Publications

evaluation of antimicrobial therapy of blood culture positive healthcare-associated infections in children.	knowledge of the quality of antimicrobial therapy (amt) used for invasive healthcare-associated infections (hais) in paediatrics is scarce. influence of the final information about the isolated pathogen on the subsequent targeted amt was investigated in our study.	2015	26539831
structure analysis uncovers a highly diverse but structurally conserved effector family in phytopathogenic fungi.	phytopathogenic ascomycete fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins. the molecular function of these effectors and the evolutionary mechanisms that generate this tremendous number of singleton genes are largely unknown. to get a deeper understanding of fungal effectors, we determined by nmr spectroscopy the 3-dimensional structures of the magnaporthe oryzae effectors avr1-co39 and avr-pia. despite a lack of sequence simi ...	2015	26506000
mechanism of aromatic amine carcinogen bypass by the y-family polymerase, dpo4.	bulky dna damage inhibits dna synthesis by replicative polymerases and often requires the action of error prone bypass polymerases. the exact mechanism governing adduct-induced mutagenesis and its dependence on the dna sequence context remains unclear. in this work, we characterize dpo4 binding conformations and activity with dna templates modified with the carcinogenic dna adducts, 2-aminofluoene (af) or n-acetyl-2-aminofluorene (aaf), using single-molecule fret (smfret) analysis and dna synthe ...	2015	26481355
port site infection in laparoscopic surgery: a review of its management.	laparoscopic surgery (ls), also termed minimal access surgery, has brought a paradigm shift in the approach to modern surgical care. early postoperative recovery, less pain, improved aesthesis and early return to work have led to its popularity both amongst surgeons and patients. its application has progressed from cholecystectomies and appendectomies to various other fields including gastrointestinal surgery, urology, gynecology and oncosurgery. however, ls has its own package of complications. ...	2015	26488021
psychrophilic pseudomonas in antarctic freshwater lake at stornes peninsula, larsemann hills over east antarctica.	the larsemann hills is an ice-free area of approximately 50 km(2), located halfway between the vestfold hills and the amery ice shelf on the south-eastern coast of prydz bay, princess elizabeth land, east antarctica (69º30's, 76º19'58″e). the ice-free area consists of two major peninsulas (stornes and broknes), four minor peninsulas, and approximately 130 islands. the larsemann hills area contains more than 150 lakes at different islands and peninsulas. nine lake water samples were collected in ...	2015	26543717
preparation of dental resins resistant to enzymatic and hydrolytic degradation in oral environments.	the short average service life of traditional dental composite restorative materials and increasing occurrence of secondary caries adjacent to composite restorations and sealants are necessitating the development of new, longer lasting compositions. novel monomers and their polymers, reinforcing fillers, and adhesive components are needed. the goal of this research is to develop resin systems for use in restorations, sealants, and other dental services that are superior in properties and enduran ...	2015	26358180
skin-derived c-terminal filaggrin-2 fragments are pseudomonas aeruginosa-directed antimicrobials targeting bacterial replication.	soil- and waterborne bacteria such as pseudomonas aeruginosa are constantly challenging body surfaces. since infections of healthy skin are unexpectedly rare, we hypothesized that the outermost epidermis, the stratum corneum, and sweat glands directly control the growth of p. aeruginosa by surface-provided antimicrobials. due to its high abundance in the upper epidermis and eccrine sweat glands, filaggrin-2 (flg2), a water-insoluble 248 kda s100 fused-type protein, might possess these innate eff ...	2015	26371476
brkautodisplay: functional display of multiple exogenous proteins on the surface of escherichia coli by using brka autotransporter.	bacterial surface display technique enables the exogenous proteins or polypeptides displayed on the bacterial surface, while maintaining their relatively independent spatial structures and biological activities. the technique makes recombinant bacteria possess the expectant functions, subsequently, directly used for many applications. many proteins could be used to achieve bacterial surface display, among them, autotransporter, a member of the type v secretion system of gram-negative bacteria, h ...	2015	26337099
ultrasound scan as a potential source of nosocomial and crossinfection: a literature review.	the authors review the main concepts regarding the importance of cleaning/disinfection of ultrasonography probes, aiming a better comprehension by practitioners and thus enabling strategies to establish a safe practice without compromising the quality of the examination and the operator productivity. in the context of biosafety, it is imperative to assume that contact with blood or body fluids represents a potential source of infection. thus, in order to implement cleaning/disinfection practice, ...	2015	26543284
a facile method for controlling the reaction equilibrium of sphingolipid ceramide n-deacylase for lyso-glycosphingolipid production.	lyso-glycosphingolipids (lyso-gsls), the n-deacylated forms of glycosphingolipids (gsls), are important synthetic intermediates for the preparation of gsl analogs. although lyso-gsls can be produced by hydrolyzing natural gsls using sphingolipid ceramide n-deacylase (scdase), the yield for this reaction is usually low because scdase also catalyzes the reverse reaction, ultimately establishing an equilibrium between hydrolysis and synthesis. in the present study, we developed an efficient method ...	2015	26130766
biosurfactant production by bacillus salmalaya for lubricating oil solubilization and biodegradation.	this study investigated the capability of a biosurfactant produced by a novel strain of bacillus salmalaya to enhance the biodegradation rates and bioavailability of organic contaminants. the biosurfactant produced by cultured strain 139si showed high physicochemical properties and surface activity in the selected medium. the biosurfactant exhibited a high emulsification index and a positive result in the drop collapse test, with the results demonstrating the wetting activity of the biosurfactan ...	2015	26295402
live-streaming: time-lapse video evidence of novel streamer formation mechanism and varying viscosity.	time-lapse videos of growing biofilms were analyzed using a background subtraction method, which removed camouflaging effects from the heterogeneous field of view to reveal evidence of streamer formation from optically dense biofilm segments. in addition, quantitative measurements of biofilm velocity and optical density, combined with mathematical modeling, demonstrated that streamer formation occurred from mature, high-viscosity biofilms. we propose a streamer formation mechanism by sudden part ...	2015	26339304
