Publications

fine tuning by human cd1e of lipid-specific immune responses.	cd1e is a member of the cd1 family that participates in lipid antigen presentation without interacting with the t-cell receptor. it binds lipids in lysosomes and facilitates processing of complex glycolipids, thus promoting editing of lipid antigens. we find that cd1e may positively or negatively affect lipid presentation by cd1b, cd1c, and cd1d. this effect is caused by the capacity of cd1e to facilitate rapid formation of cd1-lipid complexes, as shown for cd1d, and also to accelerate their tur ...	2011	21844346
Sphingomonas alpina sp. nov., a psychrophilic bacterium isolated from alpine soil.	An aerobic, Gram-negative, motile, psychrophilic bacterium, designated strain S8-3T, was isolated from alpine soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S8-3T was related to the genus Sphingomonas and had highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica S213T (98.0 %). 16S RNA gene sequence similarity between strain S8-3T and Sphingomonas paucimobilis ATCC 29837 T (the type species of the genus Sphingomonas) was 93.0 %. Strain S8-3T ...	2011	21856979
x-ray structure reveals a new class and provides insight into evolution of alkaline phosphatases.	the alkaline phosphatase (ap) is a bi-metalloenzyme of potential applications in biotechnology and bioremediation, in which phosphate monoesters are nonspecifically hydrolysed under alkaline conditions to yield inorganic phosphate. the hydrolysis occurs through an enzyme intermediate in which the catalytic residue is phosphorylated. the reaction, which also requires a third metal ion, is proposed to proceed through a mechanism of in-line displacement involving a trigonal bipyramidal transition s ...	2011	21829507
role of sphingomonas sp. strain fr1 phyr-nepr-σecfg cascade in general stress response and identification of a negative regulator of phyr.	the general stress response in alphaproteobacteria was recently described to depend on the alternative sigma factor σ(ecfg), whose activity is regulated by its anti-sigma factor nepr. the response regulator phyr, in turn, regulates nepr activity in a partner-switching mechanism according to which phosphorylation of phyr triggers sequestration of nepr by the sigma factor-like effector domain of phyr. although genes encoding predicted histidine kinases can often be found associated with phyr, litt ...	2011	21949070
poly(aspartate) hydrolases: biochemical properties and applications.	thermally synthesized poly(aspartate) (tpaa) shows potential for use in a wide variety of products and applications as a biodegradable replacement for non-biodegradable polycarboxylates, such as poly(acrylate). the tpaa molecule has unnatural structures, and the relationship between its biodegradability and structures has been investigated. two tpaa-degrading bacteria, sphingomonas sp. kt-1 and pedobacter sp. kp-2, were isolated from river water; from them, two paa-hydrolyzing enzymes, paa hydro ...	2011	21713512
changes in the bacterial community structure and diversity during bamboo retting.	microbial retting is a critical step in obtaining fiber bundles from bamboo culm using indigenous microorganisms. a cultivation-independent technique for monitoring the changes in bacteria community during bamboo retting was applied in this work. this technique involves genetic profiling of pcr-amplified small-subunit rrna and the single-strand conformation polymorphism (sscp) gel analysis of the pcr-amplified 16s rdna fragments. the study revealed that both the structure and the diversity of in ...	2011	21695788
effect of surfactants on pah biodegradation by a bacterial consortium and on the dynamics of the bacterial community during the process.	the aim of this work was to evaluate the effect of a non-biodegradable (tergitol np-10) and a biodegradable (tween-80) surfactant on growth, degradation rate and microbial dynamics of a polycyclic aromatic hydrocarbon (pahs) degrading consortium (c2pl05) from a petroleum polluted soil, applying cultivable and non cultivable techniques. growth and degradation rate were significantly lower with tergitol np-10 than that with tween-80. toxicity did not show any significant reduction with tergitol np ...	2011	21862321
Identification of the Midgut Microbiota of An. stephensi and An. maculipennis for Their Application as a Paratransgenic Tool against Malaria.	The midgut microbiota associated with Anopheles stephensi and Anopheles maculipennis (Diptera: Culicidae) was investigated for development of a paratransgenesis-based approach to control malaria transmission in Eastern Mediterranean Region (EMR). Here, we present the results of a polymerase chain reaction (PCR) and biochemical-based approaches to identify the female adult and larvae mosquitoe microbiota of these two major malaria vectors, originated from South Eastern and North of Iran. Plating ...	2011	22163022
[Isolation and identification of dominant microorganisms in rhizosphere of continuous cropping with peanut].	We isolated and identified dominant microorganisms from the rhizosphere of continuous cropping with peanut, to study the relationship between dominant microorganisms and peanut continuous cropping.	2011	21866710
