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PubMed2005

Sulfide-oxidizing activity and bacterial community structure in a fluidized bed reactor from a zero-discharge mariculture system.

In the present work we describe a comprehensive analysis of sulfide oxidation in a fluidized bed reactor (FBR) from an environmentally sustainable, zero-discharge mariculture system. The FBR received oxygen-depleted effluent from a digestion basin (DB) that is responsible for gasification of organic matter and nitrogen. The FBR is a crucial component in this recirculating system because it safeguards the fish from the toxic sulfide produced in the DB. Microscale sulfide oxidation potential and bacterial community composition within FBR biofilms were correlated to biofilter performance by integrating bulk chemical, microsensor (O2, pH, and H2S), and molecular microbial community analyses. The FBR consistently oxidized sulfide during two years of continuous operation, with an estimated average sulfide removal rate of 1.3 g of sulfide-S L(FBR)(-1) d(-1). Maximum sulfide oxidation rates within the FBR biofilms were 0.36 and 0.21 mg of sulfide-S cm(-3) h(-1) in the oxic and anoxic layers, respectively, indicating that both oxygen and nitrate serve as electron acceptors for sulfide oxidation. The estimated anoxic sulfide removal rate, as extrapolated from bench scale, autotrophic, nitrate-amended experiments, was 0.7 g of sulfide-S L(FBR)(-1) d(-1), which is approximately 50% of the total estimated sulfide removal in the FBR. Community composition analyses using denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA gene fragments from FBR samples taken at six-month intervals revealed several sequences that were closely affiliated with sulfide-oxidizing bacteria. These included the denitrifying, sulfide-oxidizing bacteria Thiomicrospira denitrificans, members of the filamentous Thiothrix genus, and sulfide-oxidizing symbionts from the Gammaproteobacteria. In addition, marine Alphaproteobacteria and Bacteroidetes species were present in all of the DGGE profiles examined. DGGE analyses showed significant shifts in the bacterial community composition between profiles over two years of sampling, indicating the presence of a diverse and dynamic microbial community within the functionally stable FBR. The FBR's combined capacity for both oxic and anoxic sulfide oxidation, as indicated by bulk chemical, microsensor, and molecular microbial analyses, gives it significant functional elasticity, which is crucial for proper performance in the dynamic environment of this mariculture system.

Aquaculture↗
PubMed2006

Enhanced covariance spectroscopy from minimal datasets.

A novel approach is described for the determination of reliable high-resolution homonuclear NMR covariance spectra from minimal datasets. It uses a sparse sampling scheme along the indirect dimension together with a comprehensive analysis of finite sampling effects that eliminates spurious correlations. The scheme, which is demonstrated for TOCSY and COSY, offers a substantial speed up over current methods, rendering it suitable for high-throughput screening applications.

Image Enhancement↗
PubMed2003

Profiling glucosinolates and phenolics in vegetative and reproductive tissues of the multi-purpose trees Moringa oleifera L. (horseradish tree) and Moringa stenopetala L.

Moringa species are important multi-purpose tropical crops, as human foods and for medicine and oil production. There has been no previous comprehensive analysis of the secondary metabolites in Moringa species. Tissues of M. oleifera from a wide variety of sources and M. stenopetala from a single source were analyzed for glucosinolates and phenolics (flavonoids, anthocyanins, proanthocyanidins, and cinnamates). M. oleifera and M. stenopetala seeds only contained 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate at high concentrations. Roots of M. oleifera and M. stenopetala had high concentrations of both 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate and benzyl glucosinolate. Leaves from both species contained 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate and three monoacetyl isomers of this glucosinolate. Only 4-(alpha-l-rhamnopyranosyloxy)-benzylglucosinolate was detected in M. oleifera bark tissue. M. oleifera leaves contained quercetin-3-O-glucoside and quercetin-3-O-(6' '-malonyl-glucoside), and lower amounts of kaempferol-3-O-glucoside and kaempferol-3-O-(6' '-malonyl-glucoside). M. oleifera leaves also contained 3-caffeoylquinic acid and 5-caffeoylquinic acid. Leaves of M. stenopetala contained quercetin 3-O-rhamnoglucoside (rutin) and 5-caffeoylquinic acid. Neither proanthocyanidins nor anthocyanins were detected in any of the tissues of either species.