multifarious activities of cellulose degrading bacteria from koala (phascolarctos cinereus) faeces.	cellulose degrading bacteria from koala faeces were isolated using caboxymethylcellulose-congo red agar, screened in vitro for different hydrolytic enzyme activities and phylogenetically characterized using molecular tools. bacillus sp. and pseudomonas sp. were the most prominent bacteria from koala faeces. the isolates demonstrated good xylanase, amylase, lipase, protease, tannase and lignin peroxidase activities apart from endoglucanase activity. furthermore many isolates grew in the presence ...	2015	26290743
identification of an endophytic antifungal bacterial strain isolated from the rubber tree and its application in the biological control of banana fusarium wilt.	banana fusarium wilt (also known as panama disease) is one of the most disastrous plant diseases. effective control methods are still under exploring. the endophytic bacterial strain itbb b5-1 was isolated from the rubber tree, and identified as serratia marcescens by morphological, biochemical, and phylogenetic analyses. this strain exhibited a high potential for biological control against the banana fusarium disease. visual agar plate assay showed that itbb b5-1 restricted the mycelial growth ...	2015	26133557
additivity of the stabilization effect of single amino acid substitutions in triple mutants of recombinant formate dehydrogenase from the soybean glycine max.	recently, we demonstrated that the amino acid substitutions ala267met and ala267met/ile272val (alekseeva et al., biochemistry, 2012), phe290asp, phe290asn and phe290ser (alekseeva et al., prot. eng. des. select, 2012) in recombinant formate dehydrogenase from soya glycine max (soyfdh) lead to a significant (up to 30-100 times) increase in the thermal stability of the enzyme. the substitutions phe290asp, phe290asn and phe290ser were introduced into double mutant soyfdh ala267met/ile272val by site ...	2015	26483960
screening the drug resistance property among aerobic pathogenic microorganisms of dental caries in north-western indian population: a preliminary study.	to evaluate the emerging drug resistance among the caries pathogens isolated from carious dentine microbiologically.	2015	26393195
treatment of uncomplicated symptomatic urinary tract infections: resistance patterns and misuse of antibiotics.	uncomplicated but symptomatic urinary tract infections (utis) are a common problem seen in practice. the study was undertaken to assess the most common pathogens responsible for uncomplicated symptomatic utis and the antimicrobial resistance pattern in a hospital in bangalore. the study also explores the issue of antibiotic usage for these patients.	2015	26288784
microbial population dynamics in response to pectobacterium atrosepticum infection in potato tubers.	endophytes are microbes and fungi that live inside plant tissues without damaging the host. herein we examine the dynamic changes in the endophytic bacterial community in potato (solanum tuberosum) tuber in response to pathogenic infection by pectobacterium atrosepticum, which causes soft rot in numerous economically important crops. we quantified community changes using both cultivation and next-generation sequencing of the 16s rrna gene and found that, despite observing significant variability ...	2015	26118792
classes of organic molecules targeted by a methanogenic microbial consortium grown on sedimentary rocks of various maturities.	organic-rich shales are populated by methanogenic consortia that are able to degrade the fossilized organic matter into methane gas. to identify the organic fraction effectively degraded, we have sequentially depleted two types of organic-rich sedimentary rocks, shale, and coal, at two different maturities, by successive solvent extractions to remove the most soluble fractions (maltenes and asphaltenes) and isolate kerogen. we show the ability of the consortia to produce methane from all rock sa ...	2015	26136731
seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient.	this research investigated spatial-temporal variation in benthic bacterial community structure, rates of denitrification and dissimilatory nitrate reduction to ammonium (dnra) processes and abundances of corresponding genes and transcripts at three sites-the estuary-head, mid-estuary and the estuary mouth (em) along the nitrate gradient of the colne estuary over an annual cycle. denitrification rates declined down the estuary, while dnra rates were higher at the estuary head and middle than the ...	2015	26082763
antagonistic effect of pseudomonas sp. cmi-1 on foodborne pathogenic listeria monocytogenes.	bacterial isolates derived from food or raw food materials of animal origin were screened for potential antagonistic activity against foodborne pathogenic listeria monocytogenes. using the agar spot method, ten out of the 94 tested bacteria showed antilisterial activity. all of the antagonistic isolates identified by sequence analysis as strains of the genus pseudomonas were able to inhibit the growth of all the examined listeria species including the ruminal pathogenic l. ivanovii and the oppor ...	2015	27904352
biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium.	three bacterial isolates identified as alcanivorax borkumensis sk2, rhodococcus erythropolis hs4 and pseudomonas stutzeri sdm, based on 16s rrna gene sequences, were isolated from crude oil enrichments of natural seawater. single strains and four bacterial consortia designed by mixing the single bacterial cultures respectively in the following ratios: (alcanivorax: pseudomonas, 1:1), (alcanivorax: rhodococcus, 1:1), (pseudomonas: rhodococcus, 1:1), and (alcanivorax: pseudomonas: rhodococcus, 1:1 ...	2015	26273252
fermentative hydrogen production from agroindustrial lignocellulosic substrates.	to achieve economically competitive biological hydrogen production, it is crucial to consider inexpensive materials such as lignocellulosic substrate residues derived from agroindustrial activities. it is possible to use (1) lignocellulosic materials without any type of pretreatment, (2) lignocellulosic materials after a pretreatment step, and (3) lignocellulosic materials hydrolysates originating from a pretreatment step followed by enzymatic hydrolysis. according to the current literature data ...	2015	26273246
the potential impact of coinfection on antimicrobial chemotherapy and drug resistance.	across a range of pathogens, resistance to chemotherapy is a growing problem in both public health and animal health. despite the ubiquity of coinfection, and its potential effects on within-host biology, the role played by coinfecting pathogens on the evolution of resistance and efficacy of antimicrobial chemotherapy is rarely considered. in this review, we provide an overview of the mechanisms of interaction of coinfecting pathogens, ranging from immune modulation and resource modulation, to d ...	2015	26028590
