Publications

bronchodilator response in adults with bronchiectasis: correlation with clinical parameters and prognostic implications.	bronchial dilation testing is an important tool to assess airway reversibility in adults with bronchiectasis. this study aims to investigate the association of bronchodilator response (bdr) and clinical parameters in bronchiectasis, and the utility of bdr to indicate lung function decline and risks of bronchiectasis exacerbations (bes).	2016	26904207
highly diverse nirk genes comprise two major clades that harbour ammonium-producing denitrifiers.	copper dependent nitrite reductase, nirk, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. distinct structural nirk classes and phylogenetic clades of nirk-type denitrifiers have previously been observed based on a limited set of nirk sequences, however, their environmental distribution or ecological strategies are currently unknown. in addition, environmental nirk-type denitrifiers are currently underestimated in pcr-dependent surveys due to primer coverage lim ...	2016	26923558
redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.	proton-coupled electron transfer (pcet), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (cunir), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. analyses of the nitrite reduction mechanism in cunir with conventional synchrotron radiation crystallography (srx) have been faced with difficulties, because x-ray photoreduction changes the native structures of metal centers and the enzyme-substrate complex. using seri ...	2016	26929369
draft genome sequence of alcaligenes faecalis strain iitr89, an indole-oxidizing bacterium.	we report the draft genome sequence of alcaligenes faecalis strain iitr89, a bacterium able to form indigo by utilizing indole as the sole carbon source. the alcaligenes species is increasingly reported for biodegradation of diverse toxicants and thus complete sequencing may provide insight into biodegradation capabilities and other phenotypes.	2016	26941148
a new thermophilic nitrilase from an antarctic hyperthermophilic microorganism.	several environmental samples from antarctica were collected and enriched to search for microorganisms with nitrilase activity. a new thermostable nitrilase from a novel hyperthermophilic archaea pyrococcus sp. m24d13 was purified and characterized. the activity of this enzyme increased as the temperatures rise from 70 up to 85°c. its optimal activity occurred at 85°c and ph 7.5. this new enzyme shows a remarkable resistance to thermal inactivation retaining more than 50% of its activity even af ...	2016	26973832
diversity of arsenite oxidase gene and arsenotrophic bacteria in arsenic affected bangladesh soils.	arsenic (as) contaminated soils are enriched with arsenotrophic bacteria. the present study analyzes the microbiome and arsenotrophic genes-from as affected soil samples of bhanga, charvadrason and sadarpur of faridpur district in bangladesh in summer (sfdsl1, 2, 3) and in winter (wfdsl1, 2, 3). total as content of the soils was within the range of 3.24-17.8 mg/kg as per atomic absorption spectroscopy. the aioa gene, conferring arsenite [as (iii)] oxidation, was retrieved from the soil sample, w ...	2016	26980601
one step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers.	the aim of this study was to characterise the microbiome of new and recurrent diabetic foot ulcers using 16s amplicon sequencing (16s as), allowing the identification of a wider range of bacterial species that may be important in the development of chronicity in these debilitating wounds. twenty patients not receiving antibiotics for the past three months were selected, with swabs taken from each individual for culture and 16s as. dna was isolated using a combination of bead beating and kit extr ...	2016	27005417
biodegradation of phenol by bacteria strain acinetobacter calcoaceticus pa isolated from phenolic wastewater.	a phenol-degrading bacterium strain pa was successfully isolated from the effluent of petrochemical wastewater. based on its morphological, physiological and biochemical characteristics, the strain pa was characterized as a gram-negative, strictly aerobic, nonmotile and short rod-shaped bacterium that utilizes phenol as a sole carbon and energy source. 16s rdna sequence analysis revealed that this strain is affiliated to acinetobacter calcoaceticus in the group of gammaproteobacteria. the strain ...	2016	27005648
unusual non-fluorescent broad spectrum siderophore activity (sid egyii) by pseudomonas aeruginosa strain egyii dsm 101801 and a new insight towards simple siderophore bioassay.	present study highlights an unusual non-fluorescent hydroxamate broad spectrum siderophore (sid egyii) activity from pseudomonas aeruginosa strain egyii dsm 101801, a soil bacterial isolate, along with simple low cost effective siderophore bioassay. detection of sid egyii activity qualitatively was proved by masking this activity against erwinia amylovora strain egy1 dsm 101800, an indicator strain, in well-cut diffusion assay containing 100 µm fecl3. sid egyii activity was expressed quantitativ ...	2016	27015845
ire1α mediates pkr activation in response to chlamydia trachomatis infection.	protein kinase rna activated (pkr) is a crucial mediator of anti-viral responses but is reported to be activated by multiple non-viral stimuli. however, mechanisms underlying pkr activation, particularly in response to bacterial infection, remain poorly understood. we have investigated mechanisms of pkr activation in human primary monocyte-derived dendritic cells in response to infection by chlamydia trachomatis. infection resulted in potent activation of pkr that was dependent on tlr4 and myd88 ...	2016	27021640
bacterial and fungal contamination risks in human oocyte and embryo cryopreservation: open versus closed vitrification systems.	to study the contamination risk in open and closed vitrification devices for oocyte/embryo cryopreservation by evaluating the contaminants present (bacteria and fungi) in the thaw medium and in liquid nitrogen (ln) storage containers.	2016	27025548
effect of supplementation of lysine producing microbes vis-a-vis source and level of dietary protein on performance and egg quality characteristics of post-peak layers.	the aim was to study the effect of supplementation of lysine producing microbes (lpm) as an in vivo source of lysine on performance and egg quality characters of post-peak layers.	2015	27047114
the genome sequence of alcaligenes faecalis nbib-017 contains genes with potentially high activities against erwinia carotovora.	alcaligenes faecalisnbib-017, a gram-negative bacterium, was isolated from soil in china. here, we provide the complete genome sequence of this bacterium, which possesses a high number of genes encoding antibacterial factors, including proteins and small molecular peptides.	2016	27056227