Chromatography, High Pressure Liquid↗
PubMed2005

Pyrazole derivatives as photosynthetic electron transport inhibitors: new leads and structure-activity relationship.

Four series of new pyrazoles, namely, 5 4-carboxypyrazolo-3-tert-butylcarboxamide and 6 4-carboxypyrazolo-3-cyclopropylcarboxamide derivatives and 10 pyrazolo[3,4-d][1,3]thiazine-4-one and 9 pyrazolo[3,4-d][1,3]thiazine-4-thione derivatives, were synthesized and screened as potential inhibitors of photosynthetic electron transport. The structures were confirmed by 1H NMR, elemental, and IR analyses. Their biological activity was evaluated in vitro as the ability to interfere with the light-driven reduction of ferricyanide by isolated spinach chloroplasts. Only a few compounds exhibited excellent inhibitory properties in the micromolar range, comparable to those of commercial herbicides sharing the same target, such as diuron, lenacil, and hexazinone. Nevertheless, most of the remaining molecules exerted a remarkable inhibition in the millimolar range. Combined with previous results on 6 pyrazolo[1,5-a][1,3,5]triazine-2,4-dione and 4 pyrazolo[1,5-c][1,3,5]thiadiazine-2-one derivatives, these data allowed a comprehensive analysis of structure-activity relationship. Molecular modeling studies were undertaken to rationalize the structural determinants of activity in terms of shape, size, and molecular fields. Results suggested that the inhibitory potential of these compounds is associated mainly with their electrostatic properties.

Electron Transport↗
PubMed2005

Evolution of self-assembled silica-tetrapropylammonium nanoparticles at elevated temperatures.

The time evolution of silica nanoparticles in solutions of tetrapropylammonium (TPA) has been studied using a combination of small-angle scattering, conductivity, and pH measurements to provide the first comprehensive analysis of nanoparticle structural and compositional changes at elevated temperatures. We have found that silica-TPA nanoparticles subjected to hydrothermal treatment (70-90 degrees C) grow via an Ostwald ripening mechanism with growth rates that depend on both pH and temperature. Small-angle X-ray (SAXS) and neutron (SANS) scattering confirm that the core-shell structure of the particles, initially present at room temperature, is maintained during heating, but an evolution toward sphericity is evidenced especially at high values of pH. SAXS absolute intensity calculations were utilized to calculate the changes in nanoparticle composition and concentration over time. These changes along with the conductivity and pH measurements and SANS contrast matching studies indicate that, upon heating, TPA becomes embedded in the core of nanoparticles giving rise to more zeolitic-looking nanomaterials.

Journal Article↗
PubMed2005

Oriented crystal growth model explains the formation of titania nanotubes.

We discuss the formation mechanism of titania nanotubes synthesized by the hydrothermal method. On the basis of a comprehensive analysis of TEM, HRTEM, FT-Raman, and N(2) adsorption data, we point out some major shortcomings of the currently accepted trititanate sheet rollup mechanism. We suggest that a novel formation mechanism, oriented nanotube crystal growth from nanoloop seeds, can explain the experimental findings better than the ones proposed so far.

Journal Article↗
PubMed2006

Surface characterization of 1-butyl-3-methylimidazolium Br-, I-, PF6-, BF4-, (CF3SO2)2N-, SCN-, CH3SO3-, CH3SO4-, and (CN)2N- ionic liquids by sum frequency generation.

