Assessing low-maturity organic matter in shales using Raman spectroscopy : effects of sample preparation and operating procedure

Laser Raman spectroscopy is used to assess the thermal maturity of organic matter in sedimentary rocks, particularly organic-rich mudstones. However, discrepancies exist between quantified Raman spectral parameters and maturity values obtained by vitrinite reflectance. This has prevented the adoption of a standard protocol for the determination of thermal maturity of organic matter (OM) by Raman spectroscopy. We have examined the factors influencing the Raman spectra obtained from low-maturity OM in potential shale gas reservoir rocks. The inconsistencies in Raman results obtained are due to three main factors that are critically evaluated: (1) different operational procedures, including experiment setup and spectral processing methods; (2) different methods of sample preparation; (3) the analysis of diverse types of OM. These factors are scrutinized to determine the sources of inconsistency and potential bias in Raman results, and guidance is offered on the development of robust and reproducible analytical protocols. We present two new Raman parameters for un-deconvolved spectra named the DA1/GA ratio (area ratio of 1100–1400 cm−1/1550–1650 cm−1) and SSA (scaled spectrum area: sum of total area between 1100 and 1700 cm−1) that offer potential maturity proxies. An automated spreadsheet procedure is presented that processes raw Raman spectra and calculates several of the most commonly used Raman parameters, including the two new variables

Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation

We present molecular dynamics simulations of unliganded human hemoglobin (Hb) A under physiological conditions, starting from the R, R2, and T state. The simulations were carried out with protonated and deprotonated HC3 histidines His(β)146, and they sum up to a total length of 5.6µs. We observe spontaneous and reproducible T→R quaternary transitions of the Hb tetramer and tertiary transitions of the α and β subunits, as detected from principal component projections, from an RMSD measure, and from rigid body rotation analysis. The simulations reveal a marked asymmetry between the α and β subunits. Using the mutual information as correlation measure, we find that the β subunits are substantially more strongly linked to the quaternary transition than the α subunits. In addition, the tertiary populations of the α and β subunits differ substantially, with the β subunits showing a tendency towards R, and the α subunits showing a tendency towards T. Based on the simulation results, we present a transition pathway for coupled quaternary and tertiary transitions between the R and T conformations of Hb

Identification of Inhibitors against Mycobacterium tuberculosis Thiamin Phosphate Synthase, an Important Target for the Development of Anti-TB Drugs

Tuberculosis (TB) continues to pose a serious challenge to human health afflicting a large number of people throughout the world. In spite of the availability of drugs for the treatment of TB, the non-compliance to 6–9 months long chemotherapeutic regimens often results in the emergence of multidrug resistant strains of Mycobacterium tuberculosis adding to the precariousness of the situation. This has necessitated the development of more effective drugs. Thiamin biosynthesis, an important metabolic pathway of M.tuberculosis, is shown to be essential for the intracellular growth of this pathogen and hence, it is believed that inhibition of this pathway would severely affect the growth of M.tuberculosis. In this study, a comparative homology model of M.tuberculosis thiamin phosphate synthase (MtTPS) was generated and employed for virtual screening of NCI diversity set II to select potential inhibitors. The best 39 compounds based on the docking results were evaluated for their potential to inhibit the MtTPS activity. Seven compounds inhibited MtTPS activity with IC50 values ranging from 20 – 100 µg/ml and two of these exhibited weak inhibition of M.tuberculosis growth with MIC99 values being 125 µg/ml and 162.5 µg/ml while one compound was identified as a very potent inhibitor of M.tuberculosis growth with an MIC99 value of 6 µg/ml. This study establishes MtTPS as a novel drug target against M.tuberculosis leading to the identification of new lead molecules for the development of antitubercular drugs. Further optimization of these lead compounds could result in more potent therapeutic molecules against Tuberculosis

Insight into the Mechanisms of Adenovirus Capsid Disassembly from Studies of Defensin Neutralization

Defensins are effectors of the innate immune response with potent antibacterial activity. Their role in antiviral immunity, particularly for non-enveloped viruses, is poorly understood. We recently found that human alpha-defensins inhibit human adenovirus (HAdV) by preventing virus uncoating and release of the endosomalytic protein VI during cell entry. Consequently, AdV remains trapped in the endosomal/lysosomal pathway rather than trafficking to the nucleus. To gain insight into the mechanism of defensin-mediated neutralization, we analyzed the specificity of the AdV-defensin interaction. Sensitivity to alpha-defensin neutralization is a common feature of HAdV species A, B1, B2, C, and E, whereas species D and F are resistant. Thousands of defensin molecules bind with low micromolar affinity to a sensitive serotype, but only a low level of binding is observed to resistant serotypes. Neutralization is dependent upon a correctly folded defensin molecule, suggesting that specific molecular interactions occur with the virion. CryoEM structural studies and protein sequence analysis led to a hypothesis that neutralization determinants are located in a region spanning the fiber and penton base proteins. This model was supported by infectivity studies using virus chimeras comprised of capsid proteins from sensitive and resistant serotypes. These findings suggest a mechanism in which defensin binding to critical sites on the AdV capsid prevents vertex removal and thereby blocks subsequent steps in uncoating that are required for release of protein VI and endosomalysis during infection. In addition to informing the mechanism of defensin-mediated neutralization of a non-enveloped virus, these studies provide insight into the mechanism of AdV uncoating and suggest new strategies to disrupt this process and inhibit infection

Raman spectroscopy as a tool to determine the thermal maturity of organic matter : application to sedimentary, metamorphic and structural geology

Raman spectrometry is a rapid, non-destructive alternative to conventional tools employed to assess the thermal alteration of organic matter (OM). Raman may be used to determine vitrinite reflectance equivalent OM maturity values for petroleum exploration, to provide temperature data for metamorphic studies, and to determine the maximum temperatures reached in fault zones. To achieve the wider utilisation of Raman, the spectrum processing method, and the positions and nomenclature of Raman bands and parameters, all need to be standardized. We assess the most widely used Raman parameters as well as the best analytical practices that have been proposed. Raman band separation and G-band full-width at half-maximum are the best parameters to estimate the maturity for rocks following diagenesis–metagenesis. For metamorphic studies, the ratios of band areas after performing deconvolution are generally used. Further work is needed on the second-order region, as well as assessing the potential of using integrated areas on the whole spectrum, to increase the calibrated temperature range of Raman parameters. Applying Raman spectroscopy on faults has potential to be able to infer both temperature and deformation processes. We propose a unified terminology for OM Raman bands and parameters that should be adopted in the future. The popular method of fitting several functions to a spectrum is generally unnecessary, as Raman parameters determined from an un-deconvoluted spectrum can track the maturity of OM. To progress the Raman application as a geothermometer a standardized approach must be developed and tested by means of an interlaboratory calibration exercise using reference materials

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