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Sample records for zebrin ii compartmentation

  1. Zebrin II compartmentation of the cerebellum in a basal insectivore, the Madagascan hedgehog tenrec Echinops telfairi

    PubMed Central

    Sillitoe, Roy V; Künzle, Heinz; Hawkes, Richard

    2003-01-01

    The mammalian cerebellum is histologically uniform. However, underlying the simple laminar architecture is a complex arrangement of parasagittal stripes and transverse zones that can be revealed by the expression of zebrin II/aldolase C. The cerebellar cortex of rodents, for example, is organized into four transverse zones: anterior, central, posterior and nodular. Within the anterior and posterior zones, parasagittal stripes of Purkinje cells expressing zebrin II alternate with those that do not. Zonal boundaries appear to be independent of cerebellar lobulation. To explore this model further, and to broaden our understanding of the evolution of cerebellar patterning, zebrin II expression has been studied in the cerebellum of the Madagascan hedgehog tenrec (Echinops telfairi), a basal insectivore with a lissiform cerebellum with only five lobules. Zebrin II expression in the tenrec reveals an array of four transverse zones as in rodents, two with homogeneous zebrin II expression, two further subdivided into stripes, that closely resembles the expression pattern described in other mammals. We conclude that a zone-and-stripe organization may be a common feature of the mammalian cerebellar vermis and hemispheres, and that zonal boundaries and cerebellar lobules and fissures form independently. PMID:14529046

  2. Zebrin II Is Expressed in Sagittal Stripes in the Cerebellum of Dragon Lizards (Ctenophorus sp.).

    PubMed

    Wylie, Douglas R; Hoops, Daniel; Aspden, Joel W; Iwaniuk, Andrew N

    2016-01-01

    Aldolase C, also known as zebrin II (ZII), is a glycolytic enzyme that is expressed in cerebellar Purkinje cells of the vertebrate cerebellum. In both mammals and birds, ZII is expressed heterogeneously, such that there are sagittal stripes of Purkinje cells with high ZII expression (ZII+) alternating with stripes of Purkinje cells with little or no expression (ZII-). In contrast, in snakes and turtles, ZII is not expressed heterogeneously; rather all Purkinje cells are ZII+. Here, we examined the expression of ZII in the cerebellum of lizards to elucidate the evolutionary origins of ZII stripes in Sauropsida. We focused on the central netted dragon (Ctenophorus nuchalis) but also examined cerebellar ZII expression in 5 other dragon species (Ctenophorus spp.). In contrast to what has been observed in snakes and turtles, we found that in these lizards, ZII is heterogeneously expressed. In the posterior part of the cerebellum, on each side of the midline, there were 3 sagittal stripes consisting of Purkinje cells with high ZII expression (ZII+) alternating with 2 sagittal stripes with weaker ZII expression (ZIIw). More anteriorly, most of the Purkinje cells were ZII+, except laterally, where the Purkinje cells did not express ZII (ZII-). Finally, all Purkinje cells in the auricle (flocculus) were ZII-. Overall, the parasagittal heterogeneous expression of ZII in the cerebellum of lizards is similar to that in mammals and birds, and contrasts with the homogenous ZII+ expression seen in snakes and turtles. We suggest that a sagittal heterogeneous expression of ZII represents the ancestral condition in stem reptiles which was lost in snakes and turtles. © 2017 S. Karger AG, Basel.

  3. Structure-function relationships between aldolase C/zebrin II expression and complex spike synchrony in the cerebellum.

    PubMed

    Tsutsumi, Shinichiro; Yamazaki, Maya; Miyazaki, Taisuke; Watanabe, Masahiko; Sakimura, Kenji; Kano, Masanobu; Kitamura, Kazuo

    2015-01-14

    Simple and regular anatomical structure is a hallmark of the cerebellar cortex. Parasagittally arrayed alternate expression of aldolase C/zebrin II in Purkinje cells (PCs) has been extensively studied, but surprisingly little is known about its functional significance. Here we found a precise structure-function relationship between aldolase C expression and synchrony of PC complex spike activities that reflect climbing fiber inputs to PCs. We performed two-photon calcium imaging in transgenic mice in which aldolase C compartments can be visualized in vivo, and identified highly synchronous complex spike activities among aldolase C-positive or aldolase C-negative PCs, but not across these populations. The boundary of aldolase C compartments corresponded to that of complex spike synchrony at single-cell resolution. Sensory stimulation evoked aldolase C compartment-specific complex spike responses and synchrony. This result further revealed the structure-function segregation. In awake animals, complex spike synchrony both within and between PC populations across the aldolase C boundary were enhanced in response to sensory stimuli, in a way that two functionally distinct PC ensembles are coactivated. These results suggest that PC populations characterized by aldolase C expression precisely represent distinct functional units of the cerebellar cortex, and these functional units can cooperate to process sensory information in awake animals. Copyright © 2015 the authors 0270-6474/15/350843-10$15.00/0.

  4. Distribution of zebrin-immunoreactive Purkinje cell terminals in the cerebellar and vestibular nuclei of birds.

    PubMed

    Wylie, Douglas R; Pakan, Janelle M P; Huynh, Hang; Graham, David J; Iwaniuk, Andrew N

    2012-05-01

    Zebrin II (aldolase C) is expressed in a subset of Purkinje cells in the mammalian and avian cerebella such that there is a characteristic parasagittal organization of zebrin-immunopositive stripes alternating with zebrin-immunonegative stripes. Zebrin is expressed not only in the soma and dendrites of Purkinje cells but also in their axonal terminals. Here we describe the distribution of zebrin immunoreactivity in both the vestibular and the cerebellar nuclei of pigeons (Columba livia) and hummingbirds (Calypte anna, Selasphorus rufus). In the medial cerebellar nucleus, zebrin-positive labeling was particularly heavy in the “shell,” whereas the “core” was zebrin negative. In the lateral cerebellar nucleus, labeling was not as heavy, but a positive shell and negative core were also observed. In the vestibular nuclear complex, zebrin-positive terminal labeling was heavy in the dorsolateral vestibular nucleus and the lateral margin of the superior vestibular nucleus. The central and medial regions of the superior nucleus were generally zebrin negative. Labeling was moderate to heavy in the medial vestibular nucleus, particulary the rostral half of the parvocellular subnucleus. A moderate amount of zebrin-positive labeling was present in the descending vestibular nucleus: this was heaviest laterally, and the central region was generally zebrin negative. Zebrin-positive terminals were also observed in the the cerebellovestibular process, prepositus hypoglossi, and lateral tangential nucleus. We discuss our findings in light of similar studies in rats and with respect to the corticonuclear projections to the cerebellar nuclei and the functional connections of the vestibulocerebellum with the vestibular nuclei. Copyright © 2011 Wiley Periodicals, Inc.

  5. Heterogeneity of Purkinje cell simple spike-complex spike interactions: zebrin- and non-zebrin-related variations.

    PubMed

    Tang, Tianyu; Xiao, Jianqiang; Suh, Colleen Y; Burroughs, Amelia; Cerminara, Nadia L; Jia, Linjia; Marshall, Sarah P; Wise, Andrew K; Apps, Richard; Sugihara, Izumi; Lang, Eric J

    2017-08-01

    Cerebellar Purkinje cells (PCs) generate two types of action potentials, simple and complex spikes. Although they are generated by distinct mechanisms, interactions between the two spike types exist. Zebrin staining produces alternating positive and negative stripes of PCs across most of the cerebellar cortex. Thus, here we compared simple spike-complex spike interactions both within and across zebrin populations. Simple spike activity undergoes a complex modulation preceding and following a complex spike. The amplitudes of the pre- and post-complex spike modulation phases were correlated across PCs. On average, the modulation was larger for PCs in zebrin positive regions. Correlations between aspects of the complex spike waveform and simple spike activity were found, some of which varied between zebrin positive and negative PCs. The implications of the results are discussed with regard to hypotheses that complex spikes are triggered by rises in simple spike activity for either motor learning or homeostatic functions. Purkinje cells (PCs) generate two types of action potentials, called simple and complex spikes (SSs and CSs). We first investigated the CS-associated modulation of SS activity and its relationship to the zebrin status of the PC. The modulation pattern consisted of a pre-CS rise in SS activity, and then, following the CS, a pause, a rebound, and finally a late inhibition of SS activity for both zebrin positive (Z+) and negative (Z-) cells, though the amplitudes of the phases were larger in Z+ cells. Moreover, the amplitudes of the pre-CS rise with the late inhibitory phase of the modulation were correlated across PCs. In contrast, correlations between modulation phases across CSs of individual PCs were generally weak. Next, the relationship between CS spikelets and SS activity was investigated. The number of spikelets/CS correlated with the average SS firing rate only for Z+ cells. In contrast, correlations across CSs between spikelet numbers and the

  6. Cadherins in cerebellar development: translation of embryonic patterning into mature functional compartmentalization.

    PubMed

    Redies, Christoph; Neudert, Franziska; Lin, Juntang

    2011-09-01

    Cadherins are cell adhesion molecules with multiple morphogenic functions in brain development, for example, in neuroblast migration and aggregation, axon navigation, neural circuit formation, and synaptogenesis. More than 100 members of the cadherin superfamily are expressed in the developing and mature brain. Most of the cadherins investigated, in particular classic cadherins and δ-protocadherins, are expressed in the cerebellum. For several cadherin subtypes, expression begins at early embryonic stages and persists until mature stages of cerebellar development. At intermediate stages, distinct Purkinje cell clusters exhibit unique rostrocaudal and mediolateral expression profiles for each cadherin. In the chicken, mouse, and other species, the Purkinje cell clusters are separated by intervening raphes of migrating granule cells. This pattern of Purkinje cell clusters/raphes is, at least in part, continuous with the parasagittal striping pattern that is apparent in the mature cerebellar cortex, for example, for zebrin II/aldolase C. Moreover, subregions of the deep cerebellar nuclei, vestibular nuclei and the olivary complex also express cadherins differentially. Neuroanatomical evidence suggests that the nuclear subregions and cortical domains that express the same cadherin subtype are connected to each other, to form neural subcircuits of the cerebellar system. Cadherins thus provide a molecular code that specifies not only embryonic structures but also functional cerebellar compartmentalization. By following the implementation of this code, it can be revealed how mature functional architecture emerges from embryonic patterning during cerebellar development. Dysfunction of some cadherins is associated with psychiatric diseases and developmental impairments and may also affect cerebellar function.

  7. Purkinje Cell Compartmentation in the Cerebellum of the Lysosomal Acid Phosphatase 2 Mutant Mouse (Nax - Naked-Ataxia Mutant Mouse)

    PubMed Central

    Bailey, Karen; Rahimi Balaei, Maryam; Mannan, Ashraf; Del Bigio, Marc R.; Marzban, Hassan

    2014-01-01

    The Acp2 gene encodes the beta subunit of lysosomal acid phosphatase, which is an isoenzyme that hydrolyzes orthophosphoric monoesters. In mice, a spontaneous mutation in Acp2 results in severe cerebellar defects. These include a reduced size, abnormal lobulation, and an apparent anterior cerebellar disorder with an absent or hypoplastic vermis. Based on differential gene expression in the cerebellum, the mouse cerebellar cortex can normally be compartmentalized anteroposteriorly into four transverse zones and mediolaterally into parasagittal stripes. In this study, immunohistochemistry was performed using various Purkinje cell compartmentation markers to examine their expression patterns in the Acp2 mutant. Despite the abnormal lobulation and anterior cerebellar defects, zebrin II and PLCβ4 showed similar expression patterns in the nax mutant and wild type cerebellum. However, fewer stripes were found in the anterior zone of the nax mutant, which could be due to a lack of Purkinje cells or altered expression of the stripe markers. HSP25 expression was uniform in the central zone of the nax mutant cerebellum at around postnatal day (P) 18–19, suggesting that HSP25 immunonegative Purkinje cells are absent or delayed in stripe pattern expression compared to the wild type. HSP25 expression became heterogeneous around P22–23, with twice the number of parasagittal stripes in the nax mutant compared to the wild type. Aside from reduced size and cortical disorganization, both the posterior zone and nodular zone in the nax mutant appeared less abnormal than the rest of the cerebellum. From these results, it is evident that the anterior zone of the nax mutant cerebellum is the most severely affected, and this extends beyond the primary fissure into the rostral central zone/vermis. This suggests that ACP2 has critical roles in the development of the anterior cerebellum and it may regulate anterior and central zone compartmentation. PMID:24722417

  8. Compartmentalization today

    Kevin T. Smith

    2006-01-01

    For more than 30 years, the compartmentdization concept has helped tree care practitioners and land managers interpret patterns of decay in living trees. Understanding these patterns can help guide the selection of treatments that meet the needs of people and communities while respecting the underlying tree biology. At its simplest, compartmentalization resists the...

  9. A radical pathway in catecholase activity with nickel(II) complexes of phenol based "end-off" compartmental ligands.

    PubMed

    Ghosh, Totan; Adhikary, Jaydeep; Chakraborty, Prateeti; Sukul, Pradip K; Jana, Mahendra Sekhar; Mondal, Tapan Kumar; Zangrando, Ennio; Das, Debasis

    2014-01-14

    Seven dinuclear and one dinuclear based dicyanamide bridged polymeric Ni(II) complexes of phenol based compartmental ligands (HL(1)-HL(4)) have been synthesized with the aim to investigate their catecholase-like activity and to evaluate the most probable mechanistic pathway involved in this process. The complexes have been characterized by routine physicochemical studies as well as by X-ray single crystal structure analyses namely [Ni2(L(2))(SCN)3(H2O)(CH3OH)] (), [Ni2(L(4))(SCN)3(CH3OH)2] (), [Ni2(L(2))(SCN)2(AcO)(H2O)] (), [Ni2(L(4))(SCN)(AcO)2] (), [Ni2(L(2))(N3)3(H2O)2] (), [Ni2(L(4))(N3)3(H2O)2] (), [Ni2(L(1))(AcO)2(N(CN)2)]n () and [Ni2(L(3))(AcO)2(N(CN)2)] (), [SCN = isothiocyanate, AcO = acetate, N3 = azide, and N(CN)2 = dicyanamide anion; L(1-4) = 2,6-bis(R2-iminomethyl)-4-R1-phenolato, where R1 = methyl and tert-butyl, R2 = N,N-dimethyl ethylene for L(1-2) and R1 = methyl and tert-butyl, R2 = 2-(N-ethyl) pyridine for L(3-4)]. A UV-vis spectrophotometric study using 3,5-di-tert butylcatechol (3,5-DTBC) reveals that all the complexes are highly active in catalyzing the aerobic oxidation of (3,5-DTBC) to 3,5-di-tert-butylbenzoquinone (3,5-DTBQ) in methanol medium with the formation of hydrogen peroxide. An EPR study confirms the generation of radicals during the catalysis. Cyclic voltammetric studies of the complexes in the presence and absence of 3,5-DTBC have been performed. Reduction of Ni(II) to Ni(I) and that of the imine bond of the ligand system have been detected at ∼-1.0 V and ∼-1.5 V, respectively. Coulometric separation of the species at -1.5 V followed by the EPR study at 77 K confirms the species as an organic radical and thus most probably reduced imine species. Spectroelectrochemical analysis at -1.5 V clearly indicates the oxidation of 3,5-DTBC and thus suggests that the radical pathway is supposed to be responsible for the catecholase-like activity exhibited by the nickel complexes. The ligand centred radical generation has further been

  10. Compartmentalization of the chick cerebellar cortex based on the link between the striped expression pattern of aldolase C and the topographic olivocerebellar projection.

    PubMed

    Vibulyaseck, Suteera; Luo, Yuanjun; Fujita, Hirofumi; Oh-Nishi, Arata; Ohki-Hamazaki, Hiroko; Sugihara, Izumi

    2015-09-01

    The avian cerebellum is organized into multiple longitudinal stripes defined by expression profiles of aldolase C (zebrin II) in Purkinje cells. The relationship between the aldolase C striped pattern and the olivocerebellar projection pattern is crucial in understanding cerebellar functional compartmentalization. We identified all aldolase C stripes across all lobules with the serial section alignment analysis method and then looked at this relationship by anterograde and retrograde labeling of olivocerebellar axons in the chick cerebellum. Aldolase C stripes were generally consistent and continuous from lobule I through VII and to the medial part of lobules VIII-IXb. The dorsal and ventral lamellas (DL, VL) of the inferior olive projected to the stripes in these areas with a simple mediolateral topographic relation. A few aldolase C stripes appeared at the lateral edge of lobules VI-VIII. Several more stripes were added in the lateral parts of lobules IXa-IXb and IXc-X. The medial column (MC) of the inferior olive projected to the stripes in lobules VIII-X, including the added lateral stripes, with a complex topographic relation. Sharp boundaries between aldolase C-positive and -negative stripes often accompanied a gap in the Purkinje cell layer and bordered topographically distinct groups of axons. Although the compartmental organization of the chick cerebellum is comparable to that of the mammalian cerebellum, several significant differences in the organization suggest partly separate evolutionary lineages of the mammalian and avian cerebella. We propose that rostral lobules may be evolved by rostral extension of medial stripes from caudal lobules in the avian cerebellum. © 2015 Wiley Periodicals, Inc.

  11. Synthesis, structural characterization and DFT calculation on a square-planar Ni(II) complex of a compartmental Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Biswas, Surajit; Dolai, Malay; Dutta, Arpan; Ali, Mahammad

    2016-12-01

    Reaction of a symmetric compartmental Schiff-base ligand, (H2L) with nickel(II) perchlorate hexahydrate in 1:1 M ratio in methanol gives rise to a mononuclear nickel(II) compound, NiL (1). The compound has been characterized by C, H, N microanalyses and UV-Vis spectra. The single crystal X-ray diffraction studies reveal a square planar geometry around the Ni(II) center. The compound crystallizes in monoclinic system with space group C2/c with a = 21.6425(6), b = 9.9481(3), c = 13.1958(4) Å, β = 107.728(2)°, V = 2706.16(14) Å3 and Z = 4. Ground state DFT optimization and TDDFT calculations on the ligand and complex were performed to get their UV-Vis spectral pattern.

  12. Synthesis, characterization and in vitro antimicrobial studies of Co(II), Ni(II) and Cu(II) complexes derived from macrocyclic compartmental ligand

    NASA Astrophysics Data System (ADS)

    El-Gammal, O. A.; Bekheit, M. M.; El-Brashy, S. A.

    2015-02-01

    New Co(II), Ni(II) and Cu(II) complexes derived from tetradentate macrocyclic nitrogen ligand, (1E,4E,8E,12E)-5,8,13,16-tetramethyl-1,4,9,12-tetrazacyclohexadeca-4,8,12,16-tetraene (EDHDH) have been synthesized. The complexes have been characterized by elemental analysis, spectral (IR, UV-Vis, 1H NMR and ESR (for Cu(II) complex)) mass, and magnetic as well as thermal analysis measurements. The complexes afforded the formulae: [Cu(EDHDH)Cl2]·2EtOH and [M(EDHDH)X2]·nH2O where M = Co(II) and Ni(II), X = Cl- or OH-, n = 1,0, respectively. The data revealed an octahedral arrangement with N4 tetradentate donor sites in addition to two Cl atoms occupying the other two sites. ESR spectrum of Cu2+ complex confirmed the suggested geometry with values of a α2and β2 indicating that the in-plane σ-bonding and in-plane π-bonding are appreciably covalent, and are consistent with very strong σ-in-plane bonding in the complexes. The molecular modeling is drawn and showed the bond length, bond angle, chemical reactivity, energy components (kcal/mol) and binding energy (kcal/mol) for all the title compounds using DFT method. Also, the thermal behavior and the kinetic parameters of degradation were determined using Coats-Redfern and Horowitz-Metzger methods. Moreover, the in vitro antibacterial studies of all compounds screened against pathogenic bacteria (two Gram +ve and two Gram -ve) to assess their inhibiting potential. The assay indicated that the inhibition potential is metal ion dependent. The ligand, EDHDH, Co(II) and Cu(II) complexes exhibited a remarkable antibacterial activity against Streptococcus Pyogenes as Gram +ve and Proteus vulgaris as Gram -ve bacterial strains. On the other hand, Ni(II) complex revealed a moderate antibacterial activity against both Gram +ve organisms and no activity against Gram -ve bacterial strain.

  13. Compartmentation of metals in foliage of Populus tremula grown on soils with mixed contamination. II. Zinc binding inside leaf cell organelles.

    PubMed

    Vollenweider, Pierre; Bernasconi, Petra; Gautschi, Hans-Peter; Menard, Terry; Frey, Beat; Günthardt-Goerg, Madeleine S

    2011-01-01

    The phytoextraction potential of plants for removing heavy metals from polluted soils is determined by their capacity to store contaminants in aboveground organs and complex them safely. In this study, the metal compartmentation, elemental composition of zinc deposits and zinc complexation within leaves from poplars grown on soil with mixed metal contamination was analysed combining several histochemical and microanalytical approaches. Zinc was the only heavy metal detected and was stored in several organelles in the form of globoid deposits showing β-metachromasy. It was associated to oxygen anions and different cations, noteworthy phosphorous. The deposit structure, elemental composition and element ratios indicated that zinc was chelated by phytic acid ligands. Maturation processes in vacuolar vs. cytoplasmic deposits were suggested by differences in size and amounts of complexed zinc. Hence, zinc complexation by phytate contributed to metal detoxification and accumulation in foliage but could not prevent toxicity reactions therein. Copyright © 2010 Elsevier Ltd. All rights reserved.

  14. A multi-stage compartmental model for HIV-infected individuals: II--application to insurance functions and health-care costs.

    PubMed

    Billard, L; Dayananda, P W A

    2014-03-01

    Stochastic population processes have received a lot of attention over the years. One approach focuses on compartmental modeling. Billard and Dayananda (2012) developed one such multi-stage model for epidemic processes in which the possibility that individuals can die at any stage from non-disease related causes was also included. This extra feature is of particular interest to the insurance and health-care industries among others especially when the epidemic is HIV/AIDS. Rather than working with numbers of individuals in each stage, they obtained distributional results dealing with the waiting time any one individual spent in each stage given the initial stage. In this work, the impact of the HIV/AIDS epidemic on several functions relevant to these industries (such as adjustments to premiums) is investigated. Theoretical results are derived, followed by a numerical study. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Cellular compartmentalization of secondary metabolism

    PubMed Central

    Kistler, H. Corby; Broz, Karen

    2015-01-01

    Fungal secondary metabolism is often considered apart from the essential housekeeping functions of the cell. However, there are clear links between fundamental cellular metabolism and the biochemical pathways leading to secondary metabolite synthesis. Besides utilizing key biochemical precursors shared with the most essential processes of the cell (e.g., amino acids, acetyl CoA, NADPH), enzymes for secondary metabolite synthesis are compartmentalized at conserved subcellular sites that position pathway enzymes to use these common biochemical precursors. Co-compartmentalization of secondary metabolism pathway enzymes also may function to channel precursors, promote pathway efficiency and sequester pathway intermediates and products from the rest of the cell. In this review we discuss the compartmentalization of three well-studied fungal secondary metabolite biosynthetic pathways for penicillin G, aflatoxin and deoxynivalenol, and summarize evidence used to infer subcellular localization. We also discuss how these metabolites potentially are trafficked within the cell and may be exported. PMID:25709603

  16. Protocell design through modular compartmentalization

    PubMed Central

    Miller, David; Booth, Paula J.; Seddon, John M.; Templer, Richard H.; Law, Robert V.; Woscholski, Rudiger; Ces, Oscar; Barter, Laura M. C.

    2013-01-01

    De novo synthetic biological design has the potential to significantly impact upon applications such as energy generation and nanofabrication. Current designs for constructing organisms from component parts are typically limited in scope, as they utilize a cut-and-paste ideology to create simple stepwise engineered protein-signalling pathways. We propose the addition of a new design element that segregates components into lipid-bound ‘proto-organelles’, which are interfaced with response elements and housed within a synthetic protocell. This design is inspired by living cells, which utilize multiple types of signalling molecules to facilitate communication between isolated compartments. This paper presents our design and validation of the components required for a simple multi-compartment protocell machine, for coupling a light transducer to a gene expression system. This represents a general design concept for the compartmentalization of different types of artificial cellular machinery and the utilization of non-protein signal molecules for signal transduction. PMID:23925982

  17. Protocell design through modular compartmentalization.

    PubMed

    Miller, David; Booth, Paula J; Seddon, John M; Templer, Richard H; Law, Robert V; Woscholski, Rudiger; Ces, Oscar; Barter, Laura M C

    2013-10-06

    De novo synthetic biological design has the potential to significantly impact upon applications such as energy generation and nanofabrication. Current designs for constructing organisms from component parts are typically limited in scope, as they utilize a cut-and-paste ideology to create simple stepwise engineered protein-signalling pathways. We propose the addition of a new design element that segregates components into lipid-bound 'proto-organelles', which are interfaced with response elements and housed within a synthetic protocell. This design is inspired by living cells, which utilize multiple types of signalling molecules to facilitate communication between isolated compartments. This paper presents our design and validation of the components required for a simple multi-compartment protocell machine, for coupling a light transducer to a gene expression system. This represents a general design concept for the compartmentalization of different types of artificial cellular machinery and the utilization of non-protein signal molecules for signal transduction.

  18. A Network Thermodynamic Approach to Compartmental Analysis

    PubMed Central

    Mikulecky, D. C.; Huf, E. G.; Thomas, S. R.

    1979-01-01

    We introduce a general network thermodynamic method for compartmental analysis which uses a compartmental model of sodium flows through frog skin as an illustrative example (Huf and Howell, 1974a). We use network thermodynamics (Mikulecky et al., 1977b) to formulate the problem, and a circuit simulation program (ASTEC 2, SPICE2, or PCAP) for computation. In this way, the compartment concentrations and net fluxes between compartments are readily obtained for a set of experimental conditions involving a square-wave pulse of labeled sodium at the outer surface of the skin. Qualitative features of the influx at the outer surface correlate very well with those observed for the short circuit current under another similar set of conditions by Morel and LeBlanc (1975). In related work, the compartmental model is used as a basis for simulation of the short circuit current and sodium flows simultaneously using a two-port network (Mikulecky et al., 1977a, and Mikulecky et al., A network thermodynamic model for short circuit current transients in frog skin. Manuscript in preparation; Gary-Bobo et al., 1978). The network approach lends itself to computation of classic compartmental problems in a simple manner using circuit simulation programs (Chua and Lin, 1975), and it further extends the compartmental models to more complicated situations involving coupled flows and non-linearities such as concentration dependencies, chemical reaction kinetics, etc. PMID:262387

  19. Compartmentalized storage tank for electrochemical cell system

    NASA Technical Reports Server (NTRS)

    Piecuch, Benjamin Michael (Inventor); Dalton, Luke Thomas (Inventor)

    2010-01-01

    A compartmentalized storage tank is disclosed. The compartmentalized storage tank includes a housing, a first fluid storage section disposed within the housing, a second fluid storage section disposed within the housing, the first and second fluid storage sections being separated by a movable divider, and a constant force spring. The constant force spring is disposed between the housing and the movable divider to exert a constant force on the movable divider to cause a pressure P1 in the first fluid storage section to be greater than a pressure P2 in the second fluid storage section, thereby defining a pressure differential.

  20. COMPARTMENTAL MODEL OF NITRATE RETENTION IN STREAMS

    EPA Science Inventory

    A compartmental modeling approach is presented to route nitrate retention along a cascade of stream reach sections. A process transfer function is used for transient storage equations with first order reaction terms to represent nitrate uptake in the free stream, and denitrifica...

  1. Compartmentalized Platforms for Neuro-pharmacological Research

    PubMed Central

    Jadhav, Amol D.; Wei, Li; Shi, Peng

    2016-01-01

    Dissociated primary neuronal cell culture remains an indispensable approach for neurobiology research in order to investigate basic mechanisms underlying diverse neuronal functions, drug screening and pharmacological investigation. Compartmentalization, a widely adopted technique since its emergence in 1970s enables spatial segregation of neuronal segments and detailed investigation that is otherwise limited with traditional culture methods. Although these compartmental chambers (e.g. Campenot chamber) have been proven valuable for the investigation of Peripheral Nervous System (PNS) neurons and to some extent within Central Nervous System (CNS) neurons, their utility has remained limited given the arduous manufacturing process, incompatibility with high-resolution optical imaging and limited throughput. The development in the area of microfabrication and microfluidics has enabled creation of next generation compartmentalized devices that are cheap, easy to manufacture, require reduced sample volumes, enable precise control over the cellular microenvironment both spatially as well as temporally, and permit highthroughput testing. In this review we briefly evaluate the various compartmentalization tools used for neurobiological research, and highlight application of the emerging microfluidic platforms towards in vitro single cell neurobiology. PMID:26813122

  2. Ras trafficking, localization and compartmentalized signalling

    PubMed Central

    Prior, Ian A.; Hancock, John F.

    2012-01-01

    Ras proteins are proto-oncogenes that are frequently mutated in human cancers. Three closely related isoforms, HRAS, KRAS and NRAS, are expressed in all cells and have overlapping but distinctive functions. Recent work has revealed how differences between the Ras isoforms in their trafficking, localization and protein-membrane orientation enable signalling specificity to be determined. We review the various strategies used to characterize compartmentalized Ras localization and signalling. Localization is an important contextual modifier of signalling networks and insights from the Ras system are of widespread relevance for researchers interested in signalling initiated from membranes. PMID:21924373

  3. Compartmental model of 18F-choline

    NASA Astrophysics Data System (ADS)

    Janzen, T.; Tavola, F.; Giussani, A.; Cantone, M. C.; Uusijärvi, H.; Mattsson, S.; Zankl, M.; Petoussi-Henß, N.; Hoeschen, C.

    2010-03-01

    The MADEIRA Project (Minimizing Activity and Dose with Enhanced Image quality by Radiopharmaceutical Administrations), aims to improve the efficacy and safety of 3D functional imaging by optimizing, among others, the knowledge of the temporal variation of the radiopharmaceuticals' uptake in and clearance from tumor and healthy tissues. With the help of compartmental modeling it is intended to optimize the time schedule for data collection and improve the evaluation of the organ doses to the patients. Administration of 18F-choline to screen for recurrence or the occurrence of metastases in prostate cancer patients is one of the diagnostic applications under consideration in the frame of the project. PET and CT images have been acquired up to four hours after injection of 18F-choline. Additionally blood and urine samples have been collected and measured in a gamma counter. The radioactivity concentration in different organs and data of plasma clearance and elimination into urine were used to set-up a compartmental model of the biokinetics of the radiopharmaceutical. It features a central compartment (blood) exchanging with organs. The structure describes explicitly liver, kidneys, spleen, plasma and bladder as separate units with a forcing function approach. The model is presented together with an evaluation of the individual and population kinetic parameters, and a revised time schedule for data collection is proposed. This optimized time schedule will be validated in a further set of patient studies.

  4. Field Testing of Compartmentalization Methods for Multifamily Construction

    SciT

    Ueno, K.; Lstiburek, J. W.

    2015-03-01

    The 2012 International Energy Conservation Code (IECC) has an airtightness requirement of 3 air changes per hour at 50 Pascals test pressure (3 ACH50) for single-family and multifamily construction (in climate zones 3–8). The Leadership in Energy & Environmental Design certification program and ASHRAE Standard 189 have comparable compartmentalization requirements. ASHRAE Standard 62.2 will soon be responsible for all multifamily ventilation requirements (low rise and high rise); it has an exceptionally stringent compartmentalization requirement. These code and program requirements are driving the need for easier and more effective methods of compartmentalization in multifamily buildings.

  5. Demonstration of nuclear compartmentalization of glutathione in hepatocytes.

    PubMed Central

    Bellomo, G; Vairetti, M; Stivala, L; Mirabelli, F; Richelmi, P; Orrenius, S

    1992-01-01

    The intracellular distribution of glutathione (GSH) in cultured hepatocytes has been investigated by using the compound monochlorobimane (BmCl), which interacts specifically with GSH to form a highly fluorescent adduct. Image analysis of BmCl-labeled hepatocytes predominantly localized the fluorescence in the nucleus; the nuclear/cytoplasmic concentration gradient was approximately three. This concentration gradient was collapsed by treatment of the cells with ATP-depleting agents. The uneven distribution of BmCl fluorescence was not attributable to (i) nonspecific interaction of BmCl with protein sulfhydryl groups, (ii) any selective nuclear localization of the GSH transferase(s) catalyzing formation of the GSH-BmCl conjugate, or (iii) any apparent alterations in cell morphology from culture conditions, suggesting that this distribution did, indeed, reflect a nuclear compartmentalization of GSH. That the nuclear pool of GSH was found more resistant to depletion by several agents than the cytoplasmic pool supports the assumption that GSH is essential in protecting DNA and other nuclear structures from chemical injury. Images PMID:1584774

  6. Compartmentalization and Transport in Synthetic Vesicles

    PubMed Central

    Schmitt, Christine; Lippert, Anna H.; Bonakdar, Navid; Sandoghdar, Vahid; Voll, Lars M.

