Publications

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
the 29(th) annual symposium of the protein society, barcelona, spain, july 22-25, 2015.		2015	26452528
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 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
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
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
a lipid-accumulating alga maintains growth in outdoor, alkaliphilic raceway pond with mixed microbial communities.	algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal "crop." in this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, chlorella vulgaris ba050. the strain c. vulgaris b ...	2015	26779138
a lipid-accumulating alga maintains growth in outdoor, alkaliphilic raceway pond with mixed microbial communities.	algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal "crop." in this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, chlorella vulgaris ba050. the strain c. vulgaris b ...	2015	26779138
multi-disciplinary antimicrobial strategies for improving orthopaedic implants to prevent prosthetic joint infections in hip and knee.	like any foreign object, orthopaedic implants are susceptible to infection when introduced into the human body. without additional preventative measures, the absolute number of annual prosthetic joint infections will continue to rise, and may exceed the capacity of health care systems in the near future. bacteria are difficult to eradicate from synovial joints due to their exceptionally diverse taxonomy, complex mechanistic attachment capabilities, and tendency to evolve antibiotic resistance. w ...	2015	26449208
multi-disciplinary antimicrobial strategies for improving orthopaedic implants to prevent prosthetic joint infections in hip and knee.	like any foreign object, orthopaedic implants are susceptible to infection when introduced into the human body. without additional preventative measures, the absolute number of annual prosthetic joint infections will continue to rise, and may exceed the capacity of health care systems in the near future. bacteria are difficult to eradicate from synovial joints due to their exceptionally diverse taxonomy, complex mechanistic attachment capabilities, and tendency to evolve antibiotic resistance. w ...	2015	26449208
p accumulation and physiological responses to different high p regimes in polygonum hydropiper for understanding a p-phytoremediation strategy.	phosphorus (p) accumulators used for phytoremediation vary in their potential to acquire p from different high p regimes. growth and p accumulation in polygonum hydropiper were both dependent on an increasing level of ihp (1-8 mm p) and on a prolonged growth period (3-9 weeks), and those of the mining ecotype (me) were higher than the non-mining ecotype (nme). biomass increments in root, stem, and leaf of both ecotypes were significantly greater in ihp relative to other organic p (po) sources (g ...	2015	26648137
bioactivities by a crude extract from the greenlandic pseudomonas sp. in5 involves the nonribosomal peptides, nunamycin and nunapeptin.	background. bioactive microbial metabolites provide a successful source of novel compounds with pharmaceutical potentials. the bacterium pseudomonas sp. in5 is a biocontrol strain isolated from a plant disease suppressive soil in greenland, which produces two antimicrobial nonribosomal peptides (nrps), nunapeptin and nunamycin. methods. in this study, we used in vitro antimicrobial and anticancer bioassays to evaluate the potential bioactivities of both a crude extract derived from pseudomonas s ...	2015	26734508
a quick and robust method for quantification of the hypersensitive response in plants.	one of the most studied defense reactions of plants against microbial pathogens is the hypersensitive response (hr). the hr is a complex multicellular process that involves programmed cell death at the site of infection. a standard method to quantify plant defense and the hr is to measure the release of cellular electrolytes into water after infiltration with pathogenic bacteria. in this type of experiment, the bacteria are typically delivered into the plant tissue through syringe infiltration. ...	2015	26734506
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
cultivable endophytic bacteria from leaf bases of agave tequilana and their role as plant growth promoters.	agave tequilana weber var. 'azul' is grown for the production of tequila, inulin and syrup. diverse bacteria inhabit plant tissues and play a crucial role for plant health and growth. in this study culturable endophytic bacteria were extracted from leaf bases of 100 healthy agave tequilana plants. in plant tissue bacteria occurred at mean population densities of 3 million cfu/g of fresh plant tissue. three hundred endophytic strains were isolated and 16s rdna sequences grouped the bacteria into ...	2014	25763038