transcriptional modulation of intestinal innate defense/inflammation genes by preterm infant microbiota in a humanized gnotobiotic mouse model.	it is known that postnatal functional maturation of the small intestine is facilitated by microbial colonization of the gut. preterm infants exhibit defects in gut maturation, weak innate immunity against intestinal infection and increased susceptibility to inflammatory disorders, all of which may be related to the inappropriate microbial colonization of their immature intestines. the earliest microbes to colonize the preterm infant gut encounter a naïve, immature intestine. thus this earliest m ...	2015	25928420
the toluene o-xylene monooxygenase enzymatic activity for the biosynthesis of aromatic antioxidants.	monocyclic phenols and catechols are important antioxidant compounds for the food and pharmaceutic industries; their production through biotransformation of low-added value starting compounds is of major biotechnological interest. the toluene o-xylene monooxygenase (tomo) from pseudomonas sp. ox1 is a bacterial multicomponent monooxygenase (bmm) that is able to hydroxylate a wide array of aromatic compounds and has already proven to be a versatile biochemical tool to produce mono- and dihydroxyl ...	2015	25915063
a redox regulatory system critical for mycobacterial survival in macrophages and biofilm development.	survival of m. tuberculosis in host macrophages requires the eukaryotic-type protein kinase g, pkng, but the underlying mechanism has remained unknown. here, we show that pkng is an integral component of a novel redox homeostatic system, rhocs, which includes the ribosomal protein l13 and renu, a nudix hydrolase encoded by a gene adjacent to pkng. studies in m. smegmatis showed that pkng expression is uniquely induced by nadh, which plays a key role in metabolism and redox homeostasis. in vitro, ...	2015	25884716
analysis of fungal ball rhinosinusitis by culturing fungal clumps under endoscopic surgery.	this study was designed to investigate the clinical microbiology of fungal ball (fb) rhinosinusitis by culturing fungal clumps collected under endoscopic surgery.	2015	26131186
encapsulating peritoneal sclerosis as a late complication of peritoneal dialysis.	encapsulating peritoneal sclerosis (eps) is a rare cause of intestinal obstruction which is characterized by fibrotic encapsulation of the bowel. although its pathogenesis is still not clear, many etiological factors have been stated.	2015	26150908
high potential application in bioremediation of selenate by proteus hauseri strain qw4.	selenium is essential for biological systems at low concentrations and toxic at higher levels. heavy metals and metalloids such as selenium are major contaminants in 40% of hazardous waste sites. thus, bioremediation has been considered as an effective means of cleaning up of selenium-contaminated sites.	2015	26622970
comparative analysis of wolbachia genomes reveals streamlining and divergence of minimalist two-component systems.	two-component regulatory systems are commonly used by bacteria to coordinate intracellular responses with environmental cues. these systems are composed of functional protein pairs consisting of a sensor histidine kinase and cognate response regulator. in contrast to the well-studied caulobacter crescentus system, which carries dozens of these pairs, the streamlined bacterial endosymbiont wolbachia pipientis encodes only two pairs: ccka/ctra and plec/pled. here, we used bioinformatic tools to co ...	2015	25809075
clinical outcomes and microbiological characteristics of severe pneumonia in cancer patients: a prospective cohort study.	pneumonia is the most frequent type of infection in cancer patients and a frequent cause of icu admission. the primary aims of this study were to describe the clinical and microbiological characteristics and outcomes in critically ill cancer patients with severe pneumonia.	2015	25803690
phytogenic compounds as alternatives to in-feed antibiotics: potentials and challenges in application.	this article summarizes current experimental knowledge on the efficacy, possible mechanisms and feasibility in the application of phytogenic products as feed additives for food-producing animals. phytogenic compounds comprise a wide range of plant-derived natural bioactive compounds and essential oils are a major group. numerous studies have demonstrated that phytogenic compounds have a variety of functions, including antimicrobial/antiviral, antioxidative and anti-inflammation effects and impro ...	2015	25806623
comparing two types of rabbit atg prior to reduced intensity conditioning allogeneic hematopoietic sct for hematologic malignancies.	different rabbit polyclonal antilymphocyte globulins (atgs) are used in allogeneic hematopoietic stem cell transplantation (allohsct) to prevent graft-versus-host disease (gvhd). we compared 2 different atgs in allohsct after reduced intensity conditioning (ric) for hematological malignancies. we reviewed 30 allohsct for hematologic malignancies performed between 2007 and 2010 with fludarabine and i.v. busulfan as conditioning regimen. patients alternatingly received thymoglobulin or atg-f. medi ...	2015	25874131
experimental design approach to the optimization of pahs bioremediation from artificially contaminated soil: application of variables screening development.	the effectiveness of bioremediation systems for pah-contaminated soil may be constrained by physicochemical properties of contaminants and environmental factors. information on what is the most effective factor in bioremediation process is essential in the decision of what stimulations can be taken to assist the biodegradation efficacy.	2015	25834738
trapping and assembly of living colloids at water-water interfaces.	we study the assembly of inert and living colloids in a two-phase water-water system that provides an environment that can sustain bacteria, providing a new structure with rich potential to confine and structure microbial communities. the water-water system, formed via phase separation of a casein and xanthan mixture, forms a 3-d structure of coexisting casein-rich and xanthan-rich phases. fluorescent labelling and confocal microscopy reveal the attachment of these living colloids, including esc ...	2015	25600991
biodegradation and detoxification of textile azo dyes by bacterial consortium under sequential microaerophilic/aerobic processes.	release of textile azo dyes to the environment is an issue of health concern while the use of microorganisms has proved to be the best option for remediation. thus, in the present study, a bacterial consortium consisting of providencia rettgeri strain hsl1 and pseudomonas sp. suk1 has been investigated for degradation and detoxification of structurally different azo dyes. the consortium showed 98-99 % decolorization of all the selected azo dyes viz. reactive black 5 (rb 5), reactive orange 16 (r ...	2015	26417357
