Publications

kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rrna gene pcr amplicon length heterogeneity	marine bacterioplankton diversity was examined by quantifying natural length variation in the 5' domain of small-subunit (ssu) rrna genes (rdna) amplified by pcr from a dna sample from the oregon coast. this new technique, length heterogeneity analysis by pcr (lh-pcr), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. relationships between the sizes of amplicons and ...	1998	9797317
algicidal effects of a novel marine pseudoalteromonas isolate (class proteobacteria, gamma subdivision) on harmful algal bloom species of the genera chattonella, gymnodinium, and heterosigma.	during a bacterial survey of the huon estuary in southern tasmania, australia, we isolated a yellow-pigmented pseudoalteromonas strain (class proteobacteria, gamma subdivision), designated strain y, that had potent algicidal effects on harmful algal bloom species. this organism was identified by 16s rrna sequencing as a strain with close affinities to pseudoalteromonas peptidysin. this bacterium caused rapid cell lysis and death (within 3 h) of gymnodinoids (including gymnodinium catenatum) and ...	1998	9687434
genetic diversity of the biofilm covering montacuta ferruginosa (mollusca, bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of pcr-amplified gene fragments coding for 16s rrna.	the shell of the bivalve montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. this biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. the aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their ...	1998	9726898
identification of a marine agarolytic pseudoalteromonas isolate and characterization of its extracellular agarase	the phenotypic and agarolytic features of an unidentified marine bacteria that was isolated from the southern pacific coast was investigated. the strain was gram negative, obligately aerobic, and polarly flagellated. on the basis of several phenotypic characters and a phylogenetic analysis of the genes coding for the 16s rrna, this strain was identified as pseudoalteromonas antarctica strain n-1. in solid agar, this isolate produced a diffusible agarase that caused agar softening around the colo ...	1998	9797294
aiia, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of erwinia carotovora.	n-acylhomoserine lactones, known as autoinducers (ais), are widely conserved signal molecules present in quorum-sensing systems of many gram-negative bacteria. ais are involved in the regulation of diverse biological functions, including expression of pathogenic genes in the plant pathogens pseudomonas solanacearum, several erwinia species, and the human pathogen pseudomonas aeruginosa. a bacterial isolate, bacillus sp. 240b1, is capable of enzymatic inactivation of ais. the gene (aiia) for ai i ...	2000	10716724
interspecific variability in sensitivity to uv radiation and subsequent recovery in selected isolates of marine bacteria.	the interspecific variability in the sensitivity of marine bacterial isolates to uv-b (295- to 320-nm) radiation and their ability to recover from previous uv-b stress were examined. isolates originating from different microenvironments of the northern adriatic sea were transferred to aged seawater and exposed to artificial uv-b radiation for 4 h and subsequently to different radiation regimens excluding uv-b to determine the recovery from uv-b stress. bacterial activity was assessed by thymidin ...	2000	10742228
identification of a novel type of cgmp phosphodiesterase that is defective in the chemotactic stmf mutants.	stmf mutants are chemotactic mutants that are defective in a cgmp phosphodiesterase (pde) activity. we identified a novel gene, pded, that harbors two cyclic nucleotide-binding domains and a metallo-beta-lactamase homology domain. similar to stmf mutants, pded-null mutants displayed extensively streaming aggregates, prolonged elevation of cgmp levels after chemotactic stimulation, and reduced cgmp-pde activity. pded transcripts were lacking in stmf mutant np377, indicating that this mutant carri ...	2002	12429831
molecular modeling of family gh16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae.	family gh16 glycoside hydrolases can be assigned to five subgroups according to their substrate specificities, including xyloglucan transglucosylases/hydrolases (xths), (1,3)-beta-galactanases, (1,4)-beta-galactanases/kappa-carrageenases, "nonspecific" (1,3/1,3;1,4)-beta-d-glucan endohydrolases, and (1,3;1,4)-beta-d-glucan endohydrolases. a structured family gh16 glycoside hydrolase database has been constructed (http://www.ghdb.uni-stuttgart.de) and provides multiple sequence alignments with fu ...	2004	15557263
in vitro laser ablation of natural marine biofilms.	we studied the efficiency of pulsed low-power laser irradiation of 532 nm from an nd:yag (neodymium-doped yttrium-aluminum-garnet) laser to remove marine biofilm developed on titanium and glass coupons. natural biofilms with thicknesses of 79.4 +/- 27.8 microm (titanium) and 107.4 +/- 28.5 microm (glass) were completely disrupted by 30 s of laser irradiation (fluence, 0.1 j/cm2). laser irradiation significantly reduced the number of diatoms and bacteria in the biofilm (paired t test; p < 0.05). ...	2004	15528562
