Journal Articles, De Gruyter

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  • Application of the Linkam TS1400XY heating stage to melt inclusion studies
    Esposito, Rosario; Klébesz, Rita; Bartoli, Omar; Klyukin, Yury I.; Moncada, Daniel; Doherty, Angela L.; Bodnar, Robert J. (De Gruyter, 2012-05-13)
    Melt inclusions (MI) trapped in igneous phenocrysts provide one of the best tools available for characterizing magmatic processes. Some MI experience post-entrapment modifications, including crystallization of material on the walls, formation of a vapor bubble containing volatiles originally dissolved in the melt, or partial to complete crystallization of the melt. In these cases, laboratory heating may be necessary to return the MI to its original homogeneous melt state, followed by rapid quenching of the melt to produce a homogeneous glass phase, before microanalyses can be undertaken. Here we describe a series of heating experiments that have been performed on crystallized MI hosted in olivine, clinopyroxene and quartz phenocrysts, using the Linkam TS1400XY microscope heating stage. During the experiments, we have recorded the melting behaviors of the MI up to a maximum temperature of 1360°C. In most of the experiments, the MI were homogenized completely (without crystals or bubbles) and remained homogeneous during quenching to room temperature. The resulting single phase MI contained a homogeneous glass phase. These tests demonstrate the applicability of the Linkam TS1400XY microscope heating stage to homogenize and quench MI to produce homogeneous glasses that can be analyzed with various techniques such as Electron Microprobe (EMP), Secondary Ion Mass Spectrometry (SIMS), Laser ablation Inductively Coupled Plasma Mass Spectrometry (LA ICP-MS), Raman spectroscopy, FTIR spectroscopy, etc. During heating experiments, the optical quality varied greatly between samples and was a function of not only the temperature of observation, but also on the amount of matrix glass attached to the phenocryst, the presence of other MI in the sample which are connected to the outside of the crystal, and the existence of mineral inclusions in the host.
  • Composition and origin of nodules from the ≈20 ka Pomici di Base (PB)-Sarno eruption of Mt. Somma – Vesuvius, Italy
    Klébesz, Rita; Bodnar, Robert J.; De Vivo, Benedetto; Török, Kálmán; Lima, Annamaria; Petrosino, Paola (De Gruyter, 2012-05-13)
    Nodules (coarse-grain “plutonic” rocks) were collected from the ca. 20 ka Pomici di Base (PB)-Sarno eruption of Mt. Somma-Vesuvius, Italy. The nodules are classified as monzonite-monzogabbro based on their modal composition. The nodules have porphyrogranular texture, and consist of An-rich plagioclase, K-feldspar, clinopyroxene (ferroan-diopside), mica (phlogopite-biotite) ± olivine and amphibole. Aggregates of irregular intergrowths of mostly alkali feldspar and plagioclase, along with mica, Fe-Ti-oxides and clinopyroxene, in the nodules are interpreted as crystallized melt pockets. Crystallized silicate melt inclusions (MI) are common in the nodules, especially in clinopyroxenes. Two types of MI have been identified. Type I consists of mica, Fe-Ti-oxides and/or dark green spinel, clinopyroxene, feldspar and a vapor bubble. Volatiles (CO2, H2O) could not be detected in the vapor bubbles by Raman spectroscopy. Type II inclusions are generally lighter in color and contain subhedral feldspar and/or glass and several opaque phases, most of which are confirmed to be oxide minerals by SEM analysis. Some of the opaque-appearing phases that are below the surface may be tiny vapor bubbles. The two types of MI have different chemical compositions. Type I MI are classified as phono-tephrite — tephri-phonolite — basaltic trachy-andesite, while Type II MI have basaltic composition. The petrography and MI geochemistry led us to conclude that the nodules represent samples of the crystal mush zone in the active plumbing system of Mt. Somma-Vesuvius that were entrained into the upwelling magma during the PB-Sarno eruption.
  • Gangue mineral textures and fluid inclusion characteristics of the Santa Margarita Vein in the Guanajuato Mining District, Mexico
    Moncada, Daniel; Bodnar, Robert J. (De Gruyter, 2012-05-13)
    Successful exploration for mineral deposits requires tools that the explorationist can use to distinguish between targets with high potential for mineralization and those with lower economic potential. In this study, we describe a technique based on gangue mineral textures and fluid inclusion characteristics that has been applied to identify an area of high potential for gold-silver mineralization in the epithermal Ag-Au deposits at Guanajuato, Mexico. The Guanajuato mining district in Mexico is one of the largest silver producing districts in the world with continuous mining activity for nearly 500 years. Previous work conducted on the Veta Madre vein system that is located in the central part of this district identified favorable areas for further exploration in the deepest levels that have been developed and explored. The resulting exploration program discovered one of the richest gold-silver veins ever found in the district. This newly discovered vein that runs parallel to the Veta Madre was named the Santa Margarita vein. Selected mineralized samples from this vein contain up to 249 g/t of Au and up to 2,280 g/t Ag. Fluid inclusions in these samples show homogenization temperatures that range from 184 to 300°C and salinities ranging from 0 to 5 wt.% NaCl. Barren samples show the same range in homogenization temperature, but salinities range only up to 3 wt.% NaCl. Evidence of boiling was observed in most of the samples based on fluid inclusions and/or quartz and calcite textures. Liquid-rich inclusions with trapped illite are closely associated with high silver grades. The presence of assemblages of vapor-rich-only fluid inclusions, indicative of intense boiling or “flashing”, shows the best correlation with high gold grades.
