Spectroscopic investigation of the polymerisation of pyrrole and thiophene within zeolite channels

The reaction of pyrrole and thiophene monomers with copper- or nickel-exchanged mordenite has been investigated using X-ray photoelectron (XPS) and photoacoustic infrared (PAIRS) spectroscopies. Because of the differing oxidising powers of the cations studied, polymerisation occurred only with copper-exchanged mordenite. PAIRS and XPS data indicated that both polypyrrole and polythiophene were partially oxidised when synthesised within the zeolite structure. IR spectra of polythiophene and polythiophene and polypyrrole showed intense bands typical of ring vibrations which could couple to the large dipole change induced by charges moving along the polythiophene chain. In addition it was noted that only vibrations typical of oxidised polymer structures were recorded, suggesting that the charge carrier was located within these segments. Furthermore, N 1s spectra contained a high binding energy peak at 402.5 eV which was attributed to a positively charged nitrogen species, in agreement with IR data. Significantly, C 1s spectra confirmed that molecular wires were formed within the confines of the zeolite lattice. Depth-profiling experiments suggested that polypyrrole was distributed throughout the entire zeolite host. By contrast, polythiophene may have been restricted to the uppermost zeolite channels owing to the ability of sulfur species to bond to CuI sites [produced by reduction of copper(II) ions during the polymerisation process], thus obstructing movement along the channels.

Ingenuity pathways analysis of urine metabonomics phenotypes toxicity of gentamicin in multiple organs

We introduce the use of Ingenuity Pathway Analysis to analyzing global metabonomics in order to characterize phenotypically biochemical perturbations and the potential mechanisms of the gentamicin-induced toxicity in multiple organs. A single dose of gentamicin was administered to Sprague Dawley rats (200 mg/kg, n = 6) and urine samples were collected at -24-0 h pre-dosage, 0-24, 24-48, 48-72 and 72-96 h post-dosage of gentamicin. The urine metabonomics analysis was performed by UPLC/MS, and the mass spectra signals of the detected metabolites were systematically deconvoluted and analyzed by pattern recognition analyses (Heatmap, PCA and PLS-DA), revealing a time-dependency of the biochemical perturbations induced by gentamicin toxicity. As result, the holistic metabolome change induced by gentamicin toxicity in the animal's organisms was characterized. Several metabolites involved in amino acid metabolism were identified in urine, and it was confirmed that gentamicin biochemical perturbations can be foreseen from these biomarkers. Notoriously, it was found that gentamicin induced toxicity in multiple organs system in the laboratory rats. The proof-of-knowledge based Ingenuity Pathway Analysis revealed gentamicin induced liver and heart toxicity, along with the previously known toxicity in kidney. The metabolites creatine, nicotinic acid, prostaglandin E2, and cholic acid were identified and validated as phenotypic biomarkers of gentamicin induced toxicity. Altogether, the significance of the use of metabonomics analyses in the assessment of drug toxicity is highlighted once more; furthermore, this work demonstrated the powerful predictive potential of the Ingenuity Pathway Analysis to study of drug toxicity and its valuable complementation for metabonomics based assessment of the drug toxicity.

Molecular characterisation and expression analysis of interferon gamma in response to natural chlamydia infection in the koala, phascolarctos cinereus

Interferon gamma (IFNγ) is a key Th1 cytokine, with a principal role in the immune response against intracellular organisms such as Chlamydia. Along with being responsible for significant morbidity in human populations, Chlamydia is also responsible for wide spread infection and disease in many animal hosts, with reports that many Australian koala subpopulations are endemically infected. An understanding of the role played by IFNγ in koala chlamydial diseases is important for the establishment of better prophylactic and therapeutic approaches against chlamydial infection in this host. A limited number of IFNγ sequences have been published from marsupials and no immune reagents to measure expression have been developed. Through preliminary analysis of the koala transcriptome, we have identified the full coding sequence of the koala IFNγ gene. Transcripts were identified in spleen and lymph node tissue samples. Phylogenetic analysis demonstrated that koala IFNγ is closely related to other marsupial IFNγ sequences and more distantly related to eutherian mammals. To begin to characterise the role of this important cytokine in the koala's response to chlamydial infection, we developed a quantitative real time PCR assay and applied it to a small cohort of koalas with and without active chlamydial disease, revealing significant differences in expression patterns between the groups. Description of the IFNγ sequence from the koala will not only assist in understanding this species' response to its most important pathogen but will also provide further insight into the evolution of the marsupial immune system