    2016-01-01

    Nanoscale vesicles have become a popular tool in life sciences. Besides liposomes that are generated from phospholipids of natural origin, polymersomes fabricated of synthetic block copolymers enjoy increasing popularity, as they represent more versatile membrane building blocks that can be selected based on their specific physicochemical properties, such as permeability, stability, or chemical reactivity. In this review, we focus on the application of simple and nested artificial vesicles in synthetic biology. First, we provide an introduction into the utilization of multicompartmented vesosomes as compartmentalized nanoscale bioreactors. In the bottom-up development of protocells from vesicular nanoreactors, the specific exchange of pathway intermediates across compartment boundaries represents a bottleneck for future studies. To date, most compartmented bioreactors rely on unspecific exchange of substrates and products. This is either based on changes in permeability of the coblock polymer shell by physicochemical triggers or by the incorporation of unspecific porin proteins into the vesicle membrane. Since the incorporation of membrane transport proteins into simple and nested artificial vesicles offers the potential for specific exchange of substances between subcompartments, it opens new vistas in the design of protocells. Therefore, we devote the main part of the review to summarize the technical advances in the use of phospholipids and block copolymers for the reconstitution of membrane proteins. PMID:26973834

  7. Compartmentation Studies on Spinach Leaf Peroxisomes 1

    PubMed Central

    Heupel, Ralf; Markgraf, Therese; Robinson, David G.; Heldt, Hans Walter

    1991-01-01

    In concurrence with earlier results, the following enzymes showed latency in intact spinach (Spinacia oleracea L.) leaf peroxisomes: malate dehydrogenase (89%), hydroxypyruvate reductase (85%), serine glyoxylate aminotransferase (75%), glutamate glyoxylate aminotransferase (41%), and catalase (70%). In contrast, glycolate oxidase was not latent. Aging of peroxisomes for several hours resulted in a reduction in latency accompanied by a partial solubilization of the above mentioned enzymes. The extent of enzyme solubilization was different, being highest with glutamate glyoxylate aminotransferase and lowest with malate dehydrogenase. Osmotic shock resulted in only a partial reduction of enzyme latency. Electron microscopy revealed that the osmotically shocked peroxisomes remained compact, with smaller particle size and pleomorphic morphology but without a continuous boundary membrane. Neither in intact nor in osmotically shocked peroxisomes was a lag phase observed in the formation of glycerate upon the addition of glycolate, serine, malate, and NAD. Apparently, the intermediates, glyoxylate, hydroxypyruvate, and NADH, were confined within the peroxisomal matrix in such a way that they did not readily leak out into the surrounding medium. We conclude that the observed compartmentation of peroxisomal metabolism is not due to the peroxisomal boundary membrane as a permeability barrier, but is a function of the structural arrangement of enzymes in the peroxisomal matrix allowing metabolite channeling. ImagesFigure 3 PMID:16668283

  8. Network thermodynamic approach compartmental analysis. Na+ transients in frog skin.

    PubMed

    Mikulecky, D C; Huf, E G; Thomas, S R

    1979-01-01

    We introduce a general network thermodynamic method for compartmental analysis which uses a compartmental model of sodium flows through frog skin as an illustrative example (Huf and Howell, 1974a). We use network thermodynamics (Mikulecky et al., 1977b) to formulate the problem, and a circuit simulation program (ASTEC 2, SPICE2, or PCAP) for computation. In this way, the compartment concentrations and net fluxes between compartments are readily obtained for a set of experimental conditions involving a square-wave pulse of labeled sodium at the outer surface of the skin. Qualitative features of the influx at the outer surface correlate very well with those observed for the short circuit current under another similar set of conditions by Morel and LeBlanc (1975). In related work, the compartmental model is used as a basis for simulation of the short circuit current and sodium flows simultaneously using a two-port network (Mikulecky et al., 1977a, and Mikulecky et al., A network thermodynamic model for short circuit current transients in frog skin. Manuscript in preparation; Gary-Bobo et al., 1978). The network approach lends itself to computation of classic compartmental problems in a simple manner using circuit simulation programs (Chua and Lin, 1975), and it further extends the compartmental models to more complicated situations involving coupled flows and non-linearities such as concentration dependencies, chemical reaction kinetics, etc.

  9. Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways

    DOE PAGES

    DeLoache, William C.; Russ, Zachary N.; Dueber, John E.

    2016-03-30

    Compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk and improving pathway efficiency, but improved tools and design rules are needed to make this strategy available to more engineered pathways. Here we focus on the Saccharomyces cerevisiae peroxisome and develop a sensitive high-throughput assay for peroxisomal cargo import. We identify an enhanced peroxisomal targeting signal type 1 (PTS1) for rapidly sequestering non-native cargo proteins. Additionally, we perform the first systematic in vivo measurements of nonspecific metabolite permeability across the peroxisomal membrane using a polymer exclusion assay. Finally, we apply these new insights to compartmentalize a two-enzymemore » pathway in the peroxisome and characterize the expression regimes where compartmentalization leads to improved product titre. Lastly, this work builds a foundation for using the peroxisome as a synthetic organelle, highlighting both promise and future challenges on the way to realizing this goal.« less

  10. Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways

    SciT

    DeLoache, William C.; Russ, Zachary N.; Dueber, John E.

    Compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk and improving pathway efficiency, but improved tools and design rules are needed to make this strategy available to more engineered pathways. Here we focus on the Saccharomyces cerevisiae peroxisome and develop a sensitive high-throughput assay for peroxisomal cargo import. We identify an enhanced peroxisomal targeting signal type 1 (PTS1) for rapidly sequestering non-native cargo proteins. Additionally, we perform the first systematic in vivo measurements of nonspecific metabolite permeability across the peroxisomal membrane using a polymer exclusion assay. Finally, we apply these new insights to compartmentalize a two-enzymemore » pathway in the peroxisome and characterize the expression regimes where compartmentalization leads to improved product titre. Lastly, this work builds a foundation for using the peroxisome as a synthetic organelle, highlighting both promise and future challenges on the way to realizing this goal.« less

  11. Macroanatomy of compartmentalization in fire scars of three western conifers

    Kevin T. Smith; Elaine Sutherland; Estelle Arbellay; Markus Stoffel; Donald Falk

    2013-01-01

    Fire scars are visible evidence of compartmentalization and closure processes that contribute to tree survival after fire injury. Preliminary observations of dissected fire scars from trees injured within the last decade showed centripetal development of wound-initiated discoloration (WID) through 2-3 decades of former sapwood in Larix occidentalis and Pseudotsuga...

  12. Compartmentalization of decayed wood associated with Armillaria mellea in several tree species

    Alex L. Shigo; Joanna T. Tippett

    1981-01-01

    Decayed wood associated with Armillaria mellea was compartmentalized according to the CODIT (Compartmentalization Of Decay In Trees) model. Compartmentalization in the sapwood began after the tree walled off the area of dead cambium associated with the inflection of the fungus. The fungus spread into dying sapwood beneath and beyond the area of...

  13. Engineering of DNA polymerase I from Thermus thermophilus using compartmentalized self-replication.

    PubMed

    Aye, Seaim Lwin; Fujiwara, Kei; Ueki, Asuka; Doi, Nobuhide

    2018-05-05

    Although compartmentalized self-replication (CSR) and compartmentalized partnered replication (CPR) are powerful tools for directed evolution of proteins and gene circuits, limitations remain in the emulsion PCR process with the wild-type Taq DNA polymerase used so far, including long run times, low amounts of product, and false negative results due to inhibitors. In this study, we developed a high-efficiency mutant of DNA polymerase I from Thermus thermophilus HB27 (Tth pol) suited for CSR and CPR. We modified the wild-type Tth pol by (i) deletion of the N-terminal 5' to 3' exonuclease domain, (ii) fusion with the DNA-binding protein Sso7d, (iii) introduction of four known effective point mutations from other DNA polymerase mutants, and (iv) codon optimization to reduce the GC content. Consequently, we obtained a mutant that provides higher product yields than the conventional Taq pol without decreased fidelity. Next, we performed four rounds of CSR selection with a randomly mutated library of this modified Tth pol and obtained mutants that provide higher product yields in fewer cycles of emulsion PCR than the parent Tth pol as well as the conventional Taq pol. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. Transient compartmentalization of RNA replicators prevents extinction due to parasites.

    PubMed

    Matsumura, Shigeyoshi; Kun, Ádám; Ryckelynck, Michael; Coldren, Faith; Szilágyi, András; Jossinet, Fabrice; Rick, Christian; Nghe, Philippe; Szathmáry, Eörs; Griffiths, Andrew D

    2016-12-09

    The appearance of molecular replicators (molecules that can be copied) was probably a critical step in the origin of life. However, parasitic replicators would take over and would have prevented life from taking off unless the replicators were compartmentalized in reproducing protocells. Paradoxically, control of protocell reproduction would seem to require evolved replicators. We show here that a simpler population structure, based on cycles of transient compartmentalization (TC) and mixing of RNA replicators, is sufficient to prevent takeover by parasitic mutants. TC tends to select for ensembles of replicators that replicate at a similar rate, including a diversity of parasites that could serve as a source of opportunistic functionality. Thus, TC in natural, abiological compartments could have allowed life to take hold. Copyright © 2016, American Association for the Advancement of Science.

  15. Compartmental shift of potassium--a result of sympathomimetic overdose.

    PubMed

    McCleave, D J; Phillips, P J; Vedig, A E

    1978-04-01

    A 17-year-old youth was admitted with a serum potassium concentration of 1.8 mmol/l after taking an overdose of pseudoephedrine and choline theophyllinate. Apart from tachycardia, tachypnoea and ankle clonus, examination was normal as was the initial electrocardiograph. The hypokalaemia resolved, but there was an overall positive potassium balance of only 13 mmol. This suggests that the sympathomimetics provoked a compartmental shift of potassium perhaps indirectly by inducing hyperglycaemia and hyperinsulinaemia, as well as directly. Other factors known to affect body potassium distribution were excluded. The fact that features commonly associated with hypokalaemia could not be demonstrated may be explained by a normal body potassium content. Severe hypokalaemia caused by a compartmental shift occurs with large doses of sympathomimetics as well as in periodic paralysis.

  16. Fractional two-compartmental model for articaine serum levels

    NASA Astrophysics Data System (ADS)

    Petronijevic, Branislava; Sarcev, Ivan; Zorica, Dusan; Janev, Marko; Atanackovic, Teodor M.

    2016-06-01

    Two fractional two-compartmental models are applied to the pharmacokinetics of articaine. Integer order derivatives are replaced by fractional derivatives, either of different, or of same orders. Models are formulated so that the mass balance is preserved. Explicit forms of the solutions are obtained in terms of the Mittag-Leffler functions. Pharmacokinetic parameters are determined by the use of the evolutionary algorithm and trust regions optimization to recover the experimental data.

  17. Digital PCR on an integrated self-priming compartmentalization chip.

    PubMed

    Zhu, Qiangyuan; Qiu, Lin; Yu, Bingwen; Xu, Yanan; Gao, Yibo; Pan, Tingting; Tian, Qingchang; Song, Qi; Jin, Wei; Jin, Qinhan; Mu, Ying

    2014-03-21

    An integrated on-chip valve-free and power-free microfluidic digital PCR device is for the first time developed by making use of a novel self-priming compartmentalization and simple dehydration control to realize 'divide and conquer' for single DNA molecule detection. The high gas solubility of PDMS is exploited to provide the built-in power of self-priming so that the sample and oil are sequentially sucked into the device to realize sample self-compartmentalization based on surface tension. The lifespan of its self-priming capability was about two weeks tested using an air-tight packaging bottle sealed with a small amount of petroleum jelly, which is significant for a practical platform. The SPC chip contains 5120 independent 5 nL microchambers, allowing the samples to be compartmentalized completely. Using this platform, three different abundances of lung cancer related genes are detected to demonstrate the feasibility and flexibility of the microchip for amplifying a single nucleic acid molecule. For maximal accuracy, within less than 5% of the measurement deviation, the optimal number of positive chambers is between 400 and 1250 evaluated by the Poisson distribution, which means one panel can detect an average of 480 to 4804 template molecules. This device without world-to-chip connections eliminates the constraint of the complex pipeline control, and is an integrated on-chip platform, which would be a significant improvement to digital PCR automation and more user-friendly.

  18. Compartmental Innervation of the Superior Oblique Muscle in Mammals.

    PubMed

    Le, Alan; Poukens, Vadims; Ying, Howard; Rootman, Daniel; Goldberg, Robert A; Demer, Joseph L

    2015-10-01

    Intramuscular innervation of mammalian horizontal rectus extraocular muscles (EOMs) is compartmental. We sought evidence of similar compartmental innervation of the superior oblique (SO) muscle. Three fresh bovine orbits and one human orbit were dissected to trace continuity of SO muscle and tendon fibers to the scleral insertions. Whole orbits were also obtained from four humans (two adults, a 17-month-old child, and a 33-week stillborn fetus), two rhesus monkeys, one rabbit, and one cow. Orbits were formalin fixed, embedded whole in paraffin, serially sectioned in the coronal plane at 10-μm thickness, and stained with Masson trichrome. Extraocular muscle fibers and branches of the trochlear nerve (CN4) were traced in serial sections and reconstructed in three dimensions. In the human, the lateral SO belly is in continuity with tendon fibers inserting more posteriorly on the sclera for infraducting mechanical advantage, while the medial belly is continuous with anteriorly inserting fibers having mechanical advantage for incycloduction. Fibers in the monkey superior SO insert more posteriorly on the sclera to favor infraduction, while the inferior portion inserts more anteriorly to favor incycloduction. In all species, CN4 bifurcates prior to penetrating the SO belly. Each branch innervates a nonoverlapping compartment of EOM fibers, consisting of medial and lateral compartments in humans and monkeys, and superior and inferior compartments in cows and rabbits. The SO muscle of humans and other mammals is compartmentally innervated in a manner that could permit separate CN4 branches to selectively influence vertical versus torsional action.

  19. Field Testing of Compartmentalization Methods for Multifamily Construction

    SciT

    Ueno, K.; Lstiburek, J.

    The 2012 IECC has an airtightness requirement of 3 air changes per hour at 50 Pascals test pressure for both single-family and multifamily construction in Climate Zones 3-8. Other programs (LEED, ASHRAE 189, ASHRAE 62.2) have similar or tighter compartmentalization requirements, driving the need for easier and more effective methods of compartmentalization in multifamily buildings. Builders and practitioners have found that fire-resistance rated wall assemblies are a major source of difficulty in air sealing/compartmentalization, particularly in townhouse construction. This problem is exacerbated when garages are “tucked in” to the units and living space is located over the garages. In thismore » project, Building Science Corporation examined the taping of exterior sheathing details to improve air sealing results in townhouse and multifamily construction, when coupled with a better understanding of air leakage pathways. Current approaches are cumbersome, expensive, time consuming, and ineffective; these details were proposed as a more effective and efficient method. The effectiveness of these air sealing methods was tested with blower door testing, including “nulled” or “guarded” testing (adjacent units run at equal test pressure to null out inter-unit air leakage, or “pressure neutralization”). Pressure diagnostics were used to evaluate unit-to-unit connections and series leakage pathways (i.e., air leakage from exterior, into the fire-resistance rated wall assembly, and to the interior).« less

  20. Rewiring and regulation of cross-compartmentalized metabolism in protists

    PubMed Central

    Ginger, Michael L.; McFadden, Geoffrey I.; Michels, Paul A. M.

    2010-01-01

    Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation. PMID:20124348

  1. Compartmental and Spatial Rule-Based Modeling with Virtual Cell.

    PubMed

    Blinov, Michael L; Schaff, James C; Vasilescu, Dan; Moraru, Ion I; Bloom, Judy E; Loew, Leslie M

    2017-10-03

    In rule-based modeling, molecular interactions are systematically specified in the form of reaction rules that serve as generators of reactions. This provides a way to account for all the potential molecular complexes and interactions among multivalent or multistate molecules. Recently, we introduced rule-based modeling into the Virtual Cell (VCell) modeling framework, permitting graphical specification of rules and merger of networks generated automatically (using the BioNetGen modeling engine) with hand-specified reaction networks. VCell provides a number of ordinary differential equation and stochastic numerical solvers for single-compartment simulations of the kinetic systems derived from these networks, and agent-based network-free simulation of the rules. In this work, compartmental and spatial modeling of rule-based models has been implemented within VCell. To enable rule-based deterministic and stochastic spatial simulations and network-free agent-based compartmental simulations, the BioNetGen and NFSim engines were each modified to support compartments. In the new rule-based formalism, every reactant and product pattern and every reaction rule are assigned locations. We also introduce the rule-based concept of molecular anchors. This assures that any species that has a molecule anchored to a predefined compartment will remain in this compartment. Importantly, in addition to formulation of compartmental models, this now permits VCell users to seamlessly connect reaction networks derived from rules to explicit geometries to automatically generate a system of reaction-diffusion equations. These may then be simulated using either the VCell partial differential equations deterministic solvers or the Smoldyn stochastic simulator. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. Functional compartmentalization of the human superficial masseter muscle.

    PubMed

    Guzmán-Venegas, Rodrigo A; Biotti Picand, Jorge L; de la Rosa, Francisco J Berral

    2015-01-01

    Some muscles have demonstrated a differential recruitment of their motor units in relation to their location and the nature of the motor task performed; this involves functional compartmentalization. There is little evidence that demonstrates the presence of a compartmentalization of the superficial masseter muscle during biting. The aim of this study was to describe the topographic distribution of the activity of the superficial masseter (SM) muscle's motor units using high-density surface electromyography (EMGs) at different bite force levels. Twenty healthy natural dentate participants (men: 4; women: 16; age 20±2 years; mass: 60±12 kg, height: 163±7 cm) were selected from 316 volunteers and included in this study. Using a gnathodynamometer, bites from 20 to 100% maximum voluntary bite force (MVBF) were randomly requested. Using a two-dimensional grid (four columns, six electrodes) located on the dominant SM, EMGs in the anterior, middle-anterior, middle-posterior and posterior portions were simultaneously recorded. In bite ranges from 20 to 60% MVBF, the EMG activity was higher in the anterior than in the posterior portion (p-value = 0.001).The center of mass of the EMG activity was displaced towards the posterior part when bite force increased (p-value = 0.001). The topographic distribution of EMGs was more homogeneous at high levels of MVBF (p-value = 0.001). The results of this study show that the superficial masseter is organized into three functional compartments: an anterior, a middle and a posterior compartment. However, this compartmentalization is only seen at low levels of bite force (20-60% MVBF).

  3. Functional Compartmentalization of the Human Superficial Masseter Muscle

    PubMed Central

    Guzmán-Venegas, Rodrigo A.; Biotti Picand, Jorge L.; de la Rosa, Francisco J. Berral

    2015-01-01

    Some muscles have demonstrated a differential recruitment of their motor units in relation to their location and the nature of the motor task performed; this involves functional compartmentalization. There is little evidence that demonstrates the presence of a compartmentalization of the superficial masseter muscle during biting. The aim of this study was to describe the topographic distribution of the activity of the superficial masseter (SM) muscle’s motor units using high-density surface electromyography (EMGs) at different bite force levels. Twenty healthy natural dentate participants (men: 4; women: 16; age 20±2 years; mass: 60±12 kg, height: 163±7 cm) were selected from 316 volunteers and included in this study. Using a gnathodynamometer, bites from 20 to 100% maximum voluntary bite force (MVBF) were randomly requested. Using a two-dimensional grid (four columns, six electrodes) located on the dominant SM, EMGs in the anterior, middle-anterior, middle-posterior and posterior portions were simultaneously recorded. In bite ranges from 20 to 60% MVBF, the EMG activity was higher in the anterior than in the posterior portion (p-value = 0.001).The center of mass of the EMG activity was displaced towards the posterior part when bite force increased (p-value = 0.001). The topographic distribution of EMGs was more homogeneous at high levels of MVBF (p-value = 0.001). The results of this study show that the superficial masseter is organized into three functional compartments: an anterior, a middle and a posterior compartment. However, this compartmentalization is only seen at low levels of bite force (20–60% MVBF). PMID:25692977

  4. Analytical properties of a three-compartmental dynamical demographic model

    NASA Astrophysics Data System (ADS)

    Postnikov, E. B.

    2015-07-01

    The three-compartmental demographic model by Korotaeyv-Malkov-Khaltourina, connecting population size, economic surplus, and education level, is considered from the point of view of dynamical systems theory. It is shown that there exist two integrals of motion, which enables the system to be reduced to one nonlinear ordinary differential equation. The study of its structure provides analytical criteria for the dominance ranges of the dynamics of Malthus and Kremer. Additionally, the particular ranges of parameters enable the derived general ordinary differential equations to be reduced to the models of Gompertz and Thoularis-Wallace.

  5. COMPARTMENTALIZED PHANTOMS FOR THE STANDARD MAN, ADOLESCENT AND CHILD

    SciT

    Hayes, R.L.; Brucer, M.

    A compartmentalized phantom for the standard man was designed and built of readily available and inexpensive materials. Similar phantoms were also designed for an adolescent and a child. The basic emphasis in the designs is on general utility so that a variety of different dosemeasurement techniques could be used on the same phantom. The designs are, however, in reasonable agreement with authropometric data reported in the literature. The phantoms proved to be extremely useful in depth-dose and energy-absorption measurements for total-body irradiation therapy. Dose measurements with beam teletherapy, brachytherapy devices, and internally distributed radioisotopes were also made. (auth)

  6. Directed evolution of polymerase function by compartmentalized self-replication.

    PubMed

    Ghadessy, F J; Ong, J L; Holliger, P

    2001-04-10

    We describe compartmentalized self-replication (CSR), a strategy for the directed evolution of enzymes, especially polymerases. CSR is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. Compartmentalization serves to isolate individual self-replication reactions from each other. In such a system, adaptive gains directly (and proportionally) translate into genetic amplification of the encoding gene. CSR has applications in the evolution of polymerases with novel and useful properties. By using three cycles of CSR, we obtained variants of Taq DNA polymerase with 11-fold higher thermostability than the wild-type enzyme or with a >130-fold increased resistance to the potent inhibitor heparin. Insertion of an extra stage into the CSR cycle before the polymerase reaction allows its application to enzymes other than polymerases. We show that nucleoside diphosphate kinase and Taq polymerase can form such a cooperative CSR cycle based on reciprocal catalysis, whereby nucleoside diphosphate kinase produces the substrates required for the replication of its own gene. We also find that in CSR the polymerase genes themselves evolve toward more efficient replication. Thus, polymerase genes and their encoded polypeptides cooperate to maximize postselection copy number. CSR should prove useful for the directed evolution of enzymes, particularly DNA or RNA polymerases, as well as for the design and study of in vitro self-replicating systems mimicking prebiotic evolution and viral replication.

  7. Building America Case Study: Field Testing of Compartmentalization Methods for Multifamily Construction (Fact Sheet)

    SciT

    Not Available

    2015-01-01

    The 2012 IECC has an airtightness requirement of 3 air changes per hour at 50 Pascals test pressure for both single family and multifamily construction in Climate Zones 3-8. Other programs (LEED, ASHRAE 189, ASHRAE 62.2) have similar or tighter compartmentalization requirements, thus driving the need for easier and more effective methods of compartmentalization in multifamily buildings.

  8. Compartmental and Data-Based Modeling of Cerebral Hemodynamics: Linear Analysis.

    PubMed

    Henley, B C; Shin, D C; Zhang, R; Marmarelis, V Z

    Compartmental and data-based modeling of cerebral hemodynamics are alternative approaches that utilize distinct model forms and have been employed in the quantitative study of cerebral hemodynamics. This paper examines the relation between a compartmental equivalent-circuit and a data-based input-output model of dynamic cerebral autoregulation (DCA) and CO2-vasomotor reactivity (DVR). The compartmental model is constructed as an equivalent-circuit utilizing putative first principles and previously proposed hypothesis-based models. The linear input-output dynamics of this compartmental model are compared with data-based estimates of the DCA-DVR process. This comparative study indicates that there are some qualitative similarities between the two-input compartmental model and experimental results.

  9. Organs-on-a-chip: a focus on compartmentalized microdevices.

    PubMed

    Moraes, Christopher; Mehta, Geeta; Lesher-Perez, Sasha Cai; Takayama, Shuichi

    2012-06-01

    Advances in microengineering technologies have enabled a variety of insights into biomedical sciences that would not have been possible with conventional techniques. Engineering microenvironments that simulate in vivo organ systems may provide critical insight into the cellular basis for pathophysiologies, development, and homeostasis in various organs, while curtailing the high experimental costs and complexities associated with in vivo studies. In this article, we aim to survey recent attempts to extend tissue-engineered platforms toward simulating organ structure and function, and discuss the various approaches and technologies utilized in these systems. We specifically focus on microtechnologies that exploit phenomena associated with compartmentalization to create model culture systems that better represent the in vivo organ microenvironment.

  10. Revealing Compartmentalized Diffusion in Living Cells with Interferometric Scattering Microscopy.

    PubMed

    de Wit, Gabrielle; Albrecht, David; Ewers, Helge; Kukura, Philipp

    2018-06-19

    The spatiotemporal organization and dynamics of the plasma membrane and its constituents are central to cellular function. Fluorescence-based single-particle tracking has emerged as a powerful approach for studying the single molecule behavior of plasma-membrane-associated events because of its excellent background suppression, at the expense of imaging speed and observation time. Here, we show that interferometric scattering microscopy combined with 40 nm gold nanoparticle labeling can be used to follow the motion of membrane proteins in the plasma membrane of live cultured mammalian cell lines and hippocampal neurons with up to 3 nm precision and 25 μs temporal resolution. The achievable spatiotemporal precision enabled us to reveal signatures of compartmentalization in neurons likely caused by the actin cytoskeleton. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  11. Synapse-specific and compartmentalized expression of presynaptic homeostatic potentiation

    PubMed Central

    Li, Xiling; Goel, Pragya; Chen, Catherine; Angajala, Varun; Chen, Xun

    2018-01-01

    Postsynaptic compartments can be specifically modulated during various forms of synaptic plasticity, but it is unclear whether this precision is shared at presynaptic terminals. Presynaptic homeostatic plasticity (PHP) stabilizes neurotransmission at the Drosophila neuromuscular junction, where a retrograde enhancement of presynaptic neurotransmitter release compensates for diminished postsynaptic receptor functionality. To test the specificity of PHP induction and expression, we have developed a genetic manipulation to reduce postsynaptic receptor expression at one of the two muscles innervated by a single motor neuron. We find that PHP can be induced and expressed at a subset of synapses, over both acute and chronic time scales, without influencing transmission at adjacent release sites. Further, homeostatic modulations to CaMKII, vesicle pools, and functional release sites are compartmentalized and do not spread to neighboring pre- or post-synaptic structures. Thus, both PHP induction and expression mechanisms are locally transmitted and restricted to specific synaptic compartments. PMID:29620520

  12. Intracellular transport and compartmentation of phosphate in plants.

    PubMed

    Versaw, Wayne K; Garcia, L Rene

    2017-10-01

    Phosphate (Pi) is an essential macronutrient with structural and metabolic roles within every compartment of the plant cell. Intracellular Pi transporters direct Pi to each organelle and also control its exchange between subcellular compartments thereby providing the means to coordinate compartmented metabolic processes, including glycolysis, photosynthesis, and respiration. In this review we summarize recent advances in the identification and functional analysis of Pi transporters that localize to vacuoles, chloroplasts, non-photosynthetic plastids, mitochondria, and the Golgi apparatus. Electrical potentials across intracellular membranes and the pH of subcellular environments will also be highlighted as key factors influencing the energetics of Pi transport, and therefore pose limits for Pi compartmentation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. The human NAD metabolome: Functions, metabolism and compartmentalization

    PubMed Central

    Nikiforov, Andrey; Kulikova, Veronika; Ziegler, Mathias

    2015-01-01

    Abstract The metabolism of NAD has emerged as a key regulator of cellular and organismal homeostasis. Being a major component of both bioenergetic and signaling pathways, the molecule is ideally suited to regulate metabolism and major cellular events. In humans, NAD is synthesized from vitamin B3 precursors, most prominently from nicotinamide, which is the degradation product of all NAD-dependent signaling reactions. The scope of NAD-mediated regulatory processes is wide including enzyme regulation, control of gene expression and health span, DNA repair, cell cycle regulation and calcium signaling. In these processes, nicotinamide is cleaved from NAD+ and the remaining ADP-ribosyl moiety used to modify proteins (deacetylation by sirtuins or ADP-ribosylation) or to generate calcium-mobilizing agents such as cyclic ADP-ribose. This review will also emphasize the role of the intermediates in the NAD metabolome, their intra- and extra-cellular conversions and potential contributions to subcellular compartmentalization of NAD pools. PMID:25837229

  14. Heart Mitochondrial TTP Synthesis and the Compartmentalization of TMP*

    PubMed Central

    Kamath, Vasudeva G.; Hsiung, Chia-Heng; Lizenby, Zachary J.; McKee, Edward E.

    2015-01-01

    The primary pathway of TTP synthesis in the heart requires thymidine salvage by mitochondrial thymidine kinase 2 (TK2). However, the compartmentalization of this pathway and the transport of thymidine nucleotides are not well understood. We investigated the metabolism of [3H]thymidine or [3H]TMP as precursors of [3H]TTP in isolated intact or broken mitochondria from the rat heart. The results demonstrated that [3H]thymidine was readily metabolized by the mitochondrial salvage enzymes to TTP in intact mitochondria. The equivalent addition of [3H]TMP produced far less [3H]TTP than the amount observed with [3H]thymidine as the precursor. Using zidovudine to inhibit TK2, the synthesis of [3H]TTP from [3H]TMP was effectively blocked, demonstrating that synthesis of [3H]TTP from [3H]TMP arose solely from the dephosphorysynthase pathway that includes deoxyuridine triphosphatelation of [3H]TMP to [3H]thymidine. To determine the role of the membrane in TMP metabolism, mitochondrial membranes were disrupted by freezing and thawing. In broken mitochondria, [3H]thymidine was readily converted to [3H]TMP, but further phosphorylation was prevented even though the energy charge was well maintained by addition of oligomycin A, phosphocreatine, and creatine phosphokinase. The failure to synthesize TTP in broken mitochondria was not related to a loss of membrane potential or inhibition of the electron transport chain, as confirmed by addition of carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone and potassium cyanide, respectively, in intact mitochondria. In summary, these data, taken together, suggest that the thymidine salvage pathway is compartmentalized so that TMP kinase prefers TMP synthesized by TK2 over medium TMP and that this is disrupted in broken mitochondria. PMID:25505243

  15. Evolution of energy metabolism and its compartmentation in Kinetoplastida

    PubMed Central

    Hannaert, Véronique; Bringaud, Frédéric; Opperdoes, Fred R; Michels, Paul AM

    2003-01-01

    Kinetoplastida are protozoan organisms that probably diverged early in evolution from other eukaryotes. They are characterized by a number of unique features with respect to their energy and carbohydrate metabolism. These organisms possess peculiar peroxisomes, called glycosomes, which play a central role in this metabolism; the organelles harbour enzymes of several catabolic and anabolic routes, including major parts of the glycolytic and pentosephosphate pathways. The kinetoplastid mitochondrion is also unusual with regard to both its structural and functional properties. In this review, we describe the unique compartmentation of metabolism in Kinetoplastida and the metabolic properties resulting from this compartmentation. We discuss the evidence for our recently proposed hypothesis that a common ancestor of Kinetoplastida and Euglenida acquired a photosynthetic alga as an endosymbiont, contrary to the earlier notion that this event occurred at a later stage of evolution, in the Euglenida lineage alone. The endosymbiont was subsequently lost from the kinetoplastid lineage but, during that process, some of its pathways of energy and carbohydrate metabolism were sequestered in the kinetoplastid peroxisomes, which consequently became glycosomes. The evolution of the kinetoplastid glycosomes and the possible selective advantages of these organelles for Kinetoplastida are discussed. We propose that the possession of glycosomes provided metabolic flexibility that has been important for the organisms to adapt easily to changing environmental conditions. It is likely that metabolic flexibility has been an important selective advantage for many kinetoplastid species during their evolution into the highly successful parasites today found in many divergent taxonomic groups. Also addressed is the evolution of the kinetoplastid mitochondrion, from a supposedly pluripotent organelle, attributed to a single endosymbiotic event that resulted in all mitochondria and

  16. Compartmental Modeling and Dosimetry of in Vivo Metabolic Studies of Leucine and Three Secretory Proteins in Humans Using Radioactive Tracers

    NASA Astrophysics Data System (ADS)

    Venkatakrishnan, Vaidehi

    1995-01-01

    Physical and mathematical models provide a systematic means of looking at biological systems. Radioactive tracer kinetic studies open a unique window to study complex tracee systems such as protein metabolism in humans. This research deals with compartmental modeling of tracer kinetic data on leucine and apolipoprotein metabolism obtained using an endogenous tritiated leucine tracer administered as a bolus, and application of compartmental modeling techniques for dosimetric evaluation of metabolic studies of radioiodinated apolipoproteins. Dr. Waldo R. Fisher, Department of Medicine, was the coordinating research supervisor and the work was carried out in his laboratory. A compartmental model for leucine kinetics in humans has been developed that emphasizes its recycling pathways which were examined over two weeks. This model builds on a previously published model of Cobelli et al, that analyzed leucine kinetic data up to only eight hours. The proposed model includes different routes for re-entry of leucine from protein breakdown into plasma accounting for proteins which turn over at different rates. This new model successfully incorporates published models of three secretory proteins: albumin, apoA-I, and VLDL apoB, in toto thus increasing its validity and utility. The published model of apoA-I, based on an exogenous radioiodinated tracer, was examined with data obtained using an endogenous leucine tracer using compartmental techniques. The analysis concludes that the major portion of apoA-I enters plasma by a fast pathway but the major fraction of apoA-I in plasma resides with a second slow pathway; further the study is suggestive of a precursor-product relationship between the two plasma apoA-I pools. The possible relevance of the latter suggestion to the aberrant kinetics of apoA-I in Tangier disease is discussed. The analysis of apoA-II data resulted in similar conclusions. A methodology for evaluating the dosimetry of radioiodinated apolipoproteins by

  17. A new approach to the compartmental analysis in pharmacokinetics: fractional time evolution of diclofenac.

    PubMed

    Popović, Jovan K; Atanacković, Milica T; Pilipović, Ana S; Rapaić, Milan R; Pilipović, Stevan; Atanacković, Teodor M

    2010-04-01

    This study presents a new two compartmental model and its application to the evaluation of diclofenac pharmacokinetics in a small number of healthy adults, during a bioequivalence trial. In the model the integer order derivatives are replaced by derivatives of real order often called fractional order derivatives. Physically that means that a history (memory) of a biological process, realized as a transfer from one compartment to another one with the mass balance conservation, is taken into account. This kind of investigations in pharmacokinetics is founded by Dokoumetzidis and Macheras through the one compartmental models while our contribution is the analysis of multi-dimensional compartmental models with the applications of the two compartmental model in evaluation of diclofenac pharmacokinetics. Two experiments were preformed with 12 healthy volunteers with two slow release 100 mg diclofenac tablet formulations. The agreement of the values predicted by the proposed model with the values obtained through experiments is shown to be good. Thus, pharmacokinetics of slow release diclofenac can be described well by a specific two compartmental model with fractional derivatives of the same order. Parameters in the model are determined by the least-squares method and the Particle Swarm Optimization (PSO) numerical procedure is used. The results show that the fractional order two compartmental model for diclofenac is superior in comparison to the classical two compartmental model. Actually this is true in general case since the classical one is a special case of the fractional one.