the endo-beta-agarases agaa and agab from the marine bacterium zobellia galactanivorans: two paralogue enzymes with different molecular organizations and catalytic behaviours.	two beta-agarase genes, agaa and agab, were functionally cloned from the marine bacterium zobellia galactanivorans. the agaa and agab genes encode proteins of 539 and 353 amino acids respectively, with theoretical masses of 60 and 40 kda. these two beta-agarases feature homologous catalytic domains belonging to family gh-16. however, agaa displays a modular architecture, consisting of the catalytic domain (agaac) and two c-terminal domains of unknown function which are processed during secretion ...	2005	15456406
calcium-induced tertiary structure modifications of endo-beta-1,3-glucanase from pyrococcus furiosus in 7.9 m guanidinium chloride.	the family 16 endo-beta-1,3 glucanase from the extremophilic archaeon pyrococcus furiosus is a laminarinase, which in 7.9 m gdmcl (guanidinium chloride) maintains a significant amount of tertiary structure without any change of secondary structure. the addition of calcium to the enzyme in 7.9 m gdmcl causes significant changes to the near-uv cd and fluorescence spectra, suggesting a notable increase in the tertiary structure which leads to a state comparable, but not identical, to the native sta ...	2005	15482259
the structure of gdp-4-keto-6-deoxy-d-mannose-3-dehydratase: a unique coenzyme b6-dependent enzyme.	l-colitose is a 3,6-dideoxysugar found in the o-antigens of some gram-negative bacteria such as escherichia coli and in marine bacteria such as pseudoalteromonas tetraodonis. the focus of this investigation, gdp-4-keto-6-deoxy-d-mannose-3-dehydratase, catalyzes the third step in colitose production, which is the removal of the hydroxyl group at c3' of gdp-4-keto-6-deoxymannose. it is an especially intriguing plp-dependent enzyme in that it acts as both a transaminase and a dehydratase. here we p ...	2006	16943443
degradation of lambda-carrageenan by pseudoalteromonas carrageenovora lambda-carrageenase: a new family of glycoside hydrolases unrelated to kappa- and iota-carrageenases.	carrageenans are sulfated galactans found in the cell walls of red seaweeds. they are classified according to the number and the position of sulfate ester groups. lambda-carrageenan is the most sulfated carrageenan and carries at least three sulfates per disaccharide unit. the sole known depolymerizing enzyme of lambda-carrageenan, the lambda-carrageenase from pseudoalteromonas carrageenovora, has been purified, cloned and sequenced. sequence analyses have revealed that the lambda-carrageenase, ...	2007	17269933
a structural study of gdp-4-keto-6-deoxy-d-mannose-3-dehydratase: caught in the act of geminal diamine formation.	di- and trideoxysugars are an important class of carbohydrates synthesized by certain plants, fungi, and bacteria. colitose, for example, is a 3,6-dideoxysugar found in the o-antigens of gram-negative bacteria such as escherichia coli, salmonella enterica, yersinia pseudotuberculosis, and vibrio cholerae, among others. these types of dideoxysugars are thought to serve as antigenic determinants and to play key roles in bacterial defense and survival. four enzymes are required for the biochemical ...	2007	17997582
molecular structure of endotoxins from gram-negative marine bacteria: an update.	marine bacteria are microrganisms that have adapted, through millions of years, to survival in environments often characterized by one or more extreme physical or chemical parameters, namely pressure, temperature and salinity. the main interest in the research on marine bacteria is due to their ability to produce several biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents. nonetheless, lipopolysaccharides (lpss), or their portions, from g ...	2007	18463721
carrageenan-induced innate immune response is modified by enzymes that hydrolyze distinct galactosidic bonds.	the common food additive carrageenan (cgn) predictably induces intestinal inflammation in animal models. mechanisms of cgn-induced nuclear factor κb and interleukin-8 (il-8) stimulation include an immune-mediated pathway involving toll-like receptor 4 (tlr4) and b-cell lymphoma/leukemia 10 (bcl10) and a reactive oxygen species (ros)-mediated pathway. to determine how the structure of cgn contributes to its initiation of inflammation through these two distinct mechanisms, we treated cgns with gal ...	2009	19864123
carrageenan-induced innate immune response is modified by enzymes that hydrolyze distinct galactosidic bonds.	the common food additive carrageenan (cgn) predictably induces intestinal inflammation in animal models. mechanisms of cgn-induced nuclear factor κb and interleukin-8 (il-8) stimulation include an immune-mediated pathway involving toll-like receptor 4 (tlr4) and b-cell lymphoma/leukemia 10 (bcl10) and a reactive oxygen species (ros)-mediated pathway. to determine how the structure of cgn contributes to its initiation of inflammation through these two distinct mechanisms, we treated cgns with gal ...	2009	19864123
research and application of marine microbial enzymes: status and prospects.	over billions of years, the ocean has been regarded as the origin of life on earth. the ocean includes the largest range of habitats, hosting the most life-forms. competition amongst microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to evolution. the evolution prompted the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. therefore, marine microbial enzymes can offer novel bio ...	2010	20631875
