deficits. bulk samples from the home, tissue from the sinuses, urine, nasal secretions, placenta, umbilical cord, and breast milk were tested for the presence of trichothecenes, aflatoxins, and ochratoxin a. the family h ...201122220187
a water-damaged home and health of occupants: a case study.a family of five and pet dog who rented a water-damaged home and developed multiple health problems. the home was analyzed for species of mold and bacteria. the diagnostics included mri for chronic sinusitis with ent and sinus surgery, and neurological testing for neurocognitive deficits. bulk samples from the home, tissue from the sinuses, urine, nasal secretions, placenta, umbilical cord, and breast milk were tested for the presence of trichothecenes, aflatoxins, and ochratoxin a. the family h ...201122220187
hydrolytic potential of a psychrotrophic pseudomonas isolated from refrigerated raw milk.the production of extracellular hydrolases by a psychrotrophic bacterium isolated from refrigerated raw milk, and identified as a pseudomonas sp. belonging to the pseudomonas jenssenii group, was studied. this bacterium produced proteolytic and lipolytic enzymes in all media investigated (skim milk, cheese whey, casein broth, and tryptone soy broth). high levels of α-glucosidase were produced in skim milk broth. hydrolytic enzymes detected in skim milk broth are of particular concern, indicating ...201124031781
novel antiphytopathogenic compound 2-heptyl-5-hexylfuran-3-carboxylic acid, produced by newly isolated pseudomonas sp. strain sjt25.pseudomonas sp. strain sjt25, which strongly antagonizes plant pathogens, was isolated from rice rhizosphere soil by a bioactivity-guided approach. a novel antiphytopathogenic compound was isolated from the fermentation broth of pseudomonas sp. sjt25 and identified as 2-heptyl-5-hexylfuran-3-carboxylic acid. this compound showed antimicrobial activities both in vitro and in vivo.201121742907
identification of outer membrane proteins from an antarctic bacterium pseudomonas syringae lz4w.subcellular fractionation of proteins is a preferred method of choice for detection and identification of proteins from complex mixtures such as bacterial cells. to characterize the membrane proteins of the antarctic bacterium pseudomonas syringae lz4w, the membrane fractions were prepared using three different methods, namely triton x-100 solubilization, sucrose density gradient, and carbonate extraction methods. the proteins were separated on one-dimensional polyacrylamide gels and analyzed us ...201121447709
evidence for polymicrobic flora translocating in peripheral blood of hiv-infected patients with poor immune response to antiretroviral therapy.in advanced hiv infection, the homeostatic balance between gastrointestinal indigenous bacteria and gut immunity fails and microbes are able to overcome the intestinal barrier and gain the systemic circulation. because microbial translocation is not fully controlled by antiviral therapy and is associated with inefficient cd4+ reconstitution, we investigated the profile of translocating bacteria in peripheral blood of 44 hiv-infected patients starting therapy with advanced cd4+ t-lymphopenia and ...201121494598
culture-independent analysis of bacterial fuel contamination provides insights into the level of concordance with the standard industry practice of aerobic cultivation.bacterial diversity in contaminated fuels has not been systematically investigated using cultivation-independent methods. the fuel industry relies on phenotypic cultivation-based contaminant identification, which may lack accuracy and neglect difficult-to-culture taxa. using industry practice aerobic cultivation, 16s rrna gene sequencing and strain genotyping, a collection of 152 unique contaminant isolates from 54 fuel samples was assembled, and demonstrated a dominance of pseudomonas (21%), bu ...201121602386
molecular basis of glyphosate resistance-different approaches through protein engineering.glyphosate (n-phosphonomethyl-glycine) is the most widely used herbicide in the world: glyphosate-based formulations exhibit broad-spectrum herbicidal activity with minimal human and environmental toxicity. the extraordinary success of this simple, small molecule is mainly attributable to the high specificity of glyphosate for the plant enzyme enolpyruvyl shikimate-3-phosphate synthase in the shikimate pathway, leading to the biosynthesis of aromatic amino acids. starting in 1996, transgenic gly ...201121668647
