The molecular structure of chloritoid: A mid-infrared and near-infrared spectroscopic study

The mineral chloritoid collected from the argillite in the bottom of Yaopo Formation of Western Beijing was characterized by mid-infrared (MIR) and near-infrared (NIR) spectroscopy. The MIR spectra showed all fundamental vibrations including the hydroxyl units, basic aluminosilicate framework and the influence of iron on the chloritoid structure. The NIR spectrum of the chloritoid showed combination (ν + δ)OH bands with the fundamental stretching (ν) and bending (δ) vibrations. Based on the chemical component data and the analysis result from the MIR and NIR spectra, the crystal structure of chloritoid from western hills of Beijing, China, can be illustrated. Therefore, the application of the technique across the entire infrared region is expected to become more routine and extend its usefulness, and the reproducibility of measurement and richness of qualitative information should be simultaneously considered for proper selection of a spectroscopic method for the unit cell structural analysis.

Infrared and Raman spectroscopic characterization of the carbonate bearing silicate mineral aerinite – Implications for the molecular structure

The mineral aerinite is an interesting mineral because it contains both silicate and carbonate units which is unusual. It is also a highly colored mineral being bright blue/purple. We have studied aerinite using a combination of techniques which included scanning electron microscopy, energy dispersive X-ray analysis, Raman and infrared spectroscopy. Raman bands at 1049 and 1072 cm−1 are assigned to the carbonate symmetric stretching mode. This observation supports the concept of the non-equivalence of the carbonate units in the structure of aerinite. Multiple infrared bands at 1354, 1390 and 1450 cm−1 supports this concept. Raman bands at 933 and 974 cm−1 are assigned to silicon–oxygen stretching vibrations. Multiple hydroxyl stretching and bending vibrations show that water is in different molecular environments in the aerinite structure.

The molecular structure of kaolinite–potassium acetate intercalation complexes: A combined experimental and molecular dynamic simulation study

The kaolinite (Kaol) intercalated with potassium acetate (Ac) was prepared and characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and thermogravimetry. Molecular dynamic simulation was performed to investigate the structure of Kaol–Ac intercalation complex and the hydrogen bonds between Kaol and intercalated Ac andwater using INTERFACE forcefield. The acetate anions andwater arranged in a bilayer structure in the interlayer space of Kaol. The potassium cations distributed in the interlayer space and strongly coordinated with acetate anions aswell aswater rather than keyed into the ditrigonal holes of tetrahedral surface of Kaol. Strong hydrogen bonds formed between the hydrogen atoms of hydroxyl on the octahedral surface and oxygen atoms of both acetate anions and water. The acetate anions andwater also weakly bonded hydrogen to the silica tetrahedral surface through their hydrogen atoms with the oxygen atoms of silica tetrahedral surface.

New insights into the molecular structure of kaolinite–methanol intercalation complexes

A series of kaolinite–methanol complexes with different basal spacings were synthesized using guest displacement reactions of the intercalation precursors kaolinite–N-methyformamide (Kaol–NMF), kaolinite–urea (Kaol–U), or kaolinite–dimethylsulfoxide (Kaol–DMSO), with methanol (Me). The interaction of methanol with kaolinite was examined using X-ray diffraction (XRD), infrared spectroscopy (IR), and nuclear magnetic resonance (NMR). Kaolinite (Kaol) initially intercalated with N-methyformamide (NMF), urea (U), or dimethylsulfoxide (DMSO) before subsequent reaction with Me formed final kaolinite–methanol (Kaol–Me) complexes characterized by basal spacing ranging between 8.6 Å and 9.6 Å, depending on the pre-intercalated reagent. Based on a comparative analysis of the three Kaol–Me displacement intercalation complexes, three types of Me intercalation products were suggested to have been present in the interlayer space of Kaol: (1) molecules grafted onto a kaolinite octahedral sheet in the form of a methoxy group (Al-O-C bond); (2) mobile Me and/or water molecules kept in the interlayer space via hydrogen bonds that could be partially removed during drying; and (3) a mixture of types 1 and 2, with the methoxy group (Al-O-C bond) grafted onto the Kaol sheet and mobile Me and/or water molecules coexisted in the system after the displacement reaction by Me. Various structural models that reflected four possible complexes of Kaol–Me were constructed for use in a complimentary computational study. Results from the calculation of the methanol kaolinite interaction indicate that the hydroxyl oxygen atom of methanol plays the dominant role in the stabilization and localization of the molecule intercalated in the interlayer space, and that water existing in the intercalated Kaol layer is inevitable.