cultivable endophytic bacteria from leaf bases of agave tequilana and their role as plant growth promoters.	agave tequilana weber var. 'azul' is grown for the production of tequila, inulin and syrup. diverse bacteria inhabit plant tissues and play a crucial role for plant health and growth. in this study culturable endophytic bacteria were extracted from leaf bases of 100 healthy agave tequilana plants. in plant tissue bacteria occurred at mean population densities of 3 million cfu/g of fresh plant tissue. three hundred endophytic strains were isolated and 16s rdna sequences grouped the bacteria into ...	2014	25763038
marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism.	little is known about the importance and/or mechanisms of biological mineral oxidation in sediments, partially due to the difficulties associated with culturing mineral-oxidizing microbes. we demonstrate that electrochemical enrichment is a feasible approach for isolation of microbes capable of gaining electrons from insoluble minerals. to this end we constructed sediment microcosms and incubated electrodes at various controlled redox potentials. negative current production was observed in incub ...	2014	25642220
marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism.	little is known about the importance and/or mechanisms of biological mineral oxidation in sediments, partially due to the difficulties associated with culturing mineral-oxidizing microbes. we demonstrate that electrochemical enrichment is a feasible approach for isolation of microbes capable of gaining electrons from insoluble minerals. to this end we constructed sediment microcosms and incubated electrodes at various controlled redox potentials. negative current production was observed in incub ...	2014	25642220
bacteria-bacteria interactions within the microbiota of the ancestral metazoan hydra contribute to fungal resistance.	epithelial surfaces of most animals are colonized by diverse microbial communities. although it is generally agreed that commensal bacteria can serve beneficial functions, the processes involved are poorly understood. here we report that in the basal metazoan hydra, ectodermal epithelial cells are covered with a multilayered glycocalyx that provides a habitat for a distinctive microbial community. removing this epithelial microbiota results in lethal infection by the filamentous fungus fusarium ...	2014	25514534
bacteria-bacteria interactions within the microbiota of the ancestral metazoan hydra contribute to fungal resistance.	epithelial surfaces of most animals are colonized by diverse microbial communities. although it is generally agreed that commensal bacteria can serve beneficial functions, the processes involved are poorly understood. here we report that in the basal metazoan hydra, ectodermal epithelial cells are covered with a multilayered glycocalyx that provides a habitat for a distinctive microbial community. removing this epithelial microbiota results in lethal infection by the filamentous fungus fusarium ...	2014	25514534
bioconversion of α-pinene by a novel cold-adapted fungus chrysosporium pannorum.	the psychrotrophic fungus chrysosporium pannorum a-1 is reported for the first time as a novel biocatalyst for o2-promoted oxidation of α-pinene. gc-ms analysis indicated that the main products of the reaction were compounds of a high commercial value, verbenol (1) and verbenone (2). exponentially growing cells (days 2-3) were about twice as active as cells in the late stationary phase in terms of the total concentration of products. the highest yields of 1 and 2 were obtained using three-day an ...	2014	25487757
bioconversion of α-pinene by a novel cold-adapted fungus chrysosporium pannorum.	the psychrotrophic fungus chrysosporium pannorum a-1 is reported for the first time as a novel biocatalyst for o2-promoted oxidation of α-pinene. gc-ms analysis indicated that the main products of the reaction were compounds of a high commercial value, verbenol (1) and verbenone (2). exponentially growing cells (days 2-3) were about twice as active as cells in the late stationary phase in terms of the total concentration of products. the highest yields of 1 and 2 were obtained using three-day an ...	2014	25487757
reactive oxygen species mediated bacterial biofilm inhibition via zinc oxide nanoparticles and their statistical determination.	the formation of bacterial biofilm is a major challenge in clinical applications. the main aim of this study is to describe the synthesis, characterization and biocidal potential of zinc oxide nanoparticles (nps) against bacterial strain pseudomonas aeruginosa. these nanoparticles were synthesized via soft chemical solution process in a very short time and their structural properties have been investigated in detail by using x-ray diffraction and transmission electron microscopy measurements. in ...	2014	25402188
