Submitted to the faculty of Indiana University in partial fulfillment of the requirements for the degree Master of Science in the department of Bioinformatics in School of Informatics of Indiana University 29 January, 2004 / Background: Toll and Toll-related proteins play an important role in antibacterial innate immunity and are widespread in insects, plants, and mammals. The completion of new genomes such as Anopheles gambiae has provided an avenue for a deeper understanding of Toll evolution. While most evolutionary analyses are performed on protein sequences, here, we present a unique phylogenetic analysis of Toll genes from the perspective of upstream regulatory regions so as to study the importance of evolutionary information inherited in such sequences. Results: In a comparative study, phylogeny on the protein products of Toll like genes showed consistency with earlier literature except for the single point of divergence between insects and mammals. On the other hand, the phylogeny based on upstream regulatory sequences (-3000 to +10) showed a broader distinction between the plants and the rest, though the tree was not well resolved probably due to poor alignment of these sequences. The phylogeny based on TFBs necessitated the development of a supervised statistical approach to determine their “evolutionary informativeness”. Employing the frequency of evolutionarily informative TFBs, a phylogeny was derived using pair-wise distances. It suggested a closer relationship between Anopheles and plants than to Drosophila and a significant homology among mammalian TLRs. Conclusions: A unique approach of using TFBs in studying evolution of Toll genes has been developed. Broadly, this approach showed results similar to the protein phylogeny. The inclusion of the evolutionary information from TFBs may be relevant to such analyses due to the selective pressure of conservation in upstream sequences.

Methylglyoxal (MGO) is a highly reactive dicarbonyl compound, formed as a metabolite from nonenzymatic and enzymatic reactions and is the leading precursor of advanced glycation end products (AGEs). AGEs contribute to ageing, type 2 diabetes mellitus (T2DM), and diabetes-related complications. However, MGO also has beneficial antibacterial activity and is the bioactive ingredient of medicinal honeys such as Manuka. Flavonoids are a group of phytochemicals that are powerful antioxidants. Polyphenols including flavonoids have been reported to trap MGO, forming adducts thereby preventing AGE formation. However, there is little to no information on the effect of adduct formation on the antioxidant properties of flavonoids and the antibacterial activity of MGO. In this study, catechin (CAT), chrysin (CHRY) and naringenin (NAR) at 0.1 mM and mixtures of each flavonoid with MGO (1:1) and (1:2) were evaluated for antioxidant and antibacterial activity. Antioxidant activity/capacity were evaluated with the total polyphenolic content (TPC), total flavonoid content (TFC), Trolox equivalent antioxidant capacity (TEAC) and the oxygen radical absorbent capacity (ORAC) assays. The bovine serum albumin (BSA)/MGO model was used to evaluate the effect on glycation. The 2’, 7’-dichlorofluorescein diacetate (DCFH-DA) assay with the L929 cell line was used to evaluate cellular antioxidant activity. Cytotoxicity was determined in the L929 cell line using the crystal violet (CV) and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) tetrazolium (MTT) assays. Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis) were used to determine antibacterial activity using the microbroth-dilution assay and subsequent changes to morphology were evaluated using scanning electron microscopy (SEM). A reduction in antioxidant content was observed for: CHRY (TPC), CAT and NAR (TFC) and in antioxidant activity for: CHRY (TEAC) and CAT (ORAC), when combined with MGO. Overall most of the antioxidant activity of the flavonoids was not affected by the addition of MGO. In the presence of BSA and MGO, all flavonoid:MGO combinations reduced formation of AGEs except NAR in combination with MGO. All flavonoids alone and in combinations did not cause cellular oxidative damage while MGO and AAPH induced increased cellular damage indicating that MGO via AGE formation makes cells more sensitive to the effects of oxidants that form radicals. Only CAT reduced the oxidative effects of MGO/AAPH. For all combinations there was no effect on cell number, although cell viability was significantly reduced for CHRY and its combinations and for NAR and NAR:MGO1. Flavonoids at 0.1 mM CAT, CHRY and NAR had no antibacterial activity against E. coli while inhibition was observed only with NAR against B. subtilis. MGO at 0.1 and 0.2 mM inhibited bacterial growth while in combination the antibacterial activity was significantly reduced. MGO as well as NAR caused major changes to bacteria morphology. In combination, the antibacterial activity of MGO was reduced, and ultrastructure changes associated with toxicity was also observed in most groups. In conclusion, flavonoids do trap MGO and this effect does not significantly alter flavonoid antioxidant activity. However, the antibacterial activity of MGO is reduced. Future studies should focus on the chemistry and the effects involved and should include dosage dependent studies. / Dissertation (MSc)--University of Pretoria, 2019. / Anatomy / MSc / Unrestricted

No description available.