an adsorption-release-biodegradation system for simultaneous biodegradation of phenol and ammonium in phenol-rich wastewater.	the feasibility of simultaneous biodegradation of phenol and ammonium in phenol-rich wastewater was evaluated in a reusable system, which contained macroporous adsorption resin and alcaligenes faecalis strain wy-01. in the system, up to 6000mg/l phenol could be completely degraded by wy-01; meanwhile, 99.03±3.95% of ammonium was removed from the initial concentration of 384mg/l. this is the first study to show the capability of single strain in simultaneous removal of ammonium and phenol in wast ...	2016	27060247
a novel triculture system (cc3) for simultaneous enzyme production and hydrolysis of common grasses through submerged fermentation.	the perennial grasses are considered as a rich source of lignocellulosic biomass, making it a second generation alternative energy source and can diminish the use of fossil fuels. in this work, four perennial grasses saccharum arundinaceum, panicum antidotale, thysanolaena latifolia, and neyraudia reynaudiana were selected to verify their potential as a substrate to produce hydrolytic enzymes and to evaluate them as second generation energy biomass. here, cellulase and hemi-cellulase producing t ...	2016	27065995
molecular epidemiology and genetic characteristics of various blaper genes in shanghai, china.	we describe the genetic characteristics and possible transmission mechanism of blaper in 25 clinical gram-negative bacilli in shanghai. blaper, including blaper-1, blaper-3, and blaper-4, was located chromosomally or in different plasmids. tn1213 harboring blaper-1 was first identified in two proteus mirabilis isolates in china. the other blaper variants were preceded by an iscr1 element inside the complex class 1 integron associated with is26, tn21, tn1696, and a miniature inverted-repeat trans ...	2016	27067315
modified deacetylcephalosporin c synthase for the biotransformation of semisynthetic cephalosporins.	deacetylcephalosporin c synthase (dacs), a 2-oxoglutarate-dependent oxygenase synthesized by streptomyces clavuligerus, transforms an inert methyl group of deacetoxycephalosporin c (daoc) into an active hydroxyl group of deacetylcephalosporin c (dac) during the biosynthesis of cephalosporin. it is a step which is chemically difficult to accomplish, but its development by use of an enzymatic method with dacs can facilitate a cost-effective technology for the manufacture of semisynthetic cephalosp ...	2016	27084018
human interleukin-2 and hen egg white lysozyme: screening for bacteriolytic activity against various bacterial cells.	the bacteriolytic activity of interleukin-2 and hen egg white lysozyme against 34 different species of microorganisms has been studied. it was found that 6 species of microorganisms are lysed in the presence of interleukin-2. all interleukin-2-sensitive microorganisms belong either to the enterobacteriaceae, bacillaceae, or the lactobacillaceae family. it was also found that 12 species of microorganisms are lysed in the presence of lysozyme, and 16 species of microorganisms are lysed in the pres ...	2016	27099789
ct-dna binding and antibacterial activity of octahedral titanium (iv) heteroleptic (benzoylacetone and hydroxamic acids) complexes.	five structurally related titanium (iv) heteroleptic complexes, [ticl2(bzac)(l(1-4))] and [ticl3(bzac)(hl(5))]; bzac = benzoylacetonate; l(1-5) = benzohydroximate (l(1)), salicylhydroximate (l(2)), acetohydroximate (l(3)), hydroxyurea (l(4)), and n-benzoyl-n-phenyl hydroxylamine (l(5)), were used for the assessment of their antibacterial activities against ten pathogenic bacterial strains. the titanium (iv) complexes (1-5) demonstrated significant level of antibacterial properties as measured us ...	2016	27119022
therapeutic manuka honey: no longer so alternative.	medicinal honey research is undergoing a substantial renaissance. from a folklore remedy largely dismissed by mainstream medicine as "alternative", we now see increased interest by scientists, clinical practitioners and the general public in the therapeutic uses of honey. there are a number of drivers of this interest: first, the rise in antibiotic resistance by many bacterial pathogens has prompted interest in developing and using novel antibacterials; second, an increasing number of reliable s ...	2016	27148246
implementation of a zebrafish health program in a research facility: a 4-year retrospective study.	in the past two decades, zebrafish (danio rerio)-based research has contributed to significant scientific advances. still, husbandry and health programs did not evolve at the same pace, as evidenced by the absence of general guidelines. health monitoring is essential to animal welfare, to permit animal exchanges across facilities, to contribute to robust experimental results, and for data reproducibility. in this study, we report a health program implemented in a zebrafish research facility to p ...	2016	27186875
exogenous cofactors for the improvement of bioremoval and biotransformation of sulfamethoxazole by alcaligenes faecalis.	sulfamethoxazole (smx), an extensively prescribed or administered antibiotic pharmaceutical product, is usually detected in aquatic environments, because of its incomplete metabolism and elimination. this study investigated the effects of exogenous cofactors on the bioremoval and biotransformation of smx by alcaligenes faecalis. high concentration (100mg·l(-1)) of exogenous vitamin c (vc), vitamin b6 (vb6) and oxidized glutathione (gssg) enhanced smx bioremoval, while the additions of vitamin b2 ...	2016	27203516
enrichment of bacterial dna for the diagnosis of blood stream infections.	blood cultures are commonly employed to identify bacterial pathogens causing sepsis. pcr assays to diagnose septicemia require extraction of bacterial dna from blood samples and thus, delay the initiation of appropriate antimicrobial treatment. the presence of abundant human dna may hamper the sensitivity of pcr in the detection of bacteria.	2016	27246723
dendritic cell-derived vegf-a plays a role in inflammatory angiogenesis of human secondary lymphoid organs and is driven by the coordinated activation of multiple transcription factors.	lymph node expansion during inflammation is essential to establish immune responses and relies on the development of blood and lymph vessels. previous work in mice has shown that this process depends on the presence of vegf-a produced by b cells, macrophages and stromal cells. in humans, however, the cell types and the mechanisms regulating the intranodal production of vegf-a remain elusive. here we show that cd11c+ cells represent the main vegf-a-producing cell population in human reactive seco ...	2016	27256980
