Publications

chemical structure and inhalation toxicity of lipopolysaccharides from bacteria on cotton.	lipopolysaccharides from different bacteria isolated from cotton were purified and chemically analyzed. their pulmonary toxicity to animals was tested in inhalation tests. lipopolysaccharides from agrobacterium and xanthomonas were shown to differ from the others in that they contained no heptose and no non-hydroxylated fatty acids with a chain length of 12, 14, or 16 carbon atoms. lipopolysaccharides from pseudomonas putida, enterobacter agglomerans, and klebsiella oxytoca were found to cause a ...	1980	7000706
comparative properties of glutamine synthetases i and ii in rhizobium and agrobacterium spp.	some properties of glutamine synthetase i (gsi) and gsii are described for a fast-growing rhizobium sp. (rhizobium trifolii t1), a slow-growing rhizobium sp. (rhizobium japonicum usda 83), and agrobacterium tumefaciens c58. gsii of the fast-growing rhizobium sp. and gsii of the agrobacterium sp. were considerably more heat labile than gsii of the slow-growing rhizobium sp. as previously shown in r. japonicum 61a76, gsi became adenylylated rapidly in all species tested in response to ammonium. gs ...	1980	6107288
ultrastructure of gram-negative cotton bacteria with different pulmonary toxicities.	the shedding of outer membrane material was observed by electron microscopy in typical gram-negative cotton bacteria, except agrobacterium sp. this finding is in accordance with the relative pulmonary toxicities of these bacteria. the presence of capsules did not seem to be correlated with the acute pulmonary toxicity of the bacteria.	1982	7054127
pulmonary toxicity of endotoxins: comparison of lipopolysaccharides from various bacterial species.	lipopolysaccharides from three gram-negative bacteria isolated from bale cotton and piggery air were analyzed for their chemical composition, and their pulmonary toxicity for guinea pigs, lethal toxicity for mice, and pyrogenicity for rabbits were measured. lipopolysaccharides from enterobacter agglomerans and citrobacter freundii had closely related chemical compositions; both were pyrogenic for rabbits and caused a dose-dependent influx of polymorphonuclear leukocytes into the airways of guine ...	1982	7056574
septicemia caused by agrobacterium sp.	agrobacterium radiobacter biovar 2 was repeatedly grown from the blood of an elderly patient receiving artificial ventilation and broad-spectrum antibiotics. no source of the organism was found, but the septicemia ceased when cefotaxime was given. sera from the patient showed a fourfold rise in antibody against the organism and higher titers than sera from all but 1 of 50 healthy blood donors. the organism did not contain the plasmid associated with plant oncogenicity. this case may be only the ...	1985	4077973
transport of gamma-butyrobetaine in an agrobacterium species isolated from soil.	an agrobacterium sp. isolated from soil by selective growth on gamma-butyrobetaine (gamma-trimethylaminobutyrate) as the sole source of both carbon and nitrogen has been shown to possess an inducible transport system for this growth substrate. this transport system has a kt of 0.5 microm and a maximal velocity of 3.8 nmol/min per mg (dry weight). the influx of gamma-butyrobetaine is optimal at ph 8.5 and operates against a concentration gradient. the transport system shows a high specificity for ...	1986	3782024
isolation of tobacco dna segments with plant promoter activity.	we constructed a promoter probe vector, pgvl120, to isolate plant dna segments with promoter activity in tobacco. plant nuclear dna sau3a fragments were inserted in front of the npt-ii sequence, and a mixture of recombinant plasmids was mobilized to agrobacterium sp. and used to transform tobacco protoplasts. by kanamycin selection, transformed plant cell lines containing npt-ii t-dnas were isolated. eight of these cell lines were regenerated and analyzed for the levels of npt-ii activity in ste ...	1986	3540612
characterization of agrobacterium tumefaciens strains isolated from grapevine tumors in china.	thirteen strains of agrobacterium tumefaciens isolated from grapevine tumors in northern china were surveyed. these strains varied in their host range properties, although all were tumorigenic on grapevines. twelve of these strains belonged to agrobacterium sp. biotype 3, and 11 strains resulted in the synthesis of the opine octopine in tumor tissue. interestingly, one strain resulted in accumulation of arginine, a previously unrecognized opine, in tumor tissue. although dna in most of these str ...	1987	3606110
