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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 ...201628119685
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 ...201628119685
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 ...201628119675
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 ...201628119675
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 ...201628066725
metabolic pathway for a new strain pseudomonas synxantha lsh-7': from chemotaxis to uptake of n-hexadecane.bacteria can use n-hexadecane as a carbon source, but it remains incompletely understood whether n-hexadecane is transformed into metabolic intermediates prior to cellular uptake or not. we newly isolated a strain identified as pseudomonas synxantha lsh-7' and conducted chemotaxis experiment of this bacterial strain towards n-hexadecane, hexadecanol and hexadecanoic acid with qualitative assays respectively. furthermore, we described the identification of extracellular alkane hydroxylase and alc ...201728051099
high levels of soluble c5b-9 complex in dialysis fluid may predict poor prognosis in peritonitis in peritoneal dialysis patients.we searched for indicators to predict the prognosis of infectious peritonitis by measuring levels of complement proteins and activation products in peritoneal dialysis (pd) fluid (pdf) of patients at early stages of peritonitis. we retrospectively analyzed the relationship between the levels of sc5b-9, c3 and c4 in pdf and the subsequent clinical prognosis.201728046064
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 ...201628018625
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 ...201627983578
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.201627927201
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 ...201627924916
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 ...201527904352
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.201627893743
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 ...201627858593
l-asparaginase production in the pseudomonas pseudoalcaligenes strain jhs-71 isolated from jooshan hot-spring.l-asparaginase has lots of medical and industrial applications. ever since l-asparaginase anti-tumor activity was first demonstrated, its production using microbial systems has attracted considerable attention owing to their cost-effective and eco-friendly nature. the aim of this study is to obtain l-asparaginase producing bacteria and determining the enzyme activity. samples were picked up from jooshan hot springs located in the sirch, kerman. the l-asparaginase producing bacteria were screened ...201627844015
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) ...201627822530
new, hybrid pectin-based biosorbents.in this work hybrid pectin-based biosorbents with secondary polysaccharide additives (gellan, carob and xanthan gum, ratio to pectin 1:1, 1:1 and 1:3, respectively) were obtained at two temperatures. the presence of these additives in prepared beads was confirmed by raman spectra. the sem micrographs show better homogeneity of blends and grater differences between structures of beads with various additives obtained at higher temperature. the sorption capacity of our hybrid biosorbents as well as ...201627812233
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. ...201427795973
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 ...201627790229
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 ...201627781152
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 ...201627760188
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 ...201627703668
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 ...201627701473
frequency of hospital acquired pneumonia and its microbiological etiology in medical intensive care unit.the objectives were to assess the frequency of hospital acquired pneumonia (hap) in patients admitted to intensive care unit (icu) and to determine the frequencies of different etiological organisms in these patients.201627648021
bacterial viability within dental calculus: an untrodden, inquisitive clinico-patho- microbiological research.chronic inflammatory periodontal diseases i.e. gingivitis and periodontitis are one of the most common afflictions faced by human beings. dental plaque, which is a pool of pathogenic microorganisms, remains to be current mainstay in etiopathogenesis. dental calculus, which is a mineralized product of this plaque remains ignored and is considered merely as an ash heap of minor significance. however, the intriguing array in disease etiopathogenesis bulldozed researchers to suspect the role of calc ...201627630958
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 ...201627611326
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 ...201627572178
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 ...201627537546
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 ...201627529821
enzymatic potential of heterotrophic bacteria from a neutral copper mine drainage.copper mine drainages are restricted environments that have been overlooked as sources of new biocatalysts for bioremediation and organic syntheses. therefore, this study aimed to determine the enzymatic activities (esterase, epoxide hydrolase and monooxygenase) of 56 heterotrophic bacteria isolated from a neutral copper mine drainage (sossego mine, canaã dos carajás, brazil). hydrolase and monooxygenase activities were detected in 75% and 20% of the evaluated bacteria, respectively. bacterial s ...201627522533