comparative void-volume analysis of psychrophilic and mesophilic enzymes: structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility.psychrophiles, cold-adapted organisms, have adapted to live at low temperatures by using a variety of mechanisms. their enzymes are active at cold temperatures by being structurally more flexible than mesophilic enzymes. even though, there are some indications of the possible structural mechanisms by which psychrophilic enzymes are catalytic active at cold temperatures, there is not a generalized structural property common to all psychrophilic enzymes.201122013889
a selective chromogenic plate, yeca, for the detection of pathogenic yersinia enterocolitica: specificity, sensitivity, and capacity to detect pathogenic y. enterocolitica from pig tonsils.a new selective chromogenic plate, yeca, was tested for its specificity, sensitivity, and accuracy to detect pathogenic y. enterocolitica from pig tonsils. we tested a panel of 26 bacterial strains on yeca and compared it to pca, cin, and yecm media. detection of pathogenic y. enterocolitica was carried out on 50 pig tonsils collected in one slaughter house. enrichment was done in psb and itc broths. streaking on yeca and cin was done in direct, after 24h incubation of itc, after 48h incubation ...201122567328
molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient dna, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. using human lung tissue and/or teeth samples from burials in eastern s ...201121765907
intensive care management of liver transplanted patients.advances in pre-transplant treatment of cirrhosis-related organ dysfunction, intraoperative patient management, and improvements in the treatment of rejection and infections have made human liver transplantation an effective and valuable option for patients with end stage liver disease. however, many important factors, related both to an increasing "marginality" of the implanted graft and unexpected perioperative complications still make immediate post-operative care challenging and the early ou ...201121487537
Influence of uranium on bacterial communities: a comparison of natural uranium-rich soils with controls.This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing ...201121998695
a naturally associated rhizobacterium of arabidopsis thaliana induces a starvation-like transcriptional response while promoting growth.plant growth promotion by rhizobacteria is a known phenomenon but the underlying mechanisms are poorly understood. we searched for plant growth-promoting rhizobacteria that are naturally associated with arabidopsis thaliana to investigate the molecular mechanisms that are involved in plant growth-promotion. we isolated a pseudomonas bacterium (pseudomonas sp. g62) from roots of field-grown arabidopsis plants that has not been described previously and analyzed its effect on plant growth, gene exp ...201122216267
repression of the antifungal activity of pseudomonas sp. strain df41 by the stringent response.the stringent response (sr) enables bacteria to adapt to nutrient limitation through production of the nucleotides guanosine tetraphosphate and guanosine pentaphosphate, collectively known as (p)ppgpp. two enzymes are responsible for the intracellular pools of (p)ppgpp: rela acts as a synthetase, while spot can function as either a synthetase or a hydrolase. we investigated how the sr affects the ability of the biological control agent pseudomonas sp. strain df41 to inhibit the fungal pathogen s ...201121705548
Investigation of the Catalytic Mechanism of the Hotdog-fold Enzyme Superfamily Pseudomonas sp. strain CBS3 4-Hydroxybenzoyl-CoA Thioesterase.The 4-hydroxybenzoyl-CoA (4-HB-CoA)1 thioesterase from Pseudomonas sp strain CBS3 catalyzes the final step of the 4-chlorobenzoate degradation pathway, which is the hydrolysis of 4-hydroxybenzoyl-CoA (4-HB-CoA) to coenzyme A (CoA) and 4-hydroxybenzoate. In previous work, X-ray structural analysis of the substrate-bound thioesterase provided evidence for the role of an active site Asp17 in nucleophilic catalysis (Thoden, J. B., Holden, H. M., Zhuang, Z., Dunaway-Mariano, D. (2002) X-ray crystallo ...201122208697
genetic approach for the fast discovery of phenazine producing bacteria.a fast and efficient approach was established to identify bacteria possessing the potential to biosynthesize phenazines, which are of special interest regarding their antimicrobial activities. sequences of phze genes, which are part of the phenazine biosynthetic pathway, were used to design one universal primer system and to analyze the ability of bacteria to produce phenazine. diverse bacteria from different marine habitats and belonging to six major phylogenetic lines were investigated. bacter ...201121673888
characterisation of phosphate solubilising bacteria in sandy loam soil under chickpea cropping system.with the aim to explore the possible role of phosphate-solubilizing bacteria (psb) in phosphorus (p) cycling in agricultural soils, we isolated psb inhabiting naturally in the sandy loam soils under chickpea cropping of patiala (punjab state). a total of 31 bacterial isolates showing solubilizing activities were isolated on pikovskaya agar plates. the potent phosphate solubilizers were selected for further characterization. these isolates were shown to belong to the genera pseudomonas and serrat ...201123729877