il-27 induced by select candida spp. via tlr7/nod2 signaling and ifn-β production inhibits fungal clearance.	candida spp. elicit cytokine production downstream of various pathogen recognition receptors, including c-type lectin-like receptors, tlrs, and nucleotide oligomerization domain (nod)-like receptors. il-12 family members il-12p70 and il-23 are important for host immunity against candida spp. in this article, we show that il-27, another il-12 family member, is produced by myeloid cells in response to selected candida spp. we demonstrate a novel mechanism for candida parapsilosis-mediated inductio ...	2016	27259855
rhizoma coptidis alkaloids alleviate hyperlipidemia in b6 mice by modulating gut microbiota and bile acid pathways.	it is hypothesized that rhizoma coptidis (rc) alkaloids exert their hypolipidemic effects primarily by targeting the gastrointestinal tract and liver. thus, this study was conducted to evaluate the antihyperlipidemic mechanisms of rc alkaloids (at a daily dose of 140mg/kg for 35days) in high-fat and high-cholesterol induced hyperlipidemic b6 mice. after treatment, serum lipid parameters were determined, the expression of lipid metabolism related genes and pathways such as the sterol regulatory e ...	2016	27287254
immunomodulatory effects of a bioactive compound isolated from dryopteris crassirhizoma on the grass carp ctenopharyngodon idella.	in the present study, we investigated effects of compound kaempferol 3-a-l-(4-o-acetyl)rhamnopyranoside-7-a-l-rhamnopyranoside (sa) isolated from dryopteris crassirhizoma during immune-related gene expression in ctenopharyngodon idella head kidney macrophages (cihkm). the expression of immune-related genes (il-1β, tnf-α, myd88, and mx1) were investigated using real-time pcr at 2 h, 8 h, 12 h, and 24 h after incubation with 1, 10, and 50 μg ml(-1) of sa. furthermore, fish were injected intraperit ...	2016	27294155
sepsis, parenteral vaccination and skin disinfection.	asbstract disinfection should be required for all skin penetrative procedures including parenteral administration of vaccines. this review analyses medically attended infectious events following parenteral vaccination in terms of their microbiological aetiology and pathogenesis. like 'clean' surgical site infections, the major pathogens responsible for these events were staphylococcal species, implicating endogenous con-tamination as a significant source of infection. as 70% isopropyl alcohol sw ...	2016	27295449
deciphering the contribution of biofilm to the pathogenesis of peritoneal dialysis infections: characterization and microbial behaviour on dialysis fluids.	infections are major complications in peritoneal dialysis (pd) with a multifactorial etiology that comprises patient, microbial and dialytic factors. this study aimed at investigating the contribution of microbial biofilms on pd catheters to recalcitrant infections and their interplay with pd related-factors. a prospective observational study was performed on 47 patients attending centro hospitalar of porto and vila nova de gaia/espinho to whom the catheter was removed due to infectious (n = 16) ...	2016	27336367
paecilomyces variotii: a fungus capable of removing ammonia nitrogen and inhibiting ammonia emission from manure.	ammonia (nh3) emissions from animal manure are a significant environmental and public concern. despite the numerous studies regarding nh3 emissions from manure, few of them have considered microbial nitrification approaches, especially fungal nitrification. in this study, a filamentous fungus was isolated from chicken manure and was used for nitrification. the species was paecilomyces variotii by morphological characteristics and 18s rdna gene sequencing. it played the biggest role in the remova ...	2016	27348533
colonization of the intestinal tract of the polyphagous pest spodoptera littoralis with the gfp-tagged indigenous gut bacterium enterococcus mundtii.	the alkaline gut of lepidopterans plays a crucial role in shaping communities of bacteria. enterococcus mundtii has emerged as one of the predominant gut microorganisms in the gastrointestinal tract of the major agricultural pest, spodoptera littoralis. therefore, it was selected as a model bacterium to study its adaptation to harsh alkaline gut conditions in its host insect throughout different stages of development (larvae, pupae, adults, and eggs). to date, the mechanism of bacterial survival ...	2016	27379058
structural insights into the catalytic reaction trigger and inhibition of d-3-hydroxybutyrate dehydrogenase.	d-3-hydroxybutyrate dehydrogenase catalyzes the reversible conversion of acetoacetate and d-3-hydroxybutyrate. these ketone bodies are both energy-storage forms of acetyl-coa. in order to clarify the structural mechanisms of the catalytic reaction with the cognate substrate d-3-hydroxybutyrate and of the inhibition of the reaction by inhibitors, the enzyme from alcaligenes faecalis has been analyzed by x-ray crystallography in liganded states with the substrate and with two types of inhibitor: m ...	2016	27380367
characterization of an indole-3-acetamide hydrolase from alcaligenes faecalis subsp. parafaecalis and its application in efficient preparation of both enantiomers of chiral building block 2,3-dihydro-1,4-benzodioxin-2-carboxylic acid.	both the enantiomers of 2,3-dihydro-1,4-benzodioxin-2-carboxylic acid are valuable chiral synthons for enantiospecific synthesis of therapeutic agents such as (s)-doxazosin mesylate, wb 4101, mkc 242, 2,3-dihydro-2-hydroxymethyl-1,4-benzodioxin, and n-[2,4-oxo-1,3-thiazolidin-3-yl]-2,3-dihydro-1,4-benzodioxin-2-carboxamide. pharmaceutical applications require these enantiomers in optically pure form. however, currently available methods suffer from one drawback or other, such as low efficiency, ...	2016	27391673
allovahlkampfia spelaea causing keratitis in humans.	free-living amoebae are present worldwide. they can survive in different environment causing human diseases in some instances. acanthamoeba sp. is known for causing sight-threatening keratitis in humans. free-living amoeba keratitis is more common in developing countries. amoebae of family vahlkampfiidae are rarely reported to cause such affections. a new genus, allovahlkampfia spelaea was recently identified from caves with no data about pathogenicity in humans. we tried to identify the causati ...	2016	27415799
serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.	relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and x-ray free-electron laser experiments. in this work, serial crystallography was used to obtain multiple structures serially from one crystal (msox) to study in crystallo enzyme catalysis. rapid, shutterless x-ray detector technology on a synchrotron mx beamline ...	2016	27437114
biochemical and molecular mechanisms of plant-microbe-metal interactions: relevance for phytoremediation.	plants and microbes coexist or compete for survival and their cohesive interactions play a vital role in adapting to metalliferous environments, and can thus be explored to improve microbe-assisted phytoremediation. plant root exudates are useful nutrient and energy sources for soil microorganisms, with whom they establish intricate communication systems. some beneficial bacteria and fungi, acting as plant growth promoting microorganisms (pgpms), may alleviate metal phytotoxicity and stimulate p ...	2016	27446148
curdlan activates dendritic cells through dectin-1 and toll-like receptor 4 signaling.	curdlan, a β-1,3-glucan isolated from alcaligenes faecalis, is an agonist of dectin-1 in various immune cells, including dendritic cells (dcs). however, whether curdlan also activates dcs through other receptors remains unknown. in this study, we found that curdlan activates dcs through dectin-1 and toll-like receptor 4 (tlr4). curdlan increased the expression levels of surface molecules (cd40, cd80, cd86, and mhc-i/ii), the production of cytokines (il-12, il-1β, tnf-α, and ifn-β), migration tow ...	2016	27449326
populations of stored product mite tyrophagus putrescentiae differ in their bacterial communities.	tyrophagus putrescentiae colonizes different human-related habitats and feeds on various post-harvest foods. the microbiota acquired by these mites can influence the nutritional plasticity in different populations. we compared the bacterial communities of five populations of t. putrescentiae and one mixed population of t. putrescentiae and t. fanetzhangorum collected from different habitats.	2016	27462300
cadmium resistance and uptake by bacterium, salmonella enterica 43c, isolated from industrial effluent.	cadmium resistant bacterium, isolated from industrial wastewater, was characterized as salmonella enterica 43c on the basis of biochemical and 16s rrna ribotyping. it is first ever reported s. enterica 43c bared extreme resistance against heavy metal consortia in order of pb(2+)>cd(2+)>as(3+)>zn(2+)>cr(6+)>cu(2+)>hg(2+). cd(2+) stress altered growth pattern of the bacterium in time dependent manner. it could remove nearly 57 % cd(2+) from the medium over a period of 8 days. kinetic and thermodyn ...	2016	27491862
bacterial and archaeal α-amylases: diversity and amelioration of the desirable characteristics for industrial applications.	industrial enzyme market has been projected to reach us$ 6.2 billion by 2020. major reasons for continuous rise in the global sales of microbial enzymes are because of increase in the demand for consumer goods and biofuels. among major industrial enzymes that find applications in baking, alcohol, detergent, and textile industries are α-amylases. these are produced by a variety of microbes, which randomly cleave α-1,4-glycosidic linkages in starch leading to the formation of limit dextrins. α-amy ...	2016	27516755
identification of novel genomic islands in liverpool epidemic strain of pseudomonas aeruginosa using segmentation and clustering.	pseudomonas aeruginosa is an opportunistic pathogen implicated in a myriad of infections and a leading pathogen responsible for mortality in patients with cystic fibrosis (cf). horizontal transfers of genes among the microorganisms living within cf patients have led to highly virulent and multi-drug resistant strains such as the liverpool epidemic strain of p. aeruginosa, namely the lesb58 strain that has the propensity to acquire virulence and antibiotic resistance genes. often these genes are ...	2016	27536294
dextran: influence of molecular weight in antioxidant properties and immunomodulatory potential.	dextrans (α-d-glucans) extracted from leuconostoc mesenteroides, with molecular weights (mw) of 10 (d10), 40 (d40) and 147 (d147) kda, were evaluated as antioxidant, anticoagulant and immunomodulatory drugs for the first time. none presented anticoagulant activity. as for the antioxidant and immunomodulatory tests, a specific test showed an increase in the dextran activity that was proportional to the increase in molecular weight. in a different assay, however, activity decreased or showed no co ...	2016	27548151
experimental studies and kinetic modeling of the growth of phenol-degrading bacteria in turbulent fluids.	understanding the interaction between microorganisms and fluid dynamics is important for aquatic ecosystems, though only sporadic attention has been focused on this topic in the past. in this study, particular attention was paid to the phenol-degrading bacterial strains microbacterium oxydans ly1 and alcaligenes faecalis ly2 subjected to controlled fluid flow under laboratory conditions. these two strains were found to be able to degrade phenols over a concentration range from 50 to 500 mg/l und ...	2016	27557974
the drosomycin multigene family: three-disulfide variants from drosophila takahashii possess antibacterial activity.	drosomycin (drs) is a strictly antifungal peptide in drosophila melanogaster, which contains four disulfide bridges (dbs) with three buried in molecular interior and one exposed on molecular surface to tie the amino- and carboxyl-termini of the molecule together (called wrapper disulfide bridge, wdb). based on computational analysis of genomes of drosophila species belonging to the oriental lineage, we identified a new multigene family of drs in drosphila takahashii that includes a total of 11 d ...	2016	27562645
detection of extended spectrum beta-lactamases resistance genes among bacteria isolated from selected drinking water distribution channels in southwestern nigeria.	extended spectrum beta-lactamases (esbl) provide high level resistance to beta-lactam antibiotics among bacteria. in this study, previously described multidrug resistant bacteria from raw, treated, and municipal taps of dwds from selected dams in southwestern nigeria were assessed for the presence of esbl resistance genes which include bla tem, bla shv, and bla ctx by pcr amplification. a total of 164 bacteria spread across treated (33), raw (66), and municipal taps (68), belonging to α-proteoba ...	2016	27563674
