180 research outputs found
Characterisation of a recombinant plasmid encoding leptospiral antigen
No full textThis thesis was scanned from the print manuscript for digital preservation and is copyright the author.
Researchers can access this thesis by asking their local university, institution or public library to
make a request on their behalf. Monash staff and postgraduate students can use the link in the References field
ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes
No full textArrayOme is a new program that calculates the size of genomes represented by microarray-based probes and facilitates recognition of key bacterial strains carrying large numbers of novel genes. Protein-coding sequences (CDS) that are contigu-ous on annotated reference templates and classified as ‘Present ’ in the test strain by hybridization to microarrays are merged into ICs (ICs). These ICs are then extended to account for flanking intergenic sequences. Finally, the lengths of all extended ICs are summated to yield the ‘microarray-visualized genome (MVG) ’ size. We tested and validated ArrayOme using both experimental and in silico-generated genomic hybridization data. MVG sizing of five sequenced Escherichia coli and Shigella strains resulted in an accuracy of 97–99%, as com-pared to true genome sizes, when the comprehens-ive ShE.coli meta-array gene sequences (6239 CDS) were used for in silico hybridization analysis. How-ever, the E.coli CFT073 genome size was underesti-mated by 14 % as this meta-array lacked probes for many CFT073 CDS. ArrayOme permits rapid recog-nition of discordances between PFGE-measured genome and MVG sizes, thereby enabling high-throughput identification of strains rich in novel genes. Gene discovery studies focused on these strains will greatly facilitate characterization of the global gene pool accessible to individual bacterial species
Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota
No full textDietary intake of L-carnitine can promote cardiovascular diseases in humans through microbial production of trimethylamine (TMA) and its subsequent oxidation to trimethylamine N-oxide (TMAO) by hepatic flavin-containing monooxygenases. Although our microbiota are responsible for TMA formation from carnitine, the underpinning molecular and biochemical mechanisms remain unclear. In this study, using bioinformatics approaches, we first identified a two-component Rieske-type oxygenase/reductase (CntAB) and associated gene cluster proposed to be involved in carnitine metabolism in representative genomes of the human microbiota. CntA belongs to a group of previously uncharacterized Rieske-type proteins and has an unusual "bridging" glutamate but not the aspartate residue, which is believed to facilitate inter-subunit electron transfer between the Rieske centre and the catalytic mononuclear iron centre. Using Acinetobacter baumannii as the model, we then demonstrate that cntAB is essential in carnitine degradation to TMA. Heterologous overexpression of cntAB enables Escherichia coli to produce TMA, confirming that these genes are sufficient in TMA formation. Site-directed mutagenesis experiments have confirmed that this unusual "bridging glutamate" residue in CntA is essential in catalysis and neither mutant (E205D, E205A) is able to produce TMA. Together, our study reveals the molecular and biochemical mechanisms underpinning carnitine metabolism to TMA in human microbiota and assigns the role of this novel group of Rieske-type proteins in microbial carnitine metabolism
Real-Time Water Quality Modeling with Ensemble Kalman Filter for State and Parameter Estimation in Water Distribution Networks
No full textThis study presents a novel approach to real-time water quality state (chlorine concentration) and reaction parameter estimation in water distribution systems (WDSs) using ensemble Kalman filter (EnKF)-based data assimilation techniques. Two different types of EnKF-based methods are used in this study: noniterative restart-EnKF (NIR-EnKF) and iterative restart-EnKF (IR-EnKF). The use of these data assimilation frameworks for addressing key uncertainties in water quality models, such as uncertainty in the source or initial concentration of chlorine and uncertainty in the wall reaction parameter, is studied. The effect of ensemble size, number and location of measurement nodes, measurement error, and noise are also studied extensively in this work. The performance of the proposed methodology is tested on two different water networks: a brushy plains network and a large, citywide WDS, the Bangalore inflow network. The results of the simulation study show that both the NIR-EnKF and IR-EnKF methods are appropriate for dealing with uncertainty in source chlorine concentration, but the IR-EnKF method performs better than the NIR-EnKF method in the case of reaction parameter uncertainty
Kinetics and Mechanistic Study for Gas Phase Tropospheric Photo-oxidation Reactions of 2,2,2-Trifluoroethyl Methacrylate with OH Radicals and Cl Atoms: An Experimental and Computational Approach