foliar endophytic fungi as potential protectors from pathogens in myrmecophytic acacia plants.	in defensive ant-plant interactions myrmecophytic plants express reduced chemical defense in their leaves to protect themselves from pathogens, and it seems that mutualistic partners are required to make up for this lack of defensive function. previously, we reported that mutualistic ants confer plants of acacia hindsii protection from pathogens, and that the protection is given by the ant-associated bacteria. here, we examined whether foliar endophytic fungi may potentially act as a new partner ...	2014	26843901
detection of metallo-beta lactamases among carbapenem-resistant pseudomonas aeruginosa.	carbapenems are important drugs used for the treatment of pseudomonas aeruginosa infections, however metallo-β-lactamases (mbl) are able to efficiently hydrolyze these classes of drugs. immediate detection of the mbl-producing p. aeruginosa is necessary in order to accurately treat infections caused by this organism.	2014	25774271
applying nightingale charts to evaluate the heterogeneity of biomedical waste in a hospital.	to evaluate the heterogeneity of biomedical waste (bw) using nightingale charts.	2014	25591088
significance of serum antibodies against hsp 60 and hsp 70 for the diagnostic of infectious diseases.	heat shock proteins (hsp) represent important antigenic targets for the immune response, playing an important role in the pathology and infectious diseases control. the purpose of this work was to investigate the levels of hsp60 and hsp70 specific antibodies in the bloodstream of patients with different bacterial infections and cancer, in order to evaluate their potential role as diagnosis markers of different infectious diseases. detection of specific anti-hsp 60 and hsp 70 serum levels was per ...	2014	25483863
dissolving mechanism of strain p17 on insoluble phosphorus of yellow-brown soil.	strain p17 was a bacterial strain identified as bacillus megaterium isolated from ground accumulating phosphate rock powder. the fermentation broth of strain p17 and the yellow-brown soil from nanjing agricultural university garden were collected to conduct this study. the simulation of fixed insoluble phosphorous forms after applying calcium superphosphate into yellow-brown soil was performed in pots, while available p and total p of soil were extremely positive correlative with those of ground ...	2014	25477929
membrane bioprocesses for pharmaceutical micropollutant removal from waters.	the purpose of this review work is to give an overview of the research reported on bioprocesses for the treatment of domestic or industrial wastewaters (ww) containing pharmaceuticals. conventional ww treatment technologies are not efficient enough to completely remove all pharmaceuticals from water. indeed, these compounds are becoming an actual public health problem, because they are more and more present in underground and even in potable waters. different types of bioprocesses are described ...	2014	25295629
nanomedicine and therapy of lung diseases.	the use of nanotechnology has significantly increased in different fields of science, including the development of drug delivery systems. currently, the most modern pharmaceutical nanocarriers, such as liposomes, micelles, nanoemulsions and polymeric nanoparticles, demonstrate extremely useful properties from the point of view of drug therapy. in this context, the development of nanocarriers for pulmonary application has been much debated by the scientific community in recent decades. although r ...	2014	25628213
outcomes of patients with healthcare-associated pneumonia: worse disease or sicker patients?	healthcare-associated pneumonia (hcap) is an entity distinct from community-acquired pneumonia (cap). hcap has a higher case-fatality rate, due either to hcap organisms or to the health status of hcap patients. the contribution of hcap criteria to case-fatality rate is unknown.	2014	25222889
the non-canonical hydroxylase structure of yfcm reveals a metal ion-coordination motif required for ef-p hydroxylation.	ef-p is a bacterial trna-mimic protein, which accelerates the ribosome-catalyzed polymerization of poly-prolines. in escherichia coli, ef-p is post-translationally modified on a conserved lysine residue. the post-translational modification is performed in a two-step reaction involving the addition of a β-lysine moiety and the subsequent hydroxylation, catalyzed by poxa and yfcm, respectively. the β-lysine moiety was previously shown to enhance the rate of poly-proline synthesis, but the role of ...	2014	25274739
abstracts, 9th german allergy congress, wiesbaden, 2-4 october 2014.		2014	26120532
isolation and characterization of atrazine mineralizing bacillus subtilis strain hb-6.	atrazine is a widely used herbicide with great environmental concern due to its high potential to contaminate soil and waters. an atrazine-degrading bacterial strain hb-6 was isolated from industrial wastewater and the 16s rrna gene sequencing identified hb-6 as a bacillus subtilis. pcr assays indicated that hb-6 contained atrazine-degrading genes trzn, atzb and atzc. the strain hb-6 was capable of utilizing atrazine and cyanuric acid as a sole nitrogen source for growth and even cleaved the s-t ...	2014	25238246