Sum frequency generation spectroscopy, SFG, was used for the surface characterization at the gas-liquid interface of the 1-butyl-3-methylimidazolium cation combined with the following anions: Br-, I-, PF6-, BF4-, (CF3SO2)2N- (imide), SCN-, CH3SO3- (MeSO3), CH3SO4- (MS), and (CN)2N- (DCN). The SFG spectra obtained for the different ionic liquids were similar independent of the anion selected; therefore, a comprehensive analysis for the surface characterization of the ionic liquids' cation was focused only on the PF6- and Br- anion combinations. For an accurate identification of the vibrational modes observed, FT-IR and Raman spectroscopy in combination with isotopic labeling with deuterium and polarized Raman spectroscopy was used. The cation orientation was determined by analysis of polarization-dependent SFG spectra. For a compound dried in a vacuum to < or = 2 x 10(-5) Torr, the cation appears to be oriented with the ring laying flat along the surface plane and the butyl chain projecting into the gas phase independent of the anion identity.

Journal Article↗
PubMed2006

Chemical reactivity indices for the complete series of chlorinated benzenes: solvent effect.

We present a comprehensive analysis to probe the effect of solvation on the reactivity of the complete series of chlorobenzenes through the conceptual density functional theory (DFT)-based global and local descriptors. We propose a multiphilic descriptor in this study to explore the nature of attack at a particular site in a molecule. It is defined as the difference between nucleophilic and electrophilic condensed philicity functions. This descriptor is capable of explaining both the nucleophilicity and electrophilicity of the given atomic sites in the molecule simultaneously. The predictive ability of this descriptor is tested on the complete series of chlorobenzenes in gas and solvent media. A structure-toxicity analysis of these entire sets of chlorobenzenes toward aquatic organisms demonstrates the importance of the electrophilicity index in the prediction of the reactivity/toxicity.

Algorithms↗
PubMed2005

Caucanolides A-F, unusual antiplasmodial constituents from a colombian collection of the gorgonian coral Pseudopterogorgia bipinnata.

Six new diterpenoids, caucanolides A-F (1-6), have been isolated from extracts of the gorgonian octocoral Pseudopterogorgia bipinnata collected near the Colombian Southwestern Caribbean Sea. The structures of 1-6 were elucidated by comprehensive analysis of spectroscopic data. The caucanolides showed in vitro antiplasmodial activity against the malaria parasite, Plasmodium falciparum. In addition to possessing structures based on novel carbon skeletons, one of these metabolites, caucanolide B (2), constitutes the only example from nature of a secondary metabolite possessing the N(1),N(1)-dimethyl-N(2)-acylformamidine functionality.

Animals↗
PubMed1999

Antifungal jujubogenin saponins from Colubrina retusa.

Antifungal assay-guided isolation of the 95% ethanol extract of the stems of Colubrina retusa yielded jujubogenin 3-O-alpha-L-arabinofuranosyl(1-->2)-[beta-D-glucopyranosyl (1-->3)]-alpha-L-arabinopyranoside (1), which showed modest growth-inhibitory effects against Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus (MICs, 50 microg/mL). In addition, two new minor saponins, jujubogenin 3-O-alpha-L-arabinofuranosyl(1-->2)-[2-O-(trans, cis)p-coumaroyl-beta-D-glucopyranosyl(1-->3)]-alpha-L-arabinopy ranosi de (2), and jujubogenin 3-O-(5-O-malonyl)-alpha-L-arabinofuranosyl (1-->2)-[beta-D-glucopyranosyl(1-->3)]-alpha-L-arabinopyranoside (3), were obtained. Saponin 2 was marginally active against only C. neoformans, with a MIC of 50 microg/mL, while 3 was inactive. NMR spectroscopy was used extensively for the structure determination of these compounds. The previously reported ambiguity of the NMR assignments of jujubogenin saponins for carbons -26 to -29 was clarified by a comprehensive analysis of the NMR spectra of 1.

Antifungal Agents↗
PubMed2006

Skeleton-rearranged pentacyclic diterpenoids possessing a cyclobutane ring from Euphorbia wallichii.