characterisation of phosphate solubilising bacteria in sandy loam soil under chickpea cropping system.with the aim to explore the possible role of phosphate-solubilizing bacteria (psb) in phosphorus (p) cycling in agricultural soils, we isolated psb inhabiting naturally in the sandy loam soils under chickpea cropping of patiala (punjab state). a total of 31 bacterial isolates showing solubilizing activities were isolated on pikovskaya agar plates. the potent phosphate solubilizers were selected for further characterization. these isolates were shown to belong to the genera pseudomonas and serrat ...201123729877
Regulation of phenylacetic acid uptake is s54 dependent in Pseudomonas putida CA-3.Styrene is a toxic and potentially carcinogenic alkenylbenzene used extensively in the polymer processing industry. Significant quantities of contaminated liquid waste are generated annually as a consequence. However, styrene is not a true xenobiotic and microbial pathways for its aerobic assimilation, via an intermediate, phenylacetic acid, have been identified in a diverse range of environmental isolates. The potential for microbial bioremediation of styrene waste has received considerable res ...201121995721
molecular characterization and snp detection of cd14 gene of crossbred cattle.cd14 is an important molecule for innate immunity that can act against a wide range of pathogens. the present paper has characterized cd14 gene of crossbred (cb) cattle (bos indicus×bos taurus). cloning and sequence analysis of cd14 cdna revealed 1119 nucleotide long open reading frame encoding 373 amino acids protein and 20 amino acids signal peptide. cb cattle cd14 gene exhibited a high percentage of nucleotide identity (59.3-98.1%) with the corresponding mammalian homologs. cattle and buffalo ...201122132326
Identification of the Midgut Microbiota of An. stephensi and An. maculipennis for Their Application as a Paratransgenic Tool against Malaria.The midgut microbiota associated with Anopheles stephensi and Anopheles maculipennis (Diptera: Culicidae) was investigated for development of a paratransgenesis-based approach to control malaria transmission in Eastern Mediterranean Region (EMR). Here, we present the results of a polymerase chain reaction (PCR) and biochemical-based approaches to identify the female adult and larvae mosquitoe microbiota of these two major malaria vectors, originated from South Eastern and North of Iran. Plating ...201122163022
genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain pseudomonas aeruginosa m18.our previously published reports have described an effective biocontrol agent named pseudomonas sp. m18 as its 16s rdna sequence and several regulator genes share homologous sequences with those of p. aeruginosa, but there are several unusual phenotypic features. this study aims to explore its strain specific genomic features and gene expression patterns at different temperatures.201121884571
the culturable intestinal microbiota of triploid and diploid juvenile atlantic salmon (salmo salar) - a comparison of composition and drug resistance.with the increased use of ploidy manipulation in aquaculture and fisheries management this investigation aimed to determine whether triploidy influences culturable intestinal microbiota composition and bacterial drug resistance in atlantic salmon (salmo salar). the results could provide answers to some of the physiological differences observed between triploid and diploid fish, especially in terms of fish health.201122094054
identification and engineering of the cytochalasin gene cluster from aspergillus clavatus nrrl 1.cytochalasins are a group of fungal secondary metabolites with diverse structures and bioactivities, including cytochalasin e produced by aspergillus clavatus, which is a potent anti-angiogenic agent. here, we report the identification and characterization of the cytochalasin gene cluster from a. clavatus nrrl 1. as a producer of cytochalasin e and k, the genome of a. clavatus was analyzed and the ∼30 kb ccs gene cluster was identified based on the presence of a polyketide synthase-nonribosomal ...201121983160
Lipoteichoic acid in Streptomyces hygroscopicus: structural model and immunomodulatory activities.Gram positive bacteria produce cell envelope macroamphiphile glycopolymers, i.e. lipoteichoic acids or lipoglycans, whose functions and biosynthesis are not yet fully understood. We report for the first time a detailed structure of lipoteichoic acid isolated from a Streptomyces species, i.e. Streptomyces hygroscopicus subsp. hygroscopicus NRRL 2387T. Chemical, MS and NMR analyses revealed a polyglycerolphosphate backbone substituted with a-glucosaminyl and a-N-acetyl-glucosaminyl residues but de ...201122028855
Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1.In all structurally characterized bacterial multicomponent monooxygenase (BMM) hydroxylase proteins, a series of hydrophobic cavities in the a-subunit trace a conserved path from the protein exterior to the carboxylate-bridged diiron active site. This study examines these cavities as a potential route for transport of dioxygen to the active site by crystallographic characterization of a xenon-pressurized sample of the hydroxylase component of phenol hydroxylase from Pseudomonas sp. OX1. Computat ...201122136180
Epidemiology of hospital-acquired urinary tract-related bloodstream infection at a university hospital.Little is known about the epidemiology of nosocomial urinary tract-related bloodstream infection. In a case series from an academic medical center, Enterococcus (28.7%) and Candida (19.6%) species were the predominant microorganisms, which suggests a potential shift from gram-negative microorganisms. A case-fatality rate of 32.8% highlights the severity of this condition.201122011543
kinetics of styrene biodegradation by pseudomonas sp. e-93486.the research into kinetics of styrene biodegradation by bacterial strain pseudomonas sp. e-93486 coming from vtt culture collection (finland) was presented in this work. microbial growth tests in the presence of styrene as the sole carbon and energy source were performed both in batch and continuous cultures. batch experiments were conducted for initial concentration of styrene in the liquid phase changed in the range of 5-90-ágôçëm(-3). the haldane model was found to be the best to fit the kine ...201121833566
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
biological control of chickpea collar rot by co-inoculation of antagonistic bacteria and compatible rhizobia.two hundred and seven bacteria were isolated from composts and macrofauna and screened for plant growth promoting and antagonistic traits. seven of the 207 isolates showed antagonistic activity against sclerotium rolfsii in plate culture. inhibition of s. rolfsii by the bacterial isolates ranged between 61 and 84%. two of the seven isolates were bacillus sp. and rest belonged to pseudomonas sp. two isolates, pseudomonas sp. cdb 35 and pseudomonas sp. bwb 21 was compatible with chickpea rhizobium ...201122282609
transferable integrons of gram-negative bacteria isolated from the gut of a wild boar in the buffer zone of a national park.the aim of this study was to determine the presence of integron-bearing gram-negative bacteria in the gut of a wild boar (sus scrofa l.) shot in the buffer zone of a national park. five gram-negative strains of escherichia coli, serratia odorifera, hafnia alvei and pseudomonas sp. were isolated. four of these strains had class 2 integrase (inti2), and one harbored class 1 integrase (inti1). the integron-positive strains were multiresistant, i.e., resistant to at least three unrelated antibiotics ...201122661922
metabolic characterization of cold active pseudomonas, arthrobacter, bacillus, and flavobacterium spp. from western himalayas.himalayan soils undergo dramatic temporal changes in their microclimatic properties. the soil habitats in the high altitude cold habitats of himalayas are little explored with respect to bacterial diversity and metabolic potentials of the bacterial species. soil habitat in western himalayas is dominated by the genera of pseudomonas, arthrobacter, bacillus, and flavobacterium. strains were found to be diverse in their metabolic potentials to utilize different carbon sources by growing them on med ...201122282631
the homogentisate and homoprotocatechuate central pathways are involved in 3- and 4-hydroxyphenylacetate degradation by burkholderia xenovorans lb400.genome characterization of the model pcb-degrading bacterium burkholderia xenovorans lb400 revealed the presence of eleven central pathways for aromatic compounds degradation, among them, the homogentisate and the homoprotocatechuate pathways. however, the functionality of these central pathways in strain lb400 has not been assessed and related peripheral pathways has not been described.201121423751
a comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in c. elegans.while caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. we applied new methods to conduct a comprehensive and comparative study of the transcriptional response of c. elegans to bacterial and fungal infection. using tiling arrays and/or rna-sequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (serr ...201121602919