synonymous codon bias and functional constraint on gc3-related dna backbone dynamics in the prokaryotic nucleoid.	while mrna stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene gc content; suggesting that structural dynamics of dna might also influence codon choice. because minor groove width is highly governed by 3-base periodicity in gc, the existence of triplet-based codons might imply a functional role for the ...	2014	25200075
rhamnolipid biosurfactants-past, present, and future scenario of global market.		2014	25228898
degradation of toluene by ortho cleavage enzymes in burkholderia fungorum flu100.	burkholderia fungorum flu100 simultaneously oxidized any mixture of toluene, benzene and mono-halogen benzenes to (3-substituted) catechols with a selectivity of nearly 100%. further metabolism occurred via enzymes of ortho cleavage pathways with complete mineralization. during the transformation of 3-methylcatechol, 4-carboxymethyl-2-methylbut-2-en-4-olide (2-methyl-2-enelactone, 2-ml) accumulated transiently, being further mineralized only after a lag phase of 2 h in case of cells pre-grown on ...	2014	25130674
degradation of toluene by ortho cleavage enzymes in burkholderia fungorum flu100.	burkholderia fungorum flu100 simultaneously oxidized any mixture of toluene, benzene and mono-halogen benzenes to (3-substituted) catechols with a selectivity of nearly 100%. further metabolism occurred via enzymes of ortho cleavage pathways with complete mineralization. during the transformation of 3-methylcatechol, 4-carboxymethyl-2-methylbut-2-en-4-olide (2-methyl-2-enelactone, 2-ml) accumulated transiently, being further mineralized only after a lag phase of 2 h in case of cells pre-grown on ...	2014	25130674
structural and functional analysis show that the escherichia coli uncharacterized protein yjcs is likely an alkylsulfatase.	sodium dodecyl sulfate (sds) is a widely used anionic surfactant in industry and research settings, and is known to have a detrimental effect to the environment. the pathway of sds degradation by bacteria is initiated by an alkylsulfatase and the oxidized product, 1-dodecanoic acid, subsequently enters into the β-oxidation pathway and is used as a carbon source. in this work, we solved the crystal structure of escherichia coli uncharacterized protein yjcs and identified that it belongs to the ty ...	2014	25066955
antibiotic susceptibilities of bacteria isolated within the oral flora of florida blacktip sharks: guidance for empiric antibiotic therapy.	sharks possess a variety of pathogenic bacteria in their oral cavity that may potentially be transferred into humans during a bite. the aim of the presented study focused on the identification of the bacteria present in the mouths of live blacktip sharks, carcharhinus limbatus, and the extent that these bacteria possess multi-drug resistance. swabs were taken from the oral cavity of nineteen live blacktip sharks, which were subsequently released. the average fork length was 146 cm (±11), suggest ...	2014	25110948
does netosis contribute to the bacterial pathoadaptation in cystic fibrosis?	significant advances in our understanding of neutrophil biology were made in the past several years. the exciting discovery that neutrophils deploy neutrophil extracellular traps (nets) to catch pathogens paved the way for a series of additional studies to define the molecular mechanisms of net generation and the biological significance of netosis in acute and chronic pathologic conditions. this review highlights the latest knowledge regarding net structures, deployment, and function, with an em ...	2014	25157250
identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (python regius).	respiratory infections are important causes of morbidity and mortality in reptiles; however, the causative agents are only infrequently identified.	2014	25106433
study of the structure-function-stability relationships in yeast d-amino acid oxidase: hydrophobization of alpha-helices.	hydrophobization of alpha-helices is one of the general approaches used for improving the thermal stability of enzymes. a total of 11 serine residues located in alpha-helices have been found based on multiple alignments of the amino acid sequences of d-amino acid oxidases from different organisms and the analysis of the 3d-structure of d-amino acid oxidase from yeast trigonopsis variabilis (tvdaao, ec 1.4.3.3). as a result of further structural analysis, eight ser residues in 67, 77, 78, 105, 27 ...	2014	25349716