genome-based insights into the resistome and mobilome of multidrug-resistant aeromonas sp. arm81 isolated from wastewater.	the draft genome of multidrug-resistant aeromonas sp. arm81 isolated from a wastewater treatment plant in warsaw (poland) was obtained. sequence analysis revealed multiple genes conferring resistance to aminoglycosides, β-lactams or tetracycline. three different β-lactamase genes were identified, including an extended-spectrum β-lactamase gene bla per-1. the antibiotic susceptibility was experimentally tested. genome sequencing also allowed us to investigate the plasmidome and transposable mobil ...	2016	27590015
genome-based insights into the resistome and mobilome of multidrug-resistant aeromonas sp. arm81 isolated from wastewater.	the draft genome of multidrug-resistant aeromonas sp. arm81 isolated from a wastewater treatment plant in warsaw (poland) was obtained. sequence analysis revealed multiple genes conferring resistance to aminoglycosides, β-lactams or tetracycline. three different β-lactamase genes were identified, including an extended-spectrum β-lactamase gene bla per-1. the antibiotic susceptibility was experimentally tested. genome sequencing also allowed us to investigate the plasmidome and transposable mobil ...	2016	27590015
improving the bioremoval of sulfamethoxazole and alleviating cytotoxicity of its biotransformation by laccase producing system under coculture of pycnoporus sanguineus and alcaligenes faecalis.	the occurrence of sulfamethoxazole (smx) in aquatic environment is a health concern. the presence of smx significantly inhibited the laccase activity of pycnoporus sanguineus with a lower removal efficiency of smx. although a laccase system with 2,20-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (abts) eliminated 100% smx within 6h, abts might cause an environmental issue. an alternative to smx elimination is the coculture of alcaligenes faecalis and p. sanguineus. the smx removal efficienc ...	2016	27591519
opportunistic infections in hiv-infected patients differ strongly in frequencies and spectra between patients with low cd4+ cell counts examined postmortem and compensated patients examined antemortem irrespective of the haart era.	aids-related mortality has changed dramatically with the onset of highly active antiretroviral therapy (haart), which has even allowed compensated hiv-infected patients to withdraw from secondary therapy directed against opportunistic pathogens. however, in recently autopsied hiv-infected patients, we observed that associations with a broad spectrum of pathogens remain, although detailed analyses are lacking. therefore, we focused on the possible frequency and spectrum shifts in pathogens associ ...	2016	27611681
primary succession of nitrogen cycling microbial communities along the deglaciated forelands of tianshan mountain, china.	structural succession and its driving factors for nitrogen (n) cycling microbial communities during the early stages of soil development (0-44 years) were studied along a chronosequence in the glacial forelands of the tianshan mountain no.1 glacier in the arid and semi-arid region of central asia. we assessed the abundance and population of functional genes affiliated with n-fixation (nifh), nitrification (bacterial and archaeal amoa), and denitrification (nirk/s and nosz) in a glacier foreland ...	2016	27625641
extraction of total nucleic acids from bacterial isolates using the biomérieux nuclisens easymag total nucleic acid extractor.	the biomerieux nuclisens easymag total nucleic acid extractor was evaluated for use on bacterial isolates in the clinical microbiology laboratory. forty eight isolates were extracted, yielding quantifiable amounts of dna for all isolates. the easymag is appropriate for dna extraction from bacterial isolates and will be incorporated in the clinical laboratory.	2016	27658494
microbial structure and nitrogen compound conversions in aerobic granular sludge reactors with non-aeration phases and acetate pulse feeding.	a technological system was developed for efficient nitrogen removal from real digester supernatant in a single reactor with shortened aeration to increase the economical aspects of wastewater treatment. the supernatant (600 mg tkn/l, low cod/n ratio of 2.2) was treated in batch reactors with aerobic granules (gsbrs) to test how one, two, or three non-aeration phases and acetate pulse feeding in the cycle affect the morphological and microbial properties of biomass. introduction of one non-aerati ...	2016	27662853
functional metagenomics of spacecraft assembly cleanrooms: presence of virulence factors associated with human pathogens.	strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. we wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. three geographically distinct cleanrooms were sampled during the ...	2016	27667984
high-throughput screening of carbohydrate-degrading enzymes using novel insoluble chromogenic substrate assay kits.	carbohydrates active enzymes (cazymes) have multiple roles in vivo and are widely used for industrial processing in the biofuel, textile, detergent, paper and food industries. a deeper understanding of cazymes is important from both fundamental biology and industrial standpoints. vast numbers of cazymes exist in nature (especially in microorganisms) and hundreds of thousands have been cataloged and described in the carbohydrate active enzyme database (cazy). however, the rate of discovery of put ...	2016	27684747
fungal cell wall agents and bacterial lipopolysaccharide in organic dust as possible risk factors for pulmonary sarcoidosis.	composition of organic dust is very complex, involving particles of microbial, animal and plant origin. several environmental exposure studies associate microbial cell wall agents in organic dust with various respiratory symptoms and diseases. the aim of the present study was to investigate the in vitro effects of the co-exposure of fungal cell wall agents (fcwas) and bacterial lipopolysaccharide (lps) on inflammatory immune responses of peripheral blood mononuclear cells (pbmcs) from patients w ...	2016	27688795
beneficial effects of spices in food preservation and safety.	spices have been used since ancient times. although they have been employed mainly as flavoring and coloring agents, their role in food safety and preservation have also been studied in vitro and in vivo. spices have exhibited numerous health benefits in preventing and treating a wide variety of diseases such as cancer, aging, metabolic, neurological, cardiovascular, and inflammatory diseases. the present review aims to provide a comprehensive summary of the most relevant and recent findings on ...	2016	27708620
anti-infective therapy without antimicrobials: apparent successful treatment of multidrug resistant osteomyelitis with hyperbaric oxygen therapy.		2016	27713861