  18. Compartmentalized partnered replication for the directed evolution of genetic parts and circuits.

    PubMed

    Abil, Zhanar; Ellefson, Jared W; Gollihar, Jimmy D; Watkins, Ella; Ellington, Andrew D

    2017-12-01

    Compartmentalized partnered replication (CPR) is an emulsion-based directed evolution method based on a robust and modular phenotype-genotype linkage. In contrast to other in vivo directed evolution approaches, CPR largely mitigates host fitness effects due to a relatively short expression time of the gene of interest. CPR is based on gene circuits in which the selection of a 'partner' function from a library leads to the production of a thermostable polymerase. After library preparation, bacteria produce partner proteins that can potentially lead to enhancement of transcription, translation, gene regulation, and other aspects of cellular metabolism that reinforce thermostable polymerase production. Individual cells are then trapped in water-in-oil emulsion droplets in the presence of primers and dNTPs, followed by the recovery of the partner genes via emulsion PCR. In this step, droplets with cells expressing partner proteins that promote polymerase production will produce higher copy numbers of the improved partner gene. The resulting partner genes can subsequently be recloned for the next round of selection. Here, we present a step-by-step guideline for the procedure by providing examples of (i) selection of T7 RNA polymerases that recognize orthogonal promoters and (ii) selection of tRNA for enhanced amber codon suppression. A single round of CPR should take ∼3-5 d, whereas a whole directed evolution can be performed in 3-10 rounds, depending on selection efficiency.

  19. Shape control and compartmentalization in active colloidal cells

    PubMed Central

    Spellings, Matthew; Engel, Michael; Klotsa, Daphne; Sabrina, Syeda; Drews, Aaron M.; Nguyen, Nguyen H. P.; Bishop, Kyle J. M.; Glotzer, Sharon C.

    2015-01-01

    Small autonomous machines like biological cells or soft robots can convert energy input into control of function and form. It is desired that this behavior emerges spontaneously and can be easily switched over time. For this purpose we introduce an active matter system that is loosely inspired by biology and which we term an active colloidal cell. The active colloidal cell consists of a boundary and a fluid interior, both of which are built from identical rotating spinners whose activity creates convective flows. Similarly to biological cell motility, which is driven by cytoskeletal components spread throughout the entire volume of the cell, active colloidal cells are characterized by highly distributed energy conversion. We demonstrate that we can control the shape of the active colloidal cell and drive compartmentalization by varying the details of the boundary (hard vs. flexible) and the character of the spinners (passive vs. active). We report buckling of the boundary controlled by the pattern of boundary activity, as well as formation of core–shell and inverted Janus phase-separated configurations within the active cell interior. As the cell size is increased, the inverted Janus configuration spontaneously breaks its mirror symmetry. The result is a bubble–crescent configuration, which alternates between two degenerate states over time and exhibits collective migration of the fluid along the boundary. Our results are obtained using microscopic, non–momentum-conserving Langevin dynamics simulations and verified via a phase-field continuum model coupled to a Navier–Stokes equation. PMID:26253763

  20. Shape control and compartmentalization in active colloidal cells.

    PubMed

    Spellings, Matthew; Engel, Michael; Klotsa, Daphne; Sabrina, Syeda; Drews, Aaron M; Nguyen, Nguyen H P; Bishop, Kyle J M; Glotzer, Sharon C

    2015-08-25

    Small autonomous machines like biological cells or soft robots can convert energy input into control of function and form. It is desired that this behavior emerges spontaneously and can be easily switched over time. For this purpose we introduce an active matter system that is loosely inspired by biology and which we term an active colloidal cell. The active colloidal cell consists of a boundary and a fluid interior, both of which are built from identical rotating spinners whose activity creates convective flows. Similarly to biological cell motility, which is driven by cytoskeletal components spread throughout the entire volume of the cell, active colloidal cells are characterized by highly distributed energy conversion. We demonstrate that we can control the shape of the active colloidal cell and drive compartmentalization by varying the details of the boundary (hard vs. flexible) and the character of the spinners (passive vs. active). We report buckling of the boundary controlled by the pattern of boundary activity, as well as formation of core-shell and inverted Janus phase-separated configurations within the active cell interior. As the cell size is increased, the inverted Janus configuration spontaneously breaks its mirror symmetry. The result is a bubble-crescent configuration, which alternates between two degenerate states over time and exhibits collective migration of the fluid along the boundary. Our results are obtained using microscopic, non-momentum-conserving Langevin dynamics simulations and verified via a phase-field continuum model coupled to a Navier-Stokes equation.

  1. Nuclear Pore-Like Structures in a Compartmentalized Bacterium

    PubMed Central

    Sagulenko, Evgeny; Green, Kathryn; Yee, Benjamin; Morgan, Garry; Leis, Andrew; Lee, Kuo-Chang; Butler, Margaret K.; Chia, Nicholas; Pham, Uyen Thi Phuong; Lindgreen, Stinus; Catchpole, Ryan; Poole, Anthony M.; Fuerst, John A.

    2017-01-01

    Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence. PMID:28146565

  2. The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context.

    PubMed

    Cremer, T; Cremer, M; Cremer, C

    2018-04-01

    4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.

  3. Pathways and Subcellular Compartmentation of NAD Biosynthesis in Human Cells

    PubMed Central

    Nikiforov, Andrey; Dölle, Christian; Niere, Marc; Ziegler, Mathias

    2011-01-01

    NAD is a vital redox carrier, and its degradation is a key element of important regulatory pathways. NAD-mediated functions are compartmentalized and have to be fueled by specific biosynthetic routes. However, little is known about the different pathways, their subcellular distribution, and regulation in human cells. In particular, the route(s) to generate mitochondrial NAD, the largest subcellular pool, is still unknown. To visualize organellar NAD changes in cells, we targeted poly(ADP-ribose) polymerase activity into the mitochondrial matrix. This activity synthesized immunodetectable poly(ADP-ribose) depending on mitochondrial NAD availability. Based on this novel detector system, detailed subcellular enzyme localizations, and pharmacological inhibitors, we identified extracellular NAD precursors, their cytosolic conversions, and the pathway of mitochondrial NAD generation. Our results demonstrate that, besides nicotinamide and nicotinic acid, only the corresponding nucleosides readily enter the cells. Nucleotides (e.g. NAD and NMN) undergo extracellular degradation resulting in the formation of permeable precursors. These precursors can all be converted to cytosolic and mitochondrial NAD. For mitochondrial NAD synthesis, precursors are converted to NMN in the cytosol. When taken up into the organelles, NMN (together with ATP) serves as substrate of NMNAT3 to form NAD. NMNAT3 was conclusively localized to the mitochondrial matrix and is the only known enzyme of NAD synthesis residing within these organelles. We thus present a comprehensive dissection of mammalian NAD biosynthesis, the groundwork to understand regulation of NAD-mediated processes, and the organismal homeostasis of this fundamental molecule. PMID:21504897

  4. Adaptive and neuroadaptive control for nonnegative and compartmental dynamical systems

    NASA Astrophysics Data System (ADS)

    Volyanskyy, Kostyantyn Y.

    Neural networks have been extensively used for adaptive system identification as well as adaptive and neuroadaptive control of highly uncertain systems. The goal of adaptive and neuroadaptive control is to achieve system performance without excessive reliance on system models. To improve robustness and the speed of adaptation of adaptive and neuroadaptive controllers several controller architectures have been proposed in the literature. In this dissertation, we develop a new neuroadaptive control architecture for nonlinear uncertain dynamical systems. The proposed framework involves a novel controller architecture with additional terms in the update laws that are constructed using a moving window of the integrated system uncertainty. These terms can be used to identify the ideal system weights of the neural network as well as effectively suppress system uncertainty. Linear and nonlinear parameterizations of the system uncertainty are considered and state and output feedback neuroadaptive controllers are developed. Furthermore, we extend the developed framework to discrete-time dynamical systems. To illustrate the efficacy of the proposed approach we apply our results to an aircraft model with wing rock dynamics, a spacecraft model with unknown moment of inertia, and an unmanned combat aerial vehicle undergoing actuator failures, and compare our results with standard neuroadaptive control methods. Nonnegative systems are essential in capturing the behavior of a wide range of dynamical systems involving dynamic states whose values are nonnegative. A sub-class of nonnegative dynamical systems are compartmental systems. These systems are derived from mass and energy balance considerations and are comprised of homogeneous interconnected microscopic subsystems or compartments which exchange variable quantities of material via intercompartmental flow laws. In this dissertation, we develop direct adaptive and neuroadaptive control framework for stabilization, disturbance

  5. Rift Valley fever trasmission dynamics described by compartmental models.

    PubMed

    Danzetta, Maria Luisa; Bruno, Rossana; Sauro, Francesca; Savini, Lara; Calistri, Paolo

    2016-11-01

    Rift Valley fever (RVF) is one of the most important zoonotic Transboundary Animal Diseases able to cross international borders and cause devastating effect on animal health and food security. Climate changes and the presence of competent vectors in the most of the current RVF-free temperate countries strongly support the inclusion of RVF virus (RVFV) among the most significant emerging viral threats for public and animal health. The transmission of RVFV is driven by complex eco-climatic factors making the epidemiology of RVF infection difficult to study and to understand. Mathematical, statistical and spatial models are often used to explain the mechanisms underlying these biological processes, providing new and effective tools to plan measures for public health protection. In this paper we performed a systematic literature review on RVF published papers with the aim of identifying and describing the most recent papers developing compartmental models for the study of RVFV transmission dynamics. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Metabolic Compartmentation – A System Level Property of Muscle Cells

    PubMed Central

    Saks, Valdur; Beraud, Nathalie; Wallimann, Theo

    2008-01-01

    Problems of quantitative investigation of intracellular diffusion and compartmentation of metabolites are analyzed. Principal controversies in recently published analyses of these problems for the living cells are discussed. It is shown that the formal theoretical analysis of diffusion of metabolites based on Fick's equation and using fixed diffusion coefficients for diluted homogenous aqueous solutions, but applied for biological systems in vivo without any comparison with experimental results, may lead to misleading conclusions, which are contradictory to most biological observations. However, if the same theoretical methods are used for analysis of actual experimental data, the apparent diffusion constants obtained are orders of magnitude lower than those in diluted aqueous solutions. Thus, it can be concluded that local restrictions of diffusion of metabolites in a cell are a system-level properties caused by complex structural organization of the cells, macromolecular crowding, cytoskeletal networks and organization of metabolic pathways into multienzyme complexes and metabolons. This results in microcompartmentation of metabolites, their channeling between enzymes and in modular organization of cellular metabolic networks. The perspectives of further studies of these complex intracellular interactions in the framework of Systems Biology are discussed. PMID:19325782

  7. Compartmental transport model of microbicide delivery by an intravaginal ring

    PubMed Central

    Geonnotti, Anthony R.; Katz, David F.

    2010-01-01

    Topical antimicrobials, or microbicides, are being developed to prevent HIV transmission through local, mucosal delivery of antiviral compounds. While hydrogel vehicles deliver the majority of current microbicide products, intravaginal rings (IVRs) are an alternative microbicide modality in preclinical development. IVRs provide a long-term dosing alternative to hydrogel use, and might provide improved user adherence. IVR efficacy requires sustained delivery of antiviral compounds to the entire vaginal compartment. A two-dimensional, compartmental vaginal drug transport model was created to evaluate the delivery of drugs from an intravaginal ring. The model utilized MRI-derived ring geometry and location, experimentally defined ring fluxes and vaginal fluid velocities, and biophysically relevant transport theory. Model outputs indicated the presence of potentially inhibitory concentrations of antiviral compounds along the entire vaginal canal within 24 hours following IVR insertion. Distributions of inhibitory concentrations of antiviral compounds were substantially influenced by vaginal fluid flow and production, while showing little change due to changes in diffusion coefficients or ring fluxes. Additionally, model results were predictive of in vivo concentrations obtained in clinical trials. Overall, this analysis initiates a mechanistic computational framework, heretofore missing, to understand and evaluate the potential of IVRs for effective delivery of antiviral compounds. PMID:20222027

  8. Compartmentalization - A Prerequisite for Maintaining and Changing an Identity.

    PubMed

    Rottmann, Philipp; Ward, Thomas; Panke, Sven

    2016-01-01

    The chemical manipulation of DNA is much more convenient than the manipulation of the bioproducts, such as enzymes, that it encodes. The optimization of bioproducts requires cycles of diversification of DNA followed by read-out of the information into the bioproduct. Maintaining the link between the information - the genotype - and the properties of the bioproduct - the phenotype - through some form of compartmentalization is therefore an essential aspect in directed evolution. While the ideal compartment is a biological cell, many projects involving more radical changes in the bioproduct, such as the introduction of novel cofactors, may not be suitable for expression of the information in cells, and alternative in vitro methods have to be applied. Consequently, the possibility to produce simple and advanced micro compartments at high rates and to combine them with the ability to translate the information into proteins represents a unique opportunity to explore demanding enzyme engineering projects that require the evaluation of at least hundreds of thousands of enzyme variants over multiple generations.

  9. Transit times and mean ages for nonautonomous and autonomous compartmental systems

    DOE PAGES

    Rasmussen, Martin; Hastings, Alan; Smith, Matthew J.; ...

    2016-04-01

    In this study, we develop a theory for transit times and mean ages for nonautonomous compartmental systems. Using the McKendrick–von Förster equation, we show that the mean ages of mass in a compartmental system satisfy a linear nonautonomous ordinary differential equation that is exponentially stable. We then define a nonautonomous version of transit time as the mean age of mass leaving the compartmental system at a particular time and show that our nonautonomous theory generalises the autonomous case. We apply these results to study a nine-dimensional nonautonomous compartmental system modeling the terrestrial carbon cycle, which is a modification of themore » Carnegie–Ames–Stanford approach model, and we demonstrate that the nonautonomous versions of transit time and mean age differ significantly from the autonomous quantities when calculated for that model.« less

  10. Bidirectionality and compartmentation of metabolic fluxes are revealed in the dynamics of isotopomer networks.

    PubMed

    Schryer, David W; Peterson, Pearu; Paalme, Toomas; Vendelin, Marko

    2009-04-17

    Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prerequisite for the intelligent design of genetically modified organisms able to realize their potential of revolutionizing food, energy, and pharmaceutical production. We describe techniques to explore the bidirectionality and compartmentalization of metabolic fluxes using information contained in the isotopic transient, and discuss the integration of kinetic models with MFA. The flux parameters of an example metabolic network were optimized to examine the compartmentalization of metabolites and and the bidirectionality of fluxes in the TCA cycle of Saccharomyces uvarum for steady-state respiratory growth.

  11. MULTIMEDIA ENVIRONMENTAL DISTRIBUTION OF TOXICS (MEND-TOX): PART I, HYBRID COMPARTMENTAL-SPATIAL MODELING FRAMEWORK

    EPA Science Inventory

    An integrated hybrid spatial-compartmental modeling approach is presented for analyzing the dynamic distribution of chemicals in the multimedia environment. Information obtained from such analysis, which includes temporal chemical concentration profiles in various media, mass ...

  12. Efficient Vaccine Distribution Based on a Hybrid Compartmental Model.

    PubMed

    Yu, Zhiwen; Liu, Jiming; Wang, Xiaowei; Zhu, Xianjun; Wang, Daxing; Han, Guoqiang

    2016-01-01

    To effectively and efficiently reduce the morbidity and mortality that may be caused by outbreaks of emerging infectious diseases, it is very important for public health agencies to make informed decisions for controlling the spread of the disease. Such decisions must incorporate various kinds of intervention strategies, such as vaccinations, school closures and border restrictions. Recently, researchers have paid increased attention to searching for effective vaccine distribution strategies for reducing the effects of pandemic outbreaks when resources are limited. Most of the existing research work has been focused on how to design an effective age-structured epidemic model and to select a suitable vaccine distribution strategy to prevent the propagation of an infectious virus. Models that evaluate age structure effects are common, but models that additionally evaluate geographical effects are less common. In this paper, we propose a new SEIR (susceptible-exposed-infectious šC recovered) model, named the hybrid SEIR-V model (HSEIR-V), which considers not only the dynamics of infection prevalence in several age-specific host populations, but also seeks to characterize the dynamics by which a virus spreads in various geographic districts. Several vaccination strategies such as different kinds of vaccine coverage, different vaccine releasing times and different vaccine deployment methods are incorporated into the HSEIR-V compartmental model. We also design four hybrid vaccination distribution strategies (based on population size, contact pattern matrix, infection rate and infectious risk) for controlling the spread of viral infections. Based on data from the 2009-2010 H1N1 influenza epidemic, we evaluate the effectiveness of our proposed HSEIR-V model and study the effects of different types of human behaviour in responding to epidemics.

  13. Efficient Vaccine Distribution Based on a Hybrid Compartmental Model

    PubMed Central

    Yu, Zhiwen; Liu, Jiming; Wang, Xiaowei; Zhu, Xianjun; Wang, Daxing; Han, Guoqiang

    2016-01-01

    To effectively and efficiently reduce the morbidity and mortality that may be caused by outbreaks of emerging infectious diseases, it is very important for public health agencies to make informed decisions for controlling the spread of the disease. Such decisions must incorporate various kinds of intervention strategies, such as vaccinations, school closures and border restrictions. Recently, researchers have paid increased attention to searching for effective vaccine distribution strategies for reducing the effects of pandemic outbreaks when resources are limited. Most of the existing research work has been focused on how to design an effective age-structured epidemic model and to select a suitable vaccine distribution strategy to prevent the propagation of an infectious virus. Models that evaluate age structure effects are common, but models that additionally evaluate geographical effects are less common. In this paper, we propose a new SEIR (susceptible—exposed—infectious šC recovered) model, named the hybrid SEIR-V model (HSEIR-V), which considers not only the dynamics of infection prevalence in several age-specific host populations, but also seeks to characterize the dynamics by which a virus spreads in various geographic districts. Several vaccination strategies such as different kinds of vaccine coverage, different vaccine releasing times and different vaccine deployment methods are incorporated into the HSEIR-V compartmental model. We also design four hybrid vaccination distribution strategies (based on population size, contact pattern matrix, infection rate and infectious risk) for controlling the spread of viral infections. Based on data from the 2009–2010 H1N1 influenza epidemic, we evaluate the effectiveness of our proposed HSEIR-V model and study the effects of different types of human behaviour in responding to epidemics. PMID:27233015

  14. The compartmentation of phosphorylated thiamine derivatives in cultured neuroblastoma cells.

    PubMed

    Bettendorff, L

    1994-05-26

    Thiamine transport in cultured neuroblastoma cells is mediated by a high-affinity carrier (KM = 40 nM). In contrast, the uptake of the more hydrophobic sulbutiamine (isobutyrylthiamine disulfide) is unsaturable and its initial transport rate is 20-times faster than for thiamine. In the cytoplasm, sulbutiamine is rapidly hydrolyzed and reduced to free thiamine, the overall process resulting in a rapid and concentrative thiamine accumulation. Incorporation of radioactivity from [14C]thiamine or [14C]sulbutiamine into intracellular thiamine diphosphate is slow in both cases. Despite the fact that the diphosphate is probably the direct precursor for both thiamine monophosphate and triphosphate, the specific radioactivity increased much faster for the latter two compounds than for thiamine diphosphate. This suggests the existence of two pools of thiamine diphosphate, the larger one having a very slow turnover (about 17 h); a much smaller, rapidly turning over pool would be the precursor of thiamine mono- and triphosphate. The turnover time for thiamine triphosphate could be estimated to be 1-2 h. When preloading the cells with [14C]sulbutiamine was followed by a chase with the same concentration of the unlabeled compound, the specific radioactivities of thiamine and thiamine monophosphate decreased exponentially as expected, but labeling of the diphosphate continued to increase slowly. Specific radioactivity of thiamine triphosphate increased first, but after 30 min it began to slowly decrease. These results show for the first time the existence of distinct thiamine diphosphate pools in the same homogeneous cell population. They also suggest a complex compartmentation of thiamine metabolism.

  15. Shape control and compartmentalization in active colloidal cells

    DOE PAGES

    Spellings, Matthew; Engel, Michael; Klotsa, Daphne; ...

    2015-08-07

    Small autonomous machines like biological cells or soft robots can convert energy input into control of function and form. It is desired that this behavior emerges spontaneously and can be easily switched over time. For this purpose, in this paper we introduce an active matter system that is loosely inspired by biology and which we term an active colloidal cell. The active colloidal cell consists of a boundary and a fluid interior, both of which are built from identical rotating spinners whose activity creates convective flows. Similarly to biological cell motility, which is driven by cytoskeletal components spread throughout themore » entire volume of the cell, active colloidal cells are characterized by highly distributed energy conversion. We demonstrate that we can control the shape of the active colloidal cell and drive compartmentalization by varying the details of the boundary (hard vs. flexible) and the character of the spinners (passive vs. active). We report buckling of the boundary controlled by the pattern of boundary activity, as well as formation of core–shell and inverted Janus phase-separated configurations within the active cell interior. As the cell size is increased, the inverted Janus configuration spontaneously breaks its mirror symmetry. The result is a bubble–crescent configuration, which alternates between two degenerate states over time and exhibits collective migration of the fluid along the boundary. Finally, our results are obtained using microscopic, non–momentum-conserving Langevin dynamics simulations and verified via a phase-field continuum model coupled to a Navier–Stokes equation.« less

  16. Radical pathway in catecholase activity with zinc-based model complexes of compartmental ligands.

    PubMed

    Guha, Averi; Chattopadhyay, Tanmay; Paul, Nanda Dulal; Mukherjee, Madhuparna; Goswami, Somen; Mondal, Tapan Kumar; Zangrando, Ennio; Das, Debasis

    2012-08-20

    Four dinuclear and three mononuclear Zn(II) complexes of phenol-based compartmental ligands (HL(1)-HL(7)) have been synthesized with the aim to investigate the viability of a radical pathway in catecholase activity. The complexes have been characterized by routine physicochemical studies as well as X-ray single-crystal structure analysis: [Zn(2)(H(2)L(1))(OH)(H(2)O)(NO(3))](NO(3))(3) (1), [Zn(2)L(2)Cl(3)] (2), [Zn(2)L(3)Cl(3)] (3), [Zn(2)(L(4))(2)(CH(3)COO)(2)] (4), [Zn(HL(5))Cl(2)] (5), [Zn(HL(6))Cl(2)] (6), and [Zn(HL(7))Cl(2)] (7) [L(1)-L(3) and L(5)-L(7) = 2,6-bis(R-iminomethyl)-4-methylphenolato, where R= N-ethylpiperazine for L(1), R = 2-(N-ethyl)pyridine for L(2), R = N-ethylpyrrolidine for L(3), R = N-methylbenzene for L(5), R = 2-(N-methyl)thiophene for L(6), R = 2-(N-ethyl)thiophene for L(7), and L(4) = 2-formyl-4-methyl-6-N-methylbenzene-iminomethyl-phenolato]. Catecholase-like activity of the complexes has been investigated in methanol medium by UV-vis spectrophotometric study using 3,5-di-tert-butylcatechol as model substrate. All complexes are highly active in catalyzing the aerobic oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) to 3,5-di-tert-butylbenzoquinone (3,5-DTBQ). Conversion of 3,5-DTBC to 3,5-DTBQ catalyzed by mononuclear complexes (5-7) is observed to proceed via formation of two enzyme-substrate adducts, ES1 and ES2, detected spectroscopically, a finding reported for the first time in any Zn(II) complex catalyzed oxidation of catechol. On the other hand, no such enzyme-substrate adduct has been identified, and 3,5-DTBC to 3,5-DTBQ conversion is observed to be catalyzed by the dinuclear complexes (1-4) very smoothly. EPR experiment suggests generation of radicals in the presence of 3,5-DTBC, and that finding has been strengthened by cyclic voltammetric study. Thus, it may be proposed that the radical pathway is probably responsible for conversion of 3,5-DTBC to 3,5-DTBQ promoted by complexes of redox-innocent Zn(II) ion. The ligand

  17. Global identifiability of linear compartmental models--a computer algebra algorithm.

    PubMed

    Audoly, S; D'Angiò, L; Saccomani, M P; Cobelli, C

    1998-01-01

    A priori global identifiability deals with the uniqueness of the solution for the unknown parameters of a model and is, thus, a prerequisite for parameter estimation of biological dynamic models. Global identifiability is however difficult to test, since it requires solving a system of algebraic nonlinear equations which increases both in nonlinearity degree and number of terms and unknowns with increasing model order. In this paper, a computer algebra tool, GLOBI (GLOBal Identifiability) is presented, which combines the topological transfer function method with the Buchberger algorithm, to test global identifiability of linear compartmental models. GLOBI allows for the automatic testing of a priori global identifiability of general structure compartmental models from general multi input-multi output experiments. Examples of usage of GLOBI to analyze a priori global identifiability of some complex biological compartmental models are provided.

  18. Co-Compartmentation of Terpene Biosynthesis and Storage via Synthetic Droplet.

    PubMed

    Zhao, Cheng; Kim, YongKyoung; Zeng, Yining; Li, Man; Wang, Xin; Hu, Cheng; Gorman, Connor; Dai, Susie Y; Ding, Shi-You; Yuan, Joshua S

    2018-03-16

    Traditional bioproduct engineering focuses on pathway optimization, yet is often complicated by product inhibition, downstream consumption, and the toxicity of certain products. Here, we present the co-compartmentation of biosynthesis and storage via a synthetic droplet as an effective new strategy to improve the bioproduct yield, with squalene as a model compound. A hydrophobic protein was designed and introduced into the tobacco chloroplast to generate a synthetic droplet for terpene storage. Simultaneously, squalene biosynthesis enzymes were introduced to chloroplasts together with the droplet-forming protein to co-compartmentalize the biosynthesis and storage of squalene. The strategy has enabled a record yield of squalene at 2.6 mg/g fresh weight without compromising plant growth. Confocal fluorescent microscopy imaging, stimulated Raman scattering microscopy, and droplet composition analysis confirmed the formation of synthetic storage droplet in chloroplast. The co-compartmentation of synthetic storage droplet with a targeted metabolic pathway engineering represents a new strategy for enhancing bioproduct yield.

  19. Subcellular compartmentalization of Cd and Zn in two bivalves. II. Significance of trophically available metal (TAM)

    Wallace, W.G.; Luoma, S.N.

    2003-01-01

    This paper examines how the subcellular partitioning of Cd and Zn in the bivalves Macoma balthica and Potamocorbula amurensis may affect the trophic transfer of metal to predators. Results show that the partitioning of metals to organelles, 'enzymes' and metallothioneins (MT) comprise a subcellular compartment containing trophically available metal (TAM; i.e. metal trophically available to predators), and that because this partitioning varies with species, animal size and metal, TAM is similarly influenced. Clams from San Francisco Bay, California, were exposed for 14 d to 3.5 ??g 1-1 Cd and 20.5 ??g 1-1 Zn, including 109Cd and 65Zn as radiotracers, and were used in feeding experiments with grass shrimp Palaemon macrodatylus, or used to investigate the subcellular partitioning of metal. Grass shrimp fed Cd-contaminated P. amurensis absorbed ???60% of ingested Cd, which was in accordance with the partitioning of Cd to the bivalve's TAM compartment (i.e. Cd associated with organelles, 'enzymes' and MT); a similar relationship was found in previous studies with grass shrimp fed Cd-contaminated oligochaetes. Thus, TAM may be used as a tool to predict the trophic transfer of at least Cd. Subcellular fractionation revealed that ???34% of both the Cd and Zn accumulated by M. balthica was associated with TAM, while partitioning to TAM in P. amurensis was metal-dependent (???60% for TAM-Cd%, ???73% for TAM-Zn%). The greater TAM-Cd% of P. amurensis than M. balthica is due to preferential binding of Cd to MT and 'enzymes', while enhanced TAM-Zn% of P. amurensis results from a greater binding of Zn to organelles. TAM for most species-metal combinations was size-dependent, decreasing with increased clam size. Based on field data, it is estimated that of the 2 bivalves, P. amurensis poses the greater threat of Cd exposure to predators because of higher tissue concentrations and greater partitioning as TAM; exposure of Zn to predators would be similar between these species.

  20. Krebs cycle metabolon formation: metabolite concentration gradient enhanced compartmentation of sequential enzymes.

    PubMed

    Wu, Fei; Pelster, Lindsey N; Minteer, Shelley D

    2015-01-25

    Dynamics of metabolon formation in mitochondria was probed by studying diffusional motion of two sequential Krebs cycle enzymes in a microfluidic channel. Enhanced directional co-diffusion of both enzymes against a substrate concentration gradient was observed in the presence of intermediate generation. This reveals a metabolite directed compartmentation of metabolic pathways.

  1. Macroanatomy and compartmentalization of recent fire scars in three North American conifers

    Kevin T. Smith; Estelle Arbellay; Donald A. Falk; Elaine Kennedy Sutherland

    2016-01-01

    Fire scars are initiated by cambial necrosis caused by localized lethal heating of the tree stem. Scars develop as part of the linked survival processes of compartmentalization and wound closure. The position of scars within dated tree ring series is the basis for dendrochronological reconstruction of fire history. Macroanatomical features were described for western...

  2. Sustainability of a Compartmentalized Host-Parasite Replicator System under Periodic Washout-Mixing Cycles

    PubMed Central

    Furubayashi, Taro

    2018-01-01

    The emergence and dominance of parasitic replicators are among the major hurdles for the proliferation of primitive replicators. Compartmentalization of replicators is proposed to relieve the parasite dominance; however, it remains unclear under what conditions simple compartmentalization uncoupled with internal reaction secures the long-term survival of a population of primitive replicators against incessant parasite emergence. Here, we investigate the sustainability of a compartmentalized host-parasite replicator (CHPR) system undergoing periodic washout-mixing cycles, by constructing a mathematical model and performing extensive simulations. We describe sustainable landscapes of the CHPR system in the parameter space and elucidate the mechanism of phase transitions between sustainable and extinct regions. Our findings revealed that a large population size of compartments, a high mixing intensity, and a modest amount of nutrients are important factors for the robust survival of replicators. We also found two distinctive sustainable phases with different mixing intensities. These results suggest that a population of simple host–parasite replicators assumed before the origin of life can be sustained by a simple compartmentalization with periodic washout-mixing processes. PMID:29373536

  3. Compartmentalization: a conceptual framework for understanding how trees grow and defend themselves

    Alex L. Shigo

    1984-01-01

    The purpose of this chapter is to describe a conceptual framework for understanding how trees grow and how they and other perennial plants defend themselves. The concept of compartmentalization has developed over many years, a synthesis of ideas from a number of investigators. It is derived from detailed studies of the gross morphology and cellular anatomy of the wood...

  4. Meningoencephalitis and Compartmentalization of the Cerebral Ventricles Caused by Enterobacter sakazakii

    PubMed Central

    Kleiman, Martin B.; Allen, Stephen D.; Neal, Patricia; Reynolds, Janet

    1981-01-01

    A necrotizing meningoencephalitis complicated by ventricular compartmentalization and abscess formation caused by Enterobacter sakazakii in a previously healthy 5-week-old female is described. A detailed description of the isolate is presented. This communication firmly establishes the pathogenicity of E. sakazakii. PMID:7287892

  5. SYNCHROTRON X-RAY ABSORPTION-EDGE COMPUTED MICROTOMOGRAPHY IMAGING OF THALLIUM COMPARTMENTALIZATION IN IBERIS INTERMEDIA

    EPA Science Inventory

    Thallium (TI) is an extremely toxic metal which, due to its similarities to K, is readily taken up by plants. Thallium is efficiently hyperaccumulated in Iberis intermedia as TI(I). Distribution and compartmentalization of TI in I. intermedia is highes...

  6. Beyond Compartmentalization: A Relational Approach towards Agency and Vulnerability of Young Migrants

    ERIC Educational Resources Information Center

    Huijsmans, Roy

    2012-01-01

    Based on fieldwork material from Lao People's Democratic Republic, this paper introduces an analytical framework that transcends compartmentalized approaches towards migration involving young people. The notions of fluid and institutionalized forms of migration illuminate key differences and commonalities in the relational fabric underpinning…

  7. A Compartmentalized Out-of-Equilibrium Enzymatic Reaction Network for Sustained Autonomous Movement

    PubMed Central

    2016-01-01

    Every living cell is a compartmentalized out-of-equilibrium system exquisitely able to convert chemical energy into function. In order to maintain homeostasis, the flux of metabolites is tightly controlled by regulatory enzymatic networks. A crucial prerequisite for the development of lifelike materials is the construction of synthetic systems with compartmentalized reaction networks that maintain out-of-equilibrium function. Here, we aim for autonomous movement as an example of the conversion of feedstock molecules into function. The flux of the conversion is regulated by a rationally designed enzymatic reaction network with multiple feedforward loops. By compartmentalizing the network into bowl-shaped nanocapsules the output of the network is harvested as kinetic energy. The entire system shows sustained and tunable microscopic motion resulting from the conversion of multiple external substrates. The successful compartmentalization of an out-of-equilibrium reaction network is a major first step in harnessing the design principles of life for construction of adaptive and internally regulated lifelike systems. PMID:27924313

  8. Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis

    PubMed Central

    Poupin, Nathalie; Mariotti, François; Huneau, Jean-François; Hermier, Dominique; Fouillet, Hélène

    2014-01-01

    Body tissues are generally 15N-enriched over the diet, with a discrimination factor (Δ15N) that varies among tissues and individuals as a function of their nutritional and physiopathological condition. However, both 15N bioaccumulation and intra- and inter-individual Δ15N variations are still poorly understood, so that theoretical models are required to understand their underlying mechanisms. Using experimental Δ15N measurements in rats, we developed a multi-compartmental model that provides the first detailed representation of the complex functioning of the body's Δ15N system, by explicitly linking the sizes and Δ15N values of 21 nitrogen pools to the rates and isotope effects of 49 nitrogen metabolic fluxes. We have shown that (i) besides urea production, several metabolic pathways (e.g., protein synthesis, amino acid intracellular metabolism, urea recycling and intestinal absorption or secretion) are most probably associated with isotope fractionation and together contribute to 15N accumulation in tissues, (ii) the Δ15N of a tissue at steady-state is not affected by variations of its P turnover rate, but can vary according to the relative orientation of tissue free amino acids towards oxidation vs. protein synthesis, (iii) at the whole-body level, Δ15N variations result from variations in the body partitioning of nitrogen fluxes (e.g., urea production, urea recycling and amino acid exchanges), with or without changes in nitrogen balance, (iv) any deviation from the optimal amino acid intake, in terms of both quality and quantity, causes a global rise in tissue Δ15N, and (v) Δ15N variations differ between tissues depending on the metabolic changes involved, which can therefore be identified using simultaneous multi-tissue Δ15N measurements. This work provides proof of concept that Δ15N measurements constitute a new promising tool to investigate how metabolic fluxes are nutritionally or physiopathologically reorganized or altered. The existence of such

  9. PET-based compartmental modeling of (124)I-A33 antibody: quantitative characterization of patient-specific tumor targeting in colorectal cancer.