identification and characterization of the spiruchostatin biosynthetic gene cluster enable yield improvement by overexpressing a transcriptional activator.	spiruchostatins a and b are members of the fk228-family of natural products with potent histone deacetylase inhibitory activities and antineoplastic activities. however, their production in the wild-type strain of pseudomonas sp. q71576 is low. to improve the yield, the spiruchostatin biosynthetic gene cluster (spi) was first identified by rapid genome sequencing and characterized by genetic mutations. this spi gene cluster encodes a hybrid biosynthetic pathway similar to that encoded by the fk2 ...	2014	24973954
comparison of bacterial community structure and dynamics during the thermophilic composting of different types of solid wastes: anaerobic digestion residue, pig manure and chicken manure.	this study investigated the impact of composting substrate types on the bacterial community structure and dynamics during composting processes. to this end, pig manure (pm), chicken manure (cm), a mixture of pm and cm (pm + cm), and a mixture of pm, cm and anaerobic digestion residue (adr) (pm + cm + adr) were selected for thermophilic composting. the bacterial community structure and dynamics during the composting process were detected and analysed by polymerase chain reaction-denaturing gradie ...	2014	24963997
a novel peptidoglycan binding protein crucial for pbp1a-mediated cell wall biogenesis in vibrio cholerae.	the bacterial cell wall, which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges (peptidoglycan, pg), is critical for maintenance of cell shape and survival. pg assembly is mediated by a variety of penicillin binding proteins (pbp) whose fundamental activities have been characterized in great detail; however, there is limited knowledge of the factors that modulate their activities in different environments or growth phases. in vibrio cholerae, the cause of cholera, ...	2014	24945690
microbial community structures and dynamics in the o3/bac drinking water treatment process.	effectiveness of drinking water treatment, in particular pathogen control during the water treatment process, is always a major public health concern. in this investigation, the application of pcr-dgge technology to the analysis of microbial community structures and dynamics in the drinking water treatment process revealed several dominant microbial populations including: α-proteobacteria, β-proteobacteria, γ-proteobacteria, bacteroidetes, actinobacteria firmicutes and cyanobacteria. α-proteobac ...	2014	24937529
melioidosis presenting as lymphadenitis: a case report.	melioidosis is an infection caused by the facultative intracellular gram-negative bacterium; burkholderia pseudomallei. it gives rise to protean clinical manifestations and has a varied prognosis. although it was rare in sri lanka increasing numbers of cases are being reported with high morbidity and mortality. here we report a case of melioidosis presenting with lymphadenitis which was diagnosed early and treated promptly with a good outcome.	2014	24927768
from community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic bacteroidetes generalists.	the microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. however, studies addressing the dynamic nature of these systems are very scarce. here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of card-fish and dgge. microbial community structure was statistically correlated with several environmental parameters, includ ...	2014	24926861
from community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic bacteroidetes generalists.	the microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. however, studies addressing the dynamic nature of these systems are very scarce. here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of card-fish and dgge. microbial community structure was statistically correlated with several environmental parameters, includ ...	2014	24926861
a novel, nested, multiplex, real-time pcr for detection of bacteria and fungi in blood.	the study describes the application of the pcr method for the simultaneous detection of dna of gram-negative bacteria, gram-positive bacteria, yeast fungi and filamentous fungi in blood and, thus, a whole range of microbial etiological agents that may cause sepsis. material for the study was sterile blood inoculated with four species of microorganisms (escherichia coli, staphylococcus aureus, candida albicans and aspergillus fumigatus) and blood collected from patients with clinical symptoms of ...	2014	24893651
teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries.	indigenous microbiota play a critical role in the lives of their vertebrate hosts. in human and mouse models it is increasingly clear that innate and adaptive immunity develop in close concert with the commensal microbiome. furthermore, several aspects of digestion and nutrient metabolism are governed by intestinal microbiota. research on teleosts has responded relatively slowly to the introduction of massively parallel sequencing procedures in microbiomics. nonetheless, progress has been made i ...	2014	24917852