characterization of the structure and function of klebsiella pneumoniae allantoin racemase.the oxidative catabolism of uric acid produces 5-hydroxyisourate (hiu), which is further degraded to (s)-allantoin by two enzymes, hiu hydrolase and 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. the intermediates of the latter two reactions, hiu and 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, are unstable in solution and decay nonstereospecifically to allantoin. in addition, nonenzymatic racemization of allantoin has been shown to occur at physiological ph. since the further br ...201121616082
isolation of xylose isomerases by sequence- and function-based screening from a soil metagenome library.abstract: background: xylose isomerase (xi) catalyses the isomerization of xylose to xylulose in bacteria and some fungi. currently, only a limited number of xi genes have been functionally expressed in saccharomyces cerevisiae, the microorganism of choice for lignocellulosic ethanol production. the objective of the present study was to search for novel xi genes in the vastly diverse microbial habitat present in soil. as the exploitation of microbial diversity is impaired by the ability to culti ...201121545702
microfluidic fluorescence in situ hybridization and flow cytometry (µflowfish).we describe an integrated microfluidic device (µflowfish) capable of performing 16s rrna fluorescence in situ hybridization (fish) followed by flow cytometric detection for identifying bacteria in natural microbial communities. the device was used for detection of species involved in bioremediation of cr(vi) and other metals in groundwater samples from a highly-contaminated environmental site (hanford, wa, usa). the µflowfish seamlessly integrates two components: a hybridization chamber formed b ...201121755095
kinetic, crystallographic, and mechanistic characterization of tomn: elucidation of a function for a 4-oxalocrotonate tautomerase homologue in the tomaymycin biosynthetic pathway.the biosynthesis of the c ring of the anti-tumor antibiotic agent, tomaymycin, is proposed to proceed through five enzyme-catalyzed steps from l-tyrosine. the genes encoding these enzymes have recently been cloned and their functions tentatively assigned, but there is limited biochemical evidence supporting the assignments of the last three steps. one enzyme, tomn, shows 58% pairwise sequence similarity with 4-oxalocrotonate tautomerase (4-ot), an enzyme found in a catabolic pathway for aromatic ...201121809870
mechanisms of nickel toxicity in microorganisms.nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. this assumption was overturned by the discovery of a nickel defense system (rcnr/rcna) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological conce ...201121799955
xenopus laevis oocytes infected with multi-drug-resistant bacteria: implications for electrical recordings.the xenopus laevis oocyte has been the workhorse for the investigation of ion transport proteins. these large cells have spawned a multitude of novel techniques that are unfathomable in mammalian cells, yet the fickleness of the oocyte has driven many researchers to use other membrane protein expression systems. here, we show that some colonies of xenopus laevis are infected with three multi-drug-resistant bacteria: pseudomonas fluorescens, pseudomonas putida, and stenotrophomonas maltophilia. o ...201121788613
multiple roles of component proteins in bacterial multicomponent monooxygenases: phenol hydroxylase and toluene/o-xylene monooxygenase from pseudomonas sp. ox1.phenol hydroxylase (ph) and toluene/o-xylene monooxygenase (tomo) from pseudomonas sp. ox1 require three or four protein components to activate dioxygen for the oxidation of aromatic substrates at a carboxylate-bridged diiron center. in this study, we investigated the influence of the hydroxylases, regulatory proteins, and electron-transfer components of these systems on substrate (phenol; nadh) consumption and product (catechol; h(2)o(2)) generation. single-turnover experiments revealed that on ...201121366224
differential effects of frozen storage on the molecular detection of bacterial taxa that inhabit the nasopharynx. 201121261963
mechanistic studies of 1-aminocyclopropane-1-carboxylate deaminase: characterization of an unusual pyridoxal 5'-phosphate-dependent reaction.1-aminocyclopropane-1-carboxylic acid (acc) deaminase (accd) is a pyridoxal 5'-phosphate (plp)-dependent enzyme that cleaves the cyclopropane ring of acc, to give α-ketobutyric acid and ammonia as products. the cleavage of the c(α)-c(β) bond of an amino acid substrate is a rare event in plp-dependent enzyme catalysis. potential chemical mechanisms involving nucleophile- or acid-catalyzed cyclopropane ring opening have been proposed for the unusual transformation catalyzed by accd, but the actual ...201121244019