    PubMed

    Zanzonico, Pat; Carrasquillo, Jorge A; Pandit-Taskar, Neeta; O'Donoghue, Joseph A; Humm, John L; Smith-Jones, Peter; Ruan, Shutian; Divgi, Chaitanya; Scott, Andrew M; Kemeny, Nancy E; Fong, Yuman; Wong, Douglas; Scheinberg, David; Ritter, Gerd; Jungbluth, Achem; Old, Lloyd J; Larson, Steven M

    2015-10-01

    The molecular specificity of monoclonal antibodies (mAbs) directed against tumor antigens has proven effective for targeted therapy of human cancers, as shown by a growing list of successful antibody-based drug products. We describe a novel, nonlinear compartmental model using PET-derived data to determine the "best-fit" parameters and model-derived quantities for optimizing biodistribution of intravenously injected (124)I-labeled antitumor antibodies. As an example of this paradigm, quantitative image and kinetic analyses of anti-A33 humanized mAb (also known as "A33") were performed in 11 colorectal cancer patients. Serial whole-body PET scans of (124)I-labeled A33 and blood samples were acquired and the resulting tissue time-activity data for each patient were fit to a nonlinear compartmental model using the SAAM II computer code. Excellent agreement was observed between fitted and measured parameters of tumor uptake, "off-target" uptake in bowel mucosa, blood clearance, tumor antigen levels, and percent antigen occupancy. This approach should be generally applicable to antibody-antigen systems in human tumors for which the masses of antigen-expressing tumor and of normal tissues can be estimated and for which antibody kinetics can be measured with PET. Ultimately, based on each patient's resulting "best-fit" nonlinear model, a patient-specific optimum mAb dose (in micromoles, for example) may be derived.

  10. The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers

    PubMed Central

    Weyland, Mathias S.; Fellermann, Harold; Hadorn, Maik; Sorek, Daniel; Lancet, Doron; Rasmussen, Steen; Füchslin, Rudolf M.

    2013-01-01

    We propose an automaton, a theoretical framework that demonstrates how to improve the yield of the synthesis of branched chemical polymer reactions. This is achieved by separating substeps of the path of synthesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of fixed successive compartments. We describe the automaton in mathematical terms and show how it can be configured automatically in order to synthesize a given branched polymer target. The algorithm we present finds an optimal path of synthesis in linear time. We discuss how the automaton models compartmentalized structures found in cells, such as the endoplasmic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers such as oligosaccharides. Lastly, we show examples of artificial branched polymers and discuss how the automaton can be configured to synthesize them with maximal yield. PMID:24489601

  11. Self-priming compartmentalization digital LAMP for point-of-care.

    PubMed

    Zhu, Qiangyuan; Gao, Yibo; Yu, Bingwen; Ren, Hao; Qiu, Lin; Han, Sihai; Jin, Wei; Jin, Qinhan; Mu, Ying

    2012-11-21

    Digital nucleic acid amplification provides unprecedented opportunities for absolute nucleic acid quantification by counting of single molecules. This technique is useful for molecular genetic analysis in cancer, stem cell, bacterial, non-invasive prenatal diagnosis in which many biologists are interested. This paper describes a self-priming compartmentalization (SPC) microfluidic chip platform for performing digital loop-mediated amplification (LAMP). The energy for the pumping is pre-stored in the degassed bulk PDMS by exploiting the high gas solubility of PDMS; therefore, no additional structures other than channels and reservoirs are required. The sample and oil are sequentially sucked into the channels, and the pressure difference of gas dissolved in PDMS allows sample self-compartmentalization without the need for further chip manipulation such as with pneumatic microvalves and control systems, and so on. The SPC digital LAMP chip can be used like a 384-well plate, so, the world-to-chip fluidic interconnections are avoided. The microfluidic chip contains 4 separate panels, each panel contains 1200 independent 6 nL chambers and can be used to detect 4 samples simultaneously. Digital LAMP on the microfluidic chip was tested quantitatively by using β-actin DNA from humans. The self-priming compartmentalization behavior is roughly predictable using a two-dimensional model. The uniformity of compartmentalization was analyzed by fluorescent intensity and fraction of volume. The results showed that the feasibility and flexibility of the microfluidic chip platform for amplifying single nucleic acid molecules in different chambers made by diluting and distributing sample solutions. The SPC chip has the potential to meet the requirements of a general laboratory: power-free, valve-free, operating at isothermal temperature, inexpensive, sensitive, economizing labour time and reagents. The disposable analytical devices with appropriate air-tight packaging should be

  12. A compartmentalized solute transport model for redox zones in contaminated aquifers: 1. Theory and development

    Abrams , Robert H.; Loague, Keith

    2000-01-01

    This paper, the first of two parts [see Abrams and Loague, this issue], takes the compartmentalized approach for the geochemical evolution of redox zones presented by Abrams et al. [1998] and embeds it within a solute transport framework. In this paper the compartmentalized approach is generalized to facilitate the description of its incorporation into a solute transport simulator. An equivalent formulation is developed which removes any discontinuities that may occur when switching compartments. Rate‐limited redox reactions are modeled with a modified Monod relationship that allows either the organic substrate or the electron acceptor to be the rate‐limiting reactant. Thermodynamic constraints are used to inhibit lower‐energy redox reactions from occurring under infeasible geochemical conditions without imposing equilibrium on the lower‐energy reactions. The procedure used allows any redox reaction to be simulated as being kinetically limited or thermodynamically limited, depending on local geochemical conditions. Empirical reaction inhibition methods are not needed. The sequential iteration approach (SIA), a technique which allows the number of solute transport equations to be reduced, is adopted to solve the coupled geochemical/solute transport problem. When the compartmentalized approach is embedded within the SIA, with the total analytical concentration of each component as the dependent variable in the transport equation, it is possible to reduce the number of transport equations even further than with the unmodified SIA. A one‐dimensional, coupled geochemical/solute transport simulation is presented in which redox zones evolve dynamically in time and space. The compartmentalized solute transport (COMPTRAN) model described in this paper enables the development of redox zones to be simulated under both kinetic and thermodynamic constraints. The modular design of COMPTRAN facilitates the use of many different, preexisting solute transport and

  13. Aspects of astrocyte energy metabolism, amino acid neurotransmitter homoeostasis and metabolic compartmentation

    PubMed Central

    Kreft, Marko; Bak, Lasse K; Waagepetersen, Helle S; Schousboe, Arne

    2012-01-01

    Astrocytes are key players in brain function; they are intimately involved in neuronal signalling processes and their metabolism is tightly coupled to that of neurons. In the present review, we will be concerned with a discussion of aspects of astrocyte metabolism, including energy-generating pathways and amino acid homoeostasis. A discussion of the impact that uptake of neurotransmitter glutamate may have on these pathways is included along with a section on metabolic compartmentation. PMID:22435484

  14. Repurposing the Saccharomyces cerevisiae peroxisome for compartmentalizing multi-enzyme pathways

    SciT

    DeLoache, William; Russ, Zachary; Samson, Jennifer

    The peroxisome of Saccharomyces cerevisiae was targeted for repurposing in order to create a synthetic organelle that provides a generalizable compartment for engineered metabolic pathways. Compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk, improving pathway efficiency, and ultimately modifying the chemical environment to be distinct from that of the cytoplasm. We focused on the Saccharomyces cerevisiae peroxisome, as this organelle is not required for viability when grown on conventional media. We identified an enhanced peroxisomal targeting signal type 1 (PTS1) for rapidly importing non-native cargo proteins. Additionally, we performed the first systematic in vivo measurementsmore » of nonspecific metabolite permeability across the peroxisomal membrane using a polymer exclusion assay and characterized the size dependency of metabolite trafficking. Finally, we applied these new insights to compartmentalize a two-enzyme pathway in the peroxisome and characterize the expression regimes where compartmentalization leads to improved product titer. This work builds a foundation for using the peroxisome as a synthetic organelle, highlighting both promise and future challenges on the way to realizing this goal.« less

  15. Co-Compartmentation of Terpene Biosynthesis and Storage via Synthetic Droplet

    SciT

    Zhao, Cheng; Kim, YongKyoung; Zeng, Yining

    Traditional bioproduct engineering focuses on pathway optimization, yet is often complicated by product inhibition, downstream consumption, and the toxicity of certain products. Here, we present the co-compartmentation of biosynthesis and storage via a synthetic droplet as an effective new strategy to improve the bioproduct yield, with squalene as a model compound. A hydrophobic protein was designed and introduced into the tobacco chloroplast to generate a synthetic droplet for terpene storage. Simultaneously, squalene biosynthesis enzymes were introduced to chloroplasts together with the droplet-forming protein to co-compartmentalize the biosynthesis and storage of squalene. The strategy has enabled a record yield of squalenemore » at 2.6 mg/g fresh weight without compromising plant growth. Confocal fluorescent microscopy imaging, stimulated Raman scattering microscopy, and droplet composition analysis confirmed the formation of synthetic storage droplet in chloroplast. The co-compartmentation of synthetic storage droplet with a targeted metabolic pathway engineering represents a new strategy for enhancing bioproduct yield.« less

  16. Co-Compartmentation of Terpene Biosynthesis and Storage via Synthetic Droplet

    DOE PAGES

    Zhao, Cheng; Kim, YongKyoung; Zeng, Yining; ...

    2018-02-13

    Traditional bioproduct engineering focuses on pathway optimization, yet is often complicated by product inhibition, downstream consumption, and the toxicity of certain products. Here, we present the co-compartmentation of biosynthesis and storage via a synthetic droplet as an effective new strategy to improve the bioproduct yield, with squalene as a model compound. A hydrophobic protein was designed and introduced into the tobacco chloroplast to generate a synthetic droplet for terpene storage. Simultaneously, squalene biosynthesis enzymes were introduced to chloroplasts together with the droplet-forming protein to co-compartmentalize the biosynthesis and storage of squalene. The strategy has enabled a record yield of squalenemore » at 2.6 mg/g fresh weight without compromising plant growth. Confocal fluorescent microscopy imaging, stimulated Raman scattering microscopy, and droplet composition analysis confirmed the formation of synthetic storage droplet in chloroplast. The co-compartmentation of synthetic storage droplet with a targeted metabolic pathway engineering represents a new strategy for enhancing bioproduct yield.« less

  17. The mechanics of cellular compartmentalization as a model for tumor spreading

    NASA Astrophysics Data System (ADS)

    Fritsch, Anatol; Pawlizak, Steve; Zink, Mareike; Kaes, Josef A.

    2012-02-01

    Based on a recently developed surgical method of Michael H"ockel, which makes use of cellular confinement to compartments in the human body, we study the mechanics of the process of cell segregation. Compartmentalization is a fundamental process of cellular organization and occurs during embryonic development. A simple model system can demonstrate the process of compartmentalization: When two populations of suspended cells are mixed, this mixture will eventually segregate into two phases, whereas mixtures of the same cell type will not. In the 1960s, Malcolm S. Steinberg formulated the so-called differential adhesion hypothesis which explains the segregation in the model system and the process of compartmentalization by differences in surface tension and adhesiveness of the interacting cells. We are interested in to which extend the same physical principles affect tumor growth and spreading between compartments. For our studies, we use healthy and cancerous breast cell lines of different malignancy as well as primary cells from human cervix carcinoma. We apply a set of techniques to study their mechanical properties and interactions. The Optical Stretcher is used for whole cell rheology, while Cell-cell-adhesion forces are directly measured with a modified AFM. In combination with 3D segregation experiments in droplet cultures we try to clarify the role of surface tension in tumor spreading.

  18. Robust global identifiability theory using potentials--Application to compartmental models.

    PubMed

    Wongvanich, N; Hann, C E; Sirisena, H R

    2015-04-01

    This paper presents a global practical identifiability theory for analyzing and identifying linear and nonlinear compartmental models. The compartmental system is prolonged onto the potential jet space to formulate a set of input-output equations that are integrals in terms of the measured data, which allows for robust identification of parameters without requiring any simulation of the model differential equations. Two classes of linear and non-linear compartmental models are considered. The theory is first applied to analyze the linear nitrous oxide (N2O) uptake model. The fitting accuracy of the identified models from differential jet space and potential jet space identifiability theories is compared with a realistic noise level of 3% which is derived from sensor noise data in the literature. The potential jet space approach gave a match that was well within the coefficient of variation. The differential jet space formulation was unstable and not suitable for parameter identification. The proposed theory is then applied to a nonlinear immunological model for mastitis in cows. In addition, the model formulation is extended to include an iterative method which allows initial conditions to be accurately identified. With up to 10% noise, the potential jet space theory predicts the normalized population concentration infected with pathogens, to within 9% of the true curve. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Diminished viral replication and compartmentalization of hepatitis C virus in hepatocellular carcinoma tissue.

    PubMed

    Harouaka, Djamila; Engle, Ronald E; Wollenberg, Kurt; Diaz, Giacomo; Tice, Ashley B; Zamboni, Fausto; Govindarajan, Sugantha; Alter, Harvey; Kleiner, David E; Farci, Patrizia

    2016-02-02

    Analysis of hepatitis C virus (HCV) replication and quasispecies distribution within the tumor of patients with HCV-associated hepatocellular carcinoma (HCC) can provide insight into the role of HCV in hepatocarcinogenesis and, conversely, the effect of HCC on the HCV lifecycle. In a comprehensive study of serum and multiple liver specimens from patients with HCC who underwent liver transplantation, we found a sharp and significant decrease in HCV RNA in the tumor compared with surrounding nontumorous tissues, but found no differences in multiple areas of control non-HCC cirrhotic livers. Diminished HCV replication was not associated with changes in miR-122 expression. HCV genetic diversity was significantly higher in livers containing HCC compared with control non-HCC cirrhotic livers. Tracking of individual variants demonstrated changes in the viral population between tumorous and nontumorous areas, the extent of which correlated with the decline in HCV RNA, suggesting HCV compartmentalization within the tumor. In contrast, compartmentalization was not observed between nontumorous areas and serum, or in controls between different areas of the cirrhotic liver or between liver and serum. Our findings indicate that HCV replication within the tumor is restricted and compartmentalized, suggesting segregation of specific viral variants in malignant hepatocytes.

  20. Verification of Compartmental Epidemiological Models using Metamorphic Testing, Model Checking and Visual Analytics

    SciT

    Ramanathan, Arvind; Steed, Chad A; Pullum, Laura L

    Compartmental models in epidemiology are widely used as a means to model disease spread mechanisms and understand how one can best control the disease in case an outbreak of a widespread epidemic occurs. However, a significant challenge within the community is in the development of approaches that can be used to rigorously verify and validate these models. In this paper, we present an approach to rigorously examine and verify the behavioral properties of compartmen- tal epidemiological models under several common modeling scenarios including birth/death rates and multi-host/pathogen species. Using metamorphic testing, a novel visualization tool and model checking, we buildmore » a workflow that provides insights into the functionality of compartmental epidemiological models. Our initial results indicate that metamorphic testing can be used to verify the implementation of these models and provide insights into special conditions where these mathematical models may fail. The visualization front-end allows the end-user to scan through a variety of parameters commonly used in these models to elucidate the conditions under which an epidemic can occur. Further, specifying these models using a process algebra allows one to automatically construct behavioral properties that can be rigorously verified using model checking. Taken together, our approach allows for detecting implementation errors as well as handling conditions under which compartmental epidemiological models may fail to provide insights into disease spread dynamics.« less

  1. Compartmentalized human immunodeficiency virus type 1 originates from long-lived cells in some subjects with HIV-1-associated dementia.

    PubMed

    Schnell, Gretja; Spudich, Serena; Harrington, Patrick; Price, Richard W; Swanstrom, Ronald

    2009-04-01

    Human immunodeficiency virus type 1 (HIV-1) invades the central nervous system (CNS) shortly after systemic infection and can result in the subsequent development of HIV-1-associated dementia (HAD) in a subset of infected individuals. Genetically compartmentalized virus in the CNS is associated with HAD, suggesting autonomous viral replication as a factor in the disease process. We examined the source of compartmentalized HIV-1 in the CNS of subjects with HIV-1-associated neurological disease and in asymptomatic subjects who were initiating antiretroviral therapy. The heteroduplex tracking assay (HTA), targeting the variable regions of env, was used to determine which HIV-1 genetic variants in the cerebrospinal fluid (CSF) were compartmentalized and which variants were shared with the blood plasma. We then measured the viral decay kinetics of individual variants after the initiation of antiretroviral therapy. Compartmentalized HIV-1 variants in the CSF of asymptomatic subjects decayed rapidly after the initiation of antiretroviral therapy, with a mean half-life of 1.57 days. Rapid viral decay was also measured for CSF-compartmentalized variants in four HAD subjects (t(1/2) mean = 2.27 days). However, slow viral decay was measured for CSF-compartmentalized variants from an additional four subjects with neurological disease (t(1/2) range = 9.85 days to no initial decay). The slow decay detected for CSF-compartmentalized variants was not associated with poor CNS drug penetration, drug resistant virus in the CSF, or the presence of X4 virus genotypes. We found that the slow decay measured for CSF-compartmentalized variants in subjects with neurological disease was correlated with low peripheral CD4 cell count and reduced CSF pleocytosis. We propose a model in which infiltrating macrophages replace CD4(+) T cells as the primary source of productive viral replication in the CNS to maintain high viral loads in the CSF in a substantial subset of subjects with HAD.

  2. DISTING: A web application for fast algorithmic computation of alternative indistinguishable linear compartmental models.

    PubMed

    Davidson, Natalie R; Godfrey, Keith R; Alquaddoomi, Faisal; Nola, David; DiStefano, Joseph J

    2017-05-01

    We describe and illustrate use of DISTING, a novel web application for computing alternative structurally identifiable linear compartmental models that are input-output indistinguishable from a postulated linear compartmental model. Several computer packages are available for analysing the structural identifiability of such models, but DISTING is the first to be made available for assessing indistinguishability. The computational algorithms embedded in DISTING are based on advanced versions of established geometric and algebraic properties of linear compartmental models, embedded in a user-friendly graphic model user interface. Novel computational tools greatly speed up the overall procedure. These include algorithms for Jacobian matrix reduction, submatrix rank reduction, and parallelization of candidate rank computations in symbolic matrix analysis. The application of DISTING to three postulated models with respectively two, three and four compartments is given. The 2-compartment example is used to illustrate the indistinguishability problem; the original (unidentifiable) model is found to have two structurally identifiable models that are indistinguishable from it. The 3-compartment example has three structurally identifiable indistinguishable models. It is found from DISTING that the four-compartment example has five structurally identifiable models indistinguishable from the original postulated model. This example shows that care is needed when dealing with models that have two or more compartments which are neither perturbed nor observed, because the numbering of these compartments may be arbitrary. DISTING is universally and freely available via the Internet. It is easy to use and circumvents tedious and complicated algebraic analysis previously done by hand. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. In vivo kinematics of a robot-assisted uni- and multi-compartmental knee arthroplasty.

    PubMed

    Watanabe, Toshifumi; Abbasi, Ali Z; Conditt, Michael A; Christopher, Jennifer; Kreuzer, Stefan; Otto, Jason K; Banks, Scott A

    2014-07-01

    There is great interest in providing reliable and durable treatments for one- and two-compartment arthritic degeneration of the cruciate-ligament intact knee. One approach is to resurface only the diseased compartments with discrete unicompartmental components, retaining the undamaged compartment(s). However, placing multiple small implants into the knee presents a greater surgical challenge than total knee arthroplasty, so it is not certain that the natural knee mechanics can be maintained or restored. The goal of this study was to determine whether near-normal knee kinematics can be obtained with a robot-assisted multi-compartmental knee arthroplasty. Thirteen patients with 15 multi-compartmental knee arthroplasties using haptic robotic-assisted bone preparation were involved in this study. Nine subjects received a medial unicompartmental knee arthroplasty (UKA), three subjects received a medial UKA and patellofemoral (PF) arthroplasty, and three subjects received medial and lateral bi-unicondylar arthroplasty. Knee motions were recorded using video-fluoroscopy an average of 13 months (6-29 months) after surgery during stair and kneeling activities. The three-dimensional position and orientation of the implant components were determined using model-image registration techniques. Knee kinematics during maximum flexion kneeling showed femoral external rotation and posterior lateral condylar translation. All knees showed femoral external rotation and posterior condylar translation with flexion during the step activity. Knees with medial UKA and PF arthroplasty showed the most femoral external rotation and posterior translation, and knees with bicondylar UKA showed the least. Knees with accurately placed uni- or bi-compartmental arthroplasty exhibited stable knee kinematics consistent with intact and functioning cruciate ligaments. The patterns of tibiofemoral motion were more similar to natural knees than commonly has been observed in knees with total knee

  4. Regulation of NAD+ metabolism, signaling and compartmentalization in the yeast Saccharomyces cerevisiae

    PubMed Central

    Kato, Michiko; Lin, Su-Ju

    2014-01-01

    Pyridine nucleotides are essential coenzymes in many cellular redox reactions in all living systems. In addition to functioning as a redox carrier, NAD+ is also a required co-substrate for the conserved sirtuin deacetylases. Sirtuins regulate transcription, genome maintenance and metabolism and function as molecular links between cells and their environment. Maintaining NAD+ homeostasis is essential for proper cellular function and aberrant NAD+ metabolism has been implicated in a number of metabolic- and age-associated diseases. Recently, NAD+ metabolism has been linked to the phosphate-responsive signaling pathway (PHO pathway) in the budding yeast Saccharomyces cerevisiae. Activation of the PHO pathway is associated with the production and mobilization of the NAD+ metabolite nicotinamide riboside (NR), which is mediated in part by PHO-regulated nucleotidases. Cross-regulation between NAD+ metabolism and the PHO pathway has also been reported; however, detailed mechanisms remain to be elucidated. The PHO pathway also appears to modulate the activities of common downstream effectors of multiple nutrient-sensing pathways (Ras-PKA, TOR, Sch9/AKT). These signaling pathways were suggested to play a role in calorie restriction-mediated beneficial effects, which have also been linked to Sir2 function and NAD+ metabolism. Here, we discuss the interactions of these pathways and their potential roles in regulating NAD+ metabolism. In eukaryotic cells, intracellular compartmentalization facilitates the regulation of enzymatic functions and also concentrates or sequesters specific metabolites. Various NAD+-mediated cellular functions such as mitochondrial oxidative phosphorylation are compartmentalized. Therefore, we also discuss several key players functioning in mitochondrial, cytosolic and vacuolar compartmentalization of NAD+ intermediates, and their potential roles in NAD+ homeostasis. To date, it remains unclear how NAD+ and NAD+ intermediates shuttle between different

  5. Regulation of NAD+ metabolism, signaling and compartmentalization in the yeast Saccharomyces cerevisiae.

    PubMed

    Kato, Michiko; Lin, Su-Ju

    2014-11-01

    Pyridine nucleotides are essential coenzymes in many cellular redox reactions in all living systems. In addition to functioning as a redox carrier, NAD(+) is also a required co-substrate for the conserved sirtuin deacetylases. Sirtuins regulate transcription, genome maintenance and metabolism and function as molecular links between cells and their environment. Maintaining NAD(+) homeostasis is essential for proper cellular function and aberrant NAD(+) metabolism has been implicated in a number of metabolic- and age-associated diseases. Recently, NAD(+) metabolism has been linked to the phosphate-responsive signaling pathway (PHO pathway) in the budding yeast Saccharomyces cerevisiae. Activation of the PHO pathway is associated with the production and mobilization of the NAD(+) metabolite nicotinamide riboside (NR), which is mediated in part by PHO-regulated nucleotidases. Cross-regulation between NAD(+) metabolism and the PHO pathway has also been reported; however, detailed mechanisms remain to be elucidated. The PHO pathway also appears to modulate the activities of common downstream effectors of multiple nutrient-sensing pathways (Ras-PKA, TOR, Sch9/AKT). These signaling pathways were suggested to play a role in calorie restriction-mediated beneficial effects, which have also been linked to Sir2 function and NAD(+) metabolism. Here, we discuss the interactions of these pathways and their potential roles in regulating NAD(+) metabolism. In eukaryotic cells, intracellular compartmentalization facilitates the regulation of enzymatic functions and also concentrates or sequesters specific metabolites. Various NAD(+)-mediated cellular functions such as mitochondrial oxidative phosphorylation are compartmentalized. Therefore, we also discuss several key players functioning in mitochondrial, cytosolic and vacuolar compartmentalization of NAD(+) intermediates, and their potential roles in NAD(+) homeostasis. To date, it remains unclear how NAD(+) and NAD(+) intermediates

  6. Development and testing of a compartmentalized reaction network model for redox zones in contaminated aquifers

    Abrams , Robert H.; Loague, Keith; Kent, Douglas B.

    1998-01-01

    The work reported here is the first part of a larger effort focused on efficient numerical simulation of redox zone development in contaminated aquifers. The sequential use of various electron acceptors, which is governed by the energy yield of each reaction, gives rise to redox zones. The large difference in energy yields between the various redox reactions leads to systems of equations that are extremely ill-conditioned. These equations are very difficult to solve, especially in the context of coupled fluid flow, solute transport, and geochemical simulations. We have developed a general, rational method to solve such systems where we focus on the dominant reactions, compartmentalizing them in a manner that is analogous to the redox zones that are often observed in the field. The compartmentalized approach allows us to easily solve a complex geochemical system as a function of time and energy yield, laying the foundation for our ongoing work in which we couple the reaction network, for the development of redox zones, to a model of subsurface fluid flow and solute transport. Our method (1) solves the numerical system without evoking a redox parameter, (2) improves the numerical stability of redox systems by choosing which compartment and thus which reaction network to use based upon the concentration ratios of key constituents, (3) simulates the development of redox zones as a function of time without the use of inhibition factors or switching functions, and (4) can reduce the number of transport equations that need to be solved in space and time. We show through the use of various model performance evaluation statistics that the appropriate compartment choice under different geochemical conditions leads to numerical solutions without significant error. The compartmentalized approach described here facilitates the next phase of this effort where we couple the redox zone reaction network to models of fluid flow and solute transport.

  7. Nilpotent singularities and dynamics in an SIR type of compartmental model with hospital resources

    NASA Astrophysics Data System (ADS)

    Shan, Chunhua; Yi, Yingfei; Zhu, Huaiping

    2016-03-01

    An SIR type of compartmental model with a standard incidence rate and a nonlinear recovery rate was formulated to study the impact of available resources of public health system especially the number of hospital beds. Cusp, focus and elliptic type of nilpotent singularities of codimension 3 are discovered and analyzed in this three dimensional model. Complex dynamics of disease transmission including multi-steady states and multi-periodicity are revealed by bifurcation analysis. Large-amplitude oscillations found in our model provide a more reasonable explanation for disease recurrence. With clinical data, our studies have practical implications for the prevention and control of infectious diseases.

  8. Atg22p, a vacuolar membrane protein involved in the amino acid compartmentalization of Schizosaccharomyces pombe.

    PubMed

    Sugimoto, Naoko; Iwaki, Tomoko; Chardwiriyapreecha, Soracom; Shimazu, Masamitsu; Kawano, Miyuki; Sekito, Takayuki; Takegawa, Kaoru; Kakinuma, Yoshimi

    2011-01-01

    The fission yeast Schizosaccharomyces pombe has a homolog of the budding yeast Atg22p, which is involved in spore formation (Mukaiyama H. et al., Microbiology, 155, 3816-3826 (2009)). GFP-tagged Atg22p in the fission yeast was localized to the vacuolar membrane. Upon disruption of atg22, the amino acid levels of the cellular fraction as well as the vacuolar fraction decreased. The uptake of several amino acids, such as lysine, histidine, and arginine, was impaired in atg22Δ cells. S. pombe Atg22p plays an important role in the compartmentalization of amino acids.

  9. Beyond compartmentalization: a relational approach towards agency and vulnerability of young migrants.

    PubMed

    Huijsmans, Roy

    2012-01-01

    Based on fieldwork material from Lao People's Democratic Republic, this paper introduces an analytical framework that transcends compartmentalized approaches towards migration involving young people. The notions of fluid and institutionalized forms of migration illuminate key differences and commonalities in the relational fabric underpinning empirically diverse migration scenarios. Applying this framework to the role of networks in becoming a young migrant, this chapter sheds light on young migrants' differential scope for exercising agency. This redirects concerns about young migrants away from descriptive and static factors towards their relational position in the process of migration, which shapes their agency and vulnerability. Copyright © 2012 Wiley Periodicals, Inc., A Wiley Company.

  10. Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus.

    PubMed

    Razin, S V; Borunova, V V; Iarovaia, O V; Vassetzky, Y S

    2014-07-01

    Becoming popular at the end of the 20th century, the concept of the nuclear matrix implies the existence of a nuclear skeleton that organizes functional elements in the cell nucleus. This review presents a critical analysis of the results obtained in the study of nuclear matrix in the light of current views on the organization of the cell nucleus. Numerous studies of nuclear matrix have failed to provide evidence of the existence of such a structure. Moreover, the existence of a filamentous structure that supports the nuclear compartmentalization appears to be unnecessary, since this function is performed by the folded genome itself.

  11. Influence of bi- and tri-compartmental knee arthroplasty on the kinematics of the knee joint.

    PubMed

    Wünschel, Markus; Lo, Jiahsuan; Dilger, Torsten; Wülker, Nikolaus; Müller, Otto

    2011-01-27

    The cruciate ligaments are important stabilizers of the knee joint and determine joint kinematics in the natural knee and after cruciate retaining arthroplasty.No in vitro data is available to biomechanically evaluate the ability of the anterior cruciate ligament (ACL) to maintain knee joint kinematics after bicruciate-retaining bi-compartmental knee arthroplasty (BKA).Therefore, the objective of the current study was to investigate the kinematics of the natural knee joint, before and after installing bicruciate-retaining BKA and posterior cruciate retaining total knee arthroplasty. Specifically, we incorporated a dynamic knee simulator to simulate weight-bearing flexions on cadaveric knee specimen before and after surgical manipulations. In this cadaveric study we investigated rotational and translational tibiofemoral kinematics during simulated weight-bearing flexions of the intact knee, after bi-compartmental knee arthroplasty (BKA+), after resecting the ACL in BKA (BKA-), and after posterior cruciate retaining total knee arthroplasty (TKA). Rotation of BKA+ is closest to the intact knee joint, whereas TKA shows significant differences from 30 to 90 degree of flexion. Within the tested flexion range (15 to 90 degree of flexion), there was no significant difference in the anterior-posterior translation among intact, BKA+, and TKA knees. Resecting the ACL in BKA leads to a significant anterior tibial translation. BKA with intact cruciate ligaments resembles rotation and translation of the natural knee during a simulated weight-bearing flexion. It is a suitable treatment option for medial and patellofemoral osteoarthritis with advantages in rotational characteristics compared to TKA.

  12. A Minimal Polymer Model Integrates an Inverted Nuclear Geometry with Conventional Hi-C Compartmentalization

    NASA Astrophysics Data System (ADS)

    Falk, Martin; Naumova, Natasha; Fudenberg, Geoffrey; Feodorova, Yana; Imakaev, Maxim; Dekker, Job; Solovei, Irina; Mirny, Leonid

    The organization of interphase nuclei differs dramatically across cell types in a functionally-relevant fashion. A striking example is found in the rod photoreceptors of nocturnal mammals, where the conventional nuclear organization is inverted. In particular, in murine rods, constitutive heterochromatin is packed into a single chromocenter in the nuclear center, which is encircled by a shell of facultative heterochromatin and then by an outermost shell of euchromatin. Surprisingly, Hi-C maps of conventional and inverted nuclei display remarkably similar compartmentalization between heterochromatin and euchromatin. Here, we simulate a de novo polymer model that is capable of replicating both conventional and inverted geometries while preserving the patterns of compartmentalization as observed by Hi-C. In this model, chromatin is a polymer composed of three classes of monomers arranged in blocks representing constitutive heterochromatin, facultative heterochromatin, and euchromatin. Different classes of monomers have different levels of attraction to each other and to the nuclear lamina. Our results indicate that preferential interactions between facultative heterochromatin and constitutive heterochromatin provide a possible mechanism to explain nuclear inversion when association with the lamina is lost.

  13. Isoform-specific tethering links the Golgi ribbon to maintain compartmentalization

    PubMed Central

    Jarvela, Timothy; Linstedt, Adam D.