  • Quartz precipitation and fluid inclusion characteristics in sub-seafloor hydrothermal systems associated with volcanogenic massive sulfide deposits
    Steele-MacInnis, Matthew; Han, Liang; Lowell, Robert P.; Rimstidt, J. Donald; Bodnar, Robert J. (De Gruyter, 2012-05-13)
    Results of a numerical modeling study of quartz dissolution and precipitation in a sub-seafloor hydrothermal system have been used to predict where in the system quartz could be deposited and potentially trap fluid inclusions. The spatial distribution of zones of quartz dissolution and precipitation is complex, owing to the fact that quartz solubility depends on many inter-related factors, including temperature, fluid salinity and fluid immiscibility, and is further complicated by the fact that quartz exhibits both prograde and retrograde solubility behavior, depending on the fluid temperature and salinity. Using the PVTX properties of H2O-NaCl, the petrographic and microthermometric properties of fluid inclusions trapped at various locations within the hydrothermal system have been predicted. Vapor-rich inclusions are trapped as a result of the retrograde temperature-dependence of quartz solubility as the convecting fluid is heated in the vicinity of the magmatic heat source. Coexisting liquid-rich and vapor-rich inclusions are also trapped in this region when quartz precipitates as a result of fluid immiscibility that lowers the overall bulk quartz solubility in the system. Fluid inclusions trapped in the shallow subsurface near the seafloor vents and in the underlying stockwork are liquid-rich with homogenization temperatures of 200–400°C and salinities close to that of seawater. Volcanogenic massive sulfide (VMS) deposits represent the uplifted and partially eroded remnants of fossil submarine hydrothermal systems, and the relationship between fluid-inclusion properties and location within the hydrothermal system described here can be used in exploration for VMS deposits to infer the direction towards potential massive sulfide ore.
  • Inhibiting foodborne pathogens Vibrio parahaemolyticus and Listeria monocytogenes using extracts from traditional medicine: Chinese gallnut, pomegranate peel, Baikal skullcap root and forsythia fruit
    Wu, Jian; Goodrich, Katheryn M.; Eifert, Joseph D.; Jahncke, Michael L.; O'Keefe, Sean F.; Welbaum, Gregory E.; Neilson, Andrew P. (De Gruyter, 2018-06-21)
    Foodborne illnesses have been a heavy burden in the United States and globally. Many medicinal herbs have been cultivated in the US and many of which contain antimicrobial compounds with the potential to be used for food preservation. Methanol/water extracts of pomegranate peel (“PP”, Punica Granatum L.), Chinese gallnut (“CG”, Galla chinensis), Forsythia fruit (“FF”, Forsythia suspensa) and Baikal skullcap root (“BS”, Scutellaria baicalensis) were tested for antimicrobial activity using the agar diffusion assay on tryptic soy agar (TSA) and microdilution assay in tryptic soy broth (TSB). CG and PP extracts showed good to excellent inhibitory effect against Vibrio parahaemolyticus and Listeria monocytogenes in both assays, with a minimum inhibitory concentration (MIC) range from 0.04 to 5 mg/mL. BS had moderate inhibitory effects against V. parahaemolyticus with an MIC of 5 mg/mL in TSB, and against L. monocytogenes with an MIC of 20 mg/mL on TSA. CG was analyzed using LC-MS and fractionated using HPLC. The major components were identified as gallic acid, digallic acid, methyl gallate, and gallotannins (oligo-galloyl-D-glucose, nGG, n = 1~10). Six fractions (I - VI) were collected and their antibacterial activities were tested against L. monocytogenes, and V. parahaemolyticus both on TSA and in TSB. On TSA, fraction III, IV and V inhibited V. parahaemolyticus but no fraction inhibited L. monocytogenes. In TSB, all fractions inhibited V. parahaemolyticus and fractions II - V inhibited L. monocytogenes. Future studies are needed to investigate the effects of medicinal plants on food products.
  • Fatgraph models of RNA structure
    Huang, Fenix; Reidys, Christian Michael; Rezazadegan, Reza (De Gruyter, 2017-02-08)
    In this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We discuss various notions of coarse-grained RNA structures and relate them to fatgraphs. We motivate and discuss the main intuition behind the fatgraph model and showcase its applicability to canonical as well as noncanonical base pairs. Recent discoveries regarding novel recursions of pseudoknotted (pk) configurations as well as their translation into context-free grammars for pk-structures are discussed. This is shown to allow for extending the concept of partition functions of sequences w.r.t. a fixed structure having non-crossing arcs to pk-structures. We discuss minimum free energy folding of pk-structures and combine these above results outlining how to obtain an inverse folding algorithm for PK structures.