Molecular cocrystals of 5-(4-bromophenyl)-1,3,4-thiadiazol-2-amine: hydrogen bonding in the structures of the 1:1 adduct with 2-(naphthalen-2-yloxy)acetic acid and the salt with 3,5-dinitrobenzoic acid

The structures of the anhydrous products from the interaction of 2-amino-5-(4-bromophenyl)-1,3,4-thiadiazole with (2-naphthoxy)acetic acid, the 1:1 adduct C8H6BrN3S . C12H10O3 (I) and 3,5-dinitrobenzoic acid, the salt C8H7BrN3S+ C7H3N2O6- (II) have been determined. In the adduct (I), a heterodimer is formed through a cyclic hydrogen-bonding motif [graph set R2/2(8)], involving carboxylic acid O-H...N(hetero)and amine N-H...O(carboxyl) interactions. The heterodimers are essentially planar with a thiadiazole to naphthyl ring dihedral angle of 15.9(2)deg. and the intramolecular thiadiazole to phenyl ring angle of 4.7(2)deg. An amine N-H...N(hetero) hydrogen bond between the heterodimers generates a one-dimensional chain structure extending down [001]. Also present are weak benzene-benzene and naphthalene-naphthalene pi-pi stacking interactions down the b axis [minimum ring centroid separation, 3.936(3) Ang.]. With the salt (II), the cation-anion association is also through a cyclic R2/2(8) motif but involving duplex N-H...O(carboxyl) hydrogen bonds, giving a heterodimer which is close to planar [dihedral angles between the thiadiazole ring and the two benzene rings, 5.00(16)deg. (intra) and 7.23(15)deg. (inter)]. A secondary centrosymmetric cyclic N-H...O(carboxyl) hydrogen-bonding association involving the second amino H-atom generates a heterotetramer. Also present in the crystal are weak pi-pi i-\p interactions between thiadiazolium rings [minimum ring centroid separation, 3.936(3)Ang.], as well as a short Br...O(nitro) interaction [3.314(4)Ang.]. The two structures reported here now provide a total of three crystallographically characterized examples of co-crystalline products from the interaction of 2-amino-5-(4-bromophenyl)-1,3,4-thiadiazole with carboxylic acids, of which only one involves proton-transfer.

Infrared and Raman spectroscopic characterization of the carbonate mineral huanghoite - and in comparison with selected rare earth carbonates

Raman spectroscopy complimented with infrared spectroscopy has been used to study the rare earth based mineral huanghoite with possible formula given as BaCe(CO3)2F and compared with the Raman spectra of a series of selected natural halogenated carbonates from different origins including bastnasite, parisite and northupite. The Raman spectrum of huanghoite displays three bands are at 1072, 1084 and 1091 cm−1 attributed to the symmetric stretching vibration. The observation of three symmetric stretching vibrations is very unusual. The position of symmetric stretching vibration varies with mineral composition. Infrared spectroscopy of huanghoite show bands at 1319, 1382, 1422 and 1470 cm−1. No Raman bands of huanghoite were observed in these positions. Raman spectra of bastnasite, parisite and northupite show a single band at 1433, 1420 and 1554 cm−1 assigned to the ν3 (CO3)2− antisymmetric stretching mode. The observation of additional Raman bands for the ν3 modes for some halogenated carbonates is significant in that it shows distortion of the carbonate anion in the mineral structure. Four Raman bands for huanghoite are observed at 687, 704, 718 and 730 cm−1and assigned to the (CO3)2− ν2 bending modes. Raman bands are observed for huanghoite at around 627 cm−1 and are assigned to the (CO3)2− ν4 bending modes. Raman bands are observed for the carbonate ν4 in phase bending modes at 722 cm−1 for bastnasite, 736 and 684 cm−1 for parisite, 714 cm−1 for northupite. Raman bands for huanghoite observed at 3259, 3484 and 3589 cm−1 are attributed to water stretching bands. Multiple bands are observed in the OH stretching region for bastnasite and parisite indicating the presence of water and OH units in their mineral structure. Vibrational spectroscopy enables new information on the structure of huanghoite to be assessed.