structure and transcription analysis of the gene encoding a cellobiase from agrobacterium sp. strain atcc 21400.	the dna sequence was determined for the cloned agrobacterium sp. strain atcc 21400 beta-glucosidase gene, abg. high-resolution nuclease s1 protection studies were used to map the abg mrna 5' and 3' termini. a putative abg promoter was identified whose sequence shows similarities to the consensus promoter of escherichia coli and with the nif promoter regions of klebsiella. the abg coding sequence was 1,374 nucleotides long. the molecular weight of the enzyme, based on the predicted amino acid seq ...	1988	2826395
purification and properties of the gamma-butyrobetaine-binding protein from an agrobacterium sp.	a binding protein for gamma-butyrobetaine was purified from osmotic shock fluid of an agrobacterium sp. it was a monomeric protein with an apparent molecular weight of 52,000 or 53,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration, respectively. the isoelectric point was 4.3, as determined by isoelectric focusing. amino acid analysis of the protein showed that asx and glx were predominant components and that the protein contained no cysteine. the d ...	1988	3182728
biodegradation of metal-edta complexes by an enriched microbial population.	a mixed culture utilizing edta as the sole carbon source was isolated from a mixed inoculum of water from the river mersey (united kingdom) and sludge from an industrial effluent treatment plant. fourteen component organisms were isolated from the culture, including representatives of the genera methylobacterium, variovorax, enterobacter, aureobacterium, and bacillus. the mixed culture biodegraded metal-edta complexes slowly; the biodegradability was in the order fe > cu > co > ni > cd. by incor ...	1998	9546167
mechanistic consequences of replacing the active-site nucleophile glu-358 in agrobacterium sp. beta-glucosidase with a cysteine residue.	retaining glycosidases achieve the hydrolysis of glycosidic bonds through the assistance of two key active-site carboxyls. one carboxyl functions as a nucleophile/leaving group, and the other acts as the acid-base catalyst. it has been suggested that a cysteine residue could fulfil the role of the active site nucleophile [hardy and poteete (1991) biochemistry 30, 9457-9463]. to test the validity of this proposal, a kinetic evaluation was conducted on the active-site nucleophile cysteine mutant ( ...	1998	9461511
the plant oncogene rold encodes a functional ornithine cyclodeaminase.	the plant oncogene rold stimulates the reproductive phase transition in plants. we define here the function of its gene product. we show that the rold protein bears sequence homology with ornithine cyclodeaminase, an uncommon enzyme of specialized-niche eubacteria and archaea that catalyzes the unusual nad(+)-dependent conversion of ornithine to proline. to confirm the prediction of the bioinformatic analysis, the rold protein was expressed in escherichia coli and purified. an ornithine-dependen ...	2001	11687622
cloning and characterization of the phosphatidylserine synthase gene of agrobacterium sp. strain atcc 31749 and effect of its inactivation on production of high-molecular-mass (1-->3)-beta-d-glucan (curdlan).	genes involved in the production of the extracellular (1-->3)-beta-glucan, curdlan, by agrobacterium sp. strain atcc 31749 were described previously (stasinopoulos et al., glycobiology 9:31-41, 1999). to identify additional curdlan-related genes whose protein products occur in the cell envelope, the transposon tnphoa was used as a specific genetic probe. one mutant was unable to produce high-molecular-mass curdlan when a previously uncharacterized gene, pss(ag), encoding a 30-kda, membrane-assoc ...	2002	12107128
different patterns of evolution for duplicated dna repair genes in bacteria of the xanthomonadales group.	dna repair genes encode proteins that protect organisms against genetic damage generated by environmental agents and by-products of cell metabolism. the importance of these genes in life maintenance is supported by their high conservation, and the presence of duplications of such genes may be easily traced, especially in prokaryotic genomes.	2004	15333143
production of l-carnitine by secondary metabolism of bacteria.	abstract: the increasing commercial demand for l-carnitine has led to a multiplication of efforts to improve its production with bacteria. the use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for l-carnitine production is discussed in the text. the different cell states of enterobacteria, such as escherichia coli and proteus sp., which can be used to produce l- ...	2007	17910757
"hot cores" in proteins: comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms.	a wide variety of stabilizing factors have been invoked so far to elucidate the structural basis of protein thermostability. these include, amongst the others, a higher number of ion-pairs interactions and hydrogen bonds, together with a better packing of hydrophobic residues. it has been frequently observed that packing of hydrophobic side chains is improved in hyperthermophilic proteins, when compared to their mesophilic counterparts. in this work, protein crystal structures from hyper/thermop ...	2008	18312638