16s rrna amplicon sequencing dataset for conventionalized and conventionally raised zebrafish larvae.data presented here contains metagenomic analysis regarding the sequential conventionalization of germ-free zebrafish embryos. zebrafish embryos that underwent a germ-free sterilization process immediately after fertilization were promptly exposed to and raised to larval stage in conventional fish water. at 6 days postfertilization (dpf), these "conventionalized" larvae were compared to zebrafish larvae that were raised in conventional fish water never undergoing the initial sterilization proces ...201627508247
fabrication of unique magnetic bionanocomposite for highly efficient removal of hexavalent chromium from water.biotreatment of hexavalent chromium has attracted widespread interest due to its cost effective and environmental friendliness. however, the difficult separation of biomass from aqueous solution and the slow hexavalent chromium bioreduction rate are bottlenecks for biotechnology application. in this approach, a core-shell structured functional polymer coated magnetic nanocomposite was prepared for enriching the hexavalent chromium. then the nanocomposite was connected to the bacteria via amines ...201627502074
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 ...201627498591
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 ...201627494717
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 ...201627486441
marine natural product inhibitors of neutrophil-associated inflammation.neutrophils are widely recognized to play an important role in acute inflammatory responses, and recent evidence has expanded their role to modulating chronic inflammatory and autoimmune diseases. reactive oxygen species (ros) and microbicidal compounds released from neutrophils that are recruited to the site of inflammation contribute to the pathogenesis of multiple inflammation-associated diseases such as chronic obstructive pulmonary disease, atherosclerosis, and hepatitis. marine organisms a ...201627472345
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 ...201627441989
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 ...201627438604
human thanatomicrobiome succession and time since death.the thanatomicrobiome (thanatos, greek for death) is a relatively new term and is the study of the microbes colonizing the internal organs and orifices after death. recent scientific breakthroughs in an initial study of the thanatomicrobiome have revealed that a majority of the microbes within the human body are the obligate anaerobes, clostridium spp., in the internal postmortem microbial communities. we hypothesized that time-dependent changes in the thanatomicrobiome within internal organs ca ...201627412051
risk factors for fecal carriage of carbapenemase producing enterobacteriaceae among intensive care unit patients from a tertiary care center in india.resistance amongst the commensal flora is a serious threat because a very highly populated ecosystem like the gut, may at a later stage, be a source of extra intestinal infections, resistant strains may spread to other host or transfer genetic resistance element to other members of micro-biota including pathogens. this study was carried out to assess fecal colonization by carbapenemase producing enterobacteriaceae (cpe) and associated risk factors among 100 patients admitted to intensive care un ...201627392139
ventricular assist devices as bridge to heart transplantation: impact on post-transplant infections.ventricular assist devices (vad) are valuable options for patients with heart failure awaiting cardiac transplantation. we assessed the impact of pre-transplant vad implantation on the incidence of post-transplant infections in a nationwide cohort of heart transplant recipients.201627391967
nosocomial urinary tract infections caused by extended-spectrum beta-lactamase uropathogens: prevalence, pathogens, risk factors, and strategies for infection control.our goal was to investigate the prevalence and antibiogram pattern of extended spectrum beta-lactamase (esbl) production among uropathogens using isolates from urine samples collected at the department of urology in the sahloul hospital, tunisia we also aimed to identify the risk factors for nosocomial urinary tract infections (utis) in patients who underwent transurethral resection of the prostate (turp) and the measures for infection control.201627330585
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 ...201627297185
exploring the mechanisms of action of human secretory rnase 3 and rnase 7 against candida albicans.human antimicrobial rnases, which belong to the vertebrate rnase a superfamily and are secreted upon infection, display a wide spectrum of antipathogen activities. in this work, we examined the antifungal activity of the eosinophil rnase 3 and the skin-derived rnase 7, two proteins expressed by innate cell types that are directly involved in the host defense against fungal infection. candida albicans has been selected as a suitable working model for testing rnase activities toward a eukaryotic p ...201627277554
silica ecosystem for synergistic biotransformation.synergistical bacterial species can perform more varied and complex transformations of chemical substances than either species alone, but this is rarely used commercially because of technical difficulties in maintaining mixed cultures. typical problems with mixed cultures on scale are unrestrained growth of one bacterium, which leads to suboptimal population ratios, and lack of control over bacterial spatial distribution, which leads to inefficient substrate transport. to address these issues, w ...201627264916
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 ...201627253975
