Matrix isolation of fullerene-derived CO 2 at ambient temperature

NASA Astrophysics Data System (ADS)

Taylor, Roger; Pénicaud, Alain; Tower, Nicole J.

1998-10-01

Heating fullerene oxides, e.g. C 120O, C 70O, C 60O and C 60O 2, in a KBr matrix at 225°C under 0.2 mbar vacuum, produces a sharp IR band at 2330 cm -1 due to matrix-isolated CO 2. The band is also obtained by heating a KBr matrix of the insoluble deposits that fullerenes form on standing in air. The matrices are extremely stable and are unchanged even by prolonged heating at 225°C under vacuum. Heating a KBr matrix of the deposit from C 84 produces also a sharp stable band at 2035 cm -1 consistent with matrix-isolated C 3. Similar treatment of C 70F 38O produces matrices containing both CO 2 and CO, the latter being of lower stability.

Identification of Candida species isolated from vulvovaginitis using matrix assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Alizadeh, Majid; Kolecka, Anna; Boekhout, Teun; Zarrinfar, Hossein; Ghanbari Nahzag, Mohamad A; Badiee, Parisa; Rezaei-Matehkolaei, Ali; Fata, Abdolmajid; Dolatabadi, Somayeh; Najafzadeh, Mohammad J

2017-12-01

Vulvovaginal candidiasis (VVC) is a common problem in women. The purpose of this study was to identify Candida isolates by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from women with vulvovaginitis that were referred to Ghaem Hospital, Mashhad, Iran. This study was conducted on 65 clinical samples isolated from women that were referred to Ghaem Hospital. All specimens were identified using phenotyping techniques, such as microscopy and culture on Sabouraud dextrose agar and corn meal agar. In addition, all isolates were processed for MALDI-TOF MS identification. Out of the 65 analyzed isolates, 61 (94%) samples were recognized by MALDI-TOF MS. However, the remaining four isolates (6%) had no reliable identification. According to the results, C. albicans (58.5%) was the most frequently isolated species, followed by C. tropicalis (16.9%), C. glabrata (7.7%), C. parapsilosis (7.7%), and guilliermondii (3.1%). As the findings indicated, MALDI TOF MS was successful in the identification of clinical Candida species. C. albicans was identified as the most common Candida species isolated from the women with VVC. Moreover, C. tropicalis was the most common species among the non- albicans Candida species.

Photochemistry of matrix isolated (trifluoromethyl)sulfonyl azide, CF₃SO₂N₃.

PubMed

Zeng, Xiaoqing; Beckers, Helmut; Willner, Helge; Neuhaus, Patrik; Grote, Dirk; Sander, Wolfram

2015-03-19

The photochemistry of matrix isolated (trifluoromethylsulfonyl) azide, CF3SO2N3, has been studied at low temperatures. Upon ArF laser irradiation (λ = 193 nm), the azide eliminates N2 and furnishes triplet [(trifluoromethyl)sulfonyl]nitrene, CF3SO2N, which has been characterized by IR and EPR spectroscopy. Upon subsequent UV light irradiation (λ = 260-400 nm) the nitrene converts to CF3N═SO2 and CF3S(O)NO through a Curtius-type rearrangement. Further two new species CF2N═SO2F and FSNO were identified together with CF2NF, SO2, F2CO, CF3NO, and SO as side products. In addition, triplet nitrene CF3N was detected by its EPR and IR spectra. The complex stepwise photodecomposition of matrix isolated CF3SO2N3 is discussed in terms of the observed photolysis products and quantum chemical calculations.

A proteinaceous organic matrix regulates carbonate mineral production in the marine teleost intestine

PubMed Central

Schauer, Kevin L.; LeMoine, Christophe M. R.; Pelin, Adrian; Corradi, Nicolas; Warren, Wesley C.; Grosell, Martin

2016-01-01

Marine teleost fish produce CaCO3 in their intestine as part of their osmoregulatory strategy. This precipitation is critical for rehydration and survival of the largest vertebrate group on earth, yet the molecular mechanisms that regulate this reaction are unknown. Here, we isolate and characterize an organic matrix associated with the intestinal precipitates produced by Gulf toadfish (Opsanus beta). Toadfish precipitates were purified using two different methods, and the associated organic matrix was extracted. Greater than 150 proteins were identified in the isolated matrix by mass spectrometry and subsequent database searching using an O. beta transcriptomic sequence library produced here. Many of the identified proteins were enriched in the matrix compared to the intestinal fluid, and three showed no substantial homology to any previously characterized protein in the NCBI database. To test the functionality of the isolated matrix, a micro-modified in vitro calcification assay was designed, which revealed that low concentrations of isolated matrix substantially promoted CaCO3 production, where high concentrations showed an inhibitory effect. High concentrations of matrix also decreased the incorporation of magnesium into the forming mineral, potentially providing an explanation for the variability in magnesium content observed in precipitates produced by different fish species. PMID:27694946

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

USGS Publications Warehouse

Kennedy, Christina M.; Campbell Grant, Evan H.; Neel, Maile C.; Fagan, William F.; Marpa, Peter P.

2011-01-01

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical nsectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban evelopment, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

Photochemical isomerizations of thiosemicarbazide, a matrix isolation study.

PubMed

Rostkowska, Hanna; Lapinski, Leszek; Kozankiewicz, Boleslaw; Nowak, Maciej J

2012-10-11

Two thione conformers of monomeric thiosemicarbazide were trapped from the gas phase into a low-temperature Ar matrix. A phototransformation converting the less stable form of the compound into the most stable conformer was induced by irradiation with near-IR (λ = 1462 nm) or UV (λ > 320 nm) light. This photoeffect allowed separation of the IR spectra of the observed thione forms. The structures of both observed isomers were identified by comparison of the separated experimental IR spectra with the spectra theoretically predicted for two most stable forms of the compound. The population ratio of the two conformers in an Ar matrix, prior to any irradiation, was estimated to be equal ≈2:1. Irradiation of matrix-isolated thiosemicarbazide with shorter-wavelength UV (λ > 270 nm) light induced a phototautomeric reaction generating thiol forms of the compound.

Potential of SiO2/ZrO2 matrix doped with CoFe2O4 magnetic nanoparticles in achieving integrated magneto-optical isolators

NASA Astrophysics Data System (ADS)

Zamani, Mehdi; Hocini, Abdesselam

2017-05-01

We have investigated the potential of the SiO2/ZrO2 matrix doped with CoFe2O4 magnetic nanoparticles in order to overcome the problem of integration of the magneto-optical isolators (MOIs). In this way, we have performed a theoretical study for the case of designing perfect and adjustable MOIs based on magnetophotonic crystals (MPCs) containing SiO2/ZrO2 matrix doped with CoFe2O4 magnetic nanoparticles as a magnetic medium. Despite the existence the attenuation coefficient for SiO2/ZrO2 matrix at wavelength 1550 nm that leads to a non-perfect transmittance, we could introduce an MPC structure having no reflectance; therefore, an ideal MOI for eliminating unwanted back-reflection could be achieved.

Survival of human pre-antral follicles after cryopreservation of ovarian tissue, follicular isolation and in vitro culture in a calcium alginate matrix.

PubMed

Amorim, Christiani A; Van Langendonckt, Anne; David, Anu; Dolmans, Marie-Madeleine; Donnez, Jacques

2009-01-01

Ovarian tissue cryopreservation is a promising technique to safeguard fertility in cancer patients. However, in some types of cancer, there is a risk of transmitting malignant cells present in the cryopreserved tissue. To avoid such a risk, pre-antral follicles could be isolated from ovarian tissue and grown in vitro. On the basis of this assumption, the aim of our study was to investigate in vitro survival and growth of pre-antral follicles after cryopreservation of ovarian tissue and follicular isolation, followed by encapsulation in alginate beads. Ovarian biopsies from four patients were frozen and thawed. Pre-antral follicles were then isolated and embedded in an alginate matrix before in vitro culture for 7 days. Small pre-antral follicles (42.98 +/- 9.06 microm) from frozen-thawed tissue can survive and develop after enzymatic isolation and in vitro culture. A total of 159 follicles were incubated in a three-dimensional system (alginate hydrogel) and, after 7 days, all of them showed an increase in size (final size 56.73 +/- 13.10 microm). The survival rate of the follicles was 90% (oocyte and all granulosa cells viable). Our preliminary results indicate that alginate hydrogels may be a suitable system for in vitro culture of isolated human pre-antral follicles. However, more studies are required to establish whether follicular morphology and functionality can be maintained using this matrix.

Polyfluorides and Neat Fluorine as Host Material in Matrix-Isolation Experiments.

PubMed

Brosi, Felix; Vent-Schmidt, Thomas; Kieninger, Stefanie; Schlöder, Tobias; Beckers, Helmut; Riedel, Sebastian

2015-11-09

The use of neat fluorine in matrix isolation is reported, as well as the formation of polyfluoride monoanions under cryogenic conditions. Purification procedures and spectroscopic data of fluorine are described, and matrix shifts of selected molecules and impurities in solid fluorine are compared to those of common matrix gases (Ar, Kr, N2 , Ne). The reaction of neat fluorine and IR-laser ablated metal atoms to yield fluorides of chromium (CrF5 ), palladium (PdF2 ), gold (AuF5 ), and praseodymium (PrF4 ) has been investigated. The fluorides have been characterized in solid fluorine by IR spectroscopy at 5 K. Also the fluorination of Kr and the photo-dismutation of XeO4 have been studied by using IR spectroscopy in neat fluorine. Formation of the [F5 ](-) ion was obtained by IR-laser ablation of platinum in the presence of fluorine and proven in a Ne matrix at 5 K by two characteristic vibrational bands of [F5 ](-) at $\\tilde \

Human umbilical cord derived matrix: A scaffold suitable for tissue engineering application.

PubMed

Dan, Pan; Velot, Émilie; Mesure, Benjamin; Groshenry, Guillaume; Bacharouche, Jalal; Decot, Véronique; Menu, Patrick

2017-01-01

Human tissue derived natural extracellular matrix (ECM) has great potential in tissue engineering. We sought to isolate extracellular matrix derived from human umbilical cord and test its potential in tissue engineering. An enzymatic method was applied to isolate and solubilized complete human umbilical cord derived matrix (hUCM). The obtained solution was analyzed for growth factors, collagen and residual DNA contents, then used to coat 2D and 3D surfaces for cell culture application. The hUCM was successfully isolated with trypsin digestion to acquire a solution containing various growth factors and collagen but no residual DNA. This hUCM solution can form a coating on 2D and 3D substrates suitable cell culture. We developed a new matrix derived from human source that can be further used in tissue engineering.

Identification of Candida species isolated from vulvovaginitis using matrix assisted laser desorption ionization-time of flight mass spectrometry

PubMed Central

Alizadeh, Majid; Kolecka, Anna; Boekhout, Teun; Zarrinfar, Hossein; Ghanbari Nahzag, Mohamad. A; Badiee, Parisa; Rezaei-Matehkolaei, Ali; Fata, Abdolmajid; Dolatabadi, Somayeh; Najafzadeh, Mohammad. J

2017-01-01

Background and Purpose: Vulvovaginal candidiasis (VVC) is a common problem in women. The purpose of this study was to identify Candida isolates by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from women with vulvovaginitis that were referred to Ghaem Hospital, Mashhad, Iran. Materials and Methods: This study was conducted on 65 clinical samples isolated from women that were referred to Ghaem Hospital. All specimens were identified using phenotyping techniques, such as microscopy and culture on Sabouraud dextrose agar and corn meal agar. In addition, all isolates were processed for MALDI-TOF MS identification. Results: Out of the 65 analyzed isolates, 61 (94%) samples were recognized by MALDI-TOF MS. However, the remaining four isolates (6%) had no reliable identification. According to the results, C. albicans (58.5%) was the most frequently isolated species, followed by C. tropicalis (16.9%), C. glabrata (7.7%), C. parapsilosis (7.7%), and guilliermondii (3.1%). Conclusion: As the findings indicated, MALDI TOF MS was successful in the identification of clinical Candida species. C. albicans was identified as the most common Candida species isolated from the women with VVC. Moreover, C. tropicalis was the most common species among the non-albicans Candida species. PMID:29707675

Differentiation of Streptococcus pneumoniae Conjunctivitis Outbreak Isolates by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry▿

PubMed Central

Williamson, Yulanda M.; Moura, Hercules; Woolfitt, Adrian R.; Pirkle, James L.; Barr, John R.; Carvalho, Maria Da Gloria; Ades, Edwin P.; Carlone, George M.; Sampson, Jacquelyn S.

2008-01-01

Streptococcus pneumoniae (pneumococcus [Pnc]) is a causative agent of many infectious diseases, including pneumonia, septicemia, otitis media, and conjunctivitis. There have been documented conjunctivitis outbreaks in which nontypeable (NT), nonencapsulated Pnc has been identified as the etiological agent. The use of mass spectrometry to comparatively and differentially analyze protein and peptide profiles of whole-cell microorganisms remains somewhat uncharted. In this report, we discuss a comparative proteomic analysis between NT S. pneumoniae conjunctivitis outbreak strains (cPnc) and other known typeable or NT pneumococcal and streptococcal isolates (including Pnc TIGR4 and R6, Streptococcus oralis, Streptococcus mitis, Streptococcus pseudopneumoniae, and Streptococcus pyogenes) and nonstreptococcal isolates (including Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus) as controls. cPnc cells and controls were grown to mid-log phase, harvested, and subsequently treated with a 10% trifluoroacetic acid-sinapinic acid matrix mixture. Protein and peptide fragments of the whole-cell bacterial isolate-matrix combinations ranging in size from 2 to 14 kDa were evaluated by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Additionally Random Forest analytical tools and dendrogramic representations (Genesis) suggested similarities and clustered the isolates into distinct clonal groups, respectively. Also, a peak list of protein and peptide masses was obtained and compared to a known Pnc protein mass library, in which a peptide common and unique to cPnc isolates was tentatively identified. Information gained from this study will lead to the identification and validation of proteins that are commonly and exclusively expressed in cPnc strains which could potentially be used as a biomarker in the rapid diagnosis of pneumococcal conjunctivitis. PMID:18708515

Synchronized flash photolysis and pulse deposition in matrix isolation experiments

NASA Technical Reports Server (NTRS)

Allamandola, Louis J.; Lucas, Donald; Pimentel, George C.

1978-01-01

An apparatus is described which permits flash photolysis of a pulse-deposited gas mixture in a matrix isolation experiment. This technique obviates the limitations of in situ photolysis imposed by the cage effect and by secondary photolysis. The matrix is deposited in pulses at 30-s intervals and photolyzed sequentially by four synchronized flashlamps approximately 1 ms before the pulse strikes the cold surface. Pulsed deposition maintains adequate isolation and causes line narrowing, which enhances spectral sensitivity. The efficacy of flash photolysis combined with pulsed deposition for producing and trapping transient species was demonstrated by infrated detection of CF3 (from photolysis of CF3I/Ar mixtures) and of ClCO (from photolysis of Cl2/CO/Ar mixtures). The apparatus was used to study the photolytic decomposition of gaseous tricarbonylironcyclobutadiene, C4H4Fe(CO)3. The results indicate that the primary photolytic step is not elimination of C4H4, as suggested earlier, but rather of CO.

Influence of different metal ions on the ultrastructure, biochemical properties, and protein localization of the K562 cell nuclear matrix.

PubMed

Neri, L M; Bortul, R; Zweyer, M; Tabellini, G; Borgatti, P; Marchisio, M; Bareggi, R; Capitani, S; Martelli, A M

1999-06-01

The higher order of chromatin organization is thought to be determined by the nuclear matrix, a mainly proteinaceous structure that would act as a nucleoskeleton. The matrix is obtained from isolated nuclei by a series of extraction steps involving the use of high salt and nonspecific nucleases, which remove chromatin and other loosely bound components. It is currently under debate whether these structures, isolated in vitro by unphysiological extraction buffers, correspond to a nucleoskeleton existing in vivo. In most cell types investigated, the nuclear matrix does not spontaneously resist these extractions steps; rather, it must be stabilized before the application of extracting agents. In this study nuclei, isolated from K562 human erythroleukemia cells, were stabilized by incubation with different metal ions (Ca2+, Cu2+, Zn2+, Cd2+), and the matrix was obtained by extraction with 2 M NaCl. By means of ultrastructural analysis of the resulting structures, we determined that, except for Ca2+, all the other metals induced a stabilization of the matrix, which retained the inner fibrogranular network and residual nucleoli. The biochemical composition, analyzed by two-dimensional gel electrophoresis separation, exhibited a distinct matrix polypeptide pattern, characteristic of each type of stabilizing ion employed. We also investigated to what extent metal ions could maintain in the final structures the original distribution of three inner matrix components, i.e. NuMA, topoisomerase IIalpha, and RNP. Confocal microscopy analysis showed that only NuMa, and, to a lesser extent, topoisomerase IIalpha, were unaffected by stabilization with divalent ions. On the contrary, the fluorescent RNP patterns detected in the resulting matrices were always disarranged, irrespective of the stabilization procedure. These results indicate that several metal ions are powerful stabilizing agents of the nuclear matrix prepared from K562 erythroleukemia cells and also strengthen the concept that NuMA and topoisomerase IIalpha may act as structural components of the nuclear matrix.

Estimation of the rotamerization constants of different conformations of N-acetylalanine: a theoretical and matrix-isolation FT-IR study.

PubMed

Boeckx, Bram; Maes, Guido

2012-02-01

The conformational landscape of N-acetylalanine has been investigated by a theoretical and matrix-isolation FT-IR study. Optimizations of N-acetylalanine structures has been conducted at successive higher levels of theory HF/3-21G, DFT(B3LYP)/6-31++G** and MP2/6-31++G**. This resulted in three stable conformations. Among these, one conformation contains an intramolecular H-bond. The vibrational properties of these conformations were calculated and used to identify the conformations in a cryogenic argon matrix. The intensities of some bands assigned to a particular conformation were used to estimate the rotamerization constants K(r12) and K(r13) for the equilibria NAA1 NAA2 and NAA1 NAA3, respectively. The obtained experimental values were in agreement with the theoretical predictions. Copyright © 2011 Elsevier B.V. All rights reserved.

Effect of protein corona magnetite nanoparticles derived from bread in vitro digestion on Caco-2 cells morphology and uptake.

PubMed

Di Silvio, Desirè; Rigby, Neil; Bajka, Balazs; Mackie, Alan; Baldelli Bombelli, Francesca

2016-06-01

Nanoparticles (NPs) in biological fluids immediately interact with proteins forming a biomolecular corona (PC) that imparts their biological identity. While several studies on the formation of the PC in human plasma have been reported, the PC of orally administrated NPs has been less investigated, mostly in the presence of a food matrix. In fact, food matrixes when digested are subject of several dynamic changes that will certainly affect the PC formed on the NPs. The lack of studies on this topic is clearly related to the difficulty in isolating representative PC NPs from such a complex environment. In this work magnetite NPs were added to in vitro simulated digestion simultaneously with bread and PC NPs were isolated after gastric and duodenal phases by sucrose gradient ultracentrifugation (UC). The PC NPs were characterized in terms of size and protein composition. Translocation studies were then performed on Caco-2 monolayers in a serum free environment and cell morphology was characterized by confocal microscopy. PC NPs isolated from gastric and duodenal phases were different in size, surface charge and protein corona composition. NP cellular uptake was enhanced by the digestive PC inducing morphology changes in the cell monolayer. Overall, in this work we were able to isolate PC NPs from digested fluids in the presence of a food matrix and study their biological response on Caco-2 cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of isolated fractures on accelerated flow in unsaturated porous rock

USGS Publications Warehouse

Su, Grace W.; Nimmo, John R.; Dragila, Maria I.

2003-01-01

Fractures that begin and end in the unsaturated zone, or isolated fractures, have been ignored in previous studies because they were generally assumed to behave as capillary barriers and remain nonconductive. We conducted a series of experiments using Berea sandstone samples to examine the physical mechanisms controlling flow in a rock containing a single isolated fracture. The input fluxes and fracture orientation were varied in these experiments. Visualization experiments using dyed water in a thin vertical slab of rock were conducted to identify flow mechanisms occurring due to the presence of the isolated fracture. Two mechanisms occurred: (1) localized flow through the rock matrix in the vicinity of the isolated fracture and (2) pooling of water at the bottom of the fracture, indicating the occurrence of film flow along the isolated fracture wall. These mechanisms were observed at fracture angles of 20 and 60 degrees from the horizontal, but not at 90 degrees. Pooling along the bottom of the fracture was observed over a wider range of input fluxes for low‐angled isolated fractures compared to high‐angled ones. Measurements of matrix water pressures in the samples with the 20 and 60 degree fractures also demonstrated that preferential flow occurred through the matrix in the fracture vicinity, where higher pressures occurred in the regions where faster flow was observed in the visualization experiments. The pooling length at the terminus of a 20 degree isolated fracture was measured as a function of input flux. Calculations of the film flow rate along the fracture were made using these measurements and indicated that up to 22% of the flow occurred as film flow. These experiments, apparently the first to consider isolated fractures, demonstrate that such features can accelerate flow through the unsaturated zone and should be considered when developing conceptual models.

Comparative matrix isolation infrared spectroscopy study of 1,3- and 1,4-diene monoterpenes (α-phellandrene and γ-terpinene).

PubMed

Marzec, K M; Reva, I; Fausto, R; Proniewicz, L M

2011-05-05

In the present work, γ-terpinene (a 1,4-diene derivative) and α-phellandrene (1,3-diene derivative) were isolated in cryogenic argon matrices and their structures, vibrational spectra, and photochemistries were characterized with the aid of FTIR spectroscopy and quantum chemical calculations performed at the DFT/B3LYP/6-311++G(d,p) level of approximation. The molecules bear one conformationally relevant internal rotation axis, corresponding to the rotation of the isopropyl group. The calculations provide evidence of three minima on the potential energy surfaces of the studied molecules, where the isopropyl group assumes the trans, gauche+, and gauche- conformations (T, G+, G-). The signatures of all these conformers were identified in the experimental matrix infrared spectra, with the T forms dominating, in agreement with the theoretical predicted abundances in gas phase at room temperature. In situ UV (λ > 200 nm) irradiation of matrix-isolated α-phellandrene led to its isomerization into an open-ring species. The photoproduct was found to exhibit the ZE configuration of its backbone, which to be formed from the reactant molecule does not require extensive structural rearrangements of both the reagent and matrix. γ-Terpinene was photostable when subjected to irradiation under the same experimental conditions. In addition, the liquid compounds at room temperature were also investigated by FTIR-ATR and FT-Raman spectroscopies.

A spectroscopic study of intermediates in the condensation of refractory smokes: Matrix isolation experiments SiO

NASA Technical Reports Server (NTRS)

Khanna, R. K.; Stranz, D. D.; Donn, D.

1980-01-01

The infrared and Raman spectra of N2 matrix isolated silicon oxides are investigated. The vibrational frequencies of SiO, Si2O2, and Si3O3 were identified and assigned on the basis of normal coordinate analyses. Heating the solid to 50 K (evaporating the matrix) leaves a residue whose infrared spectrum is identical to that of a smoke condensed at ambient temperatures. Further heating of the sample to 500 K leads to significant changes in the band shapes. Investigations of the infrared spectra at several stages of the diffusion process result in the proposal of a mechanism for the transition from molecular properties to those of the residue (bulk) material, which is characterized as Si2O3.

A spectroscopic study of intermediates in the condensation of refractory smokes - Matrix isolation experiments of SiO

NASA Technical Reports Server (NTRS)

Khanna, R. K.; Stranz, D. D.; Donn, B.

1981-01-01

The infrared and Raman spectra of N2 matrix-isolated silicon oxides were investigated. The vibrational frequencies of SiO, Si2O2, and Si3O3 were identified and assigned on the basis of normal coordinate analyses. Heating the solid to approximately 50 K (evaporating the matrix) leaves a residue whose infrared spectrum is identical to that of a smoke condensed at ambient temperatures. Further heating of the sample to approximately 500 K leads to significant changes in the band shapes. Investigations of the infrared spectra at several stages of the diffusion process enable a mechanism to be proposed for the transition from molecular properties to those of the residue (bulk) material, which has been characterized as Si2O3.

Matrix isolation sublimation: An apparatus for producing cryogenic beams of atoms and molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sacramento, R. L.; Alves, B. X.; Silva, B. A.

2015-07-15

We describe the apparatus to generate cryogenic beams of atoms and molecules based on matrix isolation sublimation. Isolation matrices of Ne and H{sub 2} are hosts for atomic and molecular species which are sublimated into vacuum at cryogenic temperatures. The resulting cryogenic beams are used for high-resolution laser spectroscopy. The technique also aims at loading atomic and molecular traps.

General theory of multistage geminate reactions of isolated pairs of reactants. I. Kinetic equations.

PubMed

Doktorov, Alexander B; Kipriyanov, Alexey A

2014-05-14

General matrix approach to the consideration of multistage geminate reactions of isolated pairs of reactants depending on reactant mobility is formulated on the basis of the concept of "effective" particles. Various elementary reactions (stages of multistage reaction including physicochemical processes of internal quantum state changes) proceeding with the participation of isolated pairs of reactants (or isolated reactants) are taken into account. Investigation has been made in terms of kinetic approach implying the derivation of general (matrix) kinetic equations for local and mean probabilities of finding any of the reaction species in the sample under study (or for local and mean concentrations). The recipes for the calculation of kinetic coefficients of the equations for mean quantities in terms of relative coordinates of reactants have been formulated in the general case of inhomogeneous reacting systems. Important specific case of homogeneous reacting systems is considered.

DIFFERENTIATION OF AEROMONAS ISOLATES OBTAINED FROM DRINKING WATER DISTRIBUTION SYSTEM USING MATRIX-ASSISTED LASER DESCRIPTION/IONIZATION-MASS SPECTROMETRY (MALDI-MS)

EPA Science Inventory

The genus Aeromonas is one of several medically significant genera that have gained prominence due to their evolving taxonomy and controversial role in human diseases. In this study, matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) was used to analyze the...

Coordination of ScO+ and YO+ by multiple Ar, Kr, and Xe atoms in noble gas matrixes: a matrix isolation infrared spectroscopic and theoretical study.

PubMed

Zhao, Yanying; Gong, Yu; Chen, Mohua; Ding, Chuanfan; Zhou, Mingfei

2005-12-29

The combination of matrix isolation infrared spectroscopic and quantum chemical calculation results provide strong evidence that scandium and yttrium monoxide cations, ScO+ and YO+, coordinate multiple noble gas atoms in forming noble gas complexes. The results showed that ScO+ coordinates five Ar, Kr, or Xe atoms, and YO+ coordinates six Ar or Kr and five Xe atoms in solid noble gas matrixes. Hence, the ScO+ and YO+ cations trapped in solid noble gas matrixes should be regarded as the [ScO(Ng)5]+ (Ng = Ar, Kr, or Xe), [YO(Ng)6]+ (Ng = Ar or Kr) or [YO(Xe)5]+ complexes. Experiments with dilute krypton or xenon in argon or krypton in xenon produced new IR bands, which are due to the stepwise formation of the [ScO(Ar)(5-n)(Kr)n]+, [ScO(Kr)(5-n)(Xe)n]+ (n = 1-5), [YO(Ar)(6-n)(Kr)n]+ (n = 1-6), and [YO(Ar)(6-n)(Xe)n]+ (n = 1-4) complexes.

Identification of Enterobacteriaceae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using the VITEK MS system.

PubMed

Richter, S S; Sercia, L; Branda, J A; Burnham, C-A D; Bythrow, M; Ferraro, M J; Garner, O B; Ginocchio, C C; Jennemann, R; Lewinski, M A; Manji, R; Mochon, A B; Rychert, J A; Westblade, L F; Procop, G W

2013-12-01

This multicenter study evaluated the accuracy of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry identifications from the VITEK MS system (bioMérieux, Marcy l'Etoile, France) for Enterobacteriaceae typically encountered in the clinical laboratory. Enterobacteriaceae isolates (n = 965) representing 17 genera and 40 species were analyzed on the VITEK MS system (database v2.0), in accordance with the manufacturer's instructions. Colony growth (≤72 h) was applied directly to the target slide. Matrix solution (α-cyano-4-hydroxycinnamic acid) was added and allowed to dry before mass spectrometry analysis. On the basis of the confidence level, the VITEK MS system provided a species, genus only, or no identification for each isolate. The accuracy of the mass spectrometric identification was compared to 16S rRNA gene sequencing performed at MIDI Labs (Newark, DE). Supplemental phenotypic testing was performed at bioMérieux when necessary. The VITEK MS result agreed with the reference method identification for 96.7% of the 965 isolates tested, with 83.8% correct to the species level and 12.8% limited to a genus-level identification. There was no identification for 1.7% of the isolates. The VITEK MS system misidentified 7 isolates (0.7 %) as different genera. Three Pantoea agglomerans isolates were misidentified as Enterobacter spp. and single isolates of Enterobacter cancerogenus, Escherichia hermannii, Hafnia alvei, and Raoultella ornithinolytica were misidentified as Klebsiella oxytoca, Citrobacter koseri, Obesumbacterium proteus, and Enterobacter aerogenes, respectively. Eight isolates (0.8 %) were misidentified as a different species in the correct genus. The VITEK MS system provides reliable mass spectrometric identifications for Enterobacteriaceae.

Matrix isolation studies of carbonic acid--the vapor phase above the β-polymorph.

PubMed

Bernard, Jürgen; Huber, Roland G; Liedl, Klaus R; Grothe, Hinrich; Loerting, Thomas

2013-05-22

Twenty years ago two different polymorphs of carbonic acid, α- and β-H2CO3, were isolated as thin, crystalline films. They were characterized by infrared and, of late, by Raman spectroscopy. Determination of the crystal structure of these two polymorphs, using cryopowder and thin film X-ray diffraction techniques, has failed so far. Recently, we succeeded in sublimating α-H2CO3 and trapping the vapor phase in a noble gas matrix, which was analyzed by infrared spectroscopy. In the same way we have now investigated the β-polymorph. Unlike α-H2CO3, β-H2CO3 was regarded to decompose upon sublimation. Still, we have succeeded in isolation of undecomposed carbonic acid in the matrix and recondensation after removal of the matrix here. This possibility of sublimation and recondensation cycles of β-H2CO3 adds a new aspect to the chemistry of carbonic acid in astrophysical environments, especially because there is a direct way of β-H2CO3 formation in space, but none for α-H2CO3. Assignments of the FTIR spectra of the isolated molecules unambiguously reveal two different carbonic acid monomer conformers (C(2v) and C(s)). In contrast to the earlier study on α-H2CO3, we do not find evidence for centrosymmetric (C(2h)) carbonic acid dimers here. This suggests that two monomers are entropically favored at the sublimation temperature of 250 K for β-H2CO3, whereas they are not at the sublimation temperature of 210 K for α-H2CO3.

The role of hydrodynamic stress on the phenotypic characteristics of single and binary biofilms of Pseudomonas fluorescens.

PubMed

Simões, M; Pereira, M O; Vieira, M J

2007-01-01

This study investigates the phenotype of turbulent (Re = 5,200) and laminar (Re = 2,000) flow-generated Pseudomonas fluorescens biofilms. Three P. fluorescens strains, the type strain ATCC 13525 and two strains isolated from an industrial processing plant, D3-348 and D3-350, were used throughout this study. The isolated strains were used to form single and binary biofilms. The biofilm physiology (metabolic activity, cellular density, mass, extracellular polymeric substances, structural characteristics and outer membrane proteins [OMP] expression) was compared. The results indicate that, for every situation, turbulent flow-generated biofilms were more active (p < 0.05), had more mass per cm(2) (p < 0.05), a higher cellular density (p < 0.05), distinct morphology, similar matrix proteins (p > 0.1) and identical (isolated strains -single and binary biofilms) and higher (type strain) matrix polysaccharides contents (p < 0.05) than laminar flow-generated biofilms. Flow-generated biofilms formed by the type strain revealed a considerably higher cellular density and amount of matrix polysaccharides than single and binary biofilms formed by the isolated strains (p < 0.05). Similar OMP expression was detected for the several single strains and for the binary situation, not dependent on the hydrodynamic conditions. Binary biofilms revealed an equal coexistence of the isolated strains with apparent neutral interactions. In summary, the biofilms formed by the type strain represent, apparently, the worst situation in a context of control. The results obtained clearly illustrate the importance of considering strain variation and hydrodynamics in biofilm development, and complement previous studies which have focused on physical aspects of structural and density differences.

Study of optoelectronic switch for satellite-switched time-division multiple access

NASA Technical Reports Server (NTRS)

Su, Shing-Fong; Jou, Liz; Lenart, Joe

1987-01-01

The use of optoelectronic switching for satellite switched time division multiple access will improve the isolation and reduce the crosstalk of an IF switch matrix. The results are presented of a study on optoelectronic switching. Tasks include literature search, system requirements study, candidate switching architecture analysis, and switch model optimization. The results show that the power divided and crossbar switching architectures are good candidates for an IF switch matrix.

Yeasts from skin colonization are able to cross the acellular dermal matrix.

PubMed

Jarros, Isabele Carrilho; Okuno, Érika; Costa, Maiara Ignacio; Veiga, Flávia Franco; de Souza Bonfim-Mendonça, Patricia; Negri, Melyssa Fernanda Norman; Svidzinski, Terezinha Inez Estivalet

2018-04-01

In recent decades, the prognosis for burn patients has improved considerably with the development of specialized care. The acellular dermal matrix (ADM) is a totally artificial acellular device that functions to control water loss, prevent penetration by bacteria and allow migration of endothelial cells and fibroblasts from patient tissues. However, little is known about its effectiveness against yeasts. The present study evaluated the capacity of colonization and migration of some human commensal yeasts. Three clinical isolates from skin scales, identified as Candida parapsilosis, Candida glabrata and Rhodotorula mucilaginosa, were used. Their ability to cross the ADM was evaluated. After three days, all isolates had crossed the ADM. C. parapsilosis showed the lowest growth, while R. mucilaginosa showed intermediate and C. glabrata the highest growth. In the plates incubated for seven days, the growth of C. parapsilosis and C. glabrata increased by 1 log over the third day. All isolates have the capacity to colonize and migrate through the matrix, increasing the potential risk to burn patients, who can develop severe and even fatal infections by invasive fungi. Copyright © 2018 Elsevier Ltd. All rights reserved.

Infrared Spectroscopy of Matrix-Isolated Neutral and Ionized Anthracoronene in Argon.

PubMed

de Barros, A L F; Mattioda, A L; Korsmeyer, J M; Ricca, A

2018-03-08

The matrix-isolated mid-IR (MIR) spectrum of neutral and ionized anthracoronene (C 36 H 18 , AnthCor) in argon has been measured experimentally, compared to the spectrum of its parent molecules, coronene and anthracene, and analyzed by comparison to a theoretical spectrum computed using density functional theory (DFT). The experimental and theoretical band positions generally agree within 0-10 cm -1 . Anthracoronene exhibits extremely intense cation and anion bands around 1330 and 1318 cm -1 . The intensity of these two bands approaches what is traditionally observed over the entire 1000-1600 cm -1 range for a typical PAH cation or anion. The matrix-isolated near-IR (NIR) through overlap region (OVR) spectrum of ionized AnthCor in argon has been reported for the first time and compared to the spectrum of its parent molecules, coronene and anthracene. The spectrum of AnthCor contains a very strong electronic transition around 6175 cm -1 , placing it outside the range of the electronic transitions typically observed for PAHs. Anthracoronene is one of the few PAHs studied to date which has exhibited the formation of anions upon UV photolysis.

Stimulation of mitochondrial pyruvate metabolism and citrulline synthesis by dexamethasone. Effect of isolation and incubation media.

PubMed Central

Martin, A D; Titheradge, M A

1984-01-01

Hepatic mitochondria isolated in 0.3 M-sucrose or 0.3 M-mannitol from rats treated for 3h with dexamethasone displayed stimulated rates of pyruvate carboxylation and decarboxylation and citrulline synthesis when compared with organelles from control animals. Mitochondria isolated in mannitol also displayed elevated rates of pyruvate carboxylation and decarboxylation when compared with those isolated in sucrose, and this stimulation was shown to be independent of the lengthy isolation procedure. Citrulline synthesis proceeded at similar rates in mitochondria isolated in either sugar. The concentration of exchangeable adenine nucleotides was identical in mitochondria isolated in sucrose or mannitol, suggesting that those prepared in the former sugar are not more permeable to metabolites than those prepared in the latter. The matrix volume of mitochondria isolated in mannitol was greater than that of mitochondria isolated in sucrose, and the effect of mannitol on pyruvate metabolism was mimicked by swelling the organelles in hypo-osmotic sucrose. Measurements of the extra-matrix volume by using [14C]sucrose or [14C]mannitol suggest that mannitol can permeate mitochondria to a greater extent than can sucrose. The possibility that mannitol elicits its effect by entering the mitochondrial matrix and so initiating swelling is discussed. PMID:6433898

Patch Size, Functional Isolation, Visibility and Matrix Permeability Influences Neotropical Primate Occurrence within Highly Fragmented Landscapes

PubMed Central

da Silva, Lucas Goulart; Ribeiro, Milton Cezar; Hasui, Érica; da Costa, Carla Aparecida; da Cunha, Rogério Grassetto Teixeira

2015-01-01

Forest fragmentation and habitat loss are among the major current extinction causes. Remaining fragments are mostly small, isolated and showing poor quality. Being primarily arboreal, Neotropical primates are generally sensitive to fragmentation effects. Furthermore, primates are involved in complex ecological process. Thus, landscape changes that negatively interfere with primate population dynamic affect the structure, composition, and ultimately the viability of the whole community. We evaluated if fragment size, isolation and visibility and matrix permeability are important for explaining the occurrence of three Neotropical primate species. Employing playback, we verified the presence of Callicebus nigrifrons, Callithrix aurita and Sapajus nigritus at 45 forest fragments around the municipality of Alfenas, Brazil. We classified the landscape and evaluated the metrics through predictive models of occurrence. We selected the best models through Akaike Selection Criterion. Aiming at validating our results, we applied the plausible models to another region (20 fragments at the neighboring municipality of Poço Fundo, Brazil). Twelve models were plausible, and three were validated, two for Sapajus nigritus (Area and Area+Visibility) and one for Callicebus nigrifrons (Area+Matrix). Our results reinforce the contribution of fragment size to maintain biodiversity within highly degraded habitats. At the same time, they stress the importance of including novel, biologically relevant metrics in landscape studies, such as visibility and matrix permeability, which can provide invaluable help for similar studies in the future and on conservation practices in the long run. PMID:25658108

Analytic Confusion Matrix Bounds for Fault Detection and Isolation Using a Sum-of-Squared- Residuals Approach

NASA Technical Reports Server (NTRS)

Simon, Dan; Simon, Donald L.

2009-01-01

Given a system which can fail in 1 or n different ways, a fault detection and isolation (FDI) algorithm uses sensor data in order to determine which fault is the most likely to have occurred. The effectiveness of an FDI algorithm can be quantified by a confusion matrix, which i ndicates the probability that each fault is isolated given that each fault has occurred. Confusion matrices are often generated with simulation data, particularly for complex systems. In this paper we perform FDI using sums of squares of sensor residuals (SSRs). We assume that the sensor residuals are Gaussian, which gives the SSRs a chi-squared distribution. We then generate analytic lower and upper bounds on the confusion matrix elements. This allows for the generation of optimal sensor sets without numerical simulations. The confusion matrix bound s are verified with simulated aircraft engine data.

Application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in the screening of vanA-positive Enterococcus faecium.

PubMed

Wang, Li-jun; Lu, Xin-xin; Wu, Wei; Sui, Wen-jun; Zhang, Gui

2014-01-01

In order to evaluate a rapid matrix-assisted laser desorption ionization-time of flight mass spectrometry (MAIDI-TOF MS) assay in screening vancomycin-resistant Enterococcus faecium, a total of 150 E. faecium clinical strains were studied, including 60 vancomycin-resistant E. faecium (VREF) isolates and 90 vancomycin-susceptible (VSEF) strains. Vancomycin resistance genes were detected by sequencing. E. faecium were identified by MALDI-TOF MS. A genetic algorithm model with ClinProTools software was generated using spectra of 30 VREF isolates and 30 VSEF isolates. Using this model, 90 test isolates were discriminated between VREF and VSEF. The results showed that all sixty VREF isolates carried the vanA gene. The performance of VREF detection by the genetic algorithm model of MALDI-TOF MS compared to the sequencing method was sensitivity = 80%, specificity = 90%, false positive rate =10%, false negative rate =10%, positive predictive value = 80%, negative predictive value= 90%. MALDI-TOF MS can be used as a screening test for discrimination between vanA-positive E. faecium and vanA-negative E. faecium.

Transplantation of an alginate-matrigel matrix containing isolated ovarian cells: first step in developing a biodegradable scaffold to transplant isolated preantral follicles and ovarian cells.

PubMed

Vanacker, Julie; Luyckx, Valérie; Dolmans, Marie-Madeleine; Des Rieux, Anne; Jaeger, Jonathan; Van Langendonckt, Anne; Donnez, Jacques; Amorim, Christiani A

2012-09-01

For women diagnosed with leukemia, transplantation of cryopreserved ovarian tissue after disease remission is not advisable. Therefore, to restore fertility in these patients, we aim to develop a biodegradable artificial ovary that offers an environment where isolated follicles and ovarian cells (OCs) can survive and grow. Four NMRI mice were ovariectomized and their ovaries used to isolate OCs. Groups of 50,000 OCs were embedded in an alginate-matrigel matrix for further fixation (fresh controls), one week of in vitro culture (IVC) or heterotopic autografting. OC proliferation (Ki67), apoptosis (TUNEL), scaffold degradation, vessel formation (CD34) and inflammation (CD45) were analyzed. Ki67-positive OCs were found in 2.3%, 9.0% and 15.5% cells of cases in fresh, IVC and grafted beads respectively, while cells were TUNEL-positive in 0%, 1.5% and 6.9% of cases. After IVC or grafting, the beads degraded, losing their original round aspect, and infiltrating blood capillaries could be observed in the grafted beads. CD34-positive cells and 22% CD45-positive cells were found around and inside the matrix. In conclusion, our results demonstrate that an alginate-based matrix is a promising proposition to graft isolated OCs. After transplantation, this matrix was able to degrade, allowed vascularization and elicited a low inflammatory response. Copyright © 2012 Elsevier Ltd. All rights reserved.

Matrix Isolation and ab initio study of the noncovalent complexes between formamide and acetylene.

PubMed

Mardyukov, Artur; Sánchez-García, Elsa; Sander, Wolfram

2009-02-12

Matrix isolation spectroscopy in combination with ab initio calculations is a powerful technique for the identification of weakly bound intermolecular complexes. Here, weak complexes between formamide and acetylene are studied, and three 1:1 complexes with binding energies of -2.96, -2.46, and -1.79 kcal/mol have been found at the MP2 level of theory (MP2/cc-pVTZ + ZPE + BSSE). The two most stable dimers A and B are identified in argon and nitrogen matrices by comparison between the experimental and calculated infrared frequencies. Both complexes are stabilized by the formamide C=O...HC acetylene and H...pi interactions. Large shifts have been observed experimentally for the C-H stretching vibrations of the acetylene molecule, in very good agreement with the calculated values. Eight 1:2 FMA-acetylene trimers (T-A to T-H) with binding energies between -5.44 and -2.62 kcal/mol (MP2/aug-cc-pVDZ + ZPE + BSSE) were calculated. The two most stable trimers T-A and T-B are very close in energy and have similar infrared spectra. Several weak bands that are in agreement with the calculated frequencies of the trimers T-A and T-B are observed under matrix isolation conditions. However, the differences are too small for a definitive assignment.

Ultraviolet Spectroscopy of Matrix-isolated Amorphous Carbon Particles

NASA Astrophysics Data System (ADS)

Schnaiter, M.; Mutschke, H.; Henning, Th.; Lindackers, D.; Strecker, M.; Roth, P.

1996-06-01

In view of the interstellar 217.5 nm and the circumstellar 230--250 nm extinction features, the UV extinction behavior of small matrix-isolated amorphous carbon grains is investigated experimentally. The particles were produced in a flame by burning acetylene with oxygen at low pressure. To prevent coagulation, the condensing primary soot grains (average diameter ~6 nm) were extracted by a molecular beam technique into a high-vacuum chamber. There they were deposited into a layer of solid argon, isolated from each other. The particle mass and size were controlled using a particle mass spectrometer. The measured UV extinction of the matrix-isolated particles is compared with measurements on samples produced in the conventional way by collecting carbon smoke on substrate as well as with scattering calculations for small spheres and ellipsoides. The laboratory data give a good representation of the circumstellar extinction feature observed in the spectrum of V348 Sgr.

Characterization of Enterotoxigenic Bacillus cereus sensu lato and Staphylococcus aureus Isolates and Associated Enterotoxin Production Dynamics in Milk or Meat-Based Broth

PubMed Central

Walker-York-Moore, Laura; Moore, Sean C.; Fox, Edward M.

2017-01-01

Bacillus cereus sensu lato species, as well as Staphylococcus aureus, are important pathogenic bacteria which can cause foodborne illness through the production of enterotoxins. This study characterised enterotoxin genes of these species and examined growth and enterotoxin production dynamics of isolates when grown in milk or meat-based broth. All B. cereus s. l. isolates harboured nheA, hblA and entFM toxin genes, with lower prevalence of bceT and hlyII. When grown at 16 °C, toxin production by individual B. cereus s. l. isolates varied depending on the food matrix; toxin was detected at cell densities below 5 log10(CFU/mL). At 16 °C no staphylococcal enterotoxin C (SEC) production was detected by S. aureus isolates, although low levels of SED production was noted. At 30 °C all S. aureus isolates produced detectable enterotoxin in the simulated meat matrix, whereas SEC production was significantly reduced in milk. Relative to B. cereus s. l. toxin production, S. aureus typically required reaching higher cell numbers to produce detectable levels of enterotoxin. Phylogenetic analysis of the sec and sel genes suggested population evolution which correlated with animal host adaptation, with subgroups of bovine isolates or caprine/ovine isolates noted, which were distinct from human isolates. Taken together, this study highlights the marked differences in the production of enterotoxins both associated with different growth matrices themselves, but also in the behaviour of individual strains when exposed to different food matrices. PMID:28714887

Characterization of Enterotoxigenic Bacillus cereus sensu lato and Staphylococcus aureus Isolates and Associated Enterotoxin Production Dynamics in Milk or Meat-Based Broth.

PubMed

Walker-York-Moore, Laura; Moore, Sean C; Fox, Edward M

2017-07-15

Bacillus cereus sensu lato species, as well as Staphylococcus aureus , are important pathogenic bacteria which can cause foodborne illness through the production of enterotoxins. This study characterised enterotoxin genes of these species and examined growth and enterotoxin production dynamics of isolates when grown in milk or meat-based broth. All B. cereus s. l. isolates harboured nheA , hblA and entFM toxin genes, with lower prevalence of bceT and hlyII . When grown at 16 °C, toxin production by individual B. cereus s. l. isolates varied depending on the food matrix; toxin was detected at cell densities below 5 log 10 (CFU/mL). At 16 °C no staphylococcal enterotoxin C (SEC) production was detected by S. aureus isolates, although low levels of SED production was noted. At 30 °C all S. aureus isolates produced detectable enterotoxin in the simulated meat matrix, whereas SEC production was significantly reduced in milk. Relative to B. cereus s. l. toxin production, S. aureus typically required reaching higher cell numbers to produce detectable levels of enterotoxin. Phylogenetic analysis of the sec and sel genes suggested population evolution which correlated with animal host adaptation, with subgroups of bovine isolates or caprine/ovine isolates noted, which were distinct from human isolates. Taken together, this study highlights the marked differences in the production of enterotoxins both associated with different growth matrices themselves, but also in the behaviour of individual strains when exposed to different food matrices.

Conformations of n-butyl imidazole: matrix isolation infrared and DFT studies.

PubMed

Ramanathan, N; Sundararajan, K; Sankaran, K

2015-03-15

Conformations of n-butyl imidazole (B-IMID) were studied using matrix isolation infrared spectroscopy by trapping in argon, xenon and nitrogen matrixes using an effusive nozzle source. The experimental studies were supported by DFT computations performed at the B3LYP/6-311++G(d,p) level. Computations identified nine unique minima for B-IMID, corresponding to conformers with tg(±)tt, tg(±)g(∓)t, tg(±)g(±)t, tg(±)tg(±), tg(±)tg(∓), tg(±)g(∓)g(∓), tg(±)g(±)g(±), tg(±)g(∓)g(±) and tg(±)g(±)g(∓) structures, given in order of increasing energy. Computations of the transition state structures connecting the higher energy conformers to the global minimum, tg(±)tt structure were carried out. The barriers for the conformer inter-conversion were found to be ∼2 kcal/mol. Natural Bond Orbital (NBO) analysis was performed to understand the reasons for conformational preferences in B-IMID. Copyright © 2014 Elsevier B.V. All rights reserved.

Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Caspofungin Susceptibility Testing of Candida and Aspergillus Species

PubMed Central

De Carolis, Elena; Vella, Antonietta; Florio, Ada R.; Posteraro, Patrizia; Perlin, David S.; Posteraro, Brunella

2012-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) was evaluated for testing susceptibility to caspofungin of wild-type and fks mutant isolates of Candida and Aspergillus. Complete essential agreement was observed with the CLSI reference method, with categorical agreement for 94.1% of the Candida isolates tested. Thus, MALDI-TOF MS is a reliable and accurate method to detect fungal isolates with reduced caspofungin susceptibility. PMID:22535984

Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry for caspofungin susceptibility testing of Candida and Aspergillus species.

PubMed

De Carolis, Elena; Vella, Antonietta; Florio, Ada R; Posteraro, Patrizia; Perlin, David S; Sanguinetti, Maurizio; Posteraro, Brunella

2012-07-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was evaluated for testing susceptibility to caspofungin of wild-type and fks mutant isolates of Candida and Aspergillus. Complete essential agreement was observed with the CLSI reference method, with categorical agreement for 94.1% of the Candida isolates tested. Thus, MALDI-TOF MS is a reliable and accurate method to detect fungal isolates with reduced caspofungin susceptibility.

Vibrational Spectrum of Matrix-isolated Propargyl Radical HCCCH2: Detection of nu8 and Overtone Bands

NASA Astrophysics Data System (ADS)

Zhang, X.; Sander, S. P.; Ellison, G. B.; Stanton, J. F.

2010-04-01

Infrared (IR) absorption spectra of matrix-isolated propargyl radical have been measured. The CH2CCH ˜X 2B1 out-of-plane bending mode (ν8) at 378 (±2) cm-1, along with several overtone and combination modes have been detected for the first time.

Photoisomerization and photochemistry of matrix-isolated 3-furaldehyde.

PubMed

Kuş, Nihal; Reva, Igor; Fausto, Rui

2010-12-02

3-Furaldehyde (3FA) was isolated in an argon matrix at 12 K and studied using FTIR spectroscopy and quantum chemistry. The molecule has two conformers, with trans and cis orientation of the O=C-C=C dihedral angle. At the B3LYP/6-311++G(d,p) level of theory, the trans form was computed to be ca. 4 kJ mol(-1) more stable than the cis form. The relative stability of the two conformers was explained using the natural bond orbital (NBO) method. In fair agreement with their calculated relative energies and the high barrier of rotamerization (ca. 34 kJ mol(-1) from trans to cis), the trans and cis conformers were trapped in an argon matrix from the compound room temperature gas phase in proportion ~7:1. The experimentally observed vibrational signatures of the two forms are in a good agreement with the theoretically calculated spectra. Broad-band UV-irradiation (λ > 234 nm) of the matrix-isolated compound resulted in partial trans → cis isomerization, which ended at a photostationary state with the trans/cis ratio being ca. 1.85:1. This result was interpreted based on results of time-dependent DFT calculations. Irradiation at higher energies (λ > 200 nm) led to decarbonylation of the compound, yielding furan, cyclopropene-3-carbaldehyde, and two C(3)H(4) isomers: cyclopropene and propadiene.

Isolation and Proteomic Characterization of the Mouse Sperm Acrosomal Matrix*

PubMed Central

Guyonnet, Benoit; Zabet-Moghaddam, Masoud; SanFrancisco, Susan; Cornwall, Gail A.

2012-01-01

A critical step during fertilization is the sperm acrosome reaction in which the acrosome releases its contents allowing the spermatozoa to penetrate the egg investments. The sperm acrosomal contents are composed of both soluble material and an insoluble material called the acrosomal matrix (AM). The AM is thought to provide a stable structure from which associated proteins are differentially released during fertilization. Because of its important role during fertilization, efforts have been put toward isolating the AM for biochemical study and to date AM have been isolated from hamster, guinea pig, and bull spermatozoa. However, attempts to isolate AM from mouse spermatozoa, the species in which fertilization is well-studied, have been unsuccessful possibly because of the small size of the mouse sperm acrosome and/or its fusiform shape. Herein we describe a procedure for the isolation of the AM from caput and cauda mouse epididymal spermatozoa. We further carried out a proteomic analysis of the isolated AM from both sperm populations and identified 501 new proteins previously not detected by proteomics in mouse spermatozoa. A comparison of the AM proteome from caput and cauda spermatozoa showed that the AM undergoes maturational changes during epididymal transit similar to other sperm domains. Together, our studies suggest the AM to be a dynamic and functional structure carrying out a variety of biological processes as implied by the presence of a diverse group of proteins including proteases, chaperones, hydrolases, transporters, enzyme modulators, transferases, cytoskeletal proteins, and others. PMID:22707618

Detection of Biomarkers of Pathogenic Naegleria fowleri Through Mass Spectrometry and Proteomics

PubMed Central

Moura, Hercules; Izquierdo, Fernando; Woolfitt, Adrian R.; Wagner, Glauber; Pinto, Tatiana; del Aguila, Carmen; Barr, John R.

2017-01-01

Emerging methods based on mass spectrometry (MS) can be used in the rapid identification of microorganisms. Thus far, these practical and rapidly evolving methods have mainly been applied to characterize prokaryotes. We applied matrix-assisted laser-desorption-ionization-time-of-flight mass spectrometry MALDI-TOF MS in the analysis of whole cells of 18 N. fowleri isolates belonging to three genotypes. Fourteen originated from the cerebrospinal fluid or brain tissue of primary amoebic meningoencephalitis patients and four originated from water samples of hot springs, rivers, lakes or municipal water supplies. Whole Naegleria trophozoites grown in axenic cultures were washed and mixed with MALDI matrix. Mass spectra were acquired with a 4700 TOF-TOF instrument. MALDI-TOF MS yielded consistent patterns for all isolates examined. Using a combination of novel data processing methods for visual peak comparison, statistical analysis and proteomics database searching we were able to detect several biomarkers that can differentiate all species and isolates studied, along with common biomarkers for all N. fowleri isolates. Naegleria fowleri could be easily separated from other species within the genus Naegleria. A number of peaks detected were tentatively identified. MALDI-TOF MS fingerprinting is a rapid, reproducible, high-throughput alternative method for identifying Naegleria isolates. This method has potential for studying eukaryotic agents. PMID:25231600

Spectroscopic Studies of Metal-Ligand-Surface Interactions

DTIC Science & Technology

1988-10-01

oo. . . .. . . . . . . . . . . 12 2. Matrix-Iso~lation Spectra of Deuterated Hydrazine......... o.... 28 3. Matrix-Isolation Spectra of MMH, UDMH ...Monon:e-;lhydrazine Survey Spectra: 3400-2700 cm- .................... 19 Monomethylhydrazine Survey Spectra: 1750-650 c- 20 UDMH Survey Spectra...3350-2650 cm- 1 . o qo .... 21 UDMH Survey Spectra: 1750-650 cm-lo.0. ...... 22 Survey Spectra of Benzene: 3150-2950 cm-1 and 23 Survey Spectra of

The Conformational Landscape of L-Threonine Matrix Isolation Infrared and {AB-INITIO Studies

NASA Astrophysics Data System (ADS)

Dubey, Pankaj; Mukhopadhyay, Anamika; Viswanathan, K. S.

2017-06-01

Amino acids, containing hydroxy side chains such as L-threonine and tyrosine play an important role in molecular recognition, such as in the docking of propofol, which is a commonly used anaesthetic. A rich conformational landscape of these amino acids makes them interesting candidates in the study of intra and intermolecular interactions. In this work, the conformational landscape of L-threonine was studied, as it can be expected to serve as a basis for understanding structure and functions of polypeptides and other biomolecules. The matrix isolation technique (MI) coupled with a high temperature effusive molecular beam (EMB) nozzle was used to trap conformers of amino acid, which were then characterized using FTIR spectroscopy. The usefulness of MI-EMB-FTIR spectroscopy is that it can trap structures corresponding to the local minima along with the global minimum and hence allows for a better exploration of the potential energy surface. A major challenge in conformational analysis of amino acids using matrix isolation FTIR arises from its non-volatile nature. A home built heating system which was mounted close to the cryotip, was used to evaporate the non-volatile amino acids. Our infrared spectra show that three conformations were trapped in the matrix. Experimental results were supported by {ab-initio calculations performed using the CCSD(T), MP2 and M06-2X methods together with 6-311++G(d,p) and aug/cc-pVDZ basis sets. The side chains of the amino acids appeared to have an influence on the preferential stabilisation of a particular backbone structure of amino acids. Factors such as entropy, anomeric effect and intramolecular H-bonding were also found to play an important role in determining conformal preferences, which will be discussed.

Matrix-Assisted Laser Desorption Ionization (MALDI)-Time of Flight Mass Spectrometry- and MALDI Biotyper-Based Identification of Cultured Biphenyl-Metabolizing Bacteria from Contaminated Horseradish Rhizosphere Soil▿

PubMed Central

Uhlik, Ondrej; Strejcek, Michal; Junkova, Petra; Sanda, Miloslav; Hroudova, Miluse; Vlcek, Cestmir; Mackova, Martina; Macek, Tomas

2011-01-01

Bacteria that are able to utilize biphenyl as a sole source of carbon were extracted and isolated from polychlorinated biphenyl (PCB)-contaminated soil vegetated by horseradish. Isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The usage of MALDI Biotyper for the classification of isolates was evaluated and compared to 16S rRNA gene sequence analysis. A wide spectrum of bacteria was isolated, with Arthrobacter, Serratia, Rhodococcus, and Rhizobium being predominant. Arthrobacter isolates also represented the most diverse group. The use of MALDI Biotyper in many cases permitted the identification at the level of species, which was not achieved by 16S rRNA gene sequence analyses. However, some isolates had to be identified by 16S rRNA gene analyses if MALDI Biotyper-based identification was at the level of probable or not reliable identification, usually due to a lack of reference spectra included in the database. Overall, this study shows the possibility of using MALDI-TOF MS and MALDI Biotyper for the fast and relatively nonlaborious identification/classification of soil isolates. At the same time, it demonstrates the dominant role of employing 16S rRNA gene analyses for the identification of recently isolated strains that can later fill the gaps in the protein-based identification databases. PMID:21821747

Photoinduced ethane formation from reaction of ethene with matrix-isolated Ti, V, or Nb atoms.

PubMed

Thompson, Matthew G K; Parnis, J Mark

2005-10-27

The reactions of matrix-isolated Ti, V, or Nb atoms with ethene (C(2)H(4)) have been studied by FTIR absorption spectroscopy. Under conditions where the ethene dimer forms, metal atoms react with the ethene dimer to yield matrix-isolated ethane (C(2)H(6)) and methane. Under lower ethene concentration conditions ( approximately 1:70 ethene/Ar), hydridic intermediates of the types HMC(2)H(3) and H(2)MC(2)H(2) are also observed, and the relative yield of hydrocarbons is diminished. Reactions of these metals with perdeuterioethene, and equimolar mixtures of C(2)H(4) and C(2)D(4), yield products that are consistent with the production of ethane via a metal atom reaction involving at least two C(2)H(4) molecules. The absence of any other observed products suggests the mechanism also involves production of small, highly symmetric species such as molecular hydrogen and metal carbides. Evidence is presented suggesting that ethane production from the ethene dimer is a general photochemical process for the reaction of excited-state transition-metal atoms with ethene at high concentrations of ethene.

A theoretical and matrix-isolation FT-IR investigation of the conformational landscape of N-acetylcysteine

NASA Astrophysics Data System (ADS)

Boeckx, Bram; Ramaekers, Riet; Maes, Guido

2010-06-01

The conformational landscape of N-acetylcysteine (NAC) has been investigated by a combined experimental matrix-isolation FT-IR and theoretical methodology. This combination is a powerful tool to study the conformational behavior of relatively small molecules. Geometry optimizations at the HF/3-21 level resulted in 438 different geometries with an energy difference smaller than 22 kJ mol -1. Among these, six conformations were detected with a relative energy difference smaller than 10 kJ mol -1 at the DFT(B3LYP)/6-31++G∗∗ level of theory. These were finally subjected to MP2/6-31++G∗∗ optimizations which resulted in five minima. The vibrational and thermodynamical properties of these conformations were calculated at both the DFT and MP2 methodologies. Experimentally NAC was isolated in an argon matrix at 16 K after being sublimated at 323 K. The most stable MP2 form appeared to be dominant in the experimental spectra but the presence of three other conformations with Δ EMP2 < 10 kJ mol -1 was also demonstrated. The experimentally observed abundance of the H-bond containing conformations appeared to be in good accordance with the predicted MP2 value.

Biomimetic soluble collagen purified from bones.

PubMed

Ferreira, Ana Marina; Gentile, Piergiorgio; Sartori, Susanna; Pagliano, Cristina; Cabrele, Chiara; Chiono, Valeria; Ciardelli, Gianluca

2012-11-01

Type I collagen has been extensively exploited as a biomaterial for biomedical applications and drug delivery; however, small molecular alterations occurring during the isolation procedure and its interaction with residual bone extracellular matrix molecules or proteins might affect the overall material biocompatibility and performance. The aim of the current work is to study the potential alterations in collagen properties and organization associated with the absence of proteoglycans, which mimic pathological conditions associated with age-related diseases. A new approach for evaluating the effect of proteoglycans on the properties of isolated type I collagen from the bone matrix is described. Additional treatment with guanidine hydrochloride was introduced to remove residual proteoglycans from the collagen matrix. The properties of the isolated collagen with/without guanidine hydrochloride treatment were investigated and compared with a commercial rabbit collagen as control. We demonstrate that the absence of proteoglycans in the isolated type I collagen affects its thermal properties, the extraction into its native structure, and its ability to hydrate and self-assemble into fibers. The fine control and tuning of all these features, linked to the absence of non-collagenous proteins as proteoglycans, offer the possibility of designing new strategies and biomaterials with advanced biomimetic properties aimed at regenerating bone tissue in the case of fragility and/or defects. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nuclear matrix and hnRNP share a common structural constituent associated with premessenger RNA.

PubMed Central

Gallinaro, H; Puvion, E; Kister, L; Jacob, M

1983-01-01

Nuclear matrix and heterogeneous nuclear ribonucleoprotein (hnRNP) were compared to establish whether premessenger RNA (premRNA) was associated with a same constituent in both structures. The isolation of nuclear matrix included the removal of chromatin and of 0.4 M KCl-soluble material. HnRNP, isolated by a standard method was also treated by 0.4 M KCl. Both isolation procedures caused the removal of DNA, histones, a fraction of small nuclear RNA and of nonhistone proteins including the hnRNP proteins in the 30 000-40 000 mol. wt. range. High resolution autoradiography showed that hnRNA remained associated with the residual fibrils in both structures. They both contained the same premRNA and maturation products as shown by the analysis of the transcripts of the early region 3 of adenovirus 2. In addition, the small nuclear RNA and protein of the salt-resistant complexes were also present in the matrix. The results are compatible with the idea that the salt-resistant complexes from hnRNP constitute the fibrils associated with premRNA in the nucleoplasmic matrix. The fibrils may be the basic unit of splicing and their organization in matrix might provide the spatial configuration necessary for regulation. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 7. PMID:6557026

E- and P-cadherin expression during murine hair follicle morphogenesis and cycling.

PubMed

Müller-Röver, S; Tokura, Y; Welker, P; Furukawa, F; Wakita, H; Takigawa, M; Paus, R

1999-08-01

The role of adhesion molecules in the control of hair follicle (HF) morphogenesis, regression and cycling is still rather enigmatic. Since the adhesion molecules E- and P-cadherin (Ecad and Pcad) are functionally important, e.g. during embryonic pattern formation, we have studied their expression patterns during neonatal HF morphogenesis and cycling in C57/BL6 mice by immunohistology and semi-quantitative RT-PCR. The expression of both cadherins was strikingly hair cycle-dependent and restricted to distinct anatomical HF compartments. During HF morphogenesis, hair bud keratinocytes displayed strong Ecad and Pcad immunoreactivity (IR). While neonatal epidermis showed Ecad IR in all epidermal layers, Pcad IR was restricted to the basal layer. During later stages of HF morphogenesis and during anagen IV-VI of the adolescent murine hair cycle, the outer root sheath showed strong E- and Pcad IR. Instead, the outermost portion of the hair matrix and the inner root sheath displayed isolated Ecad IR, while the innermost portion of the hair matrix exhibited isolated Pcad IR. During telogen, all epidermal and follicular keratinocytes showed strong Ecad IR. This is in contrast to Pcad, whose IR was stringently restricted to matrix and secondary hair germ keratinocytes which are in closest proximity to the dermal papilla. These findings suggest that isolated or combined E- and/or Pcad expression is involved in follicular pattern formation by segregating HF keratinocytes into functionally distinct subpopulations; most notably, isolated Pcad expression may segregate those hair matrix keratinocytes into one functional epithelial tissue unit, which is particularly susceptible to growth control by dermal papilla-derived morphogens. The next challenge is to define which secreted agents implicated in hair growth control modulate these follicular cadherin expression patterns, and to define how these basic parameters of HF topobiology are altered during common hair growth disorders.

Chondrocyte-based intraoperative processing strategies for the biological augmentation of a polyurethane meniscus replacement.

PubMed

Vedicherla, Srujana; Romanazzo, Sara; Kelly, Daniel J; Buckley, Conor T; Moran, Cathal J

2017-11-28

Purpose/aim of study: Menisectomies account for over 1.5 million surgical interventions in Europe annually, and there is a growing interest in regenerative strategies to improve outcomes in meniscal replacement. The overall objective of this study was to evaluate the role of intraoperatively applied fresh chondrocyte (FC) isolates compared to minced cartilage (MC) fragments, used without cell isolation, to improve bioactivity and tissue integration when combined with a polyurethane replacement. First, to optimize the intraoperative cell isolation protocol, caprine articular cartilage biopsies were digested with 750 U/ml or 3000 U/ml collagenase type II (ratio of 10 ml per g of tissue) for 30 min, 1 h or 12 h with constant agitation and compared to culture-expanded chondrocytes in terms of matrix deposition when cultured on polyurethane scaffolds. Finally, FCs and MC-augmented polyurethane scaffolds were evaluated in a caprine meniscal explant model to assess the potential enhancements on tissue integration strength. Adequate numbers of FCs were harvested using a 30 min chondrocyte isolation protocol and were found to demonstrate improved matrix deposition compared to standard culture-expanded cells in vitro. Upon evaluation in a meniscus explant defect model, both FCs and MC showed improved matrix deposition at the tissue-scaffold interface and enhanced push-out strength, fourfold and 2.5-fold, respectively, compared with the acellular implant. Herein, we have demonstrated a novel approach that could be applied intraoperatively, using FCs or MC for improved tissue integration with a polyurethane meniscal replacement.

Novel hydrophobic interaction chromatography matrix for specific isolation and simple elution of immunoglobulins (A, G, and M) from porcine serum.

PubMed

Ramos-Clamont, Gabriela; del Carmen Candia-Plata, Maria; Zamudio, Roberto Guzman; Vazquez-Moreno, Luz

2006-07-28

A new, highly acetylated agarose matrix (HA-Sepharose) was synthesized and used as a hydrophobic interaction chromatography (HIC) medium to specifically isolate immunoglobulins (Igs) from porcine serum. Recovery of Igs was in a single step and under mild conditions. HA-Sepharose adsorption was studied in terms of salt, gel acetylation time, flow rate, and protein concentration on the loading buffer. At 0.5 M Na2SO4, control with unmodified Sepharose retained a small fraction (0.70 mg/mL of matrix) of serum albumin. On the contrary HA-Sepharose retained primary Igs (IgA, IgG, and 53% of IgM) as revealed by sodium dodecyl sulphate 10% polyacrylamide gel electrophoresis (SDS-PAGE), quantitative radial immunodiffusion and immunodetection. At a flow rate of 1 mL/min, the HA-Sepharose column capacity (3.9 mg/mL of matrix) was similar to the reported capacity for the commercial thiophilic T-gel. However, HA-Sepharose showed higher recovery of IgA and IgM than the T-gel in the same salt conditions, clearly an advantage in terms of immunoglobulin recovery strategies. Acetylation changed the matrix adsorption from albumin to immunoglobulins; thus, the highly acetylated gel rendered recoveries of Igs from unprocessed porcine serum practically free of albumin.

Evaluation of VITEK mass spectrometry (MS), a matrix-assisted laser desorption ionization time-of-flight MS system for identification of anaerobic bacteria.

PubMed

Lee, Wonmok; Kim, Myungsook; Yong, Dongeun; Jeong, Seok Hoon; Lee, Kyungwon; Chong, Yunsop

2015-01-01

By conventional methods, the identification of anaerobic bacteria is more time consuming and requires more expertise than the identification of aerobic bacteria. Although the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems are relatively less studied, they have been reported to be a promising method for the identification of anaerobes. We evaluated the performance of the VITEK MS in vitro diagnostic (IVD; 1.1 database; bioMérieux, France) in the identification of anaerobes. We used 274 anaerobic bacteria isolated from various clinical specimens. The results for the identification of the bacteria by VITEK MS were compared to those obtained by phenotypic methods and 16S rRNA gene sequencing. Among the 249 isolates included in the IVD database, the VITEK MS correctly identified 209 (83.9%) isolates to the species level and an additional 18 (7.2%) at the genus level. In particular, the VITEK MS correctly identified clinically relevant and frequently isolated anaerobic bacteria to the species level. The remaining 22 isolates (8.8%) were either not identified or misidentified. The VITEK MS could not identify the 25 isolates absent from the IVD database to the species level. The VITEK MS showed reliable identifications for clinically relevant anaerobic bacteria.

Efficacy of a marine bacterial nuclease against biofilm forming microorganisms isolated from chronic rhinosinusitis.

PubMed

Shields, Robert C; Mokhtar, Norehan; Ford, Michael; Hall, Michael J; Burgess, J Grant; ElBadawey, Mohamed Reda; Jakubovics, Nicholas S

2013-01-01

The persistent colonization of paranasal sinus mucosa by microbial biofilms is a major factor in the pathogenesis of chronic rhinosinusitis (CRS). Control of microorganisms within biofilms is hampered by the presence of viscous extracellular polymers of host or microbial origin, including nucleic acids. The aim of this study was to investigate the role of extracellular DNA in biofilm formation by bacteria associated with CRS. Obstructive mucin was collected from patients during functional endoscopic sinus surgery. Examination of the mucous by transmission electron microscopy revealed an acellular matrix punctuated occasionally with host cells in varying states of degradation. Bacteria were observed in biofilms on mucosal biopsies, and between two and six different species were isolated from each of 20 different patient samples. In total, 16 different bacterial genera were isolated, of which the most commonly identified organisms were coagulase-negative staphylococci, Staphylococcus aureus and α-haemolytic streptococci. Twenty-four fresh clinical isolates were selected for investigation of biofilm formation in vitro using a microplate model system. Biofilms formed by 14 strains, including all 9 extracellular nuclease-producing bacteria, were significantly disrupted by treatment with a novel bacterial deoxyribonuclease, NucB, isolated from a marine strain of Bacillus licheniformis. Extracellular biofilm matrix was observed in untreated samples but not in those treated with NucB and extracellular DNA was purified from in vitro biofilms. Our data demonstrate that bacteria associated with CRS form robust biofilms which can be reduced by treatment with matrix-degrading enzymes such as NucB. The dispersal of bacterial biofilms with NucB may offer an additional therapeutic target for CRS sufferers.

Dimerization of the keto tautomer of acetohydroxamic acid—infrared matrix isolation and theoretical study

NASA Astrophysics Data System (ADS)

Sałdyka, Magdalena; Mielke, Zofia

2005-05-01

Dimerization of the keto tautomer of acetohydroxamic acid has been studied using FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-31+G(d,p) calculations. Analysis of CH 3CONHOH/Ar matrix spectra indicates formation of two dimers in which two intramolecular CO···H sbnd ON bonds within two interacting acetohydroxamic acid molecules are retained. A chain dimer I is stabilized by the intermolecular CO···H sbnd N hydrogen bond, whereas the cyclic dimer II is stabilized by two intermolecular N sbnd H···O(H)N bonds. Twelve vibrations were identified for dimer I and six vibrations for dimer II; the observed frequency shifts show a good agreement with the calculated ones for the structures I and II. Both dimers have comparable binding energies ( ΔEZPECPI, II = -7.02, -6.34 kcal mol -1) being less stable than calculated structures III and IV ( ΔEZPECPIII, IV = -9.50, -8.87 kcal mol -1) in which one or two intramolecular hydrogen bonds are disrupted. In the most stable 10-membered cyclic dimer III, two intermolecular CO···H sbnd ON hydrogen bonds are formed at expense of intramolecular hydrogen bonds of the same type. The formation of the less stable (AHA) 2 dimers in the studied matrixes indicates that the formation of (AHA) 2 is kinetically and not thermodynamically controlled.

Quasi-normal modes from non-commutative matrix dynamics

NASA Astrophysics Data System (ADS)

Aprile, Francesco; Sanfilippo, Francesco

2017-09-01

We explore similarities between the process of relaxation in the BMN matrix model and the physics of black holes in AdS/CFT. Focusing on Dyson-fluid solutions of the matrix model, we perform numerical simulations of the real time dynamics of the system. By quenching the equilibrium distribution we study quasi-normal oscillations of scalar single trace observables, we isolate the lowest quasi-normal mode, and we determine its frequencies as function of the energy. Considering the BMN matrix model as a truncation of N=4 SYM, we also compute the frequencies of the quasi-normal modes of the dual scalar fields in the AdS5-Schwarzschild background. We compare the results, and we finda surprising similarity.

Short communication: Lactic acid bacteria from the honeybee inhibit the in vitro growth of mastitis pathogens.

PubMed

Piccart, K; Vásquez, A; Piepers, S; De Vliegher, S; Olofsson, T C

2016-04-01

Despite the increasing knowledge of prevention and control strategies, bovine mastitis remains one of the most challenging diseases in the dairy industry. This study investigated the antimicrobial activity of 13 species of lactic acid bacteria (LAB), previously isolated from the honey crop of the honeybee, on several mastitis pathogens. The viable LAB were first reintroduced into a sterilized heather honey matrix. More than 20 different bovine mastitis isolates were tested against the mixture of the 13 LAB species in the honey medium using a dual-culture overlay assay. The mastitis isolates were identified through bacteriological culturing, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Additionally, the mastitis isolates were subjected to antimicrobial susceptibility testing through disk diffusion. Growth of all tested mastitis pathogens, including the ones displaying antimicrobial resistance to one or more antimicrobial compounds, were inhibited to some extent by the honey and LAB combination. The antibacterial effect of these LAB opens up new perspectives on alternative treatment and prevention of bovine mastitis. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Successful Identification of Clinical Dermatophyte and Neoscytalidium Species by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Alshawa, Kinda; Beretti, Jean-Luc; Lacroix, Claire; Feuilhade, Martine; Dauphin, Brunhilde; Quesne, Gilles; Hassouni, Noura; Nassif, Xavier

2012-01-01

Dermatophytes are keratinolytic fungi responsible for a wide variety of diseases of glabrous skin, nails, and hair. Their identification, currently based on morphological criteria, is hindered by intraspecies morphological variability and the atypical morphology of some clinical isolates. The aim of this study was to evaluate matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as a routine tool for identifying dermatophyte and Neoscytalidium species, both of which cause dermatomycoses. We first developed a spectral database of 12 different species of common and unusual dermatophytes and two molds responsible for dermatomycoses (Neoscytalidium dimidiatum and N. dimidiatum var. hyalinum). We then prospectively tested the performance of the database on 381 clinical dermatophyte and Neoscytalidium isolates. Correct identification of the species was obtained for 331/360 dermatophytes (91.9%) and 18/21 Neoscytalidium isolates (85.7%). The results of MALDI-TOF MS and standard identification disagreed for only 2 isolates. These results suggest that MALDI-TOF MS could be a useful tool for routine and fast identification of dermatophytes and Neoscytalidium spp. in clinical mycology laboratories. PMID:22535981

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry rapid detection of carbapenamase activity in Acinetobacter baumannii isolates.

PubMed

Abouseada, Noha; Raouf, May; El-Attar, Eman; Moez, Pacinte

2017-01-01

Carbapenamase-producing Acinetobacter baumannii are an increasing threat in hospitals and Intensive Care Units. Accurate and rapid detection of carbapenamase producers has a great impact on patient improvement and aids in implementation of infection control measures. In this study, we describe the use of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI TOF MS) to identify carbapenamase-producing A. baumannii isolates in up to 3 h. Isolates and Methods: A total of 50 A. baumannii isolates (of which 39 were carabapenamase producers) were tested using MALDI TOF MS. Isolates were incubated for 3 h with 0.25 mg/ml up to 2 mg/ml of imipenem (IMP) at 37°C. Supernatants were analysed by MALDI TOF to analyse peaks corresponding to IMP (300 Da) and an IMP metabolite (254 Da) using UltrafleXtreme (Bruker Daltonics, Bremen, Germany). All carbapenamase-producing isolates were evidenced by the disappearance or reduction in intensity of the 300 Da peak of IPM and the appearance of a 254 Da peak of the IPM metabolite. In isolates that did not produce carbapenamase, the IPM 300 Da peak remained intact. MALDI TOF is a promising tool in the field of diagnostic microbiology that has the ability to transfer identification and antimicrobial susceptibility testing time from days to hours.

