Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.

Extraction and radioimmunoassay quantitation of neuropeptide Y (NPY) and vasoactive intestinal polypeptide (VIP) from human dental pulp tissue

The measurement of neuropeptides in complex biological tissue samples requires efficient and appropriate extraction methods so that immunoreactivity is retained for subsequent radioimmunoassay detection. Since neuropeptides differ in their molecular mass, charge and hydrophobicity, no single method will suffice for the optimal extraction of various neuropeptides. In this study, dental pulp tissue was obtained from 30 human non-carious teeth. Of the three different neuropeptide extraction methods employed, boiling in acetic acid in the presence of protease inhibitors yielded the highest levels of neuropeptide Y (NPY) and vasoactive intestinal polypeptide (VIP). High pressure liquid chromatography (HPLC) analysis of dental pulp tissue verified the authenticity of the neuropeptides extracted. © 2003 Elsevier Science Ltd. All rights reserved.

Neuropeptide YY1 receptor in human dental pulp cells of noncarious and carious teeth

Aim To determine the distribution of the NPY Y1 receptor in carious and noncarious human dental pulp tissue using immunohistochemistry. A subsidiary aim was to confirm the presence of the NPY Y1 protein product in membrane fractions of dental pulp tissue from carious and noncarious teeth using western blotting. Methodology Twenty two dental pulp samples were collected from carious and noncarious extracted teeth. Ten samples were processed for immunohistochemistry using a specific antibody to the NPY Y1 receptor. Twelve samples were used to obtain membrane extracts which were electrophoresed, blotted onto nitrocellulose and probed with NPY Y1 receptor antibody. Kruskal-Wallis one-way analysis of variance was employed to test for overall statistical differences between NPY Y1 levels in noncarious, moderately carious and grossly carious teeth. Results Neuropeptide Y Y1 receptor immunoreactivity was detected on the walls of blood vessels in pulp tissue from noncarious teeth. In carious teeth NPY Y1 immunoreactvity was observed on nerve fibres, blood vessels and inflammatory cells. Western blotting indicated the presence and confirmed the variability of NPY Y1 receptor protein expression in solubilised membrane preparations of human dental pulp tissue from carious and noncarious teeth. Conclusions Neuropeptide Y Y1 is expressed in human dental pulp tissue with evidence of increased expression in carious compared with noncarious teeth, suggesting a role for NPY Y1 in modulation of caries induced pulpal inflammation. © 2008 International Endodontic Journal.

A comparative study of biopolymers and alum in the separation and recovery of pulp fibres from paper mill effluent by flocculation

Recovery of cellulose fibres from paper mill effluent has been studied using common polysaccharides or biopolymers such as Guar gum, Xanthan gum and Locust bean gum as flocculent. Guar gum is commonly used in sizing paper and routinely used in paper making. The results have been compared with the performance of alum, which is a common coagulant and a key ingredient of the paper industry. Guar gum recovered about 3.86 mg/L of fibre and was most effective among the biopolymers. Settling velocity distribution curves demonstrated that Guar gum was able to settle the fibres faster than the other biopolymers; however, alum displayed the highest particle removal rate than all the biopolymers at any of the settling velocities. Alum, Guar gum, Xanthan gum and Locust bean gum removed 97.46%, 94.68%, 92.39% and 92.46% turbidity of raw effluent at a settling velocity of 0.5 cm/min, respectively. The conditions for obtaining the lowest sludge volume index such as pH, dose and mixing speed were optimised for guar gum which was the most effective among the biopolymers. Response surface methodology was used to design all experiments, and an optimum operational setting was proposed. The test results indicate similar performance of alum and Guar gum in terms of floc settling velocities and sludge volume index. Since Guar gum is a plant derived natural substance, it is environmentally benign and offers a green treatment option to the paper mills for pulp recycling.