京都大学 / 新制・課程博士 / 博士(医学) / 甲第24479号 / 医博第4921号 / 新制||医||1062(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 安達 泰治, 教授 別所 和久, 教授 長尾 美紀 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Indiana University-Purdue University Indianapolis (IUPUI) / The functional quaternary ammonium salts (QAS) and their constructed polyQAS or PQAS were synthesized, characterized and formulated into a novel antibacterial glass-ionomer cement. Compressive strength (CS) and Streptococcus mutans (S. mutans) viability were used to evaluate the mechanical strength and antibacterial activity of the cements. Fuji II LC cement was used as control. The specimens were conditioned in distilled water at 37 oC for 24 h prior to testing. The effects of the substitute chain length, loading as well as grafting ratio of the QAS and aging on CS and S. mutans viability were investigated. Chapter 2 describes how we studied and evaluated the formulated antibacterial glass-ionomer cement by incorporating QAS chloride-containing polymer into the formulation. The results show that with PQAS addition, the studied cements showed a reduction in CS with 25-95% for Fuji II LC and 13-78% for the experimental cement and a reduction in S. mutans viability with 40-79% for Fuji II LC and 40-91% for the experimental cement. The experimental cement showed less CS reduction and higher antibacterial activity as compared to Fuji II LC. The long-term aging study indicates that the cements are permanently antibacterial with no PQAS leaching. Chapter 3 describes how we studied and evaluated the formulated antibacterial cements by changing chain length, type of halide, loading, grafting ratio and aging time. The results show that the effects of the chain length, loading and grafting ratio of the QAS were significant. Increasing chain length, loading, grafting ratio significantly enhanced antibacterial activity but reduced CS. The experimental cement showed less CS reduction and higher antibacterial activity as compared to Fuji II LC. The long-term aging study indicates that the cements are permanently antibacterial with no PQAS leaching. There was no significant difference between QAS bromide and QAS chloride, suggesting that we can use QAS bromide directly without converting bromide to chloride. In summary, we have developed a novel PQAS-containing antibacterial glass-ionomer cement. The cement has demonstrated significant antibacterial activities. Our experimental cement is a promising system because the reduced strength of the cement with addition of PQAS is still above those demonstrated by original commercial cement Fuji II LC without any PQAS addition. It appears that the experimental cement is a clinically attractive dental restorative that can be potentially used for long-lasting restorations due to its high mechanical strength and permanent antibacterial function.

No description available.

In the past two decades, few reports have confirmed the various antibacterial activities of total extract from the seeds of Nigella sativa (Black cumin). In attempts to identify the active ingredients in this extract, the seeds were extracted with hexane. The volatile oil obtained from the crude extract was shown to contain at least three distinct compounds, thymoquinone, p-cymene, and α-pinene, as confirmed by GC/MS and NMR spectroscopy. While p-cymene and α-pinene showed no antibacterial activities, thymoquinone, exhibited remarkable inhibition of the growth of various strains of bacteria. For instance, the IC50 and the Minimal Inhibitory Concentration (MIC) for thymoquinone were found to be 1.31 μg/mL and 3.6 μg/mL respectively, when tested against the gram-positive bacteria, S. aureus. It is also found that thymoquinone significantly inhibites the protein and RNA synthesis in S. aureus.

The development and evaluation of a vancomycin population pharmacokinetic model in children, pre-adolescent, and adolescent patients was performed via non linear mixed effects modeling (NONMEM) in 2 phases. In phase I, a vancomycin population pharmacokinetic model was developed based on data from 200 children (aged 2-17 years) using a two-compartment model. Variables tested for inclusion in the model were serum creatinine (SCR), age (AGE), weight (WT), height (HT), sex (SEX), and body surface area (BSA). Variables were included at the p $ In phase II, the performance of the derived model was evaluated in a naive tested population and then compared to the Schaad, et al. model via prediction error techniques (PE). The predictability of 159 measured concentrations was assessed in 68 new patients. In predicting all concentrations types, the mean prediction error (MPE) with a 95% confidence interval (CI) for both the current study model and Schaad, et al model were: $-$1.42 ($-$3.38, 0.54), and 6.01 (4.46, 7.56) mg/L, respectively. When considering only peaks, a MPE with 95% CI were 1.72 ($-$0.94, 4.38), and 7.61 (5.13, 10.09) mg/L, respectively. Finally, MPE with 95% CI for the troughs were $-$1.45 ($-$3.42, 0.52), and 3.84 (2.98, 4.70) mg/L, respectively. Maintenance dose (MD) tables were designed, based on the relationship of height and serum creatinine to clearance. In addition, a loading dose (LD) was also recommended, which was 5 mg/cm. It is recommended that the current study model be used for dosing the pediatric population while setting an initial target peak of 30 mg/L and a trough of 5-10 mg/L. This should frequently result in optimal serum vancomycin concentrations within the therapeutic window. Individualization of therapy should then be done, once the measured concentrations are available.