Characterization of Klebsiella isolates by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and determination of antimicrobial resistance with VITEK 2 advanced expert system (AES).

PubMed

Karagöz, Alper; Acar, Sümeyra; Körkoca, Hanifi

2015-01-01

The purpose of the study was to evaluate the performance of the VITEK mass spectrometry (MS) (bioMérieux, France) system for the identification of Klebsiella spp. isolated from different sources. Moreover, while assessing the ability of the VITEK 2 automated expert system (AES) to recognize antimicrobial resistance patterns, the researchers have extended the study to compare VITEK 2 with the routine antimicrobial susceptibility testing method. This study tested 51 Klebsiella spp. isolates that were isolated from environmental examples and clinical examples. Results of conventional methods and the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS were compared. Then, any differing results were compared against a reference 16S rRNA gene sequence, and when indicated, a recA sequencing analysis was done. VITEK MS correctly identified 100% of the Klebsiella spp. isolates. There were two K. oxytoca isolates incorrectly identified to the species level with conventional methods according to the 16S rRNA gene sequencing analysis. In addition, a VITEK 2 AST-N261 card was used for the detection of extended spectrum beta-lactamases (ESBL). Using the VITEK 2 AES, ESBL positivity was found at the rate of 16.3% whereas this rate was 4.08% using the disk diffusion method. MALDI-TOF MS is a rapid and accurate method for the identification of Klebsiella spp. Moreover, the bioMérieux AES provides a useful laboratory tool for the interpretation of susceptibility results.

Advanced instrumental methods for analyzing organics in solid waste: The use of gas chromatography/matrix isolation infrared spectroscopy (GC/MIIR) and supercritical fluid chromatography (SFC) for waste characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raphaelian, L.A.; Boparai, A.S.; Schneider, J.F.

1987-01-01

Objectives of this research project were: (1) to enhance the capabilities of analyzing the complex mixtures found in coal wastes by using gas chromatography/matrix isolation infrared spectroscopy (GC/MIIR); (2) to separate, by supercritical fluid chromatography (SFC), the complex mixtures found in coal wastes into a few, less-complex mixtures so that analysis by gas chromatography (GC/MS) and GC/MIIR would be simplified. Preliminary results are presented for the mass spectra and infrared spectra of xylene isomers, gas chromatogram of 12 C/sub 2/-Napthalenes, averaged IR spectrum and a comparison of matrix isolation with light-pipe infrared spectra. A SFC chromatogram of polynuclear aromatic hydrocarbonsmore » is also presented. 2 refs., 5 figs.« less

Iminopropadienones RN=C=C=C=O and bisiminopropadienes RN=C=C=C=NR: Matrix infrared spectra and anharmonic frequency calculations

NASA Astrophysics Data System (ADS)

Bégué, Didier; Baraille, Isabelle; Andersen, Heidi Gade; Wentrup, Curt

2013-10-01

Methyliminopropadienone MeN=C=C=C=O 1a was generated by flash vacuum thermolysis from four different precursors and isolated in solid argon. The matrix-isolation infrared spectrum is dominated by unusually strong anharmonic effects resulting in complex fine structure of the absorptions due to the NCCCO moiety in the 2200 cm-1 region. Doubling and tripling of the corresponding absorption bands are observed for phenyliminopropadienone PhN=C=C=C=O 1b and bis(phenylimino)propadiene PhN=C=C=C=NPh 9, respectively. Anharmonic vibrational frequency calculations allow the identification of a number of overtones and combination bands as the cause of the splittings for each molecule. This method constitutes an important tool for the characterization of reactive intermediates and unusual molecules by matrix-isolation infrared spectroscopy.

Pasture succession in the Neotropics: extending the nucleation hypothesis into a matrix discontinuity hypothesis.

PubMed

Peterson, Chris J; Dosch, Jerald J; Carson, Walter P

2014-08-01

The nucleation hypothesis appears to explain widespread patterns of succession in tropical pastures, specifically the tendency for isolated trees to promote woody species recruitment. Still, the nucleation hypothesis has usually been tested explicitly for only short durations and in some cases isolated trees fail to promote woody recruitment. Moreover, at times, nucleation occurs in other key habitat patches. Thus, we propose an extension, the matrix discontinuity hypothesis: woody colonization will occur in focal patches that function to mitigate the herbaceous vegetation effects, thus providing safe sites or regeneration niches. We tested predictions of the classical nucleation hypothesis, the matrix discontinuity hypothesis, and a distance from forest edge hypothesis, in five abandoned pastures in Costa Rica, across the first 11 years of succession. Our findings confirmed the matrix discontinuity hypothesis: specifically, rotting logs and steep slopes significantly enhanced woody colonization. Surprisingly, isolated trees did not consistently significantly enhance recruitment; only larger trees did so. Finally, woody recruitment consistently decreased with distance from forest. Our results as well as results from others suggest that the nucleation hypothesis needs to be broadened beyond its historical focus on isolated trees or patches; the matrix discontinuity hypothesis focuses attention on a suite of key patch types or microsites that promote woody species recruitment. We argue that any habitat discontinuities that ameliorate the inhibition by dense graminoid layers will be foci for recruitment. Such patches could easily be manipulated to speed the transition of pastures to closed canopy forests.

Isolation and characterization of chicken bile matrix metalloproteinase

USDA-ARS?s Scientific Manuscript database

Avian bile is rich in matrix metalloproteinases (MMP), the enzymes that cleave extracellular matrix (ECM) proteins such as collagens and proteoglycans. Changes in bile MMP expression have been correlated with hepatic and gall bladder pathologies but the significance of their expression in normal, he...

Chemical Reactions Triggered Using Electrons Photodetached from "Clean" Distributions of Anions Deposited in Cryogenic Matrices via Counterion Codeposition.

PubMed

Ludwig, Ryan M; Moore, David T

2014-09-04

Application of matrix isolation spectroscopy to ionic species is typically complicated by the presence of neutral contaminants during matrix deposition. Herein we demonstrate that simultaneous deposition of balanced currents of counterions with mass-selected ions of interest generates "clean" distributions of matrix-isolated metal carbonyl anions, where the only bands appearing in the CO-stretching region of the vibrational spectrum arise from ions. (Neutrals are initially absent.) Photodetachment by mild irradiation with visible light leads to complete conversion of the anions into their corresponding neutral species. The photodetached electrons, in turn, initiate covalent chemistry, inducing C-C bond formation following electron-capture by CO van der Waals dimers to produce trans-OCCO(-). The initial clean distribution of ions enables clear connections to be drawn between the spectral changes occurring at each experimental step, thus demonstrating the potential of the counterion codeposition technique to facilitate detailed studies of chemistry involving ions and electron transfer in cryogenic matrices.

Detection of biomarkers of pathogenic Naegleria fowleri through mass spectrometry and proteomics.

PubMed

Moura, Hercules; Izquierdo, Fernando; Woolfitt, Adrian R; Wagner, Glauber; Pinto, Tatiana; del Aguila, Carmen; Barr, John R

2015-01-01

Emerging methods based on mass spectrometry (MS) can be used in the rapid identification of microorganisms. Thus far, these practical and rapidly evolving methods have mainly been applied to characterize prokaryotes. We applied matrix-assisted laser-desorption-ionization-time-of-flight mass spectrometry MALDI-TOF MS in the analysis of whole cells of 18 N. fowleri isolates belonging to three genotypes. Fourteen originated from the cerebrospinal fluid or brain tissue of primary amoebic meningoencephalitis patients and four originated from water samples of hot springs, rivers, lakes or municipal water supplies. Whole Naegleria trophozoites grown in axenic cultures were washed and mixed with MALDI matrix. Mass spectra were acquired with a 4700 TOF-TOF instrument. MALDI-TOF MS yielded consistent patterns for all isolates examined. Using a combination of novel data processing methods for visual peak comparison, statistical analysis and proteomics database searching we were able to detect several biomarkers that can differentiate all species and isolates studied, along with common biomarkers for all N. fowleri isolates. Naegleria fowleri could be easily separated from other species within the genus Naegleria. A number of peaks detected were tentatively identified. MALDI-TOF MS fingerprinting is a rapid, reproducible, high-throughput alternative method for identifying Naegleria isolates. This method has potential for studying eukaryotic agents. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

Radioprotective Thiolamines WR-1065 and WR-33278 Selectively Denature Nonhistone Nuclear Proteins

NASA Technical Reports Server (NTRS)

Booth, Valerie K.; Roberts, Jeanette C.; Warters, Raymond L.; Wilmore, Britta H.; Lepock, James R.

2000-01-01

Differential scanning calorimetry was used to study the interactions of nuclei isolated from Chinese hamster V79 cells with the radioprotector WR-1065, other thiol compounds, and polyamines. Differential scanning calorimetry monitors denaturation of macromolecules and resolves the major nuclear components (e.g. constrained and relaxed DNA, nucleosome core, and nuclear matrix) of intact nuclei on the basis of thermal stability. WR-1065 treatment (0.5-10 mM) of isolated nuclei led to the irreversible denaturation of nuclear proteins, a fraction of which are nuclear matrix proteins. Denaturation of 50% of the total nonhistone nuclear protein content of isolated nuclei occurred after exposure to 4.7 mM WR-1065 for 20 min at 23 C. In addition, a 22% increase in the insoluble protein content of nuclei isolated from V79 cells that had been treated with 4 mM WR-1065 for 30 min at 37 C was observed, indicating that WR-1065-induced protein denaturation occurs not only in isolated nuclei but also in the nuclei of intact cells. From the extent of the increase in insoluble protein in the nucleus, protein denaturation by WR-1065 is expected to contribute to drug toxicity at concentrations greater than approximately 4 mM. WR-33278, the disulfide form of WR1065, was approximately twice as effective as the free thiol at denaturing nuclear proteins. The proposed mechanism for nucleoprotein denaturation is through direct interactions with protein cysteine groups with the formation of destabilizing protein-WR-1065 disulfides. In comparison to its effect on nuclear proteins in isolated nuclei, WR-1065 had only a very small effect on non-nuclear proteins of whole cells, isolated nuclear matrix, or the thiol-rich Ca (2+) ATPase of sarcoplasmic reticulum, indicating that WR-1065 can effectively denature protein only inside an intact nucleus, probably due to the increased concentration of the positively charged drug in the vicinity of DNA.

Improvement of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of difficult-to-identify bacteria and its impact in the workflow of a clinical microbiology laboratory.

PubMed

Rodríguez-Sánchez, Belén; Marín, Mercedes; Sánchez-Carrillo, Carlos; Cercenado, Emilia; Ruiz, Adrián; Rodríguez-Créixems, Marta; Bouza, Emilio

2014-05-01

This study evaluates matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) capability for the identification of difficult-to-identify microorganisms. A total of 150 bacterial isolates inconclusively identified with conventional phenotypic tests were further assessed by 16S rRNA sequencing and by MALDI-TOF MS following 2 methods: a) a simplified formic acid-based, on-plate extraction and b) performing a tube-based extraction step. Using the simplified method, 29 isolates could not be identified. For the remaining 121 isolates (80.7%), we obtained a reliable identification by MALDI-TOF: in 103 isolates, the identification by 16S rRNA sequencing and MALDI TOF coincided at the species level (68.7% from the total 150 analyzed isolates and 85.1% from the samples with MALDI-TOF result), and in 18 isolates, the identification by both methods coincided at the genus level (12% from the total and 14.9% from the samples with MALDI-TOF results). No discordant results were observed. The performance of the tube-based extraction step allowed the identification at the species level of 6 of the 29 unidentified isolates by the simplified method. In summary, MALDI-TOF can be used for the rapid identification of many bacterial isolates inconclusively identified by conventional methods. Copyright © 2014 Elsevier Inc. All rights reserved.

A simple non-enzymatic method for the preparation of white spot syndrome virus (WSSV) DNA from the haemolymph of Marsupenaeus japonicus using FTA matrix cards.

PubMed

Sudhakaran, R; Mekata, T; Kono, T; Supamattaya, K; Linh, N T H; Suzuki, Y; Sakai, M; Itami, T

2009-07-01

White spot syndrome virus (WSSV) is an important shrimp pathogen responsible for large economic losses for the shrimp culture industry worldwide. The nucleic acids of the virus must be adequately preserved and transported from the field to the laboratory before molecular diagnostic analysis is performed. Here, we developed a new method to isolate WSSV-DNA using Flinders Technology Associates filter paper (FTA matrix card; Whatman) without centrifugation or hazardous steps involved. FTA technology is a new method allowing the simple collection, shipment and archiving of nucleic acids from haemolymph samples providing DNA protection against nucleases, oxidation, UV damage, microbial and fungal attack. DNA samples prepared from 10-fold dilutions of moribund shrimp haemolymph using FTA matrix cards were analysed using semi-quantitative and quantitative polymerase chain reaction (PCR) and were compared with two commercially available DNA isolation methods, the blood GenomicPrep Mini Spin Kit (GE Healthcare) and the DNAzol (Invitrogen). Sequence analysis was performed for the DNA samples prepared using the various isolation procedures and no differences in the sequence among these methods were identified. Results based on the initial copy number of DNA prepared from the GenomicPrep Mini Spin Kit are a little more sensitive than the DNA prepared from FTA matrix cards, whereas the DNAzol method is not suitable for blood samples. Our data shows the efficiency of retention capacity of WSSV-DNA samples from impregnated FTA matrix cards. Matrix cards were easy to store and ship for long periods of time. They provide ease of handling and are a reliable alternative for sample collection and for molecular detection and characterization of WSSV isolates.

Matrix Isolation Spectroscopy Applied to Positron Moderatioin in Cryogenic Solids

DTIC Science & Technology

2011-07-01

Current Positron Applications • 2-γ decay exploited in Positron Emission Tomography (PET) scanners. • Positrons localize & annihilate preferentially at...Air Force  Eglin Air Force Base AFRL-RW-EG-TP-2011-024 Matrix Isolation Spectroscopy Applied to Positron Moderation in Cryogenic Solids Distribution... Spectroscopy Applied to Positron Moderation in Cryogenic Solids 5a. CONTRACT NUMBER 5b. GRANT NUMBER 62602F 5c. PROGRAM ELEMENT NUMBER 6

Composition of fibrin glues significantly influences axial vascularization and degradation in isolation chamber model.

PubMed

Arkudas, Andreas; Pryymachuk, Galyna; Hoereth, Tobias; Beier, Justus P; Polykandriotis, Elias; Bleiziffer, Oliver; Gulle, Heinz; Horch, Raymund E; Kneser, Ulrich

2012-07-01

In this study, different fibrin sealants with varying concentrations of the fibrin components were evaluated in terms of matrix degradation and vascularization in the arteriovenous loop (AVL) model of the rat. An AVL was placed in a Teflon isolation chamber filled with 500 μl fibrin gel. The matrix was composed of commercially available fibrin gels, namely Beriplast (Behring GmbH, Marburg, Germany) (group A), Evicel (Omrix Biopharmaceuticals S.A., Somerville, New Jersey, USA) (group B), Tisseel VH S/D (Baxter, Vienna, Austria) with a thrombin concentration of 4 IU/ml and a fibrinogen concentration of 80 mg/ml [Tisseel S F80 (Baxter), group C] and with an fibrinogen concentration of 20 mg/ml [Tisseel S F20 (Baxter), group D]. After 2 and 4 weeks, five constructs per group and time point were investigated using micro-computed tomography, and histological and morphometrical analysis techniques. The aprotinin, factor XIII and thrombin concentration did not affect the degree of clot degradation. An inverse relationship was found between fibrin matrix degradation and sprouting of blood vessels. By reducing the fibrinogen concentration in group D, a significantly decreased construct weight and an increased generation of vascularized connective tissue were detected. There was an inverse relationship between matrix degradation and vascularization detectable. Fibrinogen as the major matrix component showed a significant impact on the matrix properties. Alteration of fibrin gel properties might optimize formation of blood vessels.

Matrix-isolation and comparative far-IR investigation of free linear [Cl3]- and a series of alkali trichlorides.

PubMed

Redeker, F A; Beckers, H; Riedel, S

2017-11-30

Here we discuss the reaction products of laser ablated alkali chlorides and elemental chlorine. Salt ablation using this technique combined with matrix-isolation spectroscopy allows for the formation and characterization of novel anionic species. The laser ablation of solid MCl with M = Cs, Rb, and K in the presence of Cl 2 produced free [Cl 3 ] - ions which were isolated in solid noble-gas matrices. For M = Cs, Rb, K, and Na, the ion pairs M + [Cl 3 ] - are the main reaction products. Trends in the formation and bonding of these trichloride anions will be discussed. In contrast to the trifluoride analogues, the isolated ion pairs M + [Cl 3 ] - feature a systematic distortion due to metal coordination.

Are calcifying matrix vesicles in atherosclerotic lesions of cellular origin?

PubMed

Bobryshev, Yuri V; Killingsworth, Murray C; Huynh, Thuan G; Lord, Reginald S A; Grabs, Anthony J; Valenzuela, Stella M

2007-03-01

Over recent years, the role of matrix vesicles in the initial stages of arterial calcification has been recognized. Matrix calcifying vesicles have been isolated from atherosclerotic arteries and the biochemical composition of calcified vesicles has been studied. No studies have yet been carried out to examine the fine structure of matrix vesicles in order to visualize the features of the consequent stages of their calcification in arteries. In the present work, a high resolution ultrastructural analysis has been employed and the study revealed that matrix vesicles in human atherosclerotic lesions are heterogeneous with two main types which we classified. Type I calcified vesicles were presented by vesicles surrounded by two electron-dense layers and these vesicles were found to be resistant to the calcification process in atherosclerotic lesions in situ. Type II matrix vesicles were presented by vesicles surrounded by several electron-dense layers and these vesicles were found to represent calcifying vesicles in atherosclerotic lesions. To test the hypothesis that calcification of matrix vesicles surrounded by multilayer sheets may occur simply as a physicochemical process, independently from the cell regulation, we produced multilamellar liposomes and induced their calcification in vitro in a manner similar to that occurring in matrix vesicles in atherosclerotic lesions in situ.

Use of Isolated Mitochondria and Pulmonary Artery Endothelial Cell Systems in Studies of Oxygen Utilization and the Effects of Hemoglobin-Based Oxygen Carriers

DTIC Science & Technology

2008-07-16

mitochondria through the monocarboxylate transporter and feed in to the Kreb’s cycle to yield 34 ATPs via oxidative phosphorylation as follows (assuming a... Krebs (tricarboxylic acid) cycle enzyme, and is found mainly in the mitochondrial matrix (8). Therefore, its measured enzymatic activity serves as an...APPROVAL SHEET Title of Thesis: "Use of Isolated Mitochondria and Pulmonary Artery Endothelial Cell Systems in Studies of Oxygen Utilization and the

Inhibition of matrix metalloproteinase-1 and type-I procollagen expression by phenolic compounds isolated from the leaves of Quercus mongolica in ultraviolet-irradiated human fibroblast cells.

PubMed

Kim, Han Hyuk; Kim, Dong Hee; Oh, Myeong Hwan; Park, Kwang Jun; Heo, Jun Hyeok; Lee, Min Won

2015-01-01

The aim of this study was to investigate the effect of Quercus mongolica (QM) which induce anti-photoaging process of skin in vitro. Bioassay-guided isolation of 80 % Me2CO extract of the leaves of QM led to the isolation and identification of six known phenolic compounds: pedunculagin (1), (-)-epigallocatechin (2), (+)-catechin (3), quercetin 3-O-(6″-O-galloyl)-β-D-glucopyranoside (4), kaempferol-3-O-β-D-glucopyranoside-7-O-α-L-rhamnopyranoside (5) and kaempferol 3-O-(6″-galloyl)-β-D-glucopyranoside (6). The effects of compounds 1-6 on expression of matrix metalloproteinase-1 (MMP-1) and type-I procollagen were further evaluated. Among them, compound 1 showed potent inhibitory effect on MMP-1 and the increased type-I procollagen synthesis in ultraviolet B-induced human fibroblast. These results suggest that pedunculagin, an ellagitannin, is a potential candidate for the prevention and treatment of skin aging.

Difluoro-lambda(5)-phosphinonitrile F(2)P[triple bond]N: matrix isolation and photoisomerization into FP=NF.

PubMed

Zeng, Xiaoqing; Beckers, Helmut; Willner, Helge

2009-01-01

Splendid isolation: Monomeric phosphazene F(2)PN ((1)A(1)) was prepared for the first time through irradiation of F(2)PN(3) in an argon matrix with an ArF excimer laser (lambda=193 nm). Upon subsequent irradiation with a high-pressure mercury arc lamp (lambda=255 nm), F(2)PN undergoes a 1,2-fluorine shift to give iminophosphane cis-FP=NF.

Experimental and theoretical IR study of methyl thioglycolate, CH3OC(O)CH2SH, in different phases: Evidence of a dimer formation

NASA Astrophysics Data System (ADS)

Bava, Yanina B.; Tamone, Luciana M.; Juncal, Luciana C.; Seng, Samantha; Tobón, Yeny A.; Sobanska, Sophie; Picone, A. Lorena; Romano, Rosana M.

2017-07-01

The IR spectrum of methyl thioglycolate (MTG) was studied in three different phases, and interpreted with the aid of DFT calculations. The gas phase IR spectrum was explainable by the presence of the most stable conformer (syn-gauche-(-)gauche) only, while the IR spectrum of the liquid reveals strong intermolecular interactions, coincident with the formation of a dimeric form. The matrix-isolated spectra allow the identification of the second conformer (syn-gauche-gauche), in addition to the most stable form. The MTG dimer was also isolated by increasing the proportion of MTG in the matrix. The theoretical most stable structure of the dimer, which calculated IR spectrum agrees very well with the experimental one, is stabilized by a double interaction of the lone pair of the O atom of each of the Cdbnd O groups with the antibonding orbitals σ* (Ssbnd H).

C dbnd N sbnd N dbnd C conformational isomers of 2'-hydroxyacetophenone azine: FTIR matrix isolation and DFT study

NASA Astrophysics Data System (ADS)

Grzegorzek, Joanna; Mielke, Zofia; Filarowski, Aleksander

2010-07-01

2'-hydroxyacetophenone azine (APA) has been studied by matrix isolation infrared spectroscopy and quantum chemical calculations. The DFT/B3LYP/6-311++G(2d,2p) calculations demonstrated the existence of two conformers for the lowest energy E/ E configuration of APA, a s- trans and a gauche ones. The conformers are characterized by similar energies and differ in the value of a C dbnd N sbnd N dbnd C angle, that was calculated to be 180° for a planar s-trans conformer and 155° for a non-planar gauche one . The calculated barrier for conformational interconversion is also very low, ca. 1 kJ mol -1 for the conversion from a gauche conformer to a trans one. The FTIR spectra of an argon matrix doped with APA from a vapour above solid sample evidence the presence of both conformers that exhibit reversible interconversion at matrix temperatures. The comparison of the theoretical spectra with the experimental ones and reversible temperature dependence of the experimental spectra allowed for unambiguous spectroscopic characterization of the trans and gauche conformers. The experiment also demonstrated that a gauche conformer is more stable than a trans one. The spectra analysis indicates that transformation from a trans conformer to a gauche one weakens the intramolecular O sbnd H⋯N bonds in the molecule.

Matrix isolation infrared spectra of O2 and N2 insertion reactions with atomic uranium

NASA Astrophysics Data System (ADS)

Hunt, Rodney D.; Toth, L. Mac; Yustein, Jason T.; Andrews, Lester

1993-10-01

Laser ablation of refractory metals can be an effective source of vapor for matrix isolation IR studies. This combination of techniques was used for the first time to study the mechanisms of U vapor reactions with atmospheric components. U atoms and O2 were codeposited with excess Ar at 12 K. The dominant codeposition products were UO2 and UO3. In contrast, the UO yield was always small because UO2 is formed by an insertion mechanism. This mechanism was verified in the 16O2/18O2 experiments which failed to produce 16OU18O. The effects of UV photolysis and matrix annealings were also examined. The U atoms and O2 reaction requires little or no activation energy since UO2 was formed from cold reagents. New charge-transfer species, (UO2+2)(O2-2) and (UO+2)(O-2), and a weak complex, UO3-O2, were primarily produced under conditions which favored further O2 reactions. Similar U atom and N2 experiments produced only linear NUN which is also produced by an insertion mechanism. This U reaction represents the first time that atom was observed breaking and inserting into the triple bond of N2. Photolysis dramatically increased the NUN yield by 3-fold. Matrix annealings produced weak UN2-N2 and UN2-2N2 complexes.

Electronic absorption spectroscopy of matrix-isolated polycyclic aromatic hydrocarbon cations. II. The phenanthrene cation (C14H10+) and its 1-methyl derivative

NASA Technical Reports Server (NTRS)

Salama, F.; Joblin, C.; Allamandola, L. J.

1994-01-01

The ultraviolet, visible, and near infrared absorption spectra of phenanthrene (C14H10), 1-methylphenanthrene [(CH3)C14H9], and their radical ions [C14H10+; (CH3)C14H9+], formed by vacuum-ultraviolet irradiation, were measured in neon matrices at 4.2 K. The associated vibronic band systems and their spectroscopic assignments are discussed. The oscillator strengths were calculated for the phenanthrene ion and found lower than the theoretical predictions. This study presents the first spectroscopic data for phenanthrene and its methyl derivative trapped in a neon matrix where the perturbation of the isolated species by its environment is minimum; a condition crucial to astrophysical applications.

Isolation, purification and characterization of collagenase from hepatopancreas of the land snail Achatina fulica.

PubMed

Indra, D; Ramalingam, K; Babu, Mary

2005-09-01

Collagenase (matrix metalloproteinase-1, EC:3.4.24.7) was isolated from the hepatopancreas of Achatina fulica and characterized for its enzymatic activity and immunological properties. Procollagenase was isolated using ammonium sulphate precipitation and gel filtration, followed by purification by reverse-phase high performance liquid chromatography in the presence of trifluoroacetic acid and by dialysis in neutral buffer. In the presence of SDS and beta-mercaptoethanol, the procollagenase resolved into two subunits with molecular masses of 63 and 28 kDa, respectively. The 63 kDa fragment retained its ability to bind and degrade gelatin, but the 28 kDa was inactive. Analysis by 2D gel electrophoresis revealed that the 63 kDa fragment was basic (pIs 7.6, 7.8 and 8.15), while the 28 kDa fragment was acidic (pI 4.7 and 5.1). Western blot analysis confirmed the identity of collagenase, as only matrix metalloproteinase-1 rabbit antibodies against human matrix metalloproteinase-1 (N-terminal region) recognized both the isolated procollagenase and the 63 kDa fragment.

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry identification of large colony beta-hemolytic streptococci containing Lancefield groups A, C, and G.

PubMed

Jensen, Christian Salgård; Dam-Nielsen, Casper; Arpi, Magnus

2015-08-01

The aim of this study was to investigate whether large colony beta-hemolytic streptococci containing Lancefield groups A, C, and G can be adequately identified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-ToF). Previous studies show varying results, with an identification rate from below 50% to 100%. Large colony beta-hemolytic streptococci containing Lancefield groups A, C, and G isolated from blood cultures between January 1, 2007 and May 1, 2012 were included in the study. Isolates were identified to the species level using a combination of phenotypic characteristics and 16s rRNA sequencing. The isolates were subjected to MALDI-ToF analysis. We used a two-stage approach starting with the direct method. If no valid result was obtained we proceeded to an extraction protocol. Scores above 2 were considered valid identification at the species level. A total of 97 Streptococcus pyogenes, 133 Streptococcus dysgalactiae, and 2 Streptococcus canis isolates were tested; 94%, 66%, and 100% of S. pyogenes, S. dysgalactiae, and S. canis, respectively, were correctly identified by MALDI-ToF. In most instances when the isolates were not identified by MALDI-ToF this was because MALDI-ToF was unable to differentiate between S. pyogenes and S. dysgalactiae. By removing two S. pyogenes reference spectra from the MALDI-ToF database the proportion of correctly identified isolates increased to 96% overall. MALDI-ToF is a promising method for discriminating between S. dysgalactiae, S. canis, and S. equi, although more strains need to be tested to clarify this.

Large-scale production and isolation of Candida biofilm extracellular matrix.

PubMed

Zarnowski, Robert; Sanchez, Hiram; Andes, David R

2016-12-01

The extracellular matrix of biofilm is unique to the biofilm lifestyle, and it has key roles in community survival. A complete understanding of the biochemical nature of the matrix is integral to the understanding of the roles of matrix components. This knowledge is a first step toward the development of novel therapeutics and diagnostics to address persistent biofilm infections. Many of the assay methods needed for refined matrix composition analysis require milligram amounts of material that is separated from the cellular components of these complex communities. The protocol described here explains the large-scale production and isolation of the Candida biofilm extracellular matrix. To our knowledge, the proposed procedure is the only currently available approach in the field that yields milligram amounts of biofilm matrix. This procedure first requires biofilms to be seeded in large-surface-area roller bottles, followed by cell adhesion and biofilm maturation during continuous movement of the medium across the surface of the rotating bottle. The formed matrix is then separated from the entire biomass using sonication, which efficiently removes the matrix without perturbing the fungal cell wall. Subsequent filtration, dialysis and lyophilization steps result in a purified matrix product sufficient for biochemical, structural and functional assays. The overall protocol takes ∼11 d to complete. This protocol has been used for Candida species, but, using the troubleshooting guide provided, it could be adapted for other fungi or bacteria.

Evaluation of oral keratinocyte progenitor and T-lymphocite cells response during early healing after augmentation of keratinized gingiva with a 3D collagen matrix - a pilot study.

PubMed

Rusu, Darian; Calenic, Bogdan; Greabu, Maria; Kralev, Alexander; Boariu, Marius; Bojin, Florina; Anghel, Simona; Paunescu, Virgil; Vela, Octavia; Calniceanu, Horia; Stratul, Stefan-Ioan

2016-07-07

The aim of the present study is to analyze the behavior of selected populations of oral keratinocytes and T-lymphocytes, responsible for re-constructing and maintaining the oral epithelial tissue architecture, following augmentation of the keratinized oral mucosa using a 3D-collagen matrix. Different groups of oral keratinocytes were isolated from biopsies harvested from 3 patients before the surgical procedure, as well as 7 and 14 days after the augmentation procedure. T-lymphocytes were isolated from peripheral blood at same timepoints. Keratinocytes were characterized for stem and differentiation markers, such as p63, cytokeratin 10 and 14, and in vitro parameters, such as cell viability, cell size and colony-forming efficiency. T-lymphocytes were analyzed for viability and the expression of various cluster of differentiation markers. The methods included magnetic separation of cell populations, immunofluorescence, flow cytometry, and histology of oral biopsies. Both at 7 and 14 days, the majority of cells that repopulate the matrix were actively proliferating/progenitor oral keratinocytes with the phenotype integrin alfa6beta4 + CD71+. These cells display in vitro characteristics similar to the progenitor cells analyzed before the matrix placement. T-lymphocytes expressed CD8 and CD69 markers, while CD25 was absent. The study shows that two weeks after the collagen membrane placement, the healing process appeared to be histologically complete, with no abnormal immune response induced by the matrix, however, with a higher than usual content of active proliferating cells, the majority of keratinocytes being characterized as transit amplifying cells.

Identification of Weissella species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Lee, Meng-Rui; Tsai, Chia-Jung; Teng, Shih-Hua; Hsueh, Po-Ren

2015-01-01

Although some Weissella species play beneficial roles in food fermentation and in probiotic products, others such as Weissella confusa are emerging Gram-positive pathogens in immunocompromised hosts. Weissella species are difficult to identify by conventional biochemical methods and commercial automated systems and are easily misidentified as Lactobacillus and Leuconostoc species. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly being used for bacterial identification. Little, however, is known about the effectiveness of MALDI-TOF MS in identifying clinical isolates of Weissella to the species level. In this study, we evaluated whether the MALDI-TOF MS Bruker Biotyper system could accurately identify a total of 20 W. confusa and 2 W. cibaria blood isolates that had been confirmed by 16s rRNA sequencing analysis. The MALDI-TOF Biotyper system yielded no reliable identification results based on the current reference spectra for the two species (all score values <1.7). New W. confusa spectra were created by randomly selecting 3 W. confusa isolates and external validation was performed by testing the remaining 17 W. confusa isolates using the new spectra. The new main spectra projection (MSP) yielded reliable score values of >2 for all isolates with the exception of one (score value, 1.963). Our results showed that the MSPs in the current database are not sufficient for correctly identifying W. confusa or W. cibaria. Further studies including more Weissella isolates are warranted to further validate the performance of MALDI-TOF in identifying Weissella species.

Epidemiology and antifungal susceptibilities of yeast isolates causing invasive infections across urban Beijing, China.

PubMed

Guo, Li-Na; Xiao, Meng; Cao, Bin; Qu, Fen; Zhan, Yu-Liang; Hu, Yun-Jian; Wang, Xin-Ru; Liang, Guo-Wei; Gu, Hai-Tong; Qi, Jun; Yuan, Hui; Min, Rong; Wang, Fei-Yan; Liu, Lin-Juan; Wang, Hai-Bin; Jiang, Wei; Duan, Xue-Guang; Xu, Wen-Jian; Yu, Yan-Hua; Su, Jian-Rong; Zhang, Jian-Zhong; Nong, Jin-Qing; Liu, Shu-Mei; Li, Jun; Liu, Jun-Ting; Yue, Zhi-Gang; Yang, Duo; Guo, Jie; Zhao, Rui; Zhang, Ya-Nan; Yang, Xi-Ming; Liu, Xiao-Qing; Hsueh, Po-Ren; Xu, Ying-Chun

2017-09-01

To investigate the species distribution and antifungal susceptibility profiles of yeast isolates causing invasive infections across Beijing. A total of 1201 yeast isolates recovered from blood and other sterile body fluids were correctly identified by matrix-assisted laser desorption/ionization TOF MS supplemented by DNA sequencing. Antifungal susceptibility testing was performed according to the Clinical and Laboratory Standards Institute broth microdilution method. Candida (95.5%) remained the most common yeast species isolated; Candida albicans (38.8%) and Candida parapsilosis (22.6%) were the leading species of candidemia. Azole resistances were mainly observed in Candida glabrata and Candida tropicalis isolates. This study outlined the epidemiologic data of invasive yeast infections and highlighted the need for continuous monitoring of azole resistances among C. glabrata and C. tropicalis isolates in Beijing.

Biofilm-Forming Abilities of Shiga Toxin-Producing Escherichia coli Isolates Associated with Human Infections

PubMed Central

Vogeleer, Philippe; Tremblay, Yannick D. N.; Jubelin, Grégory; Jacques, Mario

2015-01-01

Forming biofilms may be a survival strategy of Shiga toxin-producing Escherichia coli to enable it to persist in the environment and the food industry. Here, we evaluate and characterize the biofilm-forming ability of 39 isolates of Shiga toxin-producing Escherichia coli isolates recovered from human infection and belonging to seropathotypes A, B, or C. The presence and/or production of biofilm factors such as curli, cellulose, autotransporter, and fimbriae were investigated. The polymeric matrix of these biofilms was analyzed by confocal microscopy and by enzymatic digestion. Cell viability and matrix integrity were examined after sanitizer treatments. Isolates of the seropathotype A (O157:H7 and O157:NM), which have the highest relative incidence of human infection, had a greater ability to form biofilms than isolates of seropathotype B or C. Seropathotype A isolates were unique in their ability to produce cellulose and poly-N-acetylglucosamine. The integrity of the biofilms was dependent on proteins. Two autotransporter genes, ehaB and espP, and two fimbrial genes, z1538 and lpf2, were identified as potential genetic determinants for biofilm formation. Interestingly, the ability of several isolates from seropathotype A to form biofilms was associated with their ability to agglutinate yeast in a mannose-independent manner. We consider this an unidentified biofilm-associated factor produced by those isolates. Treatment with sanitizers reduced the viability of Shiga toxin-producing Escherichia coli but did not completely remove the biofilm matrix. Overall, our data indicate that biofilm formation could contribute to the persistence of Shiga toxin-producing Escherichia coli and specifically seropathotype A isolates in the environment. PMID:26712549

Biofilm-Forming Abilities of Shiga Toxin-Producing Escherichia coli Isolates Associated with Human Infections.

PubMed

Vogeleer, Philippe; Tremblay, Yannick D N; Jubelin, Grégory; Jacques, Mario; Harel, Josée

2015-12-28

Forming biofilms may be a survival strategy of Shiga toxin-producing Escherichia coli to enable it to persist in the environment and the food industry. Here, we evaluate and characterize the biofilm-forming ability of 39 isolates of Shiga toxin-producing Escherichia coli isolates recovered from human infection and belonging to seropathotypes A, B, or C. The presence and/or production of biofilm factors such as curli, cellulose, autotransporter, and fimbriae were investigated. The polymeric matrix of these biofilms was analyzed by confocal microscopy and by enzymatic digestion. Cell viability and matrix integrity were examined after sanitizer treatments. Isolates of the seropathotype A (O157:H7 and O157:NM), which have the highest relative incidence of human infection, had a greater ability to form biofilms than isolates of seropathotype B or C. Seropathotype A isolates were unique in their ability to produce cellulose and poly-N-acetylglucosamine. The integrity of the biofilms was dependent on proteins. Two autotransporter genes, ehaB and espP, and two fimbrial genes, z1538 and lpf2, were identified as potential genetic determinants for biofilm formation. Interestingly, the ability of several isolates from seropathotype A to form biofilms was associated with their ability to agglutinate yeast in a mannose-independent manner. We consider this an unidentified biofilm-associated factor produced by those isolates. Treatment with sanitizers reduced the viability of Shiga toxin-producing Escherichia coli but did not completely remove the biofilm matrix. Overall, our data indicate that biofilm formation could contribute to the persistence of Shiga toxin-producing Escherichia coli and specifically seropathotype A isolates in the environment. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity.

PubMed

Linnemann, Amelia K; Krawetz, Stephen A

2009-05-01

DNA loop organization by nuclear scaffold/matrix attachment is a key regulator of gene expression that may provide a means to modulate phenotype. We have previously shown that attachment of genes to the NaCl-isolated nuclear matrix correlates with their silencing in HeLa cells. In contrast, expressed genes were associated with the lithium 3,5-diiodosalicylate (LIS)-isolated nuclear scaffold. To define their role in determining phenotype matrix attached regions (MARs) on human chromosomes 14-18 were identified as a function of expression in a primary cell line. The locations of MARs in aortic adventitial fibroblast (AoAF) cells were very stable (r = 0.909) and 96% of genes attached at MARs are silent (P < 0.001). Approximately one-third of the genes uniquely expressed in AoAF cells were associated with the HeLa cell nuclear matrix and silenced. Comparatively, 81% were associated with the AoAF cell nuclear scaffold (P < 0.001) and expressed. This suggests that nuclear scaffold/matrix association mediates a portion of cell type-specific gene expression thereby modulating phenotype. Interestingly, nuclear matrix attachment and thus silencing of specific genes that regulate proliferation and maintain the integrity of the HeLa cell genome suggests that transformation may at least in part be achieved through aberrant nuclear matrix attachment.

Influence of Culture Media on Detection of Carbapenem Hydrolysis by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Ramos, Ana Carolina; Carvalhaes, Cecília Godoy; Cordeiro-Moura, Jhonatha Rodrigo; Rockstroh, Anna Carolina; Machado, Antonia Maria Oliveira; Gales, Ana Cristina

2016-07-01

In this study, we evaluated the influence of distinct bacterial growth media on detection of carbapenemase hydrolysis by matrix-assisted laser desorption ionization-time of flight mass spectrometry. False-negative results were observed for OXA-25-, OXA-26-, and OXA-72-producing Acinetobacter baumannii isolates grown on MacConkey agar medium. The other culture media showed 100% sensitivity and 100% specificity for detecting carbapenemase. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Raman Spectroscopy.

ERIC Educational Resources Information Center

Gerrard, Donald L.

1984-01-01

Reviews literature on Raman spectroscopy from late 1981 to late 1983. Topic areas include: instrumentation and sampling; liquids and solutions; gases and matrix isolation; biological molecules; polymers; high-temperature and high-pressure studies; Raman microscopy; thin films and surfaces; resonance-enhanced and surface-enhanced spectroscopy; and…

Exploiting elastic anharmonicity in aluminum nitride matrix for phase-synchronous frequency reference generation

NASA Astrophysics Data System (ADS)

Ghatge, Mayur; Tabrizian, Roozbeh

2018-03-01

A matrix of aluminum-nitride (AlN) waveguides is acoustically engineered to realize electrically isolated phase-synchronous frequency references through nonlinear wave-mixing. AlN rectangular waveguides are cross-coupled through a periodically perforated plate that is engineered to have a wide acoustic bandgap around a desirable frequency ( f1≈509 MHz). While the coupling plate isolates the matrix from resonant vibrations of individual waveguide constituents at f1, it is transparent to the third-order harmonic waves (3f1) that are generated through nonlinear wave-mixing. Therefore, large-signal excitation of the f1 mode in a constituent waveguide generates acoustic waves at 3f1 with an efficiency defined by elastic anharmonicity of the AlN film. The phase-synchronous propagation of the third harmonic through the matrix is amplified by a high quality-factor resonance mode at f2≈1529 MHz, which is sufficiently close to 3f1 (f2 ≅ 3f1). Such an architecture enables realization of frequency-multiplied and phase-synchronous, yet electrically and spectrally isolated, references for multi-band/carrier and spread-spectrum wireless communication systems.

Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation

PubMed Central

Liu, Hongxia; Kolter, Roberto; Losick, Richard; Guo, Jian-hua

2014-01-01

Summary Bacillus subtilis and other Bacilli have long been used as biological control agents against plant bacterial diseases but the mechanisms by which the bacteria confer protection are not well understood. Our goal in this study was to isolate strains of B. subtilis that exhibit high levels of biocontrol efficacy from natural environments and to investigate the mechanisms by which these strains confer plant protection. We screened a total of sixty isolates collected from various locations across China and obtained six strains that exhibited above 50% biocontrol efficacy on tomato plants against the plant pathogen Ralstonia solanacearum under greenhouse conditions. These wild strains were able to form robust biofilms both in defined medium and on tomato plant roots and exhibited strong antagonistic activities against various plant pathogens in plate assays. We show that plant protection by those strains depended on widely conserved genes required for biofilm formation, including regulatory genes and genes for matrix production. We provide evidence suggesting that matrix production is critical for bacterial colonization on plant root surfaces. Finally, we have established a model system for studies of B. subtilis-tomato plant interactions in protection against a plant pathogen. PMID:22934631

Identification of Non-diphtheriae Corynebacterium by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Alatoom, Adnan A.; Cazanave, Charles J.; Cunningham, Scott A.; Ihde, Sherry M.

2012-01-01

We evaluated the Bruker Biotyper matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry for identification of 92 clinical isolates of Corynebacterium species in comparison to identification using rpoB or 16S rRNA gene sequencing. Eighty isolates (87%) yielded a score of ≥1.700, and all of these were correctly identified to the species level with the exception of Corynebacterium aurimucosum being misidentified as the closely related Corynebacterium minutissimum. PMID:22075579

Atmospheric trace gas analysis using matrix isolation-Fourier Transform Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Griffith, David W. T.; Schuster, Gerhard

1987-03-01

A novel cryogenic sampling method combining the matrix isolation technique with FTIR spectroscopy has been developed for atmospheric trace gas analysis. It is applicable to a wide range of molecules with detection limits typically in the 10-50 ppt range. The method is described along with some measurements of N2O, CFCl3, CF2Cl2, OCS, CS2, SO2 and PAN from samples collected at ground level and from an aircraft between 9 and 14 km.

Matrix-Isolation Spectroscopy of Reactive Organic Molecules of Relevance to Interstellar Space

NASA Astrophysics Data System (ADS)

Kopff, Laura A.; Nolan, Alex M.; Kreifels, Terese A.; Draxler, Thomas W.; Esselman, Brian J.; Burrmann, Nicola J.; McMahon, Robert J.

2010-11-01

Matrix isolation, the process of trapping a molecule in an inert gas at low temperature, provides a means for studying highly reactive intermediates, such as carbenes or radicals. Reactive species can be characterized by IR, UV-vis and/or EPR spectroscopy. Comparison of experimental and computed spectral data, as well as chemical reactivity, is used for structural assignment Triplet propynylidene is proposed to exist in the interstellar medium (ISM), due to the detection of a higher-energy isomers via rotational spectroscopy. Currently, we are exploring the structural and photochemical effects of varying substituents on the propynylidne system. A diazo precursor has been synthesized and photolyzed to produce dimethylpropynylidene in an argon matrix. A photochemical hydrogen shift to produce 1-penten-3-yne has been observed through infrared spectroscopy. Cyanocarbons are known to be abundant in the ISM and the atmosphere of Titan, however matrixisolation studies have not yet been carried out for a significant number of these compounds. Photolysis of 3-cyano-3-methyldiazirine should yield methylcyanocarbene, one of the simplest species in this family. Another molecule of interest is l-HC4N, which has been detected in the ISM, but has not yet been matrix-isolated and characterized. The study of arylcarbenes is vital to understanding the chemistry of carbon-rich environments, such as discharges, interstellar clouds, and circumstellar envelopes. The identification of small, sulfur containing molecules, and the identification of aromatics in the ISM make future thiophene and benzothiophene detections a real possibility. Studies on 2- and 3-diazomethyl substituted benzothiophenes are underway to assess their photochemical reactivity and potential for forming benzothiophene carbenes. Macrocylic polyynes are proposed to be involved in carbon condensation via the ring coalescence and annealing model to produce graphitic sheets or fullerenes. To simplify a complex system we are experimentally and computationally studying the series of ethynyl-substituted cyclobutadienes and their possible involvement in the build-up of larger carbon containing molecules in the ISM. The Bergman cyclization of cyclobutadiene has been explored computationally and the photochemical precursor is currently being synthesized.

The effects of matrix structure on movement decisions of meadow voles (Microtus pennsylvanicus)

Treesearch

Robin E. Russell; Robert K. Swihart; Bruce A. Craig

2007-01-01

The composition of the landscape between patches (the matrix) can have important effects on movement rates that potentially outweigh the effects of patch size and isolation. We conducted a small-scale experiment with radiocollared meadow voles (Microtus pennsylvanicus) to quantify the effects of matrix habitat on movement behavior of voles. Habitat...

Spectroscopy of Cosmic Carbon Analogs in Inert-Gas Matrices and in the Gas-Phase: Comparative Results and Perspectives for Astrophysics

NASA Technical Reports Server (NTRS)

Salama, Farid; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

Recent studies of the spectroscopy of large (up to approx. 50 carbon atoms) neutral and Ionized polycyclic aromatic hydrocarbons (PAHs) and Fullerenes isolated in inert gas matrices will be presented. The advantages and the limitations of matrix isolation spectroscopy for the study of the molecular spectroscopy of interstellar dust analogs will be discussed. The laboratory data will be compared to the astronomical spectra (the interstellar extinction, the diffuse interstellar bands). Finally, the spectra of PAH ions isolated in neon/argon matrices will be compared to the spectra obtained for PAH ion seeded in a supersonic expansion. The astrophysical implications and future perspectives will be discussed.

Electronic Absorption Spectra of Neutral Perylene (C20H12), Terrylene (C30H16), and Quaterrylene (C40H20) and their Positive and Negative Ions: Ne Matrix-Isolation Spectroscopy and Time Dependent Density Functional Theory Calculations

NASA Technical Reports Server (NTRS)

Halasinski, Thomas M.; Weisman, Jennifer L.; Lee, Timothy J.; Salama, Farid; Head-Gordon, Martin; Kwak, Dochan (Technical Monitor)

2002-01-01

We present a full experimental and theoretical study of an interesting series of polycyclic aromatic hydrocarbons, the oligorylenes. The absorption spectra of perylene, terrylene and quaterrylene in neutral, cationic and anionic charge states are obtained by matrix-isolation spectroscopy in Ne. The experimental spectra are dominated by a bright state that red shifts with growing molecular size. Excitation energies and state symmetry assignments are supported by calculations using time dependent density functional theory methods. These calculations also provide new insight into the observed trends in oscillator strength and excitation energy for the bright states: the oscillator strength per unit mass of carbon increases along the series.

Electrodialytic matrix isolation for metal cations.

PubMed

Ohira, Shin-Ichi; Hiroyama, Yuri; Nakamura, Koretaka; Koda, Takumi; Dasgupta, Purnendu K; Toda, Kei

2015-01-01

Electrodialytic ion transfer was studied as a matrix isolation tool for heavy metal determinations. An ion transfer device (ITD) was used for the transfer of heavy metal cations. Under optimized flow rates applied voltage and receptor composition, heavy metal ions were quantitatively transferred at concentrations spanning µg L(-1) to mg L(-1). As long as the sample pH was acidic, there was no significant sample pH effect on the transfer efficiencies. Significant salt concentrations (>1 mM NaCl), however, decreased the transfer efficiency. This could be ameliorated (up to 5 mM NaCl) by transient instead of continuous sample introduction. The device was applied to the determination of Fe, Cu and Zn in equine and bovine serum; the reproducibility was better than conventional digestion method. Copyright © 2014 Elsevier B.V. All rights reserved.

Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Seng, Piseth; Abat, Cedric; Rolain, Jean Marc; Colson, Philippe; Lagier, Jean-Christophe; Gouriet, Frédérique; Fournier, Pierre Edouard; Drancourt, Michel; La Scola, Bernard; Raoult, Didier

2013-07-01

During the past 5 years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories.

Identification of Rare Pathogenic Bacteria in a Clinical Microbiology Laboratory: Impact of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Seng, Piseth; Abat, Cedric; Rolain, Jean Marc; Colson, Philippe; Lagier, Jean-Christophe; Gouriet, Frédérique; Fournier, Pierre Edouard; Drancourt, Michel; La Scola, Bernard

2013-01-01

During the past 5 years, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories. PMID:23637301

Analysis of nosocomial Staphylococcus haemolyticus by MLST and MALDI-TOF mass spectrometry.

PubMed

Kornienko, Maria; Ilina, Elena; Lubasovskaya, Ludmila; Priputnevich, Tatiana; Falova, Oksana; Sukhikh, Gennadiy; Govorun, Vadim

2016-04-01

Coagulase-negative staphylococci (CoNS) are a major component of normal human skin and mucosae flora. However, some species of CoNS can lead to infections in immunocompromised patients and premature newborns. The choice of a rapid and reliable typing method is one of the major problems in the epidemiological monitoring of CoNS, especially Staphylococcushaemolyticus isolates. In this study, we have tested 71 isolates of S. haemolyticus obtained from newborns using the multilocus sequence typing (MLST) and the direct bacterial MALDI-TOF mass spectrometry profiling approaches. To date, there is no standard MLST scheme for investigating the diversity of S. haemolyticus strains. The novel variant of MLST scheme including the tpiA, pta, sh1200, rphE, tphK, mvaK1, and arc loki was tested. The discriminatory power was estimated by the Hunter-Gaston discriminatory index (D) as 0.95. The Composition Correlation Index Matrix (CCI matrix) was calculated to typing the isolates through the analysis of mass spectra; also, the values of the correlation index for different groups of isolates were evaluated. Closely related isolates obtained from the same hospital are characterized by increased values of correlation indices in comparison with these values of isolates collected from various hospitals. The data obtained by both methods allow to describe a clonal structure of S. haemolyticus population and to designate the presence of endemic clones of S. haemolyticus. Copyright © 2015 Elsevier B.V. All rights reserved.

Identification and Characterization of Clostridium difficile Sequence Type 37 Genotype by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Li, Ruxin; Xiao, Di; Yang, Jing; Sun, Suju; Kaplan, Samuel; Li, Zhirong; Niu, Yanan; Qiang, Cuixin; Zhai, Yu; Wang, Xiaoming; Zhao, Xingzhen; Zhao, Baoxin; Welker, Martin; Pincus, David H; Jin, Dazhi; Kamboj, Mini; Zheng, Guanghui; Zhang, Guojun; Zhang, Jianzhong; Tang, Yi-Wei; Zhao, Jianhong

2018-05-01

Clostridium difficile multilocus sequence type 37 (ST37), which mainly corresponds to ribotype 017, has been a dominant genotype circulating in China. In this study, we report the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to analyze and characterize 204 C. difficile clinical isolates, including 49 ST37 and 155 non-ST37 isolates collected in China and other countries. The distributions of two major protein peaks ( m/z 3,242 and 3,286) were significantly different between ST37 and non-ST37 prototype strains and clinical isolates. This difference was reproducible when analysis was performed on different colonies in different runs. This finding was repeated and confirmed by both bioMérieux Vitek MS and Bruker Microflex LT systems on isolates recovered from a variety of geographic regions worldwide. The combination of the two peaks was present in 47 of 49 ST37 isolates, resulting in a sensitivity of 95.9%. In contrast, the peak combination was absent in 153 of 155 non-ST37 isolates, resulting in a specificity of 98.7%. Our results suggest that MALDI-TOF MS is a rapid and reliable tool to identify C. difficile genotype ST37. Work is in progress to characterize the two molecules having peaks at m/z 3,242 and 3,286, which appear to be specific to C. difficile genotype ST37. Copyright © 2018 American Society for Microbiology.

Recognition of Streptococcus pseudoporcinus Colonization in Women as a Consequence of Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Group B Streptococcus Identification.

PubMed

Suwantarat, Nuntra; Grundy, Maureen; Rubin, Mayer; Harris, Renee; Miller, Jo-Anne; Romagnoli, Mark; Hanlon, Ann; Tekle, Tsigereda; Ellis, Brandon C; Witter, Frank R; Carroll, Karen C

2015-12-01

During a 14-month period of using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for group B streptococcus (GBS) identification, we recovered 32 (1%) Streptococcus pseudoporcinus isolates from 3,276 GBS screening cultures from female genital sources (25 isolates from pregnant women and 7 from nonpregnant women). An additional two S. pseudoporcinus isolates were identified from a urine culture and a posthysterectomy wound culture. These isolates were found to cross-react with three different GBS antigen agglutination kits, PathoDx (Remel) (93%), Prolex (Pro-Lab Diagnostics) (38%), and Streptex (Remel) (53%). New approaches to bacterial identification in routine clinical microbiology laboratories may affect the prevalence of S. pseudoporcinus. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The electronic structure of VO in its ground and electronically excited states: A combined matrix isolation and quantum chemical (MRCI) study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hübner, Olaf; Hornung, Julius; Himmel, Hans-Jörg, E-mail: hans-jorg.himmel@aci.uni-heidelberg.de

2015-07-14

The electronic ground and excited states of the vanadium monoxide (VO) molecule were studied in detail. Electronic absorption spectra for the molecule isolated in Ne matrices complement the previous gas-phase spectra. A thorough quantum chemical (multi-reference configuration interaction) study essentially confirms the assignment and characterization of the electronic excitations observed for VO in the gas-phase and in Ne matrices and allows the clarification of open issues. It provides a complete overview over the electronically excited states up to about 3 eV of this archetypical compound.

Species Identification and Delineation of Pathogenic Mucorales by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Shao, Jin; Wan, Zhe; Li, Ruoyu; Yu, Jin

2018-04-01

This study aimed to validate the effectiveness of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification of filamentous fungi of the order Mucorales. A total of 111 isolates covering six genera preserved at the Research Center for Medical Mycology of Peking University were selected for MALDI-TOF MS analysis. We emphasized the study of 23 strains of Mucor irregularis predominantly isolated from patients in China. We first used the Bruker Filamentous Fungi library (v1.0) to identify all 111 isolates. To increase the identification rate, we created a compensatory in-house database, the Beijing Medical University (BMU) database, using 13 reference strains covering 6 species, including M. irregularis , Mucor hiemalis , Mucor racemosus , Cunninghamella bertholletiae , Cunninghamella phaeospora , and Cunninghamella echinulata All 111 isolates were then identified by MALDI-TOF MS using a combination of the Bruker library and BMU database. MALDI-TOF MS identified 55 (49.5%) and 74 (66.7%) isolates at the species and genus levels, respectively, using the Bruker Filamentous Fungi library v1.0 alone. A combination of the Bruker library and BMU database allowed MALDI-TOF MS to identify 90 (81.1%) and 111 (100%) isolates at the species and genus levels, respectively, with a significantly increased accuracy rate. MALDI-TOF MS poorly identified Mucorales when the Bruker library was used alone due to its lack of some fungal species. In contrast, this technique perfectly identified M. irregularis after main spectrum profiles (MSPs) of relevant reference strains were added to the Bruker library. With an expanded Bruker library, MALDI-TOF MS is an effective tool for the identification of pathogenic Mucorales. Copyright © 2018 American Society for Microbiology.

Infrared Spectrum and UV-Induced Photochemistry of Matrix-Isolated 5-Hydroxyquinoline.

PubMed

Kuş, Nihal; Sagdinc, Seda; Fausto, Rui

2015-06-18

The structure, infrared spectrum, and photochemistry of 5-hydroxyquinoline (5HQ) were studied by matrix isolation infrared spectroscopy, complemented by theoretical calculations performed at the DFT(B3LYP)/6-311++G(d,p) level of approximation. According to the calculations, the trans conformer of 5HQ (with the OH group pointing to the opposite direction of the pyridine ring of the molecule) is more stable than the cis form (by ∼8.8 kJ mol(-1)). The main factors determining the relative stability of the two conformers were rationalized through natural bond orbital (NBO) and charge density analyses. The compound was trapped in solid nitrogen at 10 K, and its infrared spectra registered and interpreted, showing the sole presence in the matrix of the more stable trans conformer. Broadband in situ UV irradiations (λ ≥ 288 nm and λ ≥ 235 nm) allowed for the observation of different chemical transformations, which started by excitation to the S1 state of 5HQ, followed by homolytic cleavage of the O-H bond, and subsequent reattachment of the H atom to the 5HQ radical to form quinolin-5(6H)-one and quinolin-5(8H)-one. The first of these two quinolinones was found to convert to open-ring isomeric ketenes, especially when irradiation was performed at higher energy, whereas the second is rather stable under the used experimental conditions. As a whole, the observed photochemistry of matrix-isolated 5HQ closely matches those previously reported for phenol and thiophenol. A detailed mechanistic interpretation for the observed photochemical processes is here proposed, which received support from time-dependent DFT calculations.

Comparison of Saramis 4.12 and IVD 3.0 Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Mycobacteria from Solid and Liquid Culture Media

PubMed Central

Leyer, Caroline; Gregorowicz, Guillaume; Mougari, Faiza; Raskine, Laurent; Cambau, Emmanuelle

2017-01-01

ABSTRACT During the last decade, many investigators have studied matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for identification of mycobacteria. Diverse and contradictory results indicated that optimal level for routine testing has not been reached yet. This work aimed to assess Vitek MS through two distinct versions, Saramis v4.12 RUO and the IVD v3.0, under conditions close to routine laboratory practice. Overall, 111 mycobacterial isolates were subjected to protein extraction and same spectra were matched against both databases. The IVD v3.0 database proved to be superior to Saramis v4.12 and its identification rates remarkably increased, from 67% to 94% for isolates grown on Middlebrook 7H10 solid medium and from 62% to 91% for isolates grown on mycobacterial growth indicator tube (MGIT) liquid medium. With this new version, IVD v3.0, MALDI-TOF MS might be integrated into routine clinical diagnostics, although molecular techniques remain mandatory in some cases. PMID:28424252

Plasma membrane isolation using immobilized concanavalin A magnetic beads.

PubMed

Lee, Yu-Chen; Srajer Gajdosik, Martina; Josic, Djuro; Lin, Sue-Hwa

2012-01-01

Isolation of highly purified plasma membranes is the key step in constructing the plasma membrane proteome. Traditional plasma membrane isolation method takes advantage of the differential density of organelles. While differential centrifugation methods are sufficient to enrich for plasma membranes, the procedure is lengthy and results in low recovery of the membrane fraction. Importantly, there is significant contamination of the plasma membranes with other organelles. The traditional agarose affinity matrix is suitable for isolating proteins but has limitation in separating organelles due to the density of agarose. Immobilization of affinity ligands to magnetic beads allows separation of affinity matrix from organelles through magnets and could be developed for the isolation of organelles. We have developed a simple method for isolating plasma membranes using lectin concanavalin A (ConA) magnetic beads. ConA is immobilized onto magnetic beads by binding biotinylated ConA to streptavidin magnetic beads. The ConA magnetic beads are used to bind glycosylated proteins present in the membranes. The bound membranes are solubilized from the magnetic beads with a detergent containing the competing sugar alpha methyl mannoside. In this study, we describe the procedure of isolating rat liver plasma membranes using sucrose density gradient centrifugation as described by Neville. We then further purify the membrane fraction by using ConA magnetic beads. After this purification step, main liver plasma membrane proteins, especially the highly glycosylated ones and proteins containing transmembrane domains could be identified by LC-ESI-MS/MS. While not described here, the magnetic bead method can also be used to isolate plasma membranes from cell lysates. This membrane purification method should expedite the cataloging of plasma membrane proteome.

Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity

PubMed Central

Linnemann, Amelia K.; Krawetz, Stephen A.

2009-01-01

DNA loop organization by nuclear scaffold/matrix attachment is a key regulator of gene expression that may provide a means to modulate phenotype. We have previously shown that attachment of genes to the NaCl-isolated nuclear matrix correlates with their silencing in HeLa cells. In contrast, expressed genes were associated with the lithium 3,5-diiodosalicylate (LIS)-isolated nuclear scaffold. To define their role in determining phenotype matrix attached regions (MARs) on human chromosomes 14–18 were identified as a function of expression in a primary cell line. The locations of MARs in aortic adventitial fibroblast (AoAF) cells were very stable (r = 0.909) and 96% of genes attached at MARs are silent (P < 0.001). Approximately one-third of the genes uniquely expressed in AoAF cells were associated with the HeLa cell nuclear matrix and silenced. Comparatively, 81% were associated with the AoAF cell nuclear scaffold (P < 0.001) and expressed. This suggests that nuclear scaffold/matrix association mediates a portion of cell type-specific gene expression thereby modulating phenotype. Interestingly, nuclear matrix attachment and thus silencing of specific genes that regulate proliferation and maintain the integrity of the HeLa cell genome suggests that transformation may at least in part be achieved through aberrant nuclear matrix attachment. PMID:19276204

Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi?

PubMed

Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Erturan, Zayre; Ener, Beyza; Akdagli, Sevtap Arikan; Muslumanoglu, Hamza; Cetinkaya, Zafer

2015-10-01

Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis. © 2015 Blackwell Verlag GmbH.

The Effects of Q-Matrix Design on Classification Accuracy in the Log-Linear Cognitive Diagnosis Model.

PubMed

Madison, Matthew J; Bradshaw, Laine P

2015-06-01

Diagnostic classification models are psychometric models that aim to classify examinees according to their mastery or non-mastery of specified latent characteristics. These models are well-suited for providing diagnostic feedback on educational assessments because of their practical efficiency and increased reliability when compared with other multidimensional measurement models. A priori specifications of which latent characteristics or attributes are measured by each item are a core element of the diagnostic assessment design. This item-attribute alignment, expressed in a Q-matrix, precedes and supports any inference resulting from the application of the diagnostic classification model. This study investigates the effects of Q-matrix design on classification accuracy for the log-linear cognitive diagnosis model. Results indicate that classification accuracy, reliability, and convergence rates improve when the Q-matrix contains isolated information from each measured attribute.

Adenoviral transduction supports matrix expression of alginate cultured articular chondrocytes.

PubMed

Pohle, D; Kasch, R; Herlyn, P; Bader, R; Mittlmeier, T; Pützer, B M; Müller-Hilke, B

2012-09-01

The present study examines the effects of adenoviral (Ad) transduction of human primary chondrocyte on transgene expression and matrix production. Primary chondrocytes were isolated from healthy articular cartilage and from cartilage with mild osteoarthritis (OA), transduced with an Ad vector and either immediately cultured in alginate or expanded in monolayer before alginate culture. Proteoglycan production was measured using dimethylmethylene blue (DMMB) assay and matrix gene expression was quantified by real-time PCR. Viral infection of primary chondrocytes results in a stable long time transgene expression for up to 13 weeks. Ad transduction does not significantly alter gene expression and matrix production if chondrocytes are immediately embedded in alginate. However, if expanded prior to three dimension (3D) culture in alginate, chondrocytes produce not only more proteoglycans compared to non-transduced controls, but also display an increased anabolic and decreased catabolic activity compared to non-transduced controls. We therefore suggest that successful autologous chondrocyte transplantation (ACT) should combine adenoviral transduction of primary chondrocytes with expansion in monolayer followed by 3D culture. Future studies will be needed to investigate whether the subsequent matrix production can be further improved by using Ad vectors bearing genes encoding matrix proteins. Copyright © 2012 Wiley Periodicals, Inc.

Infrared study of matrix-isolated ethyl cyanide: simulation of the photochemistry in the atmosphere of Titan.

PubMed

Toumi, A; Piétri, N; Couturier-Tamburelli, I

2015-11-11

Low-temperature Ar matrix isolation has been carried out to investigate the infrared spectrum of ethyl cyanide (CH3CH2CN), a molecule present in the atmosphere of Titan. The λ > 120 nm and λ > 230 nm photolysis reactions of ethyl cyanide in an Ar matrix were also performed in order to compare the behaviour of this compound when it is submitted to high and low energetic radiations. These different wavelengths have been used with the aim to reproduce the radiation reaching the various parts of the atmosphere. Several photoproducts have been identified during photolysis such as vinyl cyanide (CH2[double bond, length as m-dash]CHCN), cyanoacetylene (HC3N), and ethylene/hydrogen cyanide (C2H4/HCN), ethylene/hydrogen isocyanide (C2H4/HNC), acetylene/hydrogen cyanide (C2H2/HCN), acetylene/hydrogen isocyanide (C2H2/HNC), and acetylene:methylenimine (C2H2:HNCH2) complexes. Ethyl isocyanide (CH3CH2NC) and a ketenimine form (CH3CH[double bond, length as m-dash]C[double bond, length as m-dash]NH) have been identified as well. Photoproduct identification and spectral assignments were done using previous studies and density functional theory (DFT) calculations with the B3LYP/cc-pVTZ basis set.

Experimental evidence for blue-shifted hydrogen bonding in the fluoroform-hydrogen chloride complex: a matrix-isolation infrared and ab initio study.

PubMed

Gopi, R; Ramanathan, N; Sundararajan, K

2014-07-24

The 1:1 hydrogen-bonded complex of fluoroform and hydrogen chloride was studied using matrix-isolation infrared spectroscopy and ab initio computations. Using B3LYP and MP2 levels of theory with 6-311++G(d,p) and aug-cc-pVDZ basis sets, the structures of the complexes and their energies were computed. For the 1:1 CHF3-HCl complexes, ab initio computations showed two minima, one cyclic and the other acyclic. The cyclic complex was found to have C-H · · · Cl and C-F · · · H interactions, where CHF3 and HCl sub-molecules act as proton donor and proton acceptor, respectively. The second minimum corresponded to an acyclic complex stabilized only by the C-F · · · H interaction, in which CHF3 is the proton acceptor. Experimentally, we could trap the 1:1 CHF3-HCl cyclic complex in an argon matrix, where a blue-shift in the C-H stretching mode of the CHF3 sub-molecule was observed. To understand the nature of the interactions, Atoms in Molecules and Natural Bond Orbital analyses were carried out to unravel the reasons for blue-shifting of the C-H stretching frequency in these complexes.

Non-human Primate and Rat Cardiac Fibroblasts show similar Extracellular Matrix-related and Cellular Adhesion Gene Responses to Substance P

PubMed Central

Meléndez, Giselle C.; Manteufel, Edward J.; Dehlin, Heather M.; Register, Thomas C.; Levick, Scott P.

2015-01-01

Background The sensory nerve neuropeptide substance P (SP) regulates cardiac fibrosis in rodents under pressure overload conditions. Interestingly, SP induces transient increase expression of specific genes in isolated rat cardiac fibroblasts, without resultant changes in cell function. This suggests that SP ‘primes’ fibroblasts, but does not directly activate them. We investigated whether these unusual findings are specific to rodent fibroblasts or are translatable to a larger animal model more closely related to humans. Methods We compared the effects of SP on genes associated with extracellular matrix (ECM) regulation, cell-cell adhesion, cell-matrix adhesion and ECM in cardiac fibroblasts isolated from a non-human primate and Sprague-Dawley rats. Results We found that rodent and non-human primate cardiac fibroblasts showed similar ECM regulation and cell adhesion gene expression responses to SP. There were, however, large discrepancies in ECM genes which did not result in collagen or laminin synthesis in rat or non-human primate fibroblasts in response to SP. Conclusions This study further supports the notion that SP serves as a ‘primer’ for fibroblasts rather than initiating direct effects and suggests that rodent fibroblasts are a suitable model for studying gene and functional responses to SP in the absence of human or non-human primate fibroblasts. PMID:25550118

Ex Situ Investigation of Anisotropic Interconnection in Silicon-Titanium-Nickel Alloy Anode Material

DOE PAGES

Cho, Jong -Soo; Alaboina, Pankaj Kumar; Kang, Chan -Soon; ...

2017-03-10

Herein we investigate the nanostructural evolution of Silicon-Titanium-Nickel (Si-Ti-Ni) ternary alloy material synthesized by melt spinning process for advanced lithium-ion battery anode. The synthesized material was found to have nano-Silicon particles dispersed in the Ti 4Ni 4Si 7 (STN) alloy buffering matrix and was characterized by X-ray diffraction (XRD), High resolution- transmission electron microscope (HR-TEM), Scanning transmission electron microscopes - energy dispersive X-ray spectrometer (STEM-EDS), and electrochemical performance test. The role of STN matrix is to accommodate the volume expansion stresses of the dispersed Si nanoparticles. However, an interesting behavior was observed during cycling. The Si nanoparticles were observed tomore » form interconnection channels growing through the weak STN matrix cracks and evolving to a network isolating the STN matrix into small puddles. In conclusion, this unique nanostructural evolution of Si particles and isolation of the STN matrix failing to offer significant buffering effect to the grown Si network eventually accelerates more volume expansions during cycling due to less mechanical confinement and leads to performance degradation and poor cycle stability.« less

Studies of matrix vesicle-induced mineralization in a gelatin gel

NASA Technical Reports Server (NTRS)

Boskey, A. L.; Boyan, B. D.; Doty, S. B.; Feliciano, A.; Greer, K.; Weiland, D.; Swain, L. D.; Schwartz, Z.

1992-01-01

Matrix vesicles isolated from fourth-passage cultures of chondrocytes were tested for their ability to induce hydroxyapatite formation in a gelatin gel in order to gain insight into the function of matrix vesicles in in situ mineralization. These matrix vesicles did not appear to be hydroxyapatite nucleators per se since the extent of mineral accumulation in the gel diffusion system was not altered by the presence of matrix vesicles alone, and in the vesicle containing gels, mineral crystals were formed whether associated with vesicles or not. In gels with these matrix vesicles and beta-glycerophosphate, despite the presence of alkaline phosphatase activity, there was no increase in mineral deposition. This suggested that in the gel system these culture-derived vesicles did not increase local phosphate concentrations. However, when known inhibitors of mineral crystal formation and growth (proteoglycan aggregates [4 mg/ml], or ATP [1 mM], or both proteoglycan and ATP) were included in the gel, more mineral was deposited in gels with the vesicles than in comparable gels without vesicles, indicating that enzymes within these vesicles were functioning to remove the inhibition. These data support the suggestion that one function of the extracellular matrix vesicles is to transport enzymes for matrix modification.

Comparison of phenotypic methods and matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for the identification of aero-tolerant Actinomyces spp. isolated from soft-tissue infections.

PubMed

Ng, L S Y; Sim, J H C; Eng, L C; Menon, S; Tan, T Y

2012-08-01

Aero-tolerant Actinomyces spp. are an under-recognised cause of cutaneous infections, in part because identification using conventional phenotypic methods is difficult and may be inaccurate. Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is a promising new technique for bacterial identification, but with limited data on the identification of aero-tolerant Actinomyces spp. This study evaluated the accuracy of a phenotypic biochemical kit, MALDI-TOF MS and genotypic identification methods for the identification of this problematic group of organisms. Thirty aero-tolerant Actinomyces spp. were isolated from soft-tissue infections over a 2-year period. Species identification was performed by 16 s rRNA sequencing and genotypic results were compared with results obtained by API Coryne and MALDI-TOF MS. There was poor agreement between API Coryne and genotypic identification, with only 33% of isolates correctly identified to the species level. MALDI-TOF MS correctly identified 97% of isolates to the species level, with 33% of identifications achieved with high confidence scores. MALDI-TOF MS is a promising new tool for the identification of aero-tolerant Actinomyces spp., but improvement of the database is required in order to increase the confidence level of identification.

The behavior of peroxisomes in vitro: mammalian peroxisomes are osmotically sensitive particles.

PubMed

Antonenkov, Vasily D; Sormunen, Raija T; Hiltunen, J Kalervo

2004-12-01

It has been known for a long time that mammalian peroxisomes are extremely fragile in vitro. Changes in the morphological appearance and leakage of proteins from purified particles demonstrate that peroxisomes are damaged during isolation. However, some properties of purified peroxisomes, e.g., the latency of catalase, imply that their membranes are not disrupted. In the current study, we tried to ascertain the mechanism of this unusual behavior of peroxisomes in vitro. Biochemical and morphological examination of isolated peroxisomes subjected to sonication or to freezing and thawing showed that the membrane of the particles seals after disruption, restoring permeability properties. Transient damage of the membrane leads to the formation of peroxisomal "ghosts" containing nucleoid but nearly devoid of matrix proteins. The rate of leakage of matrix proteins from broken particles depended inversely on their molecular size. The effect of polyethylene glycols on peroxisomal integrity indicated that these particles are osmotically sensitive. Peroxisomes suffered an osmotic lysis during isolation that was resistant to commonly used low-molecular-mass osmoprotectors, e.g., sucrose. Damage to peroxisomes was partially prevented by applying more "bulky" osmoprotectors, e.g., polyethylene glycol 1500. A method was developed for the isolation of highly purified and nearly intact peroxisomes from rat liver by using polyethylene glycol 1500 as an osmoprotector.

Imipenem-avibactam: a novel combination for the rapid detection of carbapenemase activity in Enterobacteriaceae and Acinetobacter baumannii by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Oviaño, Marina; Bou, Germán

2017-02-01

In the present study, we propose a novel matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based method for detecting carbapenemase-producing Enterobacteriaceae and Acinetobacter baumannii. For this, we analyzed a series of 131 isolates. Among them, a total of 115 Enterobacteriaceae: 79 of them carrying a carbapenemase enzyme (15bla KPC , 7bla NDM , 11bla IMP , 12bla VIM , and 34bla OXA-48 ) and 16 A. baumannii isolates: 15 of them carrying carbapenemases (10bla OXA-23, 2bla OXA-58, 2bla OXA-24 , and 1bla OXA-237 ). The rest of the isolates were noncarbapenemase producers and used as negative controls. The isolates were submitted to susceptibility testing using a combination of imipenem-avibactam and analysis by the MALDI-TOF Biotyper Compass software (Bruker Daltonik, Germany). The assay showed an overall sensitivity and specificity for carbapenemase detection of 98% and 100%, respectively. The combination of imipenem and avibactam displayed activity against KPC and OXA-48-producing Enterobacteriaceae and thus represents a new strategy for identifying and confirming these carbapenemases. However, the combination did not provide any benefit over A. baumannii. Copyright © 2016 Elsevier Inc. All rights reserved.

Studies of social group dynamics under isolated conditions. Objective summary of the literature as it relates to potential problems of long duration space flight

NASA Technical Reports Server (NTRS)

Vinograd, S. P.

1974-01-01

Scientific literature which deals with the study of human behavior and crew interaction in situations simulating long term space flight is summarized and organized. A bibliography of all the pertinent U.S. literature available is included, along with definitions of the behavioral characteristics terms employed. The summarized studies are analyzed according to behavioral factors and environmental conditions. The analysis consist of two matrices. (1) The matrix of factors studied correlates each research study area and individual study with the behavioral factors that were investigated in the study. (2) The matrix of conclusions identifies those studies whose investigators appeared to draw specific conclusions concerning questions of importance to NASA.

Performance of CarbaNP and CIM tests in OXA-48 carbapenemase-producing Enterobacteriaceae.

PubMed

Yıldız, Serap Süzük; Kaşkatepe, Banu; Avcıküçük, Havva; Öztürk, Şükran

2017-03-01

This study applied two phenotypic tests, namely "Carbapenemase Nordmann-Poirel" (CarbaNP) test and "Carbapenem Inactivation Method" (CIM), against the isolates carrying the carbapenem resistance genes. The study included 83 carbapenem-resistant Enterobacteriaceae isolates producing oxacillinase-48 (OXA-48) and 30 carbapenem-sensitive Enterobacteriaceae isolates. Out of the total isolates studied, 77 isolates (92.77%) were identified as Klebsiella pneumoniae and six isolates (7.23%) were identified as Escherichia coli by Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. Polymerase chain reaction (PCR) method used to detect resistance genes found that 74 isolates (89.16%) produced OXA-48 carbapenemase, whereas nine isolates (10.84%) produced both OXA-48 and New Delhi metallo-beta-lactamase-1 (NDM-1). The isolates producing both OXA-48 and NDM-1 were found to be positive by both phenotypic tests. Among isolates carrying only bla OXA-48 gene alone, nine isolates (13.04%) for CarbaNP test and two isolates for CIM test (2.90%) displayed false negative results, respectively. The sensitivity of CarbaNP and CIM tests was found to be 89.16% and 97.59%, respectively, whereas the specificity was determined to be 100% for both tests. These findings suggest that CarbaNP and CIM tests are useful tools to identify the carbapenemase producers. Molecular methods like PCR are recommended to verify false negative tests predicted to have OXA-48 activity.