Molecular characterisation and carotenoid quantification of pro-vitamin A biofortified genetically modified bananas in Uganda

In Uganda, a significant proportion of the population depends on the micronutrient poor East African highland banana as a food staple. Consequently, micronutrient deficiencies such as vitamin A deficiency are an important health concern in the country. To reach most vulnerable rural poor populations, staple crops can be biofortified with essential micronutrients though conventional breeding or genetic engineering. This thesis provided proof of concept that genetically modified East African highland bananas with enhanced provitamin A levels can be generated and fully characterised in Uganda. In addition, provitamin A levels present in popular banana varieties was documented.

Molecular genetic investigation of mitochondrial dysfunction in relation to migraine susceptibility

The aim of this research was to assess the role of genetic variation in mitochondrial function and how this relates to migraine pathophysiology. Using our unique Norfolk Island population, a custom in-house next generation sequencing methodology was developed. This data for the first time showed that there is a molecular genetic link between mitochondrial dysfunction and migraine susceptibility. This work has provided the foundation for further studies aimed at utilising the identified markers in improved migraine diagnostic and therapeutic strategies.

Molecular recognition of 2,4,6-trinitrotoluene by 6-aminohexanethiol and surface-enhanced Raman scattering sensor

2,4,6-trinitrotoluene (TNT) is one of the most commonly used nitro aromatic explosives in landmine, military and mining industry. This article demonstrates rapid and selective identification of TNT by surface-enhanced Raman spectroscopy (SERS) using 6-aminohexanethiol (AHT) as a new recognition molecule. First, Meisenheimer complex formation between AHT and TNT is confirmed by the development of pink colour and appearance of new band around 500 nm in UV-visible spectrum. Solution Raman spectroscopy study also supported the AHT:TNT complex formation by demonstrating changes in the vibrational stretching of AHT molecule between 2800-3000 cm−1. For surface enhanced Raman spectroscopy analysis, a self-assembled monolayer (SAM) of AHT is formed over the gold nanostructure (AuNS) SERS substrate in order to selectively capture TNT onto the surface. Electrochemical desorption and X-ray photoelectron studies are performed over AHT SAM modified surface to examine the presence of free amine groups with appropriate orientation for complex formation. Further, AHT and butanethiol (BT) mixed monolayer system is explored to improve the AHT:TNT complex formation efficiency. Using a 9:1 AHT:BT mixed monolayer, a very low detection limit (LOD) of 100 fM TNT was realized. The new method delivers high selectivity towards TNT over 2,4 DNT and picric acid. Finally, real sample analysis is demonstrated by the extraction and SERS detection of 302 pM of TNT from spiked.

Modelling CO2 adsorption and separation on experimentally-realized B40 fullerene

Searching for efficient solid sorbents for CO2 adsorption and separation is important for developing emergent carbon reduction and natural gas purification technology. This work, for the first time, has investigated the adsorption of CO2 on newly experimentally realized cage-like B40 fullerene (Zhai et al., 2014) based on density functional theory calculations. We find that the adsorption of CO2 on B40 fullerene involves a relatively large energy barrier (1.21 eV), however this can be greatly decreased to 0.35 eV by introducing an extra electron. A practical way to realize negatively charged B40 fullerene is then proposed by encapsulating a Li atom into the B40 fullerene (Li@B40). Li@B40 is found to be highly stable and can significantly enhance both the thermodynamics and kinetics of CO2 adsorption, while the adsorptions of N2, CH4 and H2 on the Li@B40 fullerene remain weak in comparison. Since B40 fullerene has been successfully synthesized in a most recent experiment, our results highlight a new promising material for CO2 capture and separation for future experimental validation.

