Characterization of a Sulfuramino Acid Lyase from Citrobacter Freundii (KP25)

L-Methionine y-Iyase (EC 4.4.1.11; LMGL) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the direct conversion of L-methionine to aketobutyrate, methanethiol and ammonia by an a,r-elimination reaction. Seventy nine LMGL-producing microorganisms isolates were screened from six local sources by the 5'5-dithiobis (2-nitrobenzoic acid) (DTNB) test. The six local sources were soil samples from around the Faculty of Food Science and Biotechnology and Central Research Laboratory, Universiti Putra Malaysia and Kuantan sea coast, soil and water samples from hot springs in Ulu Legong, Baling, Kedah and Pedas, Negeri Sembilan and intestine samples from chicken. A simple and convenient colorimetric screening method, the DTNB test detects methanethiol, which reduces DTNB contained in an agar-plate medium to form yellow colour aryl mercaptan (4 thiol-2-nitro-benzoate) around the colony of a bacterium that is able to produce LMGL. LMGL was detected from 45 (57%) of the bacterial isolates by 3-methyl-2-benzothiazolone hydrazone (MBTH) assay. LMGL activity was quantitatively assayed by determining the amount of a-ketobutyrate produced spectrophotometricalIy at 320 run after derivatization with MBTH. Twelve relatively high producers of LMGL were identified by Gram stain, 10 types of biochemical tests consisting of potassium hydroxide (KOH), catalase, oxidase, indole, citrate utilization, phenylalanine deaminase and urease tests and triple sugar iron agar (ISIA), nutrient agar and MacConkey agar reactions, and by using the Biolog test kits (Biolog, Inc., Hayward, Calif.). Enterobacter nimipressuralis, Enterobacter intermedius, Pseudomonas pyrrocinia, Ratstonia pickettii and Citrobacter freundii (C freundii) were found to be new sources for LMGL while the remaining two were Escherichia coli and Bacillus cereuslthuringiensis. The methionine-utilizing enzyme was partially purified from C freundii (KP25) isolated from soil samples of Kuantan sea coast, which contained the highest activity. The purification scheme, involving dialysis, removal of nucleic acid with deoxyribonuclease I (DNase I) and ammonium sulfate [(NH₄)₂SO₄] precipitation resulted in a purification fold of 0.6 with a recovery of 22.6% and a specific activity of 0.02 U/mg, all using methionine as the substrate. It was found that the partially purified enzyme extract from C freundii (KP25) catalyzed D-amino acids better than L-amino acids and also degraded cysteine and its S-substituted derivatives such as more effectively than methionine and its S-substituted derivatives. Hence, the result on substrate specificity of the lyase present in the enzyme extract shows the probable presence of D-cysteine desulfbydrase (EC 4.4.1.15) and the absence of LMGL. Crude enzyme extract from C. freundii (KP25) was characterized by using D- and L-cysteine instead of DL-methionine as the substrates. The temperature and pH optimum of the crude enzyme extract were 45°C and pH 9.0 in 125 mM glycine-sodium hydroxide (NaOH) buffer with each D- and L-cysteine as the substrate

The application of diastereoselective free radical reactions in carbohydrate chemistry

