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PubMed2004

Assessment of microbial populations in methyl ethyl ketone degrading biofilters by denaturing gradient gel electrophoresis.

Denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction-amplified genes coding for 16S rRNA was used to assess differences in bacterial community structure as a function of spatial location along the height of two biofilters used to treat a model waste gas stream containing methyl ethyl ketone (MEK). One of the laboratory-scale biofilters was operated as a conventional continuous-flow biofilter (CFB) and the other was operated as a sequencing batch biofilter (SBB). Both biofilters, inoculated with an identical starting culture and operated over a period lasting more than 300 days, received the same influent MEK concentration and same mass of MEK on a daily basis. The systems differed, however, in terms of the fraction of time during which contaminated air was supplied and the overall operating strategy employed. DGGE analysis indicated that microbial community structures differed as a function of height in each of the biofilters. The DGGE banding patterns also differed between the two biofilters, suggesting that operating strategies imposed on the biofilters imparted a sufficiently large selective pressure to influence microbial community structures. This may explain, in part, the superior performance of the SBB over the CFB during model transient loading conditions, and it may open new possibilities for purposely manipulating the microbial populations in biofilters treating gas-phase contaminants in a manner that leads to more favorable treatment performance.

Air Conditioning↗
PubMed2002

Malakoplakia of the pancreas with diffuse lymph-node involvement.

We report a case of malakoplakia involving the pancreas in a 74-year-old man with associated regional lymphoadenopathy. Histological examination of both pancreas and lymph nodes revealed a diffuse histiocytic infiltrate containing numerous Michaelis-Gutmann bodies. Electron microscopy supported the diagnosis of malakoplakia and showed bacterial-like structures. Differential diagnosis includes myofibroblastic inflammatory tumor and histiocytic neoplasms. Lymph-node involvement during malakoplakia is extremely rare and it has never been documented microscopically. Lymphohematogenous spread of bacteria may be the cause of the nodal involvement, which, however, does not appear to influence the clinical course of the disease.

Aged↗
PubMed2002

Bioremediation of oil by marine microbial mats.

Cyanobacterial mats developing in oil-contaminated sabkhas along the African coasts of the Gulf of Suez and in the pristine Solar Lake, Sinai, were collected for laboratory studies. Samples of both mats showed efficient degradation of crude oil in the light, followed by development of an intense bloom of Phormidium spp. and Oscillatoria spp. Isolated cyanobacterial strains, however, did not degrade crude oil in axenic cultures. Strains of sulfate-reducing bacteria and aerobic heterotrophs were capable of degrading model compounds of aliphatic and aromatic hydrocarbons. Results indicate that degradation of oil was done primarily by aerobic heterotrophic bacteria. The oxygenic photosynthesis of oil-insensitive cyanobacteria supplied the molecular oxygen for the efficient aerobic metabolism of organisms, such as Marinobacter sp. The diurnal shifts in environmental conditions at the mat surface, from highly oxic conditions in the light to anaerobic sulfide-rich habitat in the dark, may allow the combined aerobic and anaerobic degradation of crude oil at the mat surface. Hence, coastal cyanobacterial mats may be used for the degradation of coastline oil spills. Oxygen microelectrodes detected a significant inhibition of photosynthetic activity subsequent to oil addition. This prevailed for a few hours and then rapidly recovered. In addition, shifts in bacterial community structure following exposure to oil were determined by denaturing gradient gel electrophoresis of PCR-amplified fractions of 16S rRNA from eubacteria, cyanobacteria and sulfate-reducing bacteria. Since the mats used for the present study were obtained from oil-contaminated environments, they were believed to be preequilibrated for petroleum remediation. The mesocosm system at Eilat provided a unique opportunity to study petroleum degradation by mats formed under different salinities (up to 21%). These mats, dominated by cyanobacteria, can serve as close analogues to the sabkhas contaminated during the Gulf War in Kuwait and Saudi Arabia.

Biodegradation, Environmental↗
PubMed1979

Soft contact lenses from patients with giant papillary conjunctivitis.

We used scanning electron microscopy to study the surfaces of five coated soft contact lenses from subjects with giant papillary conjunctivitis. Findings were compared to the surfaces of five coated lenses from normal, asymptomatic wearers and five new, nerver-worn lenses. Lenses were from various manufacturers. All worn contact lenses differed strikingly from new, never-worn lenses. The anterior surface of worn lenses was covered with apparently adherent deposits. In only a few areas was the surface similar to new, never-worn lenses. Thick coatings on lenses from patients with giant papillary conjunctivitis and asymptomatic wearers were similar. High magnification of the coatings revealed a trabeculated morphology. Also seen was debris that resembled mucus-like material in both strand and particulate forms. On some lenses bacterial-shaped structures were scattered randomly over the surface. Smooth structures resembling cells were also seen. The posterior lens surface of all worn lenses was smoother than the anterior lens surface. The findings support our idea that the capacity to develop giant papillary conjunctivitis is influenced by individual differences more than by differences in lens deposits.