Identification Of Fatty Acid Isomers By Gas Chromatography / Matrix Isolation / Fourier Transform Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Mossoba, Magdi M.; McDonald, Richard E.; Chen, Jo-Yun T.; Page, Samuel W.

1989-12-01

Geometric and positional isomers of fatty acid methyl esters (FAME) derived from hydrogenated soybean oil and margarines were separated by silver nitrate-thin layer chromatography (AgNO3-TLC) followed by capillary gas chromatography (GC) and identified by matrix isolation / Fourier transform infrared (MI/FTIR) spectroscopyi,2. Because of the high specificity of the MI technique, it was possible to distinguish between different 18-carbon aliphatic chains of FAME positional isomers with cis or trans configuration, and to determine their degree of unsaturation. For the first time mid-IR spectra were observed for methylene-interrupted or isolated trans, trans or cis/ trans C18 FAME positional isomers. These spectra could be readily differentiated based on unique MI/FTIR spectral characteristics.

Adhesion properties of Lactobacillus rhamnosus mucus-binding factor to mucin and extracellular matrix proteins.

PubMed

Nishiyama, Keita; Nakamata, Koichi; Ueno, Shintaro; Terao, Akari; Aryantini, Ni Putu Desy; Sujaya, I Nengah; Fukuda, Kenji; Urashima, Tadasu; Yamamoto, Yuji; Mukai, Takao

2015-01-01

We previously described potential probiotic Lactobacillus rhamnosus strains, isolated from fermented mare milk produced in Sumbawa Island, Indonesia, which showed high adhesion to porcine colonic mucin (PCM) and extracellular matrix (ECM) proteins. Recently, mucus-binding factor (MBF) was found in the GG strain of L. rhamnosus as a mucin-binding protein. In this study, we assessed the ability of recombinant MBF protein from the FSMM22 strain, one of the isolates of L. rhamnosus from fermented Sumbawa mare milk, to adhere to PCM and ECM proteins by overlay dot blot and Biacore assays. MBF bound to PCM, laminin, collagen IV, and fibronectin with submicromolar dissociation constants. Adhesion of the FSMM22 mbf mutant strain to PCM and ECM proteins was significantly less than that of the wild-type strain. Collectively, these results suggested that MBF contribute to L. rhamnosus host colonization via mucin and ECM protein binding.

Comparison of biodegradation of poly(ethylene glycol)s and poly(propylene glycol)s.

PubMed

Zgoła-Grześkowiak, Agnieszka; Grześkowiak, Tomasz; Zembrzuska, Joanna; Łukaszewski, Zenon

2006-07-01

The biodegradation of poly(ethylene glycol)s (PEGs) and poly(propylene glycol)s (PPGs), both being major by-products of non-ionic surfactants biodegradation, was studied under the conditions of the River Water Die-Away Test. PEGs were isolated from a water matrix using solid-phase extraction with graphitized carbon black sorbent, then derivatized with phenyl isocyanate and determined by HPLC with UV detection. PPGs were isolated from a water matrix by liquid-liquid extraction with chloroform, then derivatized with naphthyl isocyanate and determined by HPLC with fluorescence detection. The primary biodegradation of both PEGs and PPGs reached approximately 99% during the test. The tests show different biodegradation pathways of PEG and PPG. During PEG biodegradation, their chains are shortened leading to the formation of ethylene glycol and diethylene glycol. During PPG biodegradation, no short-chained biodegradation products were found.

Identification by Molecular Methods and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Antifungal Susceptibility Profiles of Clinically Significant Rare Aspergillus Species in a Referral Chest Hospital in Delhi, India.

PubMed

Masih, Aradhana; Singh, Pradeep K; Kathuria, Shallu; Agarwal, Kshitij; Meis, Jacques F; Chowdhary, Anuradha

2016-09-01

Aspergillus species cause a wide spectrum of clinical infections. Although Aspergillus fumigatus and Aspergillus flavus remain the most commonly isolated species in aspergillosis, in the last decade, rare and cryptic Aspergillus species have emerged in diverse clinical settings. The present study analyzed the distribution and in vitro antifungal susceptibility profiles of rare Aspergillus species in clinical samples from patients with suspected aspergillosis in 8 medical centers in India. Further, a matrix-assisted laser desorption ionization-time of flight mass spectrometry in-house database was developed to identify these clinically relevant Aspergillus species. β-Tubulin and calmodulin gene sequencing identified 45 rare Aspergillus isolates to the species level, except for a solitary isolate. They included 23 less common Aspergillus species belonging to 12 sections, mainly in Circumdati, Nidulantes, Flavi, Terrei, Versicolores, Aspergillus, and Nigri Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identified only 8 (38%) of the 23 rare Aspergillus isolates to the species level. Following the creation of an in-house database with the remaining 14 species not available in the Bruker database, the MALDI-TOF MS identification rate increased to 95%. Overall, high MICs of ≥2 μg/ml were noted for amphotericin B in 29% of the rare Aspergillus species, followed by voriconazole in 20% and isavuconazole in 7%, whereas MICs of >0.5 μg/ml for posaconazole were observed in 15% of the isolates. Regarding the clinical diagnoses in 45 patients with positive rare Aspergillus species cultures, 19 (42%) were regarded to represent colonization. In the remaining 26 patients, rare Aspergillus species were the etiologic agent of invasive, chronic, and allergic bronchopulmonary aspergillosis, allergic fungal rhinosinusitis, keratitis, and mycetoma. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Identification by Molecular Methods and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and Antifungal Susceptibility Profiles of Clinically Significant Rare Aspergillus Species in a Referral Chest Hospital in Delhi, India

PubMed Central

Masih, Aradhana; Singh, Pradeep K.; Kathuria, Shallu; Agarwal, Kshitij

2016-01-01

Aspergillus species cause a wide spectrum of clinical infections. Although Aspergillus fumigatus and Aspergillus flavus remain the most commonly isolated species in aspergillosis, in the last decade, rare and cryptic Aspergillus species have emerged in diverse clinical settings. The present study analyzed the distribution and in vitro antifungal susceptibility profiles of rare Aspergillus species in clinical samples from patients with suspected aspergillosis in 8 medical centers in India. Further, a matrix-assisted laser desorption ionization–time of flight mass spectrometry in-house database was developed to identify these clinically relevant Aspergillus species. β-Tubulin and calmodulin gene sequencing identified 45 rare Aspergillus isolates to the species level, except for a solitary isolate. They included 23 less common Aspergillus species belonging to 12 sections, mainly in Circumdati, Nidulantes, Flavi, Terrei, Versicolores, Aspergillus, and Nigri. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identified only 8 (38%) of the 23 rare Aspergillus isolates to the species level. Following the creation of an in-house database with the remaining 14 species not available in the Bruker database, the MALDI-TOF MS identification rate increased to 95%. Overall, high MICs of ≥2 μg/ml were noted for amphotericin B in 29% of the rare Aspergillus species, followed by voriconazole in 20% and isavuconazole in 7%, whereas MICs of >0.5 μg/ml for posaconazole were observed in 15% of the isolates. Regarding the clinical diagnoses in 45 patients with positive rare Aspergillus species cultures, 19 (42%) were regarded to represent colonization. In the remaining 26 patients, rare Aspergillus species were the etiologic agent of invasive, chronic, and allergic bronchopulmonary aspergillosis, allergic fungal rhinosinusitis, keratitis, and mycetoma. PMID:27413188

Isolation and quantification of Quillaja saponaria Molina saponins and lipids in iscom-matrix and iscoms.

PubMed

Behboudi, S; Morein, B; Rönnberg, B

1995-12-01

In the iscom, multiple copies of antigen are attached by hydrophobic interaction to a matrix which is built up by Quillaja triterpenoid saponins and lipids. Thus, the iscom presents antigen in multimeric form in a small particle with a built-in adjuvant resulting in a highly immunogenic antigen formulation. We have designed a chloroform-methanol-water extraction procedure to isolate the triterpenoid saponins and lipids incorporated into iscom-matrix and iscoms. The triterpenoids in the triterpenoid phase were quantitated using orcinol sulfuric acid detecting their carbohydrate chains and by HPLC. The cholesterol and phosphatidylcholine in the lipid phase were quantitated by HPLC and a commercial colorimetric method for the cholesterol. The quantitative methods showed an almost total separation and recovery of triterpenoids and lipids in their respective phases, while protein was detected in all phases after extraction. The protein content was determined by the method of Lowry and by amino acid analysis. Amino acid analysis was shown to be the reliable method of the two to quantitate proteins in iscoms. In conclusion, simple, reproducible and efficient procedures have been designed to isolate and quantitate the triterpenoids and lipids added for preparation of iscom-matrix and iscoms. The procedures described should also be useful to adequately define constituents in prospective vaccines.

25 CFR Appendix A to Subpart C - IRR High Priority Project Scoring Matrix

Code of Federal Regulations, 2011 CFR

2011-04-01

... 25 Indians 1 2011-04-01 2011-04-01 false IRR High Priority Project Scoring Matrix A Appendix A to...—IRR High Priority Project Scoring Matrix Score 10 5 3 1 0 Accident and fatality rate for candidate...,000 or less 250,001-500,000 500,001-750,000 Over 750,000. Geographic isolation No external access to...

25 CFR Appendix A to Subpart C - IRR High Priority Project Scoring Matrix

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 1 2013-04-01 2013-04-01 false IRR High Priority Project Scoring Matrix A Appendix A to...—IRR High Priority Project Scoring Matrix Score 10 5 3 1 0 Accident and fatality rate for candidate...,000 or less 250,001-500,000 500,001-750,000 Over 750,000. Geographic isolation No external access to...

25 CFR Appendix A to Subpart C - IRR High Priority Project Scoring Matrix

Code of Federal Regulations, 2014 CFR

2014-04-01

... 25 Indians 1 2014-04-01 2014-04-01 false IRR High Priority Project Scoring Matrix A Appendix A to...—IRR High Priority Project Scoring Matrix Score 10 5 3 1 0 Accident and fatality rate for candidate...,000 or less 250,001-500,000 500,001-750,000 Over 750,000. Geographic isolation No external access to...

25 CFR Appendix A to Subpart C - IRR High Priority Project Scoring Matrix

Code of Federal Regulations, 2012 CFR

2012-04-01

... 25 Indians 1 2012-04-01 2011-04-01 true IRR High Priority Project Scoring Matrix A Appendix A to...—IRR High Priority Project Scoring Matrix Score 10 5 3 1 0 Accident and fatality rate for candidate...,000 or less 250,001-500,000 500,001-750,000 Over 750,000. Geographic isolation No external access to...

Infrared Matrix-Isolation Study of New Noble-Gas Compounds

NASA Astrophysics Data System (ADS)

Zhu, Cheng; Räsänen, Markku; Khriachtchev, Leonid

2016-06-01

We identify new noble-gas compounds in solid matrices using IR spectroscopy. The compounds under study belong to two types: HNgY and YNgY' where Ng is a noble-gas atom and Y and Y' are electronegative fragments. The experimental assignments are supported by ab initio calculations at the MP2(full) and CCSD(T) levels of theory with the def2-TZVPPD basis set. We have prepared and characterized two new HNgY compounds (noble-gas hydrides): HKrCCCl in a Kr matrix and HXeCCCl in a Xe matrix.I The synthesis of these compounds includes two steps: UV photolysis of HCCCl in a noble-gas matrix to form the H + CCCl fragments and annealing of the matrix to mobilize H atoms and to promote the H + Ng + CCCl = HNgCCCl reaction. An interesting observation in the experiments on HXeCCCl in a Xe matrix is the temperature-induced transformation of the three H-Xe stretching bands. This observation is explained by temperature-induced changes of local matrix morphology around the embedded HXeCCCl molecule. In these experiments, we have also obtained the IR spectrum of the CCCl radical, which is produced by photodecomposition of HCCCl. We have identified three new YNgY' compounds (fluorinated noble-gas cyanides): FKrCN in a Kr matrix and FXeCN and FXeNC in a Xe matrix.II These molecule are formed by photolysis of FCN in a noble-gas matrix due to locality of this process. The amount of these molecules increases upon thermal mobilization of the F atoms in the photolyzed matrix featuring the F + Ng + CN reaction.

The anharmonic quartic force field infrared spectra of three polycyclic aromatic hydrocarbons: Naphthalene, anthracene, and tetracene.

PubMed

Mackie, Cameron J; Candian, Alessandra; Huang, Xinchuan; Maltseva, Elena; Petrignani, Annemieke; Oomens, Jos; Buma, Wybren Jan; Lee, Timothy J; Tielens, Alexander G G M

2015-12-14

Current efforts to characterize and study interstellar polycyclic aromatic hydrocarbons (PAHs) rely heavily on theoretically predicted infrared (IR) spectra. Generally, such studies use the scaled harmonic frequencies for band positions and double harmonic approximation for intensities of species, and then compare these calculated spectra with experimental spectra obtained under matrix isolation conditions. High-resolution gas-phase experimental spectroscopic studies have recently revealed that the double harmonic approximation is not sufficient for reliable spectra prediction. In this paper, we present the anharmonic theoretical spectra of three PAHs: naphthalene, anthracene, and tetracene, computed with a locally modified version of the SPECTRO program using Cartesian derivatives transformed from Gaussian 09 normal coordinate force constants. Proper treatments of Fermi resonances lead to an impressive improvement on the agreement between the observed and theoretical spectra, especially in the C-H stretching region. All major IR absorption features in the full-scale matrix-isolated spectra, the high-temperature gas-phase spectra, and the most recent high-resolution gas-phase spectra obtained under supersonically cooled molecular beam conditions in the CH-stretching region are assigned.

The anharmonic quartic force field infrared spectra of three polycyclic aromatic hydrocarbons: Naphthalene, anthracene, and tetracene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mackie, Cameron J., E-mail: mackie@strw.leidenuniv.nl; Candian, Alessandra; Tielens, Alexander G. G. M.

2015-12-14

Current efforts to characterize and study interstellar polycyclic aromatic hydrocarbons (PAHs) rely heavily on theoretically predicted infrared (IR) spectra. Generally, such studies use the scaled harmonic frequencies for band positions and double harmonic approximation for intensities of species, and then compare these calculated spectra with experimental spectra obtained under matrix isolation conditions. High-resolution gas-phase experimental spectroscopic studies have recently revealed that the double harmonic approximation is not sufficient for reliable spectra prediction. In this paper, we present the anharmonic theoretical spectra of three PAHs: naphthalene, anthracene, and tetracene, computed with a locally modified version of the SPECTRO program using Cartesianmore » derivatives transformed from Gaussian 09 normal coordinate force constants. Proper treatments of Fermi resonances lead to an impressive improvement on the agreement between the observed and theoretical spectra, especially in the C–H stretching region. All major IR absorption features in the full-scale matrix-isolated spectra, the high-temperature gas-phase spectra, and the most recent high-resolution gas-phase spectra obtained under supersonically cooled molecular beam conditions in the CH-stretching region are assigned.« less

Spacecraft in switch matrix for wide band service applicatons in 30/20 GHz communications satellite systems

NASA Technical Reports Server (NTRS)

Cory, B. J.

1982-01-01

Bandwidth, switching speed, off-state isolation, and reliability over a ten-year mission were factors in determining the optimum available technology for satellite communications switching in 1982. A proof of concept model for a 20 x 20 coupled crossbar switch matrix designed with FET devices for microwave switching and with high speed CMOS LIS for switch crosspoint addressing was fabricated and tested. Results show the design is feasible for application in a multichannel SS-TDMA communications system. Expandibility can readily be achieved with this design. A conceptual design study for a 100 x 100 switch matrix utilizing a coupled crossbar architecture implemented with a monolithic microwave integrated circuits revealed technology needs for high capacity switch matrices.

Structure and dynamics of spin-labeled insulin entrapped in a silica matrix by the sol-gel method.

PubMed

Vanea, E; Gruian, C; Rickert, C; Steinhoff, H-J; Simon, V

2013-08-12

The structure and conformational dynamics of insulin entrapped into a silica matrix was monitored during the sol to maturated-gel transition by electron paramagnetic resonance (EPR) spectroscopy. Insulin was successfully spin-labeled with iodoacetamide and the bifunctional nitroxide reagent HO-1944. Room temperature continuous wave (cw) EPR spectra of insulin were recorded to assess the mobility of the attached spin labels. Insulin conformation and its distribution within the silica matrix were studied using double electron-electron resonance (DEER) and low-temperature cw-EPR. A porous oxide matrix seems to form around insulin molecules with pore diameters in the order of a few nanometers. Secondary structure of the encapsulated insulin investigated by Fourier transform infrared spectroscopy proved a high structural integrity of insulin even in the dried silica matrix. The results show that silica encapsulation can be used as a powerful tool to effectively isolate and functionally preserve biomolecules during preparation, storage, and release.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification.

PubMed

Bizzini, A; Greub, G

2010-11-01

Until recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for the identification of microorganisms remained confined to research laboratories. In the last 2 years, the availability of relatively simple to use MALDI-TOF MS devices, which can be utilized in clinical microbiology laboratories, has changed the laboratory workflows for the identification of pathogens. Recently, the first prospective studies regarding the performance in routine bacterial identification showed that MALDI-TOF MS is a fast, reliable and cost-effective technique that has the potential to replace and/or complement conventional phenotypic identification for most bacterial strains isolated in clinical microbiology laboratories. For routine bacterial isolates, correct identification by MALDI-TOF MS at the species level was obtained in 84.1-93.6% of instances. In one of these studies, a protein extraction step clearly improved the overall valid identification yield, from 70.3% to 93.2%. This review focuses on the current state of use of MALDI-TOF MS for the identification of routine bacterial isolates and on the main difficulties that may lead to erroneous or doubtful identifications. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

A hemagglutinating variant of Prevotella melaninogenica isolated from the oral cavity.

PubMed

Haraldsson, G; Holbrook, W P

1998-12-01

Strains resembling Prevotella melaninogenica were isolated from healthy subjects and patients with periodontal disease and were identified using: a 5-test phenotypic screen; commercial identification kits; and a 16S rRNA-based polymerase chain reaction (PCR) method. Eleven clinical isolates closely resembling P. melaninogenica, and all from patients with periodontitis, were able to agglutinate erythrocytes. In the electron microscope, hemagglutinating isolates showed fimbria-like structures, that were not seen on non-hemagglutinating isolates. Some strains were further classified with PCR-restriction fragment-length polymorphism (RFLP) of 16S rRNA genes. Amplified 16S rDNA was digested using five different endonucleases, separated with agarose gel electrophoresis, stained and photographed. Photographs were then scanned, digitized and a distance matrix calculated using Dice coefficient, where the presence or absence of a band was used as a character. The distance matrix was plotted as a phenogram. At 70% similarity six clusters were seen. Type strains of separate Prevotella species did not fall into any cluster. Hemagglutinating isolates fell into three clusters: four clustered with the type strains of P. melaninogenica and Prevotella veroralis; four with other P. melaninogenica isolates and two hemagglutinating isolates clustered together Prevotella loescheii. The PCR-RFLP results showed that the hemagglutinating strains did not form a homogenous group inside the Prevotella genus.

Enamel formation and amelogenesis imperfecta.

PubMed

Hu, Jan C-C; Chun, Yong-Hee P; Al Hazzazzi, Turki; Simmer, James P

2007-01-01

Dental enamel is the epithelial-derived hard tissue covering the crowns of teeth. It is the most highly mineralized and hardest tissue in the body. Dental enamel is acellular and has no physiological means of repair outside of the protective and remineralization potential provided by saliva. Enamel is comprised of highly organized hydroxyapatite crystals that form in a defined extracellular space, the contents of which are supplied and regulated by ameloblasts. The entire process is under genetic instruction. The genetic control of amelogenesis is poorly understood, but requires the activities of multiple components that are uniquely important for dental enamel formation. Amelogenesis imperfecta (AI) is a collective designation for the variety of inherited conditions displaying isolated enamel malformations, but the designation is also used to indicate the presence of an enamel phenotype in syndromes. Recently, genetic studies have demonstrated the importance of genes encoding enamel matrix proteins in the etiology of isolated AI. Here we review the essential elements of dental enamel formation and the results of genetic analyses that have identified disease-causing mutations in genes encoding enamel matrix proteins. In addition, we provide a fresh perspective on the roles matrix proteins play in catalyzing the biomineralization of dental enamel. Copyright 2007 S. Karger AG, Basel.

Isolation and identification of oxidation products of syringol from brines and heated meat matrix.

PubMed

Bölicke, Sarah-Maria; Ternes, Waldemar

2016-08-01

In this study we developed new extraction and detection methods (using HPLC-UV and LC-MS), making it possible to analyze the smoke phenol syringol and its oxidation products nitrososyringol, nitrosyringol, and the syringol dimer 3,3',5,5'-tetramethoxy-1,1'-biphenyl-4,4'-diol, which were identified in heated meat for the first time. Preliminary brine experiments performed with different concentrations of ascorbic acid showed that high amounts of this antioxidant also resulted in almost complete degradation of syringol and to formation of the oxidation products when the brines were heated at low pH values. Heat treatment (80°C) and subsequent simulated digestion applied to meat samples containing syringol, ascorbic acid and different concentrations of sodium nitrite produced 3,3',5,5'-tetramethoxy-1,1'-biphenyl-4,4'-diol even at a low nitrite level in the meat matrix, while nitroso- and nitrosyringol were isolated only after the digestion experiments. Increasing amounts of oxygen in the meat matrix decreased the syringol concentration and enhanced the formation of the reaction products in comparison to the samples without added oxygen. Copyright © 2016 Elsevier Ltd. All rights reserved.

Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) for rapid identification of micro-organisms in the routine clinical microbiology laboratory.

PubMed

Wattal, C; Oberoi, J K; Goel, N; Raveendran, R; Khanna, S

2017-05-01

The study evaluates the utility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) Vitek MS for identification of microorganisms in the routine clinical microbiology laboratory. From May 2013 to April 2014, microbial isolates recovered from various clinical samples were identified by Vitek MS. In case of failure to identify by Vitek MS, the isolate was identified using the Vitek 2 system (bioMerieux, France) and serotyping wherever applicable or otherwise by nucleic acid-mediated methods. All the moulds were identified by Lactophenol blue mounts, and mycobacterial isolates were identified by molecular identification systems including AccuProbe (bioMerieux, France) or GenoType Mycobacterium CM (Hain Lifescience, Germany). Out of the 12,003 isolates, the Vitek MS gave a good overall ID at the genus and or species level up to 97.7% for bacterial isolates, 92.8% for yeasts and 80% for filamentous fungi. Of the 26 mycobacteria tested, only 42.3% could be identified using the Saramis RUO (Research Use Only) database. VITEK MS could not identify 34 of the 35 yeast isolates identified as C. haemulonii by Vitek 2. Subsequently, 17 of these isolates were identified as Candida auris (not present in the Vitek MS database) by 18S rRNA sequencing. Using these strains, an in-house superspectrum of C. auris was created in the VITEK MS database. Use of MALDI-TOF MS allows a rapid identification of aerobic bacteria and yeasts in clinical practice. However, improved sample extraction protocols and database upgrades with inclusion of locally representative strains is required, especially for moulds.

Delineation of Stenotrophomonas maltophilia isolates from cystic fibrosis patients by fatty acid methyl ester profiles and matrix-assisted laser desorption/ionization time-of-flight mass spectra using hierarchical cluster analysis and principal component analysis.

PubMed

Vidigal, Pedrina Gonçalves; Mosel, Frank; Koehling, Hedda Luise; Mueller, Karl Dieter; Buer, Jan; Rath, Peter Michael; Steinmann, Joerg

2014-12-01

Stenotrophomonas maltophilia is an opportunist multidrug-resistant pathogen that causes a wide range of nosocomial infections. Various cystic fibrosis (CF) centres have reported an increasing prevalence of S. maltophilia colonization/infection among patients with this disease. The purpose of this study was to assess specific fingerprints of S. maltophilia isolates from CF patients (n = 71) by investigating fatty acid methyl esters (FAMEs) through gas chromatography (GC) and highly abundant proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and to compare them with isolates obtained from intensive care unit (ICU) patients (n = 20) and the environment (n = 11). Principal component analysis (PCA) of GC-FAME patterns did not reveal a clustering corresponding to distinct CF, ICU or environmental types. Based on the peak area index, it was observed that S. maltophilia isolates from CF patients produced significantly higher amounts of fatty acids in comparison with ICU patients and the environmental isolates. Hierarchical cluster analysis (HCA) based on the MALDI-TOF MS peak profiles of S. maltophilia revealed the presence of five large clusters, suggesting a high phenotypic diversity. Although HCA of MALDI-TOF mass spectra did not result in distinct clusters predominantly composed of CF isolates, PCA revealed the presence of a distinct cluster composed of S. maltophilia isolates from CF patients. Our data suggest that S. maltophilia colonizing CF patients tend to modify not only their fatty acid patterns but also their protein patterns as a response to adaptation in the unfavourable environment of the CF lung. © 2014 The Authors.

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi.

PubMed

McMullen, Allison R; Wallace, Meghan A; Pincus, David H; Wilkey, Kathy; Burnham, C A

2016-08-01

Invasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (including Aspergillus amoenus [n = 2] and Aspergillus calidoustus [n = 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%) Aspergillus sp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Multicenter Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Gram-Positive Aerobic Bacteria

PubMed Central

Burnham, Carey-Ann D.; Bythrow, Maureen; Garner, Omai B.; Ginocchio, Christine C.; Jennemann, Rebecca; Lewinski, Michael A.; Manji, Ryhana; Mochon, A. Brian; Procop, Gary W.; Richter, Sandra S.; Sercia, Linda; Westblade, Lars F.; Ferraro, Mary Jane; Branda, John A.

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting. PMID:23658261

Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Gram-positive aerobic bacteria.

PubMed

Rychert, Jenna; Burnham, Carey-Ann D; Bythrow, Maureen; Garner, Omai B; Ginocchio, Christine C; Jennemann, Rebecca; Lewinski, Michael A; Manji, Ryhana; Mochon, A Brian; Procop, Gary W; Richter, Sandra S; Sercia, Linda; Westblade, Lars F; Ferraro, Mary Jane; Branda, John A

2013-07-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting.

Switching Matrix For Optical Signals

NASA Technical Reports Server (NTRS)

Grove, Charles H.

1990-01-01

Proposed matrix of electronically controlled shutters switches signals in optical fibers between multiple input and output channels. Size, weight, and power consumption reduced. Device serves as building block for small, low-power, broad-band television- and data-signal-switching systems providing high isolation between nominally disconnected channels.

Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations

PubMed Central

Najbauer, Eszter E.; Bazsó, Gábor; Apóstolo, Rui; Fausto, Rui; Biczysko, Malgorzata; Barone, Vincenzo; Tarczay, György

2018-01-01

The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, 6 conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-live of (3.7±0.5)·103 s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser induced conversions revealed that the excitation of the stretching overtone of both the side-chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations. PMID:26201050

Evidence for phosphorus bonding in phosphorus trichloride-methanol adduct: a matrix isolation infrared and ab initio computational study.

PubMed

Joshi, Prasad Ramesh; Ramanathan, N; Sundararajan, K; Sankaran, K

2015-04-09

The weak interaction between PCl3 and CH3OH was investigated using matrix isolation infrared spectroscopy and ab initio computations. In a nitrogen matrix at low temperature, the noncovalent adduct was generated and characterized using Fourier transform infrared spectroscopy. Computations were performed at B3LYP/6-311++G(d,p), B3LYP/aug-cc-pVDZ, and MP2/6-311++G(d,p) levels of theory to optimize the possible geometries of PCl3-CH3OH adducts. Computations revealed two minima on the potential energy surface, of which, the global minimum is stabilized by a noncovalent P···O interaction, known as a pnictogen bonding (phosphorus bonding or P-bonding). The local minimum corresponded to a cyclic adduct, stabilized by the conventional hydrogen bonding (Cl···H-O and Cl···H-C interactions). Experimentally, 1:1 P-bonded PCl3-CH3OH adduct in nitrogen matrix was identified, where shifts in the P-Cl modes of PCl3, O-C, and O-H modes of CH3OH submolecules were observed. The observed vibrational frequencies of the P-bonded adduct in a nitrogen matrix agreed well with the computed frequencies. Furthermore, computations also predicted that the P-bonded adduct is stronger than H-bonded adduct by ∼1.56 kcal/mol. Atoms in molecules and natural bond orbital analyses were performed to understand the nature of interactions and effect of charge transfer interaction on the stability of the adducts.

Effects of landscape matrix on population connectivity of an arboreal mammal, Petaurus breviceps.

PubMed

Malekian, Mansoureh; Cooper, Steven J B; Saint, Kathleen M; Lancaster, Melanie L; Taylor, Andrea C; Carthew, Susan M

2015-09-01

Ongoing habitat loss and fragmentation is considered a threat to biodiversity as it can create small, isolated populations that are at increased risk of extinction. Tree-dependent species are predicted to be highly sensitive to forest and woodland loss and fragmentation, but few studies have tested the influence of different types of landscape matrix on gene flow and population structure of arboreal species. Here, we examine the effects of landscape matrix on population structure of the sugar glider (Petaurus breviceps) in a fragmented landscape in southeastern South Australia. We collected 250 individuals across 12 native Eucalyptus forest remnants surrounded by cleared agricultural land or exotic Pinus radiata plantations and a large continuous eucalypt forest. Fifteen microsatellite loci were genotyped and analyzed to infer levels of population differentiation and dispersal. Genetic differentiation among most forest patches was evident. We found evidence for female philopatry and restricted dispersal distances for females relative to males, suggesting there is male-biased dispersal. Among the environmental variables, spatial variables including geographic location, minimum distance to neighboring patch, and degree of isolation were the most important in explaining genetic variation. The permeability of a cleared agricultural matrix to dispersing gliders was significantly higher than that of a pine matrix, with the gliders dispersing shorter distances across the latter. Our results added to previous findings for other species of restricted dispersal and connectivity due to habitat fragmentation in the same region, providing valuable information for the development of strategies to improve the connectivity of populations in the future.

ROLE CONFLICTS OF SCHOOL PRINCIPALS.

ERIC Educational Resources Information Center

GROSS, NEAL; AND OTHERS

THE PURPOSE OF THIS STUDY WAS TO ISOLATE THE ROLE CONFLICTS TO WHICH SCHOOL PRINCIPALS ARE EXPOSED, THE METHODS USED TO RESOLVE THEM, AND THE FREQUENCY WITH WHICH THEY OCCUR. THE SOCIAL MATRIX OF ROLE CONFLICT IS BASED ON DIFFERING EXPECTATIONS OF COGNITIVE BEHAVIOR INTERPRETATIONS. THUS, WHEN PARENTS, STUDENTS, TEACHERS, OTHER ADMINISTRATORS, AND…

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new possibility for the identification and typing of anaerobic bacteria.

PubMed

Nagy, Elizabeth

2014-01-01

Anaerobic bacteria predominate in the normal flora of humans and are important, often life-threatening pathogens in mixed infections originating from the indigenous microbiota. The isolation and identification of anaerobes by phenotypic and DNA-based molecular methods at a species level is time-consuming and laborious. Following the successful adaptation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the routine laboratory identification of bacteria, the extensive development of a database has been initiated to use this method for the identification of anaerobic bacteria. Not only frequently isolated anaerobic species, but also newly recognized and taxonomically rearranged genera and species can be identified using direct smear samples or whole-cell protein extraction, and even phylogenetically closely related species can be identified correctly by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Typing of anaerobic bacteria on a subspecies level, determination of antibiotic resistance and direct identification of blood culture isolates will revolutionize anaerobe bacteriology in the near future.

Charge-Transfer Complexes and Photochemistry of Ozone with Ferrocene and n-Butylferrocene: A UV-vis Matrix-Isolation Study.

PubMed

Pinelo, Laura F; Kugel, Roger W; Ault, Bruce S

2015-10-15

The reactions of ozone with ferrocene (cp2Fe) and with n-butylferrocene (n-butyl cp2Fe) were studied using matrix isolation, UV-vis spectroscopy, and theoretical calculations. The codeposition of cp2Fe with O3 and of n-butyl cp2Fe with O3 into an argon matrix led to the production of 1:1 charge-transfer complexes with absorptions at 765 and 815 nm, respectively. These absorptions contribute to the green matrix color observed upon initial deposition. The charge-transfer complexes underwent photochemical reactions upon irradiation with red light (λ ≥ 600 nm). Theoretical UV-vis spectra of the charge-transfer complexes and photochemical products were calculated using TD-DFT at the B3LYP/6-311G++(d,2p) level of theory. The calculated UV-vis spectra were in good agreement with the experimental results. MO analysis of these long-wavelength transitions showed them to be n→ π* on the ozone subunit in the complex and indicated that the formation of the charge-transfer complex between ozone and cp2Fe or n-butyl cp2Fe affects how readily the π* orbital on O3 is populated when red light (λ ≥ 600 nm) is absorbed. 1:1 complexes of cp2Fe and n-butyl cp2Fe with O2 were also observed experimentally and calculated theoretically. These results support and enhance previous infrared studies of the mechanism of photooxidation of ferrocene by ozone, a reaction that has considerable significance for the formation of iron oxide thin films for a range of applications.

Evaluation of the Thermo Scientific SureTect Listeria species assay. AOAC Performance Tested Method 071304.

PubMed

Cloke, Jonathan; Evans, Katharine; Crabtree, David; Hughes, Annette; Simpson, Helen; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko; Leon-Velarde, Carlos; Larson, Nathan; Dave, Keron

2014-01-01

The Thermo Scientific SureTect Listeria species Assay is a new real-time PCR assay for the detection of all species of Listeria in food and environmental samples. This validation study was conducted using the AOAC Research Institute (RI) Performance Tested Methods program to validate the SureTect Listeria species Assay in comparison to the reference method detailed in International Organization for Standardization 11290-1:1996 including amendment 1:2004 in a variety of foods plus plastic and stainless steel. The food matrixes validated were smoked salmon, processed cheese, fresh bagged spinach, cantaloupe, cooked prawns, cooked sliced turkey meat, cooked sliced ham, salami, pork frankfurters, and raw ground beef. All matrixes were tested by Thermo Fisher Scientific, Microbiology Division, Basingstoke, UK. In addition, three matrixes (pork frankfurters, fresh bagged spinach, and stainless steel surface samples) were analyzed independently as part of the AOAC-RI-controlled independent laboratory study by the University ofGuelph, Canada. Using probability of detection statistical analysis, a significant difference in favour of the SureTect assay was demonstrated between the SureTect and reference method for high level spiked samples of pork frankfurters, smoked salmon, cooked prawns, stainless steel, and low-spiked samples of salami. For all other matrixes, no significant difference was seen between the two methods during the study. Inclusivity testing was conducted with 68 different isolates of Listeria species, all of which were detected by the SureTect Listeria species Assay. None of the 33 exclusivity isolates were detected by the SureTect Listeria species Assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside of the recommended parameters open to variation, which demonstrated that the assay gave reliable performance. Accelerated stability testing was additionally conducted, validating the assay shelf life.

Evaluation of the Thermo Scientific™ SureTect™ Listeria species Assay.

PubMed

Cloke, Jonathan; Evans, Katharine; Crabtree, David; Hughes, Annette; Simpson, Helen; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko

2014-03-01

The Thermo Scientific™ SureTect™ Listeria species Assay is a new real-time PCR assay for the detection of all species of Listeria in food and environmental samples. This validation study was conducted using the AOAC Research Institute (RI) Performance Tested MethodsSM program to validate the SureTect Listeria species Assay in comparison to the reference method detailed in International Organization for Standardization 11290-1:1996 including amendment 1:2004 in a variety of foods plus plastic and stainless steel. The food matrixes validated were smoked salmon, processed cheese, fresh bagged spinach, cantaloupe, cooked prawns, cooked sliced turkey meat, cooked sliced ham, salami, pork frankfurters, and raw ground beef. All matrixes were tested by Thermo Fisher Scientific, Microbiology Division, Basingstoke, UK. In addition, three matrixes (pork frankfurters, fresh bagged spinach, and stainless steel surface samples) were analyzed independently as part of the AOAC-RI-controlled independent laboratory study by the University of Guelph, Canada. Using probability of detection statistical analysis, a significant difference in favour of the SureTect assay was demonstrated between the SureTect and reference method for high level spiked samples of pork frankfurters, smoked salmon, cooked prawns, stainless steel, and low-spiked samples of salami. For all other matrixes, no significant difference was seen between the two methods during the study. Inclusivity testing was conducted with 68 different isolates of Listeria species, all of which were detected by the SureTect Listeria species Assay. None of the 33 exclusivity isolates were detected by the SureTect Listeria species Assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside of the recommended parameters open to variation, which demonstrated that the assay gave reliable performance. Accelerated stability testing was additionally conducted, validating the assay shelf life.

Complications pertaining to the detection and characterization of individual and embedded single walled carbon nanotubes by scanning electron microscopy

NASA Astrophysics Data System (ADS)

Orbaek, Alvin W.; Barron, Andrew R.

2013-03-01

Comparison of AFM and SEM images of single walled carbon nanotubes (SWNTs) grown within a dielectric matrix reveal subterranean nanotubes that are present within the matrix, and as such can be charge screened by the dielectric. Under adequate imaging conditions for the SWNT/silica sample the intensity of isolated nanotubes is found to be inversely proportional to the instrument dwell time (i.e., shorter dwell times were found to make SWNT intensities brighter). The threshold dwell time required to enable isolated tubes to be visible was found to be 10 μs moreover, the degree change in intensity was found to be nanotube specific, i.e., different SWNTs respond in a different manner at different dwell times. The results indicate that care should be taken when attempting to quantify number density and length distributions of SWNTs on or within a dielectric matrix.Comparison of AFM and SEM images of single walled carbon nanotubes (SWNTs) grown within a dielectric matrix reveal subterranean nanotubes that are present within the matrix, and as such can be charge screened by the dielectric. Under adequate imaging conditions for the SWNT/silica sample the intensity of isolated nanotubes is found to be inversely proportional to the instrument dwell time (i.e., shorter dwell times were found to make SWNT intensities brighter). The threshold dwell time required to enable isolated tubes to be visible was found to be 10 μs moreover, the degree change in intensity was found to be nanotube specific, i.e., different SWNTs respond in a different manner at different dwell times. The results indicate that care should be taken when attempting to quantify number density and length distributions of SWNTs on or within a dielectric matrix. Electronic supplementary information (ESI) available: Plots of SEM for cross over points, raw SEM images used for Fig. 5, and Fig. 6, SEM image of scattering centre, and SEM images with various scan directions at 10 μs dwell time. See DOI: 10.1039/c3nr00142c

Development of sustained release antipsychotic tablets using novel polysaccharide isolated from Delonix regia seeds and its pharmacokinetic studies

PubMed Central

Krishnaraj, Kaliaperumal; Chandrasekar, Mulla Joghi Nanjan; Nanjan, Mulla Joghi; Muralidharan, Selvadurai; Manikandan, Duraikannu

2011-01-01

A natural polysaccharide was isolated from the seeds of Delonix regia. The isolated polysaccharide could maintain aqueous equilibrium between the dosage form and the surrounding medium due to its massive competence of water absorption (80.72%) and swelling index (266.7%). The Scanning Electron Micrograph of a polysaccharide exhibits rough surface with pores and crevices, hence, the drug release will be retarded because of the drug particles entrapment in the pores and crevices. Further, the surface tension of polysaccharide is higher than that of water, which may facilitate sustained release of drugs from dosage forms. An antipsychotic drug, quetiapine fumarate has a short half-life of 6 h and administered multiple times per day. Hence the quetiapine fumarate oral sustained release tablets were formulated using this polysaccharide in the concentration of 5–30% to avoid the side effects and increase patient compliance. Dissolution of the developed tablets with 25% polysaccharide content showed a better release profile than the other batches (5–20%) at the end of 12 h. The strong matrix complex has low solubility in water, it does not dissolve rapidly and the drug continues to diffuse through the gel layer at a consistent rate. Drug release from the matrix tablets follows matrix type except F-4 and F-5 which follow first order and Hix.crow type. The bioavailability study was carried out using healthy male New Zealand white rabbits that show the AUC(0–inf) value for developed SR tablets is 1.44 times higher than the reference thus, indicating more efficient and sustained drug delivery capable of maintaining plasma drug levels better. PMID:24115903

Ubiquitination of specific mitochondrial matrix proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehmann, Gilad; Ziv, Tamar; Braten, Ori

2016-06-17

Several protein quality control systems in bacteria and/or mitochondrial matrix from lower eukaryotes are absent in higher eukaryotes. These are transfer-messenger RNA (tmRNA), The N-end rule ATP-dependent protease ClpAP, and two more ATP-dependent proteases, HslUV and ClpXP (in yeast). The lost proteases resemble the 26S proteasome and the role of tmRNA and the N-end rule in eukaryotic cytosol is performed by the ubiquitin proteasome system (UPS). Therefore, we hypothesized that the UPS might have substituted these systems – at least partially – in the mitochondrial matrix of higher eukaryotes. Using three independent experimental approaches, we demonstrated the presence of ubiquitinatedmore » proteins in the matrix of isolated yeast mitochondria. First, we show that isolated mitochondria contain ubiquitin (Ub) conjugates, which remained intact after trypsin digestion. Second, we demonstrate that the mitochondrial soluble fraction contains Ub-conjugates, several of which were identified by mass spectrometry and are localized to the matrix. Third, using immunoaffinity enrichment by specific antibodies recognizing digested ubiquitinated peptides, we identified a group of Ub-modified matrix proteins. The modification was further substantiated by separation on SDS-PAGE and immunoblots. Last, we attempted to identify the ubiquitin ligase(s) involved, and identified Dma1p as a trypsin-resistant protein in our mitochondrial preparations. Taken together, these data suggest a yet undefined role for the UPS in regulation of the mitochondrial matrix proteins. -- Highlights: •Mitochondrial matrix contains ubiquitinated proteins. •Ubiquitination occurs most probably in the matrix. •Dma1p is a ubiquitin ligase present in mitochondrial preparations.« less

Characterization and serology of the matrix protein from a nuclear-polyhedrosis virus of Trichoplusia ni before and after degradation by an endogenous proteinase.

PubMed

Eppstein, D A; Thoma, J A

1977-11-01

The intact matrix protein from a nuclear-polyhedrosis virus of the cabbage looper (Trichoplusia ni), isolated after inhibition of an endogenous serine-type proteinase, was further purified by molecular-sieve chromatography. The matrix protein was associated with carbohydrate moieties, and the carbohydrate content was determined for the two major peptides isolated after proteolysis by the endogenous proteinase. The association-dissociation interactions of the intact and proteinase-hydrolysed monomer units were characterized at high and low pH. At pH1.9, proteinase-degraded matrix protein dissociated into two different peptide fractions, FI and FII. Fraction FII, a single peptide of 9400 daltons, comprised one-third of the monomer unit of 28 000 daltons. At pH9.5, the degraded peptides were tightly associated in units equivalent to the intact monomer. These monomer equivalents associated to form a series of interconverting aggregates. The predominant aggregate sedimented at 11S and had a mol.wt greater than or equal to 200 000. Two non-cross-reacting antigens were present in the aggregate mixture. The presence of these two antigens does not reflect the presence of two different matrix proteins; rather, the expression of the antigens correlates with the degree of aggregation of the matrix protein.

Optimizing identification of clinically relevant Gram-positive organisms by use of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system.

PubMed

McElvania Tekippe, Erin; Shuey, Sunni; Winkler, David W; Butler, Meghan A; Burnham, Carey-Ann D

2013-05-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including "heavy" (H) and "light" (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or "score." We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS.

Optimizing Identification of Clinically Relevant Gram-Positive Organisms by Use of the Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System

PubMed Central

McElvania TeKippe, Erin; Shuey, Sunni; Winkler, David W.; Butler, Meghan A.

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including “heavy” (H) and “light” (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or “score.” We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS. PMID:23426925

Intrinsic fluorescence excitation-emission matrix spectral features of cottonseed protein fractions and the effects of denaturants

USDA-ARS?s Scientific Manuscript database

To better understand the functional and physicochemical properties of cottonseed protein, we investigated the intrinsic fluorescence excitation-emission matrix (EEM) spectral features of cottonseed protein isolate (CSPI) and sequentially extracted water (CSPw) and alkali (CSPa) protein fractions, an...

Formic Acid-Based Direct, On-Plate Testing of Yeast and Corynebacterium Species by Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Theel, Elitza S.; Schmitt, Bryan H.; Hall, Leslie; Cunningham, Scott A.; Walchak, Robert C.; Patel, Robin

2012-01-01

An on-plate testing method using formic acid was evaluated on the Bruker Biotyper matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry system using 90 yeast and 78 Corynebacterium species isolates, and 95.6 and 81.1% of yeast and 96.1 and 92.3% of Corynebacterium isolates were correctly identified to the genus and species levels, respectively. The on-plate method using formic acid yielded identification percentages similar to those for the conventional but more laborious tube-based extraction. PMID:22760034

Species Identification of Clinical Prevotella Isolates by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Soetens, Oriane; De Bel, Annelies; Echahidi, Fedoua; Vancutsem, Ellen; Vandoorslaer, Kristof; Piérard, Denis

2012-01-01

The performance of matrix-assisted laser desorption–ionization time of flight mass spectrometry (MALDI-TOF MS) for species identification of Prevotella was evaluated and compared with 16S rRNA gene sequencing. Using a Bruker database, 62.7% of the 102 clinical isolates were identified to the species level and 73.5% to the genus level. Extension of the commercial database improved these figures to, respectively, 83.3% and 89.2%. MALDI-TOF MS identification of Prevotella is reliable but needs a more extensive database. PMID:22301022

Formic acid-based direct, on-plate testing of yeast and Corynebacterium species by Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Theel, Elitza S; Schmitt, Bryan H; Hall, Leslie; Cunningham, Scott A; Walchak, Robert C; Patel, Robin; Wengenack, Nancy L

2012-09-01

An on-plate testing method using formic acid was evaluated on the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system using 90 yeast and 78 Corynebacterium species isolates, and 95.6 and 81.1% of yeast and 96.1 and 92.3% of Corynebacterium isolates were correctly identified to the genus and species levels, respectively. The on-plate method using formic acid yielded identification percentages similar to those for the conventional but more laborious tube-based extraction.

Formation and identification of borane radical anions isolated in solid argon

NASA Astrophysics Data System (ADS)

Lin, Meng-Yeh; Huang, Tzu-Ping; Chin, Chih-Hao; Wu, Yu-Jong

2018-02-01

The infrared (IR) spectrum of borane(3) anions (BH3-) isolated in solid Ar was recorded; two vibrational modes were observed at 2259.4 and 606.6 cm-1, which were assigned to the BH2 stretching (ν3) and out-of-plane large-amplitude (ν2) modes, respectively. These anions were produced by the electron bombardment of an Ar matrix sample containing a small proportion of B2H6 and H2 during matrix deposition or by the photolysis of single-bridged-B2H5- in an Ar matrix with the selected ultraviolet light. The band positions, relative intensity ratios, isotopic splitting pattern, and isotopic shift ratios of the observed IR features of BH3- are generally in good agreement with those predicted by the B2PLYP/aug-cc-pVTZ method.

In situ localization of nucleolin in the plant nucleolar matrix.

PubMed

Minguez, A; Moreno Diaz de la Espina, S

1996-01-10

The analysis of isolated nucleolar matrices from onion cells by light and electron microscopy, 2-D separation of proteins, and confocal microscopy has confirmed the existence of an organized nucleolar matrix with a complex protein composition to which are attached the insoluble processing complexes. In the present work, we present evidence from immunoblotting, immunofluorescence, immunogold labeling, and preferential cytochemical staining with bismuth salts that an insoluble fraction of the multifunctional protein nucleolin, is a component of the onion nucleolar matrix, and analyse its ultrastructural distribution in the described domains of the matrix.

Identification of Lactobacillus from the Saliva of Adult Patients with Caries Using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry

PubMed Central

Ma, Qingwei; Song, Yeqing; Zhang, Qian; Wang, Xiaoyan; Chen, Feng

2014-01-01

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been presented as a superior method for the detection of microorganisms in body fluid samples (e.g., blood, saliva, pus, etc.) However, the performance of MALDI-TOF MS in routine identification of caries-related Lactobacillus isolates from saliva of adult patients with caries has not been determined. In the present study, we introduced a new MALDI-TOF MS system for identification of lactobacilli. Saliva samples were collected from 120 subjects with caries. Bacteria were isolated and cultured, and each isolate was identified by both 16S rRNA sequencing and MALDI-TOF MS. The identification results obtained by MALDI-TOF MS were concordant at the genus level with those of conventional 16S rRNA-based sequencing for 88.6% of lactobacilli (62/70) and 95.5% of non-lactobacilli (21/22). Up to 96 results could be obtained in parallel on a single MALDI target, suggesting that this is a reliable high-throughput approach for routine identification of lactobacilli. However, additional reference strains are necessary to increase the sensitivity and specificity of species-level identification. PMID:25166027

Cultivable Methylobacterium species diversity in rice seeds identified with whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis.

PubMed

Okumura, Marie; Fujitani, Yoshiko; Maekawa, Masahiko; Charoenpanich, Jittima; Murage, Hunja; Kimbara, Kazuhide; Sahin, Nurettin; Tani, Akio

2017-02-01

Methylobacterium species are methylotrophic bacteria that widely inhabit plant surfaces. In addition to studies on methylotrophs as model organisms, research has also been conducted on their mechanism of plant growth promotion as well as the species-species specificity of plant-microbe interaction. We employed whole-cell matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (WC-MS) analysis, which enables the rapid and accurate identification of bacteria at the species level, to identify Methylobacterium isolates collected from the rice seeds of different cultivars harvested in Japan, Thailand, and Kenya. Rice seeds obtained from diverse geographical locations showed different communities of Methylobacterium species. We found that M. fujisawaense, M. aquaticum, M. platani, and M. radiotolerans are the most frequently isolated species, but none were isolated as common species from 18 seed samples due to the highly biased communities in some samples. These findings will contribute to the development of formulations containing selected species that promote rice growth, though it may be necessary to customize the formulations depending on the cultivars and farm conditions. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Comparison of Saramis 4.12 and IVD 3.0 Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria from Solid and Liquid Culture Media.

PubMed

Leyer, Caroline; Gregorowicz, Guillaume; Mougari, Faiza; Raskine, Laurent; Cambau, Emmanuelle; de Briel, Dominique

2017-07-01

During the last decade, many investigators have studied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for identification of mycobacteria. Diverse and contradictory results indicated that optimal level for routine testing has not been reached yet. This work aimed to assess Vitek MS through two distinct versions, Saramis v4.12 RUO and the IVD v3.0, under conditions close to routine laboratory practice. Overall, 111 mycobacterial isolates were subjected to protein extraction and same spectra were matched against both databases. The IVD v3.0 database proved to be superior to Saramis v4.12 and its identification rates remarkably increased, from 67% to 94% for isolates grown on Middlebrook 7H10 solid medium and from 62% to 91% for isolates grown on mycobacterial growth indicator tube (MGIT) liquid medium. With this new version, IVD v3.0, MALDI-TOF MS might be integrated into routine clinical diagnostics, although molecular techniques remain mandatory in some cases. Copyright © 2017 American Society for Microbiology.

Comparison of 2010-2011 H3N2 influenza A viruses isolated from swine and the A(H3N2)v isolated from humans in 2011

USDA-ARS?s Scientific Manuscript database

In the end of 2011, 12 U.S. cases of humans infected with swine H3N2 virus containing the matrix gene from pandemic H1N1 2009 virus (H1N1pdm09) were detected and named A(H3N2)v. This study used a swine model to compare the pathogenic, transmission, genetic, and antigenic properties of a human A(H3N2...

A proteomic study of the arabidopsis nuclear matrix.

PubMed

Calikowski, Tomasz T; Meulia, Tea; Meier, Iris

2003-10-01

The eukaryotic nucleus has been proposed to be organized by two interdependent nucleoprotein structures, the DNA-based chromatin and the RNA-dependent nuclear matrix. The functional composition and molecular organization of the second component have not yet been resolved. Here, we describe the isolation of the nuclear matrix from the model plant Arabidopsis, its initial characterization by confocal and electron microscopy, and the identification of 36 proteins by mass spectrometry. Electron microscopy of resinless samples confirmed a structure very similar to that described for the animal nuclear matrix. Two-dimensional gel electrophoresis resolved approximately 300 protein spots. Proteins were identified in batches by ESI tandem mass spectrometry after resolution by 1D SDS-PAGE. Among the identified proteins were a number of demonstrated or predicted Arabidopsis homologs of nucleolar proteins such as IMP4, Nop56, Nop58, fibrillarins, nucleolin, as well as ribosomal components and a putative histone deacetylase. Others included homologs of eEF-1, HSP/HSC70, and DnaJ, which have also been identified in the nucleolus or nuclear matrix of human cells, as well as a number of novel proteins with unknown function. This study is the first proteomic approach towards the characterization of a higher plant nuclear matrix. It demonstrates the striking similarities both in structure and protein composition of the operationally defined nuclear matrix across kingdoms whose unicellular ancestors have separated more than one billion years ago. Copyright 2003 Wiley-Liss, Inc.

Analyzing volatile compounds in dairy products

USDA-ARS?s Scientific Manuscript database

Volatile compounds give the first indication of the flavor in a dairy product. Volatiles are isolated from the sample matrix and then analyzed by chromatography, sensory methods, or an electronic nose. Isolation may be performed by solvent extraction or headspace analysis, and gas chromatography i...

Experimental estimation of transmissibility matrices for industrial multi-axis vibration isolation systems

NASA Astrophysics Data System (ADS)

Beijen, Michiel A.; Voorhoeve, Robbert; Heertjes, Marcel F.; Oomen, Tom

2018-07-01

Vibration isolation is essential for industrial high-precision systems to suppress external disturbances. The aim of this paper is to develop a general identification approach to estimate the frequency response function (FRF) of the transmissibility matrix, which is a key performance indicator for vibration isolation systems. The major challenge lies in obtaining a good signal-to-noise ratio in view of a large system weight. A non-parametric system identification method is proposed that combines floor and shaker excitations. Furthermore, a method is presented to analyze the input power spectrum of the floor excitations, both in terms of magnitude and direction. In turn, the input design of the shaker excitation signals is investigated to obtain sufficient excitation power in all directions with minimum experiment cost. The proposed methods are shown to provide an accurate FRF of the transmissibility matrix in three relevant directions on an industrial active vibration isolation system over a large frequency range. This demonstrates that, despite their heavy weight, industrial vibration isolation systems can be accurately identified using this approach.

Further considerations on the thermal stabilization of the nuclear matrix in mouse erythroleukemia cells.

PubMed

Martelli, A M; Falcieri, E; Gobbi, P; Manzoli, L; Cataldi, A; Rana, R A; Cocco, L

1992-04-01

The morphology and the polypeptide composition of the nuclear matrix obtained from 37 degrees C incubated nuclei has been studied in mouse erythroleukemia cells. From a structural point of view, in the absence of heat treatment, the matrix lacked identifiable nucleolar remnants and the internal fibrogranular meshwork whereas a peripheral lamina was seen. On the contrary, the matrix obtained from heat exposed nuclei displayed very electrondense nucleolar remnants and an abundant inner network. These results were obtained irrespective of the type of extracting agent (2M NaCl or 0.2 M (NH4)2SO4) used to remove histones and other soluble proteins. The heat stabilization of the matrix could not be prevented by sulfhydryl blocking chemicals such as iodoacetamide and n-ethylmaleimide, thus suggesting that heat does not stabilize the matrix by inducing the formation of disulfide bonds. Only limited differences in the polypeptide pattern of matrix isolated under different conditions were seen using one-dimensional pore gradient polyacrylamide gels stained with both Coomassie Brilliant Blue and silver despite the fact that the matrix fraction from heat treated nuclei retained about three fold more protein in comparison with controls. The same results were obtained also by means of two-dimensional non-equilibrium gel electrophoresis.

Analysis of trichothecene mycotoxins in contaminated grains by gas chromatography/matrix isolation/Fourier transform infrared spectroscopy and gas chromatography/mass spectrometry.

PubMed

Mossoba, M M; Adams, S; Roach, J A; Trucksess, M W

1996-01-01

Gas chromatography/matrix isolation/Fourier transform infrared (GC/MI/FTIR) spectroscopy and GC/mass spectrometry (MS) were used to confirm the identities of trimethylsilyl (TMS) derivatives of trichothecene mycotoxins in naturally contaminated grains. Infrared spectral bands observed in the fingerprint region were unique for 10 trichothecene standards. Characteristic absorption bands were observed for the ester (near 1750 cm-1) and ketone (near 1700 cm-1) carbonyl stretching vibrations, the acetate CH3 symmetric bend (1370 cm-1), the epoxide ring (1262 cm-1), the trimethylsilyl CH3 in-plane deformation (1253 cm-1), the ester (O)C-O asymmetric stretching vibration (near 1244 cm-1), and several other bands including intense features due to the TMS function. Infrared bands observed under cryogenic matrix isolation conditions were compared with those found at room temperature in a potassium bromide matrix for 5 of these standards. Identities of deoxynivalenol (DON) from barley and mixed feed, nivalenol from wheat and barley, and DON and fusarenon-x from sweet corn were confirmed by comparison of their infrared spectral bands with those of standards. The identity of DON in the same test samples of sweet corn was confirmed further by GC/MS. GC/MS was also used to quantitate the levels of DON (67-455 ppm) in sweet corn test samples.

Influence of the amyloid dye Congo red on curli, cellulose, and the extracellular matrix in E. coli during growth and matrix purification.

PubMed

Reichhardt, Courtney; McCrate, Oscar A; Zhou, Xiaoxue; Lee, Jessica; Thongsomboon, Wiriya; Cegelski, Lynette

2016-11-01

Microbial biofilms are communities of cells characterized by a hallmark extracellular matrix (ECM) that confers functional attributes to the community, including enhanced cohesion, adherence to surfaces, and resistance to external stresses. Understanding the composition and properties of the biofilm ECM is crucial to understanding how it functions and protects cells. New methods to isolate and characterize ECM are emerging for different biofilm systems. Solid-state nuclear magnetic resonance was used to quantitatively track the isolation of the insoluble ECM from the uropathogenic Escherichia coli strain UTI89 and understand the role of Congo red in purification protocols. UTI89 assembles amyloid-integrated biofilms when grown on YESCA nutrient agar. The ECM contains curli amyloid fibers and a modified form of cellulose. Biofilms formed by UTI89 and other E. coli and Salmonella strains are often grown in the presence of Congo red to visually emphasize wrinkled agar morphologies and to score the production of ECM. Congo red is a hallmark amyloid-binding dye and binds to curli, yet also binds to cellulose. We found that growth in Congo red enabled more facile extraction of the ECM from UTI89 biofilms and facilitates isolation of cellulose from the curli mutant, UTI89ΔcsgA. Yet, Congo red has no influence on the isolation of curli from curli-producing cells that do not produce cellulose. Sodium dodecyl sulfate can remove Congo red from curli, but not from cellulose. Thus, Congo red binds strongly to cellulose and possibly weakens cellulose interactions with the cell surface, enabling more complete removal of the ECM. The use of Congo red as an extracellular matrix purification aid may be applied broadly to other organisms that assemble extracellular amyloid or cellulosic materials. Graphical abstract Solid-state NMR was used to quantitatively track the isolation of the insoluble amyloid-associated ECM from uropathogenic E. coli and understand the role of Congo red in purification protocols.

Identification of HgO/x/ species by matrix isolation spectroscopy

NASA Technical Reports Server (NTRS)

Butler, R.; Katz, S.; Snelson, A.; Stephens, J. B.

1979-01-01

The condensation of Hg atoms in an ozone-doped argon matrix gas with irradiation from a medium-pressure mercury arc lamp at 10 K resulted in the formation of several trapped HgO(x) species. Tentative identification of HgO has been made from absorption bands appearing in the visible and IR regions of the spectrum based on (O-16)2 and (O-18)2 isotope studies. The following spectroscopic constants were obtained: nu(00) = 14634 cm, nu(1) = 548 cm, and nu(11) = 676 cm. Some qualitative evidence was obtained for the existence of HgO2.

Cryochemistry of Metal Nanoparticles

NASA Astrophysics Data System (ADS)

Sergeev, Gleb B.

2003-12-01

The interaction of metal atoms, clusters and nanoparticles with different organic and inorganic substances were studied at low temperature (10-40K). Combination of matrix isolation technique and preparative cryochemistry was applied for the investigation of activity and selectivity of metal particles of different size. Encapsulation of metal nanoparticles in polymers was studied. The metal-polymer films thus obtained exhibited satisfactory sensitivity to ammonia.

Rapid identification of clinical mycobacterial isolates by protein profiling using matrix assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Panda, A; Kurapati, S; Samantaray, J C; Myneedu, V P; Verma, A; Srinivasan, A; Ahmad, H; Behera, D; Singh, U B

2013-01-01

The purpose of this study was to evaluate the identification of Mycobacterium tuberculosis which is often plagued with ambiguity. It is a time consuming process requiring 4-8 weeks after culture positivity, thereby delaying therapeutic intervention. For a successful treatment and disease management, timely diagnosis is imperative. We evaluated a rapid, proteomic based technique for identification of clinical mycobacterial isolates by protein profiling using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Freshly grown mycobacterial isolates were used. Acetonitrile/trifluoroacetic acid extraction procedure was carried out, following which cinnamic acid charged plates were subjected to identification by MALDI-TOF MS. A comparative analysis of 42 clinical mycobacterial isolates using the MALDI-TOF MS and conventional techniques was carried out. Among these, 97.61% were found to corroborate with the standard methods at genus level and 85.36% were accurate till the species level. One out of 42 was not in accord with the conventional assays because MALDI-TOF MS established it as Mycobacterium tuberculosis (log (score)>2.0) and conventional methods established it to be non-tuberculous Mycobacterium. MALDI-TOF MS was found to be an accurate, rapid, cost effective and robust system for identification of mycobacterial species. This innovative approach holds promise for early therapeutic intervention leading to better patient care.

Structure and photochemistry of a saccharyl thiotetrazole.

PubMed

Ismael, A; Borba, A; Henriques, M S C; Paixão, J A; Fausto, R; Cristiano, M L S

2015-01-02

The molecular structure and photochemistry of 5-thiosaccharyl-1-methyltetrazole (TSMT) were studied by means of matrix-isolation FTIR spectroscopy, X-ray crystallography, and theoretical calculations. The calculations predicted two conformers of TSMT that differ in energy by more than 15 kJ mol(-1). The infrared spectrum of TSMT isolated in solid argon was fully assigned on the basis of the spectrum calculated (O3LYP/6-311++G(3df,3pd)) for the most stable conformer. In the crystal, TSMT molecules were found to assume the same conformation as for the isolated molecule, with each molecule forming four hydrogen bonds with three neighboring molecules, leading to a network of TSMT oligomers. Upon UV (λ = 265 nm) irradiation of the matrix-isolated TSMT, two photodegradation pathways were observed, both arising from cleavage of the tetrazolyl ring. Pathway a involves cleavage of the N1-N2 and N3-N4 bonds with extrusion of N2, leading to photostable diazirine and thiocarbodiimide derivatives. The photostability of the photoproduced diazirine under the conditions used precluded its rearrangement to the nitrile imine, as reported for 5-phenyltetrazole by Bégué et al. ( J. Am. Chem. Soc. 2012 , 134 , 5339 ). Pathway b involves cleavage of the C5-N1 and N4-N3 bonds, leading to a thiocyanate and methyl azide, the latter undergoing subsequent fragmentation to give CNH.

Multicenter study evaluating the Vitek MS system for identification of medically important yeasts.

PubMed

Westblade, Lars F; Jennemann, Rebecca; Branda, John A; Bythrow, Maureen; Ferraro, Mary Jane; Garner, Omai B; Ginocchio, Christine C; Lewinski, Michael A; Manji, Ryhana; Mochon, A Brian; Procop, Gary W; Richter, Sandra S; Rychert, Jenna A; Sercia, Linda; Burnham, Carey-Ann D

2013-07-01

The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates, including 58 C. albicans, 62 C. glabrata, and 53 C. krusei isolates), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n = 58) identified as Candida dubliniensis, one isolate of Candida parapsilosis (n = 73) identified as Candida pelliculosa, and three isolates of Geotrichum klebahnii (n = 6) identified as Geotrichum candidum. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories.

Teaching and Studying the Americas: Cultural Influences from Colonialism to the Present

ERIC Educational Resources Information Center

Pinn, Anthony B., Ed.; Levander, Caroline F., Ed.; Emerson, Michael O., Ed.

2010-01-01

Interdisciplinary work across the humanities and social sciences is moving beyond analysis of any one nation in isolation and instead placing urgent questions in the larger matrix of the Americas as a hemisphere. But little attention has been given to the overarching methodological, institutional, and pedagogical issues resulting from the growth…

Capsule Typing of Haemophilus influenzae by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.

PubMed

Månsson, Viktor; Gilsdorf, Janet R; Kahlmeter, Gunnar; Kilian, Mogens; Kroll, J Simon; Riesbeck, Kristian; Resman, Fredrik

2018-03-01

Encapsulated Haemophilus influenzae strains belong to type-specific genetic lineages. Reliable capsule typing requires PCR, but a more efficient method would be useful. We evaluated capsule typing by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Isolates of all capsule types (a-f and nontypeable; n = 258) and isogenic capsule transformants (types a-d) were investigated. Principal component and biomarker analyses of mass spectra showed clustering, and mass peaks correlated with capsule type-specific genetic lineages. We used 31 selected isolates to construct a capsule typing database. Validation with the remaining isolates (n = 227) showed 100% sensitivity and 92.2% specificity for encapsulated strains (a-f; n = 61). Blinded validation of a supplemented database (n = 50) using clinical isolates (n = 126) showed 100% sensitivity and 100% specificity for encapsulated strains (b, e, and f; n = 28). MALDI-TOF mass spectrometry is an accurate method for capsule typing of H. influenzae.

Matrix isolation infrared spectra, assignment and DFT investigation on reactions of iron and manganese monoxides with CH3Cl.

PubMed

Zhao, Yanying; Fan, Kexue; Huang, Yongfei; Zheng, Xuming

2013-12-01

The reactions of iron and manganese monoxide molecules (FeO, and MnO) with monochloromethane in solid argon have been studied by matrix isolation infrared spectroscopy and quantum chemistry calculations. When annealing, the reactions of FeO and MnO with CH3Cl first form the OM-(η(Cl)-CH3Cl) (MMn, Fe) complexes, which can isomerize to CH3MOCl (MMn, Fe) upon 300<λ<580 nm irradiation. The products were characterized by isotopic IR studies with CD3Cl and (13)CH3Cl and density functional calculations. Based on theoretical calculations, the OFe-(η(Cl)-CH3Cl) and OMn-(η(Cl)-CH3Cl) complexes have (5)A' and (6)A' ground state with Cs symmetry, respectively. The accurate CCSD(T) single point calculations illustrate the CH3MOCl isomerism are 13.8 and 3.1 kcal/mol lower in energy than the OM-(η(Cl)-CH3Cl) (MMn, Fe) complexes. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd

Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved frommore » 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively.« less

Evaluation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Bruker Biotyper for identification of Penicillium marneffei, Paecilomyces species, Fusarium solani, Rhizopus species, and Pseudallescheria boydii

PubMed Central

Chen, Ying-Sheng; Liu, Yen-Hung; Teng, Shih-Hua; Liao, Chun-Hsing; Hung, Chien-Ching; Sheng, Wang-Huei; Teng, Lee-Jene; Hsueh, Po-Ren

2015-01-01

We evaluated the performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), the MALDI Bruker Biotyper system (microflex LT; Bruker Daltonik GmbH, Bremen, Germany), on the identification of 50 isolates of clinically encountered molds, including Penicillium marneffei (n = 28), Paecilomyces species (n = 12), Fusarium solani (n = 6), Rhizopus species (n = 3), and Pseudallescheria boydii (n = 1). The isolates were identified to species levels by sequence analysis of the internal transcribed spacer (ITS) regions using primers ITS1 and ITS4. None of the 28 genetically well characterized isolates of P. marneffei were identified as P. marneffei by MALDI-TOF MS, because P. marneffei was not present in either Bruker general library (DB 5627) or Bruker filamentous fungi library V1.0. However, the rate of accurate identification as P. marneffei (score value ≥ 2.000) was 85.7% based on newly created database from one P. marneffei strain (NTUH-3370) by MALDI Biotyper system. Sequencing analysis of these 22 non-P. marneffei isolates of molds revealed seven Paecilomyces variotii, six F. solani, four Paecilomyces lilacinus, and one each of Paecilomyces sinensis, Rhizopus arrhizus, R. oryzae, R. microspores, and P. boydii. Although all the seven P. variotii isolates, four of the six F. solani, two of the four P. lilacinus, and two of the three isolates of Rhizopus species, and the P. boydii isolate had concordant identification results between MALDI-TOF MS and sequencing analysis, the score values of these isolates were all of <1.700. This study indicated that the MALDI Bruker Biotyper is ineffective for identifying P. marneffei and other unusual molds because of the current database limitations. Therefore, it is necessary to continuously update the MALDI-TOF MS databases. PMID:26217315

Identification of beer-spoilage bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Wieme, Anneleen D; Spitaels, Freek; Aerts, Maarten; De Bruyne, Katrien; Van Landschoot, Anita; Vandamme, Peter

2014-08-18

Applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of beer-spoilage bacteria was examined. To achieve this, an extensive identification database was constructed comprising more than 4200 mass spectra, including biological and technical replicates derived from 273 acetic acid bacteria (AAB) and lactic acid bacteria (LAB), covering a total of 52 species, grown on at least three growth media. Sequence analysis of protein coding genes was used to verify aberrant MALDI-TOF MS identification results and confirmed the earlier misidentification of 34 AAB and LAB strains. In total, 348 isolates were collected from culture media inoculated with 14 spoiled beer and brewery samples. Peak-based numerical analysis of MALDI-TOF MS spectra allowed a straightforward species identification of 327 (94.0%) isolates. The remaining isolates clustered separately and were assigned through sequence analysis of protein coding genes either to species not known as beer-spoilage bacteria, and thus not present in the database, or to novel AAB species. An alternative, classifier-based approach for the identification of spoilage bacteria was evaluated by combining the identification results obtained through peak-based cluster analysis and sequence analysis of protein coding genes as a standard. In total, 263 out of 348 isolates (75.6%) were correctly identified at species level and 24 isolates (6.9%) were misidentified. In addition, the identification results of 50 isolates (14.4%) were considered unreliable, and 11 isolates (3.2%) could not be identified. The present study demonstrated that MALDI-TOF MS is well-suited for the rapid, high-throughput and accurate identification of bacteria isolated from spoiled beer and brewery samples, which makes the technique appropriate for routine microbial quality control in the brewing industry. Copyright © 2014 Elsevier B.V. All rights reserved.

Cost Savings Realized by Implementation of Routine Microbiological Identification by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Alby, Kevin; Kerr, Alan; Jones, Melissa; Gilligan, Peter H.

2015-01-01

Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is an emerging technology for rapid identification of bacterial and fungal isolates. In comparison to conventional methods, this technology is much less labor intensive and can provide accurate and reliable results in minutes from a single isolated colony. We compared the cost of performing the bioMérieux Vitek MALDI-TOF MS with conventional microbiological methods to determine the amount saved by the laboratory by converting to the new technology. Identification costs for 21,930 isolates collected between April 1, 2013, and March 31, 2014, were directly compared for MALDI-TOF MS and conventional methodologies. These isolates were composed of commonly isolated organisms, including commonly encountered aerobic and facultative bacteria and yeast but excluding anaerobes and filamentous fungi. Mycobacterium tuberculosis complex and rapidly growing mycobacteria were also evaluated for a 5-month period during the study. Reagent costs and a total cost analysis that included technologist time in addition to reagent expenses and maintenance service agreement costs were analyzed as part of this study. The use of MALDI-TOF MS equated to a net savings of $69,108.61, or 87.8%, in reagent costs annually compared to traditional methods. When total costs are calculated to include technologist time and maintenance costs, traditional identification would have cost $142,532.69, versus $68,886.51 with the MALDI-TOF MS method, resulting in a laboratory savings of $73,646.18, or 51.7%, annually by adopting the new technology. The initial cost of the instrument at our usage level would be offset in about 3 years. MALDI-TOF MS not only represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates, it also provides a significant cost savings for the laboratory. PMID:25994167

Cost Savings Realized by Implementation of Routine Microbiological Identification by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Tran, Anthony; Alby, Kevin; Kerr, Alan; Jones, Melissa; Gilligan, Peter H

2015-08-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is an emerging technology for rapid identification of bacterial and fungal isolates. In comparison to conventional methods, this technology is much less labor intensive and can provide accurate and reliable results in minutes from a single isolated colony. We compared the cost of performing the bioMérieux Vitek MALDI-TOF MS with conventional microbiological methods to determine the amount saved by the laboratory by converting to the new technology. Identification costs for 21,930 isolates collected between April 1, 2013, and March 31, 2014, were directly compared for MALDI-TOF MS and conventional methodologies. These isolates were composed of commonly isolated organisms, including commonly encountered aerobic and facultative bacteria and yeast but excluding anaerobes and filamentous fungi. Mycobacterium tuberculosis complex and rapidly growing mycobacteria were also evaluated for a 5-month period during the study. Reagent costs and a total cost analysis that included technologist time in addition to reagent expenses and maintenance service agreement costs were analyzed as part of this study. The use of MALDI-TOF MS equated to a net savings of $69,108.61, or 87.8%, in reagent costs annually compared to traditional methods. When total costs are calculated to include technologist time and maintenance costs, traditional identification would have cost $142,532.69, versus $68,886.51 with the MALDI-TOF MS method, resulting in a laboratory savings of $73,646.18, or 51.7%, annually by adopting the new technology. The initial cost of the instrument at our usage level would be offset in about 3 years. MALDI-TOF MS not only represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates, it also provides a significant cost savings for the laboratory. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

PLE in the analysis of plant compounds. Part I. The application of PLE for HPLC analysis of caffeine in green tea leaves.

PubMed

Dawidowicz, Andrzej L; Wianowska, Dorota

2005-04-29

A broad spectrum of sample preparation methods is currently used for the isolation of pharmacologically active compounds from plant and herbal materials. The paper compares the effectiveness of infusion, microwave assisted solvent extraction (MASE), matrix solid-phase dispersion (MSPD) and pressurised liquid extraction (PLE) as sample preparation methods for the isolation of caffeine from green tea leaves. The effect of PLE variables, such as extraction temperature, pressure and time, on the yield of caffeine from the investigated matrix is discussed. The obtained results revealed that PLE, in comparison with other sample preparation methods applied, has significantly lower efficacy for caffeine isolation from green tea leaves. The evaluation of PLE conditions leads to the conclusion that elevated pressure applied in the PLE process is the factor hindering the extraction.

Orthogonal Simulation Experiment for Flow Characteristics of Ore in Ore Drawing and Influencing Factors in a Single Funnel Under a Flexible Isolation Layer

NASA Astrophysics Data System (ADS)

Chen, Qingfa; Zhao, Fuyu; Chen, Qinglin; Wang, Yuding; Zhong, Yu; Niu, Wenjing

2017-12-01

A study on the flow characteristics of ore and factors that influence these characteristics is important to master ore flow laws. An orthogonal ore-drawing numerical model was established and the flow characteristics were explored. A weight matrix was obtained and the effect of the factors was determined. It was found that (1) the entire isolation-layer interface presents a Gaussian curve morphology and marked particles in each layer show a funnel morphology; (2) the drawing amount, Q, and the isolation layer half-width, W, are correlated positively with the fall depth, H, of the isolation layer; (3) factors that affect the characteristics sequentially include the particle friction coefficient, the interface friction coefficient, the isolation layer thickness, and the particle radius, and (4) the optimal combination is an isolation layer thickness of 0.005 m, an interface friction coefficient of 0.8, a particle friction coefficient of 0.2, and a particle radius of 0.007 m.

Comparison of Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometer to BD Phoenix Automated Microbiology System for Identification of Gram-Negative Bacilli▿

PubMed Central

Saffert, Ryan T.; Cunningham, Scott A.; Ihde, Sherry M.; Monson Jobe, Kristine E.; Mandrekar, Jayawant; Patel, Robin

2011-01-01

We compared the BD Phoenix automated microbiology system to the Bruker Biotyper (version 2.0) matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) system for identification of Gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. The BD Phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. The Bruker Biotyper correctly identified 408 (93%) and 360 (82%) isolates to the genus and species level, respectively. The 440 isolates were grouped into common (308) and infrequent (132) isolates in the clinical laboratory. For the 308 common isolates, the BD Phoenix and Bruker Biotyper correctly identified 294 (95%) and 296 (96%) of the isolates to the genus level, respectively. For species identification, the BD Phoenix and Bruker Biotyper correctly identified 93% of the common isolates (285 and 286, respectively). In contrast, for the 132 infrequent isolates, the Bruker Biotyper correctly identified 112 (85%) and 74 (56%) isolates to the genus and species level, respectively, compared to the BD Phoenix, which identified only 69 (52%) and 45 (34%) isolates to the genus and species level, respectively. Statistically, the Bruker Biotyper overall outperformed the BD Phoenix for identification of Gram-negative bacilli to the genus (P < 0.0001) and species (P = 0.0005) level in this sample set. When isolates were categorized as common or infrequent isolates, there was statistically no difference between the instruments for identification of common Gram-negative bacilli (P > 0.05). However, the Bruker Biotyper outperformed the BD Phoenix for identification of infrequently isolated Gram-negative bacilli (P < 0.0001). PMID:21209160

New strategy for the survey of Toxoplasma gondii in meat for human consumption.