    2014-01-01

    Homotypic membrane tethering by the Golgi reassembly and stacking proteins (GRASPs) is required for the lateral linkage of mammalian Golgi ministacks into a ribbon-like membrane network. Although GRASP65 and GRASP55 are specifically localized to cis and medial/trans cisternae, respectively, it is unknown whether each GRASP mediates cisternae-specific tethering and whether such specificity is necessary for Golgi compartmentalization. Here each GRASP was tagged with KillerRed (KR), expressed in HeLa cells, and inhibited by 1-min exposure to light. Significantly, inactivation of either GRASP unlinked the Golgi ribbon, and the immediate effect of GRASP65-KR inactivation was a loss of cis- rather than trans-Golgi integrity, whereas inactivation of GRASP55-KR first affected the trans- and not the cis-Golgi. Thus each GRASP appears to play a direct and cisternae-specific role in linking ministacks into a continuous membrane network. To test the consequence of loss of cisternae-specific tethering, we generated Golgi membranes with a single GRASP on all cisternae. Remarkably, the membranes exhibited the full connectivity of wild-type Golgi ribbons but were decompartmentalized and defective in glycan processing. Thus the GRASP isoforms specifically link analogous cisternae to ensure Golgi compartmentalization and proper processing. PMID:24227884

  14. Detecting compartmental non-Gaussian diffusion with symmetrized double-PFG MRI.

    PubMed

    Paulsen, Jeffrey L; Özarslan, Evren; Komlosh, Michal E; Basser, Peter J; Song, Yi-Qiao

    2015-11-01

    Diffusion in tissue and porous media is known to be non-Gaussian and has been used for clinical indications of stroke and other tissue pathologies. However, when conventional NMR techniques are applied to biological tissues and other heterogeneous materials, the presence of multiple compartments (pores) with different Gaussian diffusivities will also contribute to the measurement of non-Gaussian behavior. Here we present symmetrized double PFG (sd-PFG), which can separate these two contributions to non-Gaussian signal decay as having distinct angular modulation frequencies. In contrast to prior angular d-PFG methods, sd-PFG can unambiguously extract kurtosis as an oscillation from samples with isotropic or uniformly oriented anisotropic pores, and can generally extract a combination of compartmental anisotropy and kurtosis. The method further fixes its sensitivity with respect to the time dependence of the apparent diffusion coefficient. We experimentally demonstrate the measurement of the fourth cumulant (kurtosis) of diffusion and find it consistent with theoretical predictions. By enabling the unambiguous identification of contributions of compartmental kurtosis to the signal, sd-PFG has the potential to help identify the underlying micro-structural changes corresponding to current kurtosis based diagnostics, and act as a novel source of contrast to better resolve tissue micro-structure. Copyright © 2015 John Wiley & Sons, Ltd.

  15. Detecting Compartmental non-Gaussian Diffusion with Symmetrized Double-PFG MRI

    PubMed Central

    Paulsen, Jeffrey L.; Özarslan, Evren; Komlosh, Michal E.; Basser, Peter J.; Song, Yi-Qiao

    2015-01-01

    Diffusion in tissue and porous media is known to be non-Gaussian and has been used for clinical indications of stroke and other tissue pathologies. However, when conventional NMR techniques are applied to biological tissues and other heterogeneous materials, the presence of multiple compartments (pores) with different Gaussian diffusivities will also contribute to the measurement of non-Gaussian behavior. Here we present Symmetrized Double PFG (sd-PFG), which can separate these two contributions to non-Gaussian signal decay as having distinct angular modulation frequencies. In contrast to prior angular d-PFG methods, sd-PFG can unambiguously extract kurtosis as an oscillation from samples with isotropic or uniformly oriented anisotropic pores, and can generally extract a combination of compartmental anisotropy and kurtosis. The method further fixes its sensitivity with respect to the time-dependence of the apparent diffusion coefficient. We experimentally demonstrate the measurement of the fourth moment (kurtosis) of diffusion and find it consistent with theoretical predictions. By enabling the unambiguous identification of contributions of compartmental kurtosis to the signal, sd-PFG has the potential to help identify the underlying micro-structural changes corresponding to current kurtosis based diagnostics and act as a novel source of contrast to better resolve tissue micro-structure. PMID:26434812

  16. A compartmental-spatial system dynamics approach to ground water modeling.

    PubMed

    Roach, Jesse; Tidwell, Vince

    2009-01-01

    High-resolution, spatially distributed ground water flow models can prove unsuitable for the rapid, interactive analysis that is increasingly demanded to support a participatory decision environment. To address this shortcoming, we extend the idea of multiple cell (Bear 1979) and compartmental (Campana and Simpson 1984) ground water models developed within the context of spatial system dynamics (Ahmad and Simonovic 2004) for rapid scenario analysis. We term this approach compartmental-spatial system dynamics (CSSD). The goal is to balance spatial aggregation necessary to achieve a real-time integrative and interactive decision environment while maintaining sufficient model complexity to yield a meaningful representation of the regional ground water system. As a test case, a 51-compartment CSSD model was built and calibrated from a 100,0001 cell MODFLOW (McDonald and Harbaugh 1988) model of the Albuquerque Basin in central New Mexico (McAda and Barroll 2002). Seventy-seven percent of historical drawdowns predicted by the MODFLOW model were within 1 m of the corresponding CSSD estimates, and in 80% of the historical model run years the CSSD model estimates of river leakage, reservoir leakage, ground water flow to agricultural drains, and riparian evapotranspiration were within 30% of the corresponding estimates from McAda and Barroll (2002), with improved model agreement during the scenario period. Comparisons of model results demonstrate both advantages and limitations of the CCSD model approach.

  17. Compartmentalized self-replication: a novel method for the directed evolution of polymerases and other enzymes.

    PubMed

    Ghadessy, Farid J; Holliger, Philipp

    2007-01-01

    Compartmentalized self-replication (CSR) is a novel method for the directed evolution of enzymes and, in particular, polymerases. In its simplest form, CSR consists of a simple feedback loop involving a polymerase that replicates only its own encoding gene (self-replication). Self-replication occurs in discrete, spatially separate, noncommunicating compartments formed by a heat-stable water-in-oil emulsion. Compartmentalization ensures the linkage of phenotype and genotype (i.e., it ensures that each polymerase replicates only its own encoding gene to the exclusion of those in the other compartments). As a result, adaptive gains by the polymerase directly (and proportionally) translate into genetic amplification of the encoding polymerase gene. CSR has proven to be a useful strategy for the directed evolution of polymerases directly from diverse repertoires of polymerase genes. In this chapter, we describe some of the CSR protocols used successfully to evolve variants of T. aquaticus Pol I (Taq) polymerase with novel and useful properties, such as increased thermostability or resistance to the potent inhibitor, heparin, from a repertoire of randomly mutated Taq polymerase genes.

  18. Intracellular Redox Compartmentation and ROS-Related Communication in Regulation and Signaling1[OPEN

    PubMed Central

    2016-01-01

    Recent years have witnessed enormous progress in understanding redox signaling related to reactive oxygen species (ROS) in plants. The consensus view is that such signaling is intrinsic to many developmental processes and responses to the environment. ROS-related redox signaling is tightly wedded to compartmentation. Because membranes function as barriers, highly redox-active powerhouses such as chloroplasts, peroxisomes, and mitochondria may elicit specific signaling responses. However, transporter functions allow membranes also to act as bridges between compartments, and so regulated capacity to transmit redox changes across membranes influences the outcome of triggers produced at different locations. As well as ROS and other oxidizing species, antioxidants are key players that determine the extent of ROS accumulation at different sites and that may themselves act as signal transmitters. Like ROS, antioxidants can be transported across membranes. In addition, the intracellular distribution of antioxidative enzymes may be modulated to regulate or facilitate redox signaling appropriate to the conditions. Finally, there is substantial plasticity in organellar shape, with extensions such as stromules, peroxules, and matrixules playing potentially crucial roles in organelle-organelle communication. We provide an overview of the advances in subcellular compartmentation, identifying the gaps in our knowledge and discussing future developments in the area. PMID:27208308

  19. Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils

    PubMed Central

    Álvarez-Yela, Astrid Catalina; Gómez-Cano, Fabio; Zambrano, María Mercedes; Husserl, Johana; Danies, Giovanna; Restrepo, Silvia; González-Barrios, Andrés Fernando

    2017-01-01

    Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community. PMID:28767679

  20. ADP Compartmentation Analysis Reveals Coupling between Pyruvate Kinase and ATPases in Heart Muscle

    PubMed Central

    Sepp, Mervi; Vendelin, Marko; Vija, Heiki; Birkedal, Rikke

    2010-01-01

    Abstract Cardiomyocytes have intracellular diffusion restrictions, which spatially compartmentalize ADP and ATP. However, the models that predict diffusion restrictions have used data sets generated in rat heart permeabilized fibers, where diffusion distances may be heterogeneous. This is avoided by using isolated, permeabilized cardiomyocytes. The aim of this work was to analyze the intracellular diffusion of ATP and ADP in rat permeabilized cardiomyocytes. To do this, we measured respiration rate, ATPase rate, and ADP concentration in the surrounding solution. The data were analyzed using mathematical models that reflect different levels of cell compartmentalization. In agreement with previous studies, we found significant diffusion restriction by the mitochondrial outer membrane and confirmed a functional coupling between mitochondria and a fraction of ATPases in the cell. In addition, our experimental data show that considerable activity of endogenous pyruvate kinase (PK) remains in the cardiomyocytes after permeabilization. A fraction of ATPases were inactive without ATP feedback by this endogenous PK. When analyzing the data, we were able to reproduce the measurements only with the mathematical models that include a tight coupling between the fraction of endogenous PK and ATPases. To our knowledge, this is the first time such a strong coupling of PK to ATPases has been demonstrated in permeabilized cardiomyocytes. PMID:20550890

  1. [Compartmentalization of the cell nucleus and spatial organization of the genome].

    PubMed

    Gavrilov, A A; Razin, S V

    2015-01-01

    The eukaryotic cell nucleus is one of the most complex cell organelles. Despite the absence of membranes, the nuclear space is divided into numerous compartments where different processes in- volved in the genome activity take place. The most important nuclear compartments include nucleoli, nuclear speckles, PML bodies, Cajal bodies, histone locus bodies, Polycomb bodies, insulator bodies, transcription and replication factories. The structural basis for the nuclear compartmentalization is provided by genomic DNA that occupies most of the nuclear volume. Nuclear compartments, in turn, guide the chromosome folding by providing a platform for the spatial interaction of individual genomic loci. In this review, we discuss fundamental principles of higher order genome organization with a focus on chromosome territories and chromosome domains, as well as consider the structure and function of the key nuclear compartments. We show that the func- tional compartmentalization of the cell nucleus and genome spatial organization are tightly interconnected, and that this form of organization is highly dynamic and is based on stochastic processes.

  2. Intracellular Redox Compartmentation and ROS-Related Communication in Regulation and Signaling.

    PubMed

    Noctor, Graham; Foyer, Christine H

    2016-07-01

    Recent years have witnessed enormous progress in understanding redox signaling related to reactive oxygen species (ROS) in plants. The consensus view is that such signaling is intrinsic to many developmental processes and responses to the environment. ROS-related redox signaling is tightly wedded to compartmentation. Because membranes function as barriers, highly redox-active powerhouses such as chloroplasts, peroxisomes, and mitochondria may elicit specific signaling responses. However, transporter functions allow membranes also to act as bridges between compartments, and so regulated capacity to transmit redox changes across membranes influences the outcome of triggers produced at different locations. As well as ROS and other oxidizing species, antioxidants are key players that determine the extent of ROS accumulation at different sites and that may themselves act as signal transmitters. Like ROS, antioxidants can be transported across membranes. In addition, the intracellular distribution of antioxidative enzymes may be modulated to regulate or facilitate redox signaling appropriate to the conditions. Finally, there is substantial plasticity in organellar shape, with extensions such as stromules, peroxules, and matrixules playing potentially crucial roles in organelle-organelle communication. We provide an overview of the advances in subcellular compartmentation, identifying the gaps in our knowledge and discussing future developments in the area. © 2016 American Society of Plant Biologists. All Rights Reserved.

  3. A compartmentalized solute transport model for redox zones in contaminated aquifers: 2. Field‐scale simulations

    Abrams , Robert H.; Loague, Keith

    2000-01-01

    This paper, the second of two parts [see Abrams and Loague, this issue], reports the field‐scale application of COMPTRAN (compartmentalized solute transport model) for simulating the development of redox zones. COMPTRAN is fully developed and described in the companion paper. Redox zones, which are often delineated by the relative concentrations of dissolved oxygen, have been observed around the globe. The distribution of other redox‐sensitive species is affected by redox zonation. At the U.S. Geological Survey's Cape Cod research site, an anoxic zone containing high concentrations of dissolved iron has been observed. Field data were abstracted from the Cape Cod site for the one‐dimensional and two‐dimensional COMPTRAN simulations reported in this paper. The purpose of the concept‐development simulations was to demonstrate that the compartmentalized approach reported by Abrams et al. [1998] can be linked with a solute transport model to simulate field‐scale phenomena. The results presented in this paper show that COMPTRAN successfully simulated the development of redox zones at the field scale, including trends in pH and alkalinity. Thermodynamic constraints were used to prevent lower‐energy redox reactions from occurring under infeasible geochemical conditions without imposing equilibrium among all redox species. Empirical methods of reaction inhibition were not needed for the simulations conducted for this study. COMPTRAN can be extended easily to include additional compartments and reactions and is capable of handling complex velocity fields in more than one dimension.

  4. Geo-environmental zoning using physiographic compartmentalization: a proposal for supporting sustainable decision-making.

    PubMed

    Corrêa, Claudia V S; Reis, Fábio A G V; Giordano, Lucilia C; Bressane, Adriano; Chaves, Camila J; Amaral, Ana Maria C DO; Brito, Hermes D; Medeiros, Gerson A DE

    2017-01-01

    The geo-environmental zoning represents an important strategy in the territorial management. However, it requires a logical and structured procedure. Therefore, an approach using physiographic compartmentalization is proposed and applied as case study in a region covered by the topographic maps of São José dos Campos and Jacareí, Brazil. This region has great geological and geomorphological peculiarities, beyond being a place with large human interventions because of its quickly economic growth. The methodology is based on photointerpretation techniques and remote sensing in GIS environment. As a result, seven geo-environmental zones were obtained from a weighted integration by multicriteria analysis of physiographic units with land-use classes. In conclusion, taking into account potentialities and limitations, the proposed approach can be considered able to support sustainable decision-making, being applicable in other regions.

  5. Fractional kinetics of compartmental systems: first approach with use digraph-based method

    NASA Astrophysics Data System (ADS)

    Markowski, Konrad Andrzej

    2017-08-01

    In the last two decades, integral and differential calculus of a fractional order has become a subject of great interest in different areas of physics, biology, economics and other sciences. The idea of such a generalization was mentioned in 1695 by Leibniz and L'Hospital. The first definition of the fractional derivative was introduced by Liouville and Riemann at the end of the 19th century. Fractional calculus was found to be a very useful tool for modelling the behaviour of many materials and systems. In this paper fractional calculus was applied to pharmacokinetic compartmental model. For introduced model determine all possible quasi-positive realisation based on one-dimensional digraph theory. The proposed method was discussed and illustrated in detail with some numerical examples.

  6. Model Hierarchies in Edge-Based Compartmental Modeling for Infectious Disease Spread

    PubMed Central

    Miller, Joel C.; Volz, Erik M.

    2012-01-01

    We consider the family of edge-based compartmental models for epidemic spread developed in [11]. These models allow for a range of complex behaviors, and in particular allow us to explicitly incorporate duration of a contact into our mathematical models. Our focus here is to identify conditions under which simpler models may be substituted for more detailed models, and in so doing we define a hierarchy of epidemic models. In particular we provide conditions under which it is appropriate to use the standard mass action SIR model, and we show what happens when these conditions fail. Using our hierarchy, we provide a procedure leading to the choice of the appropriate model for a given population. Our result about the convergence of models to the Mass Action model gives clear, rigorous conditions under which the Mass Action model is accurate. PMID:22911242

  7. Estimation of pharmacokinetic parameters from non-compartmental variables using Microsoft Excel.

    PubMed

    Dansirikul, Chantaratsamon; Choi, Malcolm; Duffull, Stephen B

    2005-06-01

    This study was conducted to develop a method, termed 'back analysis (BA)', for converting non-compartmental variables to compartment model dependent pharmacokinetic parameters for both one- and two-compartment models. A Microsoft Excel spreadsheet was implemented with the use of Solver and visual basic functions. The performance of the BA method in estimating pharmacokinetic parameter values was evaluated by comparing the parameter values obtained to a standard modelling software program, NONMEM, using simulated data. The results show that the BA method was reasonably precise and provided low bias in estimating fixed and random effect parameters for both one- and two-compartment models. The pharmacokinetic parameters estimated from the BA method were similar to those of NONMEM estimation.

  8. Mdm4 loss in the intestinal epithelium leads to compartmentalized cell death but no tissue abnormalities

    PubMed Central

    Valentin-Vega, Yasmine A.; Box, Neil; Terzian, Tamara; Lozano, Guillermina

    2014-01-01

    Mdm4 is a critical inhibitor of the p53 tumor suppressor. Mdm4 null mice die early during embryogenesis due to increased p53 activity. In this study, we explore the role that Mdm4 plays in the intestinal epithelium by crossing mice carrying the Mdm4 floxed allele to mice with the Villin Cre transgene. Our data show that loss of Mdm4 (Mdm4intΔ) in this tissue resulted in viable animals with no obvious morphological abnormalities. However, these mutants displayed increased p53 levels and apoptosis exclusively in the proliferative compartment of the intestinal epithelium. This phenotype was completely rescued in a p53 null background. Notably, the observed compartmentalized apoptosis in proliferative intestinal epithelial cells was not due to restricted Mdm4 expression in this region. Thus, in this specific cellular context, p53 is negatively regulated by Mdm4 exclusively in highly proliferative cells. PMID:19371999

  9. Compartmentalization of gypsum and halite associated with cyanobacteria in saline soil crusts.

    PubMed

    Canfora, Loredana; Vendramin, Elisa; Vittori Antisari, Livia; Lo Papa, Giuseppe; Dazzi, Carmelo; Benedetti, Anna; Iavazzo, Pietro; Adamo, Paola; Jungblut, Anne D; Pinzari, Flavia

    2016-06-01

    The interface between biological and geochemical components in the surface crust of a saline soil was investigated using X-ray diffraction, and variable pressure scanning electron microscopy in combination with energy dispersive X-ray spectrometry. Mineral compounds such as halite and gypsum were identified crystallized around filaments of cyanobacteria. A total of 92 genera were identified from the bacterial community based on 16S gene pyrosequencing analysis. The occurrence of the gypsum crystals, their shapes and compartmentalization suggested that they separated NaCl from the immediate microenvironment of the cyanobacteria, and that some cyanobacteria and communities of sulfur bacteria may had a physical control over the distinctive halite and gypsum structures produced. This suggests that cyanobacteria might directly or indirectly promote the formation of a protective envelope made of calcium and sulfur-based compounds. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Substrate-induced Nuclear Export and Peripheral Compartmentalization of Hepatic Glucokinase Correlates with Glycogen Deposition

    PubMed Central

    Shiota, Masa; Knobel, Susan M.; Piston, David W.; Cherrington, Alan D.; Magnuson, Mark A.

    2001-01-01

    Hepatic glucokinase (GK) is acutely regulated by binding to its nuclear-anchored regulatory protein (GKRP). Although GK release by GKRP is tightly coupled to the rate of glycogen synthesis, the nature of this association is obscure. To gain insight into this coupling mechanism under physiological stimulating conditions in primary rat hepatocytes, we analyzed the subcellular distribution of GK and GKRP with immunofluorescence, and glycogen deposition with glycogen cytochemical fluorescence, using confocal microscopyand quantitative image analysis. Following stimulation, a fraction of the GK signal translocated from the nucleus to the cytoplasm. The reduction in the nuclear to cytoplasmic ratio of GK, an index of nuclear export, correlated with a >50% increase in glycogen cytochemical fluorescence over a 60min stimulation period. Furthermore, glycogen accumulation was initially deposited in a peripheral pattern in hepatocytes similar to that of GK. These data suggest that a compartmentalization exists of both active GK and the initial sites of glycogen deposition at the hepatocyte surface. PMID:12369705

  11. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization

    PubMed Central

    Nora, Elphège P.; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H.; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A.; Bruneau, Benoit G.

    2017-01-01

    Summary The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Further, our data support that CTCF mediates transcriptional insulator function through enhancer-blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding these results provide new fundamental insights into the rules governing mammalian genome organization. PMID:28525758

  12. Fatigue in isometric contraction in a single muscle fibre: a compartmental calcium ion flow model.

    PubMed

    Kothiyal, K P; Ibramsha, M

    1986-01-01

    Fatigue in muscle is a complex biological phenomenon which has so far eluded a definite explanation. Many biochemical and physiological models have been suggested in the literature to account for the decrement in the ability of muscle to sustain a given level of force for a long time. Some of these models have been critically analysed in this paper and are shown to be not able to explain all the experimental observations. A new compartmental model based on the intracellular calcium ion movement in muscle is proposed to study the mechanical responses of a muscle fibre. Computer simulation is performed to obtain model responses in isometric contraction to an impulse and a train of stimuli of long duration. The simulated curves have been compared with experimentally observed mechanical responses of the semitendinosus muscle fibre of Rana pipiens. The comparison of computed and observed responses indicates that the proposed calcium ion model indeed accounts very well for the muscle fatigue.

  13. Generation of Compartmentalized Pressure by a Nuclear Piston Governs Cell Motility in 3D Matrix*

    PubMed Central

    Petrie, Ryan J.; Koo, Hyun; Yamada, Kenneth M.

    2017-01-01

    Cells use actomyosin contractility to move through three-dimensional (3D) extracellular matrix. Contractility affects the type of protrusions cells use to migrate in 3D, but the mechanisms are unclear. Here we found that contractility generated high-pressure lobopodial protrusions in cells migrating in a 3D matrix. In these cells, the nucleus physically divided the cytoplasm into forward and rear compartments. Actomyosin contractility with the nucleoskeleton-intermediate filament linker protein nesprin 3 pulled the nucleus forward and pressurized the front of the cell. Reducing expression of nesprin 3 reduced and equalized the intracellular pressure. Thus, the nucleus can act as a piston that physically compartmentalizes the cytoplasm and increases the hydrostatic pressure between the nucleus and the leading edge to drive lamellipodia-independent 3D cell migration. PMID:25170155

  14. Plasma Membrane is Compartmentalized by a Self-Similar Cortical Actin Meshwork

    NASA Astrophysics Data System (ADS)

    Sadegh, Sanaz; Higgins, Jenny L.; Mannion, Patrick C.; Tamkun, Michael M.; Krapf, Diego

    2017-01-01

    A broad range of membrane proteins display anomalous diffusion on the cell surface. Different methods provide evidence for obstructed subdiffusion and diffusion on a fractal space, but the underlying structure inducing anomalous diffusion has never been visualized because of experimental challenges. We addressed this problem by imaging the cortical actin at high resolution while simultaneously tracking individual membrane proteins in live mammalian cells. Our data confirm that actin introduces barriers leading to compartmentalization of the plasma membrane and that membrane proteins are transiently confined within actin fences. Furthermore, superresolution imaging shows that the cortical actin is organized into a self-similar meshwork. These results present a hierarchical nanoscale picture of the plasma membrane.

  15. Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane.

    PubMed

    Koldsø, Heidi; Reddy, Tyler; Fowler, Philip W; Duncan, Anna L; Sansom, Mark S P

    2016-09-01

    The cytoskeleton underlying cell membranes may influence the dynamic organization of proteins and lipids within the bilayer by immobilizing certain transmembrane (TM) proteins and forming corrals within the membrane. Here, we present coarse-grained resolution simulations of a biologically realistic membrane model of asymmetrically organized lipids and TM proteins. We determine the effects of a model of cytoskeletal immobilization of selected membrane proteins using long time scale coarse-grained molecular dynamics simulations. By introducing compartments with varying degrees of restraints within the membrane models, we are able to reveal how compartmentalization caused by cytoskeletal immobilization leads to reduced and anomalous diffusional mobility of both proteins and lipids. This in turn results in a reduced rate of protein dimerization within the membrane and of hopping of membrane proteins between compartments. These simulations provide a molecular realization of hierarchical models often invoked to explain single-molecule imaging studies of membrane proteins.

  16. The Plasma Membrane is Compartmentalized by a Self-Similar Cortical Actin Fractal

    NASA Astrophysics Data System (ADS)

    Sadegh, Sanaz; Higgin, Jenny; Mannion, Patrick; Tamkun, Michael; Krapf, Diego

    A broad range of membrane proteins display anomalous diffusion on the cell surface. Different methods provide evidence for obstructed subdiffusion and diffusion on a fractal space, but the underlying structure inducing anomalous diffusion has never been visualized due to experimental challenges. We addressed this problem by imaging the cortical actin at high resolution while simultaneously tracking individual membrane proteins in live mammalian cells. Our data show that actin introduces barriers leading to compartmentalization of the plasma membrane and that membrane proteins are transiently confined within actin fences. Furthermore, superresolution imaging shows that the cortical actin is organized into a self-similar fractal. These results present a hierarchical nanoscale picture of the plasma membrane and demonstrate direct interactions between the actin cortex and the cell surface.

  17. Compartmentalization of metabolic pathways in yeast mitochondria improves production of branched chain alcohols

    PubMed Central

    Avalos, José L.; Fink, Gerald R.; Stephanopoulos, Gregory

    2013-01-01

    Efforts to improve the production of a compound of interest in Saccharomyces cerevisiae have mainly involved engineering or overexpression of cytoplasmic enzymes. We show that targeted expression of metabolic pathways to mitochondria can increase production levels compared with expression of the same pathways in the cytoplasm. Compartmentalisation of the Ehrlich pathway into mitochondria increased isobutanol production by 260%, whereas overexpression of the same pathway in the cytoplasm only improved yields by 10%, compared with a strain overexpressing only the first three steps of the biosynthetic pathway. Subcellular fractionation of engineered strains reveals that targeting the enzymes of the Ehrlich pathway to the mitochondria achieves higher local enzyme concentrations. Other benefits of compartmentalization may include increased availability of intermediates, removing the need to transport intermediates out of the mitochondrion, and reducing the loss of intermediates to competing pathways. PMID:23417095

  18. Host-parasite oscillation dynamics and evolution in a compartmentalized RNA replication system.

    PubMed

    Bansho, Yohsuke; Furubayashi, Taro; Ichihashi, Norikazu; Yomo, Tetsuya

    2016-04-12

    To date, various cellular functions have been reconstituted in vitro such as self-replication systems using DNA, RNA, and proteins. The next important challenges include the reconstitution of the interactive networks of self-replicating species and investigating how such interactions generate complex ecological behaviors observed in nature. Here, we synthesized a simple replication system composed of two self-replicating host and parasitic RNA species. We found that the parasitic RNA eradicates the host RNA under bulk conditions; however, when the system is compartmentalized, a continuous oscillation pattern in the population dynamics of the two RNAs emerges. The oscillation pattern changed as replication proceeded mainly owing to the evolution of the host RNA. These results demonstrate that a cell-like compartment plays an important role in host-parasite ecological dynamics and suggest that the origin of the host-parasite coevolution might date back to the very early stages of the evolution of life.

  19. Phagocytosis-inspired behaviour in synthetic protocell communities of compartmentalized colloidal objects

    NASA Astrophysics Data System (ADS)

    Rodríguez-Arco, Laura; Li, Mei; Mann, Stephen

    2017-08-01

    The spontaneous assembly of micro-compartmentalized colloidal objects capable of controlled interactions offers a step towards rudimentary forms of collective behaviour in communities of artificial cell-like entities (synthetic protocells). Here we report a primitive form of artificial phagocytosis in a binary community of synthetic protocells in which multiple silica colloidosomes are selectively ingested by self-propelled magnetic Pickering emulsion (MPE) droplets comprising particle-free fatty acid-stabilized apertures. Engulfment of the colloidosomes enables selective delivery and release of water-soluble payloads, and can be coupled to enzyme activity within the MPE droplets. Our results highlight opportunities for the development of new materials based on consortia of colloidal objects, and provide a novel microscale engineering approach to inducing higher-order behaviour in mixed populations of synthetic protocells.

  20. Compartmental culture of embryonic stem cell-derived neurons in microfluidic devices for use in axonal biology.

    PubMed

    Shin, Hwa Sung; Kim, Hyung Joon; Min, Seul Ki; Kim, Sung Hoon; Lee, Byung Man; Jeon, Noo Li

    2010-08-01

    Axonal pathology has been clearly implicated in neurodegenerative diseases making the compartmental culture of neurons a useful research tool. Primary neurons have already been cultured in compartmental microfluidic devices but their derivation from an animal is a time-consuming and difficult work and has a limit in their sources. Embryonic stem cell (ESC)-derived neurons (ESC_Ns) overcome this limit, since ESCs can be renewed without limit and can be differentiated into ESC_Ns by robust and reproducible protocols. In this research, ESC_Ns were derived from mouse ESCs in compartmental microfluidic devices, and their axons were isolated from the somal cell bodies. Once embryoid bodies (EBs) were localized in the microfluidic culture chamber, ESC_Ns spread out from the EBs and occupied the cell culture chamber. Their axons traversed the microchannels and finally were isolated from the somata, providing an arrangement comparable to dissociated primary neurons. This ESC_N compartmental microfluidic culture system not only offers a substitute for the primary neuron counterpart system but also makes it possible to make comparisons between the two systems.

  1. Sequence Stratigraphy of the Dakota Sandstone, Eastern San Juan Basin, New Mexico, and its Relationship to Reservoir Compartmentalization

    SciT

    Varney, Peter J.

    2002-04-23

    This research established the Dakota-outcrop sequence stratigraphy in part of the eastern San Juan Basin, New Mexico, and relates reservoir quality lithologies in depositional sequences to structure and reservoir compartmentalization in the South Lindrith Field area. The result was a predictive tool that will help guide further exploration and development.

  2. Lipid droplet-associated proteins (LDAPs) are required for the dynamic regulation of neutral lipid compartmentation in plant cells

    Eukaryotic cells compartmentalize neutral lipids into organelles called lipid droplets (LDs), and while much is known about the role of LDs in storing triacylglycerols (TAGs) in seeds, their biogenesis and function in non-seed tissues is poorly understood. Recently, we identified a class of plant-sp...

  3. Nucleolar structure across evolution: the transition between bi- and tri-compartmentalized nucleoli lies within the class Reptilia.

    PubMed

    Lamaye, Françoise; Galliot, Sonia; Alibardi, Lorenzo; Lafontaine, Denis L J; Thiry, Marc

    2011-05-01

    Two types of nucleolus can be distinguished among eukaryotic cells: a tri-compartmentalized nucleolus in amniotes and a bi-compartmentalized nucleolus in all the others. However, though the nucleolus' ultrastructure is well characterized in mammals and birds, it has been so far much less studied in reptiles. In this work, we examined the ultrastructural organization of the nucleolus in various tissues from different reptilian species (three turtles, three lizards, two crocodiles, and three snakes). Using cytochemical and immunocytological methods, we showed that in reptiles both types of nucleolus are present: a bi-compartmentalized nucleolus in turtles and a tri-compartmentalized nucleolus in the other species examined in this study. Furthermore, in a given species, the same type of nucleolus is present in all the tissues, however, the importance and the repartition of those nucleolar components could vary from one tissue to another. We also reveal that, contrary to the mammalian nucleolus, the reptilian fibrillar centers contain small clumps of condensed chromatin and that their surrounding dense fibrillar component is thicker. Finally, we also report that Cajal bodies are detected in reptiles. Altogether, we believe that these results have profound evolutionarily implications since they indicate that the point of transition between bipartite and tripartite nucleoli lies at the emergence of the amniotes within the class Reptilia. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Dynamic of CSF and serum biomarkers in HIV-1 subtype C encephalitis with CNS genetic compartmentalization-case study.

    PubMed

    de Almeida, Sergio M; Rotta, Indianara; Ribeiro, Clea E; Oliveira, Michelli F; Chaillon, Antoine; de Pereira, Ana Paula; Cunha, Ana Paula; Zonta, Marise; Bents, Joao França; Raboni, Sonia M; Smith, Davey; Letendre, Scott; Ellis, Ronald J

    2017-06-01

    Despite the effective suppression of viremia with antiretroviral therapy, HIV can still replicate in the central nervous system (CNS). This was a longitudinal study of the cerebrospinal fluid (CSF) and serum dynamics of several biomarkers related to inflammation, the blood-brain barrier, neuronal injury, and IgG intrathecal synthesis in serial samples of CSF and serum from a patient infected with HIV-1 subtype C with CNS compartmentalization.The phylogenetic analyses of plasma and CSF samples in an acute phase using next-generation sequencing and F-statistics analysis of C2-V3 haplotypes revealed distinct compartmentalized CSF viruses in paired CSF and peripheral blood mononuclear cell samples. The CSF biomarker analysis in this patient showed that symptomatic CSF escape is accompanied by CNS inflammation, high levels of cell and humoral immune biomarkers, CNS barrier dysfunction, and an increase in neuronal injury biomarkers with demyelization. Independent and isolated HIV replication can occur in the CNS, even in HIV-1 subtype C, leading to compartmentalization and development of quasispecies distinct from the peripheral plasma. These immunological aspects of the HIV CNS escape have not been described previously. To our knowledge, this is the first report of CNS HIV escape and compartmentalization in HIV-1 subtype C.