comprehensive analysis of secondary dental root canal infections: a combination of culture and culture-independent approaches reveals new insights.persistence of microorganisms or reinfections are the main reasons for failure of root canal therapy. very few studies to date have included culture-independent methods to assess the microbiota, including non-cultivable microorganisms. the aim of this study was to combine culture methods with culture-independent cloning methods to analyze the microbial flora of root-filled teeth with periradicular lesions. twenty-one samples from previously root-filled teeth were collected from patients with per ...201223152922
Development of a New Strategy for Production of Medium-Chain-Length Polyhydroxyalkanoates by Recombinant Escherichia coli via Inexpensive Non-Fatty Acid Feedstocks.Pseudomonas putida KT2440 is capable of producing medium-chain-length polyhydroxyalkanoates (MCL-PHAs) when grown on unrelated carbon sources during nutrient limitation. Transcription levels of genes putatively involved in PHA biosynthesis were assessed by quantitative real-time PCR (qRT-PCR) in P. putida grown on glycerol as a sole carbon source. The results showed that two genes, phaG and the PP0763 gene, were highly upregulated among genes potentially involved in the biosynthesis of MCL-PHAs ...201222101037
The glycerophospholipid inventory of Pseudomonas putida is conserved between strains and enables growth condition-related alterations.Microorganisms, such as Pseudomonas putida, utilize specific physical properties of cellular membrane constituents, mainly glycerophospholipids, to (re-)adjust the membrane barrier to environmental stresses. Building a basis for membrane composition/function studies, we inventoried the glycerophospholipids of different Pseudomonas and challenged membranes of growing cells with n-butanol. Using a new high-resolution liquid chromatography/mass spectrometry (LC/MS) method, 127 glycerophospholipid s ...201221895997
isolation of paenibacillus sp. and variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction.prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. in this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. there was a predominance of gram positive isolates that belonged to the phyla proteobacteria and firmicutes. many primary isolates with cellulolytic activity were not p ...201223301200
engineering non-heme mono- and dioxygenases for biocatalysis.oxygenases are ubiquitous enzymes that catalyze the introduction of one or two oxygen atoms to unreactive chemical compounds. they require reduction equivalents from nadh or nadph and comprise metal ions, metal ion complexes, or coenzymes in their active site. thus, for industrial purposes, oxygenases are most commonly employed using whole cell catalysis, to alleviate the need for co-factor regeneration. biotechnological applications include bioremediation, chiral synthesis, biosensors, fine che ...201224688652
reciprocal tripartite interactions between the aedes aegypti midgut microbiota, innate immune system and dengue virus influences vector competence.dengue virus is one of the most important arboviral pathogens and the causative agent of dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. it is transmitted between humans by the mosquitoes aedes aegypti and aedes albopictus, and at least 2.5 billion people are at daily risk of infection. during their lifecycle, mosquitoes are exposed to a variety of microbes, some of which are needed for their successful development into adulthood. however, recent studies have suggested that th ...201222413032
pathology of spontaneous air sacculitis in 37 baboons and seven chimpanzees and a brief review of the literature.air sacculitis is an important clinical condition in non-human primates.201222765381
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
characterization of bacteria associated with pinewood nematode bursaphelenchus xylophilus.pine wilt disease (pwd) is a complex disease integrating three major agents: the pathogenic agent, the pinewood nematode bursaphelenchus xylophilus; the insect-vector monochamus spp.; and the host pine tree, pinus sp. since the early 80's, the notion that another pathogenic agent, namely bacteria, may play a role in pwd has been gaining traction, however the role of bacteria in pwd is still unknown. the present work supports the possibility that some b. xylophilus-associated bacteria may play a ...201223091599