taking a corneal scrape and making a diagnosis.		2015	26435585
the role of ala198 in the stability and coenzyme specificity of bacterial formate dehydrogenases.	it has been shown by an x-ray structural analysis that the amino acid residues ala198, which are located in the coenzyme-binding domain of nad(+)-dependent formate dehydrogenases (ec 1.2.1.2., fdh) from bacteria pseudomonas sp.101 and moraxella sp. c-1 (psefdh and morfdh, respectively), have non-optimal values of the angles ψ and φ. these residues were replaced with gly by site-directed mutagenesis. the mutants psefdh a198g and morfdh a198g were expressed in e.coli cells and obtained in active a ...	2015	25927002
metabolic degradation of 1,4-dichloronaphthalene by pseudomonas sp. hy.	there is increasing concern regarding the adverse health effects of polychlorinated naphthalenes (pcns). the metabolic degradation of 1,4-dichloronaphthalene (1,4-dcn) as a model pcn, was studied using a strain of pseudomonas sp. hy. the metabolites were analyzed by gas chromatography-mass spectrometry (gc-ms). a series of metabolites including dihydroxy-dichloro-naphthalene, epoxy-dichlorinated naphthalene, dichlorinated naphthol, and dichlorinated salicylic acid were identified. the time-conce ...	2015	26308037
the crystal structure of d-threonine aldolase from alcaligenes xylosoxidans provides insight into a metal ion assisted plp-dependent mechanism.	threonine aldolases catalyze the pyridoxal phosphate (plp) dependent cleavage of threonine into glycine and acetaldehyde and play a major role in the degradation of this amino acid. in nature, l- as well as d-specific enzymes have been identified, but the exact physiological function of d-threonine aldolases (dtas) is still largely unknown. both types of enantio-complementary enzymes have a considerable potential in biocatalysis for the stereospecific synthesis of various β-hydroxy amino acids, ...	2015	25884707
bioaugmentation of mesorhizobium cicer, pseudomonas spp. and piriformospora indica for sustainable chickpea production.	chickpea establishes symbiotic association with mesorhizobium to fulfill its nitrogen (n) requirement. integrating chickpea rhizosphere with potential native mesorhizobia and other plant growth promoting microorganisms can contribute multiple benefits to plants. the present investigation was undertaken to study interactions among piriformospora indica (pi) with potential plant growth promoting rhizobacteria (pgpr) viz. pseudomonas argentinensis (lpgpr1), pseudomonas sp. (lpgpr2) along with natio ...	2015	26261403
plant-microbe cross-talk in the rhizosphere: insight and biotechnological potential.	rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. the composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. recent a ...	2015	25926899
comparative genomics of pseudomonas fluorescens subclade iii strains from human lungs.	while the taxonomy and genomics of environmental strains from the p. fluorescens species-complex has been reported, little is known about p. fluorescens strains from clinical samples. in this report, we provide the first genomic analysis of p. fluorescens strains in which human vs. environmental isolates are compared.	2015	26644001
composition of the spruce budworm (choristoneura fumiferana) midgut microbiota as affected by rearing conditions.	the eastern spruce budworm (choristoneura fumiferana) is one of the most destructive forest insect pests in canada. little is known about its intestinal microbiota, which could play a role in digestion, immune protection, communication and/or development. the present study was designed to provide a first characterization of the effects of rearing conditions on the taxonomic diversity and structure of the c. fumiferana midgut microbiota, using a culture-independent approach. three diets and insec ...	2015	26636571
a fragrant neighborhood: volatile mediated bacterial interactions in soil.	there is increasing evidence that volatile organic compounds (vocs) play essential roles in communication and competition between soil microorganisms. here we assessed volatile-mediated interactions of a synthetic microbial community in a model system that mimics the natural conditions in the heterogeneous soil environment along the rhizosphere. phylogenetic different soil bacterial isolates (burkholderia sp., dyella sp., janthinobacterium sp., pseudomonas sp., and paenibacillus sp.) were inocul ...	2015	26579111
phylogenetic analysis based evolutionary study of 16s rrna in known pseudomonas sp.	molecular evolution analysis of 16s rrna sequences of native pseudomonas strains and different fluorescent pseudomonads were conducted on the basis of molecular evolutionary genetics analysis version 5.2 (mega5.2). topological evaluations show common origin for native strains with other known strains with available sequences at genbank database. phylogenetic affiliation of different pseudomonas sp based on 16s rrna gene shows that molecular divergence contributes to the genetic diversity of pseu ...	2015	26664032
biodegradation kinetics and interactions of styrene and ethylbenzene as single and dual substrates for a mixed bacterial culture.	this study examined biodegradation kinetics of styrene and ethylbenzene as representatives of alkenylbenzenes and mono-alkylbenzenes, respectively. the compounds were studied independently and as binary mixtures using a series of aerobic batch degradation experiments introduced by acclimatized mix culture. initial concentration of styrene and ethylbenzene in the liquid phase vacillated from 0 to 220 mg/l. the andrew model was applied for the biodegradation of individual substrates and the estima ...	2015	26483955
the genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles.	ribosomally synthesized and post-translationally modified peptides (ripps) are a burgeoning class of natural products with diverse activity that share a similar origin and common features in their biosynthetic pathways. the precursor peptides of these natural products are ribosomally produced, upon which a combination of modification enzymes installs diverse functional groups. this genetically encoded peptide-based strategy allows for rapid diversification of these natural products by mutation i ...	2015	26462797
fiber-optic chemical sensors and fiber-optic bio-sensors.	this review summarizes principles and current stage of development of fiber-optic chemical sensors (focs) and biosensors (fobs). fiber optic sensor (fos) systems use the ability of optical fibers (of) to guide the light in the spectral range from ultraviolet (uv) (180 nm) up to middle infrared (ir) (10 μm) and modulation of guided light by the parameters of the surrounding environment of the of core. the introduction of of in the sensor systems has brought advantages such as measurement in flamm ...	2015	26437407