No full textThe photo-oxidation reactions of 2,2,2-trifluoroethyl
methacrylate
(TFEMA) initiated by OH radicals and Cl atoms were investigated via
experimental as well as computational methodologies. The rate coefficients
for these reactions were investigated using the relative rate technique
(RR) at temperatures between 268 and 363 K. The rate coefficients
for the reaction of OH radicals with TFEMA were measured with reference
to diethyl ether and propylene. Propane and propylene were used in
the kinetic measurements as reference compounds. At 298 K, experimentally
obtained rate coefficients for the reaction of TFEMA with OH radicals
and Cl atoms are kTFEMA+OHexp–298K = (2.81 ± 0.54) ×
10–11 and kTFEMA+Clexp–298K = (1.91
± 0.44) × 10–10 cm3 molecule–1 s–1, respectively. The Arrhenius
expression obtained for the respective reactions are kTFEMA+OHexp–(268–363K) = (7.32 ± 0.62) × 10–12 exp[(400
± 53) and kTFEMA+Clexp–(268–363K) = (4.10 ±
0.78) × 10–12 exp[(1228 ± 115)/T]. To further complement our experimental findings, rate
coefficients were also calculated computationally for the reactions
of OH radicals and Cl atoms with TFEMA at CCSD(T)/cc-pVDZ//M062X/6-31+G(d,p)
and CCSD(T)/cc-pVDZ//MP2/6-31+G(d,p) levels of theory using canonical
variational transition state theory (CVT) with small curvature tunneling
(SCT) over the temperature range 200–400 K. Moreover, to analyze
the end products formed during the title reactions, qualitative analyses
were performed using gas chromatography–mass spectrometry (GC–MS)
and gas chromatography–infrared spectroscopy (GC–IR)
as analytical tools and degradation mechanisms were proposed for the
title reactions. Branching ratios, thermochemical parameters of these
reactions, and their impact on the troposphere were discussed
Strategic Design of a WO3/PdOxCarbon Shell Composite Photocatalyst: Visible Light-Mediated Selective Hydrogenation of 5Hydroxymethylfurfural
No full textThe development of visible light-assisted
heterogeneous selective
hydrogenation by utilizing solvents as a H2 source is a
sustainable and energy-saving approach. Here, we have synthesized
an efficient WO3/PdOx-carbon
shell composite photocatalyst via the solution combustion method (SCM).
The catalyst showed excellent activity for 5-hydroxymethylfurfural
(HMF) hydrogenation in H2O/MeOH (3:1) under visible light
(λ ≥ 420 nm) without the use of a pressurized external
hydrogen support. The primary product was identified as 5-bis(hydroxymethyl)furan
(BHMF) with a yield of 79.2%, which is regarded as a valuable feedstock
for polymer industries. The minor hydrogenolysis product 5-methylfurfuryl
alcohol (MFA) was also observed in proton NMR with a yield <20%.
Our findings reveal that conversion efficiency (>95%) and selectivity
(86.9%) increase drastically along with the pH range of the reaction
medium, i.e., 7.5–8.2. The photocatalyst was embedded with
both quantum-sized (0.6%) Pd particles (<5 nm) and PdO. After a
series of experiments, we found that the uniform dimension (10 nm)
of carbon shell benefits the stability of Pd particles (catalytic
active site) and enhances charge carrier mobility. The photocatalyst
is durable and reusable for up to more than six cycles without any
significant loss in its activity. The progress of the reaction and
key reactive species (•OH) were systematically investigated
by proton NMR kinetic studies and electron paramagnetic resonance
(EPR) spectroscopy. The possible reaction pathway was investigated
and explored. These studies may contribute to serving as a cost-effective
alternative method for a hydrogenating agent at an ambient condition
without the use of a pressurized external hydrogen/temperature support
under visible light
Gas Phase Kinetics and Mechanistic Insights for the Reactions of Cl atoms with Isopropyl Formate and Isobutyl Formate
No full textRate
coefficients for the reactions of Cl atoms with isopropyl
formate (IPF) and isobutyl formate (IBF) were measured experimentally
over the temperature range of 268–363 K and at 760 Torr of
nitrogen using relative rate method. Ethyl acetate and ethyl formate
were used as reference compounds for the measurement of rate coefficients
for the reaction of IPF with Cl atoms. Ethane and ethylene were used
as reference compounds for the measurement of rate coefficients for
the reaction of IBF with Cl atoms. The obtained rate coefficients
for the reactions of IPF and IBF with Cl atoms at 298 K are (1.56
± 0.47) × 10–11 and (7.60 ± 1.10)
× 10–11 cm3 molecule–1 s–1 respectively. The derived temperature dependent
Arrhenius expression for the reactions of IPF and IBF with Cl atoms
are kR1(268–363K)Experimental = (3.87 ± 0.88) ×
10–12 exp [(418 ± 70)/T] and kR2(268–363K)Experimental = (1.83 ± 0.45) × 10–11 exp [(421 ± 70)/T] cm3 molecule–1 s–1 respectively. A qualitative analysis of the
products formed during the reactions of Cl atoms with IPF and IBF
were carried out using gas chromatography–mass spectrometry
(GC–MS) and gas chromatography–infrared spectroscopy
(GC–IR) as analytical tools, and the degradation mechanisms