the gut microbiota of larvae of rhynchophorus ferrugineus oliver (coleoptera: curculionidae).	the red palm weevil (rpw) rhynchophorus ferrugineus olivier (coleoptera: curculionidae) is one of the major pests of palms. the larvae bore into the palm trunk and feed on the palm tender tissues and sap, leading the host tree to death. the gut microbiota of insects plays a remarkable role in the host life and understanding the relationship dynamics between insects and their microbiota may improve the biological control of insect pests. the purpose of this study was to analyse the diversity of t ...	2014	24884866
evolving epidemiology and antimicrobial resistance in spontaneous bacterial peritonitis: a two-year observational study.	current recommendations for empirical antimicrobial therapy in spontaneous bacterial peritonitis (sbp) are based on quite old trials. since microbial epidemiology and the management of patients have changed, whether these recommendations are still appropriate must be confirmed.	2014	24884471
u2 snrnp is required for expression of the 3' end of genes.	pre-mrna in eukaryotes is subjected to mrna processing, which includes capping, polyadenylation, and splicing. transcription and mrna processing are coupled, and this coupling stimulates mrna processing; however, the effects of mrna processing on transcription are not fully understood. in this study, we found that inhibition of u2 snrnp by a splicing inhibitor, spliceostatin a (ssa), or by an antisense oligonucleotide to u2 snrna, caused gene-specific 3'-end down-regulation. removal of ssa from ...	2014	24845214
quorum quenching mediated approaches for control of membrane biofouling.	membrane biofouling is widely acknowledged as the most frequent adverse event in wastewater treatment systems resulting in significant loss of treatment efficiency and economy. different strategies including physical cleaning and use of antimicrobial chemicals or antibiotics have been tried for reducing membrane biofouling. such traditional practices are aimed to eradicate biofilms or kill the bacteria involved, but the greater efficacy in membrane performance would be achieved by inhibiting bio ...	2014	24910534
the dimerization domain in dape enzymes is required for catalysis.	the emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. therefore dap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. the dape-encoded n-succinyl-l,l-diaminopimel ...	2014	24806882
characterization and function of the first antibiotic isolated from a vent organism: the extremophile metazoan alvinella pompejana.	the emblematic hydrothermal worm alvinella pompejana is one of the most thermo tolerant animal known on earth. it relies on a symbiotic association offering a unique opportunity to discover biochemical adaptations that allow animals to thrive in such a hostile habitat. here, by studying the pompeii worm, we report on the discovery of the first antibiotic peptide from a deep-sea organism, namely alvinellacin. after purification and peptide sequencing, both the gene and the peptide tertiary struct ...	2014	24776651
fast and economic immobilization methods described for non-commercial pseudomonas lipases.	there is an increasing interest to seek new enzyme preparations for the development of new products derived from bioprocesses to obtain alternative bio-based materials. in this context, four non-commercial lipases from pseudomonas species were prepared, immobilized on different low-cost supports, and examined for potential biotechnological applications.	2014	24755191
microbial growth and carbon use efficiency in the rhizosphere and root-free soil.	plant-microbial interactions alter c and n balance in the rhizosphere and affect the microbial carbon use efficiency (cue)-the fundamental characteristic of microbial metabolism. estimation of cue in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. we analyzed respiratory activity, microbial dna content and cue by manipulation the c and nutrients availability in the soil under beta vulgar ...	2014	24722409
sepsis in intensive care unit patients with traumatic brain injury: factors associated with higher mortality.	patients with traumatic brain injury are particularly susceptible to sepsis, which may exacerbate the systemic inflammatory response and lead to organ dysfunction. the influence of clinical variables on the mortality of intensive care unit patients with traumatic brain injury and sepsis was investigated.	2014	25028949
classification of healthcare-associated infection: a systematic review 10 years after the first proposal.	ten years after the first proposal, a consensus definition of healthcare-associated infection (hcai) has not been reached, preventing the development of specific treatment recommendations. a systematic review of all definitions of hcai used in clinical studies is made.	2014	24597462