  5. Influence of bi- and tri-compartmental knee arthroplasty on the kinematics of the knee joint

    PubMed Central

    2011-01-01

    Background The cruciate ligaments are important stabilizers of the knee joint and determine joint kinematics in the natural knee and after cruciate retaining arthroplasty. No in vitro data is available to biomechanically evaluate the ability of the anterior cruciate ligament (ACL) to maintain knee joint kinematics after bicruciate-retaining bi-compartmental knee arthroplasty (BKA). Therefore, the objective of the current study was to investigate the kinematics of the natural knee joint, before and after installing bicruciate-retaining BKA and posterior cruciate retaining total knee arthroplasty. Specifically, we incorporated a dynamic knee simulator to simulate weight-bearing flexions on cadaveric knee specimen before and after surgical manipulations. Methods In this cadaveric study we investigated rotational and translational tibiofemoral kinematics during simulated weight-bearing flexions of the intact knee, after bi-compartmental knee arthroplasty (BKA+), after resecting the ACL in BKA (BKA-), and after posterior cruciate retaining total knee arthroplasty (TKA). Results Rotation of BKA+ is closest to the intact knee joint, whereas TKA shows significant differences from 30 to 90 degree of flexion. Within the tested flexion range (15 to 90 degree of flexion), there was no significant difference in the anterior-posterior translation among intact, BKA+, and TKA knees. Resecting the ACL in BKA leads to a significant anterior tibial translation. Conclusions BKA with intact cruciate ligaments resembles rotation and translation of the natural knee during a simulated weight-bearing flexion. It is a suitable treatment option for medial and patellofemoral osteoarthritis with advantages in rotational characteristics compared to TKA. PMID:21272328

  6. Transit-time and age distributions for nonlinear time-dependent compartmental systems.

    PubMed

    Metzler, Holger; Müller, Markus; Sierra, Carlos A

    2018-02-06

    Many processes in nature are modeled using compartmental systems (reservoir/pool/box systems). Usually, they are expressed as a set of first-order differential equations describing the transfer of matter across a network of compartments. The concepts of age of matter in compartments and the time required for particles to transit the system are important diagnostics of these models with applications to a wide range of scientific questions. Until now, explicit formulas for transit-time and age distributions of nonlinear time-dependent compartmental systems were not available. We compute densities for these types of systems under the assumption of well-mixed compartments. Assuming that a solution of the nonlinear system is available at least numerically, we show how to construct a linear time-dependent system with the same solution trajectory. We demonstrate how to exploit this solution to compute transit-time and age distributions in dependence on given start values and initial age distributions. Furthermore, we derive equations for the time evolution of quantiles and moments of the age distributions. Our results generalize available density formulas for the linear time-independent case and mean-age formulas for the linear time-dependent case. As an example, we apply our formulas to a nonlinear and a linear version of a simple global carbon cycle model driven by a time-dependent input signal which represents fossil fuel additions. We derive time-dependent age distributions for all compartments and calculate the time it takes to remove fossil carbon in a business-as-usual scenario.

  7. PKA catalytic subunit compartmentation regulates contractile and hypertrophic responses to β-adrenergic signaling

    PubMed Central

    Yang, Jason H.; Polanowska-Grabowska, Renata K.; Smith, Jeffrey S.; Shields, Charles W.; Saucerman, Jeffrey J.

    2014-01-01

    β-adrenergic signaling is spatiotemporally heterogeneous in the cardiac myocyte, conferring exquisite control to sympathetic stimulation. Such heterogeneity drives the formation of protein kinase A (PKA) signaling microdomains, which regulate Ca2+ handling and contractility. Here, we test the hypothesis that the nucleus independently comprises a PKA signaling microdomain regulating myocyte hypertrophy. Spatially-targeted FRET reporters for PKA activity identified slower PKA activation and lower isoproterenol sensitivity in the nucleus (t50 = 10.60±0.68 min; EC50 = 89.00 nmol/L) than in the cytosol (t50 = 3.71±0.25 min; EC50 = 1.22 nmol/L). These differences were not explained by cAMP or AKAP-based compartmentation. A computational model of cytosolic and nuclear PKA activity was developed and predicted that differences in nuclear PKA dynamics and magnitude are regulated by slow PKA catalytic subunit diffusion, while differences in isoproterenol sensitivity are regulated by nuclear expression of protein kinase inhibitor (PKI). These were validated by FRET and immunofluorescence. The model also predicted differential phosphorylation of PKA substrates regulating cell contractility and hypertrophy. Ca2+ and cell hypertrophy measurements validated these predictions and identified higher isoproterenol sensitivity for contractile enhancements (EC50 = 1.84 nmol/L) over cell hypertrophy (EC50 = 85.88 nmol/L). Over-expression of spatially targeted PKA catalytic subunit to the cytosol or nucleus enhanced contractile and hypertrophic responses, respectively. We conclude that restricted PKA catalytic subunit diffusion is an important PKA compartmentation mechanism and the nucleus comprises a novel PKA signaling microdomain, insulating hypertrophic from contractile β-adrenergic signaling responses. PMID:24225179

  8. The role of the bi-compartmental stem cell niche in delaying cancer

    NASA Astrophysics Data System (ADS)

    Shahriyari, Leili; Komarova, Natalia L.

    2015-10-01

    In recent years, by using modern imaging techniques, scientists have found evidence of collaboration between different types of stem cells (SCs), and proposed a bi-compartmental organization of the SC niche. Here we create a class of stochastic models to simulate the dynamics of such a heterogeneous SC niche. We consider two SC groups: the border compartment, S1, is in direct contact with transit-amplifying (TA) cells, and the central compartment, S2, is hierarchically upstream from S1. The S1 SCs differentiate or divide asymmetrically when the tissue needs TA cells. Both groups proliferate when the tissue requires SCs (thus maintaining homeostasis). There is an influx of S2 cells into the border compartment, either by migration, or by proliferation. We examine this model in the context of double-hit mutant generation, which is a rate-limiting step in the development of many cancers. We discover that this type of a cooperative pattern in the stem niche with two compartments leads to a significantly smaller rate of double-hit mutant production compared with a homogeneous, one-compartmental SC niche. Furthermore, the minimum probability of double-hit mutant generation corresponds to purely symmetric division of SCs, consistent with the literature. Finally, the optimal architecture (which minimizes the rate of double-hit mutant production) requires a large proliferation rate of S1 cells along with a small, but non-zero, proliferation rate of S2 cells. This result is remarkably similar to the niche structure described recently by several authors, where one of the two SC compartments was found more actively engaged in tissue homeostasis and turnover, while the other was characterized by higher levels of quiescence (but contributed strongly to injury recovery). Both numerical and analytical results are presented.

  9. The construction of next-generation matrices for compartmental epidemic models.

    PubMed

    Diekmann, O; Heesterbeek, J A P; Roberts, M G

    2010-06-06

    The basic reproduction number (0) is arguably the most important quantity in infectious disease epidemiology. The next-generation matrix (NGM) is the natural basis for the definition and calculation of (0) where finitely many different categories of individuals are recognized. We clear up confusion that has been around in the literature concerning the construction of this matrix, specifically for the most frequently used so-called compartmental models. We present a detailed easy recipe for the construction of the NGM from basic ingredients derived directly from the specifications of the model. We show that two related matrices exist which we define to be the NGM with large domain and the NGM with small domain. The three matrices together reflect the range of possibilities encountered in the literature for the characterization of (0). We show how they are connected and how their construction follows from the basic model ingredients, and establish that they have the same non-zero eigenvalues, the largest of which is the basic reproduction number (0). Although we present formal recipes based on linear algebra, we encourage the construction of the NGM by way of direct epidemiological reasoning, using the clear interpretation of the elements of the NGM and of the model ingredients. We present a selection of examples as a practical guide to our methods. In the appendix we present an elementary but complete proof that (0) defined as the dominant eigenvalue of the NGM for compartmental systems and the Malthusian parameter r, the real-time exponential growth rate in the early phase of an outbreak, are connected by the properties that (0) > 1 if and only if r > 0, and (0) = 1 if and only if r = 0.

  10. The Golgi apparatus regulates cGMP-dependent protein kinase I compartmentation and proteolysis.

    PubMed

    Kato, Shin; Chen, Jingsi; Cornog, Katherine H; Zhang, Huili; Roberts, Jesse D

    2015-06-01

    cGMP-dependent protein kinase I (PKGI) is an important effector of cGMP signaling that regulates vascular smooth muscle cell (SMC) phenotype and proliferation. PKGI has been detected in the perinuclear region of cells, and recent data indicate that proprotein convertases (PCs) typically resident in the Golgi apparatus (GA) can stimulate PKGI proteolysis and generate a kinase fragment that localizes to the nucleus and regulates gene expression. However, the role of the endomembrane system in PKGI compartmentation and processing is unknown. Here, we demonstrate that PKGI colocalizes with endoplasmic reticulum (ER), ER-Golgi intermediate compartment, GA cisterna, and trans-Golgi network proteins in pulmonary artery SMC and cell lines. Moreover, PKGI localizes with furin, a trans-Golgi network-resident PC known to cleave PKGI. ER protein transport influences PKGI localization because overexpression of a constitutively inactive Sar1 transgene caused PKGI retention in the ER. Additionally, PKGI appears to reside within the GA because PKGI immunoreactivity was determined to be resistant to cytosolic proteinase K treatment in live cells. The GA appears to play a role in PKGI proteolysis because overexpression of inositol 1,4,5-trisphosphate receptor-associated cGMP kinase substrate, not only tethered heterologous PKGI-β to the ER and decreased its localization to the GA, but also diminished PKGI proteolysis and nuclear translocation. Also, inhibiting intra-GA protein transport with monensin was observed to decrease PKGI cleavage. These studies detail a role for the endomembrane system in regulating PKGI compartmentation and proteolysis. Moreover, they support the investigation of mechanisms regulating PKGI-dependent nuclear cGMP signaling in the pulmonary vasculature with Golgi dysfunction. Copyright © 2015 the American Physiological Society.

  11. Adaptive developmental plasticity: compartmentalized responses to environmental cues and to corresponding internal signals provide phenotypic flexibility.

    PubMed

    Mateus, Ana Rita A; Marques-Pita, Manuel; Oostra, Vicencio; Lafuente, Elvira; Brakefield, Paul M; Zwaan, Bas J; Beldade, Patrícia

    2014-11-21

    The environmental regulation of development can result in the production of distinct phenotypes from the same genotype and provide the means for organisms to cope with environmental heterogeneity. The effect of the environment on developmental outcomes is typically mediated by hormonal signals which convey information about external cues to the developing tissues. While such plasticity is a wide-spread property of development, not all developing tissues are equally plastic. To understand how organisms integrate environmental input into coherent adult phenotypes, we must know how different body parts respond, independently or in concert, to external cues and to the corresponding internal signals. We quantified the effect of temperature and ecdysone hormone manipulations on post-growth tissue patterning in an experimental model of adaptive developmental plasticity, the butterfly Bicyclus anynana. Following a suite of traits evolving by natural or sexual selection, we found that different groups of cells within the same tissue have sensitivities and patterns of response that are surprisingly distinct for the external environmental cue and for the internal hormonal signal. All but those wing traits presumably involved in mate choice responded to developmental temperature and, of those, all but the wing traits not exposed to predators responded to hormone manipulations. On the other hand, while patterns of significant response to temperature contrasted traits on autonomously-developing wings, significant response to hormone manipulations contrasted neighboring groups of cells with distinct color fates. We also showed that the spatial compartmentalization of these responses cannot be explained by the spatial or temporal compartmentalization of the hormone receptor protein. Our results unravel the integration of different aspects of the adult phenotype into developmental and functional units which both reflect and impact evolutionary change. Importantly, our findings

  12. The construction of next-generation matrices for compartmental epidemic models

    PubMed Central

    Diekmann, O.; Heesterbeek, J. A. P.; Roberts, M. G.

    2010-01-01

    The basic reproduction number ℛ0 is arguably the most important quantity in infectious disease epidemiology. The next-generation matrix (NGM) is the natural basis for the definition and calculation of ℛ0 where finitely many different categories of individuals are recognized. We clear up confusion that has been around in the literature concerning the construction of this matrix, specifically for the most frequently used so-called compartmental models. We present a detailed easy recipe for the construction of the NGM from basic ingredients derived directly from the specifications of the model. We show that two related matrices exist which we define to be the NGM with large domain and the NGM with small domain. The three matrices together reflect the range of possibilities encountered in the literature for the characterization of ℛ0. We show how they are connected and how their construction follows from the basic model ingredients, and establish that they have the same non-zero eigenvalues, the largest of which is the basic reproduction number ℛ0. Although we present formal recipes based on linear algebra, we encourage the construction of the NGM by way of direct epidemiological reasoning, using the clear interpretation of the elements of the NGM and of the model ingredients. We present a selection of examples as a practical guide to our methods. In the appendix we present an elementary but complete proof that ℛ0 defined as the dominant eigenvalue of the NGM for compartmental systems and the Malthusian parameter r, the real-time exponential growth rate in the early phase of an outbreak, are connected by the properties that ℛ0 > 1 if and only if r > 0, and ℛ0 = 1 if and only if r = 0. PMID:19892718

  13. Bioaccessibility of selenium after human ingestion in relation to its chemical species and compartmentalization in maize.

    PubMed

    Mombo, Stéphane; Schreck, Eva; Dumat, Camille; Laplanche, Christophe; Pierart, Antoine; Longchamp, Mélanie; Besson, Philippe; Castrec-Rouelle, Maryse

    2016-06-01

    Selenium is a micronutrient needed by all living organisms including humans, but often present in low concentration in food with possible deficiency. From another side, at higher concentrations in soils as observed in seleniferous regions of the world, and in function of its chemical species, Se can also induce (eco)toxicity. Root Se uptake was therefore studied in function of its initial form for maize (Zea mays L.), a plant widely cultivated for human and animal food over the world. Se phytotoxicity and compartmentalization were studied in different aerial plant tissues. For the first time, Se oral human bioaccessibility after ingestion was assessed for the main Se species (Se(IV) and Se(VI)) with the BARGE ex vivo test in maize seeds (consumed by humans), and in stems and leaves consumed by animals. Corn seedlings were cultivated in hydroponic conditions supplemented with 1 mg L(-1) of selenium (Se(IV), Se(VI), Control) for 4 months. Biomass, Se concentration, and bioaccessibility were measured on harvested plants. A reduction in plant biomass was observed under Se treatments compared to control, suggesting its phytotoxicity. This plant biomass reduction was higher for selenite species than selenate, and seed was the main affected compartment compared to control. Selenium compartmentalization study showed that for selenate species, a preferential accumulation was observed in leaves, whereas selenite translocation was very limited toward maize aerial parts, except in the seeds where selenite concentrations are generally high. Selenium oral bioaccessibility after ingestion fluctuated from 49 to 89 % according to the considered plant tissue and Se species. Whatever the tissue, selenate appeared as the most human bioaccessible form. A potential Se toxicity was highlighted for people living in seleniferous regions, this risk being enhanced by the high Se bioaccessibility.

  14. Compartmentalized PDE4A5 Signaling Impairs Hippocampal Synaptic Plasticity and Long-Term Memory.

    PubMed

    Havekes, Robbert; Park, Alan J; Tolentino, Rosa E; Bruinenberg, Vibeke M; Tudor, Jennifer C; Lee, Yool; Hansen, Rolf T; Guercio, Leonardo A; Linton, Edward; Neves-Zaph, Susana R; Meerlo, Peter; Baillie, George S; Houslay, Miles D; Abel, Ted

    2016-08-24

    Alterations in cAMP signaling are thought to contribute to neurocognitive and neuropsychiatric disorders. Members of the cAMP-specific phosphodiesterase 4 (PDE4) family, which contains >25 different isoforms, play a key role in determining spatial cAMP degradation so as to orchestrate compartmentalized cAMP signaling in cells. Each isoform binds to a different set of protein complexes through its unique N-terminal domain, thereby leading to targeted degradation of cAMP in specific intracellular compartments. However, the functional role of specific compartmentalized PDE4 isoforms has not been examined in vivo Here, we show that increasing protein levels of the PDE4A5 isoform in mouse hippocampal excitatory neurons impairs a long-lasting form of hippocampal synaptic plasticity and attenuates hippocampus-dependent long-term memories without affecting anxiety. In contrast, viral expression of a truncated version of PDE4A5, which lacks the unique N-terminal targeting domain, does not affect long-term memory. Further, overexpression of the PDE4A1 isoform, which targets a different subset of signalosomes, leaves memory undisturbed. Fluorescence resonance energy transfer sensor-based cAMP measurements reveal that the full-length PDE4A5, in contrast to the truncated form, hampers forskolin-mediated increases in neuronal cAMP levels. Our study indicates that the unique N-terminal localization domain of PDE4A5 is essential for the targeting of specific cAMP-dependent signaling underlying synaptic plasticity and memory. The development of compounds to disrupt the compartmentalization of individual PDE4 isoforms by targeting their unique N-terminal domains may provide a fruitful approach to prevent cognitive deficits in neuropsychiatric and neurocognitive disorders that are associated with alterations in cAMP signaling. Neurons exhibit localized signaling processes that enable biochemical cascades to be activated selectively in specific subcellular compartments. The

  15. A new compartmental method for the analysis of liver FDG kinetics in small animal models.

    PubMed

    Garbarino, Sara; Vivaldi, Valentina; Delbary, Fabrice; Caviglia, Giacomo; Piana, Michele; Marini, Cecilia; Capitanio, Selene; Calamia, Iolanda; Buschiazzo, Ambra; Sambuceti, Gianmario

    2015-12-01

    Compartmental analysis is a standard method to quantify metabolic processes using fluorodeoxyglucose-positron emission tomography (FDG-PET). For liver studies, this analysis is complex due to the hepatocyte capability to dephosphorylate and release glucose and FDG into the blood. Moreover, a tracer is supplied to the liver by both the hepatic artery and the portal vein, which is not visible in PET images. This study developed an innovative computational approach accounting for the reversible nature of FDG in the liver and directly computing the portal vein tracer concentration by means of gut radioactivity measurements. Twenty-one mice were subdivided into three groups: the control group 'CTR' (n = 7) received no treatment, the short-term starvation group 'STS' (n = 7) was submitted to food deprivation with free access to water within 48 h before imaging, and the metformin group 'MTF' (n = 7) was treated with metformin (750 mg/Kg per day) for 1 month. All mice underwent a dynamic micro-PET study for 50 min after an (18)F-FDG injection. The compartmental analysis considered two FDG pools (phosphorylated and free) in both the gut and liver. A tracer was carried into the liver by the hepatic artery and the portal vein, and tracer delivery from the gut was considered as the sole input for portal vein tracer concentration. Accordingly, both the liver and gut were characterized by two compartments and two exchange coefficients. Each one of the two two-compartment models was mathematically described by a system of differential equations, and data optimization was performed by applying a Newton algorithm to the inverse problems associated to these differential systems. All rate constants were stable in each group. The tracer coefficient from the free to the metabolized compartment in the liver was increased by STS, while it was unaltered by MTF. By contrast, the tracer coefficient from the metabolized to the free compartment was reduced by MTF and increased by STS. Data

  16. Vascular Nox (NADPH Oxidase) Compartmentalization, Protein Hyperoxidation, and Endoplasmic Reticulum Stress Response in Hypertension.

    PubMed

    Camargo, Livia L; Harvey, Adam P; Rios, Francisco J; Tsiropoulou, Sofia; Da Silva, Renée de Nazaré Oliveira; Cao, Zhenbo; Graham, Delyth; McMaster, Claire; Burchmore, Richard J; Hartley, Richard C; Bulleid, Neil; Montezano, Augusto C; Touyz, Rhian M

    2018-07-01

    Vascular Nox (NADPH oxidase)-derived reactive oxygen species and endoplasmic reticulum (ER) stress have been implicated in hypertension. However, relationships between these processes are unclear. We hypothesized that Nox isoforms localize in a subcellular compartment-specific manner, contributing to oxidative and ER stress, which influence the oxidative proteome and vascular function in hypertension. Nox compartmentalization (cell fractionation), O 2 - (lucigenin), H 2 O 2 (amplex red), reversible protein oxidation (sulfenylation), irreversible protein oxidation (protein tyrosine phosphatase, peroxiredoxin oxidation), and ER stress (PERK [protein kinase RNA-like endoplasmic reticulum kinase], IRE1α [inositol-requiring enzyme 1], and phosphorylation/oxidation) were studied in spontaneously hypertensive rat (SHR) vascular smooth muscle cells (VSMCs). VSMC proliferation was measured by fluorescence-activated cell sorting, and vascular reactivity assessed in stroke-prone SHR arteries by myography. Noxs were downregulated by short interfering RNA and pharmacologically. In SHR, Noxs were localized in specific subcellular regions: Nox1 in plasma membrane and Nox4 in ER. In SHR, oxidative stress was associated with increased protein sulfenylation and hyperoxidation of protein tyrosine phosphatases and peroxiredoxins. Inhibition of Nox1 (NoxA1ds), Nox1/4 (GKT137831), and ER stress (4-phenylbutyric acid/tauroursodeoxycholic acid) normalized SHR vascular reactive oxygen species generation. GKT137831 reduced IRE1α sulfenylation and XBP1 (X-box binding protein 1) splicing in SHR. Increased VSMC proliferation in SHR was normalized by GKT137831, 4-phenylbutyric acid, and STF083010 (IRE1-XBP1 disruptor). Hypercontractility in the stroke-prone SHR was attenuated by 4-phenylbutyric acid. We demonstrate that protein hyperoxidation in hypertension is associated with oxidative and ER stress through upregulation of plasmalemmal-Nox1 and ER-Nox4. The IRE1-XBP1 pathway of the ER stress

  17. Compartmental analysis of the disposition of benzo[a]pyrene in rats.

    PubMed

    Bevan, D R; Weyand, E H

    1988-11-01

    We have previously reported the disposition of benzo[a]pyrene (B[a]P) and its metabolites in male Sprague-Dawley rats following intratracheal instillation of [3H]B[a]P [Weyand, E.H. and Bevan, D.R. (1986) Cancer Res., 46, 5655-5661]. In some experiments, cannulas were implanted in the bile duct of the animals prior to administration of [3H]B[a]P [Weyand, E.H. and Bevan, D.R. (1987) Drug Metab. Disposition, 15, 442-448]. Based on these data, we have developed a compartmental model of the distribution of radioactivity to provide a quantitative description of the fate of B[a]P and its metabolites in rats. Modeling of the distribution of radioactivity was performed using the Simulation, Analysis and Modeling (SAAM) and conversational SAAM (CONSAM) computer programs. Compartments in the model included organs into which the largest amounts of radioactivity were distributed as well as pathways for excretion of radioactivity from the animals. Data from animals with and without cannulas implanted in the bile duct were considered simultaneously during modeling. Radioactivity was so rapidly absorbed from the lungs that an absorption phase into blood was not apparent at the earliest sampling times. Using the model of extrapolate to shorter times, it was predicted that the maximum amount of radioactivity was present in blood within 2 min after administration. In addition, considerable recycling of radioactivity back to lungs from blood was predicted by the model. Transfer of radioactivity from blood to liver and carcass (skin, muscle, bones, fat and associated blood) also was extensive. Carcass was modeled as the sum of two compartments to obtain agreement between the model and experimental data. The model accounted for enterohepatic circulation of B[a]P metabolites; data also required that intestinal secretion be included in the model. Quantitative data obtained from compartmental analysis included rate constants for transfer of radioactivity among compartments as well as

  18. Compartmentalization of endocannabinoids into lipid rafts in a microglial cell line devoid of caveorrlin-1

    PubMed Central

    Rimmerman, Neta; Bradshaw, Heather B; Kozela, Ewa; Levy, Rivka; Juknat, Ana; Vogel, Zvi

    2012-01-01

    BACKGROUND AND PURPOSE N-acyl ethanolamines (NAEs) and 2-arachidonoyl glycerol (2-AG) are endogenous cannabinoids and along with related lipids are synthesized on demand from membrane phospholipids. Here, we have studied the compartmentalization of NAEs and 2-AG into lipid raft fractions isolated from the caveolin-1-lacking microglial cell line BV-2, following vehicle or cannabidiol (CBD) treatment. Results were compared with those from the caveolin-1-positive F-11 cell line. EXPERIMENTAL APPROACH BV-2 cells were incubated with CBD or vehicle. Cells were fractionated using a detergent-free continuous OptiPrep density gradient. Lipids in fractions were quantified using HPLC/MS/MS. Proteins were measured using Western blot. KEY RESULTS BV-2 cells were devoid of caveolin-1. Lipid rafts were isolated from BV-2 cells as confirmed by co-localization with flotillin-1 and sphingomyelin. Small amounts of cannabinoid CB1 receptors were found in lipid raft fractions. After incubation with CBD, levels and distribution in lipid rafts of 2-AG, N-arachidonoyl ethanolamine (AEA), and N-oleoyl ethanolamine (OEA) were not changed. Conversely, the levels of the saturated N-stearoyl ethanolamine (SEA) and N-palmitoyl ethanolamine (PEA) were elevated in lipid raft fractions. In whole cells with growth medium, CBD treatment increased AEA and OEA time-dependently, while levels of 2-AG, PEA and SEA did not change. CONCLUSIONS AND IMPLICATIONS Whereas levels of 2-AG were not affected by CBD treatment, the distribution and levels of NAEs showed significant changes. Among the NAEs, the degree of acyl chain saturation predicted the compartmentalization after CBD treatment suggesting a shift in cell signalling activity. LINKED ARTICLES This article is part of a themed section on Cannabinoids in Biology and Medicine. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2012.165.issue-8. To view Part I of Cannabinoids in Biology and Medicine visit http://dx.doi.org/10

  19. Single cell digital polymerase chain reaction on self-priming compartmentalization chip.

    PubMed

    Zhu, Qiangyuan; Qiu, Lin; Xu, Yanan; Li, Guang; Mu, Ying

    2017-01-01

    Single cell analysis provides a new framework for understanding biology and disease, however, an absolute quantification of single cell gene expression still faces many challenges. Microfluidic digital polymerase chain reaction (PCR) provides a unique method to absolutely quantify the single cell gene expression, but only limited devices are developed to analyze a single cell with detection variation. This paper describes a self-priming compartmentalization (SPC) microfluidic digital polymerase chain reaction chip being capable of performing single molecule amplification from single cell. The chip can be used to detect four single cells simultaneously with 85% of sample digitization. With the optimized protocol for the SPC chip, we first tested the ability, precision, and sensitivity of our SPC digital PCR chip by assessing β-actin DNA gene expression in 1, 10, 100, and 1000 cells. And the reproducibility of the SPC chip is evaluated by testing 18S rRNA of single cells with 1.6%-4.6% of coefficient of variation. At last, by detecting the lung cancer related genes, PLAU gene expression of A549 cells at the single cell level, the single cell heterogeneity was demonstrated. So, with the power-free, valve-free SPC chip, the gene copy number of single cells can be quantified absolutely with higher sensitivity, reduced labor time, and reagent. We expect that this chip will enable new studies for biology and disease.

  20. Identification of HIV-1 genitourinary tract compartmentalization by analyzing the env gene sequences in urine.

    PubMed

    Blasi, Maria; Carpenter, J Harris; Balakumaran, Bala; Cara, Andrea; Gao, Feng; Klotman, Mary E

    2015-08-24

    HIV-1 persists indefinitely in memory CD4 T cells and other long-lived cellular reservoirs despite antiretroviral therapy. Our group had previously demonstrated that HIV-1 can establish a productive infection in renal epithelial cells and that the kidney represents a separate compartment for HIV-1 replication. Here, to better understand the viruses in this unique site, we genetically characterized and compared the viruses in blood and urine specimens from 24 HIV-1 infected patients with detectable viremia. Blood and urine samples were obtained from 35 HIV-1 positive patients. Single-genome amplification was performed on HIV-1 env RNA and DNA isolated from urine supernatants and urine-derived cell pellets, respectively, as well as from plasma and peripheral blood mononuclear cell from the same individuals. Neighbor-joining trees were constructed under the Kimura 2-parameter model. We amplified and sequenced the full-length HIV-1 envelope (env) gene from 12 of the 24 individuals, indicating that 50% of the viremic HIV-1-positive patients had viral RNA in their urine. Phylogenetic analysis of the env sequences from four individuals with more than 15 urine-derived env sequences showed that the majority of the sequences from urine formed distinct cluster(s) independent of those peripheral blood mononuclear cell and plasma-derived sequences, consistent with viral compartmentalization in the urine. Our results suggest the presence of a distinct HIV compartment in the genitourinary tract.

  1. Identification of HIV-1 Genitourinary Tract Compartmentalization by Analyzing the env Gene Sequences in Urine

    PubMed Central

    BLASI, Maria; CARPENTER, J. Harris; BALAKUMARAN, Bala; CARA, Andrea; GAO, Feng; KLOTMAN, Mary E.

    2015-01-01

    Objective HIV-1 persists indefinitely in memory CD4+ T cells and other long-lived cellular reservoirs despite antiretroviral therapy (ART). Our group had previously demonstrated that HIV-1 can establish a productive infection in renal epithelial cells and that the kidney represents a separate compartment for HIV-1 replication. Here, to better understand the viruses in this unique site, we genetically characterized and compared the viruses in blood and urine specimens from twenty-four HIV-1 infected subjects with detectable viremia. Design and Methods Blood and urine samples were obtained from 35 HIV-1 positive subjects. Single-genome amplification was performed on HIV-1 env RNA and DNA isolated from urine supernatants and urine derived cell pellets respectively, as well as from plasma and PBMC from the same individuals. Neighbor-joining trees were constructed under the Kimura 2-parameter mode. Results We amplified and sequenced the full-length HIV-1 envelope (env) gene from twelve of the twenty-four individuals, indicating that fifty percent (50%) of the viremic HIV-1 positive patients had viral RNA in their urine. Phylogenetic analysis of the env sequences from four subjects with more than fifteen urine-derived env sequences showed that the majority of the sequences from urine formed distinct cluster(s) independent of those PBMC and plasma-derived sequences, consistent with viral compartmentalization in the urine. Conclusions Our results suggest the presence of a distinct HIV compartment in the genitourinary tract. PMID:26372275

  2. Checking distributional assumptions for pharmacokinetic summary statistics based on simulations with compartmental models.

    PubMed

    Shen, Meiyu; Russek-Cohen, Estelle; Slud, Eric V

    2016-08-12

    Bioequivalence (BE) studies are an essential part of the evaluation of generic drugs. The most common in vivo BE study design is the two-period two-treatment crossover design. AUC (area under the concentration-time curve) and Cmax (maximum concentration) are obtained from the observed concentration-time profiles for each subject from each treatment under each sequence. In the BE evaluation of pharmacokinetic crossover studies, the normality of the univariate response variable, e.g. log(AUC) 1 or log(Cmax), is often assumed in the literature without much evidence. Therefore, we investigate the distributional assumption of the normality of response variables, log(AUC) and log(Cmax), by simulating concentration-time profiles from two-stage pharmacokinetic models (commonly used in pharmacokinetic research) for a wide range of pharmacokinetic parameters and measurement error structures. Our simulations show that, under reasonable distributional assumptions on the pharmacokinetic parameters, log(AUC) has heavy tails and log(Cmax) is skewed. Sensitivity analyses are conducted to investigate how the distribution of the standardized log(AUC) (or the standardized log(Cmax)) for a large number of simulated subjects deviates from normality if distributions of errors in the pharmacokinetic model for plasma concentrations deviate from normality and if the plasma concentration can be described by different compartmental models.

  3. Single cell digital polymerase chain reaction on self-priming compartmentalization chip

    PubMed Central

    Zhu, Qiangyuan; Qiu, Lin; Xu, Yanan; Li, Guang; Mu, Ying

    2017-01-01

    Single cell analysis provides a new framework for understanding biology and disease, however, an absolute quantification of single cell gene expression still faces many challenges. Microfluidic digital polymerase chain reaction (PCR) provides a unique method to absolutely quantify the single cell gene expression, but only limited devices are developed to analyze a single cell with detection variation. This paper describes a self-priming compartmentalization (SPC) microfluidic digital polymerase chain reaction chip being capable of performing single molecule amplification from single cell. The chip can be used to detect four single cells simultaneously with 85% of sample digitization. With the optimized protocol for the SPC chip, we first tested the ability, precision, and sensitivity of our SPC digital PCR chip by assessing β-actin DNA gene expression in 1, 10, 100, and 1000 cells. And the reproducibility of the SPC chip is evaluated by testing 18S rRNA of single cells with 1.6%–4.6% of coefficient of variation. At last, by detecting the lung cancer related genes, PLAU gene expression of A549 cells at the single cell level, the single cell heterogeneity was demonstrated. So, with the power-free, valve-free SPC chip, the gene copy number of single cells can be quantified absolutely with higher sensitivity, reduced labor time, and reagent. We expect that this chip will enable new studies for biology and disease. PMID:28191267

  4. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina.

    PubMed

    Zullo, Joseph M; Demarco, Ignacio A; Piqué-Regi, Roger; Gaffney, Daniel J; Epstein, Charles B; Spooner, Chauncey J; Luperchio, Teresa R; Bernstein, Bradley E; Pritchard, Jonathan K; Reddy, Karen L; Singh, Harinder

    2012-06-22

    A large fraction of the mammalian genome is organized into inactive chromosomal domains along the nuclear lamina. The mechanism by which these lamina associated domains (LADs) are established remains to be elucidated. Using genomic repositioning assays, we show that LADs, spanning the developmentally regulated IgH and Cyp3a loci contain discrete DNA regions that associate chromatin with the nuclear lamina and repress gene activity in fibroblasts. Lamina interaction is established during mitosis and likely involves the localized recruitment of Lamin B during late anaphase. Fine-scale mapping of LADs reveals numerous lamina-associating sequences (LASs), which are enriched for a GAGA motif. This repeated motif directs lamina association and is bound by the transcriptional repressor cKrox, in a complex with HDAC3 and Lap2β. Knockdown of cKrox or HDAC3 results in dissociation of LASs/LADs from the nuclear lamina. These results reveal a mechanism that couples nuclear compartmentalization of chromatin domains with the control of gene activity. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

    PubMed

    Nora, Elphège P; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A; Bruneau, Benoit G

    2017-05-18

    The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Hypothalamic metabolic compartmentation during appetite regulation as revealed by magnetic resonance imaging and spectroscopy methods

    PubMed Central

    Lizarbe, Blanca; Benitez, Ania; Peláez Brioso, Gerardo A.; Sánchez-Montañés, Manuel; López-Larrubia, Pilar; Ballesteros, Paloma; Cerdán, Sebastián

    2013-01-01

    We review the role of neuroglial compartmentation and transcellular neurotransmitter cycling during hypothalamic appetite regulation as detected by Magnetic Resonance Imaging (MRI) and Spectroscopy (MRS) methods. We address first the neurochemical basis of neuroendocrine regulation in the hypothalamus and the orexigenic and anorexigenic feed-back loops that control appetite. Then we examine the main MRI and MRS strategies that have been used to investigate appetite regulation. Manganese-enhanced magnetic resonance imaging (MEMRI), Blood oxygenation level-dependent contrast (BOLD), and Diffusion-weighted magnetic resonance imaging (DWI) have revealed Mn2+ accumulations, augmented oxygen consumptions, and astrocytic swelling in the hypothalamus under fasting conditions, respectively. High field 1H magnetic resonance in vivo, showed increased hypothalamic myo-inositol concentrations as compared to other cerebral structures. 1H and 13C high resolution magic angle spinning (HRMAS) revealed increased neuroglial oxidative and glycolytic metabolism, as well as increased hypothalamic glutamatergic and GABAergic neurotransmissions under orexigenic stimulation. We propose here an integrative interpretation of all these findings suggesting that the neuroendocrine regulation of appetite is supported by important ionic and metabolic transcellular fluxes which begin at the tripartite orexigenic clefts and become extended spatially in the hypothalamus through astrocytic networks becoming eventually MRI and MRS detectable. PMID:23781199

  7. Compartmental modelling of the pharmacokinetics of a breast cancer resistance protein.

    PubMed

    Grandjean, Thomas R B; Chappell, Mike J; Yates, James T W; Jones, Kevin; Wood, Gemma; Coleman, Tanya

    2011-11-01

    A mathematical model for the pharmacokinetics of Hoechst 33342 following administration into a culture medium containing a population of transfected cells (HEK293 hBCRP) with a potent breast cancer resistance protein inhibitor, Fumitremorgin C (FTC), present is described. FTC is reported to almost completely annul resistance mediated by BCRP in vitro. This non-linear compartmental model has seven macroscopic sub-units, with 14 rate parameters. It describes the relationship between the concentration of Hoechst 33342 and FTC, initially spiked in the medium, and the observed change in fluorescence due to Hoechst 33342 binding to DNA. Structural identifiability analysis has been performed using two methods, one based on the similarity transformation/exhaustive modelling approach and the other based on the differential algebra approach. The analyses demonstrated that all models derived are uniquely identifiable for the experiments/observations available. A kinetic modelling software package, namely FACSIMILE (MPCA Software, UK), was used for parameter fitting and to obtain numerical solutions for the system equations. Model fits gave very good agreement with in vitro data provided by AstraZeneca across a variety of experimental scenarios. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  8. Magnetic resonance imaging demonstrates compartmental muscle mechanisms of human vertical fusional vergence

    PubMed Central

    Clark, Robert A.