PubMed

Villena, Isabelle; Durand, Benoit; Aubert, Dominique; Blaga, Radu; Geers, Régine; Thomas, Myriam; Perret, Catherine; Alliot, Annie; Escotte-Binet, Sandie; Thébault, Anne; Boireau, Pascal; Halos, Lénaïg

2012-02-10

Monitoring of Toxoplasma infection in animals destined for human consumption is a great challenge for human toxoplasmosis prevention. This study aimed to compare results obtained from a naturally infected population of sheep using different tests and targeting an original matrix: meat samples and muscle fluids collected at the slaughterhouse. A commercial ELISA test was performed on diaphragm fluids from 419 ovine carcasses collected at the slaughterhouse. A MAT (modified agglutination test) was performed on heart fluids obtained from the same animals. In addition, all hearts were bioassayed in mice. Serological test agreement, the relative sensitivity of ELISA MAT and mouse bioassay as well as a correlation between titres and parasite isolation probability were statistically evaluated. The overall agreement (kappa coefficient=0.64) of ELISA on diaphragm fluids and MAT on heart fluids is substantial and subsequently both tests can be used for epidemiological studies. Relative sensitivity was higher for MAT performed on cardiac fluids (90%) than ELISA on diaphragm fluid (61%). For both serological tests, relative sensitivity is lower in lambs younger than 12 months. Relative sensitivity of mouse inoculation was 42%. A significant correlation was obtained between increasing MAT titres and probability to isolate live parasite from the heart. When the fluid titre was higher than 1:16, parasites were isolated in 65% of cases. When it was lower, isolation failed in 95% of the cases. According to our results, cardiac fluids appear to be a relevant matrix for toxoplasmosis survey in meat. Copyright © 2011 Elsevier B.V. All rights reserved.

The relaxation matrix for symmetric tops with inversion symmetry. I. Effects of line coupling on self-broadened ν1 and pure rotational bands of NH3.

PubMed

Ma, Q; Boulet, C

2016-06-14

The Robert-Bonamy formalism has been commonly used to calculate half-widths and shifts of spectral lines for decades. This formalism is based on several approximations. Among them, two have not been fully addressed: the isolated line approximation and the neglect of coupling between the translational and internal motions. Recently, we have shown that the isolated line approximation is not necessary in developing semi-classical line shape theories. Based on this progress, we have been able to develop a new formalism that enables not only to reduce uncertainties on calculated half-widths and shifts, but also to model line mixing effects on spectra starting from the knowledge of the intermolecular potential. In our previous studies, the new formalism had been applied to linear and asymmetric-top molecules. In the present study, the method has been extended to symmetric-top molecules with inversion symmetry. As expected, the inversion splitting induces a complete failure of the isolated line approximation. We have calculated the complex relaxation matrices of self-broadened NH3. The half-widths and shifts in the ν1 and the pure rotational bands are reported in the present paper. When compared with measurements, the calculated half-widths match the experimental data very well, since the inapplicable isolated line approximation has been removed. With respect to the shifts, only qualitative results are obtained and discussed. Calculated off-diagonal elements of the relaxation matrix and a comparison with the observed line mixing effects are reported in the companion paper (Paper II).

The Relaxation Matrix for Symmetric Tops with Inversion Symmetry. I. Effects of Line Coupling on Self-Broadened v (sub 1) and Pure Rotational Bands of NH3

NASA Technical Reports Server (NTRS)

Ma, Q.; Boulet, C.

2016-01-01

The Robert-Bonamy formalism has been commonly used to calculate half-widths and shifts of spectral lines for decades. This formalism is based on several approximations. Among them, two have not been fully addressed: the isolated line approximation and the neglect of coupling between the translational and internal motions. Recently, we have shown that the isolated line approximation is not necessary in developing semi-classical line shape theories. Based on this progress, we have been able to develop a new formalism that enables not only to reduce uncertainties on calculated half-widths and shifts, but also to model line mixing effects on spectra starting from the knowledge of the intermolecular potential. In our previous studies, the new formalism had been applied to linear and asymmetric-top molecules. In the present study, the method has been extended to symmetric-top molecules with inversion symmetry. As expected, the inversion splitting induces a complete failure of the isolated line approximation. We have calculated the complex relaxation matrices of selfbroadened NH3. The half-widths and shifts in the ?1 and the pure rotational bands are reported in the present paper. When compared with measurements, the calculated half-widths match the experimental data very well, since the inapplicable isolated line approximation has been removed. With respect to the shifts, only qualitative results are obtained and discussed. Calculated off-diagonal elements of the relaxation matrix and a comparison with the observed line mixing effects are reported in the companion paper (Paper II).

The OH-Initiated Oxidation of CS2 in the Presence of NO: FTIR Matrix-Isolation and Theoretical Studies.

PubMed

Bil, A; Grzechnik, K; Sałdyka, M; Mielke, Z

2016-09-01

We studied the photochemistry of the carbon disulfide-nitrous acid system with the help of Fourier transform infrared (FTIR) matrix isolation spectroscopy and theoretical methods. The irradiation of the CS2···HONO complexes, isolated in solid argon, with the filtered output of the mercury lamp (λ > 345 nm) was found to produce OCS, SO2, and HNCS; HSCN was also tentatively identified. The (13)C, (15)N, and (2)H isotopic shifts as well as literature data were used for product identifications. The evolution of the measured FTIR spectra with irradiation time and the changes in the spectra after matrix annealing indicated that the identified molecules are the products of different reaction channels: OCS being a product of another reaction path than SO2 and HNCS or HSCN. The possible reaction channels between SC(OH)S/SCS(OH) radicals and NO were studied using DFT/B3LYP/aug-cc-pVTZ method. The SC(OH)S and/or SCS(OH) intermediates are formed when HONO attached to CS2 photodissociates into OH and NO. The calculations indicated that SC(OH)S radical can form with NO two stable adducts. The more stable SC(OH)S···NO structure is a reactant for a simple one-step process leading to OCS and HONS molecules. An alternative, less-stable complex formed between SC(OH)S and NO leads to formation of OCS and HSNO. The calculations predict only one stable complex between SCS(OH) radical and NO, which can dissociate along two channels leading to HNCS and SO2 or HSCN and SO2 as the end products. The identified photoproducts indicate that both SC(OH)S and SCS(OH) adducts are intermediates in the CS2 + OH + NO reaction leading to different reaction products.

First step in developing a 3D biodegradable fibrin scaffold for an artificial ovary.

PubMed

Luyckx, Valérie; Dolmans, Marie-Madeleine; Vanacker, Julie; Scalercio, Sarah R; Donnez, Jacques; Amorim, Christiani A

2013-11-25

Although transplantation of cryopreserved ovarian tissue is a promising approach to restore fertility in cancer patients, it is not advisable for women at risk of ovarian involvement due to the threat of reintroducing malignant cells. The aim of this study was therefore to find an alternative for these patients by development of an artificial ovary. For construction of the artificial ovary matrix, we used a central composite design to investigate nine combinations of fibrinogen (mg/ml) and thrombin (IU/mL) (F/T): F1/T4, F12.5/T1, F12.5/T20, F25/T0.1, F25/T4, F25/T500, F50/T1, F50/T20 and F100/T4. From the first qualitative analyses (handling and matrix size), five combinations (F12.5/T1, F25/T4, F50/T20, F50/T1 and F100/T4) yielded positive results. They were further evaluated in order to assess fibrin matrix degradation and homogeneous cell encapsulation (density), survival and proliferation (Ki67), and atresia (TUNEL) before and after 7 days of in vitro culture. To determine the best compromise between maximizing the dynamic density (Y1) and minimizing the apoptosis rate (Y2), we used the desirability function approach. Two combinations (F12.5/T1 and F25/T4) showed greater distribution of cells before in vitro culture, reproducible degradation of the fibrin network and adequate support for isolated human ovarian stromal cells, with a high proportion of Ki67-positive cells. SEM analysis revealed a network of fibers with regular pores and healthy stromal cells after in vitro culture with both F/T combinations. This study reports two optimal F/T combinations that allow survival and proliferation of isolated human ovarian cells. Further studies are required to determine if such a scaffold will also be a suitable environment for isolated ovarian follicles.

Novel cross-linked alcohol-insoluble solid (CL-AIS) affinity gel from pea pod for pectinesterase purification.

PubMed

Wu, Ming-Chang; Lin, Guan-Hui; Wang, Yuh-Tai; Jiang, Chii-Ming; Chang, Hung-Min

2005-10-05

Alcohol-insoluble solids (AIS) from pea pod were cross-linked (CL-AIS) and used as an affinity gel matrix to isolate pectin esterases (PEs) from tendril shoots of chayote (TSC) and jelly fig achenes (JFA), and the results were compared with those isolated by ion-exchange chromatography with a commercial resin. CL-AIS gel matrix in a column displayed poor absorption and purification fold of PE; however, highly methoxylated CL-AIS (HM-CL-AIS), by exposing CL-AIS to methanolic sulfuric acid to increase the degree of esterification (DE) to 92%, facilitated the enzyme purification. The purified TSC PE and JFA PE by the HM-CL-AIS column were proofed as a single band on an SDS-PAGE gel, showing that the HM-CL-AIS column was a good matrix for purification of PE, either with alkaline isoelectric point (pI) (TSC PE) or with acidic pI (JFA PE).

Conformational changes in matrix-isolated 6-methoxyindole: Effects of the thermal and infrared light excitations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopes Jesus, A. J.; CQC, Faculty of Pharmacy, University of Coimbra, 3004-295 Coimbra; Reva, I., E-mail: reva@qui.uc.pt

2016-03-28

Conformational changes induced thermally or upon infrared excitation of matrix-isolated 6-methoxyindole were investigated. Narrowband near-infrared excitation of the first overtone of the N–H stretching vibration of each one of the two identified conformers is found to induce a selective large-scale conversion of the pumped conformer into the other one. This easily controllable bidirectional process consists in the intramolecular reorientation of the methoxy group and allowed a full assignment of the infrared spectra of the two conformers. Matrices with different conformational compositions prepared by narrow-band irradiations were subsequently used to investigate the effects of both thermal and broadband infrared excitations onmore » the conformational mixtures. Particular attention is given to the influence of the matrix medium (Ar vs. Xe) and conformational effects of exposition of the sample to the spectrometer light source during the measurements.« less

THE USE OF MATRIX-ASSISTED LASER DESORPTION/IONIZATION-MASS SPECTROMETRY FOR THE IDENTIFICATION OF AEROMONAS ISOLATES OBTAINED FROM WATER DISTRIBUTION SYSTEMS

EPA Science Inventory

Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) has long been established as a tool by which microorganisms can be characterized and identified. EPA is investigating the potential of using this technology as a way to rapidly identify Aeromonas species fo...

Relative Contribution of Matrix Structure, Patch Resources and Management to the Local Densities of Two Large Blue Butterfly Species

PubMed Central

Skórka, Piotr; Nowicki, Piotr; Bonk, Maciej; Król, Wiesław; Szpiłyk, Damian; Woyciechowski, Michal

2016-01-01

The type of matrix, the landscape surrounding habitat patches, may determine the distribution and function of local populations. However, the matrix is often heterogeneous, and its various components may differentially contribute to metapopulation processes at different spatial scales, a phenomenon that has rarely been investigated. The aim of this study was to estimate the relative importance of matrix composition and spatial scale, habitat quality, and management intensity on the occurrence and density of local populations of two endangered large blue butterflies: Phengaris teleius and P. nausithous. Presence and abundance data were assessed over two years, 2011–12, in 100 local patches within two heterogeneous regions (near Kraków and Tarnów, southern Poland). The matrix composition was analyzed at eight spatial scales. We observed high occupancy rates in both species, regions and years. With the exception of area and isolation, almost all of the matrix components contributed to Phengaris sp. densities. The different matrix components acted at different spatial scales (grassland cover within 4 and 3 km, field cover within 0.4 and 0.3 km and water cover within 4 km radii for P. teleius and P. nausithous, respectively) and provided the highest independent contribution to the butterfly densities. Additionally, the effects of a 0.4 km radius of forest cover and a food plant cover on P. teleius, and a 1 km radius of settlement cover and management intensity on P. nausithous densities were observed. Contrary to former studies we conclude that the matrix heterogeneity and spatial scale rather than general matrix type are of relevance for densities of butterflies. Conservation strategies for these umbrella species should concentrate on maintaining habitat quality and managing matrix composition at the most appropriate spatial scales. PMID:28005942

Relative Contribution of Matrix Structure, Patch Resources and Management to the Local Densities of Two Large Blue Butterfly Species.

PubMed

Kajzer-Bonk, Joanna; Skórka, Piotr; Nowicki, Piotr; Bonk, Maciej; Król, Wiesław; Szpiłyk, Damian; Woyciechowski, Michal

2016-01-01

The type of matrix, the landscape surrounding habitat patches, may determine the distribution and function of local populations. However, the matrix is often heterogeneous, and its various components may differentially contribute to metapopulation processes at different spatial scales, a phenomenon that has rarely been investigated. The aim of this study was to estimate the relative importance of matrix composition and spatial scale, habitat quality, and management intensity on the occurrence and density of local populations of two endangered large blue butterflies: Phengaris teleius and P. nausithous. Presence and abundance data were assessed over two years, 2011-12, in 100 local patches within two heterogeneous regions (near Kraków and Tarnów, southern Poland). The matrix composition was analyzed at eight spatial scales. We observed high occupancy rates in both species, regions and years. With the exception of area and isolation, almost all of the matrix components contributed to Phengaris sp. densities. The different matrix components acted at different spatial scales (grassland cover within 4 and 3 km, field cover within 0.4 and 0.3 km and water cover within 4 km radii for P. teleius and P. nausithous, respectively) and provided the highest independent contribution to the butterfly densities. Additionally, the effects of a 0.4 km radius of forest cover and a food plant cover on P. teleius, and a 1 km radius of settlement cover and management intensity on P. nausithous densities were observed. Contrary to former studies we conclude that the matrix heterogeneity and spatial scale rather than general matrix type are of relevance for densities of butterflies. Conservation strategies for these umbrella species should concentrate on maintaining habitat quality and managing matrix composition at the most appropriate spatial scales.

Preparation of on-plate immobilized metal ion affinity chromatography platform via dopamine chemistry for highly selective isolation of phosphopeptides with matrix assisted laser desorption/ionization mass spectrometry analysis.

PubMed

Shi, Chenyi; Lin, Qinrui; Deng, Chunhui

2015-04-01

In this study, a novel on-plate IMAC technique was developed for highly selective enrichment and isolation of phosphopeptides with high-throughput MALDI-TOF-MS analysis. At first, a MALDI plate was coated with polydopamine (PDA), and then Ti(4+) was immobilized on the PDA-coated plate. The obtained IMAC plate was successfully applied to the highly selective enrichment and isolation of phosphopeptides in protein digests and human serum. Because of no loss of samples, the on-plate IMAC platform exhibits excellent selectivity and sensitivity in the selective enrichment and isolation of phosphopeptides, which provides a potential technique for high selectivity in the detection of low-abundance phosphopeptides in biological samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Differential expression of neuroleukin in osseous tissues and its involvement in mineralization during osteoblast differentiation

NASA Technical Reports Server (NTRS)

Zhi, J.; Sommerfeldt, D. W.; Rubin, C. T.; Hadjiargyrou, M.

2001-01-01

Osteoblast differentiation is a multistep process that involves critical spatial and temporal regulation of cellular processes marked by the presence of a large number of differentially expressed molecules. To identify key functional molecules, we used differential messenger RNA (mRNA) display and compared RNA populations isolated from the defined transition phases (proliferation, matrix formation, and mineralization) of the MC3T3-E1 osteoblast-like cell line. Using this approach, a complementary DNA (cDNA) fragment was isolated and identified as neuroleukin (NLK), a multifunctional cytokine also known as autocrine motility factor (AMF), phosphoglucose isomerase (PGI; phosphohexose isomerase [PHI]), and maturation factor (MF). Northern analysis showed NLK temporal expression during MC3T3-E1 cell differentiation with a 3.5-fold increase during matrix formation and mineralization. Immunocytochemical studies revealed the presence of NLK in MC3T3-E1 cells as well as in the surrounding matrix, consistent with a secreted molecule. In contrast, the NLK receptor protein was detected primarily on the cell membrane. In subsequent studies, a high level of NLK expression was identified in osteoblasts and superficial articular chondrocytes in bone of 1-, 4-, and 8-month-old normal mice, as well as in fibroblasts, proliferating chondrocytes, and osteoblasts within a fracture callus. However, NLK was not evident in hypertrophic chondrocytes or osteocytes. In addition, treatment of MC3T3 cells with 6-phosphogluconic acid (6PGA; a NLK inhibitor) resulted in diminishing alkaline phosphatase (ALP) activity and mineralization in MC3T3-E1 cells, especially during the matrix formation stage of differentiating cells. Taken together, these data show specific expression of NLK in discrete populations of bone and cartilage cells and suggest a possible role for this secreted protein in bone development and regeneration.

Laser-induced emission spectroscopy of matrix-isolated carbon molecules: Experimental setup and new results on C3

NASA Astrophysics Data System (ADS)

Čermák, Ivo; Förderer, Markus; Čermáková, Iva; Kalhofer, Stefan; Stopka-Ebeler, Helmut; Monninger, Gerold; Krätschmer, Wolfgang

1998-06-01

We have studied small carbon molecules using a matrix-isolation technique. Our experimental setup is described in detail. The carbon clusters were produced by evaporating graphite and trapping the carbon-vapor molecules in solid argon, where molecular growth could be induced by controlled matrix annealing. To identify the produced molecules, absorption spectroscopy in the ultraviolet (UV)-visible and infrared (IR) spectral ranges was applied. Additional characterization of the excited and ground states of the molecules was obtained from emission and excitation spectra. The molecules were excited by a pulsed dye laser system and the emission spectra were recorded with a high-sensitivity photodiode-array spectrometer. We present our measurements on linear C3. The à 1Πu excited state of linear C3 was populated by the electronic transition à 1Πu←X˜ 1Σg+, and the corresponding excitation spectra of the C3 fluorescence (à 1Πu→X˜ 1Σg+) and phosphorescence (ã 3Πu→X˜ 1Σg+) were studied. Comparison of excitation and absorption spectra yielded information on site effects due to the matrix environment. Emission bands in the fluorescence and phosphorescence spectra up to vibrational energies of 8500 cm-1 could be observed. The radiation lifetime of the à 1Πu excited state of C3 in solid argon was found to be shorter than 10 ns. The phosphorescence transition ã 3Πu→X˜ 1Σg+ decays in about 10 ms and its rise indicates fast vibrational relaxation within the triplet system. Our data support a linear ground state geometry for C3 also in solid argon.

Tautomerism and infrared spectra of 2-thiopurine: an experimental matrix isolation and theoretical ab initio and density functional theory study

NASA Astrophysics Data System (ADS)

Stepanenko, Tetyana; Lapinski, Leszek; Nowak, Maciej J.; Kwiatkowski, Józef S.; Leszczynski, Jerzy

2001-02-01

Infrared spectra of 2-thiopurine (2-mercaptopurine, 2-purinethiol ) isolated in low-temperature Ar and N 2 matrixes are reported. These spectra indicate that the compound adopts exclusively the thiol N9H tautomeric form. The theoretical calculations of relative energies of 2-thiopurine tautomers have been carried out at the MP4(SDTQ)//HF level using the 6-31G( d, p) basis set. The thiol N9H tautomer was predicted to be the most stable of all isomers of 2-thiopurine. The infrared spectra of the tautomers of 2-thiopurine have been calculated at the DFT(B3LYP)/6-31G( d, p) level. Good agreement between the experimental spectra and the spectra calculated for thiol N9H tautomer supported the identification of the dominant tautomer. It has also allowed for the reliable assignment of the bands observed in the experimental IR spectrum.

Interstellar matrices: the chemical composition and evolution of interstellar ices as observed by ISO.

PubMed

d'Hendecourt, L; Dartois, E

2001-03-15

Matrix isolation techniques have been developed in the early sixties as a tool for studying the spectroscopic properties of out of equilibrium species (atoms, radicals, ions, reactive molecules), embedded in rare gas inert matrices at low temperatures. Cold interstellar grains surfaces are able to condense out gas phase molecules, routinely observed by radioastronomy. These grain 'mantles' can be considered as 'interstellar matrices'. However, these matrices are not clean and unreactive. They are made principally of dirty ices whose composition must be determined carefully to assess the importance of the solid state chemistry that takes place in the Interstellar Medium. Infrared spectroscopy, both in astronomy and in the laboratory, is the unique tool to determine the chemical composition of these ices. Astronomical spectra can directly be compared with laboratory ones obtained using classical matrix isolation techniques. Furthermore, dedicated experiments may be undertaken to further improve the understanding of the basic physico-chemical processes that take place in cosmic ices.

Effect of replacement of corn starch by whey protein isolate in biodegradable film blends obtained by extrusion.

PubMed

Azevedo, Viviane Machado; Borges, Soraia Vilela; Marconcini, José Manoel; Yoshida, Maria Irene; Neto, Alfredo Rodrigues Sena; Pereira, Tamara Coelho; Pereira, Camila Ferreira Gonçalves

2017-02-10

The aim of this study was to evaluate the effect of replacing corn starch by whey protein isolated (WPI) in biodegradable polymer blends developed by extrusion. X-ray diffraction showed the presence of a Vh-type crystalline arrangement. The films were homogeneous, indicating strong interfacial adhesion between the protein and the thermoplastic starch matrix (TPS) as observed in scanning electron microscopy. The addition of WPI on TPS matrix promoted an increase in the thermal stability of the materials. It was observed 58.5% decrease in the water vapor permeability. The effect of corn starch substitution by WPI on mechanical properties resulted in a more resistant and less flexible film when compared the TPS film. The addition of WPI caused greenish yellow color and less transparent films. The substitution of corn starch by WPI made it possible to obtain polymer blends with improved properties and represents an innovation for application as a packaging material. Copyright © 2016. Published by Elsevier Ltd.

On the behavior of isolated and embedded carbon nano-tubes in a polymeric matrix

NASA Astrophysics Data System (ADS)

Rahimian-Koloor, Seyed Mostafa; Moshrefzadeh-Sani, Hadi; Mehrdad Shokrieh, Mahmood; Majid Hashemianzadeh, Seyed

2018-02-01

In the classical micro-mechanical method, the moduli of the reinforcement and the matrix are used to predict the stiffness of composites. However, using the classical micro-mechanical method to predict the stiffness of CNT/epoxy nanocomposites leads to overestimated results. One of the main reasons for this overestimation is using the stiffness of the isolated CNT and ignoring the CNT nanoscale effect by the method. In the present study the non-equilibrium molecular dynamics simulation was used to consider the influence of CNT length on the stiffness of the nanocomposites through the isothermal-isobaric ensemble. The results indicated that, due to the nanoscale effects, the reinforcing efficiency of the embedded CNT is not constant and decreases with decreasing its length. Based on the results, a relationship was derived, which predicts the effective stiffness of an embedded CNT in terms of its length. It was shown that using this relationship leads to predict more accurate elastic modulus of nanocomposite, which was validated by some experimental counterparts.

Identification of Aeromonas isolates by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Lamy, Brigitte; Kodjo, Angeli; Laurent, Frédéric

2011-09-01

We evaluated the accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for identifying aeromonads with an extraction procedure. Genus-level accuracy was 100%. Compared to rpoB gene sequencing, species-level accuracy was 90.6% (29/32) for type and reference strains and 91.4% for a collection of 139 clinical and environmental isolates, making this system one of the most accurate and rapid methods for phenotypic identification. The reliability of this technique was very promising, although some improvements in database composition, taxonomy, and discriminatory power are needed. Copyright © 2011 Elsevier Inc. All rights reserved.

Research on bandgaps in two-dimensional phononic crystal with two resonators.

PubMed

Gao, Nansha; Wu, Jiu Hui; Yu, Lie

2015-02-01

In this paper, the bandgap properties of a two-dimensional phononic crystal with the two resonators is studied and embedded in a homogenous matrix. The resonators are not connected with the matrix but linked with connectors directly. The dispersion relationship, transmission spectra, and displacement fields of the eigenmodes of this phononic crystal are studied with finite-element method. In contrast to the phononic crystals with one resonators and hollow structure, the proposed structures with two resonators can open bandgaps at lower frequencies. This is a very interesting and useful phenomenon. Results show that, the opening of the bandgaps is because of the local resonance and the scattering interaction between two resonators and matrix. An equivalent spring-pendulum model can be developed in order to evaluate the frequencies of the bandgap edge. The study in this paper is beneficial to the design of opening and tuning bandgaps in phononic crystals and isolators in low-frequency range. Copyright © 2014 Elsevier B.V. All rights reserved.

Effects of lattice morphology upon reaction dynamics in matrix-isolated systems

NASA Astrophysics Data System (ADS)

Raff, Lionel M.

1992-11-01

The dynamics of the cis-d2-ethylene+F2 addition reaction and the subsequent reaction dynamics of the products isolated in vapor-deposited Ar matrices at 12 K are investigated using trajectory methods that incorporate nonstatistical sampling to enhance the reaction probabilities. The matrix-isolated cis-d2-ethylene+F2 system is generated using a combination of Monte Carlo, damped trajectory, and volume contraction methods. Transport effects of the bulk are simulated using the velocity reset procedure developed by Riley et al. [J. Chem. Phys. 88, 5934 (1988)]. The potential-energy hypersurface is the same as that employed in our previous investigations of the matrix-isolated, decomposition dynamics of 1,2-difluoroethane-d4 and the bimolecular cis-d2-ethylene+F2 system in face-centered-cubic (fcc) matrices [J. Chem. Phys. 93, 3160 (1990); 95, 8901 (1991)]. It is found that matrices generated by these methods are amorphous with numerous vacancies and other imperfections. On the average, there are approximately three vacancies about each lattice atom compared to the fcc crystal. The calculated lattice density is about 82% that for a bulk fcc Ar solid. Computed radial distribution functions resemble those expected for a liquid which exhibits some short-range order. The imperfections of the lattice remain even after substantial annealing at 50 K. The calculated energy relaxation rate to the lattice phonon modes in these amorphous matrices is about a factor of 4 less than that for a close-packed fcc lattice. The 1,2-difluoroethane product is formed primarily via an αβ-addition process, as is the case for fcc matrices. However, the prominence of this pathway is greatly reduced. The major process leading to a fluoroethylene elimination product in amorphous matrices involves an atomic addition mechanism. Such a reaction path accounts for 94% of the elimination reactions. The probability of internal rotation about the C■C double bond in the fluoroethylene product is increased fivefold over that for fcc lattices. The calculated stabilization/elimination product ratio, the cis/trans ratios of fluoroethylene products, and the HF/DF elimination ratio are all found to be in fair to good accord with the reported experimental data. It is concluded that accurate simulation of matrix-isolation experiments requires a matrix model that properly represents the lattice structure present in the experiments.

Method for the removal and recovery of mercury

DOEpatents

Easterly, Clay E.; Vass, Arpad A.; Tyndall, Richard L.

1997-01-01

The present invention is an enhanced method for the removal and recovery of mercury from mercury-contaminated matrices. The method involves contacting a mercury-contaminated matrix with an aqueous dispersant solution derived from specific intra-amoebic isolates to release the mercury from the mercury-contaminated matrix and emulsify the mercury; then, contacting the matrix with an amalgamating metal from a metal source to amalgamate the mercury to the amalgamating metal; removing the metallic source from the mercury-contaminated matrix; and heating the metallic source to vaporize the mercury in a closed system to capture the mercury vapors.

Method for the removal and recovery of mercury

DOEpatents

Easterly, C.E.; Vass, A.A.; Tyndall, R.L.

1997-01-28

The present invention is an enhanced method for the removal and recovery of mercury from mercury-contaminated matrices. The method involves contacting a mercury-contaminated matrix with an aqueous dispersant solution derived from specific intra-amoebic isolates to release the mercury from the mercury-contaminated matrix and emulsify the mercury; then, contacting the matrix with an amalgamating metal from a metal source to amalgamate the mercury to the amalgamating metal; removing the metallic source from the mercury-contaminated matrix; and heating the metallic source to vaporize the mercury in a closed system to capture the mercury vapors.

A low molecular weight serine protease: Purification and characterization from Hippasa agelenoides (funnel web) spider venom gland extract.

PubMed

Devaraja, S; Nagaraju, S; Mahadeswaraswamy, Y H; Girish, K S; Kemparaju, K

2008-07-01

Despite the long history [Kaiser, E., 1956. Enzymatic activity of spider venoms. In: Buckley, E.E., Porges, N. (Eds.), Venoms. American Association for the Advancement of Science, Washington, DC, pp. 91-93] on proteolytic activity, no study so far claims the isolation of a serine protease from the spider venom/venom gland extract. Therefore, the present study describes the isolation and characterization of a low molecular weight serine protease from Hippasa agelenoides venom gland extract. The protease (Hag-protease) was purified to homogeneity using the combination of gel-permeation and ion-exchange chromatography. The molecular mass was found to be 16.350 kDa by matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry. Hag-protease was optimally active at pH 7.5 and temperature of 37 degrees C. PMSF abolished the enzyme activity while EDTA, EGTA, IAA, 1, 10-phenanthrolene did not. It hydrolyzed proteins such as casein, fibronectin and collagen type-I dose dependently but did not degrade gelatin and collagen type-IV. The isolated protease was non-lethal and devoid of hemorrhagic, myotoxic and edema forming activities. The light microscopy of Hag-protease treated skin tissue sections at the site of injection showed extensive damage of extracellular matrix (ECM) of hypodermis without causing any damage to blood vessels and capillaries. Similar damage of ECM of muscle tissue sections without affecting myocytes was noticed. Hag-protease was found to be procoagulant in property when studied plasma recalcification time.

In vitro and in vivo approaches to study osteocyte biology.

PubMed

Kalajzic, Ivo; Matthews, Brya G; Torreggiani, Elena; Harris, Marie A; Divieti Pajevic, Paola; Harris, Stephen E

2013-06-01

Osteocytes, the most abundant cell population of the bone lineage, have been a major focus in the bone research field in recent years. This population of cells that resides within mineralized matrix is now thought to be the mechanosensory cell in bone and plays major roles in the regulation of bone formation and resorption. Studies of osteocytes had been impaired by their location, resulting in numerous attempts to isolate primary osteocytes and to generate cell lines representative of the osteocytic phenotype. Progress has been achieved in recent years by utilizing in vivo genetic technology and generation of osteocyte directed transgenic and gene deficiency mouse models. We will provide an overview of the current in vitro and in vivo models utilized to study osteocyte biology. We discuss generation of osteocyte-like cell lines and isolation of primary osteocytes and summarize studies that have utilized these cellular models to understand the functional role of osteocytes. Approaches that attempt to selectively identify and isolate osteocytes using fluorescent protein reporters driven by regulatory elements of genes that are highly expressed in osteocytes will be discussed. In addition, recent in vivo studies utilizing overexpression or conditional deletion of various genes using dentin matrix protein (Dmp1) directed Cre recombinase are outlined. In conclusion, evaluation of the benefits and deficiencies of currently used cell lines/genetic models in understanding osteocyte biology underlines the current progress in this field. The future efforts will be directed towards developing novel in vitro and in vivo models that would additionally facilitate in understanding the multiple roles of osteocytes. Copyright © 2012 Elsevier Inc. All rights reserved.

Comparison of dechlorination rates for field DNAPL vs synthetic samples: effect of sample matrix

NASA Astrophysics Data System (ADS)

O'Carroll, D. M.; Sakulchaicharoen, N.; Herrera, J. E.

2015-12-01

Nanometals have received significant attention in recent years due to their ability to rapidly destroy numerous priority source zone contaminants in controlled laboratory studies. This has led to great optimism surrounding nanometal particle injection for insitu remediation. Reported dechlorination rates vary widely among different investigators. These differences have been ascribed to differences in the iron types (granular, micro, or nano-sized iron), matrix solution chemistry and the morphology of the nZVI surface. Among these, the effects of solution chemistry on rates of reductive dechlorination of various chlorinated compounds have been investigated in several short-term laboratory studies. Variables investigated include the effect of anions or groundwater solutes such as SO4-2, Cl-, NO3-, pH, natural organic matters (NOM), surfactant, and humic acid on dechlorination reaction of various chlorinated compounds such as TCE, carbon tetrachloride (CT), and chloroform (CF). These studies have normally centered on the assessment of nZVI reactivity toward dechlorination of an isolated individual contaminant spiked into a ground water sample under ideal conditions, with limited work conducted using real field samples. In this work, the DNAPL used for the dechlorination study was obtained from a contaminatied site. This approach was selected to adequately simulate a condition where the nZVI suspension was in direct contact with DNAPL and to isolate the dechlorination activity shown by the nZVI from the groundwater matrix effects. An ideal system "synthetic DNAPL" composed of a mixture of chlorinated compounds mimicking the composition of the actual DNAPL was also dechlorinated to evaluate the DNAPL "matrix effect" on NZVI dechlorination activity. This approach allowed us to evaluate the effect of the presence of different types of organic compounds (volatile fatty acids and humic acids) found in the actual DNAPL on nZVI dechlorination activity. This presentation will help provide insights into the degradation kinetics that can be expected in the field and help with field scale implementation of nZVI.

In vitro studies on human periodontal ligament stem cell sheets enhanced by enamel matrix derivative.

PubMed

Wang, Zhongshan; Feng, Zhihong; Wu, Guofeng; Bai, Shizhu; Dong, Yan; Zhao, Yimin

2016-05-01

Numerous preclinical and clinical studies have focused on the periodontal regenerative functions of enamel matrix derivative (EMD), a heat-treated preparation derived from enamel matrix proteins (EMPs) of developing porcine teeth. In this study, periodontal ligament (PDL) stem cells (PDLSCs) were isolated, and the effects of EMD on the extracorporeal induction process and the characteristics of PDLSC sheets were investigated for their potential as a more effective stem-cell therapy. EMD-enhanced cell sheets could be induced by complete medium supplemented with 50 μg/mL vitamin C and 100 μg/mL EMD. The EMD-enhanced cell sheets appeared thicker and more compact than the normal PDLSC sheets, demonstrated more layers of cells (3-7 layers), secreted richer extracellular matrix (ECM), showed varying degrees of increases in mRNA expression of periodontal tissue-specific genes (COL I, POSTN), calcification-related genes (RUNX2, OPN, OCN) and a cementum tissue-specific gene (CAP), and possessed a better mineralization ability in terms of osteogenic differentiation in vitro. These EMD-enhanced cell sheets may represent a potential option for stem-cell therapy for PDL regeneration. Copyright © 2016 Elsevier B.V. All rights reserved.

FACS-based Isolation of Neural and Glioma Stem Cell Populations from Fresh Human Tissues Utilizing EGF Ligand

PubMed Central

Tome-Garcia, Jessica; Doetsch, Fiona; Tsankova, Nadejda M.

2018-01-01

Direct isolation of human neural and glioma stem cells from fresh tissues permits their biological study without prior culture and may capture novel aspects of their molecular phenotype in their native state. Recently, we demonstrated the ability to prospectively isolate stem cell populations from fresh human germinal matrix and glioblastoma samples, exploiting the ability of cells to bind the Epidermal Growth Factor (EGF) ligand in fluorescence-activated cell sorting (FACS). We demonstrated that FACS-isolated EGF-bound neural and glioblastoma populations encompass the sphere-forming colonies in vitro, and are capable of both self-renewal and multilineage differentiation. Here we describe in detail the purification methodology of EGF-bound (i.e., EGFR+) human neural and glioma cells with stem cell properties from fresh postmortem and surgical tissues. The ability to prospectively isolate stem cell populations using native ligand-binding ability opens new doors for understanding both normal and tumor cell biology in uncultured conditions, and is applicable for various downstream molecular sequencing studies at both population and single-cell resolution. PMID:29516026

Evaluation of the Andromas Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Aerobically Growing Gram-Positive Bacilli

PubMed Central

Farfour, E.; Leto, J.; Barritault, M.; Barberis, C.; Meyer, J.; Dauphin, B.; Le Guern, A.-S.; Leflèche, A.; Badell, E.; Guiso, N.; Leclercq, A.; Le Monnier, A.; Lecuit, M.; Rodriguez-Nava, V.; Bergeron, E.; Raymond, J.; Vimont, S.; Bille, E.; Carbonnelle, E.; Guet-Revillet, H.; Lécuyer, H.; Beretti, J.-L.; Vay, C.; Berche, P.; Ferroni, A.; Nassif, X.

2012-01-01

Matrix-associated laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a rapid and simple microbial identification method. Previous reports using the Biotyper system suggested that this technique requires a preliminary extraction step to identify Gram-positive rods (GPRs), a technical issue that may limit the routine use of this technique to identify pathogenic GPRs in the clinical setting. We tested the accuracy of the MALDI-TOF MS Andromas strategy to identify a set of 659 GPR isolates representing 16 bacterial genera and 72 species by the direct colony method. This bacterial collection included 40 C. diphtheriae, 13 C. pseudotuberculosis, 19 C. ulcerans, and 270 other Corynebacterium isolates, 32 L. monocytogenes and 24 other Listeria isolates, 46 Nocardia, 75 Actinomyces, 18 Actinobaculum, 11 Propionibacterium acnes, 18 Propionibacterium avidum, 30 Lactobacillus, 21 Bacillus, 2 Rhodococcus equi, 2 Erysipelothrix rhusiopathiae, and 38 other GPR isolates, all identified by reference techniques. Totals of 98.5% and 1.2% of non-Listeria GPR isolates were identified to the species or genus level, respectively. Except for L. grayi isolates that were identified to the species level, all other Listeria isolates were identified to the genus level because of highly similar spectra. These data demonstrate that rapid identification of pathogenic GPRs can be obtained without an extraction step by MALDI-TOF mass spectrometry. PMID:22692743

Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level.

PubMed

Cherkaoui, Abdessalam; Hibbs, Jonathan; Emonet, Stéphane; Tangomo, Manuela; Girard, Myriam; Francois, Patrice; Schrenzel, Jacques

2010-04-01

Bacterial identification relies primarily on culture-based methodologies requiring 24 h for isolation and an additional 24 to 48 h for species identification. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is an emerging technology newly applied to the problem of bacterial species identification. We evaluated two MALDI-TOF MS systems with 720 consecutively isolated bacterial colonies under routine clinical laboratory conditions. Isolates were analyzed in parallel on both devices, using the manufacturers' default recommendations. We compared MS with conventional biochemical test system identifications. Discordant results were resolved with "gold standard" 16S rRNA gene sequencing. The first MS system (Bruker) gave high-confidence identifications for 680 isolates, of which 674 (99.1%) were correct; the second MS system (Shimadzu) gave high-confidence identifications for 639 isolates, of which 635 (99.4%) were correct. Had MS been used for initial testing and biochemical identification used only in the absence of high-confidence MS identifications, the laboratory would have saved approximately US$5 per isolate in marginal costs and reduced average turnaround time by more than an 8-h shift, with no loss in accuracy. Our data suggest that implementation of MS as a first test strategy for one-step species identification would improve timeliness and reduce isolate identification costs in clinical bacteriology laboratories now.

Complex formation of blueberry (Vaccinium angustifolium) anthocyanins during freeze-drying and its influence on their biological activity.

PubMed

Correa-Betanzo, Julieta; Padmanabhan, Priya; Corredig, Milena; Subramanian, Jayasankar; Paliyath, Gopinadhan

2015-03-25

Biological activity of polyphenols is influenced by their uptake and is highly influenced by their interactions with the food matrix. This study evaluated the complex formation of blueberry polyphenols with fruit matrixes such as pectin and cellulose and their effect on the biological and antiproliferative properties of human colon cell lines HT-29 and CRL 1790. Free or complexed polyphenols were isolated by dialyzing aqueous or methanolic blueberry homogenates. Seven phenolic compounds and thirteen anthocyanins were identified in blueberry extracts. Blueberry extracts showed varying degrees of antioxidant and antiproliferative activities, as well as α-glucosidase activity. Fruit matrix containing cellulose and pectin, or purified polygalacturonic acid and cellulose, did not retain polyphenols and showed very low antioxidant or antiproliferative activities. These findings suggest that interactions between polyphenols and the food matrix may be more complex than a simple association and may play an important role in the bioefficacy of blueberry polyphenols.

Multicenter Study Evaluating the Vitek MS System for Identification of Medically Important Yeasts

PubMed Central

Westblade, Lars F.; Jennemann, Rebecca; Branda, John A.; Bythrow, Maureen; Ferraro, Mary Jane; Garner, Omai B.; Ginocchio, Christine C.; Lewinski, Michael A.; Manji, Ryhana; Mochon, A. Brian; Procop, Gary W.; Richter, Sandra S.; Rychert, Jenna A.; Sercia, Linda

2013-01-01

The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates, including 58 C. albicans, 62 C. glabrata, and 53 C. krusei isolates), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n = 58) identified as Candida dubliniensis, one isolate of Candida parapsilosis (n = 73) identified as Candida pelliculosa, and three isolates of Geotrichum klebahnii (n = 6) identified as Geotrichum candidum. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories. PMID:23658267

Full-Genome Sequence of a Reassortant H1N2 Influenza A Virus Isolated from Pigs in Brazil.

PubMed

Schmidt, Candice; Cibulski, Samuel Paulo; Muterle Varela, Ana Paula; Mengue Scheffer, Camila; Wendlant, Adrieli; Quoos Mayer, Fabiana; Lopes de Almeida, Laura; Franco, Ana Cláudia; Roehe, Paulo Michel

2014-12-18

In this study, the full-genome sequence of a reassortant H1N2 swine influenza virus is reported. The isolate has the hemagglutinin (HA) and neuraminidase (NA) genes from human lineage (H1-δ cluster and N2), and the internal genes (polymerase basic 1 [PB1], polymerase basic 2 [PB2], polymerase acidic [PA], nucleoprotein [NP], matrix [M], and nonstructural [NS]) are derived from human 2009 pandemic H1N1 (H1N1pdm09) virus. Copyright © 2014 Schmidt et al.

Rapid Identification of Bacteria in Positive Blood Culture Broths by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry▿

PubMed Central

Stevenson, Lindsay G.; Drake, Steven K.; Murray, Patrick R.

2010-01-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid, accurate method for identifying bacteria and fungi recovered on agar culture media. We report herein a method for the direct identification of bacteria in positive blood culture broths by MALDI-TOF mass spectrometry. A total of 212 positive cultures were examined, representing 32 genera and 60 species or groups. The identification of bacterial isolates by MALDI-TOF mass spectrometry was compared with biochemical testing, and discrepancies were resolved by gene sequencing. No identification (spectral score of <1.7) was obtained for 42 (19.8%) of the isolates, due most commonly to insufficient numbers of bacteria in the blood culture broth. Of the bacteria with a spectral score of ≥1.7, 162 (95.3%) of 170 isolates were correctly identified. All 8 isolates of Streptococcus mitis were misidentified as being Streptococcus pneumoniae isolates. This method provides a rapid, accurate, definitive identification of bacteria within 1 h of detection in positive blood cultures with the caveat that the identification of S. pneumoniae would have to be confirmed by an alternative test. PMID:19955282

Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Stevenson, Lindsay G; Drake, Steven K; Murray, Patrick R

2010-02-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid, accurate method for identifying bacteria and fungi recovered on agar culture media. We report herein a method for the direct identification of bacteria in positive blood culture broths by MALDI-TOF mass spectrometry. A total of 212 positive cultures were examined, representing 32 genera and 60 species or groups. The identification of bacterial isolates by MALDI-TOF mass spectrometry was compared with biochemical testing, and discrepancies were resolved by gene sequencing. No identification (spectral score of < 1.7) was obtained for 42 (19.8%) of the isolates, due most commonly to insufficient numbers of bacteria in the blood culture broth. Of the bacteria with a spectral score of > or = 1.7, 162 (95.3%) of 170 isolates were correctly identified. All 8 isolates of Streptococcus mitis were misidentified as being Streptococcus pneumoniae isolates. This method provides a rapid, accurate, definitive identification of bacteria within 1 h of detection in positive blood cultures with the caveat that the identification of S. pneumoniae would have to be confirmed by an alternative test.

The controversial nuclear matrix: a balanced point of view.

PubMed

Martelli, A M; Falcieri, E; Zweyer, M; Bortul, R; Tabellini, G; Cappellini, A; Cocco, L; Manzoli, L

2002-10-01

The nuclear matrix is defined as the residual framework after the removal of the nuclear envelope, chromatin, and soluble components by sequential extractions. According to several investigators the nuclear matrix provides the structural basis for intranuclear order. However, the existence itself and the nature of this structure is still uncertain. Although the techniques used for the visualization of the nuclear matrix have improved over the years, it is still unclear to what extent the isolated nuclear matrix corresponds to an in vivo existing structure. Therefore, considerable skepticism continues to surround the nuclear matrix fraction as an accurate representation of the situation in living cells. Here, we summarize the experimental evidence in favor of, or against, the presence of a diffuse nucleoskeleton as a facilitating organizational nonchromatin structure of the nucleus.

Microbial specificity of metallic surfaces exposed to ambient seawater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaidi, B.R.; Bard, R.F.; Tosteson, T.R.

1984-09-01

High-molecular-weight materials associated with the extracellular matrix and film found on titanium and aluminum surfaces after exposure to flowing coastal seawater were isolated. This material was purified by hydroxylapatite chromatography and subsequently employed to produce antibodies in the toad, Bufo marinus. The antibodies were immobilized on a solid support and employed to isolate adhesion-enhancing, high-molecular-weight materials from the laboratory culture media of bacterial strains recovered from the respective metallic surfaces during the course of their exposure to seawater. The adhesion-enhancing materials produced by the surface-associated bacterial strains were immunologically related to the extracellular biofouling matrix material found on the surfacesmore » from which these bacteria were isolated. The surface selectivity of these bacterial strains appeared to be based on the specificity of the interaction between adhesion-enhancing macromolecules produced by these bacteria and the surfaces in question. 30 references, 6 tables.« less

Rhetoric and the Social Matrix: Reflections from the Asian Classics.

ERIC Educational Resources Information Center

Oliver, Robert T.

As humanity seeks a new social matrix which is suited to the global conditions that have ended the isolation of communities, we must learn to understand the various rhetorics of different cultures. This paper explores at length some of the richness of rhetorical theory within the classics of the East, including the "Upanishads," and in the ideas…

Characterization of Streptococcus pneumoniae isolates from Austrian companion animals and horses.

PubMed

Ginders, Maximilian; Leschnik, Michael; Künzel, Frank; Kampner, Doris; Mikula, Claudia; Steindl, Georg; Eichhorn, Inga; Feßler, Andrea T; Schwarz, Stefan; Spergser, Joachim; Loncaric, Igor

2017-11-14

The aim of the present study was to investigate the genetic relatedness and the antimicrobial resistance profiles of a collection of Austrian Streptococcus pneumoniae isolates from companion animals and horses. A total of 12 non-repetitive isolates presumptively identified as S. pneumoniae were obtained during routinely diagnostic activities between March 2009 and January 2017. Isolates were confirmed as S. pneumoniae by bile solubility and optochin susceptibility testing, matrix-assisted laser desorption-ionization-time of flight (MALDI-TOF) mass spectrometry and sequence analysis of a part recA and the 16S rRNA genes. Isolates were further characterized by pneumolysin polymerase chain reaction (PCR) and genotyped by multilocus sequence typing (MLST). Antimicrobial susceptibility testing was performed and resistance genes were detected by specific PCR assays. All isolates were serotyped. Four sequence types (ST) (ST36, ST3546, ST6934 and ST6937) and four serotypes (3, 19A, 19F and 23F) were detected. Two isolates from twelve displayed a multidrug-resistance pheno- and genotype. This study represents the first comprehensive investigation on characteristics of S. pneumoniae isolates recovered from Austrian companion animals and horses. The obtained results indicate that common human sero- (23F) and sequence type (ST36) implicated in causing invasive pneumococcal disease (IPD) may circulate in dogs. Isolates obtained from other examined animals seem to be host-adapted.

Characterization of Staphylococcus aureus Isolated from Food Products in Western Algeria.

PubMed

Chaalal, Wafaa; Chaalal, Nadia; Bourafa, Nadjette; Kihal, Mebrouk; Diene, Seydina M; Rolain, Jean-Marc

2018-03-15

The current study aimed to characterize Staphylococcus aureus isolates from foodstuffs collected from western Algeria. A total of 153 S. aureus isolates from various raw and processed foods were obtained and identified using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. Isolates were characterized by antimicrobial susceptibility testing and toxin gene detection. Methicillin-resistant Staphylococcus aureus (MRSA) isolates were identified by detection of the mecA gene and characterized by staphylococcal cassette chromosome mec (SCCmec) typing. We found that 30.9% (153/495) of food samples were contaminated with S. aureus. Thirty-three (21.5%) S. aureus isolates were identified as MRSA, and 16.9% (26/153) carried the mecA gene. Three SCCmec types were identified of which type IV was the most common (69.2%) followed by type V (15.3%) and type II (7.6%). Two MRSA isolates were not typable with SCCmec typing. None of the examined isolates harbored mecC. Furthermore, 14.3% (22/153) of the isolates were toxigenic S. aureus. The cytotoxin gene pvl was detected in 11.1% of the S. aureus isolates. This gene was more commonly detected (76.4%) in MRSA isolates than in methicillin-suceptible Staphylococcus aureus (MSSA) isolates. The tsst-1 gene coding for toxic shock syndrome toxin was isolated rarely (3.2%) and only in MSSA isolates. According to disk diffusion test results, 70 isolates were resistant to only one antimicrobial drug, and 51 (33.3%) isolates were multidrug resistant. Other 32 isolates were susceptible to all antibiotics. Our study highlights, for the first time, a high prevalence of multidrug-resistant S. aureus isolates carrying pvl or tsst-1 found in food products in Algeria. The risk of MRSA transmission through the food chain cannot be disregarded, particularly in uncooked foods.

Requirement of vitamin C for cartilage calcification in a differentiating chick limb-bud mesenchymal cell culture.

PubMed

Boskey, A L; Stiner, D; Doty, S B; Binderman, I

1991-01-01

Mesenchymal cells isolated from stage 21-24 chick limb-buds plated in a micro-mass culture differentiate to form chondrocytes and synthesize a calcifiable matrix. In the presence of inorganic phosphate (4 mM), hydroxyapatite mineral deposits around cartilage nodules. Ascorbic acid is, in general, an essential co-factor for extracellular matrix synthesis in culture, since it is required for collagen synthesis. In this study we demonstrate that in the absence of ascorbic acid supplementation in the mesenchymal cell cultures, mineral deposition (indicated by X-ray diffraction, measurement of Ca:hydroxyproline ratio, and 45Ca uptake) does not occur. Concentrations of 10-50 micrograms/ml ascorbate were compared to find the "optimal" concentration for cell mediated mineralization; 25 micrograms/ml was selected as optimal based on matrix appearance at the EM level and the rate of 45Ca uptake. High concentrations of ascorbic acid (greater than 75 micrograms/ml), while increasing the amount of hydroxyproline in the matrix synthesized, caused some cell death and hence less cell-mediated mineralization. This study demonstrates both the need for viable cells and a proper matrix for in vitro cell-mediated mineralization, and shows that varying the concentration of L-ascorbate (vitamin C) in the medium can have a marked effect on mineralization in vitro.

Isolation and characterization of aerobic anoxygenic phototrophs from exposed soils from the Sør Rondane Mountains, East Antarctica.

PubMed

Tahon, Guillaume; Willems, Anne

2017-09-01

This study investigated the culturable aerobic phototrophic bacteria present in soil samples collected in the proximity of the Belgian Princess Elisabeth Station in the Sør Rondane Mountains, East Antarctica. Until recently, only oxygenic phototrophic bacteria (Cyanobacteria) were well known from Antarctic soils. However, more recent non-cultivation-based studies have demonstrated the presence of anoxygenic phototrophs and, particularly, aerobic anoxygenic phototrophic bacteria in these areas. Approximately 1000 isolates obtained after prolonged incubation under different growth conditions were studied and characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Representative strains were identified by sequence analysis of 16S rRNA genes. More than half of the isolates grouped among known aerobic anoxygenic phototrophic taxa, particularly with Sphingomonadaceae, Methylobacterium and Brevundimonas. In addition, a total of 330 isolates were tested for the presence of key phototrophy genes. While rhodopsin genes were not detected, multiple isolates possessed key genes of the bacteriochlorophyll synthesis pathway. The majority of these potential aerobic anoxygenic phototrophic strains grouped with Alphaproteobacteria (Sphingomonas, Methylobacterium, Brevundimonas and Polymorphobacter). Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

Antifungal Susceptibility Testing of Aspergillus spp. by Using a Composite Correlation Index (CCI)-Based Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Method Appears To Not Offer Benefit over Traditional Broth Microdilution Testing

PubMed Central

Gitman, Melissa R.; McTaggart, Lisa; Spinato, Joanna; Poopalarajah, Rahgavi; Lister, Erin; Husain, Shahid

2017-01-01

ABSTRACT Aspergillus spp. cause serious invasive lung infections, and Aspergillus fumigatus is the most commonly encountered clinically significant species. Voriconazole is considered to be the drug of choice for treating A. fumigatus infections; however, rising resistance rates have been reported. We evaluated a matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based method for the differentiation between wild-type and non-wild-type isolates of 20 Aspergillus spp. (including 2 isolates of Aspergillus ustus and 1 of Aspergillus calidoustus that were used as controls due their intrinsic low azole susceptibility with respect to the in vitro response to voriconazole). At 30 and 48 h of incubation, there was complete agreement between Cyp51A sequence analysis, broth microdilution, and MALDI-TOF MS classification of isolates as wild type or non-wild type. In this proof-of-concept study, we demonstrated that MALDI-TOF MS can be used to accurately detect A. fumigatus strains with reduced voriconazole susceptibility. However, rather than proving to be a rapid and simple method for antifungal susceptibility testing, this particular MS-based method showed no benefit over conventional testing methods. PMID:28404678

Antifungal Susceptibility Testing of Aspergillus spp. by Using a Composite Correlation Index (CCI)-Based Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Method Appears To Not Offer Benefit over Traditional Broth Microdilution Testing.

PubMed

Gitman, Melissa R; McTaggart, Lisa; Spinato, Joanna; Poopalarajah, Rahgavi; Lister, Erin; Husain, Shahid; Kus, Julianne V

2017-07-01

Aspergillus spp. cause serious invasive lung infections, and Aspergillus fumigatus is the most commonly encountered clinically significant species. Voriconazole is considered to be the drug of choice for treating A. fumigatus infections; however, rising resistance rates have been reported. We evaluated a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based method for the differentiation between wild-type and non-wild-type isolates of 20 Aspergillus spp. (including 2 isolates of Aspergillus ustus and 1 of Aspergillus calidoustus that were used as controls due their intrinsic low azole susceptibility with respect to the in vitro response to voriconazole). At 30 and 48 h of incubation, there was complete agreement between Cyp51A sequence analysis, broth microdilution, and MALDI-TOF MS classification of isolates as wild type or non-wild type. In this proof-of-concept study, we demonstrated that MALDI-TOF MS can be used to accurately detect A. fumigatus strains with reduced voriconazole susceptibility. However, rather than proving to be a rapid and simple method for antifungal susceptibility testing, this particular MS-based method showed no benefit over conventional testing methods. © Crown copyright 2017.

Poly-γ-Glutamic Acids Contribute to Biofilm Formation and Plant Root Colonization in Selected Environmental Isolates of Bacillus subtilis

PubMed Central

Yu, Yiyang; Yan, Fang; Chen, Yun; Jin, Christopher; Guo, Jian-Hua; Chai, Yunrong

2016-01-01

Bacillus subtilis is long known to produce poly-γ-glutamic acids (γ-PGA) as one of the major secreted polymeric substances. In B. subtilis, the regulation of γ-PGA production and its physiological role are still unclear. B. subtilis is also capable of forming structurally complex multicellular communities, or biofilms, in which an extracellular matrix consisting of secreted proteins and polysaccharides holds individual cells together. Biofilms were shown to facilitate B. subtilis–plant interactions. In this study, we show that different environmental isolates of B. subtilis, all capable of forming biofilms, vary significantly in γ-PGA production. This is possibly due to differential regulation of γ-PGA biosynthesis genes. In many of those environmental isolates, γ-PGA seems to contribute to robustness and complex morphology of the colony biofilms, suggesting a role of γ-PGA in biofilm formation. Our evidence further shows that in selected B. subtilis strains, γ-PGA also plays a role in root colonization by the bacteria, pinpointing a possible function of γ-PGA in B. subtilis–plant interactions. Finally, we found that several pathways co-regulate both γ-PGA biosynthesis genes and genes for the biofilm matrix in B. subtilis, but in an opposing fashion. We discussed potential biological significance of that. PMID:27891125

Consistent force field modeling of matrix isolated molecules. V. Minimum energy path potential to the conformer conversion of 1,2-difluoroethane: Ar 364, ab initio calculation of electric multipole moments and electric polarization contribution to the conversion barrier

NASA Astrophysics Data System (ADS)

Gunde, R.; Ha, T.-K.; Günthard, H. H.

1990-08-01

In this paper results of consistent force field modeling (CFF) of the potential function to conversion of the gauche (g) to the trans (t) conformer of 1,2-difluoroethane (DFE) isolated in an argon matrix will be reported. Starting point are locally stable configurations gDFE:Ar 364 (defect GH1) and tDFE:Ar 364 (TH1) obtained in previous work from CFF modeling of a cube shaped Ar 364 fragment containing one DFE molecule in its center. Using the dihedral angle of DFE as an independent parameter the minimum energy path of the conversion process gDFE:Ar 364→tDFE:Ar 364 will be determined by CFF energy minimization. Determination of the minimum energy path is found to require large numbers of energy minimization steps and to lead to a rather complicated motion of the molecule with respect to the crystal fragment. Surprisingly the molecule-matrix interactions lead to a reduction of the g-t barrier by ≈500 cal/mol and to a stabilization of the trans species by ≈500 cal/mol. This finding is a consequence of a delicate interplay of matrix-molecule and matrix-matrix interactions. Calculation of the electric polarization energy (induced dipole-first-order polarization approximation) is based on extended ab initio calculations of dipole and quadrupole moments and a bond polarizability estimate of the first-order polarizability of DFE as a function of the internal rotation angle, on Fourier expansion of multipole components and use of symmetry for reduction of the order of the linear system defining the (self-consistent) induced dipole moments of all Ar atoms. Electric polarization is found to alter the potential function of the conversion process in a profound way: the g-t barrier and the t-g energy difference are increased to ≈3000 cal/mol and to ≈1500 cal/mol respectively (≈2500 and ≈530 cal/mol respectively for free DFE). Further applications of the technique developed in this work to related problems of matrix isolated molecules, e.g., vibrational matrix shifts will be discussed.

Atomic force microscopy based nanoindentation study of onion abaxial epidermis walls in aqueous environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xi, Xiaoning; Tittmann, Bernhard; Kim, Seong H.

An atomic force microscopy based nanoindentation method was employed to study how the structure of cellulose microfibril packing and matrix polymers affect elastic modulus of fully hydrated primary plant cell walls. The isolated, single-layered abaxial epidermis cell wall of an onion bulb was used as a test system since the cellulose microfibril packing in this cell wall is known to vary systematically from inside to outside scales and the most abundant matrix polymer, pectin, can easily be altered through simple chemical treatments such as ethylenediaminetetraacetic acid and calcium ions. Experimental results showed that the pectin network variation has significant impactsmore » on the cell wall modulus, and not the cellulose microfibril packing.« less

Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Aspergillus Species Directly from Growth on Solid Agar Media

PubMed Central

Li, Ying; Wang, He; Zhao, Yu-Pei; Xu, Ying-Chun; Hsueh, Po-Ren

2017-01-01

We evaluated the accuracy of the Bruker Biotyper matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) system at identifying clinical isolates of Aspergillus species that were grown on agar media. A total of 381 non-duplicate Aspergillus isolates representing 21 different Aspergillus species identified by molecular analysis were included in this study. The Bruker Biotyper MALDI-TOF MS system was able to identify 30.2% (115/381) of the isolates to the species level (score values of ≥2.000) and 49.3% to the genus level (score values of 1.700–1.999). When the identification cutoff value was lowered from ≥2.000 to ≥1.700, the species-level identification rate increased to 79.5% with a slight rise of false identification from 2.6 to 5.0%. From another aspect, a correct species-level identification rate of 89% could be reached by the Bruker Biotyper MALDI-TOF MS system regardless of the score values obtained. The Bruker Biotyper MALDI-TOF MS system had a moderate performance in identification of Aspergillus directly inoculated on solid agar media. Continued expansion of the Bruker Biotyper MALDI-TOF MS database and adoption of alternative cutoff values for interpretation are required to improve the performance of the system for identifying highly diverse species of clinically encountered Aspergillus isolates. PMID:28706514

Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Aspergillus Species Directly from Growth on Solid Agar Media.

PubMed

Li, Ying; Wang, He; Zhao, Yu-Pei; Xu, Ying-Chun; Hsueh, Po-Ren

2017-01-01

We evaluated the accuracy of the Bruker Biotyper matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) system at identifying clinical isolates of Aspergillus species that were grown on agar media. A total of 381 non-duplicate Aspergillus isolates representing 21 different Aspergillus species identified by molecular analysis were included in this study. The Bruker Biotyper MALDI-TOF MS system was able to identify 30.2% (115/381) of the isolates to the species level (score values of ≥2.000) and 49.3% to the genus level (score values of 1.700-1.999). When the identification cutoff value was lowered from ≥2.000 to ≥1.700, the species-level identification rate increased to 79.5% with a slight rise of false identification from 2.6 to 5.0%. From another aspect, a correct species-level identification rate of 89% could be reached by the Bruker Biotyper MALDI-TOF MS system regardless of the score values obtained. The Bruker Biotyper MALDI-TOF MS system had a moderate performance in identification of Aspergillus directly inoculated on solid agar media. Continued expansion of the Bruker Biotyper MALDI-TOF MS database and adoption of alternative cutoff values for interpretation are required to improve the performance of the system for identifying highly diverse species of clinically encountered Aspergillus isolates.

Study on biofilm-forming properties of clinical isolates of Staphylococcus aureus.

PubMed

Taj, Yasmeen; Essa, Farhan; Aziz, Faisal; Kazmi, Shahana Urooj

2012-05-14

The purpose of this study was to observe the formation of biofilm, an important virulence factor, by isolates of Staphylococcus aureus (S. aureus) in Pakistan by different conventional methods and through electron microscopy. We screened 115 strains of S. aureus isolated from different clinical specimens by tube method (TM), air-liquid interface coverslip assay method, Congo red agar (CRA) method, and scanning electron microscopy (SEM). Out of 115 S. aureus isolates, 63 (54.78%) showed biofilm formation by tube method. Biofilm forming bacteria were further categorized as high producers (n = 23, 20%) and moderate producers (n = 40, 34.78%). TM coordinated well with the coverslip assay for strong biofilm-producing strains in 19 (16.5%) isolates. By coverslip method, weak producers were difficult to differentiate from biofilm negative isolates. Screening on CRA showed biofilm formation only in four (3.47%) strains. Scanning electron micrographs showed the biofilm-forming strains of S. aureus arranged in a matrix on the propylene surface and correlated well with the TM. Biofilm production is a marker of virulence for clinically relevant staphylococcal infections. It can be studied by various methods but screening on CRA is not recommended for investigation of biofilm formation in Staphylococcus aureus. Electron micrograph images correlate well with the biofilm production as observed by TM.

Versatility of Biofilm Matrix Molecules in Staphylococcus epidermidis Clinical Isolates and Importance of Polysaccharide Intercellular Adhesin Expression during High Shear Stress

PubMed Central

Schaeffer, Carolyn R.; Hoang, Tra-My N.; Sudbeck, Craig M.; Alawi, Malik; Tolo, Isaiah E.; Robinson, D. Ashley; Horswill, Alexander R.; Rohde, Holger

2016-01-01

ABSTRACT Staphylococcus epidermidis is a leading cause of hospital-associated infections, including those of intravascular catheters, cerebrospinal fluid shunts, and orthopedic implants. Multiple biofilm matrix molecules with heterogeneous characteristics have been identified, including proteinaceous, polysaccharide, and nucleic acid factors. Two of the best-studied components in S. epidermidis include accumulation-associated protein (Aap) and polysaccharide intercellular adhesin (PIA), produced by the enzymatic products of the icaADBC operon. Biofilm composition varies by strain as well as environmental conditions, and strains producing PIA-mediated biofilms are more robust. Clinically, biofilm-mediated infections occur in a variety of anatomical sites with diverse physiological properties. To test the hypothesis that matrix composition exhibits niche specificity, biofilm-related genetic and physical properties were compared between S. epidermidis strains isolated from high-shear and low-shear environments. Among a collection of 105 clinical strains, significantly more isolates from high-shear environments carried the icaADBC operon than did those from low-shear settings (43.9% versus 22.9%, P < 0.05), while there was no significant difference in the presence of aap (77.2% versus 75.0%, P > 0.05). Additionally, a significantly greater number of high-shear isolates were capable of forming biofilm in vitro in a microtiter assay (82.5% versus 45.8%, P < 0.0001). However, even among high-shear clinical isolates, less than half contained the icaADBC locus; therefore, we selected for ica-negative variants with increased attachment to abiotic surfaces to examine PIA-independent biofilm mechanisms. Sequencing of selected variants identified substitutions capable of enhancing biofilm formation in multiple genes, further highlighting the heterogeneity of S. epidermidis biofilm molecules and mechanisms. IMPORTANCE Staphylococcus epidermidis is a leading cause of infections related to biomaterials, mostly due to their ability to form biofilm. Biofilm accumulation mechanisms vary, including those that are dependent on specific proteins, environmental DNA (eDNA), or polysaccharide intercellular adhesin (PIA). We found that those isolates obtained from high-shear environments, such as the lumen of a catheter, are more likely to produce PIA-mediated biofilms than those isolates obtained from a low-shear biomaterial-related infection. This suggests that PIA functions as a mechanism that is protective against shear flow. Finally, we performed selection experiments documenting the heterogeneity of biofilm accumulation molecules that function in the absence of PIA, further documenting the biofilm-forming potential of S. epidermidis. PMID:27747298

Juvenile porcine temporomandibular joint: Three different cartilaginous structures?

PubMed

Tabeian, Hessam; Bakker, Astrid D; de Vries, Teun J; Zandieh-Doulabi, Behrouz; Lobbezoo, Frank; Everts, Vincent

2016-12-01

The temporomandibular joint (TMJ) consists of three cartilaginous structures: the fossa, disc, and condyle. In juvenile idiopathic arthritis (JIA), inflammation of the TMJ leads to destruction of the condyle, but not of the fossa or the disc. Such a different effect of inflammation might be related to differences in matrix composition of the cartilaginous structures. The matrix composition of the three TMJ structures was analyzed in juvenile porcine samples and in an in vitro system of cells isolated from each anatomical structure embedded in 3% agarose gels. The matrix of all three anatomical structures of the TMJ contained collagen type I and its gene expression was maintained after isolation. The condyle and the fossa stained positive for collagen type II and proteoglycans, but the condyle contained considerably more collagen type II and proteoglycans than the fossa. The disc contained neither collagen type II protein nor expression of its gene, and the disc did not stain positive for proteoglycans. Aggrecan gene expression was lower in the disc compared to condyle and fossa cell-isolates. In general, the cell-isolates in vitro closely mimicked the characteristic features found in the tissue. The collagen type II content of the condyle clearly distinguished this cartilaginous structure from the disc and fossa. Since autoimmunity against collagen type II is associated with JIA, the relatively abundant presence of this type of collagen in the condyle might provide an explanation why primarily this cartilaginous structure of the TMJ is affected in JIA patients. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of a New Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Platform, ASTA MicroIDSys, With Bruker Biotyper for Species Identification.

PubMed

Lee, Yangsoon; Sung, Ji Yeon; Kim, Hyunsoo; Yong, Dongeun; Lee, Kyungwon

2017-11-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, with its accuracy and speed, is widely used for bacterial identification. The ASTA MicroIDSys system (ASTA, Korea) was recently developed for species identification. We compared its performance with that of Bruker Biotyper (Bruker Daltonics, Germany). Microbes were recovered from sputum, urine, and pus samples from patients admitted to a tertiary care hospital in Korea from January to April 2016. Matrix solution (α-cyano-4-hydroxycinnamic acid) was used, and the peptide profiles acquired from the Microflex LT (Bruker Daltonics) and Tinkerbell LT (ASTA) were analyzed by using their respective software. From 5,322 isolates, Bruker Biotyper identified 163 species; fifty species from 4,919 isolates were identified more than 10 times, including Klebsiella pneumoniae (n=571), Acinetobacter baumannii (n=436), Pseudomonas aeruginosa (n=358), Escherichia coli (n=372), Staphylococcus aureus (n=511), S. epidermidis (n=444), Enterococcus faecium (n=262), E. faecalis (n=220), and Candida albicans (n=248). Identical results, confidence scores (≥ 2.0 for Bruker Biotyper), and acceptable scores (≥140 for ASTA MicroIDSys) were obtained for 86.1% of isolates. Of 4,267 isolates, 99.2% showed acceptable scores in both systems. Results from the ASTA MicroIDSys showed good agreement with those from the Bruker Biotyper. The ASTA MicroIDSys could reliably identify clinically important microorganisms. © The Korean Society for Laboratory Medicine.

Vibrational spectra (FT-IR, Raman and MI-IR) of α- and β-alanine

NASA Astrophysics Data System (ADS)

Rosado, Mário Túlio S.; Duarte, Maria Leonor R. S.; Fausto, Rui

1997-06-01

The vibrational spectra of α- and β-alaine molecules in both their zwitterionic and neutral forms are studied by FT-IR, Raman and MI-IR spectroscopy. Together with results from theoretical SCF-MO ab initio calculations, the spectroscopic data obtained under the various experimental conditions used in this study (crystalline phase; low temperature matrix isolated molecules) enable to undertake a detailed assignment of the vibrational spectra of the studied compounds.

Infrared Spectroscopy of Matrix-Isolated Polycyclic Aromatic Nitrogen Heterocycles (PANHs)

NASA Technical Reports Server (NTRS)

Mattioda, A. L.; Hudgins, D. M.; Bauschlicher, C. W.; Allamandola, L. J.; Biemesderfer, C. D.; Rosi, M.

2002-01-01

The mid-infrared spectra of the nitrogen-containing heterocyclic polycyclic aromatic compounds 1-azabenz[a]-anthracene; 2-azabenz[a]anthracene; 1-azachrysene; 2-azachrysene; 4-azachrysene; 2-azapyrene, and 7,8 benzoquinoline in their neutral and cation forms were investigated. The spectra of these species isolated in an argon matrix have been measured. Band frequencies and intensities were tabulated and these data compared with spectra computed using density functional theory at the B3LYP level. The overall agreement between experiment and theory is quite good, in keeping with earlier results on homonuclear polycyclic aromatic hydrocarbons. The differences between the spectral properties of nitrogen bearing aromatics and non-substituted, neutral polycyclic aromatic hydrocarbons will be discussed.

Preparation and characterization of bio-nanocomposite films based on soy protein isolate and montmorillonite using melt extrusion

USDA-ARS?s Scientific Manuscript database

The non-biodegradable and non-renewable nature of plastic packaging has led to a renewed interest in packaging materials based on bio-nanocomposites (biopolymer matrix reinforced with nanoparticles such as layered silicates). Bio-nanocomposite films based on soy protein isolate (SPI) and montmorillo...

Nonhemolytic Streptococcus pyogenes Isolates That Lack Large Regions of the sag Operon Mediating Streptolysin S Production▿

PubMed Central

Yoshino, Miho; Murayama, Somay Y.; Sunaoshi, Katsuhiko; Wajima, Takeaki; Takahashi, Miki; Masaki, Junko; Kurokawa, Iku; Ubukata, Kimiko

2010-01-01

Among nonhemolytic Streptococcus pyogenes (group A streptococcus) strains (n = 9) isolated from patients with pharyngitis or acute otitis media, we identified three deletions in the region from the epf gene, encoding the extracellular matrix binding protein, to the sag operon, mediating streptolysin S production. PMID:20018818

Novel approach for differentiating Shigella species and Escherichia coli by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Khot, Prasanna D; Fisher, Mark A

2013-11-01

Shigella species are so closely related to Escherichia coli that routine matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) cannot reliably differentiate them. Biochemical and serological methods are typically used to distinguish these species; however, "inactive" isolates of E. coli are biochemically very similar to Shigella species and thus pose a greater diagnostic challenge. We used ClinProTools (Bruker Daltonics) software to discover MALDI-TOF MS biomarker peaks and to generate classification models based on the genetic algorithm to differentiate between Shigella species and E. coli. Sixty-six Shigella spp. and 72 E. coli isolates were used to generate and test classification models, and the optimal models contained 15 biomarker peaks for genus-level classification and 12 peaks for species-level classification. We were able to identify 90% of E. coli and Shigella clinical isolates correctly to the species level. Only 3% of tested isolates were misidentified. This novel MALDI-TOF MS approach allows laboratories to streamline the identification of E. coli and Shigella species.

Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR+ Populations with Stem Cell Properties.

PubMed

Tome-Garcia, Jessica; Tejero, Rut; Nudelman, German; Yong, Raymund L; Sebra, Robert; Wang, Huaien; Fowkes, Mary; Magid, Margret; Walsh, Martin; Silva-Vargas, Violeta; Zaslavsky, Elena; Friedel, Roland H; Doetsch, Fiona; Tsankova, Nadejda M

2017-05-09

Characterization of non-neoplastic and malignant human stem cell populations in their native state can provide new insights into gliomagenesis. Here we developed a purification strategy to directly isolate EGFR +/- populations from human germinal matrix (GM) and adult subventricular zone autopsy tissues, and from de novo glioblastoma (GBM) resections, enriching for cells capable of binding EGF ligand ( LB EGFR + ), and uniquely compared their functional and molecular properties. LB EGFR + populations in both GM and GBM encompassed all sphere-forming cells and displayed proliferative stem cell properties in vitro. In xenografts, LB EGFR + GBM cells showed robust tumor initiation and progression to high-grade, infiltrative gliomas. Whole-transcriptome sequencing analysis confirmed enrichment of proliferative pathways in both developing and neoplastic freshly isolated EGFR + populations, and identified both unique and shared sets of genes. The ability to prospectively isolate stem cell populations using native ligand-binding capacity opens new doors onto understanding both normal human development and tumor cell biology. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Absolute quantification of olive oil DNA by droplet digital-PCR (ddPCR): Comparison of isolation and amplification methodologies.

PubMed

Scollo, Francesco; Egea, Leticia A; Gentile, Alessandra; La Malfa, Stefano; Dorado, Gabriel; Hernandez, Pilar

2016-12-15

Olive oil is considered a premium product for its nutritional value and health benefits, and the ability to define its origin and varietal composition is a key step towards ensuring the traceability of the product. However, isolating the DNA from such a matrix is a difficult task. In this study, the quality and quantity of olive oil DNA, isolated using four different DNA isolation protocols, was evaluated using the qRT-PCR and ddPCR techniques. The results indicate that CTAB-based extraction methods were the best for unfiltered oil, while Nucleo Spin-based extraction protocols showed greater overall reproducibility. The use of both qRT-PCR and ddPCR led to the absolute quantification of the DNA copy number. The results clearly demonstrate the importance of the choice of DNA-isolation protocol, which should take into consideration the qualitative aspects of DNA and the evaluation of the amplified DNA copy number. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of the Thermo Scientific SureTect Salmonella species assay. AOAC Performance Tested Method 051303.

PubMed

Cloke, Jonathan; Clark, Dorn; Radcliff, Roy; Leon-Velarde, Carlos; Larson, Nathan; Dave, Keron; Evans, Katharine; Crabtree, David; Hughes, Annette; Simpson, Helen; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko

2014-01-01

The Thermo Scientific SureTect Salmonella species Assay is a new real-time PCR assay for the detection of Salmonellae in food and environmental samples. This validation study was conducted using the AOAC Research Institute (RI) Performance Tested Methods program to validate the SureTect Salmonella species Assay in comparison to the reference method detailed in International Organization for Standardization 6579:2002 in a variety of food matrixes, namely, raw ground beef, raw chicken breast, raw ground pork, fresh bagged lettuce, pork frankfurters, nonfat dried milk powder, cooked peeled shrimp, pasteurized liquid whole egg, ready-to-eat meal containing beef, and stainless steel surface samples. With the exception of liquid whole egg and fresh bagged lettuce, which were tested in-house, all matrixes were tested by Marshfield Food Safety, Marshfield, WI, on behalf of Thermo Fisher Scientific. In addition, three matrixes (pork frankfurters, lettuce, and stainless steel surface samples) were analyzed independently as part of the AOAC-RI-controlled laboratory study by the University of Guelph, Canada. No significant difference by probability of detection or McNemars Chi-squared statistical analysis was found between the candidate or reference methods for any of the food matrixes or environmental surface samples tested during the validation study. Inclusivity and exclusivity testing was conducted with 117 and 36 isolates, respectively, which demonstrated that the SureTect Salmonella species Assay was able to detect all the major groups of Salmonella enterica subspecies enterica (e.g., Typhimurium) and the less common subspecies of S. enterica (e.g., arizoniae) and the rarely encountered S. bongori. None of the exclusivity isolates analyzed were detected by the SureTect Salmonella species Assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside of the recommended parameters open to variation (enrichment time and temperature, and lysis temperature), which demonstrated that the assay gave reliable performance. Accelerated stability testing was additionally conducted, validating the assay shelf life.