an automated genomes-to-natural products platform (gnp) for the discovery of modular natural products.	bacterial natural products are a diverse and valuable group of small molecules, and genome sequencing indicates that the vast majority remain undiscovered. the prediction of natural product structures from biosynthetic assembly lines can facilitate their discovery, but highly automated, accurate, and integrated systems are required to mine the broad spectrum of sequenced bacterial genomes. here we present a genome-guided natural products discovery tool to automatically predict, combinatorialize ...	2015	26412281
immobilization of microbes for bioremediation of crude oil polluted environments: a mini review.	petroleum hydrocarbons are the most common environmental pollutants in the world and oil spills pose a great hazard to terrestrial and marine ecosystems. oil pollution may arise either accidentally or operationally whenever oil is produced, transported, stored and processed or used at sea or on land. oil spills are a major menace to the environment as they severely damage the surrounding ecosystems. to improve the survival and retention of the bioremediation agents in the contaminated sites, bac ...	2015	26668662
unearthing the genomes of plant-beneficial pseudomonas model strains wcs358, wcs374 and wcs417.	plant growth-promoting rhizobacteria (pgpr) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (isr). in the past 30 years, the pseudomonas spp. pgpr strains wcs358, wcs374 and wcs417 of the willie commelin scholten (wcs) collection have been studied in detail in pioneering papers on the molecular basis of pgpr-me ...	2015	26198432
bacteria isolated from bats inhibit the growth of pseudogymnoascus destructans, the causative agent of white-nose syndrome.	emerging infectious diseases are a key threat to wildlife. several fungal skin pathogens have recently emerged and caused widespread mortality in several vertebrate groups, including amphibians, bats, rattlesnakes and humans. white-nose syndrome, caused by the fungal skin pathogen pseudogymnoascus destructans, threatens several hibernating bat species with extinction and there are few effective treatment strategies. the skin microbiome is increasingly understood to play a large role in determini ...	2015	25853558
a novel eurythermic and thermostale lipase lipm from pseudomonas moraviensis m9 and its application in the partial hydrolysis of algal oil.	lipases are regularly used in biotechnology to catalyse the hydrolysis of triglycerides and the synthesis of esters. microbial lipases in particular have been widely used in a variety of industrial applications. however, the current commercial microbial lipases cannot meet industrial demand due to rapid inactivation under harsh conditions. therefore, in order to identify more stable enzymes, we isolated novel eurythermic and thermostable lipase(s) from pseudomonas moraviensis m9.	2015	26463643
comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis.	changes in the airway microbiome may be important in the pathophysiology of chronic lung disease in patients with cystic fibrosis. however, little is known about the microbiome in early cystic fibrosis lung disease and the relationship between the microbiomes from different niches in the upper and lower airways. therefore, in this cross-sectional study, we examined the relationship between the microbiome in the upper (nose and throat) and lower (sputum) airways from children with cystic fibrosis ...	2015	25629612
alginate lyase: review of major sources and classification, properties, structure-function analysis and applications.	alginate lyases catalyze the degradation of alginate, a complex copolymer of α-l-guluronate and its c5 epimer β-d-mannuronate. the enzymes have been isolated from various kinds of organisms with different substrate specificities, including algae, marine mollusks, marine and terrestrial bacteria, and some viruses and fungi. with the progress of structural biology, many kinds of alginate lyases of different polysaccharide lyases families have been characterized by obtaining crystal structures, and ...	2015	25831216
efflux pump-deficient mutants as a platform to search for microbes that produce antibiotics.	pseudomonas putida dot-t1e-18 is a strain deficient in the major antibiotic efflux pump (ttgabc) that exhibits an overall increased susceptibility to a wide range of drugs when compared with the wild-type strain. we used this strain as a platform to search for microbes able to produce antibiotics that inhibit growth. a collection of 2400 isolates from soil, sediments and water was generated and a drop assay developed to identify, via growth inhibition halos, strains that prevent the growth of do ...	2015	26059350
the induction of ethylene response factor 3 (erf3) in potato as a result of co-inoculation with pseudomonas sp. r41805 and rhizophagus irregularis mucl 41833 - a possible role in plant defense.	colonization of plant rhizosphere/roots by beneficial microorganisms (e.g. plant growth promoting rhizobacteria - pgpr, arbuscular mycorrhizal fungi - amf) confers broad-spectrum resistance to virulent pathogens and is known as induced systemic resistance (isr) and mycorrhizal-induced resistance (mir). isr or mir, an indirect mechanism for biocontrol, involves complex signaling networks that are regulated by several plant hormones, the most important of which are salicylic acid (sa), jasmonic ac ...	2015	25723847
a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria.	luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ...	2015	25759807
the 29(th) annual symposium of the protein society, barcelona, spain, july 22-25, 2015.		2015	26452528
overcoming differences: the catalytic mechanism of metallo-β-lactamases.	metallo-β-lactamases are the latest resistance mechanism of pathogenic and opportunistic bacteria against carbapenems, considered as last resort drugs. the worldwide spread of genes coding for these enzymes, together with the lack of a clinically useful inhibitor, have raised a sign of alarm. inhibitor design has been mostly impeded by the structural diversity of these enzymes. here we provide a critical review of mechanistic studies of the three known subclasses of metallo-β-lactamases, analyze ...	2015	26297824
biochemistry and genetics of acc deaminase: a weapon to "stress ethylene" produced in plants.	1-aminocyclopropane-1-carboxylate deaminase (accd), a pyridoxal phosphate-dependent enzyme, is widespread in diverse bacterial and fungal species. owing to accd activity, certain plant associated bacteria help plant to grow under biotic and abiotic stresses by decreasing the level of "stress ethylene" which is inhibitory to plant growth. accd breaks down acc, an immediate precursor of ethylene, to ammonia and α-ketobutyrate, which can be further metabolized by bacteria for their growth. acc deam ...	2015	26441873