proteomic analysis of excretory-secretory products of mesocestoides corti metacestodes reveals potential suppressors of dendritic cell functions.	accumulating evidences have assigned a central role to parasite-derived proteins in immunomodulation. here, we report on the proteomic identification and characterization of immunomodulatory excretory-secretory (es) products from the metacestode larva (tetrathyridium) of the tapeworm mesocestoides corti (syn. m. vogae). we demonstrate that es products but not larval homogenates inhibit the stimuli-driven release of the pro-inflammatory, th1-inducing cytokine il-12p70 by murine bone marrow-derive ...	2016	27736880
rhizoma coptidis: a potential cardiovascular protective agent.	cardiovascular diseases (cvds) are among the leading causes of morbidity and mortality in both the developed and developing world. rhizoma coptidis (rc), known as huang lian in china, is the dried rhizome of medicinal plants from the family ranunculaceae, such as coptis chinensis franch, c. deltoidea c.y. cheng et hsiao, and c. teeta wall which has been used by chinese medicinal physicians for more than 2000 years. in china, rc is a common component in traditional medicines used to treat cvd ass ...	2016	27774066
significantly enhancing recombinant alkaline amylase production in bacillus subtilis by integration of a novel mutagenesis-screening strategy with systems-level fermentation optimization.	alkaline amylase has significant potential for applications in the textile, paper and detergent industries, however, low yield of which cannot meet the requirement of industrial application. in this work, a novel artp mutagenesis-screening method and fermentation optimization strategies were used to significantly improve the expression level of recombinant alkaline amylase in b. subtilis 168.	2016	27777616
evaluation of the antibacterial and antioxidant activities of chitosan edible films incorporated with organic essential oils obtained from four thymus species.	the aims of this study were to evaluate, (1) the antibacterial properties, (2) the total phenol content and (3) the antioxidant activity, of chitosan edible films incorporated with certified organic essential oils (eos) obtained from thymus zygis, thymus mastichina, thymus capitatus and thymus vulgaris. the agar disc diffusion method was used to determine the antibacterial activities of chitosan edible films while for the antioxidant activity, two different analytical assays were used (dpph and ...	2016	27784932
biochemical and histochemical analyses revealing endophytic alcaligenes faecalis mediated suppression of oxidative stress in abelmoschus esculentus challenged with sclerotium rolfsii.	sclerotium rolfsii is a highly aggressive pathogen that causes huge economic losses, especially in temperate climates. alcaligenes faecalis, particularly in endophytic form, has rarely been used to control this fungus. in this study, endophytic alcaligenes sp. strain bhu 12, bhu 16 (isolated from abelmoschus esculentus leaf) and bhu m7 (isolated from andrographis paniculata leaf) were reported to trigger a wide range of host defenses in okra plant against the collar-rot pathogen s. rolfsii. endo ...	2016	27816824
a new lab developed real time pcr assay for direct detection of c. difficle from stool sample without dna extraction.	clostridium difficile is a major cause of nosocomial antibiotic-associated infectious diarrhea and pseudomembranous colitis. detection of c. difficile by anaerobic bacterial culture and/or cytotoxicity assays has been largely replaced by rapid enzyme immunoassays (eia). however, due to the lack of sensitivity of stool eia, we developed a multiplex real-time pcr assay targeting the c. difficile toxin genes tcdb. stool samples from hospitalized pediatric patients suspected of having c. difficile-a ...	2016	27829823
pathogenic features of heterotrophic plate count bacteria from drinking-water boreholes.	evidence suggests that heterotrophic plate count (hpc) bacteria may be hazardous to humans with weakened health. we investigated the pathogenic potential of hpc bacteria from untreated borehole water, consumed by humans, for: their haemolytic properties, the production of extracellular enzymes such as dnase, proteinase, lipase, lecithinase, hyaluronidase and chondroitinase, the effect simulated gastric fluid has on their survival, as well as the bacteria's antibiotic-susceptible profile. hutu-80 ...	2016	27959868
characteristics of a heterotrophic nitrogen removal bacterium and its potential application on treatment of ammonium-rich wastewater.	nitrogen and organic carbon are major pollutants in wastewater causing environmental problems. alcaligenes faecalis strain nr, isolated from activated sludge, exhibited the ability to remove ammonium and organic carbon from wastewater simultaneously under sole aerobic conditions in batch culture. changes in carbon type, c/n ratio, oxygen concentration and inorganic ions significantly affected the treatment efficiency. furthermore, a continuous bioreactor, solely inoculated with a. faecalis strai ...	2017	27978438
identification of new bacteria harboring qnrs and aac(6')-ib/cr and mutations possibly involved in fluoroquinolone resistance in raw sewage and activated sludge samples from a full-scale wwtp.	wastewater treatment plants (wwtps) harbor bacteria and antimicrobial resistance genes, favoring gene exchange events and resistance dissemination. here, a culture-based and metagenomic survey of qnra, qnrb, qnrs, and aac(6')-ib genes from raw sewage (rs) and activated sludge (as) of a full-scale municipal wwtp was performed. a total of 96 bacterial isolates were recovered from nalidixic acid-enrichment cultures. bacteria harboring the aac(6')-ib gene predominated in rs, whereas qnrs-positive is ...	2017	27984803
tissue-associated bacterial alterations in rectal carcinoma patients revealed by 16s rrna community profiling.	sporadic and inflammatory forms of colorectal cancer (crc) account for more than 80% of cases. recent publications have shown mechanistic evidence for the involvement of gut bacteria in the development of both crc-forms. whereas, colon and rectal cancer have been routinely studied together as crc, increasing evidence show these to be distinct diseases. also, the common use of fecal samples to study microbial communities may reflect disease state but possibly not the tumor microenvironment. we pe ...	2016	28018861