[structure: see text] Two novel rearranged trachylobane diterpenoids, designated as wallichanol A (2) and wallichanol B (3), consisting of an unprecedented pentacyclic skeleton named wallichane with a cyclobutane ring, and a new ent-trachylobane diterpenoid, 3-oxo-ent-trachyloban-17-oic acid (1), were isolated from the roots of Euphorbia wallichii. Their structures were elucidated by comprehensive analysis of 2D-NMR spectroscopic data, with the stereochemistry of 1 confirmed by X-ray crystallographic study. All of these compounds potently block osteoclastogenesis in vitro, suggesting a potential therapeutic application in prevention of osteoporosis.

Bone Resorption↗
PubMed2006

Molecular profiling of hepatocellular carcinoma in mice with a chronic deficiency of hepatic s-adenosylmethionine: relevance in human liver diseases.

S-adenosylmethionine arises as a central molecule in the preservation of liver homeostasis as a chronic hepatic deficiency results in spontaneous development of steatohepatitis and hepatocellular carcinoma. In the present work, we have attempted a comprehensive analysis of proteins associated with hepatocarcinogenesis in MAT1A knock out mice using a combination of two-dimensional electrophoresis and mass spectrometry, to then apply the resulting information to identify hallmarks of human HCC. Our results suggest the existence of individual-specific factors that might condition the development of preneoplastic lesions. Proteomic analysis allowed the identification of 151 differential proteins in MAT1A-/- mice tumors. Among all differential proteins, 27 changed in at least 50% of the analyzed tumors, and some of these alterations were already detected months before the development of HCC in the KO liver. The expression level of genes coding for 13 of these proteins was markedly decreased in human HCC. Interestingly, seven of these genes were also found to be down-regulated in a pretumoral condition such as cirrhosis, while depletion of only one marker was assessed in less severe liver disorders.

Adult↗
PubMed2006

Quantitative proteomic and genomic profiling reveals metastasis-related protein expression patterns in gastric cancer cells.

Gastric cancer is a leading cause of death worldwide, and patients have an overall 5-year survival rate of less than 10%. Using quantitative proteomic techniques together with microarray chips, we have established comprehensive proteome and transcriptome profiles of the metastatic gastric cancer TMC-1 cells and the noninvasive gastric cancer SC-M1 cell. Our qualitative protein profiling strategy offers the first comprehensive analysis of the gastric cancer cell proteome, identifying 926 and 909 proteins from SC-M1 and TMC-1 cells, respectively. Cleavable isotope-coded affinity tagging analysis allows quantitation of a total of 559 proteins (with a protein false-positive rate of <0.005), and 240 proteins were differentially expressed (>1.3-fold) between the SC-M1 and TMC-1 cells. We identified numerous proteins not previously associated with gastric cancer. Notably, a large subset of differentially expressed proteins was associated with tumor metastasis, including proteins functioning in cell-cell and cell-extracellular matrix (cell-ECM) adhesion, cell motility, proliferation, and tumor immunity. Gene expression profiling by DNA microarray revealed differential expression (of >2-fold) of about 1000 genes. The weak correlation observed between protein and mRNA profiles highlights the important complementarities of DNA microarray and proteomics approaches. These comparative data enabled us to map the disease-perturbed cell-cell and cell-ECM adhesion and Rho GTPase-mediated cytoskeletal pathways. Further validation of a subset of genes suggests the potential use of vimentin and galectin 1 as markers for metastasis. We demonstrate that combining proteomic and genomic approaches not only provides a rapid, robust, and sensitive platform to elucidate the molecular mechanisms underlying gastric cancer metastasis but also may identify candidate diagnostic markers and therapeutic targets.

Biomarkers, Tumor↗
PubMed2006

Identification and characterization of genes susceptible to transcriptional cross-talk between the hypoxia and dioxin signaling cascades.