evaluation and biochemical characterization of a distinctive pyoverdin from a pseudomonas isolated from chickpea rhizosphere.microbial siderophores confiscate the available ferric ions around the roots and trigger a reaction resulting in plant growth promotion. in our study, a high level of siderophore production was observed from a newly isolated pseudomonas sp. from the rhizosphere of chickpea plants. under an iron depleted condition in standard succinic acid medium a 1000 μgml(-1) of siderophore production was achieved. increasing the concentration of iron showed an inverse relationship between growth and sideropho ...201224031875
plant-growth promoting effect of newly isolated rhizobacteria varies between two arabidopsis ecotypes.various rhizobacteria are known for their beneficial effects on plants, i. e. promotion of growth and induction of systemic resistance against pathogens. these bacteria are categorized as plant growth promoting rhizobacteria (pgpr) and are associated with plant roots. knowledge of the underlying mechanisms of plant growth promotion in vivo is still very limited, but interference of bacteria with plant hormone metabolism is suggested to play a major role. to obtain new growth promoting bacteria, ...201222580689
investigation of the biosynthetic potential of endophytes in traditional chinese anticancer herbs.traditional chinese medicine encompasses a rich empirical knowledge of the use of plants for the treatment of disease. in addition, the microorganisms associated with medicinal plants are also of interest as the producers of the compounds responsible for the observed plant bioactivity. the present study has pioneered the use of genetic screening to assess the potential of endophytes to synthesize bioactive compounds, as indicated by the presence of non-ribosomal peptide synthetase (nrps) and pol ...201222629306
convergent development of anodic bacterial communities in microbial fuel cells.microbial fuel cells (mfcs) are often inoculated from a single wastewater source. the extent that the inoculum affects community development or power production is unknown. the stable anodic microbial communities in mfcs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. the bog-inoculated mfcs initially produced higher power densities than the wastewater-in ...201222572637
pyrosequencing-based analysis of the microbiome associated with the horn fly, haematobia irritans.the horn fly, haematobia irritans, is one of the most economically important pests of cattle. insecticides have been a major element of horn fly management programs. growing concerns with insecticide resistance, insecticide residues on farm products, and non-availability of new generation insecticides, are serious issues for the livestock industry. alternative horn fly control methods offer the promise to decrease the use of insecticides and reduce the amount of insecticide residues on livestock ...201223028533
learning from bacteriophages - advantages and limitations of phage and phage-encoded protein applications.the emergence of bacteria resistance to most of the currently available antibiotics has become a critical therapeutic problem. the bacteria causing both hospital and community-acquired infections are most often multidrug resistant. in view of the alarming level of antibiotic resistance between bacterial species and difficulties with treatment, alternative or supportive antibacterial cure has to be developed. the presented review focuses on the major characteristics of bacteriophages and phage-en ...201223305359
a conjugative 38 kb plasmid is present in multiple subspecies of xylella fastidiosa.a ≈ 38kb plasmid (pxf-riv5) was present in the riv5 strain of xylella fastidiosa subsp. multiplex isolated from ornamental plum in southern california. the complete nucleotide sequence of pxf-riv5 is almost identical to that of pxfas01 from x. fastidiosa subsp. fastidiosa strain m23; the two plasmids vary at only 6 nucleotide positions. blast searches and phylogenetic analyses indicate pxf-riv5 and pxfas01 share some similarity to chromosomal and plasmid (pxf51) sequences of x. fastidiosa subsp. ...201223251694
re-evaluation of a bacterial antifreeze protein as an adhesin with ice-binding activity.a novel role for antifreeze proteins (afps) may reside in an exceptionally large 1.5-mda adhesin isolated from an antarctic gram-negative bacterium, marinomonas primoryensis. mpafp was purified from bacterial lysates by ice adsorption and gel electrophoresis. we have previously reported that two highly repetitive sequences, region ii (rii) and region iv (riv), divide mpafp into five distinct regions, all of which require mm ca(2+) levels for correct folding. also, the antifreeze activity is conf ...201223144980