transcriptome analysis of campylobacter jejuni polyphosphate kinase (ppk1 and ppk2) mutants.		2015	26537695
lack of negative effects on syrian hamsters and mongolian gerbils housed in the same secondary enclosure.	in cases where different species might be housed in the same room or secondary enclosure, the guide for the care and use of laboratory animals recommends that the animals should be behaviorally compatible and have the same health status. syrian hamsters and mongolian gerbils, both desert-dwelling rodents, appear to be reasonable candidates for such a combination. this study was undertaken to evaluate whether housing hamsters and gerbils in the same secondary enclosure is an acceptable practice. ...	2015	26045450
protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.	a functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. we investigated the use of protein domain architectures ...	2016	27703668
expression and characterization of thermotolerant lipase with broad ph profiles isolated from an antarctic pseudomonas sp strain ams3.	a gene encoding a thermotolerant lipase with broad ph was isolated from an antarctic pseudomonas strain ams3. the recombinant lipase ams3 was purified by single-step purification using affinity chromatography, yielding a purification fold of approximately 1.52 and a recovery of 50%. the molecular weight was approximately ∼60 kda including the strep and affinity tags. interestingly, the purified antarctic ams3 lipase exhibited broad temperature profile from 10-70 °c and stable over a broad ph ran ...	2016	27781152
a novel mva-mediated pathway for isoprene production in engineered e. coli.	to deal with the increasingly severe energy crisis and environmental consequences, biofuels and biochemicals generated from renewable resources could serve as a promising alternative for replacing petroleum as a source of fuel and chemicals, among which isoprene (2-methyl-1,3-butadiene) in particular is of great significance in that it is an important platform chemical, which has been used in industrial production of synthetic rubber for tires and coatings or aviation fuel.	2016	26786050
human contamination in public genome assemblies.	contamination in genome assembly can lead to wrong or confusing results when using such genome as reference in sequence comparison. although bacterial contamination is well known, the problem of human-originated contamination received little attention. in this study we surveyed 45,735 available genome assemblies for evidence of human contamination. we used lineage specificity to distinguish between contamination and conservation. we found that 154 genome assemblies contain fragments that with hi ...	2016	27611326
mechanistic insights into c-di-gmp-dependent control of the biofilm regulator fleq from pseudomonas aeruginosa.	bacterial biofilm formation during chronic infections confers increased fitness, antibiotic tolerance, and cytotoxicity. in many pathogens, the transition from a planktonic lifestyle to collaborative, sessile biofilms represents a regulated process orchestrated by the intracellular second-messenger c-di-gmp. a main effector for c-di-gmp signaling in the opportunistic pathogen pseudomonas aeruginosa is the transcription regulator fleq. fleq is a bacterial enhancer-binding protein (bebp) with a ce ...	2016	26712005
mechanistic insights into c-di-gmp-dependent control of the biofilm regulator fleq from pseudomonas aeruginosa.	bacterial biofilm formation during chronic infections confers increased fitness, antibiotic tolerance, and cytotoxicity. in many pathogens, the transition from a planktonic lifestyle to collaborative, sessile biofilms represents a regulated process orchestrated by the intracellular second-messenger c-di-gmp. a main effector for c-di-gmp signaling in the opportunistic pathogen pseudomonas aeruginosa is the transcription regulator fleq. fleq is a bacterial enhancer-binding protein (bebp) with a ce ...	2016	26712005
temperature and redox effect on mineral colonization in juan de fuca ridge flank subsurface crustal fluids.	to examine microbe-mineral interactions in subsurface oceanic crust, we evaluated microbial colonization on crustal minerals that were incubated in borehole fluids for 1 year at the seafloor wellhead of a crustal borehole observatory (iodp hole u1301a, juan de fuca ridge flank) as compared to an experiment that was not exposed to subsurface crustal fluids (at nearby iodp hole u1301b). in comparison to previous studies at these same sites, this approach allowed assessment of the effects of temper ...	2016	27064928
functional exploration of the polysaccharide lyase family pl6.	alginate, the main cell-wall polysaccharide of brown algae, is composed of two residues: mannuronic acid (m-residues) and, its c5-epimer, guluronic acid (g-residues). alginate lyases define a class of enzymes that cleave the glycosidic bond of alginate by β-elimination. they are classified according to their ability to recognize the distribution of m- and g-residues and are named m-, g- or mg-lyases. in the cazy database, alginate lyases have been grouped by sequence similarity into seven distin ...	2016	27438604
deciphering a survival strategy during the interspecific competition between bacillus cereus msm-s1 and pseudomonas sp. msm-m1.	interspecific competition in bacteria governs colony growth dynamics and pattern formation. here, we demonstrate an interesting phenomenon of interspecific competition between bacillus cereus msm-s1 and pseudomonas sp. msm-m1, where secretion of an inhibitor by pseudomonas sp. is used as a strategy for survival. although b. cereus grows faster than pseudomonas sp., in the presence of pseudomonas sp. the population of b. cereus reduces significantly, whereas pseudomonas sp. do not show any marked ...	2016	28018625
tracing of two pseudomonas strains in the root and rhizoplane of maize, as related to their plant growth-promoting effect in contrasting soils.	taqman-based quantitative pcr (qpcr) assays were developed to study the persistence of two well-characterized strains of plant growth-promoting rhizobacteria (pgpr), pseudomonas fluorescens pf153 and pseudomonas sp. dsmz 13134, in the root and rhizoplane of inoculated maize plants. this was performed in pot experiments with three contrasting field soils (buus, le caron and dok-m). potential cross-reactivity of the qpcr assays was assessed with indigenous pseudomonas and related bacterial species ...	2016	28119675
tracing of two pseudomonas strains in the root and rhizoplane of maize, as related to their plant growth-promoting effect in contrasting soils.	taqman-based quantitative pcr (qpcr) assays were developed to study the persistence of two well-characterized strains of plant growth-promoting rhizobacteria (pgpr), pseudomonas fluorescens pf153 and pseudomonas sp. dsmz 13134, in the root and rhizoplane of inoculated maize plants. this was performed in pot experiments with three contrasting field soils (buus, le caron and dok-m). potential cross-reactivity of the qpcr assays was assessed with indigenous pseudomonas and related bacterial species ...	2016	28119675