The aryl hydrocarbon receptor (AHR) and hypoxia inducible factors (HIFs) are transcription factors that control the adaptive response to toxicants such as dioxins and decreases in available oxygen, respectively. The AHR and HIFs utilize the same heterodimeric partner, the aryl hydrocarbon nuclear translocator (ARNT) for proper function. This requirement raises the possibility that cross-talk exists between these critical signaling systems. Single gene and reporter assays have yielded conflicting results regarding the nature of the competition for ARNT. Therefore, to determine the extent of cross-talk between the AHR and HIFs, a comprehensive analysis was performed using global gene expression analysis. The results identified 767 and 430 transcripts that are sensitive to cobalt chloride and 2,3,7,8-tetrachlorodibenzo-rho-dioxin (TCDD) stimulation, respectively, with 308 and 176, respectively, exhibiting sensitivity to cross-talk. The overlap between these two sets consists of 33 unique transcripts, including the classic target genes CYP1A1, carbonic anhydrase IX, and those involved in lipid metabolism and coagulation. Computational analysis of the regulatory region of these genes identified complex relationships between HIFs, AHR, and their respective response elements as well as other DNA motifs, including the SRF, Sp-1, NF-kB, and AP-2 binding sites. These results suggest that HIF-AHR cross-talk is limited to genes with regulatory regions that contain specific motifs and architectures.

Base Sequence↗
PubMed1999

On the phylogenetic relationships among tetraphyllidean, lecanicephalidean and diphyllidean tapeworm genera.

This study had two main objectives: (1) to construct an extensive, explicit list of characters and character states that might serve as a starting point, and perhaps even a model, for the compilation of a more complete list of characters for all cestode taxa; and (2) to use this character list to generate a hypothesis of the phylogenetic relationships among species representing most of the tetraphyllidean, lecanicephalidean and diphyllidean genera. Specimens of one species in each of 48 genera of tetraphyllideans, eight genera of lecanicephalideans, the three genera of diphyllideans, two genera of proteocephalideans and two genera of trypanorhynchs, were examined as whole-mounts and sections, with light and scanning electron microscopy. A list of 120 morphological characters was compiled. Four phylogenetic analyses were conducted using PAUP* and/or NONA. The first was a comprehensive analysis with the 56 tetraphyllidean and lecanicephalidean species as ingroups and the remaining seven species as outgroups. The second was an analysis of the three diphyllidean species as ingroups and the two proteocephalidean and the two trypanorhynch species as outgroups. The third was an analysis of the eight lecanicephalidean species and the "tetraphyllideans" Echeneibothrium sp. and Pseudanthobothrium n. sp. as ingroups and an outgroup consisting of the seven species used as outgroups in the first analysis. In the fourth analysis, the ingroup consisted of the 14 hooked tetraphyllideans (onchobothriids), and the outgroup consisted of the seven species used as outgroups in the first analysis. The results of these analyses support the following phylogenetic hypotheses: The diphyllideans are monophyletic and Echinobothrium n. sp. and Macrobothridium sp. are more closely related to one another than either is to Ditrachybothridium macrocephalum. The tetraphyllideans, lecanicephalideans and proteocephalideans are more closely related to each other than they are to the diphyllideans or the trypanorhynchs. The ordinal status of the lecanicephalideans is dubious. The lecanicephalidean species are more closely related to some of the tetraphyllidean taxa than these tetraphyllidean taxa are to the remainder of the tetraphyllidean taxa. The proteocephalideans appear to belong within the tetraphyllidean clade. The "tetraphyllidean" species Echeneibothrium sp. and Pseudanthobothrium n. sp. are members of the lecanicephalidean clade. The position of "Discobothrium" n. sp. within the lecanicephalideans is dubious. Within the tetraphyllideans, the non-acetabulate species Litobothrium daileyi, Disculiceps galapagoensis and Cathetocephalus sp. are the most basal members of the group. The family Onchobothriidae is monophyletic, as it is currently defined. Within the onchobothriids, the uniloculate species are basal to the multiloculate species; the species with unipronged hooks are basal to the species with multipronged hooks. Although relationships among the phyllobothriids, as they are currently defined, remain poorly resolved, the family Phyllobothriidae is not monophyletic. These results suggest that some aspects of the classification of the lecanicephalidean and tetraphyllidean taxa require revision. However, such revision should be based on further analyses including a broader representation of the genera and species in these groups.