    2015-01-01

    Vertical fusional vergence (VFV) normally compensates for slight vertical heterophorias. We employed magnetic resonance imaging to clarify extraocular muscle contributions to VFV induced by monocular two-prism diopter (1.15°) base-up prism in 14 normal adults. Fusion during prism viewing requires monocular infraduction. Scans were repeated without prism, and with prism shifted contralaterally. Contractility indicated by morphometric indexes was separately analyzed in medial and lateral vertical rectus and superior oblique (SO) putative compartments, and superior and inferior horizontal rectus extraocular muscle putative compartments, but in the whole inferior oblique (IO). Images confirmed appropriate VFV that was implemented by the inferior rectus (IR) medial compartment contracting ipsilateral and relaxing contralateral to prism. There was no significant contractility in the IR lateral compartment. The superior but not inferior lateral rectus (LR) compartment contracted significantly in the prism viewing eye, but not contralateral to prism. The IO contracted ipsilateral but not contralateral to the prism. In the infraducting eye, the SO medial compartment relaxed significantly, while the lateral compartment was unchanged; contralateral to prism, the SO lateral compartment contracted, while the medial compartment was unchanged. There was no contractility in the superior or medial rectus muscles in either eye. There was no globe retraction. We conclude that the vertical component of VFV is primarily implemented by IR medial compartment contraction. Since appropriate vertical rotation is not directly implemented, or is opposed, by associated differential LR and SO compartmental activity, and IO contraction, these actions probably implement a torsional component of VFV. PMID:25589593

  9. Hyperforin depletes synaptic vesicles content and induces compartmental redistribution of nerve ending monoamines.

    PubMed

    Roz, Netta; Rehavi, Moshe

    2004-10-22

    Hyperforin, a phloroglucinol derivative found in Hypericum perforatum (St. John's wort) extracts has antidepressant properties in depressed patients. Hyperforin has a unique pharmacological profile and it inhibits uptake of biogenic monoamines as well as amino acid transmitters. We have recently showed that the monoamines uptake inhibition exerted by hyperforin is related to its ability to dissipate the pH gradient across the synaptic vesicle membrane thereby interfering with vesicular monoamines storage. In the present study we demonstrate that hyperforin induces dose-dependent efflux of preloaded [3H]5HT and [3H]DA from rat brain slices. Moreover, we show that hyperforin attenuates depolarization- dependent release of monoamines, while increasing monoamine release by amphetamine or fenfluramine. It is also demonstrated that preincubation of brain slices with reserpine is associated with dose- dependent blunting of efflux due to hyperforin. Our data indicate that hyperforin-induced efflux of [3H]5HT and [3H]DA reflect elevated cytoplasmic concentrations of the two monoamines secondary to the depletion of the synaptic vesicle content and the compartmental redistribution of nerve ending monoamines. Copyright 2004 Elsevier Inc.

  10. Compartmentalized Low-Rank Recovery for High-Resolution Lipid Unsuppressed MRSI

    PubMed Central

    Bhattacharya, Ipshita; Jacob, Mathews

    2017-01-01

    Purpose To introduce a novel algorithm for the recovery of high-resolution magnetic resonance spectroscopic imaging (MRSI) data with minimal lipid leakage artifacts, from dual-density spiral acquisition. Methods The reconstruction of MRSI data from dual-density spiral data is formulated as a compartmental low-rank recovery problem. The MRSI dataset is modeled as the sum of metabolite and lipid signals, each of which is support limited to the brain and extracranial regions, respectively, in addition to being orthogonal to each other. The reconstruction problem is formulated as an optimization problem, which is solved using iterative reweighted nuclear norm minimization. Results The comparisons of the scheme against dual-resolution reconstruction algorithm on numerical phantom and in vivo datasets demonstrate the ability of the scheme to provide higher spatial resolution and lower lipid leakage artifacts. The experiments demonstrate the ability of the scheme to recover the metabolite maps, from lipid unsuppressed datasets with echo time (TE)=55 ms. Conclusion The proposed reconstruction method and data acquisition strategy provide an efficient way to achieve high-resolution metabolite maps without lipid suppression. This algorithm would be beneficial for fast metabolic mapping and extension to multislice acquisitions. PMID:27851875

  11. A Compartmental Model for Zika Virus with Dynamic Human and Vector Populations

    PubMed Central

    Lee, Eva K; Liu, Yifan; Pietz, Ferdinand H

    2016-01-01

    The Zika virus (ZIKV) outbreak in South American countries and its potential association with microcephaly in newborns and Guillain-Barré Syndrome led the World Health Organization to declare a Public Health Emergency of International Concern. To understand the ZIKV disease dynamics and evaluate the effectiveness of different containment strategies, we propose a compartmental model with a vector-host structure for ZIKV. The model utilizes logistic growth in human population and dynamic growth in vector population. Using this model, we derive the basic reproduction number to gain insight on containment strategies. We contrast the impact and influence of different parameters on the virus trend and outbreak spread. We also evaluate different containment strategies and their combination effects to achieve early containment by minimizing total infections. This result can help decision makers select and invest in the strategies most effective to combat the infection spread. The decision-support tool demonstrates the importance of “digital disease surveillance” in response to waves of epidemics including ZIKV, Dengue, Ebola and cholera. PMID:28269870

  12. Characterization and subcellular compartmentation of recombinant 4-hydroxyphenylpyruvate dioxygenase from Arabidopsis in transgenic tobacco.

    PubMed

    Garcia, I; Rodgers, M; Pepin, R; Hsieh, T F; Matringe, M

    1999-04-01

    4-Hydroxyphenylpyruvate dioxygenase (4HPPD) catalyzes the formation of homogentisate (2,5-dihydroxyphenylacetate) from p-hydroxyphenylpyruvate and molecular oxygen. In plants this enzyme activity is involved in two distinct metabolic processes, the biosynthesis of prenylquinones and the catabolism of tyrosine. We report here the molecular and biochemical characterization of an Arabidopsis 4HPPD and the compartmentation of the recombinant protein in chlorophyllous tissues. We isolated a 1508-bp cDNA with one large open reading frame of 1338 bp. Southern analysis strongly suggested that this Arabidopsis 4HPPD is encoded by a single-copy gene. We investigated the biochemical characteristics of this 4HPPD by overproducing the recombinant protein in Escherichia coli JM105. The subcellular localization of the recombinant 4HPPD in chlorophyllous tissues was examined by overexpressing its complete coding sequence in transgenic tobacco (Nicotiana tabacum), using Agrobacterium tumefaciens transformation. We performed western analyses for the immunodetection of protein extracts from purified chloroplasts and total leaf extracts and for the immunocytochemistry on tissue sections. These analyses clearly revealed that 4HPPD was confined to the cytosol compartment, not targeted to the chloroplast. Western analyses confirmed the presence of a cytosolic form of 4HPPD in cultured green Arabidopsis cells.

  13. Compartmentalization and transmission of multiple epstein-barr virus strains in asymptomatic carriers.

    PubMed

    Sitki-Green, Diane; Covington, Mary; Raab-Traub, Nancy

    2003-02-01

    Infection with the Epstein-Barr virus (EBV) is often subclinical in the presence of a healthy immune response; thus, asymptomatic infection is largely uncharacterized. This study analyzed the nature of EBV infection in 20 asymptomatic immunocompetent hosts over time through the identification of EBV strain variants in the peripheral blood and oral cavity. A heteroduplex tracking assay specific for the EBV gene LMP1 precisely identified the presence of multiple EBV strains in each subject. The strains present in the peripheral blood and oral cavity were often completely discordant, indicating the existence of distinct infections, and the strains present and their relative abundance changed considerably between time points. The possible transmission of strains between the oral cavity and peripheral blood compartments could be tracked within subjects, suggesting that reactivation in the oral cavity and subsequent reinfection of B lymphocytes that reenter the periphery contribute to the maintenance of persistence. In addition, distinct virus strains persisted in the oral cavity over many time points, suggesting an important role for epithelial cells in the maintenance of persistence. Asymptomatic individuals without tonsillar tissue, which is believed to be an important source of virus for the oral cavity, also exhibited multiple strains and a cyclic pattern of transmission between compartments. This study revealed that the majority of patients with infectious mononucleosis were infected with multiple strains of EBV that were also compartmentalized, suggesting that primary infection involves the transmission of multiple strains. Both the primary and carrier states of infection with EBV are more complex than previously thought.

  14. Proposing a Compartmental Model for Leprosy and Parameterizing Using Regional Incidence in Brazil.

    PubMed

    Smith, Rebecca Lee

    2016-08-01

    Hansen's disease (HD), or leprosy, is still considered a public health risk in much of Brazil. Understanding the dynamics of the infection at a regional level can aid in identification of targets to improve control. A compartmental continuous-time model for leprosy dynamics was designed based on understanding of the biology of the infection. The transmission coefficients for the model and the rate of detection were fit for each region using Approximate Bayesian Computation applied to paucibacillary and multibacillary incidence data over the period of 2000 to 2010, and model fit was validated on incidence data from 2011 to 2012. Regional variation was noted in detection rate, with cases in the Midwest estimated to be infectious for 10 years prior to detection compared to 5 years for most other regions. Posterior predictions for the model estimated that elimination of leprosy as a public health risk would require, on average, 44-45 years in the three regions with the highest prevalence. The model is easily adaptable to other settings, and can be studied to determine the efficacy of improved case finding on leprosy control.

  15. Lab-on-a-chip in vitro compartmentalization technologies for protein studies.

    PubMed

    Zhu, Yonggang; Power, Barbara E

    2008-01-01

    In vitro compartmentalization (IVC) is a powerful tool for studying protein-protein reactions, due to its high capacity and the versatility of droplet technologies. IVC bridges the gap between chemistry and biology as it enables the incorporation of unnatural amino acids with modifications into biological systems, through protein transcription and translation reactions, in a cell-like microdrop environment. The quest for the ultimate chip for protein studies using IVC is the drive for the development of various microfluidic droplet technologies to enable these unusual biochemical reactions to occur. These techniques have been shown to generate precise microdrops with a controlled size. Various chemical and physical phenomena have been utilized for on-chip manipulation to allow the droplets to be generated, fused, and split. Coupled with detection techniques, droplets can be sorted and selected. These capabilities allow directed protein evolution to be carried out on a microchip. With further technological development of the detection module, factors such as addressable storage, transport and interfacing technologies, could be integrated and thus provide platforms for protein studies with high efficiency and accuracy that conventional laboratories cannot achieve.

  16. Thymic selection threshold defined by compartmentalization of Ras/MAPK signalling.

    PubMed

    Daniels, Mark A; Teixeiro, Emma; Gill, Jason; Hausmann, Barbara; Roubaty, Dominique; Holmberg, Kaisa; Werlen, Guy; Holländer, Georg A; Gascoigne, Nicholas R J; Palmer, Ed

    2006-12-07

    A healthy individual can mount an immune response to exogenous pathogens while avoiding an autoimmune attack on normal tissues. The ability to distinguish between self and non-self is called 'immunological tolerance' and, for T lymphocytes, involves the generation of a diverse pool of functional T cells through positive selection and the removal of overtly self-reactive thymocytes by negative selection during T-cell ontogeny. To elucidate how thymocytes arrive at these cell fate decisions, here we have identified ligands that define an extremely narrow gap spanning the threshold that distinguishes positive from negative selection. We show that, at the selection threshold, a small increase in ligand affinity for the T-cell antigen receptor leads to a marked change in the activation and subcellular localization of Ras and mitogen-activated protein kinase (MAPK) signalling intermediates and the induction of negative selection. The ability to compartmentalize signalling molecules differentially in the cell endows the thymocyte with the ability to convert a small change in analogue input (affinity) into a digital output (positive versus negative selection) and provides the basis for establishing central tolerance.

  17. Stochastic, compartmental, and dynamic modeling of cross-contamination during mechanical smearing of cheeses.

    PubMed

    Aziza, Fanny; Mettler, Eric; Daudin, Jean-Jacques; Sanaa, Moez

    2006-06-01

    Cheese smearing is a complex process and the potential for cross-contamination with pathogenic or undesirable microorganisms is critical. During ripening, cheeses are salted and washed with brine to develop flavor and remove molds that could develop on the surfaces. Considering the potential for cross-contamination of this process in quantitative risk assessments could contribute to a better understanding of this phenomenon and, eventually, improve its control. The purpose of this article is to model the cross-contamination of smear-ripened cheeses due to the smearing operation under industrial conditions. A compartmental, dynamic, and stochastic model is proposed for mechanical brush smearing. This model has been developed to describe the exchange of microorganisms between compartments. Based on the analytical solution of the model equations and on experimental data collected with an industrial smearing machine, we assessed the values of the transfer parameters of the model. Monte Carlo simulations, using the distributions of transfer parameters, provide the final number of contaminated products in a batch and their final level of contamination for a given scenario taking into account the initial number of contaminated cheeses of the batch and their contaminant load. Based on analytical results, the model provides indicators for smearing efficiency and propensity of the process for cross-contamination. Unlike traditional approaches in mechanistic models, our approach captures the variability and uncertainty inherent in the process and the experimental data. More generally, this model could represent a generic base to use in modeling similar processes prone to cross-contamination.

  18. cGMP Signaling in the Cardiovascular System—The Role of Compartmentation and Its Live Cell Imaging

    PubMed Central

    Bork, Nadja I.; Nikolaev, Viacheslav O.

    2018-01-01

    The ubiquitous second messenger 3′,5′-cyclic guanosine monophosphate (cGMP) regulates multiple physiologic processes in the cardiovascular system. Its intracellular effects are mediated by stringently controlled subcellular microdomains. In this review, we will illustrate the current techniques available for real-time cGMP measurements with a specific focus on live cell imaging methods. We will also discuss currently accepted and emerging mechanisms of cGMP compartmentation in the cardiovascular system. PMID:29534460

  19. Subcellular Compartmentalization and Chemical Forms of Lead Participate in Lead Tolerance of Robinia pseudoacacia L. with Funneliformis mosseae

    PubMed Central

    Huang, Li; Zhang, Haoqiang; Song, Yingying; Yang, Yurong; Chen, Hui; Tang, Ming

    2017-01-01

    The effect of arbuscular mycorrhizal fungus on the subcellular compartmentalization and chemical forms of lead (Pb) in Pb tolerance plants was assessed in a pot experiment in greenhouse conditions. We measured root colonization, plant growth, photosynthesis, subcellular compartmentalization and chemical forms of Pb in black locust (Robinia pseudoacacia L.) seedlings inoculated with Funneliformis mosseae isolate (BGC XJ01A) under a range of Pb treatments (0, 90, 900, and 3000 mg Pb kg-1 soil). The majority of Pb was retained in the roots of R. pseudoacacia under Pb stress, with a significantly higher retention in the inoculated seedlings. F. mosseae inoculation significantly increased the proportion of Pb in the cell wall and soluble fractions and decreased the proportion of Pb in the organelle fraction of roots, stems, and leaves, with the largest proportion of Pb segregated in the cell wall fraction. F. mosseae inoculation increased the proportion of inactive Pb (especially pectate- and protein-integrated Pb and Pb phosphate) and reduced the proportion of water-soluble Pb in the roots, stems, and leaves. The subcellular compartmentalization of Pb in different chemical forms was highly correlated with improved plant biomass, height, and photosynthesis in the inoculated seedlings. This study indicates that F. mosseae could improve Pb tolerance in R. pseudoacacia seedlings growing in Pb polluted soils. PMID:28443111

  20. Unchanged mitochondrial organization and compartmentation of high-energy phosphates in creatine-deficient GAMT−/− mouse hearts

    PubMed Central

    Branovets, Jelena; Sepp, Mervi; Kotlyarova, Svetlana; Jepihhina, Natalja; Sokolova, Niina; Aksentijevic, Dunja; Lygate, Craig A.; Neubauer, Stefan; Birkedal, Rikke

    2013-01-01

    Disruption of the creatine kinase (CK) system in hearts of CK-deficient mice leads to changes in the ultrastructure and regulation of mitochondrial respiration. We expected to see similar changes in creatine-deficient mice, which lack the enzyme guanidinoacetate methyltransferase (GAMT) to produce creatine. The aim of this study was to characterize the changes in cardiomyocyte mitochondrial organization, regulation of respiration, and intracellular compartmentation associated with GAMT deficiency. Three-dimensional mitochondrial organization was assessed by confocal microscopy. On populations of permeabilized cardiomyocytes, we recorded ADP and ATP kinetics of respiration, competition between mitochondria and pyruvate kinase for ADP produced by ATPases, ADP kinetics of endogenous pyruvate kinase, and ATP kinetics of ATPases. These data were analyzed by mathematical models to estimate intracellular compartmentation. Quantitative analysis of morphological and kinetic data as well as derived model fits showed no difference between GAMT-deficient and wild-type mice. We conclude that inactivation of the CK system by GAMT deficiency does not alter mitochondrial organization and intracellular compartmentation in relaxed cardiomyocytes. Thus, our results suggest that the healthy heart is able to preserve cardiac function at a basal level in the absence of CK-facilitated energy transfer without compromising intracellular organization and the regulation of mitochondrial energy homeostasis. This raises questions on the importance of the CK system as a spatial energy buffer in unstressed cardiomyocytes. PMID:23792673

  1. Using pressure transient analysis to improve well performance and optimize field development in compartmentalized shelf margin deltaic reservoirs

    SciT

    Badgett, K.L.; Crawford, G.E.; Mills, W.H.

    1996-12-31

    BP Exploration`s Gulf of Mexico group developed procedures to conduct effective well tests on conventional production wells and employed them during the development drilling phase of the Mississippi Canyon 109 (MC109) field. Bottomhole pressure data were recorded during the initial few weeks of production. Typically, a 48 hour pressure buildup survey (surface shut-in) was obtained near the end of data acquisition. Data from these tests were analyzed for completion efficiency, reservoir flow capacity, reservoir heterogeneities, and drainage area. Initially wells were gravel packed for sand control, until buildup interpretations indicated skins greater than 20. Frac packing technology was then employed,more » and an immediate improvement was observed with skins dropping into the teens. Over a period of time frac packs were optimized using the test derived skins as a metric. Analysis of pressure data also played an important role in identifying reservoir compartmentalization. The two major reservoir horizons at MC 109 are interpreted as shelf margin deltas. However, each of these has distinctly different compartmentalization issues. The continuous character of the G Sand made it easier to define the depositional system and investigate reservoir compartmentalization issues using a combination of well log, 3D seismic, static pressure trends, and fluid information. In the more distal deltaic reservoirs of the J Sand however, complications with seismic amplitudes and a less reliable tie between wireline and seismic data required the use of pressure transient analysis to efficiently exploit the reservoir.« less

  2. Compartmentalized Human Immunodeficiency Virus Type 1 Originates from Long-Lived Cells in Some Subjects with HIV-1–Associated Dementia

    PubMed Central

    Schnell, Gretja; Spudich, Serena; Harrington, Patrick; Price, Richard W.; Swanstrom, Ronald

    2009-01-01

    Human immunodeficiency virus type 1 (HIV-1) invades the central nervous system (CNS) shortly after systemic infection and can result in the subsequent development of HIV-1–associated dementia (HAD) in a subset of infected individuals. Genetically compartmentalized virus in the CNS is associated with HAD, suggesting autonomous viral replication as a factor in the disease process. We examined the source of compartmentalized HIV-1 in the CNS of subjects with HIV-1–associated neurological disease and in asymptomatic subjects who were initiating antiretroviral therapy. The heteroduplex tracking assay (HTA), targeting the variable regions of env, was used to determine which HIV-1 genetic variants in the cerebrospinal fluid (CSF) were compartmentalized and which variants were shared with the blood plasma. We then measured the viral decay kinetics of individual variants after the initiation of antiretroviral therapy. Compartmentalized HIV-1 variants in the CSF of asymptomatic subjects decayed rapidly after the initiation of antiretroviral therapy, with a mean half-life of 1.57 days. Rapid viral decay was also measured for CSF-compartmentalized variants in four HAD subjects (t1/2 mean = 2.27 days). However, slow viral decay was measured for CSF-compartmentalized variants from an additional four subjects with neurological disease (t1/2 range = 9.85 days to no initial decay). The slow decay detected for CSF-compartmentalized variants was not associated with poor CNS drug penetration, drug resistant virus in the CSF, or the presence of X4 virus genotypes. We found that the slow decay measured for CSF-compartmentalized variants in subjects with neurological disease was correlated with low peripheral CD4 cell count and reduced CSF pleocytosis. We propose a model in which infiltrating macrophages replace CD4+ T cells as the primary source of productive viral replication in the CNS to maintain high viral loads in the CSF in a substantial subset of subjects with HAD

  3. Management of combined knee medial compartmental and patellofemoral osteoarthritis with lateral closing wedge osteotomy with anterior translation of the distal tibial fragment: Does the degree of anteriorization affect the functional outcome and posterior tibial slope?

    PubMed

    Sadek, Ahmed F; Osman, Mohammed K; Laklok, Mohamed A

    2016-10-01

    The aim of this study was to assess the effect of degree of anterior translation of the distal tibial fragment after lateral closing wedge high tibial osteotomy in patients having combined knee medial compartmental and patellofemoral osteoarthritis. A retrospective study was conducted on 64 patients who were operated on for combined knee medial compartmental and patellofemoral osteoarthritis, by lateral closing wedge high tibial osteotomy with anterior translation of the distal tibial fragment. They were divided into two groups; Group I comprising 32 patients (34 knees, mean age of 51.4±7years) whose degree of anterior translation was <1cm and Group II comprising 32 patients (33 knees, mean age of 52.2±8.3years) whose degree of anterior translation was >1.5cm. The final assessment was performed via: visual analog scale, postoperative Knee Society clinical rating system function score, active range of motion, time to union, degree of correction of mechanical axis, posterior tibial slope, and Insall-Salvati ratio. Group II patients exhibited statistically superior mean postoperative score and better return to their work than Group I (P=0.013, 0.076, respectively). Both groups showed statistically significant differences between the preoperative and postoperative evaluation parameters (P<0.001). The posterior tibial slope was decreased in both groups but with no significant difference (P=0.527). Lateral closing wedge high tibial osteotomy combined with anterior translation of the distal tibial fragment more than 1.5cm achieved significantly better postoperative functional knee score. Both groups exhibited comparatively decreased posterior tibial slope. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Axial compartmentation of descending and ascending thin limbs of Henle's loops

    PubMed Central

    Westrick, Kristen Y.; Serack, Bradley; Dantzler, William H.

    2013-01-01

    In the inner medulla, radial organization of nephrons and blood vessels around collecting duct (CD) clusters leads to two lateral interstitial regions and preferential intersegmental fluid and solute flows. As the descending (DTLs) and ascending thin limbs (ATLs) pass through these regions, their transepithelial fluid and solute flows are influenced by variable transepithelial solute gradients and structure-to-structure interactions. The goal of this study was to quantify structure-to-structure interactions, so as to better understand compartmentation and flows of transepithelial water, NaCl, and urea and generation of the axial osmotic gradient. To accomplish this, we determined lateral distances of AQP1-positive and AQP1-negative DTLs and ATLs from their nearest CDs, so as to gauge interactions with intercluster and intracluster lateral regions and interactions with interstitial nodal spaces (INSs). DTLs express reduced AQP1 and low transepithelial water permeability along their deepest segments. Deep AQP1-null segments, prebend segments, and ATLs lie equally near to CDs. Prebend segments and ATLs abut CDs and INSs throughout much of their descent and ascent, respectively; however, the distal 30% of ATLs of the longest loops lie distant from CDs as they approach the outer medullary boundary and have minimal interaction with INSs. These relationships occur regardless of loop length. Finally, we show that ascending vasa recta separate intercluster AQP1-positive DTLs from descending vasa recta, thereby minimizing dilution of gradients that drive solute secretion. We hypothesize that DTLs and ATLs enter and exit CD clusters in an orchestrated fashion that is important for generation of the corticopapillary solute gradient by minimizing NaCl and urea loss. PMID:23195680

  5. Axial compartmentation of descending and ascending thin limbs of Henle's loops.

    PubMed

    Westrick, Kristen Y; Serack, Bradley; Dantzler, William H; Pannabecker, Thomas L

    2013-02-01

    In the inner medulla, radial organization of nephrons and blood vessels around collecting duct (CD) clusters leads to two lateral interstitial regions and preferential intersegmental fluid and solute flows. As the descending (DTLs) and ascending thin limbs (ATLs) pass through these regions, their transepithelial fluid and solute flows are influenced by variable transepithelial solute gradients and structure-to-structure interactions. The goal of this study was to quantify structure-to-structure interactions, so as to better understand compartmentation and flows of transepithelial water, NaCl, and urea and generation of the axial osmotic gradient. To accomplish this, we determined lateral distances of AQP1-positive and AQP1-negative DTLs and ATLs from their nearest CDs, so as to gauge interactions with intercluster and intracluster lateral regions and interactions with interstitial nodal spaces (INSs). DTLs express reduced AQP1 and low transepithelial water permeability along their deepest segments. Deep AQP1-null segments, prebend segments, and ATLs lie equally near to CDs. Prebend segments and ATLs abut CDs and INSs throughout much of their descent and ascent, respectively; however, the distal 30% of ATLs of the longest loops lie distant from CDs as they approach the outer medullary boundary and have minimal interaction with INSs. These relationships occur regardless of loop length. Finally, we show that ascending vasa recta separate intercluster AQP1-positive DTLs from descending vasa recta, thereby minimizing dilution of gradients that drive solute secretion. We hypothesize that DTLs and ATLs enter and exit CD clusters in an orchestrated fashion that is important for generation of the corticopapillary solute gradient by minimizing NaCl and urea loss.

  6. Leveraging unsupervised training sets for multi-scale compartmentalization in renal pathology

    NASA Astrophysics Data System (ADS)

    Lutnick, Brendon; Tomaszewski, John E.; Sarder, Pinaki

    2017-03-01

    Clinical pathology relies on manual compartmentalization and quantification of biological structures, which is time consuming and often error-prone. Application of computer vision segmentation algorithms to histopathological image analysis, in contrast, can offer fast, reproducible, and accurate quantitative analysis to aid pathologists. Algorithms tunable to different biologically relevant structures can allow accurate, precise, and reproducible estimates of disease states. In this direction, we have developed a fast, unsupervised computational method for simultaneously separating all biologically relevant structures from histopathological images in multi-scale. Segmentation is achieved by solving an energy optimization problem. Representing the image as a graph, nodes (pixels) are grouped by minimizing a Potts model Hamiltonian, adopted from theoretical physics, modeling interacting electron spins. Pixel relationships (modeled as edges) are used to update the energy of the partitioned graph. By iteratively improving the clustering, the optimal number of segments is revealed. To reduce computational time, the graph is simplified using a Cantor pairing function to intelligently reduce the number of included nodes. The classified nodes are then used to train a multiclass support vector machine to apply the segmentation over the full image. Accurate segmentations of images with as many as 106 pixels can be completed only in 5 sec, allowing for attainable multi-scale visualization. To establish clinical potential, we employed our method in renal biopsies to quantitatively visualize for the first time scale variant compartments of heterogeneous intra- and extraglomerular structures simultaneously. Implications of the utility of our method extend to fields such as oncology, genomics, and non-biological problems.

  7. The Importance of Bank Storage in Supplying Baseflow to Rivers Flowing Through Compartmentalized, Alluvial Aquifers

    NASA Astrophysics Data System (ADS)

    Rhodes, Kimberly A.; Proffitt, Tiffany; Rowley, Taylor; Knappett, Peter S. K.; Montiel, Daniel; Dimova, Natasha; Tebo, Daniel; Miller, Gretchen R.

    2017-12-01

    As water grows scarcer in semiarid and arid regions around the world, new tools are needed to quantify fluxes of water and chemicals between aquifers and rivers. In this study, we quantify the volumetric flux of subsurface water to a 24 km reach of the Brazos River, a lowland river that meanders through the Brazos River Alluvium Aquifer (BRAA), with 8 months of high-frequency differential gaging measurements using fixed gaging stations. Subsurface discharge sources were determined using natural tracers and End-Member Mixing Analysis (EMMA). During a 4 month river stage recession following a high stage event, subsurface discharge decreased from 50 m3/s to 0, releasing a total of 1.0 × 108 m3 of water. Subsurface discharge dried up even as the groundwater table at two locations in the BRAA located 300-500 m from the river remained ˜4 m higher than the river stage. Less than 4% of the water discharged from the subsurface during the prolonged recession period resembled the chemical fingerprint of the alluvial aquifer. Instead, the chemistry of this discharged water closely resembled high stage "event" river water. Together, these findings suggest that the river is well connected to rechargeable bank storage reservoirs but disconnected from the broader alluvial aquifer. The average width of discrete bank storage zones on each side of the river, identified with Electrical Resistivity Tomography (ERT), was approximately 1.5 km. In such highly compartmentalized aquifers, groundwater pumping is unlikely to impact the exchange between the river and the alluvium.

  8. Circulating TFH cells, serological memory, and tissue compartmentalization shape human influenza-specific B cell immunity.

    PubMed

    Koutsakos, Marios; Wheatley, Adam K; Loh, Liyen; Clemens, E Bridie; Sant, Sneha; Nüssing, Simone; Fox, Annette; Chung, Amy W; Laurie, Karen L; Hurt, Aeron C; Rockman, Steve; Lappas, Martha; Loudovaris, Thomas; Mannering, Stuart I; Westall, Glen P; Elliot, Michael; Tangye, Stuart G; Wakim, Linda M; Kent, Stephen J; Nguyen, Thi H O; Kedzierska, Katherine

    2018-02-14

    Immunization with the inactivated influenza vaccine (IIV) remains the most effective strategy to combat seasonal influenza infections. IIV activates B cells and T follicular helper (T FH ) cells and thus engenders antibody-secreting cells and serum antibody titers. However, the cellular events preceding generation of protective immunity in humans are inadequately understood. We undertook an in-depth analysis of B cell and T cell immune responses to IIV in 35 healthy adults. Using recombinant hemagglutinin (rHA) probes to dissect the quantity, phenotype, and isotype of influenza-specific B cells against A/California09-H1N1, A/Switzerland-H3N2, and B/Phuket, we showed that vaccination induced a three-pronged B cell response comprising a transient CXCR5 - CXCR3 + antibody-secreting B cell population, CD21 hi CD27 + memory B cells, and CD21 lo CD27 + B cells. Activation of circulating T FH cells correlated with the development of both CD21 lo and CD21 hi memory B cells. However, preexisting antibodies could limit increases in serum antibody titers. IIV had no marked effect on CD8 + , mucosal-associated invariant T, γδ T, and natural killer cell activation. In addition, vaccine-induced B cells were not maintained in peripheral blood at 1 year after vaccination. We provide a dissection of rHA-specific B cells across seven human tissue compartments, showing that influenza-specific memory (CD21 hi CD27 + ) B cells primarily reside within secondary lymphoid tissues and the lungs. Our study suggests that a rational design of universal vaccines needs to consider circulating T FH cells, preexisting serological memory, and tissue compartmentalization for effective B cell immunity, as well as to improve targeting cellular T cell immunity. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  9. Compartmentalization of the somite and myogenesis in chick embryos are influenced by wnt expression.

    PubMed

    Wagner, J; Schmidt, C; Nikowits, W; Christ, B

    2000-12-01

    Muscles of the body and bones of the axial skeleton derive from specialized regions of somites. Somite development is influenced by adjacent structures. In particular, the dorsal neural tube and the overlying ectoderm have been shown to be necessary for the induction of myogenic precursor cells in the dermomyotome. Members of the Wnt family of signaling molecules, which are expressed in the dorsal neural tube and the ectoderm, are postulated to be responsible for this process. It is shown here that ectopically implanted Wnt-1-, -3a-, and -4-expressing cells alter the process of somite compartmentalization in vivo. An enlarged dorsal compartment results from the implantation of Wnt-expressing cells ventrally between the neural tube/notochord and epithelial somites, at the expense of the ventral compartment, the sclerotome. Thus, ectopic Wnt expression is able to override the influence of ventralizing signals arising from notochord and floor plate. This shift of the border between the two compartments was identified by an increase in the domain of Pax-3 expression and a complete loss of Pax-1 expression in somites close to the ectopic Wnt signal. The expanded expression of MyoD and desmin provides evidence that it is the myotome which increases as a result of Wnt signaling. Paraxis expression is also drastically amplified after implantation of Wnt-expressing cells indicating that Wnts are involved in the formation and maintenance of somite epithelium and suggesting that Paraxis is activated through Wnt signaling pathways. Taken together these results suggest that ectopic Wnts disturb the normal balance of signaling molecules within the somite, resulting in an enhanced recruitment of somitic cells into the myogenic lineage. Copyright 2000 Academic Press.