molecular cloning and functional expression of a δ9- fatty acid desaturase from an antarctic pseudomonas sp. a3.	fatty acid desaturase enzymes play an essential role in the synthesis of unsaturated fatty acids. pseudomonas sp. a3 was found to produce a large amount of palmitoleic and oleic acids after incubation at low temperatures. using polymerase chain reaction (pcr), a novel δ9- fatty acid desaturase gene was isolated, cloned, and successfully expressed in escherichia coli. the gene was designated as pa3fad9 and has an open reading frame of 1,185 bp which codes for 394 amino acids with a predicted mole ...	2016	27494717
moleculo long-read sequencing facilitates assembly and genomic binning from complex soil metagenomes.	soil metagenomics has been touted as the "grand challenge" for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. here, we aimed to improve soil metagenomic sequence assembly by applying the moleculo synthetic long-read sequencing technology. in total, we obtained 267 gbp of raw sequence data from a native prairie soil; these data included 109.7 gbp of short-read data (~100 bp) from the joint genome institute (jgi) ...	2016	27822530
isolation of bdellovibrio sp. from soil samples in mexico and their potential applications in control of pathogens.	in this study, two strains of bdellovibrio were isolated from soil samples using the culture-dependent technique and two members of the family enterobacteriaceae (klebsiella sp. and salmonella sp.) as prey. the bdellovibrio strains were bacteriolytic, plaque-forming, and highly motile gram-negative bacteria. we identified and confirmed the bdellovibrio strains using microscopy, pcr amplification, and sequencing of the 16s rrna gene. they were observed to be different strains based on hit locus a ...	2016	27297185
bacteria with phosphate solubilizing capacity alter mycorrhizal fungal growth both inside and outside the root and in the presence of native microbial communities.	arbuscular mycorrhizal fungi (amf) and phosphate solubilizing pseudomonas bacteria (psb) could potentially interact synergistically because psb solubilize phosphate into a form that amf can absorb and transport to the plant. however, very little is known about the interactions between these two groups of microorganisms and how they influence the growth of each other. we tested whether different strains of bacteria, that have the capacity to solubilize phosphate, are able to grow along amf hyphae ...	2016	27253975
antagonistic control of the turnover pathway for the global regulatory srna csrb by the csra and csrd proteins.	the widely conserved protein csra (carbon storage regulator a) globally regulates bacterial gene expression at the post-transcriptional level. in many species, csra activity is governed by untranslated srnas, csrb and csrc in escherichia coli, which bind to multiple csra dimers, sequestering them from lower affinity mrna targets. both the synthesis and turnover of csrb/c are regulated. their turnover requires the housekeeping endonuclease rnase e and is activated by the presence of a preferred c ...	2016	27235416
biosynthesis, chemical structure, and structure-activity relationship of orfamide lipopeptides produced by pseudomonas protegens and related species.	orfamide-type cyclic lipopeptides (clps) are biosurfactants produced by pseudomonas and involved in lysis of oomycete zoospores, biocontrol of rhizoctonia and insecticidal activity against aphids. in this study, we compared the biosynthesis, structural diversity, in vitro and in planta activities of orfamides produced by rhizosphere-derived pseudomonas protegens and related pseudomonas species. genetic characterization together with chemical identification revealed that the main orfamide compoun ...	2016	27065956
insights into functional and evolutionary analysis of carbaryl metabolic pathway from pseudomonas sp. strain c5pp.	carbaryl (1-naphthyl n-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. soil isolate, pseudomonas sp. strain c5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. the draft genome analysis of strain c5pp reveals that the carbaryl catabolic genes are organized into three putative operons, 'upper', 'middle' and 'lower'. the seq ...	2016	27924916
flagellin flic phosphorylation affects type 2 protease secretion and biofilm dispersal in pseudomonas aeruginosa pao1.	protein phosphorylation has a major role in controlling the life-cycle and infection stages of bacteria. proteome-wide occurrence of s/t/y phosphorylation has been reported for many prokaryotic systems. previously, we reported the phosphoproteome of pseudomonas aeruginosa and pseudomonas putida. in this study, we show the role of s/t phosphorylation of one motility protein, flic, in regulating multiple surface-associated phenomena of p. aeruginosa pao1. this is the first report of occurrence of ...	2016	27701473
analysis of plant growth-promoting effects of fluorescent pseudomonas strains isolated from mentha piperita rhizosphere and effects of their volatile organic compounds on essential oil composition.	many species or strains of the genus pseudomonas have been characterized as plant growth promoting rhizobacteria (pgpr). we used a combination of phenotypic and genotypic techniques to analyze the community of fluorescent pseudomonas strains in the rhizosphere of commercially grown mentha piperita (peppermint). biochemical techniques, amplified rdna restriction analysis (ardra), and 16s rrna gene sequence analysis revealed that the majority of the isolated native fluorescent strains were p. puti ...	2016	27486441
abstracts.		2016	27243148
mycobiome in the lower respiratory tract - a clinical perspective.	recently the paradigm that the healthy lung is sterile was challenged and it is now believed that the lungs harbor a diverse microbiota also contributing to the pathogenesis of various diseases. most of the research studies targeting the respiratory microbiome have focused on bacteria and their impact on lung health and lung diseases. recently, also the mycobiome has gained attention. lower respiratory tract (lrt) diseases (e.g., cystic fibrosis) and other diseases or conditions (e.g., hiv infec ...	2016	28119685
mycobiome in the lower respiratory tract - a clinical perspective.	recently the paradigm that the healthy lung is sterile was challenged and it is now believed that the lungs harbor a diverse microbiota also contributing to the pathogenesis of various diseases. most of the research studies targeting the respiratory microbiome have focused on bacteria and their impact on lung health and lung diseases. recently, also the mycobiome has gained attention. lower respiratory tract (lrt) diseases (e.g., cystic fibrosis) and other diseases or conditions (e.g., hiv infec ...	2016	28119685