naima: target amplification strategy allowing quantitative on-chip detection of gmos.	we have developed a novel multiplex quantitative dna-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. this new method named nasba implemented microarray analysis (naima) was applied to gmo detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number dna targets. in a first step, the use of tailed primers allows the multiplex synthesis of template dnas in a p ...	2008	18710880
enzymatic transglycosylation for glycoconjugate synthesis.	remarkable advances have been made in recent years in exploiting the transglycosylation activity of glycosidases and glycosynthase mutants for oligosaccharide and glycoconjugate synthesis. new glycosynthases were generated from retaining glycosidases, inverting glycosidases, and those that proceed in a mechanism of substrate-assisted catalysis. directed evolution coupled with elegant screening methods has led to the discovery of an expanding number of glycosynthase mutants that show improved cat ...	2009	19766528
r2cat: synteny plots and comparative assembly.	recent parallel pyrosequencing methods and the increasing number of finished genomes encourage the sequencing and investigation of closely related strains. although the sequencing itself becomes easier and cheaper with each machine generation, the finishing of the genomes remains difficult. instead of the desired whole genomic sequence, a set of contigs is the result of the assembly. in this applications note, we present the tool r2cat (related reference contig arrangement tool) that helps in th ...	2009	20015948
r2cat: synteny plots and comparative assembly.	recent parallel pyrosequencing methods and the increasing number of finished genomes encourage the sequencing and investigation of closely related strains. although the sequencing itself becomes easier and cheaper with each machine generation, the finishing of the genomes remains difficult. instead of the desired whole genomic sequence, a set of contigs is the result of the assembly. in this applications note, we present the tool r2cat (related reference contig arrangement tool) that helps in th ...	2009	20015948
biodegradation of the high explosive hexanitrohexaazaiso-wurtzitane (cl-20).	the aerobic biodegradability of the high explosive cl-20 by activated sludge and the white rot fungus phanerochaete chrysosporium has been investigated. although activated sludge is not effective in degrading cl-20 directly, it can mineralize the alkaline hydrolysis products. phanerochaete chrysosporium degrades cl-20 in the presence of supplementary carbon and nitrogen sources. biodegradation studies were conducted using various nutrient media under diverse conditions. variables included the cl ...	2009	19440524
the prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass.	lignocellulosic biomass is a renewable and abundant resource with great potential for bioconversion to value-added bioproducts. however, the biorefining process remains economically unfeasible due to a lack of biocatalysts that can overcome costly hurdles such as cooling from high temperature, pumping of oxygen/stirring, and, neutralization from acidic or basic ph. the extreme environmental resistance of bacteria permits screening and isolation of novel cellulases to help overcome these challeng ...	2009	19680472
study of free oligosaccharides derived from the bacterial n-glycosylation pathway.	the food-borne pathogen campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide and the most frequent antecedent in neuropathies such as the guillain-barré and miller fisher syndromes. c. jejuni was demonstrated to possess an n-linked protein glycosylation pathway that adds a conserved heptasaccharide to >40 periplasmic and membrane proteins. recently, we showed that c. jejuni also produces free heptasaccharides derived from the n-glycan pathway reminiscent of th ...	2009	19706478
studies in the modulation of experimental autoimmune encephalomyelitis.	experimental autoimmune encephalomyelitis (eae), an experimental model for multiple sclerosis, can be induced through inoculation with several different central nervous system (cns) proteins or peptides. modulation of eae, resulting in either protection from eae or enhancement of eae, can also be accomplished through either vaccination or dna immunization with molecular mimics of self-cns proteins. previously published data on this method of eae modulation will be reviewed. new data is presented ...	2010	20401539
neuroimmune pharmacological control of eae.		2010	20414732