Effect of the crown design and interface lute parameters on the stress-state of a machined crown-tooth system: A finite element analysis

The effect of preparation design and the physical properties of the interface lute on the restored machined ceramic crown-tooth complex are poorly understood. The aim of this work was to determine, by means of three-dimensional finite element analysis (3D FEA) the effect of the tooth preparation design and the elastic modulus of the cement on the stress state of the cemented machined ceramic crown-tooth complex. The three-dimensional structure of human premolar teeth, restored with adhesively cemented machined ceramic crowns, was digitized with a micro-CT scanner. An accurate, high resolution, digital replica model of a restored tooth was created. Two preparation designs, with different occlusal morphologies, were modeled with cements of 3 different elastic moduli. Interactive medical image processing software (mimics and professional CAD modeling software) was used to create sophisticated digital models that included the supporting structures; periodontal ligament and alveolar bone. The generated models were imported into an FEA software program (hypermesh version 10.0, Altair Engineering Inc.) with all degrees of freedom constrained at the outer surface of the supporting cortical bone of the crown-tooth complex. Five different elastic moduli values were given to the adhesive cement interface 1.8 GPa, 4 GPa, 8 GPa, 18.3 GPa and 40 GPa; the four lower values are representative of currently used cementing lutes and 40 GPa is set as an extreme high value. The stress distribution under simulated applied loads was determined. The preparation design demonstrated an effect on the stress state of the restored tooth system. The cement elastic modulus affected the stress state in the cement and dentin structures but not in the crown, the pulp, the periodontal ligament or the cancellous and cortical bone. The results of this study suggest that both the choice of the preparation design and the cement elastic modulus can affect the stress state within the restored crown-tooth complex.

Environmental impact assessment: looking at sediments in Nootka Sound for traces of pulp mill effluent

Senior thesis written for Oceanography 445

Electrodialytic recovery of phosphorus and organic contaminants removal from sewage sludge

Phosphorus is a macronutrient essential to life which comes from phosphate rock, a non-renewable resource. Sewage sludge from wastewater treatment plants (WWTP) is a secondary resource rich in phosphorus that can be valorized. However, organic compounds are detected in sewage sludge, due to its non-polar and hydrophobic character, being considered an environmental risk. The present dissertation aims to study the efficiency of the electrodialytic process (ED) when applied to sewage sludge aiming phosphorus recovery and organic contaminants removal. Four organic compounds were analyzed: 17α-ethynylestradiol (EE2), bisphenol A (BPA), caffeine (Caf) and oxybenzone (MBPh). The experiments took place in an ED cell with two compartments and an anion exchange membrane, with the sludge in the cathode compartment. The experiments were carried out for three days with spiked sewage sludge (six assays). One control experiment was done without current, three experiments were carried out applying a constant current of 50, 75, and 100 mA and two experiments were carried out applying sequential currents: 50 mA, 75 mA and 100 mA and the opposite (100-75-50 mA). A qualitative and quantitative analysis of microorganisms existing in the samples was also done. At the end, the pH increased in the sewage sludge favoring phosphorus recovery. In terms of phosphorus, the highest recovery was achieved in the experiment run with 100 mA, where 70.3±2.0% of total phosphorus was recovered in the electrolyte. Generally, compounds degradation was favored by the current. Caf and MBPh achieved degradation percentages of 96.2±0.2% and 84.8±1.3%, respectively, in 100 mA assay. EE2 (83.1±1.7%) and BPA (91.8±4.6%) degradations were favored by 50 mA current. A total of 35 taxa from four different groups were identified, totalizing between 81,600-273,000 individuals per gram of initial sludges. After ED, microbial community population decreased between 47-98%. Arcella gibbosa represented 61% of the total observed organisms and revealed to be more tolerant to medium changes.

Bioremediation of petroleum sludge through Phytoremediation.Land farming and Microbial enhanced oil separation

The objective of this research is to study the feasibility of bioremediating the oily sludge from a refinery site. Three different methods of waste treatment were tried i.e. phytoremediation, land farming and microbial enhanced oil separation in laboratory scale treatment systems. A multiprocess approach by combination of phytoremediation, biostimulation and microbial enhanced oil separation is also presented. The methods of analysis, experimental procedure, and results are incorporated into five chapters of this thesis entitled "Bioremediation of petroleum sludge through phytoremediation, land farming and microbial enhanced oil separation.