Identifying the molecular mediators of VN and the IGF:VN complex-stimulated breast cancer cell survival

This project has identified a molecular signature involved in functions critical to breast cancer progression and metastasis mediated by vitronectin, an abundant protein in human plasma and victornectin:insulin-like growth factor complexes. This may have significant implications in designing future therapeutic targets for patient with tumours overexpressing vitronectin and/or the components of the insulin-like growth factor system:vitronectin axis. In particular, the findings from this project have identified Cyr61 and CTGF as key mediators involved in vitroncetin- and insulin-like growth factor I: Insulin-like growth factor-binding protein:vitronectin-induced breast cancer cell survival and migration.

Substrate effects in the supramolecular assembly of 1,3,5-benzene tricarboxylic acid on graphite and graphene

The behavior of small molecules on a surface depends critically on both molecule–substrate and intermolecular interactions. We present here a detailed comparative investigation of 1,3,5-benzene tricarboxylic acid (trimesic acid, TMA) on two different surfaces: highly oriented pyrolytic graphite (HOPG) and single-layer graphene (SLG) grown on a polycrystalline Cu foil. On the basis of high-resolution scanning tunnelling microscopy (STM) images, we show that the epitaxy matrix for the hexagonal TMA chicken wire phase is identical on these two surfaces, and, using density functional theory (DFT) with a non-local van der Waals correlation contribution, we identify the most energetically favorable adsorption geometries. Simulated STM images based on these calculations suggest that the TMA lattice can stably adsorb on sites other than those identified to maximize binding interactions with the substrate. This is consistent with our net energy calculations that suggest that intermolecular interactions (TMA–TMA dimer bonding) are dominant over TMA–substrate interactions in stabilizing the system. STM images demonstrate the robustness of the TMA films on SLG, where the molecular network extends across the variable topography of the SLG substrates and remains intact after rinsing and drying the films. These results help to elucidate molecular behavior on SLG and suggest significant similarities between adsorption on HOPG and SLG.

Four mammal fossil calibrations: Balancing competing palaeontological and molecular considerations

With the introduction of relaxed-clock molecular dating methods, the role of fossil calibration has expanded from providing a timescale, to also informing the models for molecular rate variation across the phylogeny. Here I suggest fossil calibration bounds for four mammal clades, Monotremata (platypus and echidnas), Macropodoidea (kangaroos and potoroos), Caviomorpha-Phiomorpha (South American and African hystricognath rodents), and Chiroptera (bats). In each case I consider sources of uncertainty in the fossil record and provide a molecular dating analysis to examine how the suggested calibration priors are further informed by other mammal fossil calibrations and molecular data.

Molecular data extend Australian Cricotopus midge (Chironomidae) species diversity, and provide a phylogenetic hypothesis for biogeography and freshwater monitoring

Resolving species relationships and confirming diagnostic morphological characters for insect clades that are highly plastic, and/or include morphologically cryptic species, is crucial for both academic and applied reasons. Within the true fly (Diptera) family Chironomidae, a most ubiquitous freshwater insect group, the genera CricotopusWulp, 1874 and ParatrichocladiusSantos-Abreu, 1918 have long been taxonomically confusing. Indeed, until recently the Australian fauna had been examined in just two unpublished theses: most species were known by informal manuscript names only, with no concept of relationships. Understanding species limits, and the associated ecology and evolution, is essential to address taxonomic sufficiency in biomonitoring surveys. Immature stages are collected routinely, but tolerance is generalized at the genus level, despite marked variation among species. Here, we explored this issue using a multilocus molecular phylogenetic approach, including the standard mitochondrial barcode region, and tested explicitly for phylogenetic signal in ecological tolerance of species. Additionally, we addressed biogeographical patterns by conducting Bayesian divergence time estimation. We sampled all but one of the now recognized Australian Cricotopus species and tested monophyly using representatives from other austral and Asian locations. Cricotopus is revealed as paraphyletic by the inclusion of a nested monophyletic Paratrichocladius, with in-group diversification beginning in the Eocene. Previous morphological species concepts are largely corroborated, but some additional cryptic diversity is revealed. No significant relationship was observed between the phylogenetic position of a species and its ecology, implying either that tolerance to deleterious environmental impacts is a convergent trait among many Cricotopus species or that sensitive and restricted taxa have diversified into more narrow niches from a widely tolerant ancestor.