diversity and phylogeny of bacteria on zimbabwe tobacco leaves estimated by 16s rrna sequence analysis.	microorganisms play important roles in the tobacco aging process. however, microbial communities on flue-cured tobacco leaves (fctl) remain largely unknown. in this study, the total microbial genomic dna of unaged and aging fctl from zimbabwe were isolated using a culture-independent method, and the bacterial communities were investigated through analyzing two 16s rrna gene libraries. eighty-four and 65 operational taxonomic units were obtained from the libraries of the unaged and aging fctl, re ...	2011	21660545
continuous ambulatory peritoneal dialysis (capd) associated peritonitis in a child: a rare case of peritonitis caused by sphingomonous paucimobilis.	first identified in 1977, sphingomonous paucimobilis has emerged as an opportunistic human pathogen. it is primarily known to cause a range of mostly nosocomial, non-life-threatening infections that typically are easily treated by antibiotic therapy. sources of its isolation linked to clinical disease include blood, spinal fluid and leg ulcers. it has also been reported as a rare cause of peritonitis in patients on continuous ambulatory peritoneal dialysis. we present a case of a child with peri ...	2011	21375172
dehydration of the off-flavor chemical 2-methylisoborneol by the r-limonene-degrading bacteria pseudomonas sp. strain 19-rlim and sphingomonas sp. strain bir2-rlima.	the terpene 2-methylisoborneol (mib), a major cause of off-flavor in farm-raised catfish and drinking water, is transformed by various different terpene-degrading bacteria. two of these, the r-limonene-degrading strains pseudomonas sp. 19-rlim and sphingomonas sp. bir2-rlima, dehydrated mib with the formation of odorless metabolites 2-methylenebornane and 4-methylcamphene. these metabolites which have a structural resemblance to camphor, could be further transformed by camphor-degrading bacteria ...	2011	21842206
[sphingomonas paucimobilis infection with underlying submandibular sialolithiasis].	sphingomonas paucimobilis (s. paucimobilis), is a gram-negative, aerobic, non-fermentative, oxidase (+) and catalase (+) bacterium. although s. paucimobilis is isolated very rarely, it can cause both nosocomial and community-acquired infections. a patient admitted to our clinic had a complaint of swelling in the right mandibular region and pain increasing while eating for the previous week. bimanual palpation revealed a painful swelling of 1x1x1 cm in size inside the right wharton's duct. via ma ...	2011	21303318
biodiversity and geochemistry of an extremely acidic, low-temperature subterranean environment sustained by chemolithotrophy.	the geochemical dynamics and composition of microbial communities within a low-temperature (ôê+8.5-¦c), long-abandoned (>ôçâ90 years) underground pyrite mine (cae coch, located in north wales) were investigated. surface water percolating through fractures in the residual pyrite ore body that forms the roof of the mine becomes extremely acidic and iron-enriched due to microbially accelerated oxidative dissolution of the sulfide mineral. water droplets on the mine roof were found to host a very li ...	2011	21382147
crystal structure of h2o2-dependent cytochrome p450sp{alpha} with its bound fatty acid substrate: insight into the regioselective hydroxylation of fatty acids at the {alpha} position.	cytochrome p450(sp+¦) (cyp152b1) isolated from sphingomonas paucimobilis is the first p450 to be classified as a h(2)o(2)-dependent p450. p450(sp+¦) hydroxylates fatty acids with high +¦-regioselectivity. herein we report the crystal structure of p450(sp+¦) with palmitic acid as a substrate at a resolution of 1.65 ôä½. the structure revealed that the c(+¦) of the bound palmitic acid in one of the alternative conformations is 4.5 ôä½ from the heme iron. this conformation explains the highly selec ...	2011	21719702
the lin genes for +¦-hexachlorocyclohexane degradation in sphingomonas sp. mm-1 proved to be dispersed across multiple plasmids.	a +¦-hexachlorocyclohexane (hch)-degrading bacterium, sphingomonas sp. mm-1, was isolated from soil contaminated with hch isomers. cultivation of mm-1 in the presence of +¦-hch led to the detection of five +¦-hch metabolites, +¦-pentachlorocyclohexene, 2,5-dichloro-2,5-cyclohexadiene-1,4-diol, 2,5-dichlorohydroquinone, 1,2,4-trichlorobenzene, and 2,5-dichlorophenol, strongly suggesting that mm-1 has the lin genes for +¦-hch degradation originally identified in the well-studied +¦-hch-degrading s ...	2011	21389627
effect of fe-pd bimetallic nanoparticles on sphingomonas sp. ph-07 and a nano-bio hybrid process for triclosan degradation.	in this study, we have evaluated the effect of palladium-iron bimetallic nanoparticles (nfe-pd) on diphenyl ether (de) degrading bacterial strain sphingomonas sp. ph-07 as well as a sequential nano-bio hybrid process with nfe-pd as catalytic reductant and ph-07 as biocatalyst for degradation of triclosan. strain ph-07 grew well in the presence of nfe-pd up to 0.1g/l in minimal salts medium with de as carbon source. in aqueous system, tcs (17.3 µm) was completely dechlorinated within 2h by nfe-pd ...	2011	21429741