enzyme biosensors for biomedical applications: strategies for safeguarding analytical performances in biological fluids.enzyme-based chemical biosensors are based on biological recognition. in order to operate, the enzymes must be available to catalyze a specific biochemical reaction and be stable under the normal operating conditions of the biosensor. design of biosensors is based on knowledge about the target analyte, as well as the complexity of the matrix in which the analyte has to be quantified. this article reviews the problems resulting from the interaction of enzyme-based amperometric biosensors with com ...201627249001
abstracts. 201627243148
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 ...201627235416
characterisation of candida within the mycobiome/microbiome of the lower respiratory tract of icu patients.whether the presence of candida spp. in lower respiratory tract (lrt) secretions is a marker of underlying disease, intensive care unit (icu) treatment and antibiotic therapy or contributes to poor clinical outcome is unclear. we investigated healthy controls, patients with proposed risk factors for candida growth in lrt (antibiotic therapy, icu treatment with and without antibiotic therapy), icu patients with pneumonia and antibiotic therapy and candidemic patients (for comparison of truly inva ...201627206014
evidence for the induction of key components of the notch signaling pathway via deltamethrin and azamethiphos treatment in the sea louse caligus rogercresseyi.the extensive use of organophosphates and pyrethroids in the aquaculture industry has negatively impacted parasite sensitivity to the delousing effects of these antiparasitics, especially among sea lice species. the notch signaling pathway is a positive regulator of abc transporter subfamily c expression and plays a key role in the generation and modulation of pesticide resistance. however, little is known about the molecular mechanisms behind pesticide resistance, partly due to the lack of geno ...201627187362
donor site morbidity following harvest of split-thickness skin grafts in south eastern nigeria.split-thickness skin grafting is a very common procedure. few documentation of its complications exist in the literatures especially in our sub-region where excessive scarring is a major issue.201127182501
pharmacological potentials of premna integrifolia l.premna integrifolia linn. (verbenaceae) is an important constituent of the formulation of ten roots of herbs known as daśamūla and is widely used for treating various ailments in the indian system of medicine. aim of this review is to provide comprehensive information on the pharmacological activities of various parts of p. integrifolia. all the relevant universally accepted electronic databases were searched with respect to the terms "agnimanthā", "headache tree", "premna integrifolia", "premna ...201627143797
achromobacter xylosoxidans as a new microorganism strain colonizing high-density polyethylene as a key step to its biodegradation.this study presents results of research on isolation new bacteria strain achromobacter xylosoxidans able to effect on the structure of high-density polyethylene (hdpe), polymer resistant to degradation in environment. new strain of a. xylosoxidans pe-1 was isolated from the soil and identified by analysis of the 16s ribosome subunit coding sequences. the substance to be degraded was hdpe in the form of thin foil films. the foil samples were analyzed with attenuated total reflectance fourier tran ...201627072033
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 ...201627065956
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 ...201627064928
response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.gauging the microbial community structures and functions become imperative to understand the ecological processes. to understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across kadi, near ahmedabad, india. soil collected was hence used for metagenomic dna extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation.201627001503
highly stable and reusable immobilized formate dehydrogenases: promising biocatalysts for in situ regeneration of nadh.this study aimed to prepare robust immobilized formate dehydrogenase (fdh) preparations which can be used as effective biocatalysts along with functional oxidoreductases, in which in situ regeneration of nadh is required. for this purpose, candida methylica fdh was covalently immobilized onto immobead 150 support (fdhi150), immobead 150 support modified with ethylenediamine and then activated with glutaraldehyde (fdhiglu), and immobead 150 support functionalized with aldehyde groups (fdhiald). t ...201626977186
genetic and functional analysis of the biosynthesis of a non-ribosomal peptide siderophore in burkholderia xenovorans lb400.b. xenovorans lb400 is a model bacterium for the study of the metabolism of aromatic compounds. the aim of this study was the genomic and functional characterization of a non-ribosomal peptide synthetase containing gene cluster that encodes a siderophore in b. xenovorans lb400. the mba gene cluster from strain lb400 encodes proteins involved in the biosynthesis and transport of a hydroxamate-type siderophore. strain lb400 has a unique mba gene organization, although mba gene clusters have been o ...201626963250
bioaugmentation mitigates the impact of estrogen on coliform-grazing protozoa in slow sand filters.exposure to endocrine-disrupting chemicals (edcs), such as estrogens, is a growing issue for human and animal health as they have been shown to cause reproductive and developmental abnormalities in wildlife and plants and have been linked to male infertility disorders in humans. intensive farming and weather events, such as storms, flash flooding, and landslides, contribute estrogen to waterways used to supply drinking water. this paper explores the impact of estrogen exposure on the performance ...201626895622