This thesis focuses essentially on the application of diastereoselective radical reactions to the preparation of O- and C-glycosidic linkages. As such, the introduction surveys both the general area of glycoside synthesis and diastereoselective radical reactions and in particular, their use in carbohydrate chemistry. Methyl [Phenyl 4,5,7-tri-O-benzyl-3-deoxy-2-sulphonyl-β-D-arabino-2-heptulopyranoside]onate (sulphone ester) was prepared from tri-O-benzyl-D-glucal according to a method previously developed in the laboratory. The highly diastereoselective preparation of 6-C-glycosides was achieved by reductive desulphonylation of the sulphone ester with lithium naphthalenide followed by quenching with an alkyl halide and ultimately by Barton reductive decarboxylation. Diastereoselectivities in excess of 95:5 were routinely observed. Thermal elimination of phenylsulphinic acid from the sulphone ester gave the corresponding 1-carbomethoxy glycal. cw-Hydroxylation with osmium tetroxide gave exclusively the gluco-isomer. Acetonation, saponification and reductive decarboxylation gave l,2-O-isopropylidene-3,4,6-tri-O-benzyl-β-D-gluco-pyranose as a single anomer and the first example of a 1,2-trans-isopropylidene derivative of a pyranose sugar. Other β-O-gluco-pyranosides were prepared as single anomers by related process. The extension of the methodology to the preparation of β-O-manno-pyranosides was investigated. The extrapolation of the method to the preparation of furanosidic linkages was investigated. 2,3:4,6-Di-O-isopropylidene-2-keto-L-gulonic acid was chosen as starting material and methods were developed for its selective deprotection and protection. The stereoselectivity of the radical decarboxylation step was investigated. Finally, in the context of the C-glycoside synthesis, 6-trimethylsilylethoxymethyl chloride (SEM-Cl) was developed as a practical equivalent to formaldehyde in low temperature, non-aqueous aldol type reactions

A Study on the Element of Sentiment toward Knowledge Sharing among Knowledge Workers in a Virtual CoP

Ever since the usage of alternative media has grown tremendously, it was seen that the increasing amount of interactive online sites that are categorized as Web 2.0 systems has changed the communication and collaboration among knowledge workers. These systems provide greater interactivity and higher user-generated content. Social networking site is one type of online platforms that allow people to collaborate and communicate through a variety of services for social purposes (Broughton, Higgins, Hicks, & Cox, 2009). These high-flying social networking sites are driving new forms of social interaction, allowing users to intermingle and cooperate with each other in a social media dialogue nowadays by swapping ideas or posting updates and comments. It is crucial to comprehend how social relationships affect the content share between each knowledge worker in a virtual world. This project investigates how work and friend relationships can influence the utilization of social media systems for knowledge sharing. The effect of the element of sentiment among knowledge workers in a virtual Community of Practice (CoP) as they send and receive messages with their peers will be studied in this research. Different forms of emotion from knowledge workers will be investigated in this study in the workplace. A proposed research model will be proposed. A research framework will be outlined and qualitative and quantitative analysis will be used to analyze the research results

First-principles investigation of graphitic carbon nitride monolayer with embedded Fe atom

Density-functional theory calculations with spin-polarized generalized gradient approximation and Hubbard $U$ correction is carried out to investigate the mechanical, structural, electronic and magnetic properties of graphitic heptazine with embedded $\mathrm{Fe}$ atom under bi-axial tensile strain and applied perpendicular electric field. It was found that the binding energy of heptazine with embedded $\mathrm{Fe}$ atom system decreases as more tensile strain is applied and increases as more electric field strength is applied. Our calculations also predict a band gap at a peak value of 5 tensile strain but at expense of the structural stability of the system. The band gap opening at 5 tensile strain is due to distortion in the structure caused by the repulsive effect in the cavity between the lone pairs of edge nitrogen atoms and $\mathrm{d}_{{xy}}/\mathrm{d}_{x^2-y^2}$ orbital of Fe atom, hence the unoccupied $\mathrm{p}_z$-orbital is forced to shift towards higher energy. The electronic and magnetic properties of the heptazine with embedded $\mathrm{Fe}$ system under perpendicular electric field up to a peak value of 10 $\mathrm{V/nm}$ is also well preserved despite obvious buckled structure. Such properties may be desirable for diluted magnetic semiconductors, spintronics, and sensing devices