Evaluation of the Thermo Scientific™ SureTect™ Salmonella species Assay.

PubMed

Cloke, Jonathan; Clark, Dorn; Radcliff, Roy; Leon-Velarde, Carlos; Larson, Nathan; Dave, Keron; Evans, Katharine; Crabtree, David; Hughes, Annette; Simpson, Helen; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko

2014-03-01

The Thermo Scientific™ SureTect™ Salmonella species Assay is a new real-time PCR assay for the detection of Salmonellae in food and environmental samples. This validation study was conducted using the AOAC Research Institute (RI) Performance Tested MethodsSM program to validate the SureTect Salmonella species Assay in comparison to the reference method detailed in International Organization for Standardization 6579:2002 in a variety of food matrixes, namely, raw ground beef, raw chicken breast, raw ground pork, fresh bagged lettuce, pork frankfurters, nonfat dried milk powder, cooked peeled shrimp, pasteurized liquid whole egg, ready-to-eat meal containing beef, and stainless steel surface samples. With the exception of liquid whole egg and fresh bagged lettuce, which were tested in-house, all matrixes were tested by Marshfield Food Safety, Marshfield, WI, on behalf of Thermo Fisher Scientific. In addition, three matrixes (pork frankfurters, lettuce, and stainless steel surface samples) were analyzed independently as part of the AOAC-RI-controlled laboratory study by the University of Guelph, Canada. No significant difference by probability of detection or McNemars Chi-squared statistical analysis was found between the candidate or reference methods for any of the food matrixes or environmental surface samples tested during the validation study. Inclusivity and exclusivity testing was conducted with 117 and 36 isolates, respectively, which demonstrated that the SureTect Salmonella species Assay was able to detect all the major groups of Salmonella enterica subspecies enterica (e.g., Typhimurium) and the less common subspecies of S. enterica (e.g., arizoniae) and the rarely encountered S. bongori. None of the exclusivity isolates analyzed were detected by the SureTect Salmonella species Assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside of the recommended parameters open to variation (enrichment time and temperature, and lysis temperature), which demonstrated that the assay gave reliable performance. Accelerated stability testing was additionally conducted, validating the assay shelf life.

Detection of enterotoxigenic Clostridium perfringens in meat samples by using molecular methods.

PubMed

Kaneko, Ikuko; Miyamoto, Kazuaki; Mimura, Kanako; Yumine, Natsuko; Utsunomiya, Hirotoshi; Akimoto, Shigeru; McClane, Bruce A

2011-11-01

To prevent food-borne bacterial diseases and to trace bacterial contamination events to foods, microbial source tracking (MST) methods provide important epidemiological information. To apply molecular methods to MST, it is necessary not only to amplify bacterial cells to detection limit levels but also to prepare DNA with reduced inhibitory compounds and contamination. Isolates carrying the Clostridium perfringens enterotoxin gene (cpe) on the chromosome or a plasmid rank among the most important food-borne pathogens. Previous surveys indicated that cpe-positive C. perfringens isolates are present in only ∼5% of nonoutbreak food samples and then only at low numbers, usually less than 3 cells/g. In this study, four molecular assays for the detection of cpe-positive C. perfringens isolates, i.e., ordinary PCR, nested PCR, real-time PCR, and loop-mediated isothermal amplification (LAMP), were developed and evaluated for their reliability using purified DNA. For use in the artificial contamination of meat samples, DNA templates were prepared by three different commercial DNA preparation kits. The four molecular assays always detected cpe when >10³ cells/g of cpe-positive C. perfringens were present, using any kit. Of three tested commercial DNA preparation kits, the InstaGene matrix kit appeared to be most suitable for the testing of a large number of samples. By using the InstaGene matrix kit, the four molecular assays efficiently detected cpe using DNA prepared from enrichment culture specimens of meat samples contaminated with low numbers of cpe-positive C. perfringens vegetative cells or spores. Overall, the current study developed molecular assay protocols for MST to detect the contamination of foods with low numbers of cells, and at a low frequency, of cpe-positive C. perfringens isolates.

Symmetrical or Non-Symmetrical Debonds at Fiber-Matrix Interfaces: A Study by BEM and Finite Fracture Mechanics on Elastic Interfaces

NASA Astrophysics Data System (ADS)

Muñoz-Reja, Mar; Távara, Luis; Mantič, Vladislav

A recently proposed criterion is used to study the behavior of debonds produced at a fiber-matrix interface. The criterion is based on the Linear Elastic-(Perfectly) Brittle Interface Model (LEBIM) combined with a Finite Fracture Mechanics (FFM) approach, where the stress and energy criteria are suitably coupled. Special attention is given to the discussion about the symmetry of the debond onset and growth in an isolated single fiber specimen under uniaxial transverse tension. A common composite material system, glass fiber-epoxy matrix, is considered. The present methodology uses a two-dimensional (2D) Boundary Element Method (BEM) code to carry out the analysis of interface failure. The present results show that a non-symmetrical interface crack configuration (debonds at one side only) is produced by a lower critical remote load than the symmetrical case (debonds at both sides). Thus, the non-symmetrical solution is the preferred one, which agrees with the experimental evidences found in the literature.

Identification of bacteria isolated from veterinary clinical specimens using MALDI-TOF MS.

PubMed

Pavlovic, Melanie; Wudy, Corinna; Zeller-Peronnet, Veronique; Maggipinto, Marzena; Zimmermann, Pia; Straubinger, Alix; Iwobi, Azuka; Märtlbauer, Erwin; Busch, Ulrich; Huber, Ingrid

2015-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has recently emerged as a rapid and accurate identification method for bacterial species. Although it has been successfully applied for the identification of human pathogens, it has so far not been well evaluated for routine identification of veterinary bacterial isolates. This study was performed to compare and evaluate the performance of MALDI-TOF MS based identification of veterinary bacterial isolates with commercially available conventional test systems. Discrepancies of both methods were resolved by sequencing 16S rDNA and, if necessary, the infB gene for Actinobacillus isolates. A total of 375 consecutively isolated veterinary samples were collected. Among the 357 isolates (95.2%) correctly identified at the genus level by MALDI-TOF MS, 338 of them (90.1% of the total isolates) were also correctly identified at the species level. Conventional methods offered correct species identification for 319 isolates (85.1%). MALDI-TOF identification therefore offered more accurate identification of veterinary bacterial isolates. An update of the in-house mass spectra database with additional reference spectra clearly improved the identification results. In conclusion, the presented data suggest that MALDI-TOF MS is an appropriate platform for classification and identification of veterinary bacterial isolates.

ASCS online fault detection and isolation based on an improved MPCA

NASA Astrophysics Data System (ADS)

Peng, Jianxin; Liu, Haiou; Hu, Yuhui; Xi, Junqiang; Chen, Huiyan

2014-09-01

Multi-way principal component analysis (MPCA) has received considerable attention and been widely used in process monitoring. A traditional MPCA algorithm unfolds multiple batches of historical data into a two-dimensional matrix and cut the matrix along the time axis to form subspaces. However, low efficiency of subspaces and difficult fault isolation are the common disadvantages for the principal component model. This paper presents a new subspace construction method based on kernel density estimation function that can effectively reduce the storage amount of the subspace information. The MPCA model and the knowledge base are built based on the new subspace. Then, fault detection and isolation with the squared prediction error (SPE) statistic and the Hotelling ( T 2) statistic are also realized in process monitoring. When a fault occurs, fault isolation based on the SPE statistic is achieved by residual contribution analysis of different variables. For fault isolation of subspace based on the T 2 statistic, the relationship between the statistic indicator and state variables is constructed, and the constraint conditions are presented to check the validity of fault isolation. Then, to improve the robustness of fault isolation to unexpected disturbances, the statistic method is adopted to set the relation between single subspace and multiple subspaces to increase the corrective rate of fault isolation. Finally fault detection and isolation based on the improved MPCA is used to monitor the automatic shift control system (ASCS) to prove the correctness and effectiveness of the algorithm. The research proposes a new subspace construction method to reduce the required storage capacity and to prove the robustness of the principal component model, and sets the relationship between the state variables and fault detection indicators for fault isolation.

Rapid Identification and Subtyping of Helicobacter cinaedi Strains by Intact-Cell Mass Spectrometry Profiling with the Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Taniguchi, Takako; Sekiya, Ayumi; Higa, Mariko; Saeki, Yuji; Umeki, Kazumi; Okayama, Akihiko; Hayashi, Tetsuya

2014-01-01

Helicobacter cinaedi infection is recognized as an increasingly important emerging disease in humans. Although H. cinaedi-like strains have been isolated from a variety of animals, it is difficult to identify particular isolates due to their unusual phenotypic profiles and the limited number of biochemical tests for detecting helicobacters. Moreover, analyses of the 16S rRNA gene sequences are also limited due to the high levels of similarity among closely related helicobacters. This study was conducted to evaluate intact-cell mass spectrometry (ICMS) profiling using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as a tool for the identification of H. cinaedi. A total of 68 strains of H. cinaedi isolated from humans, dogs, a cat, and hamsters were examined in addition to other Helicobacter species. The major ICMS profiles of H. cinaedi were identical and differed from those of Helicobacter bilis, which show >98% sequence similarity at the 16S rRNA sequence level. A phyloproteomic analysis of the H. cinaedi strains examined in this work revealed that human isolates formed a single cluster that was distinct from that of the animal isolates, with the exception of two strains from dogs. These phyloproteomic results agreed with those of the phylogenetic analysis based on the nucleotide sequences of the hsp60 gene. Because they formed a distinct cluster in both analyses, our data suggest that animal strains may not be a major source of infection in humans. In conclusion, the ICMS profiles obtained using a MALDI-TOF MS approach may be useful for the identification and subtyping of H. cinaedi. PMID:24153128

Typing of Ochrobactrum anthropi clinical isolates using automated repetitive extragenic palindromic-polymerase chain reaction DNA fingerprinting and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry.

PubMed

Quirino, Angela; Pulcrano, Giovanna; Rametti, Linda; Puccio, Rossana; Marascio, Nadia; Catania, Maria Rosaria; Matera, Giovanni; Liberto, Maria Carla; Focà, Alfredo

2014-03-22

Ochrobactrum anthropi (O. anthropi), is a non-fermenting gram-negative bacillus usually found in the environment. Nevertheless, during the past decade it has been identified as pathogenic to immunocompromised patients. In this study, we assessed the usefulness of the automated repetitive extragenic palindromic-polymerase chain reaction (rep-PCR-based DiversiLab™ system, bioMèrieux, France) and of matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF MS) for typing of twentythree O. anthropi clinical isolates that we found over a four-months period (from April 2011 to August 2011) in bacteriemic patients admitted in the same operative unit of our hospital. Pulsed-field gel electrophoresis (PFGE), commonly accepted as the gold standard technique for typing, was also used. Analysis was carried out using the Pearson correlation coefficient to determine the distance matrice and the unweighted pair group method with arithmetic mean (UPGMA) to generate dendogram. Rep-PCR analysis identified four different patterns: three that clustered together with 97% or more pattern similarity, and one whose members showed < 95% pattern similarity. Interestingly, strains isolated later (from 11/06/2011 to 24/08/2011) displayed a pattern with 99% similarity. MALDI-TOF MS evaluation clustered the twentythree strains of O. anthropi into a single group containing four distinct subgroups, each comprising the majority of strains clustering below 5 distance levels, indicating a high similarity between the isolates. Our results indicate that these isolates are clonally-related and the methods used afforded a valuable contribution to the epidemiology, prevention and control of the infections caused by this pathogen.

Evaluation of the Vitek MS v3.0 Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Mycobacterium and Nocardia Species.

PubMed

Body, Barbara A; Beard, Melodie A; Slechta, E Susan; Hanson, Kimberly E; Barker, Adam P; Babady, N Esther; McMillen, Tracy; Tang, Yi-Wei; Brown-Elliott, Barbara A; Iakhiaeva, Elena; Vasireddy, Ravikiran; Vasireddy, Sruthi; Smith, Terry; Wallace, Richard J; Turner, S; Curtis, L; Butler-Wu, Susan; Rychert, Jenna

2018-06-01

This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of Mycobacterium and Nocardia species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the M. tuberculosis , M. abscessus , and M. avium complexes and within the M. fortuitum and M. mucogenicum groups could be differentiated. Among the 312 Nocardia isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex level. Species within the N. nova and N. transvalensis complexes could not always be differentiated. Eleven percent of the isolates (103/963) underwent repeat testing in order to get a final result. Identification of a representative set of Mycobacterium and Nocardia species was highly reproducible, with 297 of 300 (99%) replicates correctly identified using multiple kit lots, instruments, analysts, and sites. These findings demonstrate that the system is robust and has utility for the routine identification of mycobacteria and Nocardia in clinical practice. Copyright © 2018 American Society for Microbiology.

Evidence of genotypic diversity among Candida auris isolates by multilocus sequence typing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and amplified fragment length polymorphism.

PubMed

Prakash, A; Sharma, C; Singh, A; Kumar Singh, P; Kumar, A; Hagen, F; Govender, N P; Colombo, A L; Meis, J F; Chowdhary, A

2016-03-01

Candida auris is a multidrug-resistant nosocomial bloodstream pathogen that has been reported from Asian countries and South Africa. Herein, we studied the population structure and genetic relatedness among 104 global C. auris isolates from India, South Africa and Brazil using multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) fingerprinting and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). RPB1, RPB2 and internal transcribed spacer (ITS) and D1/D2 regions of the ribosomal DNA were sequenced for MLST. Further, genetic variation and proteomic assessment was carried out using AFLP and MALDI-TOF MS, respectively. Both MLST and AFLP typing clearly demarcated two major clusters comprising Indian and Brazilian isolates. However, the South African isolates were randomly distributed, suggesting different genotypes. MALDI-TOF MS spectral profiling also revealed evidence of geographical clustering but did not correlate fully with the genotyping methods. Notably, overall the population structure of C. auris showed evidence of geographical clustering by all the three techniques analysed. Antifungal susceptibility testing by the CLSI microbroth dilution method revealed that fluconazole had limited activity against 87% of isolates (MIC90, 64 mg/L). Also, MIC90 of AMB was 4 mg/L. Candida auris is emerging as an important yeast pathogen globally and requires reproducible laboratory methods for identification and typing. Evaluation of MALDI-TOF MS as a typing method for this yeast is warranted. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Infrared spectroscopy of water clusters isolated in methane matrices: Effects of isotope substitution and annealing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamakawa, Koichiro, E-mail: koichiro.yamakawa@gakushuin.ac.jp; Ehara, Namika; Ozawa, Nozomi

2016-07-15

Using infrared-active solvents of CH{sub 4} and CD{sub 4} for matrix isolation, we measured infrared spectra of H{sub 2}O and D{sub 2}O clusters at 7 K. The solute-concentration dependence of the spectrum of H{sub 2}O clusters in a CH{sub 4} matrix was investigated and was used for the peak assignment. Annealing procedures were found to promote the size growth of water clusters in methane matrices for all the combinations of (H{sub 2}O, CH{sub 4}), (H{sub 2}O, CD{sub 4}), (D{sub 2}O, CH{sub 4}), and (D{sub 2}O, CD{sub 4}). We also monitored the ν{sub 3} absorption due to methane to find themore » annealing-induced structural change only of solid CH{sub 4}. The matrix effects on the vibrations of the clusters are discussed on the basis of “T{sub c} plots”, where their frequencies are plotted as a function of the square root of the matrix critical temperature, T{sub c}. The obtained plots assure the validity of the assignment of the cluster peaks.« less

Radiation-induced transformations of isolated CH3CN molecules in noble gas matrices

NASA Astrophysics Data System (ADS)

Kameneva, Svetlana V.; Volosatova, Anastasia D.; Feldman, Vladimir I.

2017-12-01

The transformations of isolated CH3CN molecules in various solid noble-gas matrices (Ne, Ar, Kr, and Xe) under the action of X-ray irradiation at 5 K were investigated by FTIR spectroscopy. The main products are CH3NC, CH2CNH and CH2NCH molecular isomers as well as CH2CN and CH2NC radicals. The matrix has a strong effect on the distribution of reaction channels. In particular, the highest relative yield of keteneimine (CH2CNH) was found in Ne matrix, whereas the formation of CH3NC predominates in xenon. It was explained by differences in the matrix ionization energy (IE) resulting in different distributions of hot ionic reactions. The reactions of neutral excited states are mainly involved in Xe matrix with low IE, while the isomerization of the primary acetonitrile positive ions may be quite effective in Ne and Ar. Annealing of the irradiated samples results in mobilization of trapped hydrogen atoms followed by their reactions with radicals to yield parent molecule and its isomers. The scheme of the radiation-induced processes and its implications for the acetonitrile chemistry in cosmic ices are discussed.

An Innovative Carbonate Fuel Cell Matrix, Abstract #188

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hilmi, Abdelkader; Surendranath, Arun; Yuh, Chao-Yi

2015-05-28

The electrolyte matrix in direct carbonate fuel cell (DFC) is a microporous ceramic structure sandwiched between the electrodes to isolate the fuel from the oxidant, store electrolyte and facilitate ionic transport. FCE has advanced DFC electrolyte matrix over the years and demonstrated that the matrix meets the requirements for greater than 5 year life based on accelerated tests and field stack operations. However, development of advanced designs and materials that can further increase the performance and extend cell life will enable accelerated MCFC deployment. This paper will report the progress on the development of an unique and innovative matrix designmore » that offers numerous benefits to the carbonate fuel cell performance and durability. In addition, this paper will also review parameters that affect matrix material stability and approaches to extend cell life.« less

Coexistence of two electronic phases in LaTiO3+δ (0.01⩽δ⩽0.12) and their evolution with δ

NASA Astrophysics Data System (ADS)

Zhou, H. D.; Goodenough, J. B.

2005-04-01

Although LaTiO3+δ(0.01⩽δ⩽0.12) is single-phase to powder x-ray diffraction, its properties reveal that a hole-poor strongly correlated electronic phase coexists with a hole-rich itinerant-electron phase. With δ⩽0.03 , the hole-rich phase exists as a minority phase of isolated, mobile itinerant-electron clusters embedded in the hole-poor phase. With δ⩾0.08 , isolated hole-poor clusters are embedded in an itinerant-electron matrix. As δ>0.08 increases, the hole-poor clusters become smaller and more isolated until they are reduced to superparamagnetic strong-correlation fluctuations by δ=0.12 . This behavior is consistent with prediction from the virial theorem of a first-order phase change at the crossover from localized (or strongly correlated) to itinerant electronic behavior, a smaller equilibrium (Ti-O) bond length being in the itinerant-electron phase. Accordingly, the variation of volume with oxidation state does not obey Végard’s law; the itinerant-electron minority phase exerts a compressive force on the hole-poor matrix, and the hole-poor minority phase exerts a tensile stress on the hole-rich matrix.

A single dynamic observer-based module for design of simultaneous fault detection, isolation and tracking control scheme

NASA Astrophysics Data System (ADS)

Davoodi, M.; Meskin, N.; Khorasani, K.

2018-03-01

The problem of simultaneous fault detection, isolation and tracking (SFDIT) control design for linear systems subject to both bounded energy and bounded peak disturbances is considered in this work. A dynamic observer is proposed and implemented by using the H∞/H-/L1 formulation of the SFDIT problem. A single dynamic observer module is designed that generates the residuals as well as the control signals. The objective of the SFDIT module is to ensure that simultaneously the effects of disturbances and control signals on the residual signals are minimised (in order to accomplish the fault detection goal) subject to the constraint that the transfer matrix from the faults to the residuals is equal to a pre-assigned diagonal transfer matrix (in order to accomplish the fault isolation goal), while the effects of disturbances, reference inputs and faults on the specified control outputs are minimised (in order to accomplish the fault-tolerant and tracking control goals). A set of linear matrix inequality (LMI) feasibility conditions are derived to ensure solvability of the problem. In order to illustrate and demonstrate the effectiveness of our proposed design methodology, the developed and proposed schemes are applied to an autonomous unmanned underwater vehicle (AUV).

Rapid and reliable MALDI-TOF mass spectrometry identification of Candida non-albicans isolates from bloodstream infections.

PubMed

Pulcrano, Giovanna; Iula, Dora Vita; Vollaro, Antonio; Tucci, Alessandra; Cerullo, Monica; Esposito, Matilde; Rossano, Fabio; Catania, Maria Rosaria

2013-09-01

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) fingerprinting has recently become an effective instrument for rapid microbiological diagnostics and in particular for identification of micro-organisms directly in a positive blood culture. The aim of the study was to evaluate a collection of 82 stored yeast isolates from bloodstream infection, by MALDI-TOF MS; 21 isolates were identified also directly from positive blood cultures and in the presence of other co-infecting micro-organisms. Of the 82 isolates grown on plates, 64 (76%) were correctly identified by the Vitek II system and 82 (100%) by MALDI-TOF MS; when the two methods gave different results, the isolate was identified by PCR. MALDI-TOF MS was unreliable in identifying two isolates (Candida glabrata and Candida parapsilosis) directly from blood culture; however, direct analysis from positive blood culture samples was fast and effective for the identification of yeast, which is of great importance for early and adequate treatment. © 2013. Published by Elsevier B.V. All rights reserved.

Evaluation of MALDI-TOF MS (Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry) for routine identification of anaerobic bacteria.

PubMed

Rodríguez-Sánchez, Belén; Alcalá, Luis; Marín, Mercedes; Ruiz, Adrián; Alonso, Elena; Bouza, Emilio

2016-12-01

Information regarding the use of MALDI-TOF MS as an alternative to conventional laboratory methods for the rapid and reliable identification of bacterial isolates is still limited. In this study, MALDI-TOF MS was evaluated on 295 anaerobic isolates previously identified by 16S rRNA gene sequencing and with biochemical tests (Rapid ID 32A system, BioMérieux). In total, 85.8% of the isolates were identified by MALDI-TOF MS at the species level vs 49.8% using the Rapid ID 32A system (p < 0.0001). None of the isolates was discordantly identified at the genus level using MALDI-TOF MS and only 9 of them could not be identified using the method. Thus, our results show that MALDI-TOF MS is a robust and reliable tool for the identification of anaerobic isolates in the microbiology laboratory. Its implementation will reduce the turnaround time for a final identification and the number of isolates that require 16S rRNA sequencing. Copyright © 2016 Elsevier Ltd. All rights reserved.

Do isolated gallery-forest trees facilitate recruitment of forest seedlings and saplings in savannna?

NASA Astrophysics Data System (ADS)

Azihou, Akomian Fortuné; Glèlè Kakaï, Romain; Sinsin, Brice

2013-11-01

Facilitation is an ecological process that allows some species to establish in environments they can hardly afford in the absence of the process. This study investigated if the subcanopy of gallery-forest trees isolated in savanna is suitable for the early recruitment of forest woody species. We measured tree crown area as well as the density of seedlings and saplings of gallery-forest tree species beneath isolated trees and in the savanna matrix along 50 transects of 5-km long and 600 m wide located along four gallery forests. We then tested the nurse-plant effect and Janzen-Connell hypothesis beneath isolated trees. We also examined the relationships between the crown area and the density of seedlings and saplings. Among the eight identified tree species isolated in savanna, only Daniellia oliveri and Khaya senegalensis showed nurse-plant effect and promoted a significant, yet low early recruitment with a seedling-to-sapling survival of 0.044 and 0.578, respectively. The suitability of the subcanopy of isolated trees decreased with the recruitment progression and Janzen-Connell effects were absent. Seedlings had neutral association with the crown area of isolated trees which shifted to positive at the sapling stage. The species of the isolated tree and the crown area explained less than 20% of total variance, indicating that other predictive factors are important in explaining the nurse-plant effect observed in this study.

Acellular Mouse Kidney ECM can be Used as a Three-Dimensional Substrate to Test the Differentiation Potential of Embryonic Stem Cell Derived Renal Progenitors.

PubMed

Sambi, Manpreet; Chow, Theresa; Whiteley, Jennifer; Li, Mira; Chua, Shawn; Raileanu, Vanessa; Rogers, Ian M

2017-08-01

The development of strategies for tissue regeneration and bio-artificial organ development is based on our understanding of embryogenesis. Differentiation protocols attempt to recapitulate the signaling modalities of gastrulation and organogenesis, coupled with cell selection regimens to isolate the cells of choice. This strategy is impeded by the lack of optimal in vitro culture systems since traditional culture systems do not allow for the three-dimensional interaction between cells and the extracellular matrix. While artificial three-dimensional scaffolds are available, using the natural extracellular matrix scaffold is advantageous because it has a distinct architecture that is difficult to replicate. The adult extracellular matrix is predicted to mediate signaling related to tissue repair not embryogenesis but existing similarities between the two argues that the extracellular matrix will influence the differentiation of stem and progenitor cells. Previous studies using undifferentiated embryonic stem cells grown directly on acellular kidney ECM demonstrated that the acellular kidney supported cell growth but limited differentiation occurred. Using mouse kidney extracellular matrix and mouse embryonic stem cells we report that the extracellular matrix can support the development of kidney structures if the stem cells are first differentiated to kidney progenitor cells before being applied to the acellular organ.

Isolation, characterization, and aggregation of a structured bacterial matrix precursor.

PubMed

Chai, Liraz; Romero, Diego; Kayatekin, Can; Akabayov, Barak; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

2013-06-14

Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms.

Evaluation of Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry for Identification of Mycobacterium species, Nocardia species, and Other Aerobic Actinomycetes

PubMed Central

Buckwalter, S. P.; Olson, S. L.; Connelly, B. J.; Lucas, B. C.; Rodning, A. A.; Walchak, R. C.; Deml, S. M.; Wohlfiel, S. L.

2015-01-01

The value of matrix-assisted laser desorption ionization−time of flight mass spectrometry (MALDI-TOF MS) for the identification of bacteria and yeasts is well documented in the literature. Its utility for the identification of mycobacteria and Nocardia spp. has also been reported in a limited scope. In this work, we report the specificity of MALDI-TOF MS for the identification of 162 Mycobacterium species and subspecies, 53 Nocardia species, and 13 genera (totaling 43 species) of other aerobic actinomycetes using both the MALDI-TOF MS manufacturer's supplied database(s) and a custom database generated in our laboratory. The performance of a simplified processing and extraction procedure was also evaluated, and, similar to the results in an earlier literature report, our viability studies confirmed the ability of this process to inactivate Mycobacterium tuberculosis prior to analysis. Following library construction and the specificity study, the performance of MALDI-TOF MS was directly compared with that of 16S rRNA gene sequencing for the evaluation of 297 mycobacteria isolates, 148 Nocardia species isolates, and 61 other aerobic actinomycetes isolates under routine clinical laboratory working conditions over a 6-month period. MALDI-TOF MS is a valuable tool for the identification of these groups of organisms. Limitations in the databases and in the ability of MALDI-TOF MS to rapidly identify slowly growing mycobacteria are discussed. PMID:26637381

Cloud-point extraction is compatible with liquid chromatography coupled to electrospray ionization mass spectrometry for the determination of antazoline in human plasma.

PubMed

Giebułtowicz, Joanna; Kojro, Grzegorz; Piotrowski, Roman; Kułakowski, Piotr; Wroczyński, Piotr

2016-09-05

Cloud-point extraction (CPE) is attracting increasing interest in a number of analytical fields, including bioanalysis, as it provides a simple, safe and environmentally-friendly sample preparation technique. However, there are only few reports on the application of this extraction technique in liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis. In this study, CPE was used for the isolation of antazoline from human plasma. To date, only one method of antazoline isolation from plasma exists-liquid-liquid extraction (LLE). The aim of this study was to prove the compatibility of CPE and LC-ESI-MS/MS and the applicability of CPE to the determination of antazoline in spiked human plasma and clinical samples. Antazoline was isolated from human plasma using Triton X-114 as a surfactant. Xylometazoline was used as an internal standard. NaOH concentration, temperature and Triton X-114 concentration were optimized. The absolute matrix effect was carefully investigated. All validation experiments met international acceptance criteria and no significant relative matrix effect was observed. The compatibility of CPE and LC-ESI-MS/MS was confirmed using clinical plasma samples. The determination of antazoline concentration in human plasma in the range 10-2500ngmL(-1) by the CPE method led to results which are equivalent to those obtained by the widely used liquid-liquid extraction method. Copyright © 2016 Elsevier B.V. All rights reserved.

Isolation and Purification of Versican and Analysis of Versican Proteolysis

PubMed Central

Foulcer, Simon J.; Day, Anthony J.; Apte, Suneel S.

2017-01-01

Versican is a widely distributed chondroitin sulfate proteoglycan that forms large complexes with the glycosaminoglycan hyaluronan (HA). As a consequence of HA binding to its receptor CD44 and interactions of the versican C-terminal globular (G3) domain with a variety of extracellular matrix proteins, versican is a key component of well-defined networks in pericellular matrix and extracellular matrix. It is crucial for several developmental processes in the embryo and there is increasing interest in its roles in cancer and inflammation. Versican proteolysis by ADAMTS proteases is highly regulated, occurs at specific peptide bonds, and is relevant to several physiological and disease mechanisms. In this chapter, methods are described for the isolation and detection of intact and cleaved versican in tissues using morphologic and biochemical techniques. These, together with the methodologies for purification and analysis of recombinant versican and a versican fragment provided here, are likely to facilitate further progress on the biology of versican and its proteolysis. PMID:25325983

Isolation and purification of versican and analysis of versican proteolysis.

PubMed

Foulcer, Simon J; Day, Anthony J; Apte, Suneel S

2015-01-01

Versican is a widely distributed chondroitin sulfate proteoglycan that forms large complexes with the glycosaminoglycan hyaluronan (HA). As a consequence of HA binding to its receptor CD44 and interactions of the versican C-terminal globular (G3) domain with a variety of extracellular matrix proteins, versican is a key component of well-defined networks in pericellular matrix and extracellular matrix. It is crucial for several developmental processes in the embryo and there is increasing interest in its roles in cancer and inflammation. Versican proteolysis by ADAMTS proteases is highly regulated, occurs at specific peptide bonds, and is relevant to several physiological and disease mechanisms. In this chapter, methods are described for the isolation and detection of intact and cleaved versican in tissues using morphologic and biochemical techniques. These, together with the methodologies for purification and analysis of recombinant versican and a versican fragment provided here, are likely to facilitate further progress on the biology of versican and its proteolysis.

[Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics].

PubMed

Nagy, Erzsébet; Abrók, Marianna; Bartha, Noémi; Bereczki, László; Juhász, Emese; Kardos, Gábor; Kristóf, Katalin; Miszti, Cecilia; Urbán, Edit

2014-09-21

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures.

Determination of matrix composition based on solute-solute nearest-neighbor distances in atom probe tomography.

PubMed

De Geuser, F; Lefebvre, W

2011-03-01

In this study, we propose a fast automatic method providing the matrix concentration in an atom probe tomography (APT) data set containing two phases or more. The principle of this method relies on the calculation of the relative amount of isolated solute atoms (i.e., not surrounded by a similar solute atom) as a function of a distance d in the APT reconstruction. Simulated data sets have been generated to test the robustness of this new tool and demonstrate that rapid and reproducible results can be obtained without the need of any user input parameter. The method has then been successfully applied to a ternary Al-Zn-Mg alloy containing a fine dispersion of hardening precipitates. The relevance of this method for direct estimation of matrix concentration is discussed and compared with the existing methodologies. Copyright © 2010 Wiley-Liss, Inc.

Genetic, phenotypic and matrix-assisted laser desorption ionization time-of-flight mass spectrometry-based identification of anaerobic bacteria and determination of their antimicrobial susceptibility at a University Hospital in Japan.

PubMed

Yunoki, Tomoyuki; Matsumura, Yasufumi; Nakano, Satoshi; Kato, Karin; Hotta, Go; Noguchi, Taro; Yamamoto, Masaki; Nagao, Miki; Takakura, Shunji; Ichiyama, Satoshi

2016-05-01

The accuracies of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and the phenotypic method using VITEK 2 were compared to the accuracy of 16S rRNA sequence analysis for the identification of 170 clinically isolated anaerobes. The antimicrobial susceptibility of the isolates was also evaluated. Genetic analysis identified 21 Gram-positive species in 14 genera and 29 Gram-negative species in 11 genera. The most frequently isolated genera were Prevotella spp. (n = 46), Bacteroides spp. (n = 25) and Clostridium spp. (n = 25). MALDI-TOF MS correctly identified more isolates compared with VITEK 2 at the species (80 vs. 58%, respectively; p < 0.01) and genus (85 vs. 71%, respectively; p < 0.01) levels. More than 90% of the isolates of the three major genera identified (Prevotella, Bacteroides, and Clostridium species other than Clostridium difficile) were susceptible to beta-lactam/beta-lactamase inhibitor combinations, carbapenems, metronidazole and chloramphenicol. MALDI-TOF MS provided better identification results than VITEK2. Commonly used anti-anaerobic agents indicated that the isolates of the three most frequently identified anaerobic genera exhibited good antimicrobial susceptibility. Copyright © 2016 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Complete polarization characterization of single plasmonic nanoparticle enabled by a novel Dark-field Mueller matrix spectroscopy system

PubMed Central

Chandel, Shubham; Soni, Jalpa; Ray, Subir kumar; Das, Anwesh; Ghosh, Anirudha; Raj, Satyabrata; Ghosh, Nirmalya

2016-01-01

Information on the polarization properties of scattered light from plasmonic systems are of paramount importance due to fundamental interest and potential applications. However, such studies are severely compromised due to the experimental difficulties in recording full polarization response of plasmonic nanostructures. Here, we report on a novel Mueller matrix spectroscopic system capable of acquiring complete polarization information from single isolated plasmonic nanoparticle/nanostructure. The outstanding issues pertaining to reliable measurements of full 4 × 4 spectroscopic scattering Mueller matrices from single nanoparticle/nanostructures are overcome by integrating an efficient Mueller matrix measurement scheme and a robust eigenvalue calibration method with a dark-field microscopic spectroscopy arrangement. Feasibility of quantitative Mueller matrix polarimetry and its potential utility is illustrated on a simple plasmonic system, that of gold nanorods. The demonstrated ability to record full polarization information over a broad wavelength range and to quantify the intrinsic plasmon polarimetry characteristics via Mueller matrix inverse analysis should lead to a novel route towards quantitative understanding, analysis/interpretation of a number of intricate plasmonic effects and may also prove useful towards development of polarization-controlled novel sensing schemes. PMID:27212687

Analysis of Potential Radical Chemistry on Kuiper Belt Objects

NASA Astrophysics Data System (ADS)

Yanez, Maya Danielle; Hodyss, Robert; Cable, Morgan; Johnson, Paul

2017-10-01

Kuiper Belt Objects (KBOs) are of high interest following the New Horizons encounter with the Pluto system and the extended mission to 2014MU69. We aimed to clarify questions raised concerning the possible presence of organic radicals formed from photolysis on the surface of KBOs and other Trans-Neptunian Objects, and obtain laboratory spectra of these radicals for comparison to remote sensing data. We explored the photochemical generation of methyl radical from matrix-isolated CH3I in an attempt to create sufficient amounts of the methyl radical to obtain spectra in the near infrared. Both Ar and N2 matrices were studied, as well as varying guest:matrix ratios. Hydrogen lamp irradiation was found to be more effective than mercury lamp irradiation. The irradiation time was a significant factor when we switched matrices: methyl radical depleted rapidly in the N2 matrix with prolonged irradiation (~10 hours) whereas it survived for over 48 hours in some experiments with the Ar matrix. Reaction of the methyl radical with the N2 matrix to form HCN was observed. Future experiments will focus on alternate methods of radical generation in order to increase the yield of trapped radical.

In situ tissue engineering with synthetic self-assembling peptide nanofiber scaffolds, PuraMatrix, for mucosal regeneration in the rat middle-ear

PubMed Central

Akiyama, Naotaro; Yamamoto-Fukuda, Tomomi; Takahashi, Haruo; Koji, Takehiko

2013-01-01

Middle-ear mucosa maintains middle-ear pressure. However, the majority of surgical cases exhibit inadequate middle-ear mucosal regeneration, and mucosal transplantation is necessary in such cases. The aim of the present study was to assess the feasibility of transplantation of isolated mucosal cells encapsulated within synthetic self-assembling peptide nanofiber scaffolds using PuraMatrix, which has been successfully used as scaffolding in tissue engineering, for the repair of damaged middle-ear. Middle-ear bullae with mucosa were removed from Sprague Dawley (SD) transgenic rats, transfected with enhanced green fluorescent protein (EGFP) transgene and excised into small pieces, then cultured up to the third passage. After surgical elimination of middle-ear mucosa in SD recipient rats, donor cells were encapsulated within PuraMatrix and transplanted into these immunosuppressed rats. Primary cultured cells were positive for pancytokeratin but not for vimentin, and retained the character of middle-ear epithelial cells. A high proportion of EGFP-expressing cells were found in the recipient middle-ear after transplantation with PuraMatrix, but not without PuraMatrix. These cells retained normal morphology and function, as confirmed by histological examination, immunohistochemistry, and electron microscopy, and multiplied to form new epithelial and subepithelial layers together with basement membrane. The present study demonstrated the feasibility of transplantation of cultured middle-ear mucosal epithelial cells encapsulated within PuraMatrix for regeneration of surgically eliminated mucosa of the middle-ear in SD rats. PMID:23926427

In situ tissue engineering with synthetic self-assembling peptide nanofiber scaffolds, PuraMatrix, for mucosal regeneration in the rat middle-ear.

PubMed

Akiyama, Naotaro; Yamamoto-Fukuda, Tomomi; Takahashi, Haruo; Koji, Takehiko

2013-01-01

Middle-ear mucosa maintains middle-ear pressure. However, the majority of surgical cases exhibit inadequate middle-ear mucosal regeneration, and mucosal transplantation is necessary in such cases. The aim of the present study was to assess the feasibility of transplantation of isolated mucosal cells encapsulated within synthetic self-assembling peptide nanofiber scaffolds using PuraMatrix, which has been successfully used as scaffolding in tissue engineering, for the repair of damaged middle-ear. Middle-ear bullae with mucosa were removed from Sprague Dawley (SD) transgenic rats, transfected with enhanced green fluorescent protein (EGFP) transgene and excised into small pieces, then cultured up to the third passage. After surgical elimination of middle-ear mucosa in SD recipient rats, donor cells were encapsulated within PuraMatrix and transplanted into these immunosuppressed rats. Primary cultured cells were positive for pancytokeratin but not for vimentin, and retained the character of middle-ear epithelial cells. A high proportion of EGFP-expressing cells were found in the recipient middle-ear after transplantation with PuraMatrix, but not without PuraMatrix. These cells retained normal morphology and function, as confirmed by histological examination, immunohistochemistry, and electron microscopy, and multiplied to form new epithelial and subepithelial layers together with basement membrane. The present study demonstrated the feasibility of transplantation of cultured middle-ear mucosal epithelial cells encapsulated within PuraMatrix for regeneration of surgically eliminated mucosa of the middle-ear in SD rats.

Newcastle disease virus in penguins from King George Island on the Antarctic region.

PubMed

Thomazelli, Luciano M; Araujo, Jansen; Oliveira, Danielle B; Sanfilippo, Luiz; Ferreira, Carolina S; Brentano, Liana; Pelizari, Vivian H; Nakayama, Cristiane; Duarte, Rubens; Hurtado, Renata; Branco, Joaquim O; Walker, David; Durigon, Edison L

2010-11-20

Here we report the isolation of Newcastle disease virus (NDV) from cloacal swabs obtained from penguins in the South Atlantic Antarctic region (62°08S, 58°25W). Samples of 100 penguins from King George Island were tested by real-time PCR, of which 2 (2%) were positive for NDV. The positive samples were isolated in embryonated chicken eggs and their matrix and fusion proteins genes were partially sequenced. This was complemented by the serological study performed on the blood of the same specimens, which resulted in a 33.3% rate of positivity. Copyright © 2010 Elsevier B.V. All rights reserved.

Nonreciprocal optical isolation via graphene based photonic crystals

NASA Astrophysics Data System (ADS)

Roshan Entezar, S.; Karimi Habil, M.

2018-03-01

The transmission properties of a one-dimensional photonic crystal containing graphene mono-layers are studied using the transfer matrix method. It is shown that the structure can be used as a polarization-selective nonreciprocal device which discriminates between the two circularly polarized waves with different handedness impinging in the same direction. This structure may be utilized in designing optical isolators for the circularly polarized waves due to the gyrotropic behavior of the graphene mono-layers under the perpendicularly applied external magnetic field. Moreover, the effect of an external magnetic field and the chemical potential of the graphene mono-layers on the band gap of the structure are investigated.

Inhibition of Collagenase by Mycosporine-like Amino Acids from Marine Sources

PubMed Central

Hartmann, Anja; Gostner, Johanna; Fuchs, Julian E.; Chaita, Eliza; Aligiannis, Nektarios; Skaltsounis, Leandros; Ganzera, Markus

2015-01-01

Matrix metalloproteinases (MMP) play an important role in extracellular matrix remodeling. Excessive activity of these enzymes can be induced by UV light and leads to skin damage, a process known as photoaging. In this study we investigated the collagenase inhibition potential of mycosporine-like amino acids (MAA), compounds that have been isolated from marine organisms and are known photoprotectants against UV-A and UV-B. For this purpose the commonly used collagenase assay was optimized and for the first time validated in terms of relationships between enzyme-substrate concentrations, temperature, incubation time and enzyme stability. Three compounds were isolated from the marine red algae Porphyra sp. and Palmaria palmata, and evaluated for their inhibitory properties against Chlostridium histolyticum collagenase (Chc). A dose-dependent, but very moderate inhibition was observed for all substances and IC50 values of 104.0 μM for shinorine, 105.9 μM for porphyra and 158.9 μM for palythine were determined. Additionally, computer-aided docking models suggested that the MAA binding to the active site of the enzyme is a competitive inhibition. PMID:26039265

High-Resolution Infrared Spectrscopy of the Hydroxymethyl Radical in Solid Parahydrogen

NASA Astrophysics Data System (ADS)

Balabanoff, Morgan E.; Anderson, David T.

2016-06-01

Interest in the hydroxymethyl radical, CH2OH, stems primarily from its importance as a reaction intermediate. However, this radical is also of interest from a spectroscopic point of view with large amplitude COH torsional tunneling and out of plane CH2 wagging motions. The first IR detection of CH2OH was accomplished via matrix isolation spectroscopy over 40 years ago by Jacox. Reisler and co-workers detected CH2OH in the gas-phase using the sensitivity of double resonance ionization detected IR spectroscopy to probe the OH stretch, asymmetric CH stretch, and symmetric CH stretch vibrational modes with partial rotational resolution (0.4 wn). Most recently, the Nesbitt group published the first fully rotationally resolved IR spectrum of CH2OH via the Ka=0←0 band of the symmetric CH stretch. These researchers were able to unambiguously assign the identified transitions to a Watson A-reduced symmetric top Hamiltonian thereby producing improved values for the symmetric CH stretch rotational constants and vibrational band origin. However, in this same work the authors point out a number of remaining unresolved issues. Motivated by these gas-phase observations, we decided to return to the matrix isolation studies of CH2OH, however utilizing solid parahydrogen as a matrix host to improve upon the sensitivity and resolution of the previous matrix isolation studies. Based on our measurements, while the end-over-end rotation of the CH2OH radical is quenched, rotational motion around the a-axis is nearly free permitting both A-type and B-type transitions to be resolved. In the case of the OH stretch mode, both A-type and B-type transitions are observed with an energy difference that makes sense based on the gas-phase CH2OH rotational constants. However, for the symmetric CH stretch mode, the same mode recently assigned by Nesbitt and co-workers, two absorption features are also observed but the energy difference and intensities of the two features do not match predictions based on the rotational constants. M.E. Jacox, D.E. Milligan, J. Mol. Spec. 47, 148-162 (1973) L. Feng, J. Wei, H. Reisler, J. Phys. Chem. A 108, 7903-7908 (2004). M.A. Roberts, E.N. Sharp-Williams, D.J. Nesbitt, J. Phys. Chem. A 117, 7042-7049 (2013).

Detection of processed genetically modified food using CIM monolithic columns for DNA isolation.

PubMed

Jerman, Sergej; Podgornik, Ales; Cankar, Katarina; Cadet, Neza; Skrt, Mihaela; Zel, Jana; Raspor, Peter

2005-02-11

The availability of sufficient quantities of DNA of adequate quality is crucial in polymerase chain reaction (PCR)-based methods for genetically modified food detection. In this work, the suitability of anion-exchange CIM (Convective Interaction Media; BIA Separations, Ljubljana, Slovenia) monolithic columns for isolation of DNA from food was studied. Maize and its derivates corn meal and thermally pretreated corn meal were chosen as model food. Two commercially available CIM disk columns were tested: DEAE (diethylaminoethyl) and QA (quaternary amine). Preliminary separations were performed with standard solution of salmon DNA at different pH values and different NaCl concentrations in mobile phase. DEAE groups and pH 8 were chosen for further isolations of DNA from a complex matrix-food extract. The quality and quantity of isolated DNA were tested on agarose gel electrophoresis, with UV-scanning spectrophotometry, and by amplification with real-time PCR. DNA isolated in this way was of suitable quality for further PCR analyses. The described method is also applicable for DNA isolation from processed foods with decreased DNA content. Furthermore, it is more effective and less time-consuming in comparison with the existing proposed methods for isolation of DNA from plant-derived foods.

Species identification of Aspergillus, Fusarium and Mucorales with direct surface analysis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

De Carolis, E; Posteraro, B; Lass-Flörl, C; Vella, A; Florio, A R; Torelli, R; Girmenia, C; Colozza, C; Tortorano, A M; Sanguinetti, M; Fadda, G

2012-05-01

Accurate species discrimination of filamentous fungi is essential, because some species have specific antifungal susceptibility patterns, and misidentification may result in inappropriate therapy. We evaluated matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for species identification through direct surface analysis of the fungal culture. By use of culture collection strains representing 55 species of Aspergillus, Fusarium and Mucorales, a reference database was established for MALDI-TOF MS-based species identification according to the manufacturer's recommendations for microflex measurements and MALDI BioTyper 2.0 software. The profiles of young and mature colonies were analysed for each of the reference strains, and species-specific spectral fingerprints were obtained. To evaluate the database, 103 blind-coded fungal isolates collected in the routine clinical microbiology laboratory were tested. As a reference method for species designation, multilocus sequencing was used. Eighty-five isolates were unequivocally identified to the species level (≥99% sequence similarity); 18 isolates producing ambiguous results at this threshold were initially rated as identified to the genus level only. Further molecular analysis definitively assigned these isolates to the species Aspergillus oryzae (17 isolates) and Aspergillus flavus (one isolate), concordant with the MALDI-TOF MS results. Excluding nine isolates that belong to the fungal species not included in our reference database, 91 (96.8%) of 94 isolates were identified by MALDI-TOF MS to the species level, in agreement with the results of the reference method; three isolates were identified to the genus level. In conclusion, MALDI-TOF MS is suitable for the routine identification of filamentous fungi in a medical microbiology laboratory. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

A First Insight into Escherichia coli ST131 High-Risk Clone Among Extended-Spectrum Beta-Lactamase-Producing Urine Isolates in Istanbul with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry and Real-Time PCR.

PubMed

Aktaş, Elif; Otlu, Barış; Erdemir, Duygu; Ekici, Hatice; Bulut, Emin

2017-12-01

We aim to investigate, as a first insight, the presence and rates of high-risk Escherichia coli ST131 clone in Istanbul and evaluate antimicrobial resistance and CTX-M-15 production of ST131 and non-ST131 isolates. The use of MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry) to detect E. coli ST131 clone is also evaluated. A total of 203 extended-spectrum beta-lactamase (ESBL)-producing urinary isolates from a training hospital in Istanbul were investigated. Detection of E. coli ST131 was done by MALDI-TOF MS and real-time PCR melting curve analysis. The presence of CTX-M and CTX-M-15 beta-lactamases was investigated by PCR and sequence analysis. Of the 203 isolates, 81 (39.9%) and 75 (36.9%) isolates were identified as ST131 clone by PCR and MALDI-TOF MS, respectively. Resistance to ciprofloxacin was significantly higher among ST131 isolates. A total of 169 (83.5%) isolates produced CTX-M beta-lactamase, of which 72 (43%) were CTX-M-15. The production of CTX-M and CTX-M-15 were significantly higher among ST131 isolates. We have demonstrated, for the first time, high rates of ST131 clone among ESBL-producing E. coli isolates in Istanbul, a region with high rates of resistance to third-generation cephalosporins and fluoroquinolones. Further investigation of this high-risk clone and its contribution to high antimicrobial resistance in Turkey is essential. MALDI-TOF MS is a useful tool for detection of high-risk clones and associated resistance patterns, simultaneous to bacterial identification.

Effects of pH changes in water-based solvents to isolate antibacterial activated extracts of natural products

NASA Astrophysics Data System (ADS)

Buang, Yohanes; Suwari, Ola, Antonius R. B.

2017-12-01

Effects of pH changes in solvents on isolation of antibacterial activities of natural product extracts were conducted in the present study. Sarang semut (M. pendens) tubers as the model material for the study was considered to be the strategic resource of natural products based on its biochemical and therapeutical effects. The water with pH 5, 7, 9, and 13 was used as the solvents. The antibacterial activities of the resulted extracts indicated that higher the working pH, higher activities of the resulted extracts. The extent activities of the resulted extracts followed the increasing pH of the maceration system. The study also found that higher pH of the working solvent, higher the amounts of the antibacterial extracts isolated from the sample matrix of the natural product. The higher pH of the water solvents plays essential roles to promote the antibacterial activities of the natural product extracts from M. pendens tubers.

Evidence for an impact-induced magnetic fabric in Allende, and exogenous alternatives to the core dynamo theory for Allende magnetization

NASA Astrophysics Data System (ADS)

Muxworthy, Adrian R.; Bland, Phillip A.; Davison, Thomas M.; Moore, James; Collins, Gareth S.; Ciesla, Fred J.

2017-10-01

We conducted a paleomagnetic study of the matrix of Allende CV3 chondritic meteorite, isolating the matrix's primary remanent magnetization, measuring its magnetic fabric and estimating the ancient magnetic field intensity. A strong planar magnetic fabric was identified; the remanent magnetization of the matrix was aligned within this plane, suggesting a mechanism relating the magnetic fabric and remanence. The intensity of the matrix's remanent magnetization was found to be consistent and low ( 6 μT). The primary magnetic mineral was found to be pyrrhotite. Given the thermal history of Allende, we conclude that the remanent magnetization was formed during or after an impact event. Recent mesoscale impact modeling, where chondrules and matrix are resolved, has shown that low-velocity collisions can generate significant matrix temperatures, as pore-space compaction attenuates shock energy and dramatically increases the amount of heating. Nonporous chondrules are unaffected, and act as heat-sinks, so matrix temperature excursions are brief. We extend this work to model Allende, and show that a 1 km/s planar impact generates bulk porosity, matrix porosity, and fabric in our target that match the observed values. Bimodal mixtures of a highly porous matrix and nominally zero-porosity chondrules make chondrites uniquely capable of recording transient or unstable fields. Targets that have uniform porosity, e.g., terrestrial impact craters, will not record transient or unstable fields. Rather than a core dynamo, it is therefore possible that the origin of the magnetic field in Allende was the impact itself, or a nebula field recorded during transient impact heating.

Calabi-Yau structures on categories of matrix factorizations

NASA Astrophysics Data System (ADS)

Shklyarov, Dmytro

2017-09-01

Using tools of complex geometry, we construct explicit proper Calabi-Yau structures, that is, non-degenerate cyclic cocycles on differential graded categories of matrix factorizations of regular functions with isolated critical points. The formulas involve the Kapustin-Li trace and its higher corrections. From the physics perspective, our result yields explicit 'off-shell' models for categories of topological D-branes in B-twisted Landau-Ginzburg models.

Comparison of direct colony method versus extraction method for identification of gram-positive cocci by use of Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Alatoom, Adnan A; Cunningham, Scott A; Ihde, Sherry M; Mandrekar, Jayawant; Patel, Robin

2011-08-01

We evaluated Bruker Biotyper (version 2.0) matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for the identification of 305 clinical isolates of staphylococci, streptococci, and related genera by comparing direct colony testing with preparatory extraction. Isolates were previously identified by use of phenotypic testing and/or 16S rRNA gene sequencing. Manufacturer-specified score cutoffs for genus- and species-level identification were used. After excluding 7 isolates not present in the Biotyper library, the Biotyper correctly identified 284 (95%) and 207 (69%) isolates to the genus and species levels, respectively, using extraction. By using direct colony testing, the Biotyper identified 168 (56%) and 60 (20%) isolates to the genus and species levels, respectively. Overall, more isolates were identified to the genus and species levels with preparatory extraction than with direct colony testing (P < 0.0001). The analysis was repeated after dividing the isolates into two subgroups, staphylococci, streptococci, and enterococci (n = 217) and "related genera" (n = 81). For the former subgroup, the extraction method resulted in the identification of 213 (98%) and 171 (79%) isolates to the genus and species levels, respectively, whereas the direct colony method identified 136 (63%) and 56 (26%) isolates to the genus and species levels, respectively. In contrast, for the subgroup of related genera, the extraction method identified 71 (88%) and 36 (44%) isolates to the genus and species levels, respectively, while the direct colony method identified 32 (40%) and 4 (5%) isolates to the genus and species levels, respectively. For both subgroups, preparatory extraction was superior to direct colony testing for the identification of isolates to the genus and species levels (P < 0.0001). Preparatory extraction is needed for the identification of a substantial proportion of Gram-positive cocci using the Biotyper method according to manufacturer-specified score cutoffs.

Microfabricated bulk wave acoustic bandgap device

DOEpatents

Olsson, Roy H.; El-Kady, Ihab F.; McCormick, Frederick; Fleming, James G.; Fleming, Carol

2010-06-08

A microfabricated bulk wave acoustic bandgap device comprises a periodic two-dimensional array of scatterers embedded within the matrix material membrane, wherein the scatterer material has a density and/or elastic constant that is different than the matrix material and wherein the periodicity of the array causes destructive interference of the acoustic wave within an acoustic bandgap. The membrane can be suspended above a substrate by an air or vacuum gap to provide acoustic isolation from the substrate. The device can be fabricated using microelectromechanical systems (MEMS) technologies. Such microfabricated bulk wave phononic bandgap devices are useful for acoustic isolation in the ultrasonic, VHF, or UHF regime (i.e., frequencies of order 1 MHz to 10 GHz and higher, and lattice constants of order 100 .mu.m or less).

Microfabricated bulk wave acoustic bandgap device

DOEpatents

Olsson, Roy H.; El-Kady, Ihab F.; McCormick, Frederick; Fleming, James G.; Fleming, legal representative, Carol

2010-11-23

A microfabricated bulk wave acoustic bandgap device comprises a periodic two-dimensional array of scatterers embedded within the matrix material membrane, wherein the scatterer material has a density and/or elastic constant that is different than the matrix material and wherein the periodicity of the array causes destructive interference of the acoustic wave within an acoustic bandgap. The membrane can be suspended above a substrate by an air or vacuum gap to provide acoustic isolation from the substrate. The device can be fabricated using microelectromechanical systems (MEMS) technologies. Such microfabricated bulk wave phononic bandgap devices are useful for acoustic isolation in the ultrasonic, VHF, or UHF regime (i.e., frequencies of order 1 MHz to 10 GHz and higher, and lattice constants of order 100 .mu.m or less).

Simultaneous infrared and UV-visible absorption spectra of matrix-isolated carbon vapor

NASA Technical Reports Server (NTRS)

Kurtz, Joe; Huffman, Donald R.

1989-01-01

Carbon molecules were suggested as possible carriers of the diffuse interstellar bands. In particular, it was proposed that the 443 nm diffuse interstellar band is due to the same molecule which gives rise to the 447 nm absorption feature in argon matrix-isolated carbon vapor. If so, then an associated C-C stretching mode should be seen in the IR. By doing spectroscopy in both the IR and UV-visible regions on the same sample, the present work provides evidence for correlating UV-visible absorption features with those found in the IR. Early data indicates no correlation between the strongest IR feature (1997/cm) and the 447 nm band. Correlation with weaker IR features is being investigated.

Pyrolysis and Matrix-Isolation FTIR of Acetoin

NASA Astrophysics Data System (ADS)

Cole, Sarah; Ellis, Martha; Sowards, John; McCunn, Laura R.

2017-06-01

Acetoin, CH_3C(O)CH(OH)CH_3, is an additive used in foods and cigarettes as well as a common component of biomass pyrolysate during the production of biofuels, yet little is known about its thermal decomposition mechanism. In order to identify thermal decomposition products of acetoin, a gas-phase mixture of approximately 0.3% acetoin in argon was subject to pyrolysis in a resistively heated SiC microtubular reactor at 1100-1500 K. Matrix-isolation FTIR spectroscopy was used to identify pyrolysis products. Many products were observed in analysis of the spectra, including acetylene, propyne, ethylene, and vinyl alcohol. These results provide clues to the overall mechanism of thermal decomposition and are important for predicting emissions from many industrial and residential processes.

Advanced large scale GaAs monolithic IF switch matrix subsystem

NASA Technical Reports Server (NTRS)

Ch'en, D. R.; Petersen, W. C.; Kiba, W. M.

1992-01-01

Attention is given to a novel chip design and packaging technique to overcome the limitations due to the high signal isolation requirements of advanced communications systems. A hermetically sealed 6 x 6 monolithic GaAs switch matrix subsystem with integral control electronics based on this technique is presented. An 0-dB insertion loss and 60-dB crosspoint isolation over a 3.5-to-6-GHz band were achieved. The internal controller portion of the switching subsystem provides crosspoint control via a standard RS-232 computer interface and can be synchronized with an external systems control computer. The measured performance of this advanced switching subsystem is fully compatible with relatively static 'switchboard' as well as dynamic TDMA modes of operation.

Proglobulin processing enzyme in vacuoles isolated from developing pumpkin cotyledons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hara-Nishimura, I.; Nishimura, M.

1987-10-01

The enzymic conversion of proglobulin to globulin catalyzed by the extracts of vacuoles isolated from developing pumpkin (Cucurbita sp. cv Kurokawa Amakuri Nankin) cotyledons was investigated. The endoplasmic reticulum fraction isolated from the developing cotyledons pulse-labeled with (/sup 35/S)methionine was shown to contain mainly the radiolabeled proglobulin, which was used as a substrate for assaying the proteolytic processing in vitro. The vacuolar extracts catalyzed the proteolytic processing of the proglobulin molecule to produce globulin containing two kinds of polypeptide chains, ..gamma.. and delta. The pH optimum for the vacuole-mediated conversion was at pH 5.0. The proteolytic processing of proglobulin bymore » the vacuolar extracts was inhibited in the presence of various thiol reagents, e.g. p-chloromercuribenzoate, N-ethylmaleimide, iodoacetic acid, Hg/sup 2 +/, and Cu/sup 2 +/, but not phenylmethylsulfonyl fluoride, EDTA, o-phenanthroline, leupeptin, antipain, pepstatin, chymostatin, or pumpkin trypsin inhibitor, and was activated in the presence of dithiothreitol and cysteine, indicating that the processing enzyme is a thiol protease. The suborganellar fractionation of the vacuoles showed that the processing activity was localized in the matrix fraction, but not in the membrane or crystalloid fractions. During the seed development, the enzyme was shown to increase, exhibiting the maximal activity at the late developmental stage. The matrix fraction of the protein bodies isolated from the dry castor bean (Ricinus communis) exhibited the processing activity toward the pumpkin proglobulin molecules in the same manner as that by the matrix fraction of pumpkin vacuoles.« less

Observation of Trans-Ethanol and Gauche-Ethanol Complexes with Benzene Using Matrix Isolation Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Amicangelo, Jay; Silbaugh, Matthew J.

2016-06-01

Ethanol can exist in two conformers, one in which the OH group is trans to the methyl group (trans-ethanol) and the other in which the OH group is gauche to the methyl group (gauche-ethanol). Matrix isolation infrared spectra of ethanol deposited in 20 K argon matrices display distinct infrared peaks that can be assigned to the trans-ethanol and gauche-ethanol conformers, particularly with the O-H stretching vibrations. Given this, matrix isolation experiments were performed in which ethanol (C_2H_5OH) and benzene (C_6H_6) were co-deposited in argon matrices at 20 K in order to determine if conformer specific ethanol complexes with benzene could be observed in the infrared spectra. New infrared peaks that can be attributed to the trans-ethanol and gauche-ethanol complexes with benzene have been observed near the O-H stretching vibrations of ethanol. The initial identification of the new infrared peaks as being due to the ethanol-benzene complexes was established by performing a concentration study (1:200 to 1:1600 S/M ratios), by comparing the co-deposition spectra with the spectra of the individual monomers, by matrix annealing experiments (35 K), and by performing experiments using isotopically labeled ethanol (C_2D_5OD) and benzene (C_6D_6). Quantum chemical calculations were also performed for the C_2H_5OH-C_6H_6 complexes using density functional theory (B3LYP) and ab initio (MP2) methods. Stable minima were found for the both the trans-ethanol and gauche-ethanol complexes with benzene at both levels of theory and were predicted to have similar interaction energies. Both complexes can be characterized as H-π complexes, in which the ethanol is above the benzene ring with the hydroxyl hydrogen interacting with the π cloud of the ring. The theoretical O-H stretching frequencies for the complexes were predicted to be shifted from the monomer frequencies and from each other and these results were used to make the conformer specific infrared peak assignments. Barnes, A. J.; Hallam, H. E. Trans. Faraday Soc., 1970, 66, 1932-1940.

Kidney stone matrix proteins ameliorate calcium oxalate monohydrate induced apoptotic injury to renal epithelial cells.

PubMed

Narula, Shifa; Tandon, Simran; Singh, Shrawan Kumar; Tandon, Chanderdeep

2016-11-01

Kidney stone formation is a highly prevalent disease, affecting 8-10% of the human population worldwide. Proteins are the major constituents of human kidney stone's organic matrix and considered to play critical role in the pathogenesis of disease but their mechanism of modulation still needs to be explicated. Therefore, in this study we investigated the effect of human kidney stone matrix proteins on the calcium oxalate monohydrate (COM) mediated cellular injury. The renal epithelial cells (MDCK) were exposed to 200μg/ml COM crystals to induce injury. The effect of proteins isolated from human kidney stone was studied on COM injured cells. The alterations in cell-crystal interactions were examined by phase contrast, polarizing, fluorescence and scanning electron microscopy. Moreover, its effect on the extent of COM induced cell injury, was quantified by flow cytometric analysis. Our study indicated the antilithiatic potential of human kidney stone proteins on COM injured MDCK cells. Flow cytometric analysis and fluorescence imaging ascertained that matrix proteins decreased the extent of apoptotic injury caused by COM crystals on MDCK cells. Moreover, the electron microscopic studies of MDCK cells revealed that matrix proteins caused significant dissolution of COM crystals, indicating cytoprotection against the impact of calcium oxalate injury. The present study gives insights into the mechanism implied by urinary proteins to restrain the pathogenesis of kidney stone disease. This will provide a better understanding of the formation of kidney stones which can be useful for the proper management of the disease. Copyright © 2016 Elsevier Inc. All rights reserved.

A technique for detecting matrix proteins in the crystalline spicule of the sea urchin embryo.

PubMed

Cho, J W; Partin, J S; Lennarz, W J

1996-02-06

The presence of proteins associated with the CaCO3-containing biocrystals found in a wide variety of marine organisms is well established. In these organisms, including the primitive skeleton (spicule) of the sea urchin embryo, the structural and functional role of these proteins either in the biomineralization process or in control of the structural features of the biocrystals is unclear. Recently, one of the matrix proteins of the sea urchin spicule, SM 30, has been shown to contain a carbohydrate chain (the 1223 epitope) that has been implicated in the process whereby Ca2+ is deposited as CaCo3. Because an understanding of the localization of this protein, as well as other proteins found within the spicule, is central to understanding their function, we undertook to develop methods to localize spicule matrix proteins in intact spicules, using immunogold techniques and scanning electron microscopy. Gold particles indicative of this matrix glycoprotein could not be detected on the surface of spicules that had been isolated from embryo homogenates and treated with alkaline hypochlorite to remove any associated membranous material. However, when isolated spicules were etched for 2 min with dilute acetic acid (10 mM) to expose more internal regions of the crystal, SM 30 and perhaps other proteins bearing the 1223 carbohydrate epitope were detected in the calcite matrix. These results, indicating that these two antigens are widely distributed in the spicule, suggest that this technique should be applicable to any matrix protein for which antibodies are available.

Near-infrared and ultraviolet induced isomerization of crotonic acid in N{sub 2} and Xe cryomatrices: First observation of two high-energy trans C–O conformers and mechanistic insights

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuş, Nihal; Department of Physics, Anadolu University, 26470 Eskişehir; Fausto, Rui, E-mail: rfausto@ci.uc.pt

2014-12-21

E-crotonic acid was isolated in cryogenic solid N{sub 2} and xenon matrices, and subjected to Laser ultraviolet (UV) and near-infrared (NIR) irradiations. In the deposited matrices, the two low-energy cis C–O E-cc and E-ct conformers, which are the only forms significantly populated in the gas phase, were observed. UV irradiation (λ= 250 nm) of the compound in N{sub 2} matrix allows for experimental detection, not just of the two low-energy cis C–O isomers of Z-crotonic acid previously observed in the experiments carried out in argon matrix [Z-cc and Z-ct; R. Fausto, A. Kulbida, and O. Schrems, J. Chem. Soc., Faradaymore » Trans. 91, 3755–3770 (1995)] but also of the never observed before high-energy forms of both E- and Z-crotonic acids bearing the carboxylic acid group in the trans arrangement (E-tc and Z-tc conformers). In turn, NIR irradiation experiments in the N{sub 2} matrix allow to produce the high-energy E-tc trans C–O conformer in a selective way, from the initially deposited E-cc form. The vibrational signatures of all the 6 rotameric structures of the crotonic acids experimentally observed, including those of the new trans C–O forms, were determined and the individual spectra fully assigned, also with support of theoretically obtained data. On the other hand, as found before for the compound isolated in argon matrix, the experiments performed in xenon matrix failed to experimental detection of the trans C–O forms. This demonstrates that in noble gas matrices these forms are not stable long enough to allow for their observation by steady state spectroscopy techniques. In these matrices, the trans C–O forms convert spontaneously into their cis C–O counterparts, by tunnelling. Some mechanistic details of the studied processes were extracted and discussed.« less

The use of Matrix-assisted laser desorption ionization-time of flight mass spectrometry in the identification of Francisella tularensis.

PubMed

Karatuna, Onur; Celebi, Bekir; Can, Simge; Akyar, Isin; Kilic, Selcuk

2016-01-15

Francisella tularensis is the cause of the zoonotic disease tularemia and is classified among highly pathogenic bacteria (HPB) due to its low infection dose and potential for airborne transmission. In the case of HBP, there is a pressing need for rapid, accurate and reliable identification. Phenotypic identification of Francisella species is inappropriate for clinical microbiology laboratories because it is time-consuming, hazardous and subject to variable interpretation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was recently evaluated as a useful tool for the rapid identification of a variety of microorganisms. In this study, we evaluated the use of MALDI-TOF MS for the rapid identification of Francisella tularensis and differentiation of its subspecies. Using national collection of Francisella isolates from the National Tularemia Reference Laboratory (Public Health Institute of Turkey, Ankara), a total of 75 clinical isolates were investigated by species and subspecies-specific polymerase chain reaction (PCR) test and MALDI-TOF MS. All isolates were originally identified as F. tularensis subsp. holarctica due to RD1 subspecies-specific PCR result. For all isolates MALDI-TOF MS provided results in concordance with subspecies-specific PCR analysis. Although PCR-based methods are effective in identifying Francisella species, they are labor-intensive and take longer periods of time to obtain the results when compared with MALDI-TOF MS. MALDI-TOF MS appeared to be a rapid, reliable and cost-effective identification technique for Francisella spp. Shorter analysis time and low cost make this an appealing new option in microbiology laboratories.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Burkholderia pseudomallei from Asia and Australia and differentiation between Burkholderia species

PubMed Central

Suttisunhakul, Vichaya; Pumpuang, Apinya; Ekchariyawat, Peeraya; Wuthiekanun, Vanaporn; Elrod, Mindy G.; Turner, Paul; Currie, Bart J.; Phetsouvanh, Rattanaphone; Dance, David A. B.; Limmathurotsakul, Direk; Peacock, Sharon J.

2017-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for rapid bacterial identification. Studies of Burkholderia pseudomallei identification have involved small isolate numbers drawn from a restricted geographic region. There is a need to expand the reference database and evaluate B. pseudomallei from a wider geographic distribution that more fully captures the extensive genetic diversity of this species. Here, we describe the evaluation of over 650 isolates. Main spectral profiles (MSP) for 26 isolates of B. pseudomallei (N = 5) and other Burkholderia species (N = 21) were added to the Biotyper database. MALDI-TOF MS was then performed on 581 B. pseudomallei, 19 B. mallei, 6 B. thailandensis and 23 isolates representing a range of other bacterial species. B. pseudomallei originated from northeast and east Thailand (N = 524), Laos (N = 12), Cambodia (N = 14), Hong Kong (N = 4) and Australia (N = 27). All 581 B. pseudomallei were correctly identified, with 100% sensitivity and specificity. Accurate identification required a minimum inoculum of 5 x 107 CFU/ml, and identification could be performed on spiked blood cultures after 24 hours of incubation. Comparison between a dendrogram constructed from MALDI-TOF MS main spectrum profiles and a phylogenetic tree based on recA gene sequencing demonstrated that MALDI-TOF MS distinguished between B. pseudomallei and B. mallei, while the recA tree did not. MALDI-TOF MS is an accurate method for the identification of B. pseudomallei, and discriminates between this and other related Burkholderia species. PMID:28384252

The use of matrix-assisted laser desorption ionization-time of flight mass spectrometry in the identification of Francisella tularensis

PubMed Central

Karatuna, Onur; Çelebi, Bekir; Can, Simge; Akyar, Işın; Kiliç, Selçuk

2016-01-01

Francisella tularensis is the cause of the zoonotic disease tularemia and is classified among highly pathogenic bacteria (HPB) due to its low infection dose and potential for airborne transmission. In the case of HBP, there is a pressing need for rapid, accurate and reliable identification. Phenotypic identification of Francisella species is inappropriate for clinical microbiology laboratories because it is time-consuming, hazardous and subject to variable interpretation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was recently evaluated as a useful tool for the rapid identification of a variety of microorganisms. In this study, we evaluated the use of MALDI-TOF MS for the rapid identification of Francisella tularensis and differentiation of its subspecies. Using national collection of Francisella isolates from the National Tularemia Reference Laboratory (Public Health Institution of Turkey, Ankara), a total of 75 clinical isolates were investigated by species and subspecies-specific polymerase chain reaction (PCR) test and MALDI-TOF MS. All isolates were originally identified as F. tularensis subsp. holarctica according to region of difference 1 (RD1) subspecies-specific PCR results. For all isolates MALDI-TOF MS provided results in concordance with subspecies-specific PCR analysis. Although PCR-based methods are effective in identifying Francisella species, they are labor-intensive and take longer periods of time to obtain the results when compared with MALDI-TOF MS. MALDI-TOF MS appeared to be a rapid, reliable and cost-effective identification technique for Francisella spp. Shorter analysis time and low cost make this an appealing new option in microbiology laboratories. PMID:26773181

Pro-angiogenic capacities of microvesicles produced by skin wound myofibroblasts.

PubMed

Merjaneh, Mays; Langlois, Amélie; Larochelle, Sébastien; Cloutier, Chanel Beaudoin; Ricard-Blum, Sylvie; Moulin, Véronique J

2017-08-01

Wound healing is a very highly organized process where numerous cell types are tightly regulated to restore injured tissue. Myofibroblasts are cells that produce new extracellular matrix and contract wound edges. We previously reported that the human myofibroblasts isolated from normal wound (WMyos) produced microvesicles (MVs) in the presence of the serum. In this study, MVs were further characterized using a proteomic strategy and potential functions of the MVs were determined. MV proteins isolated from six WMyo populations were separated using two-dimensional differential gel electrophoresis. Highly conserved spots were selected and analyzed using mass spectrometry resulting in the identification of 381 different human proteins. Using the DAVID database, clusters of proteins involved in cell motion, apoptosis and adhesion, but also in extracellular matrix production (21 proteins, enrichment score: 3.32) and in blood vessel development/angiogenesis (19 proteins, enrichment score: 2.66) were identified. Another analysis using the functional enrichment analysis tool FunRich was consistent with these results. While the action of the myofibroblasts on extracellular matrix formation is well known, their angiogenic potential is less studied. To further characterize the angiogenic activity of the MVs, they were added to cultured microvascular endothelial cells to evaluate their influence on cell growth and migration using scratch test and capillary-like structure formation in Matrigel ® . The addition of a MV-enriched preparation significantly increased endothelial cell growth, migration and capillary formation compared with controls. The release of microvesicles by the wound myofibroblasts brings new perspectives to the field of communication between cells during the normal healing process.

The Isolation and Characterization of Glycosylated Phosphoproteins from Herring Fish Bones*

PubMed Central

Zhou, Hai-Yan; Salih, Erdjan; Glimcher, Melvin J.

2010-01-01

Past studies of bone extracellular matrix phosphoproteins such as osteopontin and bone sialoprotein have yielded important biological information regarding their role in calcification and the regulation of cellular activity. Most of these studies have been limited to proteins extracted from mammalian and avian vertebrates and nonvertebrates. The present work describes the isolation and purification of two major highly glycosylated and phosphorylated extracellular matrix proteins of 70 and 22 kDa from herring fish bones. The 70-kDa phosphoprotein has some characteristics of osteopontin with respect to amino acid composition and susceptibility to thrombin cleavage. Unlike osteopontin, however, it was found to contain high levels of sialic acid similar to bone sialoprotein. The 22-kDa protein has very different properties such as very high content of phosphoserine (∼270 Ser(P) residues/1000 amino acid residues), Ala, and Asx residues. The N-terminal amino acid sequence analysis of both the 70-kDa (NPIMA(M)ETTS(M)DSKVNPLL) and the 22-kDa (NQDMAMEASSDPEAA) fish phosphoproteins indicate that these unique amino acid sequences are unlike any published in protein databases. An enzyme-linked immunosorbent assay revealed that the 70-kDa phosphoprotein was present principally in bone and in calcified scales, whereas the 22-kDa phosphoprotein was detected only in bone. Immunohistological analysis revealed diffusely positive immunostaining for both the 70- and 22-kDa phosphoproteins throughout the matrix of the bone. Overall, this work adds additional support to the concept that the mechanism of biological calcification has common evolutionary and fundamental bases throughout vertebrate species. PMID:20833721

First step in developing a 3D biodegradable fibrin scaffold for an artificial ovary

PubMed Central

2013-01-01

Background Although transplantation of cryopreserved ovarian tissue is a promising approach to restore fertility in cancer patients, it is not advisable for women at risk of ovarian involvement due to the threat of reintroducing malignant cells. The aim of this study was therefore to find an alternative for these patients by development of an artificial ovary. Methods For construction of the artificial ovary matrix, we used a central composite design to investigate nine combinations of fibrinogen (mg/ml) and thrombin (IU/mL) (F/T): F1/T4, F12.5/T1, F12.5/T20, F25/T0.1, F25/T4, F25/T500, F50/T1, F50/T20 and F100/T4. From the first qualitative analyses (handling and matrix size), five combinations (F12.5/T1, F25/T4, F50/T20, F50/T1 and F100/T4) yielded positive results. They were further evaluated in order to assess fibrin matrix degradation and homogeneous cell encapsulation (density), survival and proliferation (Ki67), and atresia (TUNEL) before and after 7 days of in vitro culture. To determine the best compromise between maximizing the dynamic density (Y1) and minimizing the apoptosis rate (Y2), we used the desirability function approach. Results Two combinations (F12.5/T1 and F25/T4) showed greater distribution of cells before in vitro culture, reproducible degradation of the fibrin network and adequate support for isolated human ovarian stromal cells, with a high proportion of Ki67-positive cells. SEM analysis revealed a network of fibers with regular pores and healthy stromal cells after in vitro culture with both F/T combinations. Conclusion This study reports two optimal F/T combinations that allow survival and proliferation of isolated human ovarian cells. Further studies are required to determine if such a scaffold will also be a suitable environment for isolated ovarian follicles. PMID:24274108

Infrared matrix isolation and theoretical studies of reactions of ozone with bicyclic alkenes: α-pinene, norbornene, and norbornadiene.