Vibrational spectroscopic study of the uranyl selenite mineral derriksite Cu4UO2(SeO3)2(OH)6⋅H2O

Raman spectrum of the mineral derriksite Cu4UO2(SeO3)2(OH)6⋅H2O was studied and complemented by the infrared spectrum of this mineral. Both spectra were interpreted and partly compared with the spectra of demesmaekerite, marthozite, larisaite, haynesite and piretite. Observed Raman and infrared bands were attributed to the (UO2)2+, (SeO3)2−, (OH)− and H2O vibrations. The presence of symmetrically distinct hydrogen bonded molecule of water of crystallization and hydrogen bonded symmetrically distinct hydroxyl ions was inferred from the spectra in the derriksite unit cell. Approximate U–O bond lengths in uranyl and O–H⋯O hydrogen bond lengths were calculated from the Raman and infrared spectra of derriksite.

Assessment of the molecular structure of natrodufrénite – NaFe2+Fe3+5(PO4)4(OH)6•2(H2O), a secondary pegmatite phosphate mineral from Minas Gerais, Brazil

The mineral natrodufrénite a secondary pegmatite phosphate mineral from Minas Gerais, Brazil, has been studied by a combination of scanning electron microscopy and vibrational spectroscopic techniques. Electron probe analysis shows the formula of the studied mineral as (Na0.88Ca0.12)∑1.00(Mn0.11Mg0.08Ca0.04Zr0.01Cu0.01)∑0.97(Al0.02)∑4.91(PO4)3.96(OH6.15F0.07)6.22⋅2.05(H2O). Raman spectroscopy identifies an intense peak at 1003 cm−1 assigned to the ν1 symmetric stretching mode. Raman bands are observed at 1059 and 1118 cm−1 and are attributed to the ν3 antisymmetric stretching vibrations. A comparison is made with the spectral data of other hydrate hydroxy phosphate minerals including cyrilovite and wardite. Raman bands at 560, 582, 619 and 668 cm−1 are assigned to the ν4 bending modes and Raman bands at 425, 444, 477 and 507 cm−1 are due to the ν2 bending modes. Raman bands in the 2600–3800 cm−1 spectral range are attributed to water and OH stretching vibrations. Vibrational spectroscopy enables aspects of the molecular structure of natrodufrénite to be assessed.

Molecular genetics of migraine

Migraine is a common neurological disorder with a significantly heritable component. It is a complex disease and despite numerous molecular genetic studies, the exact pathogenesis causing the neurological disturbance remains poorly understood. Although several known molecular mechanisms have been associated with an increased risk for developing migraine, there remains significant scope for future studies. The majority of studies have investigated the most plausible candidate genes involved in common migraine pathogenesis utilising criteria that takes into account a combination of physiological functionality in conjunction with regions of genomic association. Thus, far genes involved in neurological, vascular or hormonal pathways have been identified and investigated on this basis. Genome-wide association studies (GWAS) studies have helped to identify novel regions that may be associated with migraine and have aided in providing the basis for further molecular investigations. However, further studies utilising sequencing technologies are required to characterise the genetic basis for migraine.