characterization of 3-phosphoglycerate kinase from corynebacterium glutamicum and its impact on amino acid production.	corynebacterium glutamicum cg1790/pgk encodes an enzyme active as a 3-phosphoglycerate kinase (pgk) (ec 2.7.2.3) catalyzing phosphoryl transfer from 1,3-biphosphoglycerate (bpg) to adp to yield 3-phosphoglycerate (3-pg) and atp in substrate chain phosphorylation.	2014	24593686
comparison of substrate specificity of escherichia coli p-aminobenzoyl-glutamate hydrolase with pseudomonas carboxypeptidase g.	reduced folic acid derivatives support biosynthesis of dna, rna and amino acids in bacteria as well as in eukaryotes, including humans. while the genes and steps for bacterial folic acid synthesis are known, those associated with folic acid catabolism are not well understood. a folate catabolite found in both humans and bacteria is p-aminobenzoyl-glutamate (paba-glu). the enzyme p-aminobenzoyl-glutamate hydrolase (pgh) breaks down paba-glu and is part of an apparent operon, the abg region, in e. ...	2014	27795973
structural characterization of a hypothetical protein: a potential agent involved in trimethylamine metabolism in catenulispora acidiphila.	catenulispora acidiphila is a newly identified lineage of actinomycetes that produces antimicrobial activities and represents a promising source of novel antibiotics and secondary metabolites. among the discovered protein coding genes, 68 % were assigned a putative function, while the remaining 32 % are genes encoding "hypothetical" proteins. caci_0382 is one of the "hypothetical" proteins that has very few homologs. sequence analysis shows that the protein belongs to the ntf2-like protein famil ...	2014	24562475
genomics-based exploration of virulence determinants and host-specific adaptations of pseudomonas syringae strains isolated from grasses.	the pseudomonas syringae species complex has recently been named the number one plant pathogen, due to its economic and environmental impacts, as well as for its role in scientific research. the bacterium has been repeatedly reported to cause outbreaks on bean, cucumber, stone fruit, kiwi and olive tree, as well as on other crop and non-crop plants. it also serves as a model organism for research on the type iii secretion system (t3ss) and plant-pathogen interactions. while most of the current w ...	2014	25437611
pcrg protects the two long helical oligomerization domains of pcrv, by an interaction mediated by the intramolecular coiled-coil region of pcrg.	pcrv is a hydrophilic translocator of type three secretion system (ttss) and a structural component of the functional translocon. c-terminal helix of pcrv is essential for its oligomerization at the needle tip. conformational changes within pcrv regulate the effector translocation. pcrg is a cytoplasmic regulator of ttss and forms a high affinity complex with pcrv. c-terminal residues of pcrg control the effector secretion.	2014	24460624
a multidisciplinary intervention to reduce infections of esbl- and ampc-producing, gram-negative bacteria at a university hospital.	in response to a considerable increase in the infections caused by esbl/ampc-producing klebsiella pneumonia in 2008, a multidisciplinary intervention, with a main focus on antimicrobial stewardship, was carried out at one university hospital. four other hospitals were used as controls. stringent guidelines for antimicrobial treatment and prophylaxis were disseminated throughout the intervention hospital; cephalosporins were restricted for prophylaxis use only, fluoroquinolones for empiric use in ...	2014	24466106
microbial enhanced heavy oil recovery by the aid of inhabitant spore-forming bacteria: an insight review.	crude oil is the major source of energy worldwide being exploited as a source of economy, including oman. as the price of crude oil increases and crude oil reserves collapse, exploitation of oil resources in mature reservoirs is essential for meeting future energy demands. as conventional recovery methods currently used have become less efficient for the needs, there is a continuous demand of developing a new technology which helps in the upgradation of heavy crude oil. microbial enhanced oil re ...	2014	24550702
ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (agalychnis callidryas).	amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. the conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. in addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. this ...	2014	24416427
public health implications of contamination of franc cfa (xaf) circulating in buea (cameroon) with drug resistant pathogens.	studies in different parts of the world have implicated money as a vehicle for transmission of pathogens. such information which is necessary to facilitate infection control strategies is lacking in many sub-saharan countries including cameroon. this study analyzed the franc de la communauté financiere d'afrique (franc cfa), the currency used in cameroon and other countries in the central african sub-region, as a potential vehicle for transmission of pathogenic bacteria and fungi, particularly d ...	2014	24401290