PubMed

Kugel, Roger W; Ault, Bruce S

2015-01-15

The reactions of ozone with three bicyclic alkenes, α-pinene, norbornene, and norbornadiene, were studied by low-temperature (14 K), argon matrix isolation infrared spectroscopy including (18)O isotope-labeling studies. Theoretical calculations of some of the proposed reaction intermediates and products were carried out using the Gaussian 09 suite of programs, applying density functional theory (DFT), the B3LYP functional, and the 6-311G++(d,2p) basis set. In the α-pinene/ozone system, the thermal reaction between α-pinene and ozone was too slow to observe under the twin-jet or merged-jet deposition conditions of these experiments. However, red light (λ ≥ 600 nm) irradiation of the argon matrixes containing α-pinene and ozone caused new infrared peaks to appear that could be readily assigned to reaction products of α-pinene with O((3)P) resulting from ozone photolysis: α-pinene oxide (with an epoxide ring) and two isomeric ketones. Norbornene and norbornadiene were both found to react with ozone in the gas phase during twin-jet or merged-jet deposition of these mixtures with argon. New peaks observed in the infrared spectra were assigned to the primary ozonides, Criegee intermediates, and secondary ozonides of norbornene and norbornadiene, indicating that the bulk of these reactions proceeded via the "classic" Criegee mechanism for ozonolysis of alkenes. Calculated infrared frequencies and molecular energies support these conclusions. Ultraviolet irradiation of these mixtures resulted in complete decomposition of the early intermediates and the formation of acids, aldehydes, alcohols, carbon dioxide, and carbon monoxide. In any case, no evidence for "unusual" chemistry, prompted by the bicyclic nature of the reactants, was observed.

Compression-induced structural and mechanical changes of fibrin-collagen composites.

PubMed

Kim, O V; Litvinov, R I; Chen, J; Chen, D Z; Weisel, J W; Alber, M S

2017-07-01

Fibrin and collagen as well as their combinations play an important biological role in tissue regeneration and are widely employed in surgery as fleeces or sealants and in bioengineering as tissue scaffolds. Earlier studies demonstrated that fibrin-collagen composite networks displayed improved tensile mechanical properties compared to the isolated protein matrices. Unlike previous studies, here unconfined compression was applied to a fibrin-collagen filamentous polymer composite matrix to study its structural and mechanical responses to compressive deformation. Combining collagen with fibrin resulted in formation of a composite hydrogel exhibiting synergistic mechanical properties compared to the isolated fibrin and collagen matrices. Specifically, the composite matrix revealed a one order of magnitude increase in the shear storage modulus at compressive strains>0.8 in response to compression compared to the mechanical features of individual components. These material enhancements were attributed to the observed structural alterations, such as network density changes, an increase in connectivity along with criss-crossing, and bundling of fibers. In addition, the compressed composite collagen/fibrin networks revealed a non-linear transformation of their viscoelastic properties with softening and stiffening regimes. These transitions were shown to depend on protein concentrations. Namely, a decrease in protein content drastically affected the mechanical response of the networks to compression by shifting the onset of stiffening to higher degrees of compression. Since both natural and artificially composed extracellular matrices experience compression in various (patho)physiological conditions, our results provide new insights into the structural biomechanics of the polymeric composite matrix that can help to create fibrin-collagen sealants, sponges, and tissue scaffolds with tunable and predictable mechanical properties. Copyright © 2016 Elsevier B.V. All rights reserved.

Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry to identify MLST clade 4 Clostridium difficile isolates.

PubMed

Cheng, Jing-Wei; Liu, Chang; Kudinha, Timothy; Xiao, Meng; Yu, Shu-Ying; Yang, Chun-Xia; Wei, Ming; Liang, Guo-Wei; Shao, Dong-Hua; Kong, Fanrong; Tong, Zhao-Hui; Xu, Ying-Chun

2018-04-26

Clostridium difficile is the leading cause of health care-associated infections. Previous studies suggest that C. difficile MLST clade 4 strains with higher drug resistance rates constitute the major clone spreading in China. Thus development of a rapid and accurate typing method for these strains is needed to monitor the epidemiology of this clone and to guide clinical treatment. A total of 160 non-duplicate C. difficile isolates recovered from three large teaching hospitals in Beijing were studied. All the 41 clade 4 C. difficile isolates clustered together on the PCA dendrogram. Spectra peak statistics revealed that five markers (2691.43Da, 2704.91Da, 2711.93Da, 3247.27Da and 3290.76Da) can easily and reliably distinguish between clade 4 and non-clade 4 isolates, with area under the curve (AUC) values of 0.991, 0.997, 0.973, 1 and 1, respectively. In conclusion, MALDI-TOF MS is a very simple and accurate method for identifying C. difficile MLST clade 4 strains. Copyright © 2018 Elsevier Inc. All rights reserved.

Genetic variation of coat protein gene among the isolates of Rice tungro spherical virus from tungro-endemic states of the India.

PubMed

Mangrauthia, Satendra K; Malathi, P; Agarwal, Surekha; Ramkumar, G; Krishnaveni, D; Neeraja, C N; Madhav, M Sheshu; Ladhalakshmi, D; Balachandran, S M; Viraktamath, B C

2012-06-01

Rice tungro disease, one of the major constraints to rice production in South and Southeast Asia, is caused by a combination of two viruses: Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV). The present study was undertaken to determine the genetic variation of RTSV population present in tungro endemic states of Indian subcontinent. Phylogenetic analysis based on coat protein sequences showed distinct divergence of Indian RTSV isolates into two groups; one consisted isolates from Hyderabad (Andhra Pradesh), Cuttack (Orissa), and Puducherry and another from West Bengal, Coimbatore (Tamil Nadu), and Kanyakumari (Tamil Nadu). The results obtained from phylogenetic study were further supported with the SNPs (single nucleotide polymorphism), INDELs (insertion and deletion) and evolutionary distance analysis. In addition, sequence difference count matrix revealed 2-68 nucleotides differences among all the Indian RTSV isolates taken in this study. However, at the protein level these differences were not significant as revealed by Ka/Ks ratio calculation. Sequence identity at nucleotide and amino acid level was 92-100% and 97-100%, respectively, among Indian isolates of RTSV. Understanding of the population structure of RTSV from tungro endemic regions of India would potentially provide insights into the molecular diversification of this virus.

MT1-MMP is a crucial promotor of synovial invasion in human rheumatoid arthritis

PubMed Central

Miller, Mary-Clare; Manning, Hugh B.; Jain, Abhilash; Troeberg, Linda; Dudhia, Jayesh; Essex, David; Sandison, Ann; Seiki, Motoharu; Nanchahal, Jagdeep; Nagase, Hideaki; Itoh, Yoshifumi

2010-01-01

Objective A hallmark of rheumatoid arthritis (RA) is invasion of the synovial pannus into cartilage and this step requires degradation of the collagen matrix. The aim of this study was to explore the role of one of the collagen-degrading matrix metalloproteinases (MMPs), membrane-type 1 MMP (MT1-MMP), in synovial pannus invasiveness. Methods Expression and localization of MT1-MMP in human RA pannus were investigated by Western blot analysis of primary synovial cells and immunohistochemistry of RA joints specimens. The functional role of MT1-MMP was analyzed by 3D collagen invasion assays and a cartilage invasion assay in the presence or absence of tissue inhibitor of metalloproteinase (TIMP)-1, TIMP-2, or GM6001. The effect of adenoviral expression of a dominant negative MT1-MMP construct lacking a catalytic domain was also examined. Results MT1-MMP was highly expressed at the pannus-cartilage junction of RA joints. Freshly isolated rheumatoid synovial tissues and isolated RA synovial fibroblasts invaded into a 3D collagen matrix in an MT1-MMP-dependent manner. Invasion was blocked by TIMP-2 and GM6001, but not by TIMP-1. It was also inhibited by the over-expression of a dominant negative MT1-MMP which inhibits collagenolytic activity and proMMP-2 activation by MT1-MMP on the cell surface. Synovial fibroblasts also invaded into cartilage in an MT1-MMP-dependent manner. This process was further enhanced by removing aggrecan from the cartilage matrix. Conclusion MT1-MMP is an essential collagen-degrading proteinase during pannus invasion in human RA. Specific inhibition of MT1-MMP-dependent invasion may form a novel therapeutic strategy for RA. PMID:19248098

Effect of 3D-scaffold formation on differentiation and survival in human neural progenitor cells.

PubMed

Ortinau, Stefanie; Schmich, Jürgen; Block, Stephan; Liedmann, Andrea; Jonas, Ludwig; Weiss, Dieter G; Helm, Christiane A; Rolfs, Arndt; Frech, Moritz J

2010-11-11

3D-scaffolds have been shown to direct cell growth and differentiation in many different cell types, with the formation and functionalisation of the 3D-microenviroment being important in determining the fate of the embedded cells. Here we used a hydrogel-based scaffold to investigate the influences of matrix concentration and functionalisation with laminin on the formation of the scaffolds, and the effect of these scaffolds on human neural progenitor cells cultured within them. In this study we used different concentrations of the hydrogel-based matrix PuraMatrix. In some experiments we functionalised the matrix with laminin I. The impact of concentration and treatment with laminin on the formation of the scaffold was examined with atomic force microscopy. Cells from a human fetal neural progenitor cell line were cultured in the different matrices, as well as in a 2D culture system, and were subsequently analysed with antibody stainings against neuronal markers. In parallel, the survival rate of the cells was determined by a live/dead assay. Atomic force microscopy measurements demonstrated that the matrices are formed by networks of isolated PuraMatrix fibres and aggregates of fibres. An increase of the hydrogel concentration led to a decrease in the mesh size of the scaffolds and functionalisation with laminin promoted aggregation of the fibres (bundle formation), which further reduces the density of isolated fibres. We showed that laminin-functionalisation is essential for human neural progenitor cells to build up 3D-growth patterns, and that proliferation of the cells is also affected by the concentration of matrix. In addition we found that 3D-cultures enhanced neuronal differentiation and the survival rate of the cells compared to 2D-cultures. Taken together, we have demonstrated a direct influence of the 3D-scaffold formation on the survival and neuronal differentiation of human neural progenitor cells. These findings emphasize the importance of optimizing 3D-scaffolds protocols prior to in vivo engraftment of stem and progenitor cells in the context of regenerative medicine.

Early detection of metallo-β-lactamase NDM-1- and OXA-23 carbapenemase-producing Acinetobacter baumannii in Libyan hospitals.

PubMed

Mathlouthi, Najla; El Salabi, Allaaeddin Ali; Ben Jomàa-Jemili, Mariem; Bakour, Sofiane; Al-Bayssari, Charbel; Zorgani, Abdulaziz A; Kraiema, Abdulmajeed; Elahmer, Omar; Okdah, Liliane; Rolain, Jean-Marc; Chouchani, Chedly

2016-07-01

Acinetobacter baumannii is an opportunistic pathogen causing various nosocomial infections. The aim of this study was to characterise the molecular support of carbapenem-resistant A. baumannii clinical isolates recovered from two Libyan hospitals. Bacterial isolates were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antibiotic susceptibility testing was performed using disk diffusion and Etest methods, and carbapenem resistance determinants were studied by PCR amplification and sequencing. Multilocus sequence typing (MLST) was performed for typing of the isolates. All 36 imipenem-resistant isolates tested were identified as A. baumannii. The blaOXA-23 gene was detected in 29 strains (80.6%). The metallo-β-lactamase blaNDM-1 gene was detected in eight isolates (22.2%), showing dissemination of multidrug-resistant (MDR) A. baumannii in Tripoli Medical Center and Burn and Plastic Surgery Hospital in Libya, including one isolate that co-expressed the blaOXA-23 gene. MLST revealed several sequence types (STs). Imipenem-resistant A. baumannii ST2 was the predominant clone (16/36; 44.4%). This study shows that NDM-1 and OXA-23 contribute to antibiotic resistance in Libyan hospitals and represents the first incidence of the association of these two carbapenemases in an autochthonous MDR A. baumannii isolated from patients in Libya, indicating that there is a longstanding infection control problem in these hospitals. Copyright © 2016 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

The differentiation and isolation of mouse embryonic stem cells toward hepatocytes using galactose-carrying substrata.

PubMed

Meng, Qingyuan; Haque, Amranul; Hexig, Bayar; Akaike, Toshihiro

2012-02-01

A simple culture system to achieve the differentiation of embryonic stem (ES) cells toward hepatocytes with high efficiency is crucial in providing a cell source for the medical application. In this study, we report the effect of a matrix-dependent enrichment of ES cell-derived hepatocytes using immobilized poly(N-p-vinylbenzyl-4-O-β-D-galactopyranosyl-D-gluconamide) (PVLA) with E-cadherin-IgG Fc (E-cad-Fc) as a galactose-carrying substratum. PVLA and E-cad-Fc were confirmed to be stably co-adsorbed onto polystyrene surface by quartz crystal microbalance (QCM). We showed that the E-cad-Fc/PVLA hybrid substratum was efficient in culturing primary hepatocytes and maintaining liver functions, on which the undifferentiated ES cells also maintained high proliferative capability. Furthermore, ES cell-derived hepatocytes on this hybrid matrix expressed elevated level of liver specific genes and functions together with early expression of definitive hepatocyte marker, asialoglycoprotein receptor (ASGPR). Finally, we isolated a high percentage of cells (about 60%) with ASGPR expression after re-seeding onto PVLA-coated surface, and observed the elimination of the poorly differentiated cells (Gata6(+) and Sox17(+)) and the ones toward another cell lineage (brachyury(+) and Pdx1(+)). The system uses a glycopolymer as an extracellular substratum for isolation and enrichment of ES cell-derived hepatocytes with adequate homogeneity and functionality. Copyright © 2011 Elsevier Ltd. All rights reserved.

Matrix isolation infrared spectroscopic and theoretical study of 1,1,1-trifluoro-2-chloroethane (HCFC-133a)

NASA Astrophysics Data System (ADS)

Rodrigues, Gessenildo Pereira; Lucena, Juracy Régis; Ventura, Elizete; Andrade do Monte, Silmar; Reva, Igor; Fausto, Rui

2013-11-01

The molecular structure and infrared spectrum of the atmospheric pollutant 1,1,1-trifluoro-2-chloroethane (HCFC-133a; CF3CH2Cl) in the ground electronic state were characterized experimentally and theoretically. Excited state calculations (at the CASSCF, MR-CISD, and MR-CISD+Q levels) have also been performed in the range up to ˜9.8 eV. The theoretical calculations show the existence of one (staggered) conformer, which has been identified spectroscopically for the monomeric compound isolated in cryogenic (˜10 K) argon and xenon matrices. The observed infrared spectra of the matrix-isolated HCFC-133a were interpreted with the aid of MP2/aug-cc-pVTZ calculations and normal coordinate analysis, which allowed a detailed assignment of the observed spectra to be carried out, including identification of bands due to different isotopologues (35Cl and 37Cl containing molecules). The calculated energies of the several excited states along with the values of oscillator strengths and previous results obtained for CFCs and HCFCs suggest that the previously reported photolyses of the title compound at 147 and 123.6 nm [T. Ichimura, A. W. Kirk, and E. Tschuikow-Roux, J. Phys. Chem. 81, 1153 (1977)] are likely to be initiated in the n-4s and n-4p Rydberg states, respectively.

Effect of type and content of modified montmorillonite on the structure and properties of bio-nanocomposite films based on soy protein isolate and montmorillonite

USDA-ARS?s Scientific Manuscript database

The non-biodegradable and non-renewable nature of plastic packaging has led to a renewed interest in packaging materials based on bio-nanocomposites (biopolymer matrix reinforced with nanoparticles such as layered silicates). Bio-nanocomposite films based on soy protein isolate (SPI) and modified mo...

Application and evaluation of the matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry method to identify Moraxella bovoculi and Moraxella bovis isolates from cattle

USDA-ARS?s Scientific Manuscript database

Infectious bovine keratoconjunctivitis (IBK) is an economically significant disease caused by Moraxella bovis. Moraxella bovoculi, although not reported to cause IBK, has been isolated from bovine eyes during IBK outbreaks more frequently then M. bovis. Identification of M. bovis and M. bovoculi ca...

Detection of Escherichia coli sequence type 131 by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: implications for infection control policies?

PubMed

Lafolie, J; Sauget, M; Cabrolier, N; Hocquet, D; Bertrand, X

2015-07-01

Sequence type 131 (ST131) is a predominant lineage among extraintestinal pathogenic Escherichia coli. It plays a major role in the worldwide dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. The ST131 pandemic is mainly the result of clonal expansion of the single well-adapted subclone H30-Rx, which is acquired in hospitals more frequently than other ESBL-producing E. coli clones. To develop a rapid method using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify ST131 for infection control purposes. Peak biomarkers of ST131 were identified from the mass spectrum profiles of 109 E. coli isolates (including 50 ST131 isolates). The models accurately identified ST131 isolates from mass spectrum profiles obtained with and without protein extraction. The rapid identification of ST131 isolates with MALDI-TOF MS can be easily implemented in the laboratory, and could help to target infection control measures in patients carrying multi-drug-resistant E. coli that are more likely to spread. Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Multiyear Surveillance for Avian Influenza Virus in Waterfowl from Wintering Grounds, Texas Coast, USA

PubMed Central

Ferro, Pamela J.; Budke, Christine M.; Peterson, Markus J.; Cox, Dayna; Roltsch, Emily; Merendino, Todd; Nelson, Matt

2010-01-01

We studied the prevalence of influenza A virus in wintering waterfowl from the Central Flyway on the Gulf Coast of Texas. Of 5,363 hunter-harvested migratory and resident waterfowl and wetland-associated game birds sampled during 3 consecutive hunting seasons (September–January 2006–07, 2007–08, and 2008–09), real-time reverse transcription–PCR detected influenza A matrix sequences in 8.5% of samples, H5 in 0.7%, and H7 in 0.6%. Virus isolation yielded 134 influenza A viruses, including N1–N9, H1–H7, H10, and H11 subtypes. Low-pathogenicity H7 subtype was isolated during January, September, and November 2007 and January 2008; low-pathogenicity H5 subtype was isolated during November and December 2007. PMID:20678315

Biomechanics of isolated tomato (Solanum lycopersicum L.) fruit cuticles: the role of the cutin matrix and polysaccharides.

PubMed

López-Casado, Gloria; Matas, Antonio J; Domínguez, Eva; Cuartero, Jesús; Heredia, Antonio

2007-01-01

The mechanical characteristics of the cuticular membrane (CM), a complex composite biopolymer basically composed of a cutin matrix, waxes, and hydrolysable polysaccharides, have been described previously. The biomechanical behaviour and quantitative contribution of cutin and polysaccharides have been investigated here using as experimental material mature green and red ripe tomato fruits. Treatment of isolated CM with anhydrous hydrogen fluoride in pyridine allowed the selective elimination of polysaccharides attached to or incrusted into the cutin matrix. Cutin samples showed a drastic decrease in elastic modulus and stiffness (up to 92%) compared with CM, which clearly indicates that polysaccharides incorporated into the cutin matrix are responsible for the elastic modulus, stiffness, and the linear elastic behaviour of the whole cuticle. Reciprocally, the viscoelastic behaviour of CM (low elastic modulus and high strain values) can be assigned to the cutin. These results applied both to mature green and red ripe CM. Cutin elastic modulus, independently of the degree of temperature and hydration, was always significantly higher for the ripe than for the green samples while strain was lower; the amount of phenolics in the cutin network are the main candidates to explain the increased rigidity from mature green to red ripe cutin. The polysaccharide families isolated from CM were pectin, hemicellulose, and cellulose, the main polymers associated with the plant cell wall. The three types of polysaccharides were present in similar amounts in CM from mature green and red ripe tomatoes. Physical techniques such as X-ray diffraction and Raman spectroscopy indicated that the polysaccharide fibres were mainly randomly oriented. A tomato fruit CM scenario at the supramolecular level that could explain the observed CM biomechanical properties is presented and discussed.

Engineering Interfaces in Metal Matrix Composites (Volume 3)

DTIC Science & Technology

1988-06-10

Howard S. Landis and James A. Cornie Interfaces with Controlled Toughness as Mechanical Fuses to Isolate Fibers from Damage -Vijay Gupta, All S. Argon and...protect the re- inforcing fiber from damage resulting from fracture of surrounding fibers or from misfitting reaction products between the matrix and...properties to govern the decoupling of the fiber from its damaging surroundings, while maintaining full wetting contact along the interface between

Selection of potential probiotic Enterococcus faecium isolated from Portuguese fermented food.

PubMed

Barbosa, Joana; Borges, Sandra; Teixeira, Paula

2014-11-17

Four Enterococcus faecium strains isolated from fermented products were evaluated for potential use as probiotic strains. In addition to efaAfm gene, commonly found in E. faecium food isolates, none of the isolates possessed virulence genes and none had positive reactions for the production of tyramine, histamine, putrescine and cadaverine in the screening medium used. All of these four isolates proved to be resistant to 65 °C. E. faecium 119 did not show antimicrobial activity against any of the target bacteria investigated. E. faecium 85 and 101 inhibited Listeria innocua and E. faecium DSMZ 13590. The strain E. faecium 120 inhibited seven target bacteria (Listeria monocytogenes 7946, L. monocytogenes 7947, L. innocua 2030c, L. innocua NCTC 11286, E. faecium DSMZ 13590, Enterococcus faecalis ATCC 29212 and Staphylococcus aureus ATCC 29213) and was chosen as the representative to assess the ability to survive gastrointestinal tract passage simulation, as well as the protective role of two food matrices (skim milk and Alheira) during its passage. For both matrices used, no significant differences (p<0.05) were obtained between the types of digestion - quick and slow passage simulation. In the skim milk matrix the isolate was reduced to values below the detection limit of the enumeration technique by the end of the two digestions, in contrast to the Alheira matrix, for which isolate 120 showed a reduction of only ca. 1 log CFU/ml. The E. faecium strain 120 was shown to be a potential candidate for further investigations as a potential probiotic culture. Copyright © 2014. Published by Elsevier B.V.

Effects of solid-medium type on routine identification of bacterial isolates by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Anderson, Neil W; Buchan, Blake W; Riebe, Katherine M; Parsons, Lauren N; Gnacinski, Stacy; Ledeboer, Nathan A

2012-03-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid method for the identification of bacteria. Factors that may alter protein profiles, including growth conditions and presence of exogenous substances, could hinder identification. Bacterial isolates identified by conventional methods were grown on various media and identified using the MALDI Biotyper (Bruker Daltonics, Billerica, MA) using a direct smear method and an acid extraction method. Specimens included 23 Pseudomonas isolates grown on blood agar, Pseudocel (CET), and MacConkey agar (MAC); 20 Staphylococcus isolates grown on blood agar, colistin-nalidixic acid agar (CNA), and mannitol salt agar (MSA); and 25 enteric isolates grown on blood agar, xylose lysine deoxycholate agar (XLD), Hektoen enteric agar (HE), salmonella-shigella agar (SS), and MAC. For Pseudomonas spp., the identification rate to genus using the direct method was 83% from blood, 78% from MAC, and 94% from CET. For Staphylococcus isolates, the identification rate to genus using the direct method was 95% from blood, 75% from CNA, and 95% from MSA. For enteric isolates, the identification rate to genus using the direct method was 100% from blood, 100% from MAC, 100% from XLD, 92% from HE, and 87% from SS. Extraction enhanced identification rates. The direct method of MALDI-TOF analysis of bacteria from selective and differential media yields identifications of varied confidence. Notably, Staphylococci spp. from CNA exhibit low identification rates. Extraction enhances identification rates and is recommended for colonies from this medium.

Characterization of OXA-48-like-producing Enterobacteriaceae isolated from river water in Algeria.

PubMed

Tafoukt, Rima; Touati, Abdelaziz; Leangapichart, Thongpan; Bakour, Sofiane; Rolain, Jean-Marc

2017-09-01

The spread of carbapenemase-producing Enterobacteriaceae (CPE) is a significant problem for healthcare worldwide. The prevalence of carbapenem-resistant Enterobacteriaceae (CPE) in water environments in Algeria are unknown. The aim of this study was to screen for the presence of CPE isolates in the Soummam River in Bejaia, Algeria. Isolates of Enterobacteriaceae recovered from twelve samples of river water and showing reduced susceptibility to carbapenems were included in this study. The isolates were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Isolates were subjected to antimicrobial susceptibility testing and the modified Carba NP test. Carbapenemase and extended-spectrum β-lactamase (ESBL) determinants were studied by PCR amplification and sequencing. The clonal relatedness between isolates was studied by Multilocus Sequence Typing (MLST) method. A total of 20 carbapenem-resistant Enterobacteriaceae strains were included in this study, identified as Escherichia coli (n = 12), Klebsiella pneumoniae (n = 3), Raoultella ornithinolytica (n = 3), Citrobacter freundii (n = 1) and Citrobacter braakii (n = 1). Carbapenemase genes identified in this study included bla OXA-48 , observed in 17 isolates (9 E. coli, 3 K. pneumoniae, 3 R. ornithinolytica, 1 C. freundii and 1 C. braakii), and bla OXA-244 , a variant of bla OXA-48 , was found in three E. coli isolates. MLST showed that 12 E. coli strains belonged to six different sequence types (ST559, ST38, ST212, ST3541, 1972 and ST2142), and we identified three different STs in K. pneumoniae isolates, including ST133, ST2055, and a new sequence type: ST2192. This study showed the presence of OXA-48-like-producing Enterobacteriaceae in water environments and highlighted the potential role of aquatic environments as reservoirs of clinically relevant antimicrobial-resistant bacteria, with the potential to spread throughout the community. Copyright © 2017 Elsevier Ltd. All rights reserved.

Phylogenetic and physiological diversity of microorganisms isolated from a deep greenland glacier ice core

NASA Technical Reports Server (NTRS)

Miteva, V. I.; Sheridan, P. P.; Brenchley, J. E.

2004-01-01

We studied a sample from the GISP 2 (Greenland Ice Sheet Project) ice core to determine the diversity and survival of microorganisms trapped in the ice at least 120,000 years ago. Previously, we examined the phylogenetic relationships among 16S ribosomal DNA (rDNA) sequences in a clone library obtained by PCR amplification from genomic DNA extracted from anaerobic enrichments. Here we report the isolation of nearly 800 aerobic organisms that were grouped by morphology and amplified rDNA restriction analysis patterns to select isolates for further study. The phylogenetic analyses of 56 representative rDNA sequences showed that the isolates belonged to four major phylogenetic groups: the high-G+C gram-positives, low-G+C gram-positives, Proteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group. The most abundant and diverse isolates were within the high-G+C gram-positive cluster that had not been represented in the clone library. The Jukes-Cantor evolutionary distance matrix results suggested that at least 7 isolates represent new species within characterized genera and that 49 are different strains of known species. The isolates were further categorized based on the isolation conditions, temperature range for growth, enzyme activity, antibiotic resistance, presence of plasmids, and strain-specific genomic variations. A significant observation with implications for the development of novel and more effective cultivation methods was that preliminary incubation in anaerobic and aerobic liquid prior to plating on agar media greatly increased the recovery of CFU from the ice core sample.

Investigation of interaction between magnetic silica particles and lambda phage DNA fragment.

PubMed

Smerkova, Kristyna; Dostalova, Simona; Vaculovicova, Marketa; Kynicky, Jindrich; Trnkova, Libuse; Kralik, Miroslav; Adam, Vojtech; Hubalek, Jaromir; Provaznik, Ivo; Kizek, Rene

2013-12-01

Nucleic acids belong to the most important molecules and therefore the understanding of their properties, function and behavior is crucial. Even though a range of analytical and biochemical methods have been developed for this purpose, one common step is essential for all of them - isolation of the nucleic acid from the from complex sample matrix. The use of magnetic particles for the separation of nucleic acids has many advantages over other isolation methods. In this study, an isolation procedure for extraction of DNA was optimized. Each step of the isolation process including washing, immobilization and elution was optimized and therefore the efficiency was increased from 1.7% to 28.7% and the total time was shortened from 75 to 30min comparing to the previously described method. Quantification of the particular parameter influence was performed by square-wave voltammetry using hanging drop mercury electrode. Further, we compared the optimized method with standard chloroform extraction and applied on isolation of DNA from Staphylococcus aureus and Escherichia coli. Copyright © 2013 Elsevier B.V. All rights reserved.

An in vitro force measurement assay to study the early mechanical interaction between corneal fibroblasts and collagen matrix.

PubMed

Roy, P; Petroll, W M; Cavanagh, H D; Chuong, C J; Jester, J V

1997-04-10

An in vitro force measurement assay has been developed to quantify the forces exerted by single corneal fibroblasts during the early interaction with a collagen matrix. Corneal fibroblasts were sparsely seeded on top of collagen matrices whose stiffness was predetermined by micromanipulation with calibrated fine glass microneedles. The forces exerted by individual cells were calculated from time-lapse videomicroscopic recordings of the 2-D elastic distortion of the matrix. In additional experiments, the degree of permanent reorganization of the collagen matrices was assessed by lysing the cells with 1% Triton X-100 solution at the end of a 2-hour incubation and recording the subsequent relaxation. The data suggest that a cell can exert comparable centripetal force during either extension of a cell process or partial retraction of an extended pseudopodia. The rates of force associated with pseudopodial extension and partial retraction were 0.180 +/- 0.091 (x 10(-8)) N/min (n = 8 experiments) and 0.213 +/- 0.063 (x 10(-8)) N/min (n = 8 experiments), respectively. Rupture of pseudopodial adhesion associated with cell locomotion causes a release of force on the matrix and a complete recoil of the pseudopodia concerned; a simultaneous release of force on the matrix was also observed at the opposite end of the cell. Lysis of cells resulted in 84 +/- 18% relaxation of the matrix, suggesting that little permanent remodeling of matrix is produced by the actions of isolated migrating cells.

Isolation, separation, and characterization of epithelial and connective cells from rat palate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terranova, Victor Paul

1979-01-01

Epithelial and connective tissue cells were isolated from rat palate by sequential collagenase, hyaluronidase and trypsin digestion of the extracellular matrix. Differences between the two populations were noted with respect to total cell protein, total cell water, proline uptake and incorporation, percent collagen synthesized, effects of parathyroid hormone, metabolism of D-valine and cell density. Basal epithelial cells were subsequently separated from the heterogeneous epithelial cell population on shallow linear density gradients by velocity centrifugation. The type of collagen synthesized by the basal epithelial cells was compared to the type of collagen synthesized by the connective tissue cells by means ofmore » labeled amino acid incorporation ratios. Cells isolated from the epithelial and connective tissue were compared. From these studies it can be concluded that epithelial and connective tissue cells can be isolated from rat palate as viable and distinct populations with respect to the biochemical parameters examined. Furthermore, subpopulations can be separated and biochemically characterized.« less

Comparison of species identification of endocarditis associated viridans streptococci using rnpB genotyping and 2 MALDI-TOF systems.

PubMed

Isaksson, Jenny; Rasmussen, Magnus; Nilson, Bo; Stadler, Liselott Svensson; Kurland, Siri; Olaison, Lars; Ek, Elisabeth; Herrmann, Björn

2015-04-01

Streptococcus spp. are important causes of infective endocarditis but challenging in species identification. This study compared identification based on sequence determination of the rnpB gene with 2 systems of matrix-assisted laser desorption ionization-time of flight mass spectrometry, MALDI Biotyper (Bruker) and VITEK MS IVD (bioMérieux). Blood culture isolates of viridans streptococci from 63 patients with infective endocarditis were tested. The 3 methods showed full agreement for all 36 isolates identified in the Anginosus, Bovis, and Mutans groups or identified as Streptococcus cristatus, Streptococcus gordonii, or Streptococcus sanguinis. None of the methods could reliably identify the 23 isolates to the species level when designated as Streptococcus mitis, Streptococcus oralis, or Streptococcus tigurinus. In 7 isolates classified to the Mitis group, the rnpB sequences deviated strikingly from all reference sequences, and additional analysis of sodA and groEL genes indicated the occurrence of yet unidentified Streptococcus spp. Copyright © 2015 Elsevier Inc. All rights reserved.

Immunogold detection of glycoprotein antigens in sea urchin embryos.

PubMed

Benson, N C; Benson, S C; Wilt, F

1989-01-01

Four developmental stages of sea urchin embryos were labeled with colloidal gold in an attempt to elucidate the intracellular trafficking patterns within the cells that produce the glycoprotein matrix of the embryonic spicule. The primary mesenchyme cells (PMCs) form a syncytium and secrete an organic matrix on which calcium carbonate is laid down to form an endoskeletal spicule. The organic matrix has been isolated and characterized as glycoprotein consisting of four major bands. Polyclonal antibodies to these glycoproteins were used to label embryos from the mesenchyme blastula, early gastrula, late gastrula, and plutei stages of development. The label is concentrated in the Golgi complex and associated vesicles, in secretory vesicles, and in the organic matrix. The density of the labeling increases as development proceeds.

BMP2 induced osteogenic differentiation of human umbilical cord stem cells in a peptide-based hydrogel scaffold

NASA Astrophysics Data System (ADS)

Lakshmana, Shruthi M.

Craniofacial tissue loss due to traumatic injuries and congenital defects is a major clinical problem around the world. Cleft palate is the second most common congenital malformation in the United States occurring with an incidence of 1 in 700. Some of the problems associated with this defect are feeding difficulties, speech abnormalities and dentofacial anomalies. Current treatment protocol offers repeated surgeries with extended healing time. Our long-term goal is to regenerate bone in the palatal region using tissue-engineering approaches. Bone tissue engineering utilizes osteogenic cells, osteoconductive scaffolds and osteoinductive signals. Mesenchymal stem cells derived from human umbilical cord (HUMSCs) are highly proliferative with the ability to differentiate into osteogenic precursor cells. The primary objective of the study was to characterize HUMSCs and culture them in a 3D hydrogel scaffold and investigate their osteogenic potential. PuraMatrix(TM) is an injectable 3D nanofiber scaffold capable of self-assembly when exposed to physiologic conditions. Our second objective was to investigate the effect of Bone Morphogenic Protein 2 (BMP2) in enhancing the osteogenic differentiation of HUMSCs encapsulated in PuraMatrix(TM). We isolated cells isolated from Wharton's Jelly region of the umbilical cord obtained from NDRI (New York, NY). Isolated cells satisfied the minimal criteria for mesenchymal stem cells (MSCs) as defined by International Society of Cell Therapy in terms of plastic adherence, fibroblastic phenotype, surface marker expression and osteogenic differentiation. Flow Cytometry analysis showed that cells were positive for CD73, CD90 and CD105 while negative for hematopoietic marker CD34. Alkaline phosphatase activity (ALP) of HUMSCs showed peak activity at 2 weeks (p<0.05). Cells were encapsulated in 0.2% PuraMatrix(TM) at cell densities of 10x104, 20x104, 40x10 4 and 80x104. Cell viability with WST and proliferation with Live-Dead cell assays showed viable cells at all cell concentrations (p<0.05). A two- fold upregulation of ALP gene was seen for cells encapsulated in PuraMatrix(TM) with osteogenic medium compared to cells in culture medium (p<0.05). HUMSCs encapsulated in PuraMatrix(TM) were treated with BMP2 at doses of 50ng/ml, 100ng/ml and 200ng/ml. A significant upregulation of ALP gene in BMP2 treated cells was seen compared to HUMSCs treated in osteogenic medium (p<0.05). Peak osteogenic activity was noted at BMP2 dose of 100ng/ml (p<0.05). We have developed a composite system of HUMSCs, PuraMatrix(TM) and BMP2 for repair of bone defects that is injectable precluding additional surgeries.

Aspergillus tubingensis: a major filamentous fungus found in the airways of patients with lung disease.

PubMed

Gautier, Magali; Normand, Anne-Cécile; L'Ollivier, Coralie; Cassagne, Carole; Reynaud-Gaubert, Martine; Dubus, Jean-Christophe; Brégeon, Fabienne; Hendrickx, Marijke; Gomez, Carine; Ranque, Stéphane; Piarroux, Renaud

2016-07-01

The black Aspergillus group comprises A. niger and 18 other species, which are morphologically indistinguishable. Among this species subset, A. tubingensis, described in less than 30 human cases before 2014, is primarily isolated from ear, nose, and throat samples. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has emerged as a powerful technique to identify microbes in diagnostic settings. We applied this method to identify 1,720 filamentous fungi routinely isolated from clinical samples our laboratory over a two-year study period. Accordingly, we found 85 isolates of A. niger, 58 of A. tubingensis, and six other black Aspergillus (4 A. carbonarius and 2 A. japonicus). A. tubingensis was the fifth most frequent mold isolated in our mycology laboratory, primarily isolated from respiratory samples (40/58 isolates). In this study, we mainly aimed to describe the clinical pattern of Aspergillus tubingensisWe analyzed the clinical features of the patients in whom A. tubingensis had been isolated from 40 respiratory samples. Thirty patients suffered from cystic fibrosis, chronic obstructive pulmonary disease or other types of chronic respiratory failure. Strikingly, 20 patients were experiencing respiratory acute exacerbation at the time the sample was collected. Antifungal susceptibility testing of 36 A. tubingensis isolates showed lower amphotericin B MICs (P < 10(-4)) and higher itraconazole and voriconazole MICs (P < 10(-4) and P = .0331, respectively) compared with 36 A. niger isolates. Further studies are required to better establish the role that this fungus plays in human diseases, especially in the context of cystic fibrosis and chronic pulmonary diseases. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Examinations of the matrix isolation fourier transform infrared spectra of organic compounds: Part XII

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coleman, W. M., III; Gordon, B. M.; Lawrence, B. M.

1989-02-01

Matrix isolation Fourier transform infrared spectra (MI/FT-IR), massspectra (MS), carbon-13 Nuclear Magnetic Resonance (/sup 13/C-NMR) spectra,condensed-phase infrared spectra, and vapor-phase infrared (IR)spectra are presented for a series of terpene compounds. Subtle differencesin positional and configurational isomers commonly found withterpenes could be easily detected by the MI/FT-IR spectra. The resultsare comparable in some aspects to those obtainable from /sup 13/C-NMR andthin-film IR; however, most importantly, they are acquired at the lownanogram level for MI/FT-IR, as compared to the milligram level forthe other techniques. These results represent an advance in the technologyavailable for the analysis of complex mixtures such as essential oilscontainingmore » terpene-like molecules.« less

Prospective Evaluation of a Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System in a Hospital Clinical Microbiology Laboratory for Identification of Bacteria and Yeasts: a Bench-by-Bench Study for Assessing the Impact on Time to Identification and Cost-Effectiveness

PubMed Central

Tan, K. E.; Ellis, B. C.; Lee, R.; Stamper, P. D.; Zhang, S. X.

2012-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been found to be an accurate, rapid, and inexpensive method for the identification of bacteria and yeasts. Previous evaluations have compared the accuracy, time to identification, and costs of the MALDI-TOF MS method against standard identification systems or commercial panels. In this prospective study, we compared a protocol incorporating MALDI-TOF MS (MALDI protocol) with the current standard identification protocols (standard protocol) to determine the performance in actual practice using a specimen-based, bench-by-bench approach. The potential impact on time to identification (TTI) and costs had MALDI-TOF MS been the first-line identification method was quantitated. The MALDI protocol includes supplementary tests, notably for Streptococcus pneumoniae and Shigella, and indications for repeat MALDI-TOF MS attempts, often not measured in previous studies. A total of 952 isolates (824 bacterial isolates and 128 yeast isolates) recovered from 2,214 specimens were assessed using the MALDI protocol. Compared with standard protocols, the MALDI protocol provided identifications 1.45 days earlier on average (P < 0.001). In our laboratory, we anticipate that the incorporation of the MALDI protocol can reduce reagent and labor costs of identification by $102,424 or 56.9% within 12 months. The model included the fixed annual costs of the MALDI-TOF MS, such as the cost of protein standards and instrument maintenance, and the annual prevalence of organisms encountered in our laboratory. This comprehensive cost analysis model can be generalized to other moderate- to high-volume laboratories. PMID:22855510

Molecular and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Characterization of Clinically Significant Melanized Fungi in India.

PubMed

Singh, Ashutosh; Singh, Pradeep Kumar; Kumar, Anil; Chander, Jagdish; Khanna, Geetika; Roy, Pradip; Meis, Jacques F; Chowdhary, Anuradha

2017-04-01

Melanized or black fungi are a heterogeneous group of fungi causing cutaneous to systemic diseases with high mortality. These fungi are rarely reported as agents of human infections, primarily due to difficulties in their classical identification. In this study, we examined, using molecular methods and matrix-assisted laser desorption ioniazation-time of flight mass spectrometry (MALDI-TOF MS), the diversity of melanized fungi (MF) isolated from patients in 19 medical centers in India. Overall, during a 4-year period, 718 (5.3%) clinical specimens yielded MF. Of these, 72 (10%) isolates had clinical significance and were identified primarily by sequencing the internal transcribed spacer and large subunit (LSU) regions. MF represented 21 genera comprising 29 species, the majority of them belonging to the orders Pleosporales (50%) and Chaetothyriales (22%). Among the 29 fungal species identified in this study, only 6 (20%) species were identified by the MALDI-TOF MS due to the limited commercial database of Bruker Daltonics for MF. However, a 100% identification rate of 20 additional species identified in this study was obtained by constructing an in-house database using 24- to 96-h-old liquid cultures. Further, the CLSI broth microdilution method revealed low MICs for posaconazole (≤1 μg/ml) and voriconazole (≤2 μg/ml) in 96% and 95% of isolates, respectively. Skin/subcutaneous and sino-nasal and pulmonary phaeohyphomycosis due to MF were diagnosed in 21.4% ( n = 15) and 28.5% ( n = 20) of cases. Also, 10% of patients had central nervous system involvement ( n = 7), and 3 cases of fungal osteomyelitis due to Cladophialophora bantiana and Corynespora spp. were observed. Copyright © 2017 American Society for Microbiology.

Prospective evaluation of a matrix-assisted laser desorption ionization-time of flight mass spectrometry system in a hospital clinical microbiology laboratory for identification of bacteria and yeasts: a bench-by-bench study for assessing the impact on time to identification and cost-effectiveness.

PubMed

Tan, K E; Ellis, B C; Lee, R; Stamper, P D; Zhang, S X; Carroll, K C

2012-10-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been found to be an accurate, rapid, and inexpensive method for the identification of bacteria and yeasts. Previous evaluations have compared the accuracy, time to identification, and costs of the MALDI-TOF MS method against standard identification systems or commercial panels. In this prospective study, we compared a protocol incorporating MALDI-TOF MS (MALDI protocol) with the current standard identification protocols (standard protocol) to determine the performance in actual practice using a specimen-based, bench-by-bench approach. The potential impact on time to identification (TTI) and costs had MALDI-TOF MS been the first-line identification method was quantitated. The MALDI protocol includes supplementary tests, notably for Streptococcus pneumoniae and Shigella, and indications for repeat MALDI-TOF MS attempts, often not measured in previous studies. A total of 952 isolates (824 bacterial isolates and 128 yeast isolates) recovered from 2,214 specimens were assessed using the MALDI protocol. Compared with standard protocols, the MALDI protocol provided identifications 1.45 days earlier on average (P < 0.001). In our laboratory, we anticipate that the incorporation of the MALDI protocol can reduce reagent and labor costs of identification by $102,424 or 56.9% within 12 months. The model included the fixed annual costs of the MALDI-TOF MS, such as the cost of protein standards and instrument maintenance, and the annual prevalence of organisms encountered in our laboratory. This comprehensive cost analysis model can be generalized to other moderate- to high-volume laboratories.

Detecting Seismic Activity with a Covariance Matrix Analysis of Data Recorded on Seismic Arrays

NASA Astrophysics Data System (ADS)

Seydoux, L.; Shapiro, N.; de Rosny, J.; Brenguier, F.

2014-12-01

Modern seismic networks are recording the ground motion continuously all around the word, with very broadband and high-sensitivity sensors. The aim of our study is to apply statistical array-based approaches to processing of these records. We use the methods mainly brought from the random matrix theory in order to give a statistical description of seismic wavefields recorded at the Earth's surface. We estimate the array covariance matrix and explore the distribution of its eigenvalues that contains information about the coherency of the sources that generated the studied wavefields. With this approach, we can make distinctions between the signals generated by isolated deterministic sources and the "random" ambient noise. We design an algorithm that uses the distribution of the array covariance matrix eigenvalues to detect signals corresponding to coherent seismic events. We investigate the detection capacity of our methods at different scales and in different frequency ranges by applying it to the records of two networks: (1) the seismic monitoring network operating on the Piton de la Fournaise volcano at La Réunion island composed of 21 receivers and with an aperture of ~15 km, and (2) the transportable component of the USArray composed of ~400 receivers with ~70 km inter-station spacing.

Structure and properties of hybrid composite materials

NASA Astrophysics Data System (ADS)

Chernyshova, T. A.; Kobeleva, L. I.; Bolotova, L. K.; Katin, I. V.

2013-03-01

The structure and interfacial interaction are studied in the hybrid aluminum-matrix composite materials fabricated by reactive casting combined with mechanical mixing of fillers with a metallic melt. The following types of hardening are considered: hardening by ceramic particles and by the phases formed as isolated inclusions or coatings on ceramic particles during in situ reactions. The hardness and tribological properties of the composite materials as functions of their compositions are discussed.

Studies of Biosilicification; The Role of Proteins, Carbohydrates and Model Compounds in Structure Control

DTIC Science & Technology

2005-12-31

No. carbons Pore volume data. Resolution of complex monosaccharide mixtures from plant cell wall isolates by high pH anion exchange chromatography. To...interwoven polysaccharide chains embedded in a gel matrix of galacturonic acid rich polysaccharides connected by calcium bridges. This network also...picomolar levels). Also, it allows the determination of intact monosaccharides without pre or post column derivatisation, decreasing the time of

Heterotrophic monitoring at a drinking water treatment plant by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry after different drinking water treatments.

PubMed

Sala-Comorera, Laura; Blanch, Anicet R; Vilaró, Carles; Galofré, Belén; García-Aljaro, Cristina

2017-10-01

The aim of this work was to assess the suitability of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for routine heterotrophic monitoring in a drinking water treatment plant. Water samples were collected from raw surface water and after different treatments during two campaigns over a 1-year period. Heterotrophic bacteria were studied and isolates were identified by MALDI-TOF MS. Moreover, the diversity index and the coefficient of population similarity were also calculated using biochemical fingerprinting of the populations studied. MALDI-TOF MS enabled us to characterize and detect changes in the bacterial community composition throughout the water treatment plant. Raw water showed a large and diverse population which was slightly modified after initial treatment steps (sand filtration and ultrafiltration). Reverse osmosis had a significant impact on the microbial diversity, while the final chlorination step produced a shift in the composition of the bacterial community. Although MALDI-TOF MS could not identify all the isolates since the available MALDI-TOF MS database does not cover all the bacterial diversity in water, this technique could be used to monitor bacterial changes in drinking water treatment plants by creating a specific protein profile database for tracking purposes.

Isolation of peroxisome-deficient mutants of Saccharomyces cerevisiae.

PubMed Central

Erdmann, R; Veenhuis, M; Mertens, D; Kunau, W H

1989-01-01

Two mutants of Saccharomyces cerevisiae affected in peroxisomal assembly (pas mutants) have been isolated and characterized. Each strain contains a single mutation that results in (i) the inability to grow on oleic acid, (ii) accumulation of peroxisomal matrix enzymes in the cytosol, and (iii) absence of detectable peroxisomes at the ultrastructural level. These lesions (pas1-1 and pas2) are shown to be nonallelic and recessive. Crossing of pas1-1 and pas2 strains resulted in diploid cells that had regained the ability to grow on oleic acid as sole carbon source and to form peroxisomes. These pas mutants may provide useful tools for future studies on the molecular mechanisms involved in peroxisomal assembly. Images PMID:2568633

Dangling bond defects in SiC: An ab initio study

NASA Astrophysics Data System (ADS)

Tuttle, Blair R.

2018-01-01

We report first-principles microscopic calculations of the properties of defects with dangling bonds in crystalline 3 C -SiC. Specifically, we focus on hydrogenated Si and C vacancies, divacancies, and multivacancies. The latter is a generic model for an isolated dangling bond within a bulk SiC matrix. Hydrogen serves to passivate electrically active defects to allow the isolation of a single dangling-bond defect. We used hybrid density-functional methods to determine energetics and electrical activity. The present results are compared to previous 3 C -SiC calculations and experiments. Finally, we identify homopolar carbon dangling-bond defects as the leakage causing defects in nanoporous SiC alloys.

Device for collecting and analyzing matrix-isolated samples

DOEpatents

Reedy, Gerald T.

1979-01-01

A gas-sample collection device is disclosed for matrix isolation of individual gas bands from a gas chromatographic separation and for presenting these distinct samples for spectrometric examination. The device includes a vacuum chamber containing a rotatably supported, specular carrousel having a number of external, reflecting surfaces around its axis of rotation for holding samples. A gas inlet is provided for depositing sample and matrix material on the individual reflecting surfaces maintained at a sufficiently low temperature to cause solidification. Two optical windows or lenses are installed in the vacuum chamber walls for transmitting a beam of electromagnetic radiation, for instance infrared light, through a selected sample. Positioned within the chamber are two concave mirrors, the first aligned to receive the light beam from one of the lenses and focus it to the sample on one of the reflecting surfaces of the carrousel. The second mirror is aligned to receive reflected light from that carrousel surface and to focus it outwardly through the second lens. The light beam transmitted from the sample is received by a spectrometer for determining absorption spectra.

D2O clusters isolated in rare-gas solids: Dependence of infrared spectrum on concentration, deposition rate, heating temperature, and matrix material

NASA Astrophysics Data System (ADS)

Shimazaki, Yoichi; Arakawa, Ichiro; Yamakawa, Koichiro

2018-04-01

The infrared absorption spectra of D2O monomers and clusters isolated in rare-gas matrices were systematically reinvestigated under the control of the following factors: the D2O concentration, deposition rate, heating temperature, and rare-gas species. We clearly show that the cluster-size distribution is dependent on not only the D2O concentration but also the deposition rate of a sample; as the rate got higher, smaller clusters were preferentially formed. Under the heating procedures at different temperatures, the cluster-size growth was successfully observed. Since the monomer diffusion was not enough to balance the changes in the column densities of the clusters, the dimer diffusion was likely to contribute the cluster growth. The frequencies of the bonded-OD stretches of (D2O)k with k = 2-6 were almost linearly correlated with the square root of the critical temperature of the matrix material. Additional absorption peaks of (D2O)2 and (D2O)3 in a Xe matrix were assigned to the species trapped in tight accommodation sites.

Isolation and characterization of chicken bile matrix metalloproteinase.

PubMed

Packialakshmi, B; Liyanage, R; Rasaputra, K S; Lay, Jackson O; Rath, N C

2014-06-01

Avian bile is rich in matrix metalloproteinases (MMP), the enzymes that cleave extracellular matrix proteins such as collagens and proteoglycans. Changes in bile MMP expression have been correlated with hepatic and gall bladder pathologies, but the significance of their expression in normal, healthy bile is not understood. We hypothesized that the MMP in bile may aid the digestion of native collagens that are resistant to conventional gastric proteases. Hence, the objective of this study was to characterize the bile MMP and check its regulation in association with dietary factors. We used substrate zymography, azocoll protease assay, and gelatin affinity chromatography to identify and purify the MMP from chicken bile. Using zymography and SDS PAGE, 5 bands at 70, 64, 58, 50, and 42 kDa were detected. The bands corresponding to 64, 50, and 42 kDa were identified as MMP2 using trypsin in-gel digestion and matrix-assisted laser desorption time-of-flight mass spectrometry and peptide mass fingerprinting. Chickens fed diets containing gelatin supplements showed higher levels of MMP expression in the bile by both azocoll assay and zymography. We conclude that the bile MMP may be associated with the digestion of collagens and other extracellular matrix proteins in avian diets. Poultry Science Association Inc.

Morphological and Inter Simple Sequence Repeat (ISSR) markers analyses of Corynespora cassiicola isolates from rubber plantations in Malaysia.

PubMed

Nghia, Nguyen Anh; Kadir, Jugah; Sunderasan, E; Puad Abdullah, Mohd; Malik, Adam; Napis, Suhaimi

2008-10-01

Morphological features and Inter Simple Sequence Repeat (ISSR) polymorphism were employed to analyse 21 Corynespora cassiicola isolates obtained from a number of Hevea clones grown in rubber plantations in Malaysia. The C. cassiicola isolates used in this study were collected from several states in Malaysia from 1998 to 2005. The morphology of the isolates was characteristic of that previously described for C. cassiicola. Variations in colony and conidial morphology were observed not only among isolates but also within a single isolate with no inclination to either clonal or geographical origin of the isolates. ISSR analysis delineated the isolates into two distinct clusters. The dendrogram created from UPGMA analysis based on Nei and Li's coefficient (calculated from the binary matrix data of 106 amplified DNA bands generated from 8 ISSR primers) showed that cluster 1 encompasses 12 isolates from the states of Johor and Selangor (this cluster was further split into 2 sub clusters (1A, 1B), sub cluster 1B consists of a unique isolate, CKT05D); while cluster 2 comprises of 9 isolates that were obtained from the other states. Detached leaf assay performed on selected Hevea clones showed that the pathogenicity of representative isolates from cluster 1 (with the exception of CKT05D) resembled that of race 1; and isolates in cluster 2 showed pathogenicity similar to race 2 of the fungus that was previously identified in Malaysia. The isolate CKT05D from sub cluster 1B showed pathogenicity dissimilar to either race 1 or race 2.

Optimization of the conditions of isolation and culture of dairy goat male germline stem cells (mGSC).

PubMed

Zhu, Haijing; Liu, Chao; Li, Mingzhao; Sun, Junwei; Song, Wencong; Hua, Jinlian

2013-02-01

Male germline stem cells (mGSC) reside in the basement of seminiferous tubules of the testis and have the capacity of self-renewal and differentiation into sperm throughout the life of animals. Reports on mice and human mGSC have demonstrated that mGSC are an unlimited resource of pluripotent stem cells for sperm production. The conditions of isolation and culture of mouse and human mGSC are well developed; however, the systematic culture conditions of dairy goat mGSC are still deficient although there have been several reports of successful cultures. With the present research, several key elements of isolation and culture of dairy goat mGSC have been determined. Details for the conditions of isolation of dairy testicular spermatogonium cells were optimized, and effects of several extracellular matrix types, ages of dairy goat, and cytokines on enrichment and culture of mGSC were compared. Biological characteristics of the cells were also evaluated by RT-PCR and immunofluorescent staining. The results indicated there is one kind of enzyme cocktail (CTHD (1mg/ml collagenase, 10μg/ml DNase, 1mg/ml hyaluronidase and 1mg/ml trypsin) combined TD (0.25% trypsin and 10mg/ml DNaseI)) that can be used to successfully isolate dairy goat testicular spermatogonium cells efficiently; and fibronectin as well as laminin were efficient extracellular matrix to enrich mGSC among the extracellular matrix types evaluated. Age of dairy goat clearly influenced the cultures of dairy goat mGSC with the efficiency of establishment of an mGSC line being greater if the age of the dairy goat is younger. Some cytokines e.g. BIO (A GSK3 inhibitor, 6-bromoindirubin-3'-oxime) and basic fibroblast growth factor (bFGF) acted positively on the maintenance of proliferation and pluripotency of mGSC. Leukemia inhibitory factor (LIF) might, however, inhibit the proliferation of dairy goat mGSC. These cultured mGSC maintained similar characteristics as mouse and human mGSC. These results provide an efficient system to isolate and culture of dairy goat mGSC. Copyright © 2012 Elsevier B.V. All rights reserved.

Casein kinase II protein kinase is bound to lamina-matrix and phosphorylates lamin-like protein in isolated pea nuclei

NASA Technical Reports Server (NTRS)

Li, H.; Roux, S. J.

1992-01-01

A casein kinase II (CK II)-like protein kinase was identified and partially isolated from a purified envelope-matrix fraction of pea (Pisum sativum L.) nuclei. When [gamma-32P]ATP was directly added to the envelope-matrix preparation, the three most heavily labeled protein bands had molecular masses near 71, 48, and 46 kDa. Protein kinases were removed from the preparation by sequential extraction with Triton X-100, EGTA, 0.3 M NaCl, and a pH 10.5 buffer, but an active kinase still remained bound to the remaining lamina-matrix fraction after these treatments. This kinase had properties resembling CK II kinases previously characterized from animal and plant sources: it preferred casein as an artificial substrate, could use GTP as efficiently as ATP as the phosphoryl donor, was stimulated by spermine, was calcium independent, and had a catalytic subunit of 36 kDa. Some animal and plant CK II kinases have regulatory subunits near 29 kDa, and a lamina-matrix-bound protein of this molecular mass was recognized on immunoblot by anti-Drosophila CK II polyclonal antibodies. Also found associated with the envelope-matrix fraction of pea nuclei were p34cdc2-like and Ca(2+)-dependent protein kinases, but their properties could not account for the protein kinase activity bound to the lamina. The 71-kDa substrate of the CK II-like kinase was lamin A-like, both in its molecular mass and in its cross-reactivity with anti-intermediate filament antibodies. Lamin phosphorylation is considered a crucial early step in the entry of cells into mitosis, so lamina-bound CK II kinases may be important control points for cellular proliferation.

Isolation and Characterization of Chick Epiphyseal Cartilage Matrix Vesicle Proteolipid

DTIC Science & Technology

1988-01-01

Epiphyseal growth plate cartilage from the proximal portion of 49-52 day old broiler strain chickens was digested in collagenase for 15 hours. Plasma...cartilage from the proximal portion of 49-52 day old broiler strain chickens was digested in collagenase for 15 hours. Plasma membranes and matrix...ATPASE ACTIVITY. Epiphyseal growth plate cartilage from the proximal portion of 49-52 day old broiler strain chickens was digested in collagenase for 15

Isolation and Characterization of Bacteria Colonizing Acartia tonsa Copepod Eggs and Displaying Antagonist Effects against Vibrio anguillarum, Vibrio alginolyticus and Other Pathogenic Strains

PubMed Central

Zidour, Mahammed; Chevalier, Mickaël; Belguesmia, Yanath; Cudennec, Benoit; Grard, Thierry; Drider, Djamel; Souissi, Sami; Flahaut, Christophe

2017-01-01

Copepods represent a major source of food for many aquatic species of commercial interest for aquaculture such as mysis shrimp and early stages of fishes. For the purpose of this study, the culturable mesophilic bacterial flora colonizing Acartia tonsa copepod eggs was isolated and identified. A total of 175 isolates were characterized based on their morphological and biochemical traits. The majority of these isolates (70%) were Gram-negative bacteria. Matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was used for rapid identification of bacterial isolates. Here, 58% of isolates were successfully identified at the genus level and among them, 54% were identified at the species level. These isolates belong to 12 different genera and 29 species. Five strains, identified as Bacillus pumilus, named 18 COPS, 35A COPS, 35R COPS, 38 COPS, and 40A COPS, showed strong antagonisms against several potential fish pathogens including Vibrio alginolyticus, V. anguillarum, Listeria monocytogenes, and Staphylococcus aureus. Furthermore, using a differential approach, we show that the antimicrobial activity of the 35R COPS strain is linked primarily to the production of antimicrobial compounds of the amicoumacin family, as demonstrated by the specific UV-absorbance and the MS/MS fragmentation patterns of these compounds. PMID:29085344

Characterization of Staphylococcus caprae Clinical Isolates Involved in Human Bone and Joint Infections, Compared with Goat Mastitis Isolates.

PubMed

d'Ersu, J; Aubin, G G; Mercier, P; Nicollet, P; Bémer, P; Corvec, S

2016-01-01

Staphylococcus caprae is an emerging microorganism in human bone and joint infections (BJI). The aim of this study is to describe the features of S. caprae isolates involved in BJI (H for human) compared with those of isolates recovered in goat mastitis (A for animal). Fourteen isolates of each origin were included. Identifications were performed using a Vitek 2 GP ID card, tuf gene sequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Vitek MS. Molecular typing was carried out using pulsed-field gel electrophoresis (PFGE) and DiversiLab technology. The crystal violet method was used to determine biofilm-forming ability. Virulence factors were searched by PCR. Vitek MS technology provides an accurate identification for the two types of isolates compared to that of gold-standard sequencing (sensitivity, 96.4%), whereas the Vitek 2 GP ID card was more effective for H isolates. Molecular typing methods revealed two distinct lineages corresponding to the origin despite few overlaps: H and A. In our experimental conditions, no significant difference was observed in biofilm production ability between H and A isolates. Nine isolates (5 H isolates and 4 A isolates) behaved as weak producers while one A isolate was a strong producer. Concerning virulence factors, the autolysin atlC and the serine aspartate adhesin (sdrZ) genes were detected in 24 isolates (86%), whereas the lipase gene was always detected, except in one H isolate (96%). The ica operon was present in 23 isolates (82%). Fibrinogen-binding (fbe) or collagen-binding (cna) genes were not detected by using primers designed for Staphylococcus aureus or Staphylococcus epidermidis, even in low stringency conditions. Although S. caprae probably remains underestimated in human infections, further studies are needed to better understand the evolution and the adaptation of this species to its host. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Isolation of bacterial metabolites as natural inducers for larval settlement in the marine polychaete Hydroides elegans (Haswell).

PubMed

Harder, Tilmann; Lau, Stanley Chun Kwan; Dahms, Hans-Uwe; Qian, Pei-Yuan

2002-10-01

The bacterial component of marine biofilms plays an important role in the induction of larval settlement in the polychaete Hydroides elegans. In this study, we provide experimental evidence that bacterial metabolites comprise the chemical signal for larval settlement. Bacteria were isolated from biofilms, purified and cultured according to standard procedures. Bacterial metabolites were isolated from spent culture broth by chloroform extraction as well as by closed-loop stripping and adsorption of volatile components on surface-modified silica gel. A pronounced biological activity was exclusively observed when concentrated metabolites were adsorbed on activated charcoal. Larvae did not respond to waterbome metabolites when prevented from contacting the bacterial film surface. These results indicate that an association of the chemical signal with a sorbent-like substratum may be an essential cofactor for the expression of biological activity. The functional role of bacterial exopolymers as an adsorptive matrix for larval settlement signals is discussed.

Structural analysis of proanthocyanidins isolated from fruit stone of Chinese hawthorn with potent antityrosinase and antioxidant activity.

PubMed

Chai, Wei-Ming; Chen, Chih-Min; Gao, Yu-Sen; Feng, Hui-Ling; Ding, Yu-Mei; Shi, Yan; Zhou, Han-Tao; Chen, Qing-Xi

2014-01-08

Proanthocyanidins were isolated from fruit stone of Chinese hawthorn (Crataegus pinnatifida Bge. var. major N.E.Br.). Their structures were analyzed and elucidated by methods of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and high performance liquid chromatography electrospray ionization mass spectrometry (HPLC-ESI-MS). The results demonstrated that these compounds are complicated mixtures of homo- and heteropolymers consisting of procyanidin/procyanidin gallate and prodelphinidin. They possessed structural heterogeneity in monomer units, polymer length, and interflavan linkage (A-type and B-type). Their antityrosinase and antioxidant activity were then investigated. The results revealed that they can inhibit tyrosinase activities, including the monophenolase activity and the diphenolase activity. In addition, proanthocyanidins possessed potent antioxidant activity. Our studies revealed that proanthocyanidins isolated from fruit stone of Chinese hawthorn may be applied in food, agriculture, pharmaceutical, and cosmetic industries.

Hyperfine structure of the MnH X 7Sigma + state: A large gas-to-matrix shift in the Fermi contact interaction

NASA Astrophysics Data System (ADS)

Varberg, Thomas D.; Field, Robert W.; Merer, Anthony J.

1990-06-01

Sub-Doppler spectra of the A 7Π-X 7Σ+ (0,0) band of gas phase MnH near 5680 Å were recorded by intermodulated fluorescence spectroscopy. The spectra reveal hyperfine splittings arising from both the 55Mn and 1H nuclear spins. Internal hyperfine perturbations have been observed between the different spin components of the ground state at low N`. From a preliminary analysis of several rotational lines originating from the isolated and unperturbed F1(J`=3) spin component of the X 7Σ+(N`=0) level, the 55Mn Fermi contact interaction in the ground state has been measured as bF=Aiso =276(1) MHz. This value is 11% smaller than the value obtained by Weltner et al. from an electron-nuclear double resonance (ENDOR) study of MnH in an argon matrix at 4 K. This unprecedented gas-to-matrix shift in the Fermi contact parameter is discussed.

Infrared spectra of group III A metal oxides

NASA Technical Reports Server (NTRS)

Lynch, D. A., Jr.

1972-01-01

The measurement of infrared frequencies of metal-oxygen species which could be formed in the matrix and to investigate with an oxygen-18 enrichment study the controversy on the vibrational assignments for the suboxide. Several new molecules, Al3O2, Ga3O, In3O, In4O2, IntaO, IntaO2, and In2WO4, were found by mass spectrometric sampling to exist in extremely minor concentrations in the vapor phase. The latter three species were formed by reaction with the crucible materials and were unimportant for an infrared analysis. The infrared spectroscopic measurements were obtained by the matrix isolation technique of molecular beam sampling. The MO2 species were formed by direct reaction between metal and O2 in the matrix. A C2v structure and an O-M-O bond angle near 40 deg was favored for these molecules by analogy with a similar investigation of the alkali metals. The vibrational frequencies which were determined are given.

Formation of bone-like mineralized matrix by periodontal ligament cells in vivo: a morphological study in rats.

PubMed

Hiraga, Toru; Ninomiya, Tadashi; Hosoya, Akihiro; Takahashi, Masafumi; Nakamura, Hiroaki

2009-01-01

Periodontal ligament (PDL) is a unique connective tissue that not only connects cementum and alveolar bone to support teeth, but also plays an important role in reconstructing periodontal tissues. Previous studies have suggested that PDL cells have osteogenic potential; however, they lack precise histological examinations. Here, we studied bone-like matrix formation by PDL cells in rats using morphological techniques. Rat and human PDL cells exhibited substantial alkaline phosphatase activity and induced mineralization in vitro. RT-PCR analyses showed that PDL cells expressed the osteoblast markers, Runx2, osterix, and osteocalcin. These results suggest that PDL cells share similar phenotypes with osteoblasts. To examine the bone-like matrix formation in vivo, PDL cells isolated from green fluorescent protein (GFP)-transgenic rats were inoculated with hydroxyapatite (HA) disks into wild-type rats. Five weeks after the implantation, the pores in HA disks were occupied by GFP-positive cells. Mineralized matrix formation was also found on the surface of HA pores. At 12 weeks, some of the pores were filled with bone-like mineralized matrices (BLMM), which were positive for the bone matrix proteins, osteopontin, bone sialoprotein, and osteocalcin. Immunohistochemical examination revealed that most of the osteoblast- and osteocyte-like cells on or in the BLMM were GFP-positive, suggesting that the BLMM were directly formed by the inoculated PDL cells. On the pore surfaces, Sharpey's fiber-like structures embedded in cementum-like mineralized layers were also observed. These results collectively suggest that PDL cells have the ability to form periodontal tissues and could be a useful source for regenerative therapies of periodontal diseases.

Polymer Soft-Landing Isolation of Acetylene on Polystyrene and Poly(vinylpyridine): A Novel Approach to Probing Hydrogen Bonding in Polymers.

PubMed

Li, Yike; Samet, Cindy

2015-09-17

Hydrogen-bonded complexes of acetylene (Ac) with the polymers polystyrene (PS), poly(4-vinylpyridine) (P4VP), and poly(2-vinylpyridine) (P2VP) have been characterized for the first time at 16 K in a "polymer soft-landing isolation" experiment which is being pioneered in our research laboratory. In particular, changes in vibrational modes of Ac provide ample evidence for hydrogen-bonded complexes between Ac and the phenyl groups of PS or the pyridyl groups of P4VP and P2VP. With PS, the proton on the top Ac molecule of the classic T-shaped Ac dimer interacts with the π cloud of the benzene (Bz) ring to form a C-H---π interaction, while the π cloud of the lower Ac forms a second C-H---π interaction with a proton on the Bz ring. An analogous (ring)1-(Ac)2 double interaction occurs between an Ac dimer and the pyridine (Pyr) rings on both P2VP and P4VP, yielding a C-H---N and C-H---π interaction. With P4VP and P2VP a second bridged (ring)2-(Ac)2 product is formed, with the Ac dimer forming nearly collinear C-H---N hydrogen bonds to adjacent Pyr rings. On P2VP this bridged product is the only one after extensive annealing. These complexes in which Ac acts as both proton donor and acceptor have not previously been observed in conventional matrix isolation experiments. This study is the second from our laboratory employing this method, which represents a slight modification of the traditional matrix isolation technique.

Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK® MS system.

PubMed

Garner, O; Mochon, A; Branda, J; Burnham, C-A; Bythrow, M; Ferraro, M; Ginocchio, C; Jennemann, R; Manji, R; Procop, G W; Richter, S; Rychert, J; Sercia, L; Westblade, L; Lewinski, M

2014-04-01

Accurate and timely identification of anaerobic bacteria is critical to successful treatment. Classic phenotypic methods for identification require long turnaround times and can exhibit poor species level identification. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an identification method that can provide rapid identification of anaerobes. We present a multi-centre study assessing the clinical performance of the VITEK(®) MS in the identification of anaerobic bacteria. Five different test sites analysed a collection of 651 unique anaerobic isolates comprising 11 different genera. Multiple species were included for several of the genera. Briefly, anaerobic isolates were applied directly to a well of a target plate. Matrix solution (α-cyano-4-hydroxycinnamic acid) was added and allowed to dry. Mass spectra results were generated with the VITEK(®) MS, and the comparative spectral analysis and organism identification were determined using the VITEK(®) MS database 2.0. Results were confirmed by 16S rRNA gene sequencing. Of the 651 isolates analysed, 91.2% (594/651) exhibited the correct species identification. An additional eight isolates were correctly identified to genus level, raising the rate of identification to 92.5%. Genus-level identification consisted of Actinomyces, Bacteroides and Prevotella species. Fusobacterium nucleatum, Actinomyces neuii and Bacteroides uniformis were notable for an increased percentage of no-identification results compared with the other anaerobes tested. VITEK(®) MS identification of clinically relevant anaerobes is highly accurate and represents a dramatic improvement over other phenotypic methods in accuracy and turnaround time. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Pathotypic characterization of Newcastle disease virus isolated from vaccinated chicken in West Java, Indonesia.

PubMed

Putri, Dwi Desmiyeni; Handharyani, Ekowati; Soejoedono, Retno Damajanti; Setiyono, Agus; Mayasari, Ni Luh Putu Ika; Poetri, Okti Nadia

2017-04-01

This research was conducted to differentiate and characterize eight Newcastle disease virus (NDV) isolates collected from vaccinated chicken at commercial flocks in West Java, Indonesia, in 2011, 2014 and 2015 by pathotype specific primers. A total of eight NDV isolates collected from clinical outbreaks among commercial vaccinated flocks in West Java, Indonesia, in 2011, 2014, and 2015 were used in this study. Reverse transcription-polymerase chain reaction was used to detect and differentiate virulence of NDV strains, using three sets of primers targeting their M and F gene. First primers were universal primers to detect NDV targeting matrix (M) gene. Other two sets of primers were specific for the fusion (F) gene cleavage site sequence of virulent and avirulent NDV strains. Our results showed that three isolates belong to NDV virulent strains, and other five isolates belong to NDV avirulent strains. The nucleotide sequence of the F protein cleavage site showed 112 K/R-R-Q/R-K-R/G-F 117 on NDV virulent strains and 112 G-K/R-Q-G-R-L 117 on NDV avirulent strain. Result from the current study suggested that NDV virulent strain were circulating among vaccinated chickens in West Java, Indonesia; this might possess a risk of causing ND outbreaks and causing economic losses within the poultry industry.

Evaluation of the Thermo Scientific SureTect Listeria monocytogenes Assay.

PubMed

Cloke, Jonathan; Leon-Velarde, Carlos; Larson, Nathan; Dave, Keron; Evans, Katharine; Crabtree, David; Hughes, Annette; Hopper, Craig; Simpson, Helen; Withey, Sophie; Oleksiuk, Milena; Holopainen, Jani; Wickstrand, Nina; Kauppinen, Mikko

2014-01-01

The Thermo Scientific SureTect Listeria monocytogenes Assay is a new real-time PCR assay for the detection of Listeria monocytogenes in food and environmental samples. This assay was validated using the AOAC Research Institute (AOAC-RI) Performance Tested Methods program in comparison to the reference method detailed in International Organization for Standardization 11290-1:1996, including Amendment 1:2004 with the following foods and food contact surfaces: smoked salmon, processed cheese, fresh bagged spinach, fresh cantaloupe, cooked prawns (chilled product), cooked sliced turkey meat (chilled product), ice cream, pork frankfurters, salami, ground raw beef meat (12% fat), plastic, and stainless steel. All matrixes were tested by Thermo Fisher Scientific, Microbiology Division, Basingstoke, UK. In addition, three matrixes (pork frankfurters, bagged lettuce, and stainless steel) were analyzed independently as part of the AOAC-RI controlled laboratory study by the University of Guelph, Canada. Using probability of detection (POD) statistical analysis, a significant difference was demonstrated between the candidate and reference methods for salami, cooked sliced turkey and ice cream in favor of the SureTect assay. For all other matrixes, no significant difference by POD was seen between the two methods during the study. Inclusivity and exclusivity testing was also conducted with 53 and 30 isolates, respectively, which demonstrated that the SureTect assay was able to detect all serotypes of L. monocytogenes. None of the exclusivity isolates analyzed were detected by the SureTect assay. Ruggedness testing was conducted to evaluate the performance of the assay with specific method deviations outside the recommended parameters open to variation, i.e., enrichment time and temperature and lysis temperature, which demonstrated that the assay gave reliable performance. Accelerated stability testing was also conducted, validating the assay shelf life.

Effect of Methyl Substitution on the N-H···O Interaction in Complexes of Pyrrole with Water, Methanol, and Dimethyl Ether: Matrix Isolation Infrared Spectroscopy and ab Initio Computational Studies.

PubMed

Sarkar, Shubhra; Ramanathan, N; Sundararajan, K

2018-03-08

Hydrogen-bonded interactions of pyrrole with water and methanol have been studied using matrix isolation infrared spectroscopy and compared with the calculation performed on dimethyl ether. Computations carried out at MP2/aug-cc-pVDZ level of theory yielded two minima for the pyrrole-water and pyrrole-methanol complexes. The global and local minima correspond to the N-H···O and O-H···π complexes, respectively, where the N-H group of pyrrole interacts with oxygen of water/methanol and O-H of water and methanol interacts with the π cloud of pyrrole. Computations performed on the pyrrole-dimethyl ether gave only N-H···O type complex. From the experimental vibrational wavenumber shifts in the N-H stretching and N-H bending modes of pyrrole, as well as in the O-H stretching modes of water and methanol, the 1:1 N-H···O complexes were discerned. The strength of the N-H···O hydrogen bond and the corresponding shift in the N-H stretching vibrational wavenumbers increases in the order pyrrole-water < pyrrole-methanol < pyrrole-dimethyl ether, where a proton is successively replaced by a methyl group. Apart from the 1:1 complexes, higher clusters of 2:1 and 1:2 pyrrole-water and pyrrole-methanol complexes were also generated in N 2 matrix. Atoms in molecules and natural bond orbital analyses were carried out at the MP2/aug-cc-pVDZ level to understand the nature of interaction in the 1:1 pyrrole-water, pyrrole-methanol and pyrrole-dimethyl ether complexes.

Genotypic and Phenotypic Characteristics Associated with Biofilm Formation by Human Clinical Escherichia coli Isolates of Different Pathotypes

PubMed Central

Schiebel, Juliane; Böhm, Alexander; Nitschke, Jörg; Burdukiewicz, Michał; Weinreich, Jörg; Ali, Aamir; Roggenbuck, Dirk; Rödiger, Stefan

2017-01-01

ABSTRACT Bacterial biofilm formation is a widespread phenomenon and a complex process requiring a set of genes facilitating the initial adhesion, maturation, and production of the extracellular polymeric matrix and subsequent dispersal of bacteria. Most studies on Escherichia coli biofilm formation have investigated nonpathogenic E. coli K-12 strains. Due to the extensive focus on laboratory strains in most studies, there is poor information regarding biofilm formation by pathogenic E. coli isolates. In this study, we genotypically and phenotypically characterized 187 human clinical E. coli isolates representing various pathotypes (e.g., uropathogenic, enteropathogenic, and enteroaggregative E. coli). We investigated the presence of biofilm-associated genes (“genotype”) and phenotypically analyzed the isolates for motility and curli and cellulose production (“phenotype”). We developed a new screening method to examine the in vitro biofilm formation ability. In summary, we found a high prevalence of biofilm-associated genes. However, we could not detect a biofilm-associated gene or specific phenotype correlating with the biofilm formation ability. In contrast, we did identify an association of increased biofilm formation with a specific E. coli pathotype. Enteroaggregative E. coli (EAEC) was found to exhibit the highest capacity for biofilm formation. Using our image-based technology for the screening of biofilm formation, we demonstrated the characteristic biofilm formation pattern of EAEC, consisting of thick bacterial aggregates. In summary, our results highlight the fact that biofilm-promoting factors shown to be critical for biofilm formation in nonpathogenic strains do not reflect their impact in clinical isolates and that the ability of biofilm formation is a defined characteristic of EAEC. IMPORTANCE Bacterial biofilms are ubiquitous and consist of sessile bacterial cells surrounded by a self-produced extracellular polymeric matrix. They cause chronic and device-related infections due to their high resistance to antibiotics and the host immune system. In nonpathogenic Escherichia coli, cell surface components playing a pivotal role in biofilm formation are well known. In contrast, there is poor information for their role in biofilm formation of pathogenic isolates. Our study provides insights into the correlation of biofilm-associated genes or specific phenotypes with the biofilm formation ability of commensal and pathogenic E. coli. Additionally, we describe a newly developed method enabling qualitative biofilm analysis by automated image analysis, which is beneficial for high-throughput screenings. Our results help to establish a better understanding of E. coli biofilm formation. PMID:28986371

Genotypic and Phenotypic Characteristics Associated with Biofilm Formation by Human Clinical Escherichia coli Isolates of Different Pathotypes.