Studies on pulp propogation in single mode optical fibres

Studies on pulse propagation in single mode optical fibers have attracted interest from a wide area of science and technology as they have laid down the foundation for an in-depth understanding of the underlying physical principles, especially in the field of optical telecommunications. The foremost among them is discovery of the optical soliton which is considered to be one of the most significant events of the twentieth century owing to its fantastic ability to propagate undistorted over long distances and to remain unaflected after collision with each other. To exploit the important propertia of optical solitons, innovative mathematical models which take into account proper physical properties of the single mode optical fibers demand special attention. This thesis contains a theoretical analysis of the studies on soliton pulse propagation in single mode optical fibers.

Influence of dissolved organic matter on the solubility of heavy metals in sewage-sludge-amended soils

Sewage-sludge-amended soils generally contain elevated levels of organic matter and heavy metals compared to control soils. Because organic matter is known to complex with heavy metals, the solubility behavior of the organic matter in such soils may exert a significant influence on the solubility of the metals. Little is known about such a process. Using batch experiments in which the solubility of organic matter in a heavily sludge-amended soil was artificially manipulated, we show that the solubilities of the heavy metals copper (Cu), nickel (Ni), and lead (Pb) show a strong positive relationship to the solubility of organic matter, particularly at high pH. The results suggest that under field conditions, spatiotemporal variations in the solid-solution partitioning of organic matter may have a bearing on the environmental significance (mobility and bioavailability) of these heavy metals.

Multivariate analysis of phenol mineralisation by combined hydrodynamic cavitation and heterogeneous advanced Fenton processing

Phenolic compounds in wastewaters are difficult to treat using the conventional biological techniques such as activated sludge processes because of their bio-toxic and recalcitrant properties and the high volumes released from various chemical, pharmaceutical and other industries. In the current work, a modified heterogeneous advanced Fenton process (AFP) is presented as a novel methodology for the treatment of phenolic wastewater. The modified AFP, which is a combination of hydrodynamic cavitation generated using a liquid whistle reactor and the AFP is a promising technology for wastewaters containing high organic content. The presence of hydrodynamic cavitation in the treatment scheme intensifies the Fenton process by generation of additional free radicals. Also, the turbulence produced during the hydrodynamic cavitation process increases the mass transfer rates as well as providing better contact between the pseudo-catalyst surfaces and the reactants. A multivariate design of experiments has been used to ascertain the influence of hydrogen peroxide dosage and iron catalyst loadings on the oxidation performance of the modified AFP. High er TOC removal rates were achieved with increased concentrations of hydrogen peroxide. In contrast, the effect of catalyst loadings was less important on the TOC removal rate under conditions used in this work although there is an optimum value of this parameter. The concentration of iron species in the reaction solution was measured at 105 min and its relationship with the catalyst loadings and hydrogen peroxide level is presented.

Differences in glutamic acid and 5'-ribonucleotide contents between flesh and pulp of tomatoes and the relationship with umami taste

A difference in taste characteristics between the outer flesh and the inner pulp of tomatoes has been observed; in particular the pulp, which contains the seeds, had more umami taste. Analysis of the free amino acids and 5 '-ribonucleotides in the different parts of 13 varieties of tomatoes showed that in all cases the pulp contained higher levels of glutamic acid, 5 '-adenosine monophosphate (AMP), 5 '-guanosine monophosphate, 5 '-uridine monophosphate, and 5 '-cytidine monophosphate. The mean concentration of glutamic acid in the flesh was 1.26 g/kg and that in the pulp 4.56 g/kg but in some varieties the difference between pulp and flesh was more than 6-fold. For AMP, the mean concentration in the flesh was 80 mg/kg and that in the pulp was 295 mg/kg with one variety showing an 11-fold difference between pulp and flesh. These differences in concentration of these compounds, which are known to possess umami characteristics, provide an explanation for the perceived difference in umami taste between the flesh and pulp of tomatoes.