Adult↗
PubMed1978

Redox potentials of the photosynthetic bacterial cytochromes c2 and the structural bases for variability.

The cytochromes c2 of the Rhodospirillaceae show a much greater variation in redox potential and its pH dependence than the mitochondrial cytochromes c that have been studied. It is proposed that the range of redox potential for cytochromes c2 functioning as the immediate electron donor to photo-oxidised bacteriochlorophyll may be 345-395 mV at pH 5. Closely related cytochromes c2 with different redox potentials show patterns of amino acid substitution which are consistent with changes in hydrophobicity near the haem being at least a partial determinant of redox potential. More distantly related cytochromes are difficult to compare because of the large number of amino acid substitutions and the probability that there are subtle changes in overall peptide chain folding. The redox potential versus pH curves can be analysed in terms of either one ionisation in the oxidised form or two in the oxidised form and one in the reduced. The pK in the oxidised form at higher pH values can be correlated with the pK for the disappearance or shift of the near infrared absorption band located near 695 nm. The structural bases of these ionisations are not known but the possible involvement of the haem propionate residues is discussed.

Amino Acids↗
PubMed1991

Molecular cloning and characterization of the promoter region of the mouse regulatory subunit RII beta of type II cAMP-dependent protein kinase.

The promoter and exon 1 of the regulatory subunit (RII beta) of type II cAMP-dependent protein kinase were isolated from a mouse genomic library. The 5'-flanking DNA lacked TATA and CAAT sites but contained GC rich regions typically found in constitutively expressed house keeping genes. Fusion gene constructs, containing RII beta 5'-flanking sequences and the bacterial CAT structural gene, were transfected into NB2a neuroblastoma cells and CHO cells. The NB2a cells expressed high levels of CAT activity. CHO cells expressed CAT activity at 5% of the level seen in the NB2a cells. Transfection of deletion constructs into both cell lines was used to define the core promoter and enhancer elements. The core promoter was situated between bp -291/-121. An enhancer element was located between bp -1426/-1018.

Amino Acid Sequence↗
PubMed1994

Induced circular dichroism study of the aqueous solution complexation of cello-oligosaccharides and related polysaccharides with aromatic dyes.

Acetobacter xylinum, grown in the presence of low levels of the water-soluble dye Calcofluor White ST produces a pellicle of cellulose that has no detectable crystallinity. Biological factors of this sort are probably more important than physical factors in controlling the higher order structures of celluloses. Circular dichroism (CD) is induced by complexes that are formed by specific interactions between chiral oligosaccharides and dye molecules. Using CD, equilibrium constants were measured for the association reactions between various dyes with a series of cello-oligosaccharides (n = 2-6), methylcellulose, hydroxypropylcellulose (HPC), amylose, cyclomalto-oligosaccharides (cyclodextrins), and the linear malto-oligosaccharides (n = 3-7). Possible structural features of the complexes are discussed. Dyes that are capable of binding to the higher cello-oligomers in aqueous solutions are the same dyes that modify the solid structure of bacterial cellulose. An analogy between the binding of water-soluble dyes to cello-oligosaccharides and the binding of the cellulose-degrading enzyme, cellobiohydrolase I, to cellulose is discussed.

Acetobacter↗
PubMed1989

Synthesis of paf-acether from exogenous precursors by the prokaryote Escherichia coli.

Paf-acether (paf) is a potent mediator of inflammatory diseases and septic shock. Using normal-phase HPLC, a paf-like activity was found in culture supernatants from E. coli. Prokaryotic paf exhibited the same biological and physico-chemical properties as eukaryotic cells and synthetic paf. Further, reverse-phase HPLC indicates that paf generated by bacteria is predominantly of the hexadecyl and octadecyl species. When cultures were supplemented with lyso-paf, a dramatic increase in paf production was observed. The purity and molecular structure of bacterial paf were further characterized by mass spectral analysis. These results could be of importance considering the pathogenetic role of enterobacteria. Further, it appears that the competence to form and release paf is an early phylogenetic development.

Animals↗
PubMed1993

The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate.