glycin-rich antimicrobial peptide yd1 from b. amyloliquefaciens, induced morphological alteration in and showed affinity for plasmid dna of e. coli.	antimicrobial peptides (amps), low-molecular-weight proteins with broad-spectrum antimicrobial activity, are the most promising candidates for the development of novel antimicrobials. a powerful cationic glycine-rich amp yd1 (mw ~ 1.0 kda) was purified from bacillus amyloliquefaciens cbsyd1 isolated from traditional korean fermented food kimchi, for the treatment of multidrug-resistant (mdr) bacteria. strain cbsyd1 was identified 99.79% similar to bacillus amyloliquefaciens subsp. plantarum fzb4 ...	2017	28050849
evaluation of aerial microbial pollutants in al-haram al-nabawi during pilgrimage of 2013.	al-madinah al-munawwarah is the second holiest site in islam. the possibility of new emerging microbes is valid due to the increased number of pilgrims. the objectives of the current study were to estimate the numbers of fungi and bacteria inside and outside al-haram al-nabawi and to find whether new bacterial and fungal species have emerged compared to previous studies. air samples were collected twice a day from 12 spots and four directions during the pilgrim year of 2013 for four consecutive ...	2015	28053593
evaluation of aerial microbial pollutants in al-haram al-nabawi during pilgrimage of 2013.	al-madinah al-munawwarah is the second holiest site in islam. the possibility of new emerging microbes is valid due to the increased number of pilgrims. the objectives of the current study were to estimate the numbers of fungi and bacteria inside and outside al-haram al-nabawi and to find whether new bacterial and fungal species have emerged compared to previous studies. air samples were collected twice a day from 12 spots and four directions during the pilgrim year of 2013 for four consecutive ...	2015	28053593
pyruvic oxime dioxygenase from heterotrophic nitrifier alcaligenes faecalis is a nonheme fe((ii))-dependent enzyme homologous to class ii aldolase.	pyruvic oxime dioxygenase (pod), a key enzyme in heterotrophic nitrification, was purified from alcaligenes faecalis, and the molecular and catalytic characteristics were reexamined. pod was purified as the homotetramer of the subunit whose molecular weight was 30,000. the deduced amino acid sequence of pod was homologous with a class ii aldolase that has been regarded as the zn((ii))-dependent enzyme catalyzing aldol reactions. the recombinant protein showed weak pod activity, and was activated ...	2017	28059164
burkholderia contaminans biofilm regulating operon and its distribution in bacterial genomes.	biofilm formation by burkholderia spp. is a principal cause of lung chronic infections in cystic fibrosis patients. a "lacking biofilm production" (lbp) strain b. contaminans gimc4587:bct370-19 has been obtained by insertion modification of clinical strain with plasposon mutagenesis. it has an interrupted transcriptional response regulator (rr) gene. the focus of our investigation was a two-component signal transduction system determination, including this rr. b. contaminans clinical and lbp str ...	2016	28070515
resource recovery from wastewater by biological technologies: opportunities, challenges, and prospects.	limits in resource availability are driving a change in current societal production systems, changing the focus from residues treatment, such as wastewater treatment, toward resource recovery. biotechnological processes offer an economic and versatile way to concentrate and transform resources from waste/wastewater into valuable products, which is a prerequisite for the technological development of a cradle-to-cradle bio-based economy. this review identifies emerging technologies that enable res ...	2016	28111567
resource recovery from wastewater by biological technologies: opportunities, challenges, and prospects.	limits in resource availability are driving a change in current societal production systems, changing the focus from residues treatment, such as wastewater treatment, toward resource recovery. biotechnological processes offer an economic and versatile way to concentrate and transform resources from waste/wastewater into valuable products, which is a prerequisite for the technological development of a cradle-to-cradle bio-based economy. this review identifies emerging technologies that enable res ...	2016	28111567
characterization of novel acidobacteria exopolysaccharides with potential industrial and ecological applications.	acidobacteria have been described as one of the most abundant and ubiquitous bacterial phyla in soil. however, factors contributing to this ecological success are not well elucidated mainly due to difficulties in bacterial isolation. acidobacteria may be able to survive for long periods in soil due to protection provided by secreted extracellular polymeric substances that include exopolysaccharides (epss). here we present the first study to characterize epss derived from two strains of acidobact ...	2017	28117455
metal induced changes in trivalent chromium resistant alcaligenes faecalis vitsim2.	the changes induced in bacterial strains under stress conditions provide an insight into metal resistance strategies. trivalent chromium resistant bacterium were isolated and identified by 16s rrna gene sequencing and designated as alcaligenes faecalis vitsim2. the growth pattern was monitored. the organism also showed resistance to copper, cadmium, and certain antibiotics. the differentially expressed proteins in sds page were identified by mass spectrometry as flagellin and 50s ribosomal l36 p ...	2017	28217898
biodegradation of picolinic acid by a newly isolated bacterium alcaligenes faecalis strain jq135.	we isolated a bacterial strain jq135 from municipal wastewater, which was capable of efficiently degrading picolinic acid (pa). based on the physico-biochemical characteristics and 16s rdna analysis, strain jq135 was identified as alcaligenes faecalis. in addition, strain jq135 produced an orange pigment when cultured in the luria-bertani medium, which is different from the previously reported strains of a. faecalis. during the degradation of pa by the resting strain jq135 cells, only one interm ...	2017	28243718
insight into the bacterial diversity of fermentation woad dye vats as revealed by pcr-dgge and pyrosequencing.	the bacterial diversity in fermenting dye vats with woad (isatis tinctoria l.) prepared and maintained in a functional state for approximately 12 months was examined using a combination of culture-dependent and -independent pcr-dgge analyses and next-generation sequencing of 16s rrna amplicons. an extremely complex ecosystem including taxa potentially contributing to both indigo reduction and formation, as well as indigo degradation was found. pcr-dgge analyses revealed the presence of paenibaci ...	2017	28246965