were proposed on the basis of end products. To rationalize our experimentally
obtained results, computational calculations were performed to calculate
the temperature dependent rate coefficients for these reactions over
the temperature range of 200–400 K at CCSD(T)/cc-pVDZ//MP2/6-31+G(d,
p) level of theory using canonical variational transition state theory
(CVT) with small curvature tunneling (SCT). Detailed discussions on
the thermochemistry of the reactions, branching ratios, and atmospheric
implications are discussed in the manuscript
Innovating Against Odds: A Medical Student\u27s Research Journey in a Resource-Constrained Environment
No full text"You need not know the R in Research to embark on the journey; a strong motivation is enough to set things in motion and let the journey unfold naturally." In this article, I share my journey as a medical student starting research in a Resource-Constrained Environment. I talk about the learning curve, milestones, setbacks, and presenting my research work. I\u27ve created a simple guide for fellow students in similar situations to do impactful research. Beyond studies, the shared journey with my research partner formed a lasting bond, showing how teamwork fosters understanding and innovation. I also discuss institutional barriers, especially the toxic research culture not talked about much. I stress the importance of raising awareness about these challenges for medical students and the need for a supportive and ethical research environment. It\u27s crucial to create a space where aspiring researchers can thrive without unethical practices, emphasizing the value of knowledge pursuit over personal ambitions
GC-MS ANALYSIS OF BIOACTIVE COMPONENTS FROM THE ETHANOL EXTRACT OF AVICENNIA MARINA LEAVES
No full textObjectives: To investigate the phytoconstitutent of ethanol extract of Avicennia marina using GC-MS. Methods:  GC-MS analysis of the leaves extract were performed using a Clarus 500 Perkin- Elmer (Auto System XL) Gas Chromatograph equipped and coupled to a mass detector Turbo mass gold – Perking Elmer Turbomas 5.2 spectrometer with an Elite-1 (100% Dimethyl ply siloxane), 300 m x 0.25 mm x 1 μm df capillary column. Results: The result of the GC-MS analysis confirmed the presence of twelve compounds. The most of the prevailing compounds are squalene ; 2R,3S-butane-1,2,3,4-tetraol; Palmitic acid; Hexadecanoic acid, ethyl ester; 3,7,11,15-Tetramethyl-2-hexadecen-1ol; Phytol; (E)-9-Octadecenoic acid ethyl ester; Dodecanoic acid; Octadecanoic acid, 2-methyl-,methyl ester; 3Cyclohexen-1 carboxaldehyde,3-methyl; cis-9-Hexadecenal; 3,7-dimethyl-2, 6-octadienyl ester etc. Conclusion: This study concluded that the plant leaves contains rich amount of phytoconstituents. These bioactive components are very useful to cure many diseases and also used in many pharmaceutical industries. Keywords: Avicennia marina, GC-MS, Bioactive compounds
Design of a compact microstrip patch antenna with a CSRR loaded substrate
No full textSince the advent of the wireless communications era, microstrip antennas have been used extensively due to their compact planar profile. These antennas are easily mounted to surfaces of aircrafts, satellites making them to be an ideal communicating interface. Microstrip patch antennas are based upon the principles of microstrip line theory and they are generally fabricated on a printed circuit board, due to which the cost of producing microstrip patch antennas are very low.
The length of a patch antenna is directly dependent on its operating resonant frequency. The radiating edges of the antenna is approximately equal to half the wavelength corresponding to its resonant frequency. The phase difference of the E-field between the two resonant edges is an integral multiple of the value ‘π’. By the inclusion of a complementary split ring resonating (CSRR) structure to the antenna, the length of the resonating patch can be adjusted independent to the λ/2 constraint, which can lead to decrease in patch size.
The objective of this thesis is to study and design a highly compact patch antenna with a CSRR loaded to the antenna structure, validate the results through theoretical simulations and then practically verify the results after fabrication. From the analysis of various CSRR structures, an optimal design methodology for size reduction will be attempted. The proposed structure is designed to radiate at 2.45 GHz. The methodology proposed in this thesis can be made use in the design of antennas with resonant frequencies in the other ranges as well.
All the antenna designs showcased in this study were designed and theoretically verified through the Computer Simulation Technology studio suite using the Microwave and RF module. By simulating the final antenna structure, it is observed that it radiates at 2.45 GHZ with gain 5.71 dB. The fabricated antenna upon testing displays a shift in resonant frequency to 2.80 GHz with gain 3.31 dB due to the presence of air gap between the composite substrate structure.Master of Science (Communications Engineering
- …