The family of lipases (triacylglycerol-acyl-hydrolases EC 3.1.1.3) constitutes an interesting class of enzymes because of their ability to interact with lipid-water interfaces, their wide range of substrate specificities, and their potential industrial applications. Here we report the first crystal structure of a bacterial lipase, from Pseudomonas glumae. The structure is formed from three domains, the largest of which contains a subset of the alpha/beta hydrolase fold and a calcium site. Asp263, the acidic residue in the catalytic triad, has previously been mutated into an alanine with only a modest reduction in activity.

Amino Acid Sequence↗
PubMed1985

A non-immune interaction between the light chain of human immunoglobulin and a surface component of a Peptococcus magnus strain.

The immunoglobulin-binding capacity of a Peptococcus magnus strain was studied in a sensitive binding assay using purified human immunoglobulin preparations. The P. magnus strain 312 was capable of binding 48% of polyclonal IgG. Twenty-four of 40 purified myeloma proteins (60%) representing immunoglobulin classes A, G and M showed definite reactivity with an uptake level ranging from 45 to 90%. The remaining 16 monoclonal proteins were non-reactive, binding less than 15%. One myeloma protein with antistaphylolysin and two with antistreptolysin O specificity, i.e. monoclonal proteins with defined antigen specificity, were highly reactive. Binding capacity was observed in all four IgG subclasses and in Ig classes A and M. Twenty-three of 27 myeloma proteins of kappa type were reactive but only one of 13 myeloma proteins of lambda type interacted with the P. magnus strain. Isotope-labelled Fab gamma, F(ab')2 gamma and F(ab')2 alpha fragments were effectively bound by the strain. IgG Fc fragments were completely non-reactive. Isolated light immunoglobulin chains inhibited in a dose-dependent way the uptake of intact IgG to bacteria. Purified heavy chains were non-inhibitory. Isotope-labelled antistaphylolysin IgG F(ab')2 fragments preincubated with staphylolysin were as reactive as free antibody fragments, suggesting that the bacterial binding structure is located outside the antibody-combining site. The immunoglobulin reactivity of P. magnus was not affected by heating the bacteria to 80 degrees C for 5 min nor by treatment with trypsin or sodium metaperiodate. Digestion of 2 X 10(9) organisms with 100 micrograms of pepsin and papain reduced the binding by 58 and 90%, respectively. These data indicate that the binding of immunoglobulin to P. magnus is a non-immune reactivity mediated by a heat-stable surface protein interacting with specific sites on the light chain of the immunoglobulin molecule.

Antibodies, Monoclonal↗
PubMed1981

Structure and architecture of the bacterial virus fd. An infrared linear dichroism study.

Oriented gels of intact bacterial virus fd have been invetigated by infrared linear dichroism. Infrared absorption band maxima and dichroism indicate an alpha-helix content of the major coat protein of 95-100%. The alpha-helical rods of the coat protein are aligned parallel to the long axis of the virion with an inclination roughly estimated to approximately 37 degree. The presence of DNA infrared bands at 968, 885, 830 and 799 cm-1, the absence of a band at 860 cm-1 and the perpendicular polarization of the symmetric PO-2 stretching vibration at 1085 cm-1 are all indicative of a B-type backbone conformation in the single-stranded DNA. We find no evidence for specific interaction between aromatic side groups (phenylalanine, tyrosine) and the DNA bases. Our results independently confirm most features of the model of Marvin and co-workers [2,15 ] based on low-resolution X-ray diffraction studies. However, our findings contradict their suggestion of an A-type DNA in the bacterial virus fd. Two results are consistent with rigid and stable order in the virus. First, over a 4-day period, 65% of the peptide hydrogens remain unexchanged with deuterium. Second, changes in the relative humidity of the sample do not result in any shifts in the DNA spectrum that are characteristic of free DNA.

Coliphages↗
PubMedDate not supplied

Overproduction of a gastrointestinal hormone, secretin, in Escherichia coli cells and its chemical characterization.

A cloned synthetic DNA fragment coding for 27-desamidosecretin (DAS), which differs from natural porcine secretin by the lack of the amide group at the carboxyl-terminal valine residue, was fused to the beta-galactosidase gene (lacZ) at the EcoRI site near the 3'-terminus of the gene. The fusion gene was efficiently expressed in Escherichia coli, yielding 1.15 X 10(6) fused-protein molecules per cell. After the treatment of the fused protein with cyanogen bromide, DAS was purified by a combination of ion-exchange column chromatography and reverse-phase high-performance liquid chromatography (HPLC). The structure of bacterial DAS was confirmed by tryptic mapping and amino acid composition analyses. The bacterial DAS was not amidated at its carboxyl-terminal valine residue. Nevertheless, it stimulated pancreatic secretion in rats as does authentic porcine secretin, indicating that the carboxyl-terminal amide is not essential to secretin activity.