adenylate cyclase acya regulates development, aflatoxin biosynthesis and fungal virulence in aspergillus flavus.	aspergillus flavus is one of the most important opportunistic pathogens of crops and animals. the carcinogenic mycotoxin, aflatoxins produced by this pathogen cause a health problem to human and animals. since cyclic amp signaling controls a range of physiological processes, like fungal development and infection when responding to extracellular stimuli in fungal pathogens, in this study, we investigated the function of adenylate cyclase, a core component of camp signaling, in aflatoxins biosynth ...	2016	28066725
process-oriented review of bacterial quorum quenching for membrane biofouling mitigation in membrane bioreactors (mbrs).	quorum quenching (qq) has been developed over the last few years to overcome practical issues related to membrane biofouling, which is currently the major difficulty thwarting the extensive development of membrane bioreactors (mbrs). qq is the disruption of quorum sensing (qs), cell-to-cell communication enabling the bacteria to harmonize their behavior. the production of biofilm, which is recognized as a major part of the biocake formed on a membrane surface, and which leads to biofouling, has ...	2016	27983578
epidemiology and risk factors for pneumonia severity and mortality in bangladeshi children <5 years of age before 10-valent pneumococcal conjugate vaccine introduction.	pneumonia is the leading infectious cause of morbidity and mortality in young children in bangladesh. we present the epidemiology of pneumonia in bangladeshi children <5 years before 10-valent pneumococcal conjugate vaccine introduction and investigate factors associated with disease severity and mortality.	2016	27927201
trends of bacterial keratitis culture isolates in jerusalem; a 13- years analysis.	to describe the trends in pathogens and antibacterial resistance of corneal culture isolates in infectious keratitis during a period of 13 years at hadassah-hebrew university medical center.	2016	27893743
structure and dynamics underlying elementary ligand binding events in human pacemaking channels.	although molecular recognition is crucial for cellular signaling, mechanistic studies have relied primarily on ensemble measures that average over and thereby obscure underlying steps. single-molecule observations that resolve these steps are lacking due to diffraction-limited resolution of single fluorophores at relevant concentrations. here, we combined zero-mode waveguides with fluorescence resonance energy transfer (fret) to directly observe binding at individual cyclic nucleotide-binding do ...	2016	27858593
genotyping and descriptive proteomics of a potential zoonotic canine strain of giardia duodenalis, infective to mice.	the zoonotic potential of giardiasis, as proposed by who since the late 70's, has been largely confirmed in this century. the genetic assemblages a and b of giardia duodenalis are frequently isolated from human and canine hosts. most of the assemblage a strains are not infective to adult mice, which can limit the range of studies regarding to biology of g. duodenalis, including virulence factors and the interaction with host immune system. this study aimed to determine the infectivity in mice of ...	2016	27760188
killing two birds with one stone: natural rice rhizospheric microbes reduce arsenic uptake and blast infections in rice.	our recent work has shown that a rice thizospheric natural isolate, a pantoea sp (hereafter ea106) attenuates arsenic (as) uptake in rice. in parallel, yet another natural rice rhizospheric isolate, a pseudomonas chlororaphis (hereafter ea105), was shown to inhibit rice blast pathogen magnaporthe oryzae. considering the above, we envisaged to evaluate the importance of mixed stress regime in rice plants subjected to both as toxicity and blast infections. plants subjected to as regime showed incr ...	2016	27790229
use of ferrous iron by metallo-β-lactamases.	metallo-β-lactamases (mbls) catalyse the hydrolysis of almost all β-lactam antibacterials including the latest generation carbapenems and are a growing worldwide clinical problem. it is proposed that mbls employ one or two zinc ion cofactors in vivo. isolated mbls are reported to use transition metal ions other than zinc, including copper, cadmium and manganese, with iron ions being a notable exception. we report kinetic and biophysical studies with the di-iron(ii)-substituted metallo-β-lactamas ...	2016	27498591
insights into the biodegradation of weathered hydrocarbons in contaminated soils by bioaugmentation and nutrient stimulation.	the potential for biotransformation of weathered hydrocarbon residues in soils collected from two commercial oil refinery sites (soil a and b) was studied in microcosm experiments. soil a has previously been subjected to on-site bioremediation and it was believed that no further degradation was possible while soil b has not been subjected to any treatment. a number of amendment strategies including bioaugmentation with hydrocarbon degrader, biostimulation with nutrients and soil grinding, were a ...	2016	27441989
specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity.	root microbiota is a crucial determinant of plant productivity and stress tolerance. here, we hypothesize that the superior halo-tolerance of seepweed suaeda salsa is tightly linked to a specialized belowground microbiome. to test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16s rrna gene and fungal nuclear rrna internal transcribed spacer profiling. data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and ...	2016	27572178
modestobacter lacusdianchii sp. nov., a phosphate-solubilizing actinobacterium with ability to promote microcystis growth.	a novel actinobacterium, designated strain jxj cy 19t, was isolated from a culture mat of microcystis aeruginosa fachb-905 collected from dianchi lake, south-west china. 16s rrna gene sequences comparison of strain jxj cy 19t and the available sequences in the genbank database showed that the strain was closely related to modestobacter marinus 42h12-1t (99.1% similarity) and modestobacter roseus klbmp 1279t (99.0%). the isolate had meso-diaminopimelic in the cell wall with whole-cell sugars of m ...	2016	27537546
microbiota in breast milk of chinese lactating mothers.	the microbiota of breast milk from chinese lactating mothers at different stages of lactation was examined in the framework of a maternal infant nutrition growth (ming) study investigating the dietary habits and breast milk composition in chinese urban mothers. we used microbiota profiling based on the sequencing of fragments of 16s rrna gene and specific qpcr for bifidobacteria, lactobacilli and total bacteria to study microbiota of the entire breast milk collected using standard protocol witho ...	2016	27529821