a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ...	2010	20141328
biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium zobellia galactanivorans.	zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. notably, this marine bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycoside hydrolase family 16. although β-agarases are specific for the neutral agarobiose moieties, the recently discovered β-porphyranases degrade the sulfated polymers found in various quantities in natural agars. here, we report the biochemical and stru ...	2012	22778272
characterization of bacteria in ballast water using maldi-tof mass spectrometry.	to evaluate a rapid and cost-effective method for monitoring bacteria in ballast water, several marine bacterial isolates were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms). since international maritime organization (imo) regulations are concerned with the unintended transportation of pathogenic bacteria through ballast water, emphasis was placed on detecting species of vibrio, enterococci and coliforms. seawater samples collected fr ...	2012	22685576
characterization of a κ-carrageenase from marine cellulophaga lytica strain n5-2 and analysis of its degradation products.	a carrageenan-degrading marine cellulophaga lytica strain n5-2 was isolated from the sediment of carrageenan production base. a κ-carrageenase (ec 3.2.1.83) with high activity was purified to electrophoretic homogeneity from the culture supernatant by a procedure of ammonium sulfate precipitation, dialyzing and gel filtration on sephadexg-200 and sephadexg-75. the purified enzyme was verified as a single protein on sds-page, and whose molecular weight was 40.8 kda. the κ-carrageenase yielded a h ...	2013	24351836
discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium pseudoalteromonas carrageenovora.	carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. these polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. as a result of the screeni ...	2014	25207269
gram-negative marine bacteria: structural features of lipopolysaccharides and their relevance for economically important diseases.	gram-negative marine bacteria can thrive in harsh oceanic conditions, partly because of the structural diversity of the cell wall and its components, particularly lipopolysaccharide (lps). lps is composed of three main parts, an o-antigen, lipid a, and a core region, all of which display immense structural variations among different bacterial species. these components not only provide cell integrity but also elicit an immune response in the host, which ranges from other marine organisms to human ...	2014	24796306
the cultivable surface microbiota of the brown alga ascophyllum nodosum is enriched in macroalgal-polysaccharide-degrading bacteria.	bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. yet the water column, which has been studied largely by metagenomic approaches, is poor in such bacteria and their algal-polysaccharide-degrading enzymes. even more surprisingly, the few published studies on seaweed-associated microbiomes have revealed low abundances of such bacteria and their specific enzymes. however, as macroalgal cell-wall polysaccharides do not accumulate in n ...	2015	26734000
editorial: marine biomolecules.		2015	26347859
progress in the development of gelling agents for improved culturability of microorganisms.	gelling agents are required for formulating both solid and semisolid media, vital for the isolation of microorganisms. gelatin was the first gelling agent to be discovered but it soon paved the way for agar, which has far superior material qualities. source depletion, issues with polymerase-chain-reaction and inability to sustain extermophiles etc., necessitate the need of other gelling agents. many new gelling agents, such as xantham gum, gellan gum, carrageenan, isubgol, and guar gum have been ...	2015	26257708
seaweed hydrocolloid production: an update on enzyme assisted extraction and modification technologies.	agar, alginate, and carrageenans are high-value seaweed hydrocolloids, which are used as gelation and thickening agents in different food, pharmaceutical, and biotechnological applications. the annual global production of these hydrocolloids has recently reached 100,000 tons with a gross market value just above us$ 1.1 billion. the techno-functional properties of the seaweed polysaccharides depend strictly on their unique structural make-up, notably degree and position of sulfation and presence ...	2015	26023840
selection of the n-acylhomoserine lactone-degrading bacterium alteromonas stellipolaris pqq-42 and of its potential for biocontrol in aquaculture.	the production of virulence factors by many pathogenic microorganisms depends on the intercellular communication system called quorum sensing, which involves the production and release of signal molecules known as autoinducers. based on this, new-therapeutic strategies have emerged for the treatment of a variety of infections, such as the enzymatic degradation of signaling molecules, known as quorum quenching (qq). in this study, we present the screening of qq activity amongst 450 strains isolat ...	2016	27242684
matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity.	sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. however, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. in the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity a ...	2016	27749924