Direct pulp capping with a self-etching adhesive system: Histopathologic evaluation in dogs` teeth

Objective. This study evaluated histopathologically the response of pulp and periradicular tissues after pulp capping with an all-in-one self-etching adhesive system in dogs` teeth. Study design. Forty teeth of 4 dogs were assigned to 3 groups according to the pulp capping material: G1 (n = 20): self-etching adhesive system; G2 (n = 10): Ca(OH)(2); G3 (n = 10): zinc oxide-eugenol. The animals were killed 7 and 70 days after pulp capping. The pieces containing the pulp-capped teeth were removed and processed for histologic analysis. Results. At 7 days, no dentin bridge formation was observed; G1 and G3 exhibited inflammatory pulpal alterations, whereas G2 presented only mild inflammatory infiltrate in the pulp tissue adjacent to the capping material, the remainder being intact. At 70 days, no specimen in G1 or G3 presented dentin bridge formation. The remaining pulp tissue exhibited severe inflammatory alterations and areas of necrosis. In G2, all specimens showed dentin bridge formation and absence of inflammation and mineralized tissue resorption. No bacteria were identified using Brown and Brenn staining techniques in all 3 groups at any observation period. Conclusion. According to the conditions of this study, direct pulp capping with the self-etching adhesive system did not allow pulp tissue repair and failed histopathologically in 100% of the cases. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2009; 108: e34-e40)

Comparative Histopathological Analysis of Human Pulps after Class I Cavity Preparation with a High-Speed Air-Turbine Handpiece or Er:YAG Laser

The purpose of this study was to comparatively evaluate the response of human pulps after cavity preparation with different devices. Deep class I cavities were prepared in sound mandibular premolars using either a high-speed air-turbine handpiece (Group 1) or an Er: YAG laser (Group 2). Following total acid etching and the application of an adhesive system, all cavities were restored with composite resin. Fifteen days after the clinical procedure, the teeth were extracted and processed for analysis under optical microscopy. In Group 1 in which the average for the remaining dentin thickness (RDT) between the cavity floor and the coronal pulp was 909.5 mu m, a discrete inflammatory response occurred in only one specimen with an RDT of 214 mu m. However, tissue disorganization occurred in most specimens. In Group 2 (average RDT = 935.2 mu m), the discrete inflammatory pulp response was observed in only one specimen (average RDT = 413 mu m). It may be concluded that the high-speed air-turbine handpiece caused greater structural alterations in the pulp, although without inducing inflammatory processes.

Flow injection analysis of ethyl xanthate by gas diffusion and UV detection as CS(2) for process monitoring of sulfide ore flotation

A sensitive and robust analytical method for spectrophotometric determination of ethyl xanthate, CH(3)CH(2)OCS(2)(-) at trace concentrations in pulp solutions from froth flotation process is proposed. The analytical method is based on the decomposition of ethyl xanthate. EtX(-), with 2.0 mol L(-1) HCl generating ethanol and carbon disulfide. CS(2). A gas diffusion cell assures that only the volatile compounds diffuse through a PTFE membrane towards an acceptor stream of deionized water, thus avoiding the interferences of non-volatile compounds and suspended particles. The CS(2) is selectively detected by UV absorbance at 206 nm (epsilon = 65,000 L mol(-1) cm(-1)). The measured absorbance is directly proportional to EtX(-) concentration present in the sample solutions. The Beer`s law is obeyed in a 1 x 10(-6) to 2 x 10(-4) mol L(-1) concentration range of ethyl xanthate in the pulp with an excellent correlation coefficient (r = 0.999) and a detection limit of 3.1 x 10(-7) mol L(-1), corresponding to 38 mu g L. At flow rates of 200 mu L min(-1) of the donor stream and 100 mu L min(-1) of the acceptor channel a sampling rate of 15 injections per hour could be achieved with RSD < 2.3% (n = 10, 300 mu L injections of 1 x 10(-5) mol L(-1) EtX(-)). Two practical applications demonstrate the versatility of the FIA method: (i) evaluation the free EtX(-) concentration during a laboratory study of the EtX(-) adsorption capacity on pulverized sulfide ore (pyrite) and (ii) monitoring of EtX(-) at different stages (from starting load to washing effluents) of a flotation pilot plant processing a Cu-Zn sulfide ore. (C) 2010 Elsevier By. All rights reserved.