phenolic acids act as signaling molecules in plant-microbe symbioses.	phenolic acids are the main polyphenols made by plants. these compounds have diverse functions and are immensely important in plant-microbe interactions/symbiosis. phenolic compounds act as signaling molecules in the initiation of legumerhizobia symbioses, establishment of arbuscular mycorrhizal symbioses and can act as agents in plant defense. flavonoids are a diverse class of polyphenolic compounds that have received considerable attention as signaling molecules involved in plant-microbe inter ...	2010	20400851
molecular basis of glyphosate resistance-different approaches through protein engineering.	glyphosate (n-phosphonomethyl-glycine) is the most widely used herbicide in the world: glyphosate-based formulations exhibit broad-spectrum herbicidal activity with minimal human and environmental toxicity. the extraordinary success of this simple, small molecule is mainly attributable to the high specificity of glyphosate for the plant enzyme enolpyruvyl shikimate-3-phosphate synthase in the shikimate pathway, leading to the biosynthesis of aromatic amino acids. starting in 1996, transgenic gly ...	2011	21668647
testing pollen of single and stacked insect-resistant bt-maize on in vitro reared honey bee larvae.	the ecologically and economic important honey bee (apis mellifera) is a key non-target arthropod species in environmental risk assessment (era) of genetically modified (gm) crops. honey bee larvae are directly exposed to transgenic products by the consumption of gm pollen. but most era studies only consider responses of adult bees, although bt-proteins primarily affect the larval phases of target organisms. we adopted an in vitro larvae rearing system, to assess lethal and sublethal effects of b ...	2011	22194811
polymerases in nonhomologous end joining: building a bridge over broken chromosomes.	repair of double-strand breaks in chromosomal dna is essential. unfortunately, a paradigm central to most dna repair pathways--damaged dna is replaced by polymerases, by using an intact, undamaged complementary strand as a template--no longer works. the nonhomologous end joining (nhej) pathway nevertheless still uses dna polymerases to help repair double-strand breaks. bacteria use a member of the archaeo-eukaryal primase superfamily, whereas eukaryotes use multiple members of the polymerase x f ...	2011	20649463
formation of se (0) nanoparticles by duganella sp. and agrobacterium sp. isolated from se-laden soil of north-east punjab, india.	selenium (se) is an essential trace element, but is toxic at high concentrations. depending upon the geological background, the land use or on anthropogenic pollution, different amounts of se may be present in soil. its toxicity is related to the oxyanions selenate and selenite as they are water soluble and bioavailable. microorganisms play an important role in se transformations in soil and its cycling in the environment by transforming water-soluble oxyanions into water insoluble, non-toxic el ...	2012	22607265
production and downstream processing of (1→3)-β-d-glucan from mutant strain of agrobacterium sp. atcc 31750.	we isolated a mutant that produced higher levels of curdlan than the wild strain agrobacterium sp. atcc 31750 by chemical mutagenesis using n-methyl-n-nitro-nitrosoguanidine. the mutant strain produced 66 g/l of curdlan in 120 h with a yield of (0.88) while, the wild strain produced 41 g/l in 120 h with a yield of (0.62) in a stirred bioreactor. the mutant could not produce curdlan when the ph was shifted from 7.0 to 5.5 after nitrogen depletion as followed for wild strain. in contrast, ph optim ...	2012	22681895
novel amidases of two aminobacter sp. strains: biotransformation experiments and elucidation of gene sequences.	the amidase activities of two aminobacter sp. strains (dsm24754 and dsm24755) towards the aryl-substituted substrates phenylhydantoin, indolylmethyl hydantoin, d,l-6-phenyl-5,6-dihydrouracil (phedu) and para-chloro-d,l-6-phenyl-5,6-dihydrouracil were compared. both strains showed hydantoinase and dihydropyrimidinase activity by hydrolyzing all substrates to the corresponding n-carbamoyl-α- or n-carbamoyl-β-amino acids. however, carbamoylase activity and thus a further degradation of these produc ...	2012	22738219
integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome.	tongue diagnosis is a unique method in traditional chinese medicine (tcm). this is the first investigation on the association between traditional tongue diagnosis and the tongue coating microbiome using next-generation sequencing. the study included 19 gastritis patients with a typical white-greasy or yellow-dense tongue coating corresponding to tcm cold or hot syndrome respectively, as well as eight healthy volunteers. an illumina paired-end, double-barcode 16s rrna sequencing protocol was desi ...	2012	23226834