Identification of molecular genetic factors that influence migraine

Migraine is a common neurological disorder with a strong genetic basis. However, the complex nature of the disorder has meant that few genes or susceptibility loci have been identified and replicated consistently to confirm their involvement in migraine. Approaches to genetic studies of the disorder have included analysis of the rare migraine subtype, familial hemiplegic migraine with several causal genes identified for this severe subtype. However, the exact genetic contributors to the more common migraine subtypes are still to be deciphered. Genome-wide studies such as genome-wide association studies and linkage analysis as well as candidate genes studies have been employed to investigate genes involved in common migraine. Neurological, hormonal and vascular genes are all considered key factors in the pathophysiology of migraine and are a focus of many of these studies. It is clear that the influence of individual genes on the expression of this disorder will vary. Furthermore, the disorder may be dependent on gene–gene and gene–environment interactions that have not yet been considered. In addition, identifying susceptibility genes may require phenotyping methods outside of the International Classification of Headache Disorders II criteria, such as trait component analysis and latent class analysis to better define the ambit of migraine expression.

Genetics of menstrual migraine : the molecular evidence

Migraine is considered to be a multifactorial disorder in which genetic, environmental, and, in the case of menstrual and menstrually related migraine, hormonal events influence the phenotype. Certainly, the role of female sex hormones in migraine has been well established, yet the mechanism behind this well-known relationship remains unclear. This review focuses on the potential role of hormonally related genes in migraine, summarizes results of candidate gene studies to date, and discusses challenges and issues involved in interpreting hormone-related gene results. In light of the molecular evidence presented, we discuss future approaches for analysis with the view to elucidate the complex genetic architecture that underlies the disorder.

A molecular genetic approach for forensic animal species identification

This study investigated potential markers within chromosomal, mitochondrial DNA (mtDNA) and ribosomal RNA (rRNA) with the aim of developing a DNA based method to allow differentiation between animal species. Such discrimination tests may have important applications in the forensic science, agriculture, quarantine and customs fields. DNA samples from five different animal individuals within the same species for 10 species of animal (including human) were analysed. DNA extraction and quantitation followed by PCR amplification and GeneScan visualisation formed the basis of the experimental analysis. Five gene markers from three different types of genes were investigated. These included genomic markers for the β-actin and TP53 tumor suppressor gene. Mitochondrial DNA markers, designed by Bataille et al. [Forensic Sci. Int. 99 (1999) 165], examined the Cytochrome b gene and Hypervariable Displacement Loop (D-Loop) region. Finally, a ribosomal RNA marker for the 28S rRNA gene optimised by Naito et al. [J. Forensic Sci. 37 (1992) 396] was used as a possible marker for speciation. Results showed a difference of only several base pairs between all species for the β-actin and 28S markers, with the exception of Sus scrofa (pig) β-actin fragment length, which produced a significantly smaller fragment. Multiplexing of Cytochrome b and D-Loop markers gave limited species information, although positive discrimination of human DNA was evident. The most specific and discriminatory results were shown using the TP53 gene since this marker produced greatest fragment size differences between animal species studied. Sample differentiation for all species was possible following TP53 amplification, suggesting that this gene could be used as a potential animal species identifier.

Molecular mechanisms of migraine

Migraine is a common complex disorder that affects a large portion of the population and thus incurs a substantial economic burden on society. The disorder is characterized by recurrent headaches that are unilateral and usually accompanied by nausea, vomiting, photophobia, and phonophobia. The range of clinical characteristics is broad and there is evidence of comorbidity with other neurological diseases, complicating both the diagnosis and management of the disorder. Although the class of drugs known as the triptans (serotonin 5-HT1B/1D agonists) has been shown to be effective in treating a significant number of patients with migraine, treatment may in the future be further enhanced by identifying drugs that selectively target molecular mechanisms causing susceptibility to the disease. Genetically, migraine is a complex familial disorder in which the severity and susceptibility of individuals is most likely governed by several genes that may be different among families. Identification of the genomic variants involved in genetic predisposition to migraine should facilitate the development of more effective diagnostic and therapeutic applications. Genetic profiling, combined with our knowledge of therapeutic response to drugs, should enable the development of specific, individually-tailored treatment.