Molecular and functional characterizations of a Kunitz-type serine protease inhibitor FcKuSPI of the shrimp Fenneropenaeus chinensis

Serine proteinase inhibitors play important and diverse roles in biological processes such as coagulation, defense mechanisms, and immune responses. Here, we identified and characterized a Kunitz-type proteinase inhibitor, designated FcKuSPI, of the BPTI/Kunitz family of serine proteinase inhibitors from the hemocyte cDNA library of the shrimp Fenneropenaeus chinensis. The deduced amino acid sequence of FcKuSPI comprises 80 residues with a putative signal peptide of 15 amino acids. The predicted molecular weight of the mature peptide is 7.66 kDa and its predicted isoelectric point is 8.84. FcKuSPI includes a Kunitz domain containing six conserved cysteine residues that are predicted to form three disulfide bonds. FcKuSPI shares 44e53% homology with BPTI/Kunitz family members from other species. FcKuSPI mRNAwas expressed highly in the hemocytes and moderately in muscle in healthy shrimp. Recombinant FcKuSPI protein demonstrated anti-protease activity against trypsin and anticoagulant activity against citrated human plasma in a dose-dependent manner in in vitro assays.

Atlantic-Mediterranean and within-Mediterranean molecular variation in Coris julis (L. 1758) (Teleostei, Labridae)

Sequence variation in the mitochondrial control region was studied in the Mediterranean rainbow wrasse (Coris julis), a species with pronounced pelagic larval phase inhabiting the Mediterranean Sea and the adjacent coastal eastern Atlantic Ocean. A total of 309 specimens from 19 sampling sites were analysed with the aim of elucidating patterns of molecular variation between the Atlantic and the Mediterranean as well as within the Mediterranean Sea. Phylogeographic analyses revealed a pronounced structuring into a Mediterranean and an Atlantic group. Samples from a site at the Moroccan Mediterranean coast in the Alboran Sea showed intermediate frequencies of “Mediterranean” and “Atlantic” haplotypes. We recognised a departure from molecular neutrality and a star-like genealogy for samples from the Mediterranean Sea, which we propose to have happened due to a recent demographic expansion. The results are discussed in the light of previous studies on molecular variation in fish species between the Atlantic and the Mediterranean and within the Mediterranean.

Molecular cloning, expression and immunological characterisation of Pas n 1, the major allergen of Bahia grass Paspalum notatum pollen

Bahia grass, Paspalum notatum, is a clinically important subtropical grass with a prolonged pollination season from spring to autumn. We aimed to clone and characterise the major Bahia grass pollen allergen, Pas n 1. Grass pollen-allergic patients presenting to a tertiary hospital allergy clinic were tested for IgE reactivity with Bahia grass pollen extract by skin prick testing, ImmunoCAP, ELISA and immunoblotting. Using primers deduced from the N-terminal peptide sequence of a group 1 allergen of Bahia grass pollen extract separated by two-dimensional gel electrophoresis, the complete Pas n 1 cDNA was obtained by rapid amplification of cDNA ends and cloned. Biological relevance of recombinant Pas n 1 expressed in Escherichia coli was assessed by serum IgE reactivity and basophil activation. Twenty-nine of 34 (85%) consecutive patients presenting with grass pollen allergy were skin prick test positive to Bahia grass pollen. The Pas n 1 cDNA has sequence homology with the β-expansin 1 glycoprotein family and is more closely related to the maize pollen group 1 allergen (85% identity) than to ryegrass Lol p 1 or Timothy grass Phl p 1 (64 and 66% identity, respectively). rPas n 1 reacted with serum IgE in 47 of 55 (85%) Bahia grass pollen-allergic patients, activated basophils and inhibited serum IgE reactivity with the 29 kDa band of Bahia grass pollen extract. In conclusion the cDNA for the major group 1 allergen of the subtropical Bahia grass pollen, Pas n 1, was identified and cloned. rPas n 1 is immunologically active and is a valuable reagent for diagnosis and specific immunotherapy of grass pollen allergy.