enhanced cellulose degradation by targeted integration of a cohesin-fused β-glucosidase into the clostridium thermocellum cellulosome.	the conversion of recalcitrant plant-derived cellulosic biomass into biofuels is dependent on highly efficient cellulase systems that produce near-quantitative levels of soluble saccharides. similar to other fungal and bacterial cellulase systems, the multienzyme cellulosome system of the anaerobic, cellulolytic bacterium clostridium thermocellum is strongly inhibited by the major end product cellobiose. cellobiose-induced inhibition can be relieved via its cleavage to noninhibitory glucose by t ...	2012	22689961
analysis of the secretome and identification of novel constituents from culture filtrate of bacillus calmette-guerin using high-resolution mass spectrometry.	tuberculosis (tb) is an infectious bacterial disease that causes morbidity and mortality, especially in developing countries. although its efficacy against tb has displayed a high degree of variability (0%-80%) in different trials, mycobacterium bovis bacillus calmette-guérin (bcg) has been recognized as an important weapon for preventing tb worldwide for over 80 years. because secreted proteins often play vital roles in the interaction between bacteria and host cells, the secretome of mycobacte ...	2013	23616670
evolutionary diversification and characterization of the eubacterial gene family encoding dxr type ii, an alternative isoprenoid biosynthetic enzyme.	isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. in most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (mep) pathway. the production of mep is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (dxr-i) but a few organisms use an alternative dxr-like enzyme (dxr-ii).	2013	24004839
phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils.	phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. the p content in average soil is about 0.05% (w/w) but only 0.1% of the total p is available to plant because of poor solubility and its fixation in soil (illmer and schinner, soil biol biochem 27:257-263, 1995). an adequate supply of p ...	2013	25674415
ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (agalychnis callidryas).	amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. the conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. in addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. this ...	2014	24416427
mutation scanning in a single and a stacked genetically modified (gm) event by real-time pcr and high resolution melting (hrm) analysis.	genetic mutations must be avoided during the production and use of seeds. in the european union (eu), directive 2001/18/ec requires any dna construct introduced via transformation to be stable. establishing genetic stability is critical for the approval of genetically modified organisms (gmos). in this study, genetic stability of two gmos was examined using high resolution melting (hrm) analysis and real-time polymerase chain reaction (pcr) employing scorpion primers for amplification. the genet ...	2014	25365178
structural analysis of glucans.	glucans are most widespread polysaccharides in the nature. there is a large diversity in their molecular weight and configuration depending on the original source. according to the anomeric structure of glucose units it is possible to distinguish linear and branched α-, β- as well as mixed α,β-glucans with various glycoside bond positions and molecular masses. isolation of glucans from raw sources needs removal of ballast compounds including proteins, lipids, polyphenols and other polysaccharide ...	2014	25332993
regulatory framework for gene editing and other new breeding techniques (nbts) in argentina.	"new breeding techniques" (nbts) are a group of recent innovations in plant breeding using molecular biology tools. it is becoming evident that nbts can introduce advantageous traits for agriculture that could be commercially available very soon however, there is still a need of clarifying its regulatory status, particularly in regards to worldwide regulations on genetically modified organisms (gmos). this article reviews the meaning of the nbts concept, performs an overall regulatory analysis o ...	2015	26552666
proteolytic cleavage driven by glycosylation.	proteolytic processing of human host cell factor 1 (hcf-1) to its mature form was recently shown, unexpectedly, to occur in a udp-glcnac-dependent fashion within the transferase active site of o-glcnac-transferase (ogt) (lazarus, m. b., jiang, j., kapuria, v., bhuiyan, t., janetzko, j., zandberg, w. f., vocadlo, d. j., herr, w., and walker, s. (2013) science 342, 1235-1239). an interesting mechanism involving formation and then intramolecular rearrangement of a covalent glycosyl ester adduct of ...	2015	26515062