Theoretical studies on mechanical and electronic properties of ss-triazine sheet

Mechanical and electronic properties of $s$-triazine are studied using first-principles calculations based on density functional theory. The in-plane stiffness and bulk modulus for $s$-triazine sheet are found to be less than that of heptazine. The reduction can be related to the nature of the covalent bonds connecting the adjacent sheets and the number of atoms per unit cell. The Poisson's ratio of $s$-triazine is half the value to that of graphene. Additionally, the calculated values of the two critical strains (elastic and yielding points) of $s$-triazine sheet are in the same order of magnitude to that for heptazine which was calculated using MD simulations in the literature. It is also demonstrated that $s$-triazine sheet can withstand larger tension in the plastic region. These results established a stable mechanical property for $s$-triazine sheet. We found a linear relationship of bandgap as a function of bi-axial tensile strain within the harmonic elastic region. The reduced steric repulse of the lone pairs ($\mathrm{p}_x$-, $\mathrm {p}_y$-) causes the $\mathrm {p}_z$-like orbital to shift to high energy, and consequently an increase in the bandgap. We find no electronic properties modulation of the $s$-triazine sheet under electric field up to a peak value of 10 V/nm. Such noble properties may be useful in future nanomaterial applications.Comment: Manuscript submitted to Philosophical Magazine Journa

Adsorption of atoms and molecules on s-triazine sheet with embedded manganese atom: First-principles calculations

The mechanical, structural, electronic and magnetic properties of s-triazine sheet (C6N6) with embedded Mn atom (Mn-C6N6) is investigated under the influence of external environment using density functional theory. Our results show that Mn-C6N6 system is structurally and mechanically stable. The binding energy of Mn embedded in C6N6 sheet can be modulated under the influence of symmetric deformation and perpendicular electric field respectively. The semiconducting property of pure C6N6 sheet is maintained upon embedment of Mn atom in the porous site. It is also found that small increment in bi-axial tensile strain enhances the band gap (from 0.630 eV at zero strain to 0.802 eV at 5% strain) while the magnetic moment of the embedded Mn atom is preserved. The electronic and magnetic properties of the Mn-C6N6 systems are maintained up to 10 V/nm in electric field strength. We also explore the geometries, electronic and magnetic properties of Mn-C6N6 with adsorbed atoms and molecules. The Mn-C6N6 with adsorbed O atom and O2 molecule systems shows half-metallic character whereas the remaining systems preserve their semiconducting property. The total magnetic moment per unit cell in most of the systems is found to reduce as compared to that of the Mn-C6N6 sheet. The reduction in magnetic moment can be related to the strong interactions among the Mn atom and the surrounding atoms which lead to the formation of low-spin configurations. Overall, our results indicate that the Mn-C6N6 systems with and without adsorbed atoms and molecules can serve as potential candidates for future spintronics and catalysis applications.Comment: 14 pages, 6 figure

Molecular dynamics simulations and photoluminescence measurements of annealed ZnO surfaces

The effect of thermal annealing on wurtzite ZnO, terminated by two surfaces, (0 0 0 $\bar 1$) (which is oxygen-terminated) and (0 0 0 1) (which is Zn-terminated), is investigated via molecular dynamics simulation using reactive force field (ReaxFF). As a result of annealing at a threshold temperature range of 700~K < T_{\mbox{\small t}} \leq 800~K, surface oxygen atoms begin to sublimate from the (0 0 0 $\bar 1$) surface, while no atom leaves the (0 0 0 1) surface. The ratio of oxygen leaving the surface increases with temperature $T$ (for T \geq T_{\mbox{\small t}}). The relative luminescence intensity of the secondary peak in the photoluminescence (PL) spectra, interpreted as a measurement of amount of vacancies on the sample surfaces, qualitatively agrees with the threshold behavior as found in the MD simulations. Our simulations have also revealed the formation of oxygen dimers on the surface and evolution of partial charge distribution during the annealing process. Our MD simulation based on the ReaxFF is consistent with experimental observations.Comment: 26 pages, 11 figures. Manuscript submitted to Physica

Molecular evolution of the mammalian epiblast

Ph.DDOCTOR OF PHILOSOPH