planktonic microbes in the gulf of maine area.	in the gulf of maine area (goma), as elsewhere in the ocean, the organisms of greatest numerical abundance are microbes. viruses in goma are largely cyanophages and bacteriophages, including podoviruses which lack tails. there is also evidence of mimivirus and chlorovirus in the metagenome. bacteria in goma comprise the dominant sar11 phylotype cluster, and other abundant phylotypes such as sar86-like cluster, sar116-like cluster, roseobacter, rhodospirillaceae, acidomicrobidae, flavobacteriales ...	2011	21698243
(r,s)-dichlorprop herbicide in agricultural soil induces proliferation and expression of multiple dioxygenase-encoding genes in the indigenous microbial community.	we investigated the effect of (r,s)-dichlorprop herbicide addition to soil microcosms on the degrading indigenous microbial community by targeting multiple a-ketoglutarate-dependent (a-kg) dioxygenase-encoding genes (rdpa, sdpa and tfda group i) at both gene and transcript level. the soil microbial community responded with high growth of potential degraders as measured by the abundance of dioxygenase-encoding genes using quantitative real-time pcr (qpcr). rdpa dna was not detectable in unamended ...	2011	21418495
testosterone-mineralizing culture enriched from swine manure: characterization of degradation pathways and microbial community composition.	environmental releases and fate of steroid sex hormones from livestock and wastewater treatment plants are of increasing regulatory concern. despite the detection of these hormones in manures, biosolids, and the environment, little attention has been paid to characterization of fecal bacteria capable of hormone degradation. the enrichments of (swine) manure-borne bacteria capable of aerobic testosterone degradation were prepared and the testosterone mineralization pathway was elucidated. six dna ...	2011	21740029
the effects of metabolite molecules produced by drinking water-isolated bacteria on their single and multispecies biofilms.	the elucidation of the mechanisms by which diverse species survive and interact in drinking water (dw) biofilm communities may allow the identification of new biofilm control strategies. the purpose of the present study was to investigate the effects of metabolite molecules produced by bacteria isolated from dw on biofilm formation. six opportunistic bacteria, viz. acinetobacter calcoaceticus, burkholderia cepacia, methylobacterium sp., mycobacterium mucogenicum, sphingomonas capsulata and staph ...	2011	21732713
computational study on the interaction of a ring-hydroxylating dioxygenase from sphingomonas chy-1 with pahs.	the massive computational resources available in the framework of a grid paradigm approach represent an emerging tool in the bioinformatics field. in this paper, we used the above approach in the rapid determination of the interactions between the ring-hydroxylating dioxygenase, comprised six enzymatic subunits, and polycyclic aromatic hydrocarbons (pahs) in their optimal positions. the results were obtained by simulating enzyme dynamics at 300 k through molecular dynamics calculations. for the ...	2011	21441049
modeling sorption and biodegradation of phenanthrene in mangrove sediment slurry.	a mathematical model, combining both sorption and biodegradation process, was developed to predict the biodegradation of phenanthrene by sphingomonas sp. in different sediment slurries. the model includes two sorption parameters, α (the partition coefficient) and 1/k (the diffusion resistance); a kinetic parameter k (the first order rate constant); and a sediment parameter, a(v) (the specific sediment surface area in unit volume of slurry). these parameters were evaluated and verified in three t ...	2011	21474240
culturable bacterial diversity at the princess elisabeth station (utsteinen, sør rondane mountains, east antarctica) harbours many new taxa.	we studied the culturable heterotrophic bacterial diversity present at the site of the new princess elisabeth station at utsteinen (dronning maud land, east antarctica) before construction. about 800 isolates were picked from two terrestrial microbial mat samples after incubation on several growth media at different temperatures. they were grouped using rep-pcr fingerprinting and partial 16s rrna gene sequencing. phylogenetic analysis of the complete 16s rrna gene sequences of 93 representatives ...	2011	21501941
effects of solids retention time on the performance of bioreactors bioaugmented with a 17β-estradiol-utilizing bacterium, sphingomonas strain kc8.	this study investigated the performance of lab-scale sequencing batch reactors (sbrs) that were inoculated with nitrifying activated sludge and bioaugmented with a sphingomonas strain kc8 (a 17β-estradiol-degrading bacterium). the bioaugmented sbrs were supplied with synthetic wastewater (average initial total organic carbon (toc)=175mgl(-1) and average initial ammonia-n=25mgl(-1)) and daily dose of 17β-estradiol (1mgl(-1)) and operated under three solid retention times (srts) of 5, 10, and 20d. ...	2011	21543102
a diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis.	there is a concern of whether the structure and diversity of a microbial community can be effectively revealed by short-length pyrosequencing reads. in this study, we performed a microbial community analysis on a sample from a high-efficiency denitrifying quinoline-degrading bioreactor and compared the results generated by pyrosequencing with those generated by clone library technology. by both technologies, 16s rrna gene analysis indicated that the bacteria in the sample were closely related to ...	2011	21538111
sphingomonas jejuensis sp. nov., isolated from marine sponge hymeniacidon flavia.	a gram-negative, non-motile, rod shaped, and orange-pigmented chemoheterotrophic bacterium, strain ms-31(t) was isolated from the marine sponge hymeniacidon flavia, collected from near jeju island, korea. the strain ms-31(t) was subjected to a polyphasic taxonomic study. the phylogenetic analysis based on the 16s rrna gene sequences revealed that the novel isolate could be affiliated within the genus sphingomonas. the strain ms-31(t) showed 95.6% of 16s rrna gene sequence similarity with the mos ...	2011	21538244
transcriptomic analysis of phenanthrene degrading sphingomonas biofilms exposed to environmentally relevant solute and matric stresses.		2011	21539200
sphingomonas endophytica sp. nov., a novel bacterium isolated from artemisia annua l.	a novel bacterium (strain yim 65583(t)) belonging to the genus sphingomonas was isolated from a surface-sterilized tissue of artemisia annua l., which was collected from yunnan province, south-west china. its morphology, physiology, biochemical features were consistent with those members of the genus sphingomonas. 16s rrna gene sequence of strain yim 65583(t) further confirmed that it should be classified as a member of the genus sphingomonas and was most closely related to sphingomonas phyllosp ...	2011	21873515
interactions of leptospira with environmental bacteria from surface water.	leptospires can persist for months in nutrient-poor aqueous environments prior to transmission to a mammalian host. interactions with environmental bacteria and biofilm formation are possible mechanisms of persistence of leptospires in the environment. bacteria isolated from rivers in the ecuadorian rainforest were tested for their ability to support leptospiral viability. we found that co-culture with sphingomonas spp., but not flavobacterium spp. or delftia spp., enabled survival of l. biflexa ...	2011	21479795
growth of chlorella vulgaris and associated bacteria in photobioreactors.	the aim of this study was to test three flat plate photobioreactor configurations for growth of chlorella vulgaris under non-axenic conditions and to characterize and quantify associated bacterial communities. the photobioreactor cultivations were conducted using tap water-based media to introduce background bacterial population. growth of algae was monitored over time with three independent methods. additionally, the quantity and quality of eukaryotes and bacteria were analysed using culture-in ...	2012	21936882
novel low-temperature-active, salt-tolerant and proteases-resistant endo-1,4-β-mannanase from a new sphingomonas strain.	sphingomonas sp. jb13, isolated from slag of a >20-year-old phosphate rock-stacking site, showed the highest 16s rdna (1343bp) identity of 97.2% with sphingomonas sp. erb1-3 (fj948169) and <97% identities with other identified sphingomonas strains. a mannanase-coding gene (1191bp) was cloned and encodes a 396-residue polypeptide (manajb13) showing the highest amino acid sequence identities of 56.2% with the putative glycosyl hydrolase (gh) family 26 endo-1,4-β-mannanase from rhodothermus marinus ...	2012	22265897
coenzyme q(10) production by immobilized sphingomonas sp. zute03 via a conversion-extraction coupled process in a three-phase fluidized bed reactor.	a three-phase fluidized bed reactor (tpfbr) was designed to evaluate the potential of coq(10) production by gel-entrapped sphingomonas sp. zute03 via a conversion-extract coupled process. in the reactor, the coq(10) yield reached 46.99mg/l after 8h of conversion; a high-level yield of about 45mg/l was maintained even after 15 repetitions (8h/batch). to fully utilize the residual precursor (para-hydroxybenzoic acid, phb) in the aqueous phase, the organic phase was replaced with new solution conta ...	2012	22226200
sphingomonas laterariae lnb2t sp. nov. isolated from hexachlorocyclohexane (hch) contaminated dumpsite in lucknow.	a gram-negative, non-motile, cream coloured and rod shaped bacterial strain named lnb2t was isolated from a brick kiln area situated in an open hexachlorocyclohexane (hch) dumpsite at ummari village (lucknow, india) and was subjected to polyphasic taxonomic approach. strain lnb2t showed 16s rrna gene sequence similarity of 98.0 % with its closest relative sphingomonas haloaromaticamans a175t and 97.3 % with sphingomonas histidinilytica um2t. strain lnb2t formed a monophyletic group in a cluster ...	2012	22247216