PubMed

Schiebel, Juliane; Böhm, Alexander; Nitschke, Jörg; Burdukiewicz, Michał; Weinreich, Jörg; Ali, Aamir; Roggenbuck, Dirk; Rödiger, Stefan; Schierack, Peter

2017-12-15

Bacterial biofilm formation is a widespread phenomenon and a complex process requiring a set of genes facilitating the initial adhesion, maturation, and production of the extracellular polymeric matrix and subsequent dispersal of bacteria. Most studies on Escherichia coli biofilm formation have investigated nonpathogenic E. coli K-12 strains. Due to the extensive focus on laboratory strains in most studies, there is poor information regarding biofilm formation by pathogenic E. coli isolates. In this study, we genotypically and phenotypically characterized 187 human clinical E. coli isolates representing various pathotypes (e.g., uropathogenic, enteropathogenic, and enteroaggregative E. coli ). We investigated the presence of biofilm-associated genes ("genotype") and phenotypically analyzed the isolates for motility and curli and cellulose production ("phenotype"). We developed a new screening method to examine the in vitro biofilm formation ability. In summary, we found a high prevalence of biofilm-associated genes. However, we could not detect a biofilm-associated gene or specific phenotype correlating with the biofilm formation ability. In contrast, we did identify an association of increased biofilm formation with a specific E. coli pathotype. Enteroaggregative E. coli (EAEC) was found to exhibit the highest capacity for biofilm formation. Using our image-based technology for the screening of biofilm formation, we demonstrated the characteristic biofilm formation pattern of EAEC, consisting of thick bacterial aggregates. In summary, our results highlight the fact that biofilm-promoting factors shown to be critical for biofilm formation in nonpathogenic strains do not reflect their impact in clinical isolates and that the ability of biofilm formation is a defined characteristic of EAEC. IMPORTANCE Bacterial biofilms are ubiquitous and consist of sessile bacterial cells surrounded by a self-produced extracellular polymeric matrix. They cause chronic and device-related infections due to their high resistance to antibiotics and the host immune system. In nonpathogenic Escherichia coli , cell surface components playing a pivotal role in biofilm formation are well known. In contrast, there is poor information for their role in biofilm formation of pathogenic isolates. Our study provides insights into the correlation of biofilm-associated genes or specific phenotypes with the biofilm formation ability of commensal and pathogenic E. coli Additionally, we describe a newly developed method enabling qualitative biofilm analysis by automated image analysis, which is beneficial for high-throughput screenings. Our results help to establish a better understanding of E. coli biofilm formation. Copyright © 2017 American Society for Microbiology.

Development of a microwave 20 x 20 switch matrix for 30/20 GHz SS-TDMA application

NASA Technical Reports Server (NTRS)

Cory, B. J.; Berkowitz, M.; Wallis, R.; Schiavone, A.; Shieh, D.; Campbell, J.

1982-01-01

The design and fabrication of a 3-8 GHz, 20 x 20 Satellite Switched-Time Division Multiple Access IF switch matrix applicable to a 30/20 GHz communications satellite are described. An assessment of switch architecture in 1980 concluded that the GaAs FET-based coupled crossbar switch matrix, incorporating high speed CMOS LSI logic for switch crosspoint addressing, would be the optimum technology available for communications satellite switching by 1982. This assessment was based on such factors as switching speed, bandwidth, off-state isolation, and reliability, over a 10-year mission life. A proof-of-concept model's construction and testing are presented.

Identification by using MALDI-TOF mass spectrometry of lactic acid bacteria isolated from non-commercial yogurts in southern Anatolia, Turkey.

PubMed

Karaduman, Ayse; Ozaslan, Mehmet Ozaslan; Kilic, Ibrahim H; Bayil-Oguzkan, Sibel; Kurt, Bekir S; Erdogan, Nese

2017-03-01

Yogurt is a dairy product obtained by bacterial fermentation of milk. Commercial yogurts are produced using standard starters while, in the production of non-commercial yogurt, the microbiota is quite different since yogurts are used as starter for years. To determine the final characteristics of the fermented product it is necessary to know the biochemical properties of the starter cultures, such as acidity, aroma and flavor. This can only be achieved by identifying and characterizing the bacteria in starter cultures. In our study, 208 non-commercial yogurt samples were collected from 9 different locations in Anatolia, southern Turkey. Their pH and lactic acid bacteria profiles were analyzed. Isolated bacteria were identified by MALDI-TOF MS (matrix-assisted laser sesorption-ionization time-of-flight, mass spectrometry), which is a fast and reliable method for identification of bacterial isolates compared to classical laboratory methods. In this study, 41% of the isolates were identified by using this method, which is 99.9% and 34.0% confidence. The isolates contained two genera (Enterococcus and Lactobacillus) and four species. Afterwards, the four lactic acid bacteria were characterized physiologically and biochemically and we found that they differed from lactic acid bacteria used in commercial yogurt production. [Int Microbiol 20(1): 25-30 (2017)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Mesenchymal stem cells reside in anterior cruciate ligament remnants in situ.

PubMed

Fu, Weili; Li, Qi; Tang, Xin; Chen, Gang; Zhang, Chenghao; Li, Jian

2016-07-01

It has been reported that the anterior cruciate ligament (ACL) has certain self-healing ability after acute injury or with primary suture repair. Many studies have confirmed that a remnant preservation technique with ACL reconstruction contributes to biological augmentation for ACL healing. However, it remains unclear whether mesenchymal stem cells (MSC) reside in ACL remnants in situ. The aim of this study was to investigate the methods of culture and identification of MSC derived from the remnants of ACL rupture patients and to analyse these MSC's properties. The cells of ACL remnants from the ACL rupture patients were isolated by the methods of enzymatic digestion and cultured in vitro to the third passage under the microscope to observe their morphology and growth status. The third passage of isolated cells was analysed for the identification of immunophenotype, osteogenic, adipogenic and chondrogenic differentiation. On the third to fifth days of in vitro culture, a few cells of long fusiform shape appeared and were adherent to the plastic walls. On the sixth to ninth days, cells clustered and colonies were observed. The third passage cells showed uniform cell morphology and good proliferation, with appearance of the typical surface markers of MSC, CD29, CD44, CD90 and CD105. The surface markers of CD34 and CD45 of haematopoietic stem cells were not expressed. Under appropriate conditions of in vitro culture, isolated cells could be differentiated into osteoblasts that deposit mineralised matrix and express early osteogenic markers, adipocytes that accumulate lipid droplets in cytoplasm and chondrocytes that secrete chondrogenic-specific matrix aggrecan and collagen II. Real-time polymerase chain reaction (PCR) analysis demonstrated that the specific mRNA expression of osteogenesis, adipogenesis and chondrogenesis increased significantly compared with the control groups at day zero. Stem cells derived in situ from the human ACL stump were successfully isolated and characterised. Those isolated cells were identified as MSC according to their adherent ability, morphology, surface markers and multilineage differentiation potential. MSC derived from ACL remnants could be a potential source of seeding cells for ligament regeneration.

Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Seng, Piseth; Drancourt, Michel; Gouriet, Frédérique; La Scola, Bernard; Fournier, Pierre-Edouard; Rolain, Jean Marc; Raoult, Didier

2009-08-15

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry accurately identifies both selected bacteria and bacteria in select clinical situations. It has not been evaluated for routine use in the clinic. We prospectively analyzed routine MALDI-TOF mass spectrometry identification in parallel with conventional phenotypic identification of bacteria regardless of phylum or source of isolation. Discrepancies were resolved by 16S ribosomal RNA and rpoB gene sequence-based molecular identification. Colonies (4 spots per isolate directly deposited on the MALDI-TOF plate) were analyzed using an Autoflex II Bruker Daltonik mass spectrometer. Peptidic spectra were compared with the Bruker BioTyper database, version 2.0, and the identification score was noted. Delays and costs of identification were measured. Of 1660 bacterial isolates analyzed, 95.4% were correctly identified by MALDI-TOF mass spectrometry; 84.1% were identified at the species level, and 11.3% were identified at the genus level. In most cases, absence of identification (2.8% of isolates) and erroneous identification (1.7% of isolates) were due to improper database entries. Accurate MALDI-TOF mass spectrometry identification was significantly correlated with having 10 reference spectra in the database (P=.01). The mean time required for MALDI-TOF mass spectrometry identification of 1 isolate was 6 minutes for an estimated 22%-32% cost of current methods of identification. MALDI-TOF mass spectrometry is a cost-effective, accurate method for routine identification of bacterial isolates in <1 h using a database comprising > or =10 reference spectra per bacterial species and a 1.9 identification score (Brucker system). It may replace Gram staining and biochemical identification in the near future.

Antimicrobial activity and hydrophobicity of edible whey protein isolate films formulated with nisin and/or glucose oxidase.

PubMed

Murillo-Martínez, María M; Tello-Solís, Salvador R; García-Sánchez, Miguel A; Ponce-Alquicira, Edith

2013-04-01

The use of edible antimicrobial films has been reported as a means to improve food shelf life through gradual releasing of antimicrobial compounds on the food surface. This work reports the study on the incorporation of 2 antimicrobial agents, nisin (N), and/or glucose oxidase (GO), into the matrix of Whey protein isolate (WPI) films at pH 5.5 and 8.5. The antimicrobial activity of the edible films was evaluated against Listeria innocua (ATCC 33090), Brochothrix thermosphacta (NCIB10018), Escherichia coli (JMP101), and Enterococcus faecalis (MXVK22). In addition, the antimicrobial activity was related to the hydrophobicity and water solubility of the WPI films. The greatest antibacterial activity was observed in WPI films containing only GO. The combined addition of N and GO resulted in films with lower antimicrobial activity than films with N or GO alone. In most cases, a pH effect was observed as greater antimicrobial response at pH 5.5 as well as higher film matrix hydrophobicity. WPI films supplemented with GO can be used in coating systems suitable for food preservation. © 2013 Institute of Food Technologists®

Potential of Pseudoshikonin I Isolated from Lithospermi Radix as Inhibitors of MMPs in IL-1β-Induced SW1353 Cells.

PubMed

Lee, Dae Young; Choi, Soo-Im; Han, Se Hee; Lee, Ye-Joo; Choi, Jong-Gil; Lee, Young-Seob; Choi, Je Hun; Lee, Seung-Eun; Kim, Geum-Soog

2016-08-18

Pseudoshikonin I, the new bioactive constituent of Lithospermi radix, was isolated from this methanol extract by employing reverse-phase medium-pressure liquid chromatography (MPLC) using acetonitrile/water solvent system as eluents. The chemical structure was determined based on spectroscopic techniques, including 1D NMR (¹H, (13)C, DEPT), 2D NMR (gCOSY, gHMBC, gHMQC), and QTOF/MS data. In this study, we demonstrated the effect of pseudoshikonin I on matrix-metalloproteinase (MMPs) activation and expression in interleukin (IL)-1β-induced SW1353 chondrosarcoma cells. MMPs are considered important for the maintenance of the extracellular matrix. Following treatment with PS, active MMP-1, -2, -3, -9, -13 and TIMP-2 were quantified in the SW1353 cell culture supernatants using a commercially available ELISA kit. The mRNA expression of MMPs in SW1353 cells was measured by RT-PCR. Pseudoshikonin I treatment effectively protected the activation on all tested MMPs in a dose-dependent manner. TIMP-2 mRNA expression was significantly upregulated by pseudoshikonin I treatment. Overall, we elucidated the inhibitory effect of pseudoshikonin on MMPs, and we suggest its use as a potential novel anti-osteoarthritis agent.

Identification of a mitochondrial alcohol dehydrogenase in Schizosaccharomyces pombe: new insights into energy metabolism

PubMed Central

Crichton, Paul G.; Affourtit, Charles; Moore, Anthony L.

2006-01-01

In the present study we have shown that mitochondria isolated from Schizosaccharomyces pombe exhibit antimycin A-sensitive oxygen uptake activity that is exclusively dependent on ethanol and is inhibited by trifluoroethanol, a potent inhibitor of ADH (alcohol dehydrogenase). Ethanol-dependent respiratory activity has, to our knowledge, not been reported in S. pombe mitochondria to date, which is surprising as it has been concluded previously that only one ADH gene, encoding a cytosolic enzyme, occurs in this yeast. Spectrophotometric enzyme assays reveal that ADH activity in isolated mitochondria is increased ∼16-fold by Triton X-100, which demonstrates that the enzyme is located in the matrix. Using genetic knockouts, we show conclusively that the novel mitochondrial ADH is encoded by adh4 and, as such, is unrelated to ADH isoenzymes found in mitochondria of other yeasts. By performing a modular-kinetic analysis of mitochondrial electron transfer, we furthermore show how ethanol-dependent respiratory activity (which involves oxidation of matrix-located NADH) compares with that observed when succinate or externally added NADH are used as substrates. This analysis reveals distinct kinetic differences between substrates which fully explain the lack of respiratory control generally observed during ethanol oxidation in yeast mitochondria. PMID:16999687

UV-tunable laser induced phototransformations of matrix isolated anethole.

PubMed

Krupa, Justyna; Wierzejewska, Maria; Nunes, Cláudio M; Fausto, Rui

2014-03-14

A matrix isolation study of the infrared spectra and structure of anethole (1-methoxy-4-(1-propenyl)benzene) has been carried out, showing the presence of two E conformers (AE1, AE2) of the molecule in the as-deposited matrices. Irradiation using ultraviolet-tunable laser light at 308-307 nm induced conformationally selective phototransformations of these forms into two less stable Z conformers (AZ1, AZ2). The back reactions were also detected upon irradiation at 301 nm. On the whole, the obtained results allow for full assignment of the infrared spectra of all the four experimentally observed anethole isomers and showed that the narrowband UV-induced E-Z photoisomerization is an efficient and selective way to interconvert the two isomers of anethole into each other, with conformational discrimination. Photolysis of anethole was observed as well, with initial methoxyl O-C bond cleavage and formation of CH3 and p-propenylphenoxy (AR) radicals, followed by radical recombination to form 2-methyl-4-propenyl-2,4-cyclohexadienone, which subsequently undergoes ring-opening generating several conformers of long-chain conjugated ketenes. Interpretation of the experimental observations was supported by density functional theory (B3LYP and B2PLYD) calculations.

Matrix-assisted laser desorption ionization time of flight mass spectrometry and diagnostic testing for prosthetic joint infection in the clinical microbiology laboratory.

PubMed

Peel, Trisha N; Cole, Nicolynn C; Dylla, Brenda L; Patel, Robin

2015-03-01

Identification of pathogen(s) associated with prosthetic joint infection (PJI) is critical for patient management. Historically, many laboratories have not routinely identified organisms such as coagulase-negative staphylococci to the species level. The advent of matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has enhanced clinical laboratory capacity for accurate species-level identification. The aim of this study was to describe the species-level identification of microorganisms isolated from periprosthetic tissue and fluid specimens using MALDI-TOF MS alongside other rapid identification tests in a clinical microbiology laboratory. Results of rapid identification of bacteria isolated from periprosthetic joint fluid and/or tissue specimens were correlated with clinical findings at Mayo Clinic, Rochester, Minnesota, between May 2012 and May 2013. There were 178 PJI and 82 aseptic failure (AF) cases analyzed, yielding 770 organisms (median, 3/subject; range, 1-19/subject). MALDI-TOF MS was employed for the identification of 455 organisms (59%) in 197 subjects (123 PJIs and 74 AFs), with 89% identified to the species level using this technique. Gram-positive bacteria accounted for 68% and 93% of isolates in PJI and AF, respectively. However, the profile of species associated with infection compared to specimen contamination differed. Staphylococcus aureus and Staphylococcus caprae were always associated with infection, Staphylococcus epidermidis and Staphylococcus lugdunensis were equally likely to be a pathogen or a contaminant, whereas the other coagulase-negative staphylococci were more frequently contaminants. Most streptococcal and Corynebacterium isolates were pathogens. The likelihood that an organism was a pathogen or contaminant differed with the prosthetic joint location, particularly in the case of Propionibacterium acnes. MALDI-TOF MS is a valuable tool for the identification of bacteria isolated from patients with prosthetic joints, providing species-level identification that may inform culture interpretation of pathogens versus contaminants. Copyright © 2015 Elsevier Inc. All rights reserved.

Genotypic characterization of Escherichia coli O157:H7 isolates from different sources in the North-West Province, South Africa, using enterobacterial repetitive intergenic consensus PCR analysis.

PubMed

Ateba, Collins Njie; Mbewe, Moses

2014-05-30

In many developing countries, proper hygiene is not strictly implemented when animals are slaughtered and meat products become contaminated. Contaminated meat may contain Escherichia coli (E. coli) O157:H7 that could cause diseases in humans if these food products are consumed undercooked. In the present study, a total of 94 confirmed E. coli O157:H7 isolates were subjected to the enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR) typing to generate genetic fingerprints. The ERIC fragments were resolved by electrophoresis on 2% (w/v) agarose gels. The presence, absence and intensity of band data were obtained, exported to Microsoft Excel (Microsoft Office 2003) and used to generate a data matrix. The unweighted pair group method with arithmetic mean (UPGMA) and complete linkage algorithms were used to analyze the percentage of similarity and matrix data. Relationships between the various profiles and/or lanes were expressed as dendrograms. Data from groups of related lanes were compiled and reported on cluster tables. ERIC fragments ranged from one to 15 per isolate, and their sizes varied from 0.25 to 0.771 kb. A large proportion of the isolates produced an ERIC banding pattern with three duplets ranging in sizes from 0.408 to 0.628 kb. Eight major clusters (I-VIII) were identified. Overall, the remarkable similarities (72% to 91%) between the ERIC profiles for the isolate from animal species and their corresponding food products indicated some form of contamination, which may not exclude those at the level of the abattoirs. These results reveal that ERIC PCR analysis can be reliable in comparing the genetic profiles of E. coli O157:H7 from different sources in the North-West Province of South Africa.

Isolation of a matrix that binds medial Golgi enzymes

PubMed Central

1994-01-01

Rat liver Golgi stacks were extracted with Triton X-100 at neutral pH. After centrifugation the low speed pellet contained two medial-Golgi enzymes, N-acetylglucosaminyltransferase I and mannosidase II, but no enzymes or markers from other parts of the Golgi apparatus. Both were present in the same structures which appeared, by electron microscopy, to be small remnants of cisternal membranes. The enzymes could be removed by treatment with low salt, leaving behind a salt pellet, which we term the matrix. Removal of salt caused specific re-binding of both enzymes to the matrix, with an apparent dissociation constant of 3 nM for mannosidase II. Re-binding was abolished by pretreatment of intact Golgi stacks with proteinase K, suggesting that the matrix was present between the cisternae. PMID:8106542

Isolation and characterization of antimicrobial food components.

PubMed

Papetti, Adele

2012-04-01

Nowadays there is an evident growing interest in natural antimicrobial compounds isolated from food matrices. According to the type of matrix, different isolation and purification steps are needed and as these active compounds belong to different chemical classes, also different chromatographic and electrophoretic methods coupled with various detectors (the most used diode array detector and mass spectrometer) have to be performed. This review covers recent steps made in the fundamental understanding of sample preparation methods as well as of analytical tools useful for the complete characterization of bioactive food compounds. The most commonly used methods for extraction of natural antimicrobial compounds are the conventional liquid-liquid or solid-liquid extraction and the modern techniques such as pressurized liquid extraction, microwave-assisted extraction, ultrasound-assisted extraction, solid-phase micro-extraction, supercritical fluid extraction, and matrix solid phase dispersion. The complete characterization of the compounds is achieved using both monodimensional chromatographic processes (LC, nano-LC, GC, and CE coupled with different type of detectors) and, recently, using comprehensive two-dimensional systems (LC×LC and GC×GC). Copyright © 2011 Elsevier Ltd. All rights reserved.

Flash Vacuum Pyrolysis: Techniques and Reactions.

PubMed

Wentrup, Curt

2017-11-20

Flash vacuum pyrolysis (FVP) had its beginnings in the 1940s and 1950s, mainly through mass spectrometric detection of pyrolytically formed free radicals. In the 1960s many organic chemists started performing FVP experiments with the purpose of isolating new and interesting compounds and understanding pyrolysis processes. Meanwhile, many different types of apparatus and techniques have been developed, and it is the purpose of this review to present the most important methods as well as a survey of typical reactions and observations that can be achieved with the various techniques. This includes preparative FVP, chemical trapping reactions, matrix isolation, and low temperature spectroscopy of reactive intermediates and unstable molecules, the use of online mass, photoelectron, microwave, and millimeterwave spectroscopies, gas-phase laser pyrolysis, pulsed pyrolysis with supersonic jet expansion, very low pressure pyrolysis for kinetic investigations, solution-spray and falling-solid FVP for involatile compounds, and pyrolysis over solid supports and reagents. Moreover, the combination of FVP with matrix isolation and photochemistry is a powerful tool for investigations of reaction mechanism. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Observation of Transient Surface-Bound Intermediates by Interfacial Matrix Stabilization Spectroscopy (imss)

NASA Astrophysics Data System (ADS)

Jarrah, Nina K.; Moore, David T.

2014-06-01

Interfacial matrix stabilization spectroscopy is a new technique based on matrix isolation spectroscopy, but where a cryogenic matrix is deposited over the top of a film sample, in order to characterize interactions between the substrate and molecular dopants. The IMSS technique harnesses the well-established ability of cryogenic matrices to trap and stabilize transient species, although in this case it is applied to intermediates relevant to heterogeneous catalysis. In this proof-of-concept study, we present data for CO and O2 reactants binding to TiO2 and Au/TiO2 nanoparticle films, where in the latter case the Au nanoparticles were created by de-wetting of a 22.5 nm overlayer at 450 K. The films are first pre-saturated with CO at 40 K, then cooled to 20 K, at which point an argon matrix is deposited over the top of them. The spectra are then annealed in stages over a range of temperatures between 20 and 40 K. In all cases, the presence of the Ar matrix alters the appearance of the CO bands, revealing additional structure, such as a broad feature at 2150 wn, which is typically attributed to CO interacting with OH groups on the TiO2 surface, but is not observed at 40 K for these samples in the absence of the matrix. The interpretation is that the matrix induces a caging-effect that prevents molecules from desorbing from weak binding sites from which they would be "pumped away" in the vacuum chamber if the matrix were not present. Perhaps the most interesting feature of these spectra is a small but sharp band at 2112 wn that appears ONLY when O2 is added to the argon matrix as a dopant. This transient band grows in following annealing at 32 K, but then disappears upon annealing above 34 K, suggesting that it may correspond to a reactive intermediate. The band occurs for samples both with and without Au present on the TiO2 surface, but shows a larger intensity in the latter case. Possible assignments for the observed band in light of previous studies from the literature will be discussed in detail.

Genome Sequence of Lactobacillus brevis Strain D6, Isolated from Smoked Fresh Cheese.

PubMed

Kant, Ravi; Uroić, Ksenija; Hynönen, Ulla; Kos, Blaženka; Šušković, Jagoda; Palva, Airi

2016-04-07

The autochthonousLactobacillus brevisstrain D6, isolated from smoked fresh cheese, carries a 45-kDa S-layer protein. Strain D6 has shown adhesion to extracellular matrix proteins and to Caco-2 intestinal epithelial cells, as well as immunomodulatory potential and beneficial milk technological properties. Hence, it could be used as a potential probiotic starter culture for cheese production. Copyright © 2016 Kant et al.

Genome Sequence of Lactobacillus brevis Strain D6, Isolated from Smoked Fresh Cheese

PubMed Central

Uroić, Ksenija; Hynönen, Ulla; Kos, Blaženka; Šušković, Jagoda

2016-01-01

The autochthonous Lactobacillus brevis strain D6, isolated from smoked fresh cheese, carries a 45-kDa S-layer protein. Strain D6 has shown adhesion to extracellular matrix proteins and to Caco-2 intestinal epithelial cells, as well as immunomodulatory potential and beneficial milk technological properties. Hence, it could be used as a potential probiotic starter culture for cheese production. PMID:27056237

The demosponge Halichondria (Halichondria) panicea (Pallas, 1766) as a novel source of biosurfactant-producing bacteria.

PubMed

Rizzo, Carmen; Syldatk, Christoph; Hausmann, Rudolf; Gerçe, Berna; Longo, Caterina; Papale, Maria; Conte, Antonella; De Domenico, Emilio; Michaud, Luigi; Lo Giudice, Angelina

2018-06-01

The Mediterranean sponge Halichondria (Halichondria) panicea was explored as a novel matrix for the isolation of biosurfactant-producing bacteria. A total of 38 (out of 56) isolates gave a good response to the employed screening tests (e.g., stable emulsion detection, surface tension measurement, hemolytic activity, and blue agar plate assay) and were selected for further analyses. The thin layer chromatography revealed a possible glucidic composition of biosurfactants. Most promising strains, i.e., those able to produce stable emulsion with percentage higher than 30% and yellow spots on TLC plates, were affiliated to the genera Pseudovibrio, Acinetobacter, and Bacillus. The biosurfactant production by two isolates (i.e., Acinetobacter sp. SpN134 and Pseudovibrio sp. SpE85) was evaluated under different culture conditions, in terms of temperature, NaCl concentration, and pH. Surface tension reduction ability was more stable than the emulsification, and resulted differently influenced by salinity, temperature, and pH. Acinetobacter sp. SpN134 resulted particularly efficient and competitive if compared with other well-known biosurfactant producers. Data suggest that sponges may represent a promising matrix for the isolation of biosurfactant-producing bacteria, reinforcing the growing interest towards filter-feeding organisms as underexplored sources of specialized bacteria. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lactate is oxidized outside of the mitochondrial matrix in rodent brain.

PubMed

Herbst, Eric A F; George, Mitchell A J; Brebner, Karen; Holloway, Graham P; Kane, Daniel A

2018-05-01

The nature and existence of mitochondrial lactate oxidation is debated in the literature. Obscuring the issue are disparate findings in isolated mitochondria, as well as relatively low rates of lactate oxidation observed in permeabilized muscle fibres. However, respiration with lactate has yet to be directly assessed in brain tissue with the mitochondrial reticulum intact. To determine if lactate is oxidized in the matrix of brain mitochondria, oxygen consumption was measured in saponin-permeabilized mouse brain cortex samples, and rat prefrontal cortex and hippocampus (dorsal) subregions. While respiration in the presence of ADP and malate increased with the addition of lactate, respiration was maximized following the addition of exogenous NAD + , suggesting maximal lactate metabolism involves extra-matrix lactate dehydrogenase. This was further supported when NAD + -dependent lactate oxidation was significantly decreased with the addition of either low-concentration α-cyano-4-hydroxycinnamate or UK-5099, inhibitors of mitochondrial pyruvate transport. Mitochondrial respiration was comparable between glutamate, pyruvate, and NAD + -dependent lactate oxidation. Results from the current study demonstrate that permeabilized brain is a feasible model for assessing lactate oxidation, and support the interpretation that lactate oxidation occurs outside the mitochondrial matrix in rodent brain.

An affordable method to obtain cultured endothelial cells from peripheral blood

PubMed Central

Bueno-Betí, Carlos; Novella, Susana; Lázaro-Franco, Macarena; Pérez-Cremades, Daniel; Heras, Magda; Sanchís, Juan; Hermenegildo, Carlos

2013-01-01

The culture of endothelial progenitor cells (EPC) provides an excellent tool to research on EPC biology and vascular regeneration and vasculogenesis. The use of different protocols to obtain EPC cultures makes it difficult to obtain comparable results in different groups. This work offers a systematic comparison of the main variables of most commonly used protocols for EPC isolation, culture and functional evaluation. Peripheral blood samples from healthy individuals were recovered and mononuclear cells were cultured. Different recovery and culture conditions were tested: blood volume, blood anticoagulant, coating matrix and percentage of foetal bovine serum (FBS) in culture media. The success of culture procedure, first colonies of endothelial cells appearance time, correlation with number of circulating EPC (cEPC) and functional comparison with human umbilical vein endothelial cells (HUVEC) were studied. The use of heparin, a minimum blood volume of 30 ml, fibronectin as a coating matrix and endothelial growing media-2 supplemented with 20% FBS increased the success of obtaining EPC cultures up to 80% of the processed samples while reducing EPC colony appearance mean time to a minimum of 13 days. Blood samples exhibiting higher cEPC numbers resulted in reduced EPC colony appearance mean time. Cells isolated by using this combination were endothelial cell-like EPCs morphological and phenotypically. Functionally, cultured EPC showed decreased growing and vasculogenic capacity when compared to HUVEC. Thus, above-mentioned conditions allow the isolation and culture of EPC with smaller blood volumes and shorter times than currently used protocols. PMID:24118735

Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility.

PubMed

Walker, J; Fox, A J; Edwards-Jones, V; Gordon, D B

2002-02-01

Intact cell mass spectrometry (ICMS) rapidly analyses the surface composition of microorganisms providing rapid, discriminatory fingerprints for identification and subtyping of important nosocomial pathogens such as methicillin resistant Staphylocccus aureus (MRSA). In this study, ICMS using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI TOF/MS) was assessed for the identification and subtyping of MRSA. An intra- and inter-laboratory reproducibility study was carried out and the effects of culture media (an important source of variation for ICMS) were also studied. Several media used for the cultural identification of MRSA were examined using a panel of well-characterised staphylococcal isolates (n=26). Six MRSA isolates were analysed over a 1-month period for intra-laboratory reproducibility on the same instrument and three different culture media. Spectra were consistent for each isolate between the four experiments on the same culture medium. Individual isolates produced different spectral profiles on different culture media. Spectra from organisms grown on Columbia blood agar contained more peaks (approximately 120) compared to Columbia agar (approximately 50) and methicillin mannitol salt agar (approximately 25). All 26 staphylococcal isolates were subjected to an inter-laboratory study on two MALDI instruments. For each isolate, the overall spectral profile was the same for each of the two instruments but the baseline threshold values was adjusted due to instrument differences in detector sensitivities. Differences between certain regions of the spectra reproducibly identified isolates belonging to the two major MRSA strains (EMRSA phage group 15 and 16). These results demonstrate ICMS with appropriate media selection is a rapid and reproducible technique for identification and discrimination of MRSA.

A fast-initializing digital equalizer with on-line tracking for data communications

NASA Technical Reports Server (NTRS)

Houts, R. C.; Barksdale, W. J.

1974-01-01

A theory is developed for a digital equalizer for use in reducing intersymbol interference (ISI) on high speed data communications channels. The equalizer is initialized with a single isolated transmitter pulse, provided the signal-to-noise ratio (SNR) is not unusually low, then switches to a decision directed, on-line mode of operation that allows tracking of channel variations. Conditions for optimal tap-gain settings are obtained first for a transversal equalizer structure by using a mean squared error (MSE) criterion, a first order gradient algorithm to determine the adjustable equalizer tap-gains, and a sequence of isolated initializing pulses. Since the rate of tap-gain convergence depends on the eigenvalues of a channel output correlation matrix, convergence can be improved by making a linear transformation on to obtain a new correlation matrix.

Photochemistry of fluorinated 4-iodophenylnitrenes: matrix isolation and spectroscopic characterization of phenylnitrene-4-yls.

PubMed

Grote, Dirk; Sander, Wolfram

2009-10-02

The photochemistry of a series of fluorinated p-iodophenyl azides 2 has been investigated using matrix isolation IR and EPR spectroscopy. In all cases, the corresponding phenylnitrenes 1 were formed as primary photoproducts. Further irradiation of the nitrenes 1 resulted in the formation of azirines 3, ketenimines 4, and nitreno radicals 5. The yield of 5 depends on the number of ortho fluorine substituents: with two ortho fluorine atoms the highest yield is observed, whereas without fluorine atoms the yield is too low for IR spectroscopic detection. The interconversion between the isomers 1, 3, and 4 proved to be rather complex. If the fluorine atoms are distributed unsymmetrically, two isomers of azirines 3 and ketenimines 4 can be formed. The yields of these isomers depend critically on the irradiation conditions.

The Infrared Spectrum of Matrix Isolated Aminoacetonitrile: A Precursor to the Amino Acid Glycine

NASA Technical Reports Server (NTRS)

Bernstein, Max P.; Bauschlicher, Charles W., Jr.; Sandford, Scott A.

2003-01-01

We present infrared (IR) spectral data from matrix isolation experiments and density functional theory calculations on the pre-biologically interesting molecule aminoacetonitrile, a precursor to glycine. We find that this nitrile has an unusually weak nitrile (C=N) stretch in the infrared, in contrast to expectations based on measurements and models of other nitriles under astrophysical conditions. The absence of an observable nitrile absorption feature in the infrared will make the IR search for this molecule considerably more difficult, and will raise estimates of upper limits on nitriles in interstellar and outer Solar System ices. This is also of relevance to assessing the formation routes of the amino acid glycine, since aminoacetonitrile is the putative precursor to glycine via the Strecker synthesis, the mechanism postulated to have produced the amino acids in meteorites.

Poly-N-acetylglucosamine mediates biofilm formation and antibiotic resistance in Actinobacillus pleuropneumoniae

PubMed Central

Izano, Era A.; Sadovskaya, Irina; Vinogradov, Evgeny; Mulks, Martha H.; Velliyagounder, Kabilan; Ragunath, Chandran; Kher, William B.; Ramasubbu, Narayanan; Jabbouri, Saïd; Perry, Malcolm B.; Kaplan, Jeffrey B.

2007-01-01

Most field isolates of the swine pathogen Actinobacillus pleuropneumoniae form tenacious biofilms on abiotic surfaces in vitro. We purified matrix polysaccharides from biofilms produced by A. pleuropneumoniae field isolates IA1 and IA5 (serotypes 1 and 5, respectively), and determined their chemical structures by using NMR spectroscopy. Both strains produced matrix polysaccharides consisting of linear chains of N-acetyl-D-glucosamine (GlcNAc) residues in β(1,6) linkage (poly-β-1,6-GlcNAc or PGA). A small percentage of the GlcNAc residues in each polysaccharide were N-deacetylated. These structures were nearly identical to those of biofilm matrix polysaccharides produced by Escherichia coli, Staphylococcus aureus and S. epidermidis. PCR analyses indicated that a gene encoding the PGA-specific glycoside transferase enzyme PgaC was present on the chromosome of 15 out of 15 A. pleuropneumoniae reference strains (serotypes 1-12) and 76 out of 77 A. pleuropneumoniae field isolates (serotypes 1, 5 and 7). A pgaC mutant of strain IA5 failed to form biofilms in vitro, as did wild-type strains IA1 and IA5 when grown in broth supplemented with the PGA-hydrolyzing enzyme dispersin B. Treatment of IA5 biofilms with dispersin B rendered them more sensitive to killing by ampicillin. Our findings suggest that PGA functions as a major biofilm adhesin in A. pleuropneumoniae. Biofilm formation may have relevance to the colonization and pathogenesis of A. pleuropneumoniae in pigs. PMID:17412552

Evaluation of MALDI-TOF-MS for the Identification of Yeast Isolates Causing Bloodstream Infection.

PubMed

Turhan, Ozge; Ozhak-Baysan, Betil; Zaragoza, Oscar; Er, Halil; Sarıtas, Zubeyde Eres; Ongut, Gozde; Ogunc, Dilara; Colak, Dilek; Cuenca-Estrella, Manuel

2017-04-01

Infections due to Candida species are major causes of morbidity and mortality in humans, causing a diverse spectrum of clinical disease ranging from superficial and mucosal infections to invasive disease. Several authors have demonstrated that mortality is closely linked to both timing of therapy and/or source control. The rapid identification of pathogenic species is helpful to start timely and effective antifungal therapy. The aim of this study was to assess the performance of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system for the correct and rapid identification of yeast isolates causing bloodstream infection. Between January 2014 and January 2015, a total of 117 yeast like organisms isolated from blood culture samples of 117 episodes from 102 patients who had blood stream infections were included in the study. The isolates were identified by MALDI-TOF MS. The results were compared with those obtained by the standard mycological methods and/or sequence analysis. One hundred and seventeen yeast isolates including 115 Candida spp and two non-Candida yeasts were analysed. The Biotyper correctly identified 115 (98.3%) isolates to the genus level and 102 (87.2%) isolates to the species level using the manufacturer's recommended cutoff scores. The Bruker Biotyper is a rapid, easy, inexpensive, and highly reliable system for the identification of yeast isolates. Early identification with MALDI-TOF MS would save time for determination of antifungal susceptibility and proper treatment strategy. The expansion of the database of the library by addition of less common species will improve the performance of the system.

Matrix-assisted laser-induced gas-phase aggregation of C 60 oxides

NASA Astrophysics Data System (ADS)

Barrow, Mark P.; Tower, Nicole J.; Taylor ^*, , Roger; Drewello, Thomas

1998-08-01

Matrix-assisted laser desorption/ionisation of C 60 oxides, in conjunction with reflectron time-of-flight mass spectrometry, leads to an unprecedented gas-phase aggregation resulting in the formation of C 120O n- ·. products. The analysis of the product distribution obtained for oxides of varying oxygen content strongly suggests that the structures of these species are closely related to oxo-bridged isolated fullerene cages rather than to species featuring a fused giant fullerene core.

Isolation and characterization of a carrot nucleolar protein with structural and sequence similarity to the vertebrate PESCADILLO protein.

PubMed

Ueda, Kenji; Xu, Zheng-Jun; Miyagi, Nobuaki; Ono, Michiyuki; Wabiko, Hiroetsu; Masuda, Kiyoshi; Inoue, Masayasu

2013-07-01

The nuclear matrix is involved in many nuclear events, but its protein architecture in plants is still not fully understood. A cDNA clone was isolated by immunoscreening with a monoclonal antibody raised against nuclear matrix proteins of Daucus carota L. Its deduced amino acid sequence showed about 40% identity with the PESCADILLO protein of zebrafish and humans. Primary structure analysis of the protein revealed a Pescadillo N-terminus domain, a single breast cancer C-terminal domain, two nuclear localization signals, and a potential coiled-coil region as also found in animal PESCADILLO proteins. Therefore, we designated this gene DcPES1. Although DcPES1 mRNA was detected in all tissues examined, its levels were highest in tissues with proliferating cells. Immunofluorescence using specific antiserum against the recombinant protein revealed that DcPES1 localized exclusively in the nucleolus. Examination of fusion proteins with green fluorescent protein revealed that the N-terminal portion was important for localization to the nucleoli of tobacco and onion cells. Moreover, when the nuclear matrix of carrot cells was immunostained with an anti-DcPES1 serum, the signal was detected in the nucleolus. Therefore, the DcPES1 protein appears to be a component of or tightly bound to components of the nuclear matrix. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Curcumin Quantum Dots Mediated Degradation of Bacterial Biofilms.

PubMed

Singh, Ashish K; Prakash, Pradyot; Singh, Ranjana; Nandy, Nabarun; Firdaus, Zeba; Bansal, Monika; Singh, Ranjan K; Srivastava, Anchal; Roy, Jagat K; Mishra, Brahmeshwar; Singh, Rakesh K

2017-01-01

Bacterial biofilm has been reported to be associated with more than 80% of bacterial infections. Curcumin, a hydrophobic polyphenol compound, has anti-quorum sensing activity apart from having antimicrobial action. However, its use is limited by its poor aqueous solubility and rapid degradation. In this study, we attempted to prepare quantum dots of the drug curcumin in order to achieve enhanced solubility and stability and investigated for its antimicrobial and antibiofilm activity. We utilized a newer two-step bottom up wet milling approach to prepare Curcumin Quantum Dots (CurQDs) using acetone as a primary solvent. Minimum inhibitory concentration against select Gram-positive and Gram-negative bacteria was performed. The antibiofilm assay was performed at first using 96-well tissue culture plate and subsequently validated by Confocal Laser Scanning Microscopy. Further, biofilm matrix protein was isolated using formaldehyde sludge and TCA/Acetone precipitation method. Protein extracted was incubated with varying concentration of CurQDs for 4 h and was subjected to SDS-PAGE. Molecular docking study was performed to observe interaction between curcumin and phenol soluble modulins as well as curli proteins. The biophysical evidences obtained from TEM, SEM, UV-VIS, fluorescence, Raman spectroscopy, and zeta potential analysis confirmed the formation of curcumin quantum dots with increased stability and solubility. The MICs of curcumin quantum dots, as observed against both select gram positive and negative bacterial isolates, was observed to be significantly lower than native curcumin particles. On TCP assay, Curcumin observed to be having antibiofilm as well as biofilm degrading activity. Results of SDS-PAGE and molecular docking have shown interaction between biofilm matrix proteins and curcumin. The results indicate that aqueous solubility and stability of Curcumin can be achieved by preparing its quantum dots. The study also demonstrates that by sizing down the particle size has not only enhanced its antimicrobial properties but it has also shown its antibiofilm activities. Further, study is needed to elucidate the exact nature of interaction between curcumin and biofilm matrix proteins.

Identification and Characterization of the Lysine-Rich Matrix Protein Family in Pinctada fucata: Indicative of Roles in Shell Formation.

PubMed

Liang, Jian; Xie, Jun; Gao, Jing; Xu, Chao-Qun; Yan, Yi; Jia, Gan-Chu; Xiang, Liang; Xie, Li-Ping; Zhang, Rong-Qing

2016-12-01

Mantle can secret matrix proteins playing key roles in regulating the process of shell formation. The genes encoding lysine-rich matrix proteins (KRMPs) are one of the most highly expressed matrix genes in pearl oysters. However, the expression pattern of KRMPs is limited and the functions of them still remain unknown. In this study, we isolated and identified six new members of lysine-rich matrix proteins, rich in lysine, glycine and tyrosine, and all of them are basic matrix proteins. Combined with four members of the KRMPs previously reported, all these proteins can be divided into three subclasses according to the results of phylogenetic analyses: KRMP1-3 belong to subclass KPI, KRMP4-5 belong to KPII, and KRMP6-10 belong to KPIII. Three subcategories of lysine-rich matrix proteins are highly expressed in the D-phase, the larvae and adult mantle. Lysine-rich matrix proteins are involved in the shell repairing process and associated with the formation of the shell and pearl. What's more, they can cause abnormal shell growth after RNA interference. In detail, KPI subgroup was critical for the beginning formation of the prismatic layer; both KPII and KPIII subgroups participated in the formation of prismatic layer and nacreous layer. Compared with different temperatures and salinity stimulation treatments, the influence of changes in pH on KRMPs gene expression was the greatest. Recombinant KRMP7 significantly inhibited CaCO 3 precipitation, changed the morphology of calcite, and inhibited the growth of aragonite in vitro. Our results are beneficial to understand the functions of the KRMP genes during shell formation.

Stimulatory effects of advanced glycation endproducts (AGEs) on fibronectin matrix assembly.

PubMed

Pastino, Alexandra K; Greco, Todd M; Mathias, Rommel A; Cristea, Ileana M; Schwarzbauer, Jean E

2017-05-01

Advanced glycation endproducts (AGEs) are a heterogeneous group of compounds that form via non-enzymatic glycation of proteins throughout our lifespan and at a higher rate in certain chronic diseases such as diabetes. AGEs contribute to the progression of fibrosis, in part by stimulating cellular pathways that affect gene expression. Long-lived ECM proteins are targets for non-enzymatic glycation but the question of whether the AGE-modified ECM leads to excess ECM accumulation and fibrosis remains unanswered. In this study, cellular changes due to AGE accretion in the ECM were investigated. Non-enzymatic glycation of proteins in a decellularized fibroblast ECM was achieved by incubating the ECM in a solution of methylglyoxal (MGO). Mass spectrometry of fibronectin (FN) isolated from the glycated matrix identified twenty-eight previously unidentified MGO-derived AGE modification sites including functional sites such as the RGD integrin-binding sequence. Mesangial cells grown on the glycated, decellularized matrix assembled increased amounts of FN matrix. Soluble AGE-modified bovine serum albumin (BSA) also stimulated FN matrix assembly and this effect was reduced by function-blocking antibodies against the receptor for AGE (RAGE). These results indicate that cells respond to AGEs by increasing matrix assembly and that RAGE is involved in this response. This raises the possibility that the accumulation of ECM during the progression of fibrosis may be enhanced by cell interactions with AGEs on a glycated ECM. Copyright © 2016 Elsevier B.V. All rights reserved.

Matrix-isolation and computational study of the HXeY⋯H2O complexes (Y = Cl, Br, and I).

PubMed

Tsuge, Masashi; Berski, Sławomir; Räsänen, Markku; Latajka, Zdzisław; Khriachtchev, Leonid

2014-01-28

The HXeY⋯H2O complexes (Y = Cl, Br, and I) are studied theoretically and experimentally. The calculations at the CCSD(T)/def2-TZVPPD level of theory predict two stable structures for Y = Cl and Br and one structure for Y = I, with interaction energies up to about -7 kcal mol(-1). In the experiments, we have identified several infrared absorption bands originating from the H-Xe stretching mode of these complexes in a xenon matrix. The monomer-to-complex frequency shifts of this mode are up to +82 cm(-1) (Y = Cl), +101 cm(-1) (Y = Br), and +138 cm(-1) (Y = I), i.e., the shift is smaller for more strongly bound molecules. Based on the agreement of the experimental and theoretical results, the observed bands are assigned to the most stable planar structure with an O-H⋯Y-Xe hydrogen bond.

Efficient photochemistry of coronene:water complexes

NASA Astrophysics Data System (ADS)

Noble, J. A.; Jouvet, C.; Aupetit, C.; Moudens, A.; Mascetti, J.

2017-03-01

The photochemistry of ices with polycyclic aromatic hydrocarbons (PAHs) has been extensively studied, but to date no investigation has been made of PAHs in interaction with low numbers (n< 4) of molecules of water. We performed photochemical matrix isolation studies of coronene:water complexes, probing the argon matrix with FTIR spectroscopy. We find that coronene readily reacts with water upon irradiation with a mercury vapour lamp to produce oxygenated PAH photoproducts, and we postulate a reaction mechanism via a charge transfer Rydberg state. This result suggests that oxygenated PAHs should be widely observed in regions of the ISM with sufficiently high water abundances, for example near the edges of molecular clouds where water molecules begin to form, but before icy layers are observed, that is at AV< 3. In order to explain the low derived observational abundances of oxygenated PAHs, additional destruction routes must be invoked.

Pyrrole multimers and pyrrole-acetylene hydrogen bonded complexes studied in N2 and para-H2 matrixes using matrix isolation infrared spectroscopy and ab initio computations

NASA Astrophysics Data System (ADS)

Sarkar, Shubhra; Ramanathan, N.; Gopi, R.; Sundararajan, K.

2017-12-01

Hydrogen bonded interaction of pyrrole multimer and acetylene-pyrrole complexes were studied in N2 and p-H2 matrixes. DFT computations showed T-shaped geometry for the pyrrole dimer and cyclic complex for the trimer and tetramer were the most stable structures, stabilized by Nsbnd H⋯π interactions. The experimental vibrational wavenumbers observed in N2 and p-H2 matrixes for the pyrrole multimers were correlated with the computed wavenumbers. Computations performed at MP2/aug-cc-pVDZ level of theory showed that C2H2 and C4H5N forms 1:1 hydrogen-bonded complexes stabilized by Csbnd H⋯π interaction (Complex A), Nsbnd H⋯π interaction (Complex B) and π⋯π interaction (Complex C), where the former complex is the global minimum and latter two complexes were the first and second local minima, respectively. Experimentally, 1:1 C2H2sbnd C4H5N complexes A (global minimum) and B (first local minimum) were identified from the shifts in the Nsbnd H stretching, Nsbnd H bending, Csbnd H bending region of pyrrole and Csbnd H asymmetric stretching and bending region of C2H2 in N2 and p-H2 matrixes. Computations were also performed for the higher complexes and found two minima corresponding to the 1:2 C2H2sbnd C4H5N and three minima for the 2:1 C2H2sbnd C4H5N complexes. Experimentally the global minimum 1:2 and 2:1 C2H2sbnd C4H5N complexes were identified in N2 and p-H2 matrixes.

An adapted isolation procedure reveals Photobacterium spp. as common spoilers on modified atmosphere packaged meats.

PubMed

Hilgarth, M; Fuertes-Pèrez, S; Ehrmann, M; Vogel, R F

2018-04-01

The genus Photobacterium comprises species of marine bacteria, commonly found in open-ocean and deep-sea environments. Some species (e.g. Photobacterium phosphoreum) are associated with fish spoilage. Recently, culture-independent studies have drawn attention to the presence of photobacteria on meat. This study employed a comparative isolation approach of Photobacterium spp. and aimed to develop an adapted isolation procedure for recovery from food samples, as demonstrated for different meats: Marine broth is used for resuspending and dilution of food samples, followed by aerobic cultivation on marine broth agar supplemented with meat extract and vancomycin at 15°C for 72 h. Identification of spoilage-associated microbiota was carried out via Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry using a database supplemented with additional mass spectrometry profiles of Photobacterium spp. This study provides evidence for the common abundance of multiple Photobacterium species in relevant quantities on various modified atmosphere packaged meats. Photobacterium carnosum was predominant on beef and chicken, while Photobacterium iliopiscarium represented the major species on pork and Photobacterium phosphoreum on salmon, respectively. This study demonstrates highly frequent isolation of multiple photobacteria (Photobacterium carnosum, Photobacterium phosphoreum, and Photobacterium iliopiscarium) from different modified-atmosphere packaged spoiled and unspoiled meats using an adapted isolation procedure. The abundance of photobacteria in high numbers provides evidence for the hitherto neglected importance and relevance of Photobacterium spp. to meat spoilage. © 2018 The Society for Applied Microbiology.

Application of MALDI-TOF MS fingerprinting as a quick tool for identification and clustering of foodborne pathogens isolated from food products.

PubMed

Elbehiry, Ayman; Marzouk, Eman; Hamada, Mohamed; Al-Dubaib, Musaad; Alyamani, Essam; Moussa, Ihab M; AlRowaidhan, Anhar; Hemeg, Hassan A

2017-10-01

Foodborne pathogens can be associated with a wide variety of food products and it is very important to identify them to supply safe food and prevent foodborne infections. Since traditional techniques are timeconsuming and laborious, this study was designed for rapid identification and clustering of foodborne pathogens isolated from various restaurants in Al-Qassim region, Kingdom of Saudi Arabia (KSA) using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Sixty-nine bacterial and thirty-two fungal isolates isolated from 80 food samples were used in this study. Preliminary identification was carried out through culture and BD Phoenix™ methods. A confirmatory identification technique was then performed using MALDI-TOF MS. The BD Phoenix results revealed that 97% (67/69 isolates) of bacteria were correctly identified as 75% Enterobacter cloacae, 95.45% Campylobacter jejuni and 100% for Escherichia coli, Salmonella enterica, Staphylococcus aureus, Acinetobacter baumannii, and Klebsiella pneumoniae. While 94.44% (29/32 isolates) of fungi were correctly identified as 77.77% Alternaria alternate, 88.88% Aspergillus niger and 100% for Aspergillus flavus, Penicillium digitatum, Candida albicans and Debaryomyces hansenii. However, all bacterial and fungal isolates were 100% properly identified by MALDI-TOF MS fingerprinting with a score value ≥2.00. A gel view illustrated that the spectral peaks for the identified isolates fluctuate between 3,000 and 10,000 Da. The results of main spectra library (MSP) dendrogram showed that the bacterial and fungal isolates matched with 19 and 9 reference strains stored in the Bruker taxonomy, respectively. Our results indicated that MALDI-TOF MS is a promising technique for fast and accurate identification of foodborne pathogens.

In Vitro Efficacy of Nonantibiotic Treatments on Biofilm Disruption of Gram-Negative Pathogens and an In Vivo Model of Infectious Endometritis Utilizing Isolates from the Equine Uterus

PubMed Central

McCue, Patrick M.; Borlee, Grace I.; Loncar, Kristen D.; Hennet, Margo L.

2015-01-01

In this study, we evaluated the ability of the equine clinical treatments N-acetylcysteine, EDTA, and hydrogen peroxide to disrupt in vitro biofilms and kill equine reproductive pathogens (Escherichia coli, Pseudomonas aeruginosa, or Klebsiella pneumoniae) isolated from clinical cases. N-acetylcysteine (3.3%) decreased biofilm biomass and killed bacteria within the biofilms of E. coli isolates. The CFU of recoverable P. aeruginosa and K. pneumoniae isolates were decreased, but the biofilm biomass was unchanged. Exposure to hydrogen peroxide (1%) decreased the biofilm biomass and reduced the CFU of E. coli isolates, K. pneumoniae isolates were observed to have a reduction in CFU, and minimal effects were observed for P. aeruginosa isolates. Chelating agents (EDTA formulations) reduced E. coli CFU but were ineffective at disrupting preformed biofilms or decreasing the CFU of P. aeruginosa and K. pneumoniae within a biofilm. No single nonantibiotic treatment commonly used in equine veterinary practice was able to reduce the CFU and biofilm biomass of all three Gram-negative species of bacteria evaluated. An in vivo equine model of infectious endometritis was also developed to monitor biofilm formation, utilizing bioluminescence imaging with equine P. aeruginosa isolates from this study. Following infection, the endometrial surface contained focal areas of bacterial growth encased in a strongly adherent “biofilm-like” matrix, suggesting that biofilms are present during clinical cases of infectious equine endometritis. Our results indicate that Gram-negative bacteria isolated from the equine uterus are capable of producing a biofilm in vitro, and P. aeruginosa is capable of producing biofilm-like material in vivo. PMID:26719448

In Vitro Efficacy of Nonantibiotic Treatments on Biofilm Disruption of Gram-Negative Pathogens and an In Vivo Model of Infectious Endometritis Utilizing Isolates from the Equine Uterus.

PubMed

Ferris, Ryan A; McCue, Patrick M; Borlee, Grace I; Loncar, Kristen D; Hennet, Margo L; Borlee, Bradley R

2016-03-01

In this study, we evaluated the ability of the equine clinical treatments N-acetylcysteine, EDTA, and hydrogen peroxide to disrupt in vitro biofilms and kill equine reproductive pathogens (Escherichia coli, Pseudomonas aeruginosa, or Klebsiella pneumoniae) isolated from clinical cases. N-acetylcysteine (3.3%) decreased biofilm biomass and killed bacteria within the biofilms of E. coli isolates. The CFU of recoverable P. aeruginosa and K. pneumoniae isolates were decreased, but the biofilm biomass was unchanged. Exposure to hydrogen peroxide (1%) decreased the biofilm biomass and reduced the CFU of E. coli isolates, K. pneumoniae isolates were observed to have a reduction in CFU, and minimal effects were observed for P. aeruginosa isolates. Chelating agents (EDTA formulations) reduced E. coli CFU but were ineffective at disrupting preformed biofilms or decreasing the CFU of P. aeruginosa and K. pneumoniae within a biofilm. No single nonantibiotic treatment commonly used in equine veterinary practice was able to reduce the CFU and biofilm biomass of all three Gram-negative species of bacteria evaluated. An in vivo equine model of infectious endometritis was also developed to monitor biofilm formation, utilizing bioluminescence imaging with equine P. aeruginosa isolates from this study. Following infection, the endometrial surface contained focal areas of bacterial growth encased in a strongly adherent "biofilm-like" matrix, suggesting that biofilms are present during clinical cases of infectious equine endometritis. Our results indicate that Gram-negative bacteria isolated from the equine uterus are capable of producing a biofilm in vitro, and P. aeruginosa is capable of producing biofilm-like material in vivo. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Development of a systematic feedback isolation approach for targeted strains from mixed culture systems.

PubMed

Poudel, Pramod; Tashiro, Yukihiro; Miyamoto, Hirokuni; Miyamoto, Hisashi; Okugawa, Yuki; Sakai, Kenji

2017-01-01

Elucidation of functions of bacteria in a mixed culture system (MCS) such as composting, activated sludge system is difficult, since the system is complicating with many unisolated bacteria. Here, we developed a systematic feedback isolation strategy for the isolation and rapid screening of multiple targeted strains from MCS. Six major strains (Corynebacterium sphenisci, Bacillus thermocloacae, Bacillus thermoamylovorans, Bacillus smithii, Bacillus humi, and Bacillus coagulans), which are detected by denaturing gradient gel electrophoresis (DGGE) analysis in our previous study on MCS for l-lactic acid production, were targeted for isolation. Based on information of suitable cultivation conditions (e.g., media, pH, temperature) from the literature, feedback isolation was performed to form 136 colonies. The following direct colony matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was optimised as the second screening to narrow down 20 candidate colonies from similar spectra patterns with six closest type strains. This step could distinguish bacteria at the species level with distance similarity scores ≥0.55 corresponding to 16S rRNA gene sequence similarity ≥98.2%, suggesting that this is an effective technique to minimize isolates close to targeted type strains. Analysis of 16S rRNA gene sequences indicated that two targeted strains and one strain related to the target had successfully been isolated, showing high similarities (99.5-100%) with the sequences from the DGGE bands, and that the other candidates were affiliated with three strains that were closely related to the target species. This study proposes a new method for systematic feedback isolation that may be useful for isolating targeted strains from MCS for further investigation. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Stable Binding of Alternative Protein-enriched Food Matrices with Concentrated Cranberry Bioflavonoids for Functional Food Applications

PubMed Central

Grace, Mary H.; Guzman, Ivette; Roopchand, Diana E.; Moskal, Kristin; Cheng, Diana M.; Pogrebnyak, Natasha; Raskin, Ilya; Howell, Amy; Lila, Mary Ann

2013-01-01

Defatted soy flour (DSF), soy protein isolate (SPI), hemp protein isolate (HPI), medium roast peanut flour (MPF) and pea protein isolate (PPI) stably bind and concentrate cranberry (CB) polyphenols, creating protein/polyphenol-enriched matrices. Proanthocyanidins (PAC) in the enriched matrices ranged from 20.75 mg/g (CB-HPI) to 10.68 mg/g (CB-SPI). Anthocyanins (ANC) ranged from 3.19 mg/g (CB-DSF) to 1.68 mg/g (CB-SPI), while total phenolics (TP) ranged from 37.61 mg/g (CB-HPI) to 21.29 mg/g (CB-SPI). LC-MS indicated that the enriched matrices contained all identifiable ANC, PAC and flavonols present in CB juice. Complexation with SPI stabilized and preserved the integrity of the CB polyphenolic components for at least 15 weeks at 37 °C. PAC isolated from enriched matrices demonstrated comparable anti-adhesion bioactivity to PAC isolated directly from CB juice (MIC 0.4 to 0.16 mg/mL), indicating their potential utility for maintenance of urinary tract health. Approximately 1.0 g of polyphenol-enriched matrix delivered the same amount of PAC available in one cup (300 mL) of commercial CB juice cocktail; which has been shown clinically to be the prophylactic dose for reducing recurring urinary tract infections. CB-SPI inhibited gram- positive and gram-negative bacterial growth. Nutritional and sensory analyses indicated that the targeted CB-matrix combinations have high potential for incorporation in functional food formulations. PMID:23786629

Matrix-isolation studies on the radiation-induced chemistry in H₂O/CO₂ systems: reactions of oxygen atoms and formation of HOCO radical.

PubMed

Ryazantsev, Sergey V; Feldman, Vladimir I

2015-03-19

The radiation-induced transformations occurring upon X-ray irradiation of solid CO2/H2O/Ng systems (Ng = Ar, Kr, Xe) at 8-10 K and subsequent annealing up to 45 K were studied by Fourier transform infrared spectroscopy. The infrared (IR) spectra of deposited matrices revealed the presence of isolated monomers, dimers, and intermolecular H2O···CO2 complexes. Irradiation resulted in effective decomposition of matrix-isolated carbon dioxide and water yielding CO molecules and OH radicals, respectively. Annealing of the irradiated samples led to formation of O3, HO2, and a number of xenon hydrides of HXeY type (in the case of xenon matrices). The formation of these species was used for monitoring of the postirradiation thermally induced chemical reactions involving O and H atoms generated by radiolysis. It was shown that the radiolysis of CO2 in noble-gas matrices produced high yields of stabilized oxygen atoms. In all cases, the temperatures at which O atoms become mobile and react are lower than those of H atoms. Dynamics and reactivity of oxygen atoms was found to be independent of the precursor nature. In addition, the formation of HOCO radicals was observed in all the noble-gas matrices at remarkably low temperatures. The IR spectra of HOCO and DOCO were first characterized in krypton and xenon matrices. It was concluded that the formation of HOCO was mainly due to the radiation-induced evolution of the weakly bound H2O···CO2 complexes. This result indicates the significance of weak intermolecular interactions in the radiation-induced chemical processes in inert low-temperature media.

Validation of a New Web Application for Identification of Fungi by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Becker, P.; Gabriel, F.; Cassagne, C.; Accoceberry, I.; Gari-Toussaint, M.; Hasseine, L.; De Geyter, D.; Pierard, D.; Surmont, I.; Djenad, F.; Donnadieu, J. L.; Piarroux, M.; Hendrickx, M.; Piarroux, R.

2017-01-01

ABSTRACT Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry has emerged as a reliable technique to identify molds involved in human diseases, including dermatophytes, provided that exhaustive reference databases are available. This study assessed an online identification application based on original algorithms and an extensive in-house reference database comprising 11,851 spectra (938 fungal species and 246 fungal genera). Validation criteria were established using an initial panel of 422 molds, including dermatophytes, previously identified via DNA sequencing (126 species). The application was further assessed using a separate panel of 501 cultured clinical isolates (88 mold taxa including dermatophytes) derived from five hospital laboratories. A total of 438 (87.35%) isolates were correctly identified at the species level, while 26 (5.22%) were assigned to the correct genus but the wrong species and 37 (7.43%) were not identified, since the defined threshold of 20 was not reached. The use of the Bruker Daltonics database included in the MALDI Biotyper software resulted in a much higher rate of unidentified isolates (39.76 and 74.30% using the score thresholds 1.7 and 2.0, respectively). Moreover, the identification delay of the online application remained compatible with real-time online queries (0.15 s per spectrum), and the application was faster than identifications using the MALDI Biotyper software. This is the first study to assess an online identification system based on MALDI-TOF spectrum analysis. We have successfully applied this approach to identify molds, including dermatophytes, for which diversity is insufficiently represented in commercial databases. This free-access application is available to medical mycologists to improve fungal identification. PMID:28637907

Validation of a New Web Application for Identification of Fungi by Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Normand, A C; Becker, P; Gabriel, F; Cassagne, C; Accoceberry, I; Gari-Toussaint, M; Hasseine, L; De Geyter, D; Pierard, D; Surmont, I; Djenad, F; Donnadieu, J L; Piarroux, M; Ranque, S; Hendrickx, M; Piarroux, R

2017-09-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has emerged as a reliable technique to identify molds involved in human diseases, including dermatophytes, provided that exhaustive reference databases are available. This study assessed an online identification application based on original algorithms and an extensive in-house reference database comprising 11,851 spectra (938 fungal species and 246 fungal genera). Validation criteria were established using an initial panel of 422 molds, including dermatophytes, previously identified via DNA sequencing (126 species). The application was further assessed using a separate panel of 501 cultured clinical isolates (88 mold taxa including dermatophytes) derived from five hospital laboratories. A total of 438 (87.35%) isolates were correctly identified at the species level, while 26 (5.22%) were assigned to the correct genus but the wrong species and 37 (7.43%) were not identified, since the defined threshold of 20 was not reached. The use of the Bruker Daltonics database included in the MALDI Biotyper software resulted in a much higher rate of unidentified isolates (39.76 and 74.30% using the score thresholds 1.7 and 2.0, respectively). Moreover, the identification delay of the online application remained compatible with real-time online queries (0.15 s per spectrum), and the application was faster than identifications using the MALDI Biotyper software. This is the first study to assess an online identification system based on MALDI-TOF spectrum analysis. We have successfully applied this approach to identify molds, including dermatophytes, for which diversity is insufficiently represented in commercial databases. This free-access application is available to medical mycologists to improve fungal identification. Copyright © 2017 American Society for Microbiology.

Isolation, Characterization, and Differentiation of Dental Pulp Stem Cells in Ferrets.

PubMed

Homayounfar, Negar; Verma, Prashant; Nosrat, Ali; El Ayachi, Ikbale; Yu, Zongdong; Romberg, Elaine; Huang, George T-J; Fouad, Ashraf F

2016-03-01

The ferret canine tooth has been introduced as a suitable model for studying dental pulp regeneration. The aim of this study was to isolate and characterize ferret dental pulp stem cells (fDPSCs) and their differentiation potential. Dental pulp stem cells were isolated from freshly extracted ferret canine teeth. The cells were examined for the expression of stem cell markers STRO-1, CD90, CD105, and CD146. The osteo/odontogenic and adipogenic differentiation potential of fDPSCs was evaluated. Osteogenic and odontogenic marker genes were evaluated using quantitative real-time polymerase chain reaction (qRT-PCR) on days 1, 4, and 8 after osteo/odontogenic induction of fDPSCs including dentin sialophosphoprotein (DSPP), dentin matrix protein-1, osteopontin, and alkaline phosphatase. Human dental pulp cells were used as the control. The results were analyzed using 3-way analysis of variance. fDPSCs were positive for STRO1, CD90, and CD105 and negative for CD146 markers with immunohistochemistry. fDPSCs showed strong osteogenic and weak adipogenic potential. The overall expression of DSPP was not significantly different between fDPSCs and human dental pulp cells. The expression of DSPP in osteo/odontogenic media was significantly higher in fDPSCs on day 4 (P < .01). The overall expression of dentin matrix protein-1, osteopontin, and alkaline phosphatase was significantly higher in fDPSCs (P = .0005). fDPSCs were positive for several markers of dental pulp stem cells resembling human DPSCs and appeared to show a stronger potential to differentiate to osteoblastic rather than odontoblastic lineage. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

GIS-based approach for quantifying landscape connectivity of Javan Hawk-Eagle habitat

NASA Astrophysics Data System (ADS)

Nurfatimah, C.; Syartinilia; Mulyani, Y. A.

2018-05-01

Javan Hawk-Eagle (Nisaetus bartelsi; JHE) is a law-protected endemic raptor which currently faced the decreased in number and size of habitat patches that will lead to patch isolation and species extinction. This study assessed the degree of connectivity between remnant habitat patches in central part of Java by utilizing Conefor Sensinode software as an additional tool for ArcGIS. The connectivity index was determined by three fractions which are infra, flux and connector. Using connectivity indices successfully identified 4 patches as core habitat, 9 patches as stepping-stone habitat and 6 patches as isolated habitat were derived from those connectivity indices. Those patches then being validated with land cover map derived from Landsat 8 of August 2014. 36% of core habitat covered by natural forest, meanwhile stepping stone habitat has 55% natural forest and isolated habitat covered by 59% natural forest. Isolated patches were caused by zero connectivity (PCcon = 0) and the patch size which too small to support viable JHE population. Yet, the condition of natural forest and the surrounding matrix landscape in isolated patches actually support the habitat need. Thus, it is very important to conduct the right conservation management system based on the condition of each patches.

Identification of p63+ keratinocyte progenitor cells in circulation and their matrix-directed differentiation to epithelial cells.

PubMed

Nair, Renjith P; Krishnan, Lissy K

2013-04-11

In the event of chronic diabetes or burn wounds, accomplishing skin regeneration is a major concern. Autologous skin grafting is the most effective remedy, but the tissue harvest may create more nonhealing wounds. Currently available skin substitutes have a limited clinical outcome because of immune reactions arising from the xenobiotic scaffold or allogenous cells. Autologous stem cells that can be collected without an additional injury may be a viable option for skin-tissue engineering. Presence of a low number of keratinocyte progenitor cells (KPCs) within the peripheral blood mononuclear cell (PBMNC) population has been indicated. Identification, isolation, expansion, and differentiation of KPCs is necessary before they are considered for skin regeneration, which is the focus of this study. Culture of isolated human PBMNCs on a cell-specific matrix was carried out to induce differentiation of KPCs. Flow cytometry and reverse transcriptase polymerase chain reaction were done for epithelial stem cell marker p63 and lineage markers cytokeratin 5 and cytokeratin 14, to track differentiation. Proliferation was confirmed by quantifying the proliferating cell nuclear antigen-expressing cells. Immunostaining with epithelial cell markers, involucrin and filaggrin, was carried out to establish terminal differentiation. Microscopic analysis confirmed growth and survival of KPCs on the dermal fibroblast monolayer and on a transplantable fibrin sheet. We demonstrated that KPCs are p63(+) and CD34-. The specifically designed composition of the extracellular matrix was found to support selective adhesion, proliferation, and differentiation of p63(+) KPCs. The PBMNC culture for 12 days under controlled conditions resulted in a homogenous population that expressed cytokeratins, and >90% of the cells were found to proliferate. Subculture for 5 days resulted in expression of filaggrin and involucrin, suggesting terminal differentiation. Transfer of matrix-selected KPCs to a dermal fibroblast monolayer or fibrin supported cell proliferation and showed typical hexagonal morphology of keratinocytes within 15 days. Circulating KPCs were identified with p63, which differentiated into keratinocytes with expression of the cytokeratins, involucrin and filaggrin. Components of the specifically designed matrix favored KPC attachment, directed differentiation, and may turn out to be a potential vehicle for cell transplantation.

Identification of p63+ keratinocyte progenitor cells in circulation and their matrix-directed differentiation to epithelial cells

PubMed Central

2013-01-01

Introduction In the event of chronic diabetes or burn wounds, accomplishing skin regeneration is a major concern. Autologous skin grafting is the most effective remedy, but the tissue harvest may create more nonhealing wounds. Currently available skin substitutes have a limited clinical outcome because of immune reactions arising from the xenobiotic scaffold or allogenous cells. Autologous stem cells that can be collected without an additional injury may be a viable option for skin-tissue engineering. Presence of a low number of keratinocyte progenitor cells (KPCs) within the peripheral blood mononuclear cell (PBMNC) population has been indicated. Identification, isolation, expansion, and differentiation of KPCs is necessary before they are considered for skin regeneration, which is the focus of this study. Methods Culture of isolated human PBMNCs on a cell-specific matrix was carried out to induce differentiation of KPCs. Flow cytometry and reverse transcriptase polymerase chain reaction were done for epithelial stem cell marker p63 and lineage markers cytokeratin 5 and cytokeratin 14, to track differentiation. Proliferation was confirmed by quantifying the proliferating cell nuclear antigen-expressing cells. Immunostaining with epithelial cell markers, involucrin and filaggrin, was carried out to establish terminal differentiation. Microscopic analysis confirmed growth and survival of KPCs on the dermal fibroblast monolayer and on a transplantable fibrin sheet. Results We demonstrated that KPCs are p63+ and CD34-. The specifically designed composition of the extracellular matrix was found to support selective adhesion, proliferation, and differentiation of p63+ KPCs. The PBMNC culture for 12 days under controlled conditions resulted in a homogenous population that expressed cytokeratins, and >90% of the cells were found to proliferate. Subculture for 5 days resulted in expression of filaggrin and involucrin, suggesting terminal differentiation. Transfer of matrix-selected KPCs to a dermal fibroblast monolayer or fibrin supported cell proliferation and showed typical hexagonal morphology of keratinocytes within 15 days. Conclusions Circulating KPCs were identified with p63, which differentiated into keratinocytes with expression of the cytokeratins, involucrin and filaggrin. Components of the specifically designed matrix favored KPC attachment, directed differentiation, and may turn out to be a potential vehicle for cell transplantation. PMID:23578397

Genetic Diversity and Differentiation of Colletotrichum spp. Isolates Associated with Leguminosae Using Multigene Loci, RAPD and ISSR

PubMed Central

Mahmodi, Farshid; Kadir, J. B.; Puteh, A.; Pourdad, S. S.; Nasehi, A.; Soleimani, N.

2014-01-01

Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3) verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4%) and (15.5–19.9), respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers. PMID:25288981

Evaluation of Bruker Biotyper and Vitek MS for the identification of Candida tropicalis on different solid culture media.

PubMed

Wang, He; Li, Ying; Fan, Xin; Chiueh, Tzong-Shi; Xu, Ying-Chun; Hsueh, Po-Ren

2017-11-11

The aim of this study was to investigate the performance of the Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and Vitek MS systems for identification of genetically-confirmed blood isolates of Candida tropicalis that had been grown on several types of culture media commonly used for primary fungal isolation. Isolates included 105 from the National China Hospital Invasive Fungal Surveillance Net program (CHIF-NET) and 120 from National Taiwan University Hospital (NTUH). Culture media tested for CHIF-NET isolates included trypticase soy agar supplemented with 5% sheep blood (BAP), Sabouraud dextrose agar (SDA-C), CHROMagar, China blue agar (CBA), chocolate agar supplemented with vancomycin (CAP-VA), and MacConkey agar (MAC). Culture media used for NTUH isolates included BAP, SDA, CHROMagar, eosin methylene blue (EMB), inhibitory mold agar (IMA), Mycosel agar, and cornmeal agar (CMA). The Bruker Biotyper correctly identified all CHIF-NET isolates to the species level on all six agar media tested and correctly identified the majority of NTUH isolates with the exception of isolates grown on SDA (85.8%) and CMA (52.5%). The Vitek MS system correctly identified all CHIF-NET isolates to the species level with the exception of isolates grown on CHROMagar (84.8%), and correctly identified the majority of NTUH isolates with the exception of isolates grown on SDA (51.7%), Mycosel agar (57.5%), and CMA (9.2%) for NTUH isolates. Clinical microbiologists should be aware that different culture media can affect the performance of the Bruker Biotyper MALDI-TOF MS and Vitek MS systems in identifying C. tropicalis. Copyright © 2017. Published by Elsevier B.V.

Silver colloidal nanoparticles: effect on matrix composition and structure of Candida albicans and Candida glabrata biofilms.

PubMed

Monteiro, D R; Silva, S; Negri, M; Gorup, L F; de Camargo, E R; Oliveira, R; Barbosa, D B; Henriques, M

2013-04-01

The aim of this study was to assess the effect of different silver nanoparticles (SN) concentrations on the matrix composition and structure of Candida albicans and Candida glabrata biofilms. Candida biofilms were developed in 6-well microtiter plates during 48 h. After, these biofilms were exposed to 13.5 or 54 μg SN ml(-1) for 24 h. Then, extracellular matrices were extracted from biofilms and analysed chemically in terms of proteins, carbohydrates and DNA. To investigate the biofilm structure, scanning electron microscopy (SEM) and epifluorescence microscopy were used. SN interfered with the matrix composition of Candida biofilms tested in terms of protein, carbohydrate and DNA, except for the protein content of C. albicans biofilm. By SEM, Candida biofilms treated with SN revealed structural differences, when compared with the control groups. Further, SN showed a trend of agglomeration within the biofilms. Epifluorescence microscopy images suggest that SN induced damage on cell walls of the Candida isolates tested. In general, irrespective of concentration, SN affected the matrix composition and structure of Candida biofilms and these findings may be related to the mechanisms of biocide action of SN. This study reveals new insights about the behaviour of SN when in contact with Candida biofilms. SN may contribute to the development of therapies to prevent or control Candida infections. © 2012 The Society for Applied Microbiology.

Methodological effects in Fourier transform infrared (FTIR) spectroscopy: Implications for structural analyses of biomacromolecular samples

NASA Astrophysics Data System (ADS)

Kamnev, Alexander A.; Tugarova, Anna V.; Dyatlova, Yulia A.; Tarantilis, Petros A.; Grigoryeva, Olga P.; Fainleib, Alexander M.; De Luca, Stefania

2018-03-01

A set of experimental data obtained by Fourier transform infrared (FTIR) spectroscopy (involving the use of samples ground and pressed with KBr, i.e. in a polar halide matrix) and by matrix-free transmission FTIR or diffuse reflectance infrared Fourier transform (DRIFT) spectroscopic methodologies (involving measurements of thin films or pure powdered samples, respectively) were compared for several different biomacromolecular substances. The samples under study included poly-3-hydroxybutyrate (PHB) isolated from cell biomass of the rhizobacterium Azospirillum brasilense; dry PHB-containing A. brasilense biomass; pectin (natural carboxylated heteropolysaccharide of plant origin; obtained from apple peel) as well as its chemically modified derivatives obtained by partial esterification of its galacturonide-chain hydroxyl moieties with palmitic, oleic and linoleic acids. Significant shifts of some FTIR vibrational bands related to polar functional groups of all the biomacromolecules under study, induced by the halide matrix used for preparing the samples for spectroscopic measurements, were shown and discussed. A polar halide matrix used for preparing samples for FTIR measurements was shown to be likely to affect band positions not only per se, by affecting band energies or via ion exchange (e.g., with carboxylate moieties), but also by inducing crystallisation of metastable amorphous biopolymers (e.g., PHB of microbial origin). The results obtained have important implications for correct structural analyses of polar, H-bonded and/or amphiphilic biomacromolecular systems using different methodologies of FTIR spectroscopy.

Biofilms produced by Burkholderia cenocepacia: influence of media and solid supports on composition of matrix exopolysaccharides.

PubMed

Pellizzoni, Elena; Ravalico, Fabio; Scaini, Denis; Delneri, Ambra; Rizzo, Roberto; Cescutti, Paola

2016-02-01

Bacteria usually grow forming biofilms, which are communities of cells embedded in a self-produced dynamic polymeric matrix, characterized by a complex three-dimensional structure. The matrix holds cells together and above a surface, and eventually releases them, resulting in colonization of other surfaces. Although exopolysaccharides (EPOLs) are important components of the matrix, determination of their structure is usually performed on samples produced in non-biofilm conditions, or indirectly through genetic studies. Among the Burkholderia cepacia complex species, Burkholderia cenocepacia is an important pathogen in cystic fibrosis (CF) patients and is generally more aggressive than other species. In the present investigation, B. cenocepacia strain BTS2, a CF isolate, was grown in biofilm mode on glass slides and cellulose membranes, using five growth media, one of which mimics the nutritional content of CF sputum. The structure of the matrix EPOLs was determined by 1H-NMR spectroscopy, while visualization of the biofilms on glass slides was obtained by means of confocal laser microscopy, phase-contrast microscopy and atomic force microscopy. The results confirmed that the type of EPOLs biosynthesized depends both on the medium used and on the type of support, and showed that mucoid conditions do not always lead to significant biofilm production, while bacteria in a non-mucoid state can still form biofilm containing EPOLs.