analysis for the presence of determinants involved in the transport of mercury across bacterial membrane from polluted water bodies of india.mercury, which is ubiquitous and recalcitrant to biodegradation processes, threatens human health by escaping to the environment via various natural and anthropogenic activities. non-biodegradability of mercury pollutants has necessitated the development and implementation of economic alternatives with promising potential to remove metals from the environment. enhancement of microbial based remediation strategies through genetic engineering approaches provides one such alternative with a promisi ...201626887227
recent developments in using advanced sequencing technologies for the genomic studies of lignin and cellulose degrading microorganisms.lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. lignocellulose is an abundant renewable biomaterial present on the earth. it has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. based on the plant materials they de ...201626884714
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 ...201426843901
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.201626786050
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 ...201526779138
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 ...201526779138
cross-regulation between the phz1 and phz2 operons maintain a balanced level of phenazine biosynthesis in pseudomonas aeruginosa pao1.gene duplication often provides selective advantages for the survival of microorganisms in adapting to varying environmental conditions. p. aeruginosa pao1 possesses two seven-gene operons [phz1 (phza1b1c1d1e1f1g1) and phz2 (phza2b2c2d2e2f2g2)] that are involved in the biosynthesis of phenazine-1-carboxylic acid and its derivatives. although the two operons are highly homologous and their functions are well known, it is unclear how the two phz operons coordinate their expressions to maintain the ...201626735915
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 ...201526734508
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. ...201526734506
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 ...201626712005
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 ...201626712005
ultrasound assessment of thrombotic complications in pediatric patients with tunneled central venous catheters.central venous access consists in inserting a vascular catheter to the vena cava and placing its tip in the vicinity of the opening to the right atrium. in the patients of the clinic of pediatrics, hematology and oncology at the academic clinical centre of the medical university in gdańsk, such implantation procedures are conducted 40-50 times in a year using broviac/hickman catheters that are placed in the subclavian vein. in the ultrasound and biopsy laboratory at the clinic mentioned above, a ...201326673005
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 ...201526668662
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 ...201526664032
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 ...201526648137
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.201526644001
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 ...201526636571
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.201526622970
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 ...201526579111
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 ...201526543717
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, ...201526543284
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.201526539831
transcriptome analysis of campylobacter jejuni polyphosphate kinase (ppk1 and ppk2) mutants. 201526537695
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 ...201526506000
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. ...201526488021
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 ...201526483960
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 ...201526483955
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 ...201526481355
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 m9.201526463643
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 ...201526462797
the 29(th) annual symposium of the protein society, barcelona, spain, july 22-25, 2015. 201526452528
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 ...201526449208
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 ...201526449208
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 ...201526441873
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 ...201526437407
taking a corneal scrape and making a diagnosis. 201526435585
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 ...201526417357
antioxidative, antimicrobial and cytotoxic properties of isatis floribunda boiss. ex bornm. extracts.the isatis species has antibacterial, anticancer and antiviral properties and these important endemic plants grow widely in various parts of anatolian-turkey. in the present study, the antioxidant activities of isatis floribunda boiss. ex bornm. flower and root extracts were determined with total antioxidant activity, free radical scavenging activity, ferric ion reducing power, and cupric ion reducing antioxidant capacity assay. the total phenolic compounds and flavonoids were also examined for ...201326417224
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 ...201526412281
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.201526393195
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