Animals↗
PubMed2001

Phylogeny of the Acanthocephala based on morphological characters.

Only four previous studies of relationships among acanthocephalans have included cladistic analyses, and knowledge of the phylogeny of the group has not kept pace with that of other taxa. The purpose of this study is to provide a more comprehensive analysis of the phylogenetic relationships among members of the phylum Acanthocephala using morphological characters. The most appropriate outgroups are those that share a common early cell-cleavage pattern (polar placement of centrioles), such as the Rotifera, rather than the Priapulida (meridional placement of centrioles) to provide character polarity based on common ancestry rather than a general similarity likely due to convergence of body shapes. The phylogeny of 22 species of the Acanthocephala was evaluated based on 138 binary and multistate characters derived from comparative morphological and ontogenetic studies. Three assumptions of cement gland structure were tested: (i) the plesiomorphic type of cement glands in the Rotifera, as the sister group, is undetermined; (ii) non-syncytial cement glands are plesiomorphic; and (iii) syncytial cement glands are plesiomorphic. The results were used to test an early move of Tegorhynchus pectinarius to Koronacantha and to evaluate the relationship between Tegorhynchus and Illiosentis. Analysis of the data-set for each of these assumptions of cement gland structure produced the same single most parsimonious tree topology. Using Assumptions i and ii for the cement glands, the trees were the same length (length = 404 steps, CI = 0.545, CIX = 0.517, HI = 0.455, HIX = 0.483, RI = 0.670, RC = 0.365). Using Assumption iii, the tree was three steps longer (length = 408 steps, CI = 0.539, CIX = 0.512, HI = 0.461, HIX = 0.488, RI = 0.665, RC = 0.359). The tree indicates that the Palaeacanthocephala and Eoacanthocephala both are monophyletic and are sister taxa. The members of the Archiacanthocephala are basal to the other two clades, but do not themselves form a clade. The results provide strong support for the Palaeacanthocephala and the Eoacanthocephala and the hypothesis that the Eoacanthocephala is the most primitive group is not supported. Little support for the Archiacanthocephala as a monophyletic group was provided by the analysis. Support is provided for the recognition of Tegorhynchus and Illiosentis as distinct taxa, as well as the transfer of T. pectinarius to Koronacantha.

Acanthocephala↗
PubMed2001

Characterisation of strains of enteroaggregative Escherichia coli isolated during the infectious intestinal disease study in England.

Strains of Escherichia coli, hybridising with a DNA probe for enteroaggregative E. coli (EAggEC), were isolated from patients with infectious intestinal disease (IID) or gastro-enteritis, and healthy controls during the study of IID in England. Of 3506 cases presenting with an IID, 160 (4.6%) had faecal EAggEC as compared with 46 (1.7%) of 2772 healthy controls, 53% of EAggEC isolated from each of the 'case' and the 'control' groups adhered in a 'stacked-brick' formation. Strains from cases and controls belonged to over 39 and 14 different serogroups respectively, and approximately half of the strains isolated did not react with antisera in the current somatic antigen serotyping scheme. Forty-nine cases with EAggEC (31%) had a known history of foreign travel. Over 50% of strains isolated from cases and controls were resistant to one or more of eight antimicrobials, and antimicrobial resistance was not statistically significantly more common among cases with a known history of foreign travel (p = 0.57). These data form part of the largest investigation carried out on these organisms in the UK to date and provide the most comprehensive analysis of strains of EAggEC isolated from the general population of England.

Case-Control Studies↗