Vibrational spectroscopic characterization of the phosphate mineral barbosalite Fe2+Fe3+2(PO4)2(OH)2 : implications for the molecular structure

Natural single-crystal specimens of barbosalite from Brazil, with general formula Fe2+Fe3+ 2 (PO4)2(OH)2 were investigated by Raman and infrared spectroscopy. The mineral occurs as secondary products in granitic pegmatites. The Raman spectrum of barbosalite is characterized by bands at 1020, 1033 and 1044 cm−1 cm−1, assigned to ν1 symmetric stretching mode of the HOPO3- 3 and PO3- 4 units. Raman bands at around 1067, 1083 and 1138 cm−1 are attributed to both the HOP and PO antisymmetric stretching vibrations. The set of Raman bands observed at 575, 589 and 606 cm−1 are assigned to the ν4 out of plane bending modes of the PO4 and H2PO4 units. Raman bands at 439, 461, 475 and 503 cm−1 are attributed to the ν2 PO4 and H2PO4 bending modes. Strong Raman bands observed at 312, 346 cm−1 with shoulder bands at 361, 381 and 398 cm−1 are assigned to FeO stretching vibrations. No bands which are attributable to water vibrations were found. Vibrational spectroscopy enables aspects of the molecular structure of barbosalite to be assessed.

Infrared and Raman spectroscopic characterization of the arsenate mineral ceruleite Cu2Al7(AsO4)4(OH)13⋅11.5(H2O)

The molecular structure of the arsenate mineral ceruleite has been assessed using a combination of Raman and infrared spectroscopy. The most intense band observed at 903 cm-1 is assigned to the (AsO4)3- symmetric stretching vibrational mode. The infrared spectrum shows intense bands at 787, 827 and 886 cm-1, ascribed to the triply degenerate m3 antisymmetric stretching vibration. Raman bands observed at 373, 400, 417 and 430 cm-1 are attributed to the m2 vibrational mode. Three broad bands for ceruleite found at 3056, 3198 and 3384 cm-1 are assigned to water OH stretching bands. By using a Libowitzky empirical equation, hydrogen bond distances of 2.65 and 2.75 Å are calculated. Vibrational spectra enable the molecular structure of the ceruleite mineral to be determined and whilst similarities exist in the spectral patterns with the roselite mineral group, sufficient differences exist to be able to determine the identification of the minerals.

Raman, infrared and near-infrared spectroscopic characterization of the herderite-hydroxylherderite mineral series

Natural single-crystal specimens of the herderite-hydroxylherderite series from Brazil, with general formula CaBePO4(F,OH), were investigated by electron microprobe, Raman, infrared and near-infrared spectroscopies. The minerals occur as secondary products in granitic pegmatites. Herderite and hydroxylherderite minerals show extensive solid solution formation. The Raman spectra of hydroxylherderite are characterized by bands at around 985 and 998 cm-1, assigned to ν1 symmetric stretching mode of the HOPO33- and PO43- units. Raman bands at around 1085, 1128 and 1138 cm-1 are attributed to both the HOP and PO antisymmetric stretching vibrations. The set of Raman bands observed at 563, 568, 577, 598, 616 and 633 cm-1 are assigned to the ν4 out of plane bending modes of the PO4 and H2PO4 units. The OH Raman stretching vibrations of hydroxylherderite were observed ranging from 3626 cm-1 to 3609 cm-1. The infrared stretching vibrations of hydroxylherderites were observed between 3606 cm-1 and 3599 cm-1. By using a Libowitzky type function, hydrogen bond distances based upon the OH stretching bands were calculated. Characteristic NIR bands at around 6961 and 7054 cm-1 were assigned to the first overtone of the fundamental, whilst NIR bands at 10194 and 10329 cm-1 are assigned to the second overtone of the fundamental OH stretching vibration. Insight into the structure of the herderite-hydroxylherderite series is assessed by vibrational spectroscopy.