biosynthesis and characterization of polyhydroxyalkanoates copolymers produced by pseudomonas putida bet001 isolated from palm oil mill effluent.the biosynthesis and characterization of medium chain length poly-3-hydroxyalkanoates (mcl-pha) produced by pseudomonas putida bet001 isolated from palm oil mill effluent was studied. the biosynthesis of mcl-pha in this newly isolated microorganism follows a growth-associated trend. mcl-pha accumulation ranging from 49.7 to 68.9% on cell dry weight (cdw) basis were observed when fatty acids ranging from octanoic acid (c(8:0)) to oleic acid (c(18:1)) were used as sole carbon and energy source. mo ...201223028854
an ultrasensitive enzymatic method for measuring mevalonic acid in serum.we have developed a simple, precise, and ultrasensitive enzymatic method for measuring serum mevalonic acid (mva) concentration, which is thought to be a good indicator of the in vivo cholesterol biosynthesis rate. this assay is based on an enzyme cycling reaction and makes use of hmg-coa reductase (hmgr), thio-nad, nadh, and coa. mva participates in the hmgr cycling reaction, and its level is measured based on the production of thio-nadh, which is determined from the change in absorbance at 405 ...201222715156
identification of the para-nitrophenol catabolic pathway, and characterization of three enzymes involved in the hydroquinone pathway, in peudomonas sp. 1-7.para-nitrophenol (pnp), a priority environmental pollutant, is hazardous to humans and animals. however, the information relating to the pnp degradation pathways and their enzymes remain limited.201222380602
reduction of chromium-vi by chromium resistant lactobacilli: a prospective bacterium for bioremediation.chromium is a toxic heavy metal, which primarily exists in two inorganic forms, cr (vi) and cr (iii). highly soluble hexavalent chromium is carcinogenic due to its oxidizing nature. it is well established that the intestinal bacteria including lactobacilli have regulatory effect on intestinal homeostasis and a breakdown in the relationship between intestinal cells and bacteria results in the manifestation of gastrointestinal (gi) disorders. in this study cr (vi) resistance was developed in lacto ...201222736899
accuracy of rapid tests for malaria and treatment outcomes for malaria and non-malaria cases among under-five children in rural ghana.who now recommends test-based management of malaria across all transmission settings. the accuracy of rapid diagnostic test (rdt) and the outcome of treatment based on the result of tests will influence acceptability of and adherence to the new guidelines.201222514617
mineralization of acephate, a recalcitrant organophosphate insecticide is initiated by a pseudomonad in environmental samples.an aerobic bacterium capable of breaking down the pesticide acephate (o,s-dimethyl acetyl phosphoramidothioic acid) was isolated from activated sludge collected from a pesticide manufacturing facility. a phylogenetic tree based on the 16 s rrna gene sequence determined that the isolate lies within the pseudomonads. the isolate was able to grow in the presence of acephate at concentrations up to 80 mm, with maximum growth at 40 mm. hplc and lc-ms/ms analysis of spent medium from growth experiment ...201222496729
changes in bacterial composition of zucchini flowers exposed to refrigeration temperatures.microbial spoilage is one of the main factors affecting the quality of fresh fruits and vegetables, leading to off-flavor, fermented aroma, and tissue decay. the knowledge of microbial growth kinetics is essential for estimating a correct risk assessment associated with consuming raw vegetables and better managing the development of spoilage microorganisms. this study shows, for the first time, that only a part of total microbial community, originally present on fresh harvested female zucchini f ...201222566759
two separate gene clusters encode the biosynthetic pathway for the meroterpenoids austinol and dehydroaustinol in aspergillus nidulans.meroterpenoids are a class of fungal natural products that are produced from polyketide and terpenoid precursors. an understanding of meroterpenoid biosynthesis at the genetic level should facilitate engineering of second-generation molecules and increasing production of first-generation compounds. the filamentous fungus aspergillus nidulans has previously been found to produce two meroterpenoids, austinol and dehydroaustinol. using targeted deletions that we created, we have determined that, su ...201222329759
saber: a computational method for identifying active sites for new reactions.a software suite, saber (selection of active/binding sites for enzyme redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (barker and thornton, bioinformatics 2003;19:1644-1649). saber is used to explore the protein data bank (pdb) to locate proteins with a specific 3d arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. as a proof-of-principle test, saber was used t ...201222492397
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