proteolytic cleavage driven by glycosylation.	proteolytic processing of human host cell factor 1 (hcf-1) to its mature form was recently shown, unexpectedly, to occur in a udp-glcnac-dependent fashion within the transferase active site of o-glcnac-transferase (ogt) (lazarus, m. b., jiang, j., kapuria, v., bhuiyan, t., janetzko, j., zandberg, w. f., vocadlo, d. j., herr, w., and walker, s. (2013) science 342, 1235-1239). an interesting mechanism involving formation and then intramolecular rearrangement of a covalent glycosyl ester adduct of ...	2015	26515062
crdr function in a curdlan-producing agrobacterium sp. atcc31749 strain.	agrobacterium sp. atcc31749 is an efficient curdlan producer at low ph and under nitrogen starvation. the helix-turn-helix transcriptional regulatory protein (crdr) essential for curdlan production has been analyzed, but whether crdr directly acts to cause expression of the curdlan biosynthesis operon (crdasc) is uncertain. to elucidate the molecular function of crdr in curdlan biosynthesis, we constructed a crdr knockout mutant along with pbqcrdr and pbqncrdr vectors with crdr expression driven ...	2015	25880528
thermodynamic matchers for the construction of the cuckoo rna family.	rna family models describe classes of functionally related, non-coding rnas based on sequence and structure conservation. the most important method for modeling rna families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous rnas. however, the performance of covariance models in finding remote homologs is poor for rna families with high sequence conservation, while for families with high structure but low sequence conservation, the ...	2015	25779873
enzymological characterization of atm, the first laccase from agrobacterium sp. s5-1, with the ability to enhance in vitro digestibility of maize straw.	laccase is an enzyme that catalyzes oxidation of phenolic compounds, diamines and aromatic amines. in this study, a novel laccase-like gene (atm) in a ligninolyitic isolate agrobacterium sp. s5-1 from soil humus was identified and heterologously expressed in escherichia coli. atm exhibited its maximal activity at ph 4.5 and at 50°c. this enzyme was tolerant to high temperature, a broad range of ph, heavy metal ions (co3+, mn2+, cu2+ and ni2+, 20 mm) and all tested organic solvents. furthermore, ...	2015	26010258
a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria.	luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ...	2015	25759807
expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution.	high selectivity and exquisite control over the outcome of reactions entice chemists to use biocatalysts in organic synthesis. however, many useful reactions are not accessible because they are not in nature's known repertoire. in this review, we outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. we begin with examples of how nature has discovered new catalytic functions and how such evolutionary progression has been recapitulated in the laboratory ...	2015	25649694
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 ...	2016	27508247
production of selenium nanoparticles in pseudomonas putida kt2440.	selenium (se) is an essential element for the cell that has multiple applications in medicine and technology; microorganisms play an important role in se transformations in the environment. here we report the previously unidentified ability of the soil bacterium pseudomonas putida kt2440 to synthesize nanoparticles of elemental selenium (nano-se) from selenite. our results show that p. putida is able to reduce selenite aerobically, but not selenate, to nano-se. kinetic analysis indicates that, i ...	2016	27845437
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
an integrated multi-omics analysis of the nk603 roundup-tolerant gm maize reveals metabolism disturbances caused by the transformation process.	glyphosate tolerant genetically modified (gm) maize nk603 was assessed as 'substantially equivalent' to its isogenic counterpart by a nutrient composition analysis in order to be granted market approval. we have applied contemporary in depth molecular profiling methods of nk603 maize kernels (sprayed or unsprayed with roundup) and the isogenic corn to reassess its substantial equivalence status. proteome profiles of the maize kernels revealed alterations in the levels of enzymes of glycolysis an ...	2016	27991589
polar flagella rotation in vibrio parahaemolyticus confers resistance to bacteriophage infection.	bacteriophage has been recognized as a novel approach to treat bacterial infectious diseases. however, phage resistance may reduce the efficacy of phage therapy. here, we described a mechanism of bacterial resistance to phage infections. in gram-negative enteric pathogen vibrio parahaemolyticus, we found that polar flagella can reduce the phage infectivity. deletion of polar flagella, but not the lateral flagella, can dramatically promote the adsorption of phage to the bacteria and enhances the ...	2016	27189325