Effect of Uniaxial Tensile Cyclic Loading Regimes on Matrix Organization and Tenogenic Differentiation of Adipose-Derived Stem Cells Encapsulated within 3D Collagen Scaffolds

PubMed Central

Stasuk, Alexander

2017-01-01

Adipose-derived mesenchymal stem cells have become a popular cell choice for tendon repair strategies due to their relative abundance, ease of isolation, and ability to differentiate into tenocytes. In this study, we investigated the solo effect of different uniaxial tensile strains and loading frequencies on the matrix directionality and tenogenic differentiation of adipose-derived stem cells encapsulated within three-dimensional collagen scaffolds. Samples loaded at 0%, 2%, 4%, and 6% strains and 0.1 Hz and 1 Hz frequencies for 2 hours/day over a 7-day period using a custom-built uniaxial tensile strain bioreactor were characterized in terms of matrix organization, cell viability, and musculoskeletal gene expression profiles. The results displayed that the collagen fibers of the loaded samples exhibited increased matrix directionality with an increase in strain values. Gene expression analyses demonstrated that ASC-encapsulated collagen scaffolds loaded at 2% strain and 0.1 Hz frequency showed significant increases in extracellular matrix genes and tenogenic differentiation markers. Importantly, no cross-differentiation potential to osteogenic, chondrogenic, and myogenic lineages was observed at 2% strain and 0.1 Hz frequency loading condition. Thus, 2% strain and 0.1 Hz frequency were identified as the appropriate mechanical loading regime to induce tenogenic differentiation of adipose-derived stem cells cultured in a three-dimensional environment. PMID:29375625

Thioperoxy derivative generated by UV-induced transformation of N-hydroxypyridine-2(1H)-thione isolated in low-temperature matrixes.

PubMed

Lapinski, Leszek; Gerega, Anna; Sobolewski, Andrzej L; Nowak, Maciej J

2008-01-17

Photochemical transformations of N-hydroxypyridine-2(1H)-thione and its deuterated isotopologue were studied using the matrix-isolation technique. Low-temperature Ar and N2 matrixes containing monomers of this compound were irradiated with continuous-wave near-UV light. Photogeneration of two products was observed in these experiments. The relative population of these photogenerated species was found to be dependent on the wavelength of the UV light used for irradiation. By comparison of the IR spectra of the photoproducts with the spectra simulated theoretically at the DFT(B3LYP)/6-311++G(d, p) level, the final and the intermediate products were identified as rotameric forms of 2-hydroxysulfanyl-pyridine. This is the first report on generation of this thioperoxy derivative of pyridine. The mechanism of photogeneration of 2-hydroxysulfanyl-pyridine involves a photoinduced cleavage of the N-O bond in N-hydroxypyridine-2(1H)-thione, generation of the .OH radical weakly bound with the remaining pyridylthiyl radical, and recombination of these two radicals by formation of the new -S-O- bond. A theoretical model supporting this interpretation was constructed on the basis of approximate coupled cluster (CC2) calculations of the potential energy surfaces of the ground and first excited singlet electronic states of the system. After electronic excitation of the monomeric N-hydroxypyridine-2(1H)-thione, the molecule evolves to the conical intersection with the potential energy surface of the ground state and then to the global minimum corresponding to 2-hydroxysulfanyl-pyridine.

Effect of gel re-organization and tensional forces on alpha2beta1 integrin levels in dermal fibroblasts.

PubMed

Jenkins, G; Redwood, K L; Meadows, L; Green, M R

1999-07-01

Mechanical forces are known to play an important role in regulating cell function in a wide range of biological systems. This is of particular relevance to dermal fibroblast function, given that the skin is known to be held under an intrinsic natural tension. To understand more about the generation of force by dermal fibroblasts and their ability to respond to changes in it, we have studied the role of the beta1 integrin receptors expressed by dermal fibroblasts in their ability to generate tensional forces within a collagen type I matrix and the effect of altered tensional force on integrin expression by dermal fibroblasts. Using a purpose-built culture force monitor, function-blocking antibodies directed towards the beta1 receptors dramatically reduced the tensional forces generated by dermal fibroblasts in a 3D collagen I matrix. However, the specific involvement of alpha1 or alpha2 subunits could not be demonstrated. Analysis of cellular response demonstrated that cells isolated from contracting collagen gels expressed fourfold higher levels of alpha2 mRNA than cells isolated from fully restrained gels. The levels of beta1 messenger RNA were relatively unaffected by reductions in force. Cells exposed to single reductions in force, however, did not exhibit alterations in either alpha1 or beta1 mRNA levels. We propose, therefore that alpha2beta1 integrin receptor levels in dermal fibroblasts are not altered in response to single reductions of gel tension, but do change following a continual change in force and associated matrix re-organization

Random Matrix Theory Approach to Chaotic Coherent Perfect Absorbers

NASA Astrophysics Data System (ADS)

Li, Huanan; Suwunnarat, Suwun; Fleischmann, Ragnar; Schanz, Holger; Kottos, Tsampikos

2017-01-01

We employ random matrix theory in order to investigate coherent perfect absorption (CPA) in lossy systems with complex internal dynamics. The loss strength γCPA and energy ECPA, for which a CPA occurs, are expressed in terms of the eigenmodes of the isolated cavity—thus carrying over the information about the chaotic nature of the target—and their coupling to a finite number of scattering channels. Our results are tested against numerical calculations using complex networks of resonators and chaotic graphs as CPA cavities.

Supercritical fluid chromatography applied to the highly selective isolation of urinary steroid hormones prior to GC/MS analysis.

PubMed

Doué, Mickael; West, Caroline; Bichon, Emmanuelle; Le Bizec, Bruno; Lesellier, Eric

2018-06-01

To assess the presence of prohibited anabolic substances used to promote growth in livestock, calf urine is the most relevant matrix. However, the sample preparation methods (required to remove unwanted matrix components and fractionate isobaric species that may be unresolved by gas chromatography- mass spectrometry GC/MS) are long and complex. In this context, semi-preparative supercritical fluid chromatography (SFC) was considered to possibly simplify the sample preparation in reducing the number of procedures. Fifteen stationary phases were screened with SFC combined with UV and evaporative light-scattering detection (ELSD), among which two columns (Cosmosil π-NAP and Princeton DIOL) were retained for their ability to isolate steroid hormones from other matrix components and, for the second column, for the additional possibility to fractionate steroid hormones into different families (estrogens, mono-hydroxylated and di-hydroxylated androgens). The fractions were further analysed with GC/MS showing the benefit of class fractionation. The final method allows for significant time, solvent and money savings compared to the previously widely used method (solid-phase extraction combined with semi-preparative high-performance liquid chromatography). Copyright © 2018 Elsevier B.V. All rights reserved.

Galectin-1 induces cell adhesion to the extracellular matrix and apoptosis of non-adherent human colon cancer Colo201 cells.

PubMed

Horiguchi, Natsuko; Arimoto, Kei-ichiro; Mizutani, Atsushi; Endo-Ichikawa, Yoko; Nakada, Hiroshi; Taketani, Shigeru

2003-12-01

To isolate cDNAs for molecules involved in cell adhesion to the extracellular matrix, expression cloning with non-adherent colon cancer Colo201 cells was carried out. Four positive clones were isolated and, when sequenced, one was found to be galectin-1, a beta-galactoside-binding protein. When cultured on fibronectin-, laminin-, and collagen-coated and non-coated dishes, the adherent galectin-1 cDNA-transfected Colo201 cells increased and spread somewhat. Immunofluorescence staining revealed that galectin-1 was expressed inside and outside of Colo201 cells. The adhesion was dependent on the carbohydrate-recognition domain of galectin-1 since lactose inhibited the adhesion and exogenously-added galectin-1 caused the adhesion. PD58059, an inhibitor of mitogen-activated protein kinase, or LY294002, a phosphoinositide 3-OH kinase inhibitor, decreased the adhesion. Furthermore, the expression of galectin-1 in Colo201 cells induced apoptotic cell death, while exogenously-added galectin-1 did not cause apoptosis. These results indicate that galectin-1 plays a role in both cell-matrix interactions and the inhibition of Colo201 cell proliferation, and suggest that galectin-1 expressed in cells could be associated with apoptosis.

Refined separation of combined Fe–Hf from rock matrices for isotope analyses using AG-MP-1M and Ln-Spec chromatographic extraction resins

PubMed Central

Cheng, Ting; Nebel, Oliver; Sossi, Paolo A.; Chen, Fukun

2014-01-01

A combined procedure for separating Fe and Hf from a single rock digestion is presented. In a two-stage chromatographic extraction process, a purified Fe fraction is first quantitatively separated from the rock matrix using AG-MP-1M resin in HCl. Hafnium is subsequently isolated using a modified version of a commonly applied method using Eichrom LN-Spec resin. Our combined method includes:•Purification of Fe from the rock matrix using HCl, ready for mass spectrometric analysis.•Direct loading of the matrix onto the resin that is used for Hf purification.•Collection of a Fe-free Hf fraction. PMID:26150946

Conformers, infrared spectrum and UV-induced photochemistry of matrix-isolated furfuryl alcohol.

PubMed

Araujo-Andrade, C; Gómez-Zavaglia, A; Reva, I D; Fausto, R

2012-03-08

The infrared spectra of furfuryl alcohol (2-furanmethanol, FFA) were investigated for FFA monomers isolated in low-temperature argon matrices. The structural interpretation of the obtained experimental spectra was assisted by analysis of the molecule's conformational landscape. According to the DFT(B3LYP)/6-311++G(d,p) calculations, five different minimum energy structures were found on the potential energy surface of the molecule. They can be defined by the orientation of the OCCO and CCOH dihedral angles: GG', GG, TG, TT, GT (G = +gauche, G' = -gauche, T = trans) and have a symmetry equivalent configuration: GG' = G'G, GG = G'G', TG = TG', GT = G'T. When zero-point energies are taken into account, only three (GG', GG, and TT) out of the five unique minima correspond to stable structures. The most stable conformer GG' (OCCO, 72.7°; CCOH, -59.3°), which in gas phase at room temperature accounts for ∼65% of the total population, was the only form isolated in the argon matrices at 14 K. The other two relevant forms convert into conformer GG' during matrix deposition. The low temperature glassy and crystalline states of FFA were also obtained and their infrared spectra assigned, suggesting the sole existence of the GG' conformer also in these phases. The photochemical behavior of FFA induced in situ, by tunable UV-laser, was also studied. The longest wavelength resulting in photochemical changes in the structure of the irradiated sample was found to be λ = 229 nm. Such UV irradiation of the matrix-isolated FFA led to production of formaldehyde and different isomeric C(4)H(4)O species. Cycloprop-2-ene-1-carbaldehyde and buta-2,3-dienal (two conformers) are the main initial C(4)H(4)O photoproducts formed upon short-time excitation at λ = 229 nm. But-3-ynal (two conformers) was the principal photoproduct resulting from prolonged excitation at λ= 229 nm, being consumed upon irradiation at shorter wavelengths (λ < 227.5 nm). Vinyl ketene is produced from FFA in the trans conformation and undergoes isomerization to the cis form upon irradiation at λ < 227.5 nm. Cyclopropene, propyne, allene, and CO were also identified in the irradiated matrices (in particular at the later stages of irradiation), suggesting that the photoproduced aldehydes partially decarbonylate during the performed photochemical experiments.

Different effects of energy dependent irradiation of red and green lights on proliferation of human umbilical cord matrix-derived mesenchymal cells.

PubMed

Dehghani Soltani, Samereh; Babaee, Abdolreza; Shojaei, Mohammad; Salehinejad, Parvin; Seyedi, Fatemeh; JalalKamali, Mahshid; Nematollahi-Mahani, Seyed Noureddin

2016-02-01

Light-emitting diodes (LED) have recently been introduced as a potential factor for proliferation of various cell types in vitro. Nowadays, stem cells are widely used in regenerative medicine. Human umbilical cord matrix-derived mesenchymal (hUCM) cells can be more easily isolated and cultured than adult mesenchymal stem cells. The aim of this study was to evaluate the effect of red and green lights produced by LED on the proliferation of hUCM cells. hUCM cells were isolated from the umbilical cord, and light irradiation was applied at radiation energies of 0.318, 0.636, 0.954, 1.59, 3.18, 6.36, 9.54, and 12.72 J/cm(2). Irradiation of the hUCM cells shows a significant (p < 0.05) increase in cell number as compared to controls after 40 h. In addition, cell proliferation on days 7, 14, and 21 in irradiated groups were significantly (p < 0.001) higher than that in the non-irradiated groups. The present study clearly demonstrates the ability of red and green lights irradiation to promote proliferation of hUCM cells in vitro. The energy applied to the cells through LED irradiation is an effective factor with paradoxical alterations. Green light inserted a much profound effect at special dosages than red light.

Speciation and Sources of Brown Carbon in Precipitation at Seoul, Korea: Insights from Excitation-Emission Matrix Spectroscopy and Carbon Isotopic Analysis.

PubMed

Yan, Ge; Kim, Guebuem

2017-10-17

Brown carbon (BrC) plays a significant role in the Earth's radiative balance, yet its sources and chemical composition remain poorly understood. In this work, we investigated BrC in the atmospheric environment of Seoul by characterizing dissolved organic matter in precipitation using excitation-emission matrix (EEM) fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC). The two independent fluorescent components identified by PARAFAC were attributed to humic-like substance (HULIS) and biologically derived material based on their significant correlations with measured HULIS isolated using solid-phase extraction and total hydrolyzable tyrosine. The year-long observation shows that HULIS contributes to 66 ± 13% of total fluorescence intensity of our samples on average. By using dual carbon ( 13 C and 14 C) isotopic analysis conducted on isolated HULIS, the HULIS fraction of BrC was found to be primarily derived from biomass burning and emission of terrestrial biogenic gases and particles (>70%), with minor contributions from fossil-fuel combustion. The knowledge derived from this study could contribute to the establishment of a characterizing system of BrC components identified by EEM spectroscopy. Our work demonstrates that, EEM fluorescence spectroscopy is a powerful tool in BrC study, on the basis of its chromophore resolving power, allowing investigation into individual components of BrC by other organic matter characterization techniques.

Extracellular matrix-associated proteins form an integral and dynamic system during Pseudomonas aeruginosa biofilm development.

PubMed

Zhang, Weipeng; Sun, Jin; Ding, Wei; Lin, Jinshui; Tian, Renmao; Lu, Liang; Liu, Xiaofen; Shen, Xihui; Qian, Pei-Yuan

2015-01-01

Though the essential role of extracellular matrix in biofilm development has been extensively documented, the function of matrix-associated proteins is elusive. Determining the dynamics of matrix-associated proteins would be a useful way to reveal their functions in biofilm development. Therefore, we applied iTRAQ-based quantitative proteomics to evaluate matrix-associated proteins isolated from different phases of Pseudomonas aeruginosa ATCC27853 biofilms. Among the identified 389 proteins, 54 changed their abundance significantly. The increased abundance of stress resistance and nutrient metabolism-related proteins over the period of biofilm development was consistent with the hypothesis that biofilm matrix forms micro-environments in which cells are optimally organized to resist stress and use available nutrients. Secreted proteins, including novel putative effectors of the type III secretion system were identified, suggesting that the dynamics of pathogenesis-related proteins in the matrix are associated with biofilm development. Interestingly, there was a good correlation between the abundance changes of matrix-associated proteins and their expression. Further analysis revealed complex interactions among these modulated proteins, and the mutation of selected proteins attenuated biofilm development. Collectively, this work presents the first dynamic picture of matrix-associated proteins during biofilm development, and provides evidences that the matrix-associated proteins may form an integral and well regulated system that contributes to stress resistance, nutrient acquisition, pathogenesis and the stability of the biofilm.

Propolis Modifies Collagen Types I and III Accumulation in the Matrix of Burnt Tissue.

PubMed

Olczyk, Pawel; Wisowski, Grzegorz; Komosinska-Vassev, Katarzyna; Stojko, Jerzy; Klimek, Katarzyna; Olczyk, Monika; Kozma, Ewa M

2013-01-01

Wound healing represents an interactive process which requires highly organized activity of various cells, synthesizing cytokines, growth factors, and collagen. Collagen types I and III, serving as structural and regulatory molecules, play pivotal roles during wound healing. The aim of this study was to compare the propolis and silver sulfadiazine therapeutic efficacy throughout the quantitative and qualitative assessment of collagen types I and III accumulation in the matrix of burnt tissues. Burn wounds were inflicted on pigs, chosen for the evaluation of wound repair because of many similarities between pig and human skin. Isolated collagen types I and III were estimated by the surface plasmon resonance method with a subsequent collagenous quantification using electrophoretic and densitometric analyses. Propolis burn treatment led to enhanced collagens and its components expression, especially during the initial stage of the study. Less expressed changes were observed after silver sulfadiazine (AgSD) application. AgSD and, with a smaller intensity, propolis stimulated accumulation of collagenous degradation products. The assessed propolis therapeutic efficacy, throughout quantitatively and qualitatively analyses of collagen types I and III expression and degradation in wounds matrix, may indicate that apitherapeutic agent can generate favorable biochemical environment supporting reepithelization.

The Mukundpura meteorite, a new fall of CM chondrite

NASA Astrophysics Data System (ADS)

Ray, Dwijesh; Shukla, Anil D.

2018-02-01

Mukundpura is a new CM chondrite fell near Jaipur, Rajasthan, India on June 6, 2017 at 5:15 IST. The fall was observed by local villager. According to eyewitness, the meteorite was fragmented into several pieces once the object hit the ground. Based on petrography, mineralogy and bulk composition, Mukundpura is classified as CM2 chondrite. The chondrules are mainly similar to type I (Olivine: Fo99). Olivines are often found associated with pyroxene (Wo10-35En62-87Fs2-7) phenocryst. However, occurrences of forsteritic and fayalitic olivine (Fa58-71) as isolated mineral clast in matrix are not uncommon. Other types of chondrules include porphyritic pyroxene (En86Fs14) and barred olivine (Fa32.7±0.3) clast. Chondrules are commonly rimmed by fine-grained accretionary dust mantles. Phyllosilicates are the most dominant secondary mineral in matrix and largely associated with poorly characterised phases (PCP). FeO/SiO2 and S/SiO2 of PCP are 2.7 and 0.4 respectively. Other phases in matrix generally include calcite (pure CaCO3), Fe-Ni metal and sulphides. Spinel and perovskite occur occasionally as inclusions. The spherical or elliptical shaped metals (within chondrule or in isolated grains) are low-Ni type (kamacite <7.5 wt%) and resembles the solar Ni/Co ratio. However, Ni content in metal rarely exceeds 8.5 wt% (up to 23 wt%, taenite). Pyrrhotite (Fe ∼62 wt%; S ∼38 wt%) and pentlandite (Fe ∼31-33 wt%, Ni ∼28-32 wt%, S ∼33 wt%)) are the common sulphides occur as isolated grains within the matrix, however, the former is the most dominant. The bulk chemical composition of Mukundpura is largely similar to other CM type chondrite (e.g. Paris CM). Based on petrography, we infer a modest aqueous alteration stage for Mukundpura while the effect of thermal metamorphism was negligible.

Identification of anaerobic bacteria by Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry with on-plate formic acid preparation.

PubMed

Schmitt, Bryan H; Cunningham, Scott A; Dailey, Aaron L; Gustafson, Daniel R; Patel, Robin

2013-03-01

Identification of anaerobic bacteria using phenotypic methods is often time-consuming; methods such as 16S rRNA gene sequencing are costly and may not be readily available. We evaluated 253 clinical isolates of anaerobic bacteria using the Bruker MALDI Biotyper (Bruker Daltonics, Billerica, MA) matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system with a user-supplemented database and an on-plate formic acid-based preparation method and compared results to those of conventional identification using biochemical testing or 16S rRNA gene sequencing. A total of 179 (70.8%) and 232 (91.7%) isolates were correctly identified to the species and genus levels, respectively, using manufacturer-recommended score cutoffs. MALDI-TOF MS offers a rapid, inexpensive method for identification of anaerobic bacteria.

GPU-accelerated simulations of isolated black holes

NASA Astrophysics Data System (ADS)

Lewis, Adam G. M.; Pfeiffer, Harald P.

2018-05-01

We present a port of the numerical relativity code SpEC which is capable of running on NVIDIA GPUs. Since this code must be maintained in parallel with SpEC itself, a primary design consideration is to perform as few explicit code changes as possible. We therefore rely on a hierarchy of automated porting strategies. At the highest level we use TLoops, a C++ library of our design, to automatically emit CUDA code equivalent to tensorial expressions written into C++ source using a syntax similar to analytic calculation. Next, we trace out and cache explicit matrix representations of the numerous linear transformations in the SpEC code, which allows these to be performed on the GPU using pre-existing matrix-multiplication libraries. We port the few remaining important modules by hand. In this paper we detail the specifics of our port, and present benchmarks of it simulating isolated black hole spacetimes on several generations of NVIDIA GPU.

Tricyanomethane and Its Ketenimine Tautomer: Generation from Different Precursors and Analysis in Solution, Argon Matrix, and as a Single Crystal.

PubMed

Banert, Klaus; Chityala, Madhu; Hagedorn, Manfred; Beckers, Helmut; Stüker, Tony; Riedel, Sebastian; Rüffer, Tobias; Lang, Heinrich

2017-08-01

Solutions of azidomethylidenemalononitrile were photolyzed at low temperatures to produce the corresponding 2H-azirine and tricyanomethane, which were analyzed by low-temperature NMR spectroscopy. The latter product was also observed after short thermolysis of the azide precursor in solution whereas irradiation of the azide isolated in an argon matrix did not lead to tricyanomethane, but to unequivocal detection of the tautomeric ketenimine by IR spectroscopy for the first time. When the long-known "aquoethereal" greenish phase generated from potassium tricyanomethanide, dilute sulfuric acid, and diethyl ether was rapidly evaporated and sublimed, a mixture of hydronium tricyanomethanide and tricyanomethane was formed instead of the previously claimed ketenimine tautomer. Under special conditions of sublimation, single crystals of tricyanomethane could be isolated, which enabled the analysis of the molecular structure by X-ray diffraction. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Wide spread of OXA-23-producing carbapenem-resistant Acinetobacter baumannii belonging to clonal complex II in different hospitals in Lebanon.

PubMed

Al Atrouni, Ahmad; Hamze, Monzer; Jisr, Tamima; Lemarié, Carole; Eveillard, Matthieu; Joly-Guillou, Marie-Laure; Kempf, Marie

2016-11-01

To investigate the molecular epidemiology of Acinetobacter baumannii strains isolated from different hospitals in Lebanon. A total of 119 non-duplicate Acinetobacter strains were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and partial rpoB gene sequencing. Antibiotic susceptibility testing was performed by disc diffusion method and all identified carbapenem-resistant isolates were investigated by PCR assays for the presence of the carbapenemase-encoding genes. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used for molecular typing. Of the 119 A. baumannii isolates, 76.5% were resistant to carbapenems. The most common carbapenemase was the OXA-23-type, found in 82 isolates. The study of population structure using MLST revealed the presence of 30 sequence types (STs) including 18 new ones, with ST2 being the most commonly detected, accounting for 61% of the isolates typed. PFGE performed on all strains of ST2 identified a major cluster of 53 isolates, in addition to three other minor clusters and ten unique profiles. This study highlights the wide dissemination of highly related OXA-23-producing carbapenem-resistant A. baumannii belonging to the international clone II in Lebanon. Thus, appropriate infection control measures are recommended in order to control the geographical spread of this clone in this country. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Distribution of pericellular matrix molecules in the temporomandibular joint and their chondroprotective effects against inflammation

PubMed Central

Chu, Wern Cui; Zhang, Shipin; Sng, Timothy J; Ong, Yu Jie; Tan, Wen-Li; Ang, Vivien Y; Foldager, Casper B; Toh, Wei Seong

2017-01-01

The objectives of this study were to (1) determine the distribution and synthesis of pericellular matrix (PCM) molecules (collagen VI, collagen IV and laminin) in rat temporomandibular joint (TMJ) and (2) investigate the effects of PCM molecules on chondrocytes against inflammation in osteoarthritis. Four zones (fibrous, proliferating, mature and hypertrophic) of condylar cartilage and three bands (anterior, intermediate and posterior) of disc were analysed by immunohistochemistry for the presence of PCM molecules in rat TMJs. Isolated chondrocytes were pre-treated with PCM molecules before being subjected to interleukin (IL)-1β treatment to stimulate inflammation. The responses of the chondrocytes were analysed using gene expression, nitric oxide release and matrix metalloproteinase (MMP)-13 production measures. Histomorphometric analyses revealed that the highest areal deposition of collagen VI (67.4%), collagen IV (45.7%) and laminin (52.4%) was in the proliferating zone of TMJ condylar cartilage. No significant difference in the distribution of PCM molecules was noted among the three bands of the TMJ disc. All three PCM molecules were expressed intracellularly by chondrocytes cultured in the monolayer. Among the PCM molecules, pre-treatment with collagen VI enhanced cellular proliferation, ameliorated IL-1β-induced MMP-3, MMP-9, MMP-13 and inducible nitric oxide synthase gene expression, and attenuated the downregulation of cartilage matrix genes, including collagen I, aggrecan and cartilage oligomeric matrix protein (COMP). Concurrently, collagen VI pretreatment inhibited nitric oxide and MMP-13 production. Our study demonstrates for the first time the distribution and role of PCM molecules, particularly collagen VI, in the protection of chondrocytes against inflammation. PMID:28282029

Isolation of plasmodesmata from Arabidopsis suspension culture cells.

PubMed

Grison, Magali S; Fernandez-Calvino, Lourdes; Mongrand, Sébastien; Bayer, Emmanuelle M F

2015-01-01

Due to their position firmly anchored within the plant cell wall, plasmodesmata (PD) are notoriously difficult to isolate from plant tissue. Yet, getting access to isolated PD represents the most straightforward strategy for the identification of their molecular components. Proteomic and lipidomic analyses of such PD fractions have provided and will continue to provide critical information on the functional and structural elements that define these membranous nano-pores. Here, we describe a two-step simple purification procedure that allows isolation of pure PD-derived membranes from Arabidopsis suspension cells. The first step of this procedure consists in isolating cell wall fragments containing intact PD while free of contamination from other cellular compartments. The second step relies on an enzymatic degradation of the wall matrix and the subsequent release of "free" PD. Isolated PD membranes provide a suitable starting material for the analysis of PD-associated proteins and lipids.

Optimization of Unnicked β2-Glycoprotein I and High Avidity Anti-β2-Glycoprotein I Antibodies Isolation

PubMed Central

Artenjak, Andrej; Leonardi, Adrijana; Križaj, Igor; Ambrožič, Aleš; Sodin-Semrl, Snezna; Božič, Borut; Čučnik, Saša

2014-01-01

Patient biological material for isolation of β2-glycoprotein I (β2GPI) and high avidity IgG anti-β2-glycoprotein I antibodies (HAv anti-β2GPI) dictates its full utilization. The aim of our study was to evaluate/improve procedures for isolation of unnicked β2GPI and HAv aβ2GPI to gain unmodified proteins in higher yields/purity. Isolation of β2GPI from plasma was a stepwise procedure combining nonspecific and specific methods. For isolation of polyclonal HAv aβ2GPI affinity chromatographies with immobilized protein G and human β2GPI were used. The unknown protein found during isolation was identified by liquid chromatography electrospray ionization mass spectrometry and the nonredundant National Center for Biotechnology Information database. The average mass of the isolated unnicked purified β2GPI increased from 6.56 mg to 9.94 mg. In the optimized isolation procedure the high molecular weight protein (proteoglycan 4) was successfully separated from β2GPI in the 1st peaks with size exclusion chromatography. The average efficiency of the isolation procedure for polyclonal HAv anti-β2GPI from different matrixes was 13.8%, as determined by our in-house anti-β2GPI ELISA. We modified the in-house isolation and purification procedures of unnicked β2GPI and HAv anti-β2GPI, improving the purity of antigen and antibodies as well as increasing the number of tests routinely performed with the in-house ELISA by ~50%. PMID:24741579

The localization of occluded matrix proteins in calcareous spicules of sea urchin larvae.

PubMed

Seto, Jong; Zhang, Yang; Hamilton, Patricia; Wilt, Fred

2004-10-01

The sea urchin embryo forms calcareous endoskeletal spicules composed of calcite and an occluded protein matrix. Though the latter is approximately 0.1% of of the mass, the composite has substantially altered material properties, e.g., conchoidal fracture planes and increased hardness. Experiments were conducted to examine the localization of matrix proteins occluded in the mineral by use of immunocytochemistry coupled with scanning electron microscopy (SEM). The isolated, unfixed spicules were etched under relatively gentle conditions and exposed to affinity purified antibodies made against two different matrix proteins, as well as an antibody to the entire constellation of matrix proteins. Immunogold tagged secondary antibody was used to observe antibody localization in the back scatter mode of SEM. All proteins examined were very widely distributed throughout the calcite, supporting a model of the structure in which a multiprotein assemblage is woven with fine texture around microcrystalline domains of calcite. Gentle etching revealed a laminar arrangement of calcite solubility, consistent with a stepwise deposition of matrix and mineral to increase girth of the spicule.

Low-temperature matrix effects on orientational motion of Methyl radical trapped in gas solids: Angular tunneling vs. libration

NASA Astrophysics Data System (ADS)

Dmitriev, Yurij A.; Zelenetckii, Ilia A.; Benetis, Nikolas P.

2018-05-01

EPR investigation of the lineshape of matrix -isolated methyl radical, CH3, spectra recorded in solid N2O and CO2 was carried out. Reversible temperature-dependent line width anisotropy was observed in both matrices. This effect is a fingerprint of the extra-slow radical rotation about the in-plane C2 axes. The rotation was found to be anisotropic and closely correlated to the orientational dynamics of the matrix molecules. It was suggested that a recently discovered "hoping precession" effect of matrix molecules in solid CO2 is a common feature of matrices of the linear molecules CO, N2O, and CO2. A new low-temperature matrix effect, referred to as "libration trap", was proposed which accounts for the changing CH3 reorientational motion about the radical C3-axis from rotation to libration. Temperature dependence of the intensity of the EPR satellites produced by these nonrotating-but librating methyls was presented. This allowed for a rough estimation of the rotation hindering potential due to correlation mismatch between the radical and the nearest matrix molecules' librations.

Evaluation of species-specific PCR, Bruker MS, VITEK MS and the VITEK 2 system for the identification of clinical Enterococcus isolates.

PubMed

Fang, H; Ohlsson, A-K; Ullberg, M; Ozenci, V

2012-11-01

The purpose of this investigation was to compare the performance of species-specific polymerase chain reaction (PCR), matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and phenotypic identification systems for the identification of Enterococcus species. A total of 132 clinical isolates were investigated by the following: (1) a multiplex real-time PCR assay targeting ddl Enterococcus faecium, ddl Enterococcus faecalis, vanC1 and vanC2/C3 genes, and a high-resolution melting (HRM) analysis of the groESL gene for the differentiation of Enterococcus casseliflavus and Enterococcus gallinarum; (2) Bruker MS; (3) VITEK MS; and (4) the VITEK 2 system. 16S rRNA gene sequencing was used as a reference method in the study. The 132 isolates were identified as 32 E. faecalis, 63 E. faecium, 16 E. casseliflavus and 21 E. gallinarum. The multiplex PCR, Bruker MS and VITEK MS were able to identify all the isolates correctly at the species level. The VITEK 2 system could identify 131/132 (99.2 %) and 121/132 (91.7 %) of the isolates at the genus and species levels, respectively. The HRM-groESL assay identified all (21/21) E. gallinarum isolates and 81.3 % (13/16) of the E. casseliflavus isolates. The PCR methods described in the present study are effective in identifying the enterococcal species. MALDI-TOF MS is a rapid, reliable and cost-effective identification technique for enterococci. The VITEK 2 system is less efficient at detecting non-faecalis and non-faecium Enterococcus species.

One-step repair for cartilage defects in a rabbit model: a technique combining the perforated decalcified cortical-cancellous bone matrix scaffold with microfracture.

PubMed

Dai, Linghui; He, Zhenming; Zhang, Xin; Hu, Xiaoqing; Yuan, Lan; Qiang, Ming; Zhu, Jingxian; Shao, Zhenxing; Zhou, Chunyan; Ao, Yingfang

2014-03-01

Cartilage repair still presents a challenge to clinicians and researchers alike. A more effective, simpler procedure that can produce hyaline-like cartilage is needed for articular cartilage repair. A technique combining microfracture with a biomaterial scaffold of perforated decalcified cortical-cancellous bone matrix (DCCBM; composed of cortical and cancellous parts) would create a 1-step procedure for hyaline-like cartilage repair. Controlled laboratory study. For the in vitro portion of this study, mesenchymal stem cells (MSCs) were isolated from bone marrow aspirates of New Zealand White rabbits. Scanning electron microscopy (SEM), confocal microscopy, and 1,9-dimethylmethylene blue assay were used to assess the attachment, proliferation, and cartilage matrix production of MSCs grown on a DCCBM scaffold. For the in vivo experiment, full-thickness defects were produced in the articular cartilage of the trochlear groove of 45 New Zealand White rabbits, and the rabbits were then assigned to 1 of 3 treatment groups: perforated DCCBM combined with microfracture (DCCBM+M group), perforated DCCBM alone (DCCBM group), and microfracture alone (M group). Five rabbits in each group were sacrificed at 6, 12, or 24 weeks after the operation, and the repair tissues were analyzed by histological examination, assessment of matrix staining, SEM, and nanoindentation of biomechanical properties. The DCCBM+M group showed hyaline-like articular cartilage repair, and the repair tissues appeared to have better matrix staining and revealed biomechanical properties close to those of the normal cartilage. Compared with the DCCBM+M group, there was unsatisfactory repair tissues with less matrix staining in the DCCBM group and no matrix staining in the M group, as well as poor integration with normal cartilage and poor biomechanical properties. The DCCBM scaffold is suitable for MSC growth and hyaline-like cartilage repair induction when combined with microfracture. Microfracture combined with a DCCBM scaffold is a promising method that can be performed and adopted into clinical treatment for articular cartilage injuries.

Direct Identification and Antimicrobial Susceptibility Testing of Bacteria From Positive Blood Culture Bottles by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and the Vitek 2 System

PubMed Central

Jo, Sung Jin; Park, Kang Gyun; Han, Kyungja; Park, Dong Jin

2016-01-01

Background We evaluated the reliability and accuracy of the combined use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial identification and Vitek 2 antimicrobial susceptibility testing (AST) for bacteria from positive blood culture bottles. Methods Direct identification and AST were performed in parallel to the standard methods in monomicrobial positive blood culture bottles. In total, 254 isolates grown on aerobic and/or anaerobic bottles were identified with MALDI-TOF Vitek MS (bioMérieux, France), and 1,978 microorganism/antimicrobial agent combinations were assessed. For isolates from anaerobic bottles, an aliquot of the culture broth was centrifuged, washed, and filtered through a nylon mesh. For isolates from aerobic/pediatric bottles, a lysis step using 9.26% ammonium chloride solution and 2% saponin solution was included. Results The overall correct identification rate was 81.8% (208/254) and that for gram-positive/gram-negative isolates was 73.9%/92.6%, respectively, and it was 81.8%, 87.6%, and 57.9% for isolates from aerobic, anaerobic, and pediatric bottles, respectively. Identification was not possible in 45 cases, and most of these isolates were streptococci (N=14) and coagulase-negative staphylococci (N=11). Misidentification occurred only in one case. Compared with standard methods, direct AST showed 97.9% (1,936/1,978) agreement with very major error of 0.25%, major error of 0.05%, and minor error of 1.8%. Conclusions This simple and cost-effective sample preparation method gives reliable results for the direct identification and AST of bacteria. For the identification of streptococci and coagulase-negative staphylococci, the method should be further improved. PMID:26709258

Direct Identification and Antimicrobial Susceptibility Testing of Bacteria From Positive Blood Culture Bottles by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and the Vitek 2 System.

PubMed

Jo, Sung Jin; Park, Kang Gyun; Han, Kyungja; Park, Dong Jin; Park, Yeon-Joon

2016-03-01

We evaluated the reliability and accuracy of the combined use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial identification and Vitek 2 antimicrobial susceptibility testing (AST) for bacteria from positive blood culture bottles. Direct identification and AST were performed in parallel to the standard methods in monomicrobial positive blood culture bottles. In total, 254 isolates grown on aerobic and/or anaerobic bottles were identified with MALDI-TOF Vitek MS (bioMérieux, France), and 1,978 microorganism/antimicrobial agent combinations were assessed. For isolates from anaerobic bottles, an aliquot of the culture broth was centrifuged, washed, and filtered through a nylon mesh. For isolates from aerobic/pediatric bottles, a lysis step using 9.26% ammonium chloride solution and 2% saponin solution was included. The overall correct identification rate was 81.8% (208/254) and that for gram-positive/gram-negative isolates was 73.9%/92.6%, respectively, and it was 81.8%, 87.6%, and 57.9% for isolates from aerobic, anaerobic, and pediatric bottles, respectively. Identification was not possible in 45 cases, and most of these isolates were streptococci (N=14) and coagulase-negative staphylococci (N=11). Misidentification occurred only in one case. Compared with standard methods, direct AST showed 97.9% (1,936/1,978) agreement with very major error of 0.25%, major error of 0.05%, and minor error of 1.8%. This simple and cost-effective sample preparation method gives reliable results for the direct identification and AST of bacteria. For the identification of streptococci and coagulase-negative staphylococci, the method should be further improved.

Rapid antifungal susceptibility testing by matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis.

PubMed

Vella, Antonietta; De Carolis, Elena; Vaccaro, Luisa; Posteraro, Patrizia; Perlin, David S; Kostrzewa, Markus; Posteraro, Brunella; Sanguinetti, Maurizio

2013-09-01

The widespread use of antifungal agents, which is likely to expand with their enhanced availability, has promoted the emergence of drug-resistant strains. Antifungal susceptibility testing (AFST) is now an essential procedure for guiding appropriate antifungal therapy. Recently, we developed a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based method that enables the detection of fungal isolates with reduced echinocandin susceptibility, relying on the proteome changes that are detectable after a 15-h exposure of fungal cells to serial drug concentrations. Here, we describe a simplified version of this approach that facilitates discrimination of the susceptible and resistant isolates of Candida albicans after a 3-h incubation in the presence of "breakpoint" level drug concentrations of the echinocandin caspofungin (CSF). Spectra at concentrations of 0 (null), 0.03 (intermediate), and 32 (maximal) μg/ml of CSF were used to create individual composite correlation index (CCI) matrices for 65 C. albicans isolates, including 13 fks1 mutants. Isolates are then classified as susceptible or resistant to CSF if the CCI values of spectra at 0.03 and 32 μg/ml are higher or lower, respectively, than the CCI values of spectra at 0.03 and 0 μg/ml. In this way, the drug resistance of C. albicans isolates to echinocandin antifungals can be quickly assessed. Furthermore, the isolate categorizations determined using MALDI-TOF MS-based AFST (ms-AFST) were consistent with the wild-type and mutant FKS1 genotypes and the AFST reference methodology. The ms-AFST approach may provide a rapid and reliable means of detecting emerging antifungal resistance and accelerating the initiation of appropriate antifungal treatment.

Hydrogel Dressing with a Nano-Formula against Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa Diabetic Foot Bacteria.

PubMed

El-Naggar, Moustafa Y; Gohar, Yousry M; Sorour, Magdy A; Waheeb, Marian G

2016-02-01

This study proposes an alternative approach for the use of chitosan silver-based dressing for the control of foot infection with multidrug-resistant bacteria. Sixty-five bacterial isolates were isolated from 40 diabetic patients. Staphylococcus aureus (37%) and Pseudomonas aeruginosa (18.5%) were the predominant isolates in the ulcer samples. Ten antibiotics were in vitro tested against diabetic foot clinical bacterial isolates. The most resistant S. aureus and P. aeruginosa isolates were then selected for further study. Three chitosan sources were tested individually for chelating silver nanoparticles. Squilla chitosan silver nanoparticles (Sq. Cs-Ag(0)) showed the maximum activity against the resistant bacteria when mixed with amikacin that showed the maximum synergetic index. This, in turn, resulted in the reduction of the amikacin MIC value by 95%. For evaluation of the effectiveness of the prepared dressing using Artemia salina as the toxicity biomarker, the LC50 was found to be 549.5, 18,000, and 10,000 μg/ml for amikacin, Sq. Cs-Ag(0), and dressing matrix, respectively. Loading the formula onto chitosan hydrogel dressing showed promising antibacterial activities, with responsive healing properties for the wounds in normal rats of those diabetic rats (polymicrobial infection). It is quite interesting to note that no emergence of any side effect on either kidney or liver biomedical functions was noticed.

Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque.

PubMed

Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan

2016-02-10

Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium.

Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque

PubMed Central

Goh, Share-Yuan; Khan, Saad Ahmed; Tee, Kok Keng; Abu Kasim, Noor Hayaty; Yin, Wai-Fong; Chan, Kok-Gan

2016-01-01

Cell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium. PMID:26860259

On the isolation of elemental carbon (EC) for micro-molar 14C accelerator mass spectrometry: development of a hybrid reference material for 14C-EC accuracy assurance, and a critical evaluation of the thermal optical kinetic (TOK) EC isolation procedure

NASA Astrophysics Data System (ADS)

Currie, L. A.; Kessler, J. D.

2005-10-01

The primary objective of the research reported here has been the development of a hybrid reference material (RM) to serve as a test of accuracy for elemental carbon (EC) isotopic (14C) speciation measurements. Such measurements are vital for the quantitative apportionment of fossil and biomass sources of "soot" (EC), the tracer of fire that has profound effects on health, atmospheric visibility, and climate. Previous studies of 14C-EC measurement quality, carried out with NIST SRM 1649a (Urban Dust), showed a range of results, but since the "truth" was not known for this natural matrix RM, one had to rely on isotopic-chemical consistency evidence (14C in PAH, EC) of measurement validity (Currie et al., 2002). Components of the new Hybrid RM (DiesApple), however, have known 14C and EC composition, and they are nearly orthogonal (isotopically and chemically). NIST SRM 2975 (Forklift Diesel Soot) has little or no 14C, and its major compositional component is EC; SRM 1515 (Apple Leaves) has the 14C content of biomass-C, and it has little or no EC. Thus, the Hybrid RM can serve as an absolute isotopic test for the absence of EC-mimicking pyrolysis-C (char) from SRM 1515 in the EC isolate of the Hybrid RM, as well as a test for conservation of its dominant soot fraction throughout the isolation procedure.

The secondary objective was to employ the Hybrid RM for the comparative evaluation of the thermal optical kinetic (TOK) and thermal optical transmission (TOT) methods for the isolation of EC for micro-molar carbon accelerator mass spectrometry (AMS). As part of this process, the relatively new TOK method was subjected to a critical evaluation and significant development. Key findings of our study are: (1) both methods exhibited biomass-C "leakage"; for TOT, the EC fraction isolated for AMS contained about 8% of the original biomass-C; for TOK, the refractory carbon (RC) isolated contained about 3% of the original biomass-C.; (2) the initial isothermal oxidation stage of the TOK method substantially reduced the transfer of artifact char to the RC fraction, improving isolation capabilities; (3) the Hybrid RM was not equal to the sum of its parts, with matrix interactions inducing premature loss of EC which, however, could be quantified and minimized; (4) the three-stage TOK method provided a superior capability for carbonate quantification at the sub-micromolar level, with "reagent-free" removal of carbonate-C from EC - essential for low-level EC-14C AMS.

Osthole Suppresses the Migratory Ability of Human Glioblastoma Multiforme Cells via Inhibition of Focal Adhesion Kinase-Mediated Matrix Metalloproteinase-13 Expression

PubMed Central

Tsai, Cheng-Fang; Yeh, Wei-Lan; Chen, Jia-Hong; Lin, Chingju; Huang, Shiang-Suo; Lu, Dah-Yuu

2014-01-01

Glioblastoma multiforme (GBM) is the most common type of primary and malignant tumor occurring in the adult central nervous system. GBM often invades surrounding regions of the brain during its early stages, making successful treatment difficult. Osthole, an active constituent isolated from the dried C. monnieri fruit, has been shown to suppress tumor migration and invasion. However, the effects of osthole in human GBM are largely unknown. Focal adhesion kinase (FAK) is important for the metastasis of cancer cells. Results from this study show that osthole can not only induce cell death but also inhibit phosphorylation of FAK in human GBM cells. Results from this study show that incubating GBM cells with osthole reduces matrix metalloproteinase (MMP)-13 expression and cell motility, as assessed by cell transwell and wound healing assays. This study also provides evidence supporting the potential of osthole in reducing FAK activation, MMP-13 expression, and cell motility in human GBM cells. PMID:24599080

Phenetic, genetic diversity and symbiotic compatibility of rhizobial strains nodulating pigeon pea in Northern India.

PubMed

Arora, Naveen Kumar; Khare, Ekta; Singh, Sachin; Tewari, Sakshi

2018-01-01

Pigeon pea ( Cajanus cajan ) is one of the most important legumes grown in the northern province of Uttar Pradesh, India. However, its productively in Uttar Pradesh is lower than the average yield of adjoining states. During the course of the present study, a survey of pigeon pea growing agricultural fields was carried out and it was found that 80% of plants were inadequately nodulated. The study was aimed to evaluate the pigeon pea symbiotic compatibility and nodulation efficiency of root nodulating bacteria isolated from various legumes, and to explore the phenetic and genetic diversity of rhizobial population nodulating pigeon pea growing in fields of Uttar Pradesh. Amongst all the 96 isolates, 40 isolates showed nodulation in pigeon pea. These 40 isolates were further characterized by phenotypic, biochemical and physiological tests. Intrinsic antibiotic resistance pattern was taken to generate similarity matrix revealing 10 phenons. The study shows that most of the isolates nodulating pigeon pea in this region were rapid growers. The dendrogram generated using the NTSYSpc software grouped RAPD patterns into 19 clusters. The high degree of phenetic and genetic diversity encountered is probably because of a history of mixed cropping of legumes. The assessment of diversity is a very important tool and can be used to improve the nodulation and quality of pigeon pea crop. It is also concluded that difference between phenetic and RAPD clustering pattern is an indication that rhizobial diversity of pigeon pea is not as yet completely understood and settled.

Technical note: Method for isolation of the bovine sweat gland and conditions for in vitro culture.

PubMed

Hamzaoui, S; Burger, C A; Collier, J L; Collier, R J

2018-05-01

Apocrine sweat glands in bovine skin are involved in thermoregulation. Human, horse, and sheep sweat gland epithelial cells have been isolated and grown in vitro. The present study was conducted to identify a method to isolate bovine sweat glands and culture apocrine bovine sweat gland epithelial cells in vitro. Mechanical shearing, collagenase digestion, centrifugation, and neutral red staining were used to identify and isolate the apocrine glands from skin. Bovine sweat glands in situ and after isolation comprised 2 major cell types consisting of a single layer of cuboidal epithelial cells resting on a layer of myoepithelial cells. In situ, the glands were embedded in a collagen matrix primarily comprising fibroblasts, and some of these cells were also present in the isolated material. The isolated material was transferred to complete medium (keratinocyte serum-free medium, bovine pituitary extract, and human recombinant epidermal growth factor + 2.5% fetal bovine serum) in a T 25 flask (Falcon, Franklin Lakes, NJ) with media film and then incubated at 37°C for 24 h. After sweat glands adhered to the bottom of the flask, an additional 2 mL of complete medium was added and the medium was changed every 3 d. Isolated apocrine sweat glands and bovine sweat gland epithelial cells were immunostained for cytokeratin and fibroblast specific protein, indicating fibroblast-free cultures. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Comparison of MALDI-TOF MS, nucleic acid hybridization and the MPT64 immunochromatographic test for the identification of M. tuberculosis and non-tuberculosis Mycobacterium species.

PubMed

Şamlı, Asuman; İlki, Arzu

2016-10-01

Mycobacteria are an important cause of morbidity in humans. Rapid and accurate mycobacterial identification is important for improving patient outcomes. However, identification of Mycobacterium species is not easy, due to the slow and fastidious growth of mycobacteria. Recently, biochemical, sequencing, and probing methods have come to be used for identification. This study compared the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of M.tuberculosis and non-tuberculosis Mycobacteria (NTM) to those of nucleic acid hybridization (NAH) and the MPT64 immunochromatographic test. A total of 69 isolates from Marmara University Hospital, Microbiology Laboratory obtained between 2012 and 2013 were included in our study. All strains were grown on Lowenstein-Jensen and Middlebrook 7H9 medium. Among the 69 isolates, 56 (81%) were isolated as Mycobacterium tuberculosis complex (MTC), and 13 (19%) were isolated as NTM by the MPT64 ICT. NAH was able to identify all isolates to the species level. The isolated NTM included M. intracellulare (n:5), M. lentiflavum (n:3), M. xenopi (n:2), M. malmoense (n:1), M. abscessus (n:1), and M. avium (n:1). MALDI-TOF MS identified 88% of the mycobacterial isolates. All M. tuberculosis strains were identified correctly, but the ratio was 38.5% for NTM. Mycobacterial identification using MALDI-TOF MS takes 45 minutes and costs 3 Euro/test, whereas mycobacterial identification using NAH takes 6-7 hours and costs 30 Euro/test. In conclusion, MALDI-TOF MS has the potential to identify mycobacteria in the clinical laboratory setting by reducing identification turnaround time and laboratory costs for isolate referral.

Improved Tandem Affinity Purification Tag and Methods for Isolation of Proteins and Protein Complexes from Schizosaccharomyces pombe.

PubMed

Zilio, Nicola; Boddy, Michael N

2017-03-01

The tandem affinity purification (TAP) method uses an epitope that contains two different affinity purification tags separated by a site-specific protease site to isolate a protein rapidly and easily. Proteins purified via the TAP tag are eluted under mild conditions, allowing them to be used for structural and biochemical analyses. The original TAP tag contains a calmodulin-binding peptide and the IgG-binding domain from protein A separated by a tobacco etch virus (TEV) protease cleavage site. After capturing the Protein A epitope on an IgG resin, bound proteins are released by incubation with the TEV protease and then isolated on a calmodulin matrix in the presence of calcium; elution from this resin is achieved by chelating calcium with EGTA. However, because the robustness of the calmodulin-binding step in this procedure is highly variable, we replaced the calmodulin-binding peptide with three copies of the FLAG epitope, (3× FLAG)-TEV-Protein A, which can be isolated using an anti-FLAG resin. Elution from this matrix is achieved in the presence of an excess of a 3× FLAG peptide. In addition to allowing proteins to be released under mild conditions, elution by the 3× FLAG peptide adds an extra layer of specificity to the TAP procedure, because it liberates only FLAG-tagged proteins. © 2017 Cold Spring Harbor Laboratory Press.

Morphology and structure features of ZnAl{sub 2}O{sub 4} spinel nanoparticles prepared by matrix-isolation-assisted calcination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Xuelian, E-mail: xueliandu@126.com; Li, Liqiang; Zhang, Wenxing

2015-01-15

Graphical abstract: The substrate ZnO as the isolation medium is effective in preventing the sintering and agglomeration of ZnAl{sub 2}O{sub 4} nanoparticles, and it also prevents their contamination. High purity, well-dispersed, and single-crystal ZnAl{sub 2}O{sub 4} nanoparticles with 3.72 eV band gap were obtained. - Abstract: Well-dispersed ZnAl{sub 2}O{sub 4} spinel nanoparticles with an average crystalline size of 25.7 nm were synthesized successfully and easily by polymer-network and matrix-isolation-assisted calcination. The product microstructure and features were investigated by X-ray diffractometry, thermogravimetric and differential thermal analysis, Fourier transform-infrared spectroscopy, N{sub 2} adsorption–desorption isotherms, and energy dispersive X-ray spectra. The morphology andmore » optical performance of the as-prepared ZnAl{sub 2}O{sub 4} nanoparticles were characterized by scanning electron microscope, transmission electron microscopy, and photoluminescence spectrometer. Experimental results indicate that excess ZnO acted as the isolation medium is effective in preventing the sintering and agglomeration of ZnAl{sub 2}O{sub 4} nanoparticles, and it also prevents their contamination. Then, high purity and well-dispersed ZnAl{sub 2}O{sub 4} nanoparticles with single-crystal structure were obtained.« less

Gas chromatography/matrix-isolation apparatus

DOEpatents

Reedy, G.T.

1986-06-10

A gas-sample collection device provides matrix isolation of individual gas bands from a gas chromatographic separation and for the spectroscopic analysis of the individual sample bands. The device includes a vacuum chamber containing a rotatably supported, specular carousel having at least one reflecting surface for holding a sample deposited thereon. A gas inlet is provided for depositing a mixture of sample and matrix material on the reflecting surface which is maintained at a sufficiently low temperature to cause solidification. A first parabolic mirror directs an incident beam of electromagnetic radiation, such as in the infrared (IR) spectrum, from a source onto the sample/matrix mixture while a second parabolic mirror directs a second beam of electromagnetic radiation reflected by the specular surface to an IR spectrometer for determining the absorption spectra of the sample material deposited on the reflecting surface. The pair of off-axis parabolic mirrors having a common focal point are positioned outside of the vacuum chamber and may be displaced in combination for improved beam positioning and alignment. The carousel is provided with an aperture for each reflecting surface to facilitate accurate positioning of the incident beam relative to the gas-samples under analysis. Improved gas-sample deposition is insured by the use of a long focal length stereomicroscope positioned outside of the vacuum chamber for monitoring sample formation through a window, while the sample collector is positioned outside of the zone bounded by the incident and reflected electromagnetic beams for improved sample access and monitoring. 10 figs.

Gas chromatography/matrix-isolation apparatus

DOEpatents

Reedy, Gerald T.

1986-01-01

A gas-sample collection device provides matrix isolation of individual gas bands from a gas chromatographic separation and for the spectroscopic analysis of the individual sample bands. The device includes a vacuum chamber containing a rotatably supported, specular carousel having at least one reflecting surface for holding a sample deposited thereon. A gas inlet is provided for depositing a mixture of sample and matrix material on the reflecting surface which is maintained at a sufficiently low temperature to cause solidification. A first parabolic mirror directs an incident beam of electromagnetic radiation, such as in the infrared (IR) spectrum, from a source onto the sample/matrix mixture while a second parabolic mirror directs a second beam of electromagnetic radiation reflected by the specular surface to an IR spectrometer for determining the absorption spectra of the sample material deposited on the reflecting surface. The pair of off-axis parabolic mirrors having a common focal point are positioned outside of the vacuum chamber and may be displaced in combination for improved beam positioning and alignment. The carousel is provided with an aperture for each reflecting surface to facilitate accurate positioning of the incident beam relative to the gas-samples under analysis. Improved gas-sample deposition is insured by the use of a long focal length stereomicroscope positioned outside of the vacuum chamber for monitoring sample formation through a window, while the sample collector is positioned outside of the zone bounded by the incident and reflected electromagnetic beams for improved sample access and monitoring.

Potential Use of {sup 18}F-fluorodeoxyglucose Positron Emission Tomography–Based Quantitative Imaging Features for Guiding Dose Escalation in Stage III Non-Small Cell Lung Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fried, David V., E-mail: dvfried@mdanderson.org; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas; Mawlawi, Osama

2016-02-01

Purpose: To determine whether previously identified quantitative image features (QIFs) based on {sup 18}F-fluorodeoxyglucose positron emission tomography (FDG-PET) (co-occurrence matrix energy and solidity) are able to isolate subgroups of patients who would receive a benefit or detriment from dose escalation in terms of overall survival (OS) or progression-free survival (PFS). Methods and Materials: Subgroups of a previously analyzed 225 patient cohort were generated with the use of 5-percentile increment cutoff values of disease solidity and primary tumor co-occurrence matrix energy. The subgroups were analyzed with a log-rank test to determine whether there was a difference in OS and PFS betweenmore » patients treated with 60 to 70 Gy and those receiving 74 Gy. Results: In the entire patient cohort, there was no statistical difference in terms of OS or PFS between patients receiving 74 Gy and those receiving 60 to 70 Gy. It was qualitatively observed that as disease solidity and primary co-occurrence matrix energy increased, patients receiving 74 Gy had an improved OS and PFS compared with those receiving 60 to 70 Gy. The opposite trend (detriment of receiving 74 Gy) was also observed regarding low values of disease solidity and primary co-occurrence matrix energy. Conclusions: FDG-PET–based QIFs were found to be capable of isolating subgroups of patients who received a benefit or detriment from dose escalation.« less

Direct identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from positive blood culture bottles: An opportunity to customize growth conditions for fastidious organisms causing bloodstream infections.

PubMed

Sharma, Megha; Gautam, Vikas; Mahajan, Monika; Rana, Sudesh; Majumdar, Manasi; Ray, Pallab

2017-10-01

Culture-negative bacteraemia has been an enigmatic entity with respect to its aetiological agents. In an attempt to actively identify those positive blood cultures that escape isolation and detection on routine workflow, an additional step of MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) based detection was carried out directly from the flagged blood culture bottles. Blood samples from 200 blood culture bottles that beeped positive with automated (BACTEC) system and showed no growth of organism on routine culture media, were subjected to analysis by MALDI-TOF MS. Forty seven of the 200 (23.5%) bacterial aetiology could be established by bottle-based method. Based on these results, growth on culture medium could be achieved for the isolates by providing special growth conditions to the fastidious organisms. Direct identification by MALDI-TOF MS from BACTEC-positive bottles provided an opportunity to isolate those fastidious organisms that failed to grow on routine culture medium by providing them with necessary alterations in growth environment.

Diversity in biofilm formation and production of curli fimbriae and cellulose of Salmonella Typhimurium strains of different origin in high and low nutrient medium.

PubMed

Castelijn, Greetje A A; van der Veen, Stijn; Zwietering, Marcel H; Moezelaar, Roy; Abee, Tjakko

2012-01-01

The biofilm forming behavior of 51 Salmonella Typhimurium strains was determined in Tryptone Soya Broth (TSB) and 20 times diluted TSB (1/20TSB) at 25°C and 37°C. The results indicated that biofilm forming behavior is influenced by environmental conditions and associated with the origin of the strains. Clinical, outbreak-associated and retail product isolates showed dense biofilm formation in both media at 25°C, and in TSB also at 37°C. However, industrial isolates only showed dense biofilm formation in 1/20TSB at 25°C. By enumeration of biofilm cells, LIVE/DEAD staining and SEM analysis of biofilms it was found that the ratio of cells and extracellular matrix is affected by environmental conditions. Indeed, the genes involved in curli fimbriae and cellulose production are highly induced during biofilm formation at 25°C in 1/20TSB. This indicates that these are important matrix components during biofilm formation in 1/20TSB at 25°C and that other factors contribute to biofilm formation of clinical, outbreak-associated and retail product isolates at 37°C and/or nutrient-rich conditions.

Performance of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identifying Clinical Malassezia Isolates

PubMed Central

Machouart, Marie; Morio, Florent; Sabou, Marcela; Kauffmann-LaCroix, Catherine; Contet-Audonneau, Nelly; Candolfi, Ermanno; Letscher-Bru, Valérie

2016-01-01

ABSTRACT The genus Malassezia comprises commensal yeasts on human skin. These yeasts are involved in superficial infections but are also isolated in deeper infections, such as fungemia, particularly in certain at-risk patients, such as neonates or patients with parenteral nutrition catheters. Very little is known about Malassezia epidemiology and virulence. This is due mainly to the difficulty of distinguishing species. Currently, species identification is based on morphological and biochemical characteristics. Only molecular biology techniques identify species with certainty, but they are time-consuming and expensive. The aim of this study was to develop and evaluate a matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) database for identifying Malassezia species by mass spectrometry. Eighty-five Malassezia isolates from patients in three French university hospitals were investigated. Each strain was identified by internal transcribed spacer sequencing. Forty-five strains of the six species Malassezia furfur, M. sympodialis, M. slooffiae, M. globosa, M. restricta, and M. pachydermatis allowed the creation of a MALDI-TOF database. Forty other strains were used to test this database. All strains were identified by our Malassezia database with log scores of >2.0, according to the manufacturer's criteria. Repeatability and reproducibility tests showed a coefficient of variation of the log score values of <10%. In conclusion, our new Malassezia database allows easy, fast, and reliable identification of Malassezia species. Implementation of this database will contribute to a better, more rapid identification of Malassezia species and will be helpful in gaining a better understanding of their epidemiology. PMID:27795342

Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identifying Clinical Malassezia Isolates.

PubMed

Denis, Julie; Machouart, Marie; Morio, Florent; Sabou, Marcela; Kauffmann-LaCroix, Catherine; Contet-Audonneau, Nelly; Candolfi, Ermanno; Letscher-Bru, Valérie

2017-01-01

The genus Malassezia comprises commensal yeasts on human skin. These yeasts are involved in superficial infections but are also isolated in deeper infections, such as fungemia, particularly in certain at-risk patients, such as neonates or patients with parenteral nutrition catheters. Very little is known about Malassezia epidemiology and virulence. This is due mainly to the difficulty of distinguishing species. Currently, species identification is based on morphological and biochemical characteristics. Only molecular biology techniques identify species with certainty, but they are time-consuming and expensive. The aim of this study was to develop and evaluate a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) database for identifying Malassezia species by mass spectrometry. Eighty-five Malassezia isolates from patients in three French university hospitals were investigated. Each strain was identified by internal transcribed spacer sequencing. Forty-five strains of the six species Malassezia furfur, M. sympodialis, M. slooffiae, M. globosa, M. restricta, and M. pachydermatis allowed the creation of a MALDI-TOF database. Forty other strains were used to test this database. All strains were identified by our Malassezia database with log scores of >2.0, according to the manufacturer's criteria. Repeatability and reproducibility tests showed a coefficient of variation of the log score values of <10%. In conclusion, our new Malassezia database allows easy, fast, and reliable identification of Malassezia species. Implementation of this database will contribute to a better, more rapid identification of Malassezia species and will be helpful in gaining a better understanding of their epidemiology. Copyright © 2016 Denis et al.

Direct identification of pathogens from positive blood cultures using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry.

PubMed

Rodríguez-Sánchez, B; Sánchez-Carrillo, C; Ruiz, A; Marín, M; Cercenado, E; Rodríguez-Créixems, M; Bouza, E

2014-07-01

In recent years, matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has proved a rapid and reliable method for the identification of bacteria and yeasts that have already been isolated. The objective of this study was to evaluate this technology as a routine method for the identification of microorganisms directly from blood culture bottles (BCBs), before isolation, in a large collection of samples. For this purpose, 1000 positive BCBs containing 1085 microorganisms have been analysed by conventional phenotypic methods and by MALDI-TOF MS. Discrepancies have been resolved using molecular methods: the amplification and sequencing of the 16S rRNA gene or the Superoxide Dismutase gene (sodA) for streptococcal isolates. MALDI-TOF predicted a species- or genus-level identification of 81.4% of the analysed microorganisms. The analysis by episode yielded a complete identification of 814 out of 1000 analysed episodes (81.4%). MALDI-TOF identification is available for clinicians within hours of a working shift, as oppose to 18 h later when conventional identification methods are performed. Moreover, although further improvement of sample preparation for polymicrobial BCBs is required, the identification of more than one pathogen in the same BCB provides a valuable indication of unexpected pathogens when their presence may remain undetected in Gram staining. Implementation of MALDI-TOF identification directly from the BCB provides a rapid and reliable identification of the causal pathogen within hours. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Activity-guided identification of acetogenins as novel lipophilic antioxidants present in avocado pulp (Persea americana).

PubMed

Rodríguez-Sánchez, Dariana; Silva-Platas, Christian; Rojo, Rocío P; García, Noemí; Cisneros-Zevallos, Luis; García-Rivas, Gerardo; Hernández-Brenes, Carmen

2013-12-30

Avocado fruit is a rich source of health-related lipophilic phytochemicals such as monounsaturated fatty acids, tocopherols, carotenes, acetogenins and sterols. However, limited information is available on the contribution of specific phytochemicals to the overall antioxidant capacity (AOC) of the fruit. Centrifugal partition chromatography was used as fractionation tool, guided by an in vitro chemical assay of oxygen radical absorbance capacity (ORAC). Subsequent experiments focused on isolation and characterization of the chemical nature of the main contributors to lipophilic AOC of avocado pulp. ORAC values obtained for acetogenins were contrasted with results from an isolated kidney mitochondria membrane lipid peroxidation bioassay. The present study established that lipophilic AOC of the pulp was significantly higher than its hydrophilic AOC. Our results confirmed the presence of acetogenins in the fractions with highest lipophilic AOC, and for the first time linked them as contributors to lipophilic-ORAC values. Further HPLC-PDA/MS-TOF analysis led to structural elucidation of two novel acetogenins, not previously reported as present in avocado pulp, along with five already known related-compounds. Antioxidant properties observed for avocado pulp acetogenins by the ORAC assay suggested that, in the presence of an emulsifying agent, acetogenins could serve as novel lipophilic antioxidants in a food matrix. Results from isolated mitochondria lipid peroxidation bioassay, indicated that L-ORAC values which may have relevance for food matrix applications, should not be interpreted to have a direct relevance in health-related claims, compounds need to be evaluated considering the complexity of biological systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Matrix-isolation and ab initio study of HKrCCCl and HXeCCCl

NASA Astrophysics Data System (ADS)

Zhu, Cheng; Räsänen, Markku; Khriachtchev, Leonid

2015-12-01

We report on two new noble-gas molecules, HKrCCCl and HXeCCCl, prepared in low-temperature Kr and Xe matrices. These molecules are made by UV photolysis of HCCCl in the matrices and subsequent thermal annealing. The HCCCl precursor is produced by microwave discharge of a mixture of a matrix gas with trichloroethylene (HClC=CCl2). The assignments of the new noble-gas molecules are supported by deuteration experiments and quantum chemical calculations at the MP2(full) and CCSD(T) levels of theory with the def2-TZVPPD basis set. No evidence of ClXeCCH, which is computationally reliably stable, is found in the experiments. ClKrCCH as well as the Ar compounds HArCCCl and ClArCCH are not observed either, which is in agreement with the calculations.

Magneto-photonic crystal microcavities based on magnetic nanoparticles embedded in Silica matrix

NASA Astrophysics Data System (ADS)

Hocini, Abdesselam; Moukhtari, Riad; Khedrouche, Djamel; Kahlouche, Ahmed; Zamani, Mehdi

2017-02-01

Using the three-dimensional finite difference time domain method (3D FDTD) with perfectly matched layers (PML), optical and magneto-optical properties of two-dimensional magneto-photonic crystals micro-cavity is studied. This micro-cavity is fabricated by SiO2/ZrO2 or SiO2/TiO2 matrix doped with magnetic nanoparticles, in which the refractive index varied in the range of 1.51-1.58. We demonstrate that the Q factor for the designed cavity increases as the refractive index increases, and we find that the Q factor decreases as the volume fraction VF% due to off-diagonal elements increases. These magnetic microcavities may serve as a fundamental structure in a variety of ultra compact magneto photonic devices such as optical isolators, circulators and modulators in the future.

Surface morphological properties of Ag-Al2O3 nanocermet layers using dip-coating technique

NASA Astrophysics Data System (ADS)

Muhammad, Nor Adhila; Suhaimi, Siti Fatimah; Zubir, Zuhana Ahmad; Daud, Sahhidan

2017-12-01

Ag-Al2O3 nanocermet layer was deposited on Cu coated glass substrate using dip-coating technique. The aim of this study was to observe the surface morphology properties of Ag-Al2O3 nanocermet layers after annealing process at 350°C in H2. The surface morphology of Ag-Al2O3 nanocermet will be characterized by Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and X-Ray Diffractometer (XRD), respectively. The results show that nearly isolated Ag particles having a large and small size were present in the Al2O3 dielectric matrix after annealing process. The face centered cubic crystalline structure of Ag nanoparticles inclusion in the amorphous alumina dielectric matrix was confirmed using XRD pattern and supported by EDX spectra analysis.

Matrix photochemical study and conformational analysis of CH3C(O)NCS and CF3C(O)NCS.

PubMed

Ramos, Luis A; Ulic, Sonia E; Romano, Rosana M; Beckers, Helmut; Willner, Helge; Della Védova, Carlos O

2014-01-30

The vapor of acetyl isocyanide, CH3C(O)NCS, and trifluoroacetyl isocyanide, CF3C(O)NCS, were isolated in solid Ar at 15 K. The existence of rotational isomerism was confirmed when the matrixes were irradiated with broad-band UV-vis light (200 ≤ λ ≤ 800 nm) and also by temperature-dependent Ar-matrix IR spectroscopy. The initial spectra showed the vapor of CH3C(O)NCS and CF3C(O)NCS consist of two conformers syn-syn and syn-anti (with the C═O bond syn with respect to the C-H or C-F bond and syn or anti with respect to the N═C double bond). When CH3C(O)NCS is irradiated, simultaneously with the randomization process, H2CCO and HSCN are produced. In the case of the photolysis of CF3C(O)NCS, the main products are CF3NCS and CO. The assignment of the IR bands to the different photoproducts was made on the basis of the usual criteria, taking account reported antecedents in the literature.

A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere

PubMed Central

Sumer, Huseyin; Craig, Jeffrey M.; Sibson, Mandy; Choo, K.H. Andy

2003-01-01

Human neocentromeres are fully functional centromeres that arise at previously noncentromeric regions of the genome. We have tested a rapid procedure of genomic array analysis of chromosome scaffold/matrix attachment regions (S/MARs), involving the isolation of S/MAR DNA and hybridization of this DNA to a genomic BAC/PAC array. Using this procedure, we have defined a 2.5-Mb domain of S/MAR-enriched chromatin that fully encompasses a previously mapped centromere protein-A (CENP-A)-associated domain at a human neocentromere. We have independently verified this procedure using a previously established fluorescence in situ hybridization method on salt-treated metaphase chromosomes. In silico sequence analysis of the S/MAR-enriched and surrounding regions has revealed no outstanding sequence-related predisposition. This study defines the S/MAR-enriched domain of a higher eukaryotic centromere and provides a method that has broad application for the mapping of S/MAR attachment sites over large genomic regions or throughout a genome. PMID:12840048

Hydrostatic pressure modulates mRNA expressions for matrix proteins in human meniscal cells.

PubMed

Suzuki, Toru; Toyoda, Takashi; Suzuki, Hiroshi; Hisamori, Noriyuki; Matsumoto, Hideo; Toyama, Yoshiaki

2006-01-01

There have been few reports describing the effects of mechanical loading on the metabolism of meniscal cells. The aim of this study was to investigate the effects of hydrostatic pressure on meniscal cell metabolism. Human meniscal cells were cultured in alginate beads for 3 days. They were then subjected to 4 MPa hydrostatic pressure for 4 hours in either a static or cyclic (1 Hz) mode using a specially designed and constructed system. Immediately after the pressure application, the messenger RNA levels for aggrecan, type I collagen, matrix metalloproteinases (MMP) -1, -3, -9, -13 and tissue inhibitors of metalloproteinases (TIMP) -1 and -2 were measured. It was found that the application of static hydrostatic pressure caused a significant decrease in mRNA expression for MMP-1 and -13 (p<0.05). In contrast, the application of cyclic hydrostatic pressure was associated with a significant increase in type I collagen (p<0.01), TIMP-1 and -2 mRNA expression (p<0.01). These results would suggest that hydrostatic pressure in isolation can modulate mRNA expressions for matrix proteins in meniscal cells.

The Green's matrix and the boundary integral equations for analysis of time-harmonic dynamics of elastic helical springs.

PubMed

Sorokin, Sergey V

2011-03-01

Helical springs serve as vibration isolators in virtually any suspension system. Various exact and approximate methods may be employed to determine the eigenfrequencies of vibrations of these structural elements and their dynamic transfer functions. The method of boundary integral equations is a meaningful alternative to obtain exact solutions of problems of the time-harmonic dynamics of elastic springs in the framework of Bernoulli-Euler beam theory. In this paper, the derivations of the Green's matrix, of the Somigliana's identities, and of the boundary integral equations are presented. The vibrational power transmission in an infinitely long spring is analyzed by means of the Green's matrix. The eigenfrequencies and the dynamic transfer functions are found by solving the boundary integral equations. In the course of analysis, the essential features and advantages of the method of boundary integral equations are highlighted. The reported analytical results may be used to study the time-harmonic motion in any wave guide governed by a system of linear differential equations in a single spatial coordinate along its axis. © 2011 Acoustical Society of America

Study of a novel three-dimensional scaffold to repair bone defect in rabbit.

PubMed

Chen, Yushu; Bai, Bo; Zhang, Shujiang; Ye, Jing; Zhai, Haohan; Chen, Yi; Zhang, Linlin; Zeng, Yanjun

2014-05-01

Both decalcified bone matrix (DBM) and fibrin gel possess good biocompatibility, so they are used as scaffolds to culture bone marrow mesenchymal stem cells (BMSCs). The feasibility and efficacy of using compound material being made of decalcified bone matrix and fibrin gel as a three-dimensional scaffold for bone growth were investigated. BMSCs were isolated from the femur of rabbit, then seeded in prepared scaffolds after incubation for 28 days in vitro. In vivo: 30 New Zealand White Rabbits received bone defect in left radius and divided three treatment groups randomly: (1) BMSCs/decalcified bone matrix/fibrin glue as experimental group; (2) decalcified bone matrix/fibrin glue without cells as control group; (3) nothing was implanted into the bone defects as blank group. The observation period of specimens was 12 weeks, and were analyzed bone formation in terms of serum proteomics (2D-PAGE and MALDI-TOF-TOF-MS), hematoxylin-eosin (HE) staining, ALP staining, and Osteopontin immunofluorescence detection. The experimental group present in three peculiar kinds of proteins, whose Geninfo identifier (GI) number were 136466, 126722803, and 126723746, respectively, correspond to TTR protein, ALB protein, RBP4 protein, and the histological inspections were superior to the other group. The content of osteopontin in experimental group was significantly higher than control group (p <  0.05). The overall results indicated that a combined material being made of BMSCs/decalcified bone matrix/fibrin glue can result in successful bone formation and decalcified bone matrix/fibrin glue admixtures can be used as a scaffold for bone tissue engineering. Copyright © 2013 Wiley Periodicals, Inc.

Bromo-oxidation reaction in enzyme-entrapped alginate hollow microfibers

PubMed Central

Asthana, Amit; Lee, Kwang Ho; Shin, Su-Jung; Perumal, Jayakumar; Butler, Lauren; Lee, Sang-Hoon; Kim, Dong-Pyo

2011-01-01

In this article, the authors present the fabrication of an enzyme-entrapped alginate hollow fiber using a microfluidic device. Further use of enzyme-entrapped alginate hollow fibers as a biocatalytic microchemical reactor for chemical synthesis is also deliberated in this article. To ensure that there is no enzyme leaching from the fiber, fiber surfaces were coated with chitosan. To confine the mobility of reactants and products within the porous hollow fibers the entire fibers were embedded into a transparent polydimethylsiloxane (PDMS) matrix which also works as a support matrix. A vanadium-containing bromoperoxidase enzyme isolated from Corallina confusa was used as a model enzyme to demonstrate the use of these alginate hollow-fiber reactors in bromo-oxidation of phenol red to bromophenol blue at different dye flow rates. Stability of the entrapped enzyme at different temperatures and the effect of the chitosan coating on the reaction conversion were also studied. It was observed that molecules as big as 27 kDa can be retained in the matrix after coating with chitosan while molecules with molecular-weight of around 378 Da can still diffuse in and out of the matrix. The kinetic conversion rate in this microfluidic bioreactor was more than 41-fold faster when compared with the standard test-tube procedure. PMID:21799723

Mitochondrial matrix delivery using MITO-Porter, a liposome-based carrier that specifies fusion with mitochondrial membranes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yasuzaki, Yukari; Yamada, Yuma; Harashima, Hideyoshi, E-mail: harasima@pharm.hokudai.ac.jp

2010-06-25

Mitochondria are the principal producers of energy in cells of higher organisms. It was recently reported that mutations and defects in mitochondrial DNA (mtDNA) are associated with various mitochondrial diseases including a variety of neurodegenerative and neuromuscular diseases. Therefore, an effective mitochondrial gene therapy and diagnosis would be expected to have great medical benefits. To achieve this, therapeutic agents need to be delivered into the innermost mitochondrial space (mitochondrial matrix), which contains the mtDNA pool. We previously reported on the development of MITO-Porter, a liposome-based carrier that introduces macromolecular cargos into mitochondria via membrane fusion. In this study, we providemore » a demonstration of mitochondrial matrix delivery and the visualization of mitochondrial genes (mtDNA) in living cells using the MITO-Porter. We first prepared MITO-Porter containing encapsulated propidium iodide (PI), a fluorescent dye used to stain nucleic acids to detect mtDNA. We then confirmed the emission of red-fluorescence from PI by conjugation with mtDNA, when the carriers were incubated in the presence of isolated rat liver mitochondria. Finally, intracellular observation by confocal laser scanning microscopy clearly verified that the MITO-Porter delivered PI to the mitochondrial matrix.« less