encapsulating peritoneal sclerosis - a rare and serious complication of peritoneal dialysis: case series.	encapsulating peritoneal sclerosis is a pathological entity mainly associated with peritoneal dialysis (pd). the clinical syndrome is characterized by various degrees of intestinal obstruction due to thickening, sclerosis and calcification of peritoneum resulting in the encapsulation and cocooning of the bowel. it is a rare but potentially devastating complication associated with a considerable morbidity and mortality.	2014	25870687
prophylactic antibody treatment and intramuscular immunization reduce infectious human rhinovirus 16 load in the lower respiratory tract of challenged cotton rats.	human rhinoviruses (hrv) represent the single most important etiological agents of the common cold and are the most frequent cause of acute respiratory infections in humans. currently the performance of available animal models for immunization studies using hrv challenge is very limited. the cotton rat (sigmodon hispidus) is a well-recognized model for the study of human respiratory viral infections. in this work we show that, without requiring any genetic modification of either the host or the ...	2014	25328560
novel assay to measure the plasmid mobilizing potential of mixed microbial communities.	mobilizable plasmids lack necessary genes for complete conjugation and are therefore non-self-transmissible. instead, they rely on the conjugation system of conjugal plasmids to be horizontally transferred to new recipients. while community permissiveness, the fraction of a mixed microbial community that can receive self-transmissible conjugal plasmids, has been studied, the intrinsic ability of a community to mobilize plasmids that lack conjugation systems is unexplored. here, we present a nove ...	2014	25566238
draft genome sequence analysis of a pseudomonas putida w15oct28 strain with antagonistic activity to gram-positive and pseudomonas sp. pathogens.	pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. p. putida w15oct28, isolated from a stream in brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens staphylococcus aureus, pseudomonas aeruginosa, and the plant pathogen pseudomonas syringae, an unusual characteristic for p. putida. the active compound production only occurred in media with low iron content and w ...	2014	25369289
interactions of non-natural halogenated substrates with d-specific dehalogenase (dehd) mutants using in silico studies.	the d-2-haloacid dehalogenase of d-specific dehalogenase (dehd) from rhizobium sp. rc1 catalyses the hydrolytic dehalogenation of d-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding l-hydroxyalkanoic acids. our investigations were focused on dehd mutants: r134a and y135a. we examined the possible interactions between these mutants with haloalkanoic acids and characterized the key catalytic residues in the wild-type dehalogenase, to design deh ...	2014	26019583
chromobacterium csp_p reduces malaria and dengue infection in vector mosquitoes and has entomopathogenic and in vitro anti-pathogen activities.	plasmodium and dengue virus, the causative agents of the two most devastating vector-borne diseases, malaria and dengue, are transmitted by the two most important mosquito vectors, anopheles gambiae and aedes aegypti, respectively. insect-bacteria associations have been shown to influence vector competence for human pathogens through multi-faceted actions that include the elicitation of the insect immune system, pathogen sequestration by microbes, and bacteria-produced anti-pathogenic factors. t ...	2014	25340821
bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.	some previous studies have identified bacteria in semen as being a potential factor in male infertility. however, only few types of bacteria were taken into consideration while using pcr-based or culturing methods. here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. ninety-six semen samples collected were examined for bacterial communities, measuring seven cli ...	2014	25340531
characterization of the medium- and long-chain n-alkanes degrading pseudomonas aeruginosa strain sjtd-1 and its alkane hydroxylase genes.	a gram-negative aliphatic hydrocarbon-degrading bacterium sjtd-1 isolated from oil-contaminated soil was identified as pseudomonas aeruginosa by comparative analyses of the 16s rrna sequence, phenotype, and physiological features. sjtd-1 could efficiently mineralize medium- and long-chain n-alkanes (c12-c30) as its sole carbon source within seven days, showing the most optimal growth on n-hexadecane, followed by n-octadecane, and n-eicosane. in 36 h, 500 mg/l of tetradecane, hexadecane, and octa ...	2014	25165808