Amino Acid Sequence↗
PubMed1992

Histidine ammonia-lyase from Streptomyces griseus.

Histidine ammonia-lyase (histidase; HutH) has been purified to homogeneity from Streptomyces griseus and the N-terminal amino acid (aa) sequence used to clone the histidase-encoding structural gene, hutH. The purified enzyme shows typical saturation kinetics and is inhibited competitively by D-histidine and histidinol phosphate. High concentrations of K.cyanide inactivate HutH unless the enzyme is protected by the substrate or histidinol phosphate. On the basis of the nucleotide sequence, the hutH structural gene would encode a protein of 53 kDa with an N terminus identical to that determined for the purified enzyme. Immediately upstream from hutH is a region that strongly resembles a class of Streptomyces promoters active during vegetative growth; however, there is no obvious ribosome-binding site adjacent to the hutH translation start codon. The deduced aa sequence of an upstream partial open reading frame shows no similarity with other proteins, including HutP of Bacillus subtilis and HutU of Pseudomonas putida. Promoter-probe analysis indicates that promoter activity maps within the DNA surrounding the hutH start codon. Pairwise comparisons of the primary structures of bacterial and mammalian histidases, together with the unique kinetic properties and gene organization, suggest that streptomycete histidase may represent a distinct family of histidases.

Amino Acid Sequence↗
PubMed2005

A synthesized cationic tetradecapeptide from hornet venom kills bacteria and neutralizes lipopolysaccharide in vivo and in vitro.

Sepsis is a complex clinical syndrome that results from a harmful host response to infection, in which foreign bacteria and lipopolysaccharide (LPS) are potent activators of different immune cells, including monocytes and macrophages. To date, there are currently few effective adjuvant therapies in clinical use except activated protein C focusing on the coagulation system. Mastoparans (MPs) are wasp venom cationic amphiphilic tetradecapeptides; these are capable of modulating various cellular activities, including stimulation of GTP-binding protein, phospholipase C and can bind to a phospholipid bilayer. Masroparan-1 (MP-1, INLKAIAALAKKLL-NH2), a tetradecapeptide toxin isolated from hornet venom, was synthesized chemically. In this study, Escherichia coli 25922 (E. coli 25922) and LPS were used to induce sepsis in an animal model. We found that MP-1 treatment at 3 mg/kg protected mice from otherwise lethal bacteria and LPS challenges. MP-1 has antibacterial capabilities against Gram-negative and Gram-positive bacteria. Its antibacterial action against E. coli may result from the destruction of bacterial membrane structures. In addition, treatment of murine peritoneal macrophages with MP-1 potently inhibited the respiratory burst. This effect maybe related to an inhibition of NADPH oxidase in the membrane. Furthermore, MP-1, bound with high-affinity to LPS and lipid A with dissociation equilibrium constants of 484 and 456 nM, respectively, and neutralized LPS in a dose-dependent manner. MP-1 also significantly reduced the expression of TLR4, TNF-alpha and IL-6 mRNA and the release of cytokines in LPS-stimulated murine peritoneal macrophages. Our results shows that the MP-1-mediated protection of mice from lethal challenge by live bacteria and LPS was associated with its bactericidal action and inhibition of inflammatory responses by macrophages to both bacteria and LPS (the release of cytokines and reactive oxygen species).

Animals↗
PubMed2004

Effects of decreased resource availability, protozoan grazing and viral impact on a structure of bacterioplankton assemblage in a canyon-shaped reservoir.

We conducted a transplant experiment to elucidate the effects of different levels of grazing pressure, nutrient availability, especially phosphorus, and the impact of viruses on the changes in the structure of bacterioplankton assemblage in a meso-eutrophic reservoir. A sample taken from the nutrient-rich inflow part of the reservoir was size-fractionated and incubated in dialysis bags in both inflow and dam area. The structure of bacterial assemblage was examined by fluorescence in situ hybridization using oligonucleotide probes with different levels of specificity. In terms of the relative proportions of different bacterial groups, we found very few significant changes in the bacterioplankton composition after transplanting the treatments to the nutrient-poor dam area. However, we observed marked shifts in morphology and biomass towards the development of filaments, flocs and "vibrio-like" morphotypes of selected probe-defined groups of bacteria induced by increased grazing pressure. Despite the very high abundances of viruses in all the treatments, their effects on bacterioplankton were rather negligible.

Animals↗