new molecular packing in a crystal of pseudoazurin from alcaligenes faecalis: a double-helical arrangement of blue copper.	pseudoazurin from the denitrifying bacterium alcaligenes faecalis (afpaz) is a blue copper protein and functions as an electron donor to copper-containing nitrite reductase (cunir). conventionally, afpaz has been crystallized using highly concentrated ammonium sulfate as a precipitant. here, a needle-like crystal of afpaz grown in a solution containing a macromolecular precipitant, polyethylene glycol 8000 (peg 8000), is reported. the crystal belonged to space group p61, with unit-cell parameter ...	2017	28291752
production, purification and characterization of halophilic organic solvent tolerant protease from marine crustacean shell wastes and its efficacy on deproteinization.	the quantum of marine fish wastes produced by fish processing industries has necessitated to search new methods for its disposal. hence, this study is focused on production and purification of halophilic organic solvent tolerant protease (hosp) from marine alcaligenes faecalis apcmst-mkw6 using marine shell wastes as substrate. the candidate bacterium was isolated from the marine sediment of manakudi coast and identified as a. faecalis apcmst-mkw6. the purified protease showed 16.39-fold purity, ...	2016	28330229
synthesis and antimicrobial properties of 4-acylaminobenzenethiosulfoacid s-esters.	a series of esters of 4-acetyl, 4-trifluoroacetyl- and 4-(3-chloropropionyl)aminobenzenethiosulfoacids (twenty-four compounds) were synthesized and characterized by elemental analysis, (1)h nmr and ir spectroscopy. the antibacterial activity of the novel candidates has been screened using the agar diffusion or serial dilution methods against representative gram-positive (staphylococcus aureus, bacillus subtilis, bacillus mesentericus, mycobacterium sp., mycobacterium luteum), gram-negative (aero ...	2017	28344478
a cocktail of volatile compounds emitted from alcaligenes faecalis jbcs1294 induces salt tolerance in arabidopsis thaliana by modulating hormonal pathways and ion transporters.	in our previous study we showed that volatile organic compounds (vocs) from alcaligenes faecalis jbcs1294 (jbcs1294) induced tolerance to salt stress in arabidopsis thaliana by influencing the auxin and gibberellin pathways and upregulating the expression of key ion transporters. the aim of this study was to evaluate the contribution of each voc and blends of the vocs on the induction of salt tolerance and signaling pathways. the key vocs emitted from jbcs1294 were dissolved in lanolin and appli ...	2017	28448840
using phenotype microarrays in the assessment of the antibiotic susceptibility profile of bacteria isolated from wastewater in on-site treatment facilities.	the scope of the study was to apply phenotype biolog microarray (pm) technology to test the antibiotic sensitivity of the bacterial strains isolated from on-site wastewater treatment facilities. in the first step of the study, the percentage values of resistant bacteria from total heterotrophic bacteria growing on solid media supplemented with various antibiotics were determined. in the untreated wastewater, the average shares of kanamycin-, streptomycin-, and tetracycline-resistant bacteria wer ...	2017	28451946
an alcaligenes strain emulates bacillus thuringiensis producing a binary protein that kills corn rootworm through a mechanism similar to cry34ab1/cry35ab1.	crops expressing bacillus thuringiensis (bt)-derived insecticidal protein genes have been commercially available for over 15 years and are providing significant value to growers. however, there remains the need for alternative insecticidal actives due to emerging insect resistance to certain bt proteins. a screen of bacterial strains led to the discovery of a two-component insecticidal protein named afip-1a/1b from an alcaligenes faecalis strain. this protein shows selectivity against coleoptera ...	2017	28596570
enzymatic hydrolysis of poly(ethyleneterephthalate) used for and analysed by pore modification of track-etched membranes.	the potential of limited enzymatic poly(ethylene terephthalate) (pet) surface hydrolysis for the modification of track-etched (te) membranes was investigated. cutinases 1 and 2 from thermobifida cellulosilytica as well as a fusion protein of cutinase 1 with the polymer binding module from the polyhydroxyalkanoate depolymerase of alcaligenes faecalis (thc_cut1_pbm) were shown to hydrolyse highly crystalline pet te membranes with a pore diameter of ∼120nm at very narrow size distribution. furtherm ...	2017	28698130
biodegradation of ochratoxin a by alcaligenes faecalis isolated from soil.	the aim of this study is to report on the hydrolytic action of alcaligenes faecalis isolated from soil samples and its ability to degrade ochratoxin a.	2017	28708280
application of magnetic oms-2 in sequencing batch reactor for treating dye wastewater as a modulator of microbial community.	the potential and mechanism of synthesized magnetic octahedral molecular sieve (fe3o4@oms-2) nanoparticles in enhancing the aerobic microbial ability of sequencing batch reactor (sbr) for treating dye wastewater have been revealed in this study. the addition of fe3o4@oms-2 of 0.25g/l enhanced the decolorization of sbrs with an operation cycle of 24h by more than 20%. the 16s rrna gene high-throughput sequencing indicated fe3o4@oms-2 increased the microbial richness and diversity of sbrs, and mor ...	2017	28711831
bacterial species and mycotoxin contamination associated with locust bean, melon and their fermented products in south-western nigeria.	the microbiological safety of spontaneously fermented foods is not always guaranteed due to the undefined fermenting microbial consortium and processing materials. in this study, two commonly consumed traditional condiments (iru and ogiri) and their respective raw seeds (locust bean and melon) purchased from markets in south-western nigeria were assessed for bacterial diversity and mycotoxin contamination using 16s rrna gene sequencing and liquid chromatography tandem mass spectrometry (lc-ms/ms ...	2017	28759798
genomic characterization of vim metallo-β-lactamase-producing alcaligenes faecalis from gaza, palestine.	carbapenemase-producing gram-negative bacteria (cp-gnb) have increasingly spread worldwide, and different families of carbapenemases have been identified in various bacterial species. here we report the identification of five vim metallo-β-lactamase-producing alcaligenes faecalis, associated with a small outbreak in a large hospital in gaza, palestine. next generation sequencing analysis showed blavim-2 is harbored by a chromosomal genomic island among three strains, while blavim-4 is carried by ...	2017	28848020