In order for a drug, or any material used for the purpose of eliciting a change in an organisms’ physical or chemical state, to be effective it must reach the intended target intact and for a sustained rate over time. Drug delivery systems encapsulate a drug to protect it from degradation, prevent side reactions, increase solubility, improve accumulation rates at target sites, and release drugs at a controlled rate. Controlled and sustained release of drugs is achieved by degradation of the carrier triggered by breaking dynamic chemical bonds caused by changes in the chemical environment such as pH or redox conditions. Slow, first order kinetic release of drugs increase therapeutic efficacy while also reducing side effects and other cytotoxicity issues. Up and coming drug delivery systems include hydrogels and nanocarriers such as vesicles. Hydrogel drug delivery systems are unique three-dimensional networks of crosslinked hydrophilic polymers that contain anywhere from 50-90 wt% of water. Drugs can be loaded via encapsulation during the gelation process or may be covalently bound to the polymer backbone before gelation. Amphiphilic molecules or polymers that self-assemble in aqueous solutions to form supramolecular nanostructures, such as vesicles, can encapsulate hydrophilic drugs in the aqueous interior or hydrophobic drugs in the lipophilic bilayer membrane. This study seeks to embed vesicles into a hydrogel to create a hybrid drug delivery system which may be applied as a coating to medical devices to prevent bacterial adhesion and growth, injected directly to a target site, or as an additive for wound dressings. This hybrid system mitigates burst release from the hydrogel, as well as stabilizes the vesicles to afford a longer shelf life. Vesicles are prepared from a novel supramolecular amphiphile composed of thio-alkyl modified��-cyclodextrin as a macrocyclic host, and an adamantyl-dithiopropionic acid modified poly(ethylene glycol) as a linear guest. This host-guest system forms inclusion complexes that self-assemble to bilayered vesicles, which may encapsulate a payload, in aqueous solutions. These vesicles serve as three-dimensional multivalent junctions to form a hydrogel, which may encapsulate a second payload, through a dynamic disulfide exchange crosslinking reaction. This novel drug delivery system will be capable of dual and selective release of two different encapsulated payloads. A pH sensitive acid labile bond embedded in the crosslinker will cleave under acidic conditions to release the payload enclosed in the hydrogel matrix, while a disulfide bond embedded in the supramolecular amphiphile of the free vesicle can be cleaved in the presence of naturally occurring antioxidant glutathione, GSH, to release the second payload. It has been discovered that vesicles efficaciously form, can encapsulate a payload, and are stable for several weeks, up to a month. Vesicle stability is examined in the presence of both intracellular and extracellular concentrations of GSH, and it is found that vesicles are more stable in extracellular concentrations of GSH. Crosslinking of vesicles is attempted at several molecular weights of linear thiol terminated poly(ethylene glycol) crosslinker, concentrations ratios of crosslinker: vesicle, pHs, and temperatures. It can be concluded that the crosslinking density with the linear crosslinker is not high enough to form a hydrogel. Future studies will include 4-arm crosslinkers which are predicted to increase the number of crosslinking points and hence the crosslinking density.

Microbe resistence is a serious issue, especially as they have become resistant to most well known drugs. Therefore this is considered as a global problem and is now dealt with at a poitical level. Since no new classes of antimicrobial agents have been discovered in the past three deacdes, the development of new drugs is extremely urgent. Therefore the aim of this project was to synthesise derivatives of benzimidazole, and then assesses their antimicrobial activities in vitro by using disc (well) diffusion and MICs tests. A total of 69 benzimidazole derivatives, with substituents at positions 1, 2, and 5, were synthesised, characterised and tested against selected bacteria and fungi. In addition, six bezimidazole silver complexes were prepared and evaluated for their antimicrobial behavior. The SAR showed that the antimicrobial activity of the compounds depended on the substituents attached to the bicyclic heterocycle. Some promising results were obtained. In particular, 5 compounds displayed antibacterial activity against two MRSA strains with MIC values corresponding to ciprofloxacin, which can be considered significant. The compounds have some common features; four possess 5-chloro or 5-bromo substituents; two are derivatives of (S)-2- ethanaminebenzimidazole and the others are derivative of one 2-(chloromethyl)-1Hbenzo[d]imidazole, (1H-benzo[d]imidazol-2-yl)methanethiol and 2-(methoxymethyl)-1-methyl-1H-benzo[d]imidazole. The results from the antifungal screening were very interesting as there were 26 compounds, including two silver complexes, which were potent fungicides against the selected fungal species. They showed equivalent or greater potentency in their MIC values than amphotericin B. In particular, the 5-fluoro, 5-chloro and 5-bromo benzimidazole showed broad spectrum activity. / Saudi Culture Bureau and King Saud University