  10. Amyloid-β protein precursor regulates phosphorylation and cellular compartmentalization of microtubule associated protein tau.

    PubMed

    Nizzari, Mario; Barbieri, Federica; Gentile, Maria Teresa; Passarella, Daniela; Caorsi, Calentina; Diaspro, Alberto; Taglialatela, Maurizio; Pagano, Aldo; Colucci-D'Amato, Luca; Florio, Tullio; Russo, Claudio

    2012-01-01

    Tau is a multifunctional protein detected in different cellular compartments in neuronal and non-neuronal cells. When hyperphosphorylated and aggregated in atrophic neurons, tau is considered the culprit for neuronal death in familial and sporadic tauopathies. With regards to Alzheimer's disease (AD) pathogenesis, it is not yet established whether entangled tau represents a cause or a consequence of neurodegeneration. In fact, it is unquestionably accepted that amyloid-β protein precursor (AβPP) plays a pivotal role in the genesis of the disease, and it is postulated that the formation of toxic amyloid-β peptides from AβPP is the primary event that subsequently induces abnormal tau phosphorylation. In this work, we show that in the brain of AD patients there is an imbalance between the nuclear and the cytoskeletal pools of phospho-tau. We observed that in non-AD subjects, there is a stable pool of phospho-tau which remains strictly confined to neuronal nuclei, while nuclear localization of phospho-tau is significantly underrepresented in neurons of AD patients bearing neurofibrillary tangles. A specific phosphorylation of tau is required during mitosis in vitro and in vivo, likely via a Grb2-ERK1/2 signaling cascade. In differentiated neuronal A1 cells, the overexpression of AβPP modulates tau phosphorylation, altering the ratio between cytoskeletal and nuclear pools, and correlates with cell death. Altogether our data provide evidence that AβPP, in addition to amyloid formation, modulates the phosphorylation of tau and its subcellular compartmentalization, an event that may lead to the formation of neurofibrillary tangles and to neurodegeneration when occurring in postmitotic neurons.

  11. Two Compartmentalized Inner Receptors for the Tetramethylammonium Guest within a Keplerate-Type Capsule.

    PubMed

    Watfa, Nancy; Haouas, Mohamed; Floquet, Sébastien; Hijazi, Akram; Naoufal, Daoud; Taulelle, Francis; Cadot, Emmanuel

    2016-09-19

    The host-guest interactions between the spherical porous Keplerate anion, [Mo132O372(CH3CO2)30(H2O)72](42-) (abbreviated {Mo132}) and the tetramethylammonium cation have been investigated extensively by one- and two-dimensional (EXSY, ROESY, and DOSY) and variable-temperature NMR. Evidence of two inner receptor sites specific for a NMe4(+) guest appears consistent with a quite striking compartmentalization phenomenon. ROESY NMR analyses showed that both sites exhibit a close spatial proximity with the hanging inner acetate groups, while a quantitative EXSY study revealed that these two sites are differentiated by their exchange rates. These NMR data support the hypothesis that these two inner sites could be delimited by the hanging inner acetate groups forming triangular (S1) or pentagonal (S2) hydrophobic pockets on the inner side of the capsule wall. Furthermore, the stability constants associated with the trapping process of the NMe4(+) guest on both the S1 and S2 sites have been determined, showing that the stability constant of the S1 sites decreases significantly as the concentration of the capsule increases gradually, while that of the S2 sites remains nearly unaffected. Such an observation has been interpreted as a result of the plugging process of the {Mo9O9} pores by the counterions NH4(+), which causes unfavorable electrostatic interactions for the NMe4(+) coordination on the proximal S1 site. Finally, the thermodynamic parameters of the NMe4(+) transfer from the solvated situation to the interior of the capsule were estimated from variable-temperature NMR experiments that provide the split of the global process into two successive events corresponding to the plugging and transfer across the inorganic shell.

  12. Consequences of plant invasions on compartmentalization and species’ roles in plant–pollinator networks

    PubMed Central

    Albrecht, Matthias; Padrón, Benigno; Bartomeus, Ignasi; Traveset, Anna

    2014-01-01

    Compartmentalization—the organization of ecological interaction networks into subsets of species that do not interact with other subsets (true compartments) or interact more frequently among themselves than with other species (modules)—has been identified as a key property for the functioning, stability and evolution of ecological communities. Invasions by entomophilous invasive plants may profoundly alter the way interaction networks are compartmentalized. We analysed a comprehensive dataset of 40 paired plant–pollinator networks (invaded versus uninvaded) to test this hypothesis. We show that invasive plants have higher generalization levels with respect to their pollinators than natives. The consequences for network topology are that—rather than displacing native species from the network—plant invaders attracting pollinators into invaded modules tend to play new important topological roles (i.e. network hubs, module hubs and connectors) and cause role shifts in native species, creating larger modules that are more connected among each other. While the number of true compartments was lower in invaded compared with uninvaded networks, the effect of invasion on modularity was contingent on the study system. Interestingly, the generalization level of the invasive plants partially explains this pattern, with more generalized invaders contributing to a lower modularity. Our findings indicate that the altered interaction structure of invaded networks makes them more robust against simulated random secondary species extinctions, but more vulnerable when the typically highly connected invasive plants go extinct first. The consequences and pathways by which biological invasions alter the interaction structure of plant–pollinator communities highlighted in this study may have important dynamical and functional implications, for example, by influencing multi-species reciprocal selection regimes and coevolutionary processes. PMID:24943368

  13. Sodium and Potassium Fluxes and Compartmentation in Roots of Atriplex and Oat 1

    PubMed Central

    Mills, David; Robinson, Kenneth; Hodges, Thomas K.

    1985-01-01

    K+ and Na+ fluxes and ion content have been studied in roots of Atriplex nummularia Lindl. and Avena sativa L. cv Goodfield grown in 3 millimolar K+ with or without 3 or 50 millimolar NaCl. Compartmental analysis was carried out with entire root systems under steady-state conditions. Increasing ambient Na+ concentrations from 0 to 50 millimolar altered K+, in Atriplex, as follows: slightly decreased the cytoplasmic content (Qc), the vacuolar content (Qv), and the plasma membrane influx and efflux. Xylem transport for K+ decreased by 63% in Atriplex. For oat roots, similar increases in Na+ altered K+ parameters as follows: plasma membrane influx and efflux decreased by about 80%. Qc decreased by 65%, and xylem transport decreased by 91%. No change, however, was observed in Qv for K+. Increasing ambient Na+ resulted in higher (3 to 5-fold) Na+ fluxes across the plasma membrane and in Qc of both species. In Atriplex, Na+ fluxes across the tonoplast and Qv increased as external Na+ was increased. In oat, however, no significant change was observed in Na+ flux across the tonoplast or in Qv as external Na+ was increased. In oat roots, Na+ reduced K+ uptake markedly; in Atriplex, this was not as pronounced. However, even at high Na+ levels, the influx transport system at the plasma membrane of both species preferred K+ over Na+. Based upon the Ussing-Teorell equation, it was concluded that active inward transport of K+ occurred across the plasma membrane, and passive movement of K+ occurred across the tonoplast in both species. Na+, in oat roots, was actively pumped out of the cytoplasm to the exterior, whereas, in Atriplex, Na+ was passively distributed between the free space, cytoplasm, and vacuole. PMID:16664273

  14. Sodium and potassium fluxes and compartmentation in roots of atriplex and oat.

    PubMed

    Mills, D; Robinson, K; Hodges, T K

    1985-07-01

    K(+) and Na(+) fluxes and ion content have been studied in roots of Atriplex nummularia Lindl. and Avena sativa L. cv Goodfield grown in 3 millimolar K(+) with or without 3 or 50 millimolar NaCl. Compartmental analysis was carried out with entire root systems under steady-state conditions.Increasing ambient Na(+) concentrations from 0 to 50 millimolar altered K(+), in Atriplex, as follows: slightly decreased the cytoplasmic content (Q(c)), the vacuolar content (Q(v)), and the plasma membrane influx and efflux. Xylem transport for K(+) decreased by 63% in Atriplex. For oat roots, similar increases in Na(+) altered K(+) parameters as follows: plasma membrane influx and efflux decreased by about 80%. Q(c) decreased by 65%, and xylem transport decreased by 91%. No change, however, was observed in Q(v) for K(+). Increasing ambient Na(+) resulted in higher (3 to 5-fold) Na(+) fluxes across the plasma membrane and in Q(c) of both species. In Atriplex, Na(+) fluxes across the tonoplast and Q(v) increased as external Na(+) was increased. In oat, however, no significant change was observed in Na(+) flux across the tonoplast or in Q(v) as external Na(+) was increased. In oat roots, Na(+) reduced K(+) uptake markedly; in Atriplex, this was not as pronounced. However, even at high Na(+) levels, the influx transport system at the plasma membrane of both species preferred K(+) over Na(+).Based upon the Ussing-Teorell equation, it was concluded that active inward transport of K(+) occurred across the plasma membrane, and passive movement of K(+) occurred across the tonoplast in both species. Na(+), in oat roots, was actively pumped out of the cytoplasm to the exterior, whereas, in Atriplex, Na(+) was passively distributed between the free space, cytoplasm, and vacuole.

  15. Using magnetic resonance imaging to determine the compartmental prevalence of knee joint structural damage.

    PubMed

    Stefanik, J J; Niu, J; Gross, K D; Roemer, F W; Guermazi, A; Felson, D T

    2013-05-01

    To describe the prevalence of magnetic resonance imaging (MRI) detected structural damage in the patellofemoral joint (PFJ) and tibiofemoral joint (TFJ) in a population-based cohort. A secondary aim was to evaluate the patterns of compartmental involvement in knees with pain, between men and women, and in different age and body mass index (BMI) categories. We studied 970 knees, one knee per subject, from the Framingham Osteoarthritis Study, a population-based cohort study of persons 51-92 years old. Cartilage damage and bone marrow lesions (BMLs) were assessed using the Whole Organ Magnetic Resonance Imaging Score (WORMS). The prevalence of isolated PFJ, isolated TFJ, and mixed structural damage was determined using the following definitions: any cartilage damage, full thickness cartilage loss, any BML, and the combination of full thickness cartilage loss with any BML. The mean age and BMI was 63.4 years and 28.6 m/kg(2), respectively; 57% were female. Isolated PFJ damage occurred in 15-20% of knees and isolated TFJ damage occurred in 8-17% of knees depending on the definition used. The prevalence of isolated PFJ damage was greater than isolated TFJ damage using all definitions except the any BML definition. This pattern was similar between genders and among age and BMI categories. In those with knee pain, isolated PFJ was at least as common as TFJ damage depending on the definition used. Using MRI to assess knee joint structural damage, isolated PFJ damage was at least as common as, if not more common than, isolated TFJ damage. Copyright © 2013 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  16. Ultrafast Diffusion of a Fluorescent Cholesterol Analog in Compartmentalized Plasma Membranes

    PubMed Central

    Hiramoto-Yamaki, Nao; Tanaka, Kenji A K; Suzuki, Kenichi G N; Hirosawa, Koichiro M; Miyahara, Manami S H; Kalay, Ziya; Tanaka, Koichiro; Kasai, Rinshi S; Kusumi, Akihiro; Fujiwara, Takahiro K

    2014-01-01

    Cholesterol distribution and dynamics in the plasma membrane (PM) are poorly understood. The recent development of Bodipy488-conjugated cholesterol molecule (Bdp-Chol) allowed us to study cholesterol behavior in the PM, using single fluorescent-molecule imaging. Surprisingly, in the intact PM, Bdp-Chol diffused at the fastest rate ever found for any molecules in the PM, with a median diffusion coefficient (D) of 3.4 µm2/second, which was ∼10 times greater than that of non-raft phospholipid molecules (0.33 µm2/second), despite Bdp-Chol's probable association with raft domains. Furthermore, Bdp-Chol exhibited no sign of entrapment in time scales longer than 0.5 milliseconds. In the blebbed PM, where actin filaments were largely depleted, Bdp-Chol and Cy3-conjugated dioleoylphosphatidylethanolamine (Cy3-DOPE) diffused at comparable Ds (medians = 5.8 and 6.2 µm2/second, respectively), indicating that the actin-based membrane skeleton reduces the D of Bdp-Chol only by a factor of ∼2 from that in the blebbed PM, whereas it reduces the D of Cy3-DOPE by a factor of ∼20. These results are consistent with the previously proposed model, in which the PM is compartmentalized by the actin-based membrane-skeleton fence and its associated transmembrane picket proteins for the macroscopic diffusion of all of the membrane molecules, and suggest that the probability of Bdp-Chol passing through the compartment boundaries, once it enters the boundary, is ∼10× greater than that of Cy3-DOPE. Since the compartment sizes are greater than those of the putative raft domains, we conclude that raft domains coexist with membrane-skeleton-induced compartments and are contained within them. PMID:24506328

  17. Compartmentalization and Transmission of Multiple Epstein-Barr Virus Strains in Asymptomatic Carriers

    PubMed Central

    Sitki-Green, Diane; Covington, Mary; Raab-Traub, Nancy

    2003-01-01

    Infection with the Epstein-Barr virus (EBV) is often subclinical in the presence of a healthy immune response; thus, asymptomatic infection is largely uncharacterized. This study analyzed the nature of EBV infection in 20 asymptomatic immunocompetent hosts over time through the identification of EBV strain variants in the peripheral blood and oral cavity. A heteroduplex tracking assay specific for the EBV gene LMP1 precisely identified the presence of multiple EBV strains in each subject. The strains present in the peripheral blood and oral cavity were often completely discordant, indicating the existence of distinct infections, and the strains present and their relative abundance changed considerably between time points. The possible transmission of strains between the oral cavity and peripheral blood compartments could be tracked within subjects, suggesting that reactivation in the oral cavity and subsequent reinfection of B lymphocytes that reenter the periphery contribute to the maintenance of persistence. In addition, distinct virus strains persisted in the oral cavity over many time points, suggesting an important role for epithelial cells in the maintenance of persistence. Asymptomatic individuals without tonsillar tissue, which is believed to be an important source of virus for the oral cavity, also exhibited multiple strains and a cyclic pattern of transmission between compartments. This study revealed that the majority of patients with infectious mononucleosis were infected with multiple strains of EBV that were also compartmentalized, suggesting that primary infection involves the transmission of multiple strains. Both the primary and carrier states of infection with EBV are more complex than previously thought. PMID:12525618

  18. Compartmentalized cyanophycin metabolism in the diazotrophic filaments of a heterocyst-forming cyanobacterium

    PubMed Central

    Burnat, Mireia; Herrero, Antonia; Flores, Enrique

    2014-01-01

    Heterocyst-forming cyanobacteria are multicellular organisms in which growth requires the activity of two metabolically interdependent cell types, the vegetative cells that perform oxygenic photosynthesis and the dinitrogen-fixing heterocysts. Vegetative cells provide the heterocysts with reduced carbon, and heterocysts provide the vegetative cells with fixed nitrogen. Heterocysts conspicuously accumulate polar granules made of cyanophycin [multi-L-arginyl-poly (L-aspartic acid)], which is synthesized by cyanophycin synthetase and degraded by the concerted action of cyanophycinase (that releases β-aspartyl-arginine) and isoaspartyl dipeptidase (that produces aspartate and arginine). Cyanophycin synthetase and cyanophycinase are present at high levels in the heterocysts. Here we created a deletion mutant of gene all3922 encoding isoaspartyl dipeptidase in the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. The mutant accumulated cyanophycin and β-aspartyl-arginine, and was impaired specifically in diazotrophic growth. Analysis of an Anabaena strain bearing an All3922-GFP (green fluorescent protein) fusion and determination of the enzyme activity in specific cell types showed that isoaspartyl dipeptidase is present at significantly lower levels in heterocysts than in vegetative cells. Consistently, isolated heterocysts released substantial amounts of β-aspartyl-arginine. These observations imply that β-aspartyl-arginine produced from cyanophycin in the heterocysts is transferred intercellularly to be hydrolyzed, producing aspartate and arginine in the vegetative cells. Our results showing compartmentalized metabolism of cyanophycin identify the nitrogen-rich molecule β-aspartyl-arginine as a nitrogen vehicle in the unique multicellular system represented by the heterocyst-forming cyanobacteria. PMID:24550502

  19. Compartmentalized cyanophycin metabolism in the diazotrophic filaments of a heterocyst-forming cyanobacterium.

    PubMed

    Burnat, Mireia; Herrero, Antonia; Flores, Enrique

    2014-03-11

    Heterocyst-forming cyanobacteria are multicellular organisms in which growth requires the activity of two metabolically interdependent cell types, the vegetative cells that perform oxygenic photosynthesis and the dinitrogen-fixing heterocysts. Vegetative cells provide the heterocysts with reduced carbon, and heterocysts provide the vegetative cells with fixed nitrogen. Heterocysts conspicuously accumulate polar granules made of cyanophycin [multi-L-arginyl-poly (L-aspartic acid)], which is synthesized by cyanophycin synthetase and degraded by the concerted action of cyanophycinase (that releases β-aspartyl-arginine) and isoaspartyl dipeptidase (that produces aspartate and arginine). Cyanophycin synthetase and cyanophycinase are present at high levels in the heterocysts. Here we created a deletion mutant of gene all3922 encoding isoaspartyl dipeptidase in the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. The mutant accumulated cyanophycin and β-aspartyl-arginine, and was impaired specifically in diazotrophic growth. Analysis of an Anabaena strain bearing an All3922-GFP (green fluorescent protein) fusion and determination of the enzyme activity in specific cell types showed that isoaspartyl dipeptidase is present at significantly lower levels in heterocysts than in vegetative cells. Consistently, isolated heterocysts released substantial amounts of β-aspartyl-arginine. These observations imply that β-aspartyl-arginine produced from cyanophycin in the heterocysts is transferred intercellularly to be hydrolyzed, producing aspartate and arginine in the vegetative cells. Our results showing compartmentalized metabolism of cyanophycin identify the nitrogen-rich molecule β-aspartyl-arginine as a nitrogen vehicle in the unique multicellular system represented by the heterocyst-forming cyanobacteria.

  20. Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus.

    PubMed

    Ceja-Navarro, Javier A; Nguyen, Nhu H; Karaoz, Ulas; Gross, Stephanie R; Herman, Donald J; Andersen, Gary L; Bruns, Thomas D; Pett-Ridge, Jennifer; Blackwell, Meredith; Brodie, Eoin L

    2014-01-01

    Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by (15)N2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni-Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N2 that is important for this beetle to subsist on woody biomass.

  1. Early ovarian cancer surgery with indocyanine-green-guided targeted compartmental lymphadenectomy (TCL, pelvic part).

    PubMed

    Kimmig, Rainer; Buderath, Paul; Rusch, Peter; Mach, Pawel; Aktas, Bahriye

    2017-09-01

    Para-aortic indocyanine-green (ICG)-guided targeted compartmental lymphadenectomy is feasible in early ovarian cancer; systematic pelvic and para-aortic lymphadenectomy could potentially be avoided if thoroughly investigated sentinel nodes could predict whether residual nodes will be involved or free of disease. In contrast to advanced ovarian cancer, where the therapeutic potential of lymphadenectomy will soon be clarified by the results of the Arbeitsgemeinschaft Gynäkologische Onkologie lymphadenectomy in ovarian neoplasms (AGO LION) trial, systematic lymphadenectomy seems to be mandatory for diagnostic and also therapeutic purposes in early ovarian cancer. Sentinel node biopsy or resection of the regional lymphatic network may reduce morbidity compared to systematic lymphadenectomy as shown already for other entities. Apart from the ovarian mesonephric pathway, a second Müllerian uterine pathway exists for lymphatic drainage of the ovary. Lymphatic valves apparently do not exist at this level of the utero-ovarian network since injection of radioactivity into the ovarian ligaments also labelled pelvic nodes. We applied ICG using 4×0.5 mL of a 1.66 mg/mL ICG solution for transcervical injection into the fundal and midcorporal myometrium at each side [10] instead of injection into the infundibulopelvic ligament, since the utero-ovarian drainage was intact. In this case a 1.8 cm cancer of the right ovary was removed in continuity with its draining lymphatic vessels and at least the first 2 sentinel nodes in each channel "en bloc" as shown in this video for the pelvic part, consistent with the loco-regional ontogenetic approach. This could potentially avoid most of systematic lymphadenectomies in early ovarian cancer. Copyright © 2017. Asian Society of Gynecologic Oncology, Korean Society of Gynecologic Oncology

  2. Compartmentalized acyl-CoA metabolism in skeletal muscle regulates systemic glucose homeostasis.

    PubMed

    Li, Lei O; Grevengoed, Trisha J; Paul, David S; Ilkayeva, Olga; Koves, Timothy R; Pascual, Florencia; Newgard, Christopher B; Muoio, Deborah M; Coleman, Rosalind A

    2015-01-01

    The impaired capacity of skeletal muscle to switch between the oxidation of fatty acid (FA) and glucose is linked to disordered metabolic homeostasis. To understand how muscle FA oxidation affects systemic glucose, we studied mice with a skeletal muscle-specific deficiency of long-chain acyl-CoA synthetase (ACSL)1. ACSL1 deficiency caused a 91% loss of ACSL-specific activity and a 60-85% decrease in muscle FA oxidation. Acsl1(M-/-) mice were more insulin sensitive, and, during an overnight fast, their respiratory exchange ratio was higher, indicating greater glucose use. During endurance exercise, Acsl1(M-/-) mice ran only 48% as far as controls. At the time that Acsl1(M-/-) mice were exhausted but control mice continued to run, liver and muscle glycogen and triacylglycerol stores were similar in both genotypes; however, plasma glucose concentrations in Acsl1(M-/-) mice were ∼40 mg/dL, whereas glucose concentrations in controls were ∼90 mg/dL. Excess use of glucose and the likely use of amino acids for fuel within muscle depleted glucose reserves and diminished substrate availability for hepatic gluconeogenesis. Surprisingly, the content of muscle acyl-CoA at exhaustion was markedly elevated, indicating that acyl-CoAs synthesized by other ACSL isoforms were not available for β-oxidation. This compartmentalization of acyl-CoAs resulted in both an excessive glucose requirement and severely compromised systemic glucose homeostasis. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  3. Action potential processing in a detailed Purkinje cell model reveals a critical role for axonal compartmentalization

    PubMed Central

    Masoli, Stefano; Solinas, Sergio; D'Angelo, Egidio

    2015-01-01

    The Purkinje cell (PC) is among the most complex neurons in the brain and plays a critical role for cerebellar functioning. PCs operate as fast pacemakers modulated by synaptic inputs but can switch from simple spikes to complex bursts and, in some conditions, show bistability. In contrast to original works emphasizing dendritic Ca-dependent mechanisms, recent experiments have supported a primary role for axonal Na-dependent processing, which could effectively regulate spike generation and transmission to deep cerebellar nuclei (DCN). In order to account for the numerous ionic mechanisms involved (at present including Nav1.6, Cav2.1, Cav3.1, Cav3.2, Cav3.3, Kv1.1, Kv1.5, Kv3.3, Kv3.4, Kv4.3, KCa1.1, KCa2.2, KCa3.1, Kir2.x, HCN1), we have elaborated a multicompartmental model incorporating available knowledge on localization and gating of PC ionic channels. The axon, including initial segment (AIS) and Ranvier nodes (RNs), proved critical to obtain appropriate pacemaking and firing frequency modulation. Simple spikes initiated in the AIS and protracted discharges were stabilized in the soma through Na-dependent mechanisms, while somato-dendritic Ca channels contributed to sustain pacemaking and to generate complex bursting at high discharge regimes. Bistability occurred only following Na and Ca channel down-regulation. In addition, specific properties in RNs K currents were required to limit spike transmission frequency along the axon. The model showed how organized electroresponsive functions could emerge from the molecular complexity of PCs and showed that the axon is fundamental to complement ionic channel compartmentalization enabling action potential processing and transmission of specific spike patterns to DCN. PMID:25759640

  4. Validation of Bayesian analysis of compartmental kinetic models in medical imaging.

    PubMed

    Sitek, Arkadiusz; Li, Quanzheng; El Fakhri, Georges; Alpert, Nathaniel M

    2016-10-01

    Kinetic compartmental analysis is frequently used to compute physiologically relevant quantitative values from time series of images. In this paper, a new approach based on Bayesian analysis to obtain information about these parameters is presented and validated. The closed-form of the posterior distribution of kinetic parameters is derived with a hierarchical prior to model the standard deviation of normally distributed noise. Markov chain Monte Carlo methods are used for numerical estimation of the posterior distribution. Computer simulations of the kinetics of F18-fluorodeoxyglucose (FDG) are used to demonstrate drawing statistical inferences about kinetic parameters and to validate the theory and implementation. Additionally, point estimates of kinetic parameters and covariance of those estimates are determined using the classical non-linear least squares approach. Posteriors obtained using methods proposed in this work are accurate as no significant deviation from the expected shape of the posterior was found (one-sided P>0.08). It is demonstrated that the results obtained by the standard non-linear least-square methods fail to provide accurate estimation of uncertainty for the same data set (P<0.0001). The results of this work validate new methods for a computer simulations of FDG kinetics. Results show that in situations where the classical approach fails in accurate estimation of uncertainty, Bayesian estimation provides an accurate information about the uncertainties in the parameters. Although a particular example of FDG kinetics was used in the paper, the methods can be extended for different pharmaceuticals and imaging modalities. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  5. Barcoding of GPCR trafficking and signaling through the various trafficking roadmaps by compartmentalized signaling networks.

    PubMed

    Bahouth, Suleiman W; Nooh, Mohammed M

    2017-08-01

    Proper signaling by G protein coupled receptors (GPCR) is dependent on the specific repertoire of transducing, enzymatic and regulatory kinases and phosphatases that shape its signaling output. Activation and signaling of the GPCR through its cognate G protein is impacted by G protein-coupled receptor kinase (GRK)-imprinted "barcodes" that recruit β-arrestins to regulate subsequent desensitization, biased signaling and endocytosis of the GPCR. The outcome of agonist-internalized GPCR in endosomes is also regulated by sequence motifs or "barcodes" within the GPCR that mediate its recycling to the plasma membrane or retention and eventual degradation as well as its subsequent signaling in endosomes. Given the vast number of diverse sequences in GPCR, several trafficking mechanisms for endosomal GPCR have been described. The majority of recycling GPCR, are sorted out of endosomes in a "sequence-dependent pathway" anchored around a type-1 PDZ-binding module found in their C-tails. For a subset of these GPCR, a second "barcode" imprinted onto specific GPCR serine/threonine residues by compartmentalized kinase networks was required for their efficient recycling through the "sequence-dependent pathway". Mutating the serine/threonine residues involved, produced dramatic effects on GPCR trafficking, indicating that they played a major role in setting the trafficking itinerary of these GPCR. While endosomal SNX27, retromer/WASH complexes and actin were required for efficient sorting and budding of all these GPCR, additional proteins were required for GPCR sorting via the second "barcode". Here we will review recent developments in GPCR trafficking in general and the human β 1 -adrenergic receptor in particular across the various trafficking roadmaps. In addition, we will discuss the role of GPCR trafficking in regulating endosomal GPCR signaling, which promote biochemical and physiological effects that are distinct from those generated by the GPCR signal transduction

  6. Bioaccumulation of trace metals in octocorals depends on age and tissue compartmentalization

    PubMed Central

    Hwang, Jiang-Shiou; Huang, Ke Li; Huang, Mu-Yeh; Liu, Xue-Jun; Khim, Jong Seong; Wong, Chong Kim

    2018-01-01

    Trace metal dynamics have not been studied with respect to growth increments in octocorals. It is particularly unknown whether ontogenetic compartmentalization of trace metal accumulation is species-specific. We studied here for the first time the intracolonial distribution and concentrations of 18 trace metals in the octocorals Subergorgia suberosa, Echinogorgia complexa and E. reticulata that were retrieved from the northern coast of Taiwan. Levels of trace metals were considerably elevated in corals collected at these particular coral habitats as a result of diverse anthropogenic inputs. There was a significant difference in the concentration of metals among octocorals except for Sn. Both species of Echinogorgia contained significantly higher concentrations of Cu, Zn and Al than Subergorgia suberosa. We used for the first time exponential growth curves that describe an age-specific relationship of octocoral trace metal concentrations of Cu, Zn, Cd, Cr and Pb where the distance from the grip point was reflecting younger age as linear regressions. The larger colony (C7) had a lower accumulation rate constant than the smaller one (C6) for Cu, Zn, Cd, Cr and Pb, while other trace metals showed an opposite trend. The Cu concentration declined exponentially from the grip point, whereas the concentrations of Zn, Cd, Cr and Pb increased exponentially. In S. suberosa and E. reticulata, Zn occurred primarily in coenosarc tissues and Zn concentrations increased with distance from the grip point in both skeletal and coenosarc tissues. Metals which appeared at high concentrations (e.g. Ca, Zn and Fe) generally tended to accumulate in the outer coenosarc tissues, while metals with low concentrations (e.g. V) tended to accumulate in the soft tissues of the inner skeleton. PMID:29684058

  7. The ancient claudin Dni2 facilitates yeast cell fusion by compartmentalizing Dni1 into a membrane subdomain.

    PubMed

    Curto, M-Ángeles; Moro, Sandra; Yanguas, Francisco; Gutiérrez-González, Carmen; Valdivieso, M-Henar

    2018-05-01

    Dni1 and Dni2 facilitate cell fusion during mating. Here, we show that these proteins are interdependent for their localization in a plasma membrane subdomain, which we have termed the mating fusion domain. Dni1 compartmentation in the domain is required for cell fusion. The contribution of actin, sterol-dependent membrane organization, and Dni2 to this compartmentation was analysed, and the results showed that Dni2 plays the most relevant role in the process. In turn, the Dni2 exit from the endoplasmic reticulum depends on Dni1. These proteins share the presence of a cysteine motif in their first extracellular loop related to the claudin GLWxxC(8-10 aa)C signature motif. Structure-function analyses show that mutating each Dni1 conserved cysteine has mild effects, and that only simultaneous elimination of several cysteines leads to a mating defect. On the contrary, eliminating each single cysteine and the C-terminal tail in Dni2 abrogates Dni1 compartmentation and cell fusion. Sequence alignments show that claudin trans-membrane helixes bear small-XXX-small motifs at conserved positions. The fourth Dni2 trans-membrane helix tends to form homo-oligomers in Escherichia plasma membrane, and two concatenated small-XXX-small motifs are required for efficient oligomerization and for Dni2 export from the yeast endoplasmic reticulum. Together, our results strongly suggest that Dni2 is an ancient claudin that blocks Dni1 diffusion from the intercellular region where two plasma membranes are in close proximity, and that this function is required for Dni1 to facilitate cell fusion.

  8. Multiple Facets of cAMP Signalling and Physiological Impact: cAMP Compartmentalization in the Lung

    PubMed Central

    Oldenburger, Anouk; Maarsingh, Harm; Schmidt, Martina

    2012-01-01

    Therapies involving elevation of the endogenous suppressor cyclic AMP (cAMP) are currently used in the treatment of several chronic inflammatory disorders, including chronic obstructive pulmonary disease (COPD). Characteristics of COPD are airway obstruction, airway inflammation and airway remodelling, processes encompassed by increased airway smooth muscle mass, epithelial changes, goblet cell and submucosal gland hyperplasia. In addition to inflammatory cells, airway smooth muscle cells and (myo)fibroblasts, epithelial cells underpin a variety of key responses in the airways such as inflammatory cytokine release, airway remodelling, mucus hypersecretion and airway barrier function. Cigarette smoke, being next to environmental pollution the main cause of COPD, is believed to cause epithelial hyperpermeability by disrupting the barrier function. Here we will focus on the most recent progress on compartmentalized signalling by cAMP. In addition to G protein-coupled receptors, adenylyl cyclases, cAMP-specific phospho-diesterases (PDEs) maintain compartmentalized cAMP signalling. Intriguingly, spatially discrete cAMP-sensing signalling complexes seem also to involve distinct members of the A-kinase anchoring (AKAP) superfamily and IQ motif containing GTPase activating protein (IQGAPs). In this review, we will highlight the interaction between cAMP and the epithelial barrier to retain proper lung function and to alleviate COPD symptoms and focus on the possible molecular mechanisms involved in this process. Future studies should include the development of cAMP-sensing multiprotein complex specific disruptors and/or stabilizers to orchestrate cellular functions. Compartmentalized cAMP signalling regulates important cellular processes in the lung and may serve as a therapeutic target. PMID:24281338

  9. [CLINICAL APPLICATION OF OXFORD MOBILE-BEARING BIPOLAR PROSTHESIS UNICOMPARTMENTAL KNEE ARTHROPLASTY FOR SINGLE COMPARTMENTAL KNEE OSTEOARTHRITIS].

    PubMed

    Wang, Shangzeng; Cheng, Shao; Wang, Yisheng

    2016-01-01

    To evaluate the effectiveness of Oxford mobile-bearing bipolar prosthesis unicompartmental knee arthroplasty (UKA) in the treatment of single compartmental knee osteoarthritis. Between June 2011 and July 2013, 22 cases of single compartmental knee osteoarthritis were treated by Oxford mobile-bearing bipolar prosthesis UKA. Of 22 cases, 8 were male and 14 were female with an average age of 65 years (range, 45-80 years); the left knee was involved in 12 cases, and the right knee in 10 cases, with a mean disease duration of 32.5 months (range, 8-90 months). The mean weight was 55.2 kg (range, 50-65 kg), and the mean body mass index was 20.8 kg/m2 (range, 17-25 kg/m2). Osteoarthritis involved in the single knee medial compartment in all patients. Knee society score (KSS) and range of motion (ROM) were measured to evaluate the knee joint function. Primary healing of incision was obtained in all patients, and there was no complication of infection, bedsore, or deep venous thrombosis. Postoperative follow-up was 2-4 years (mean, 3.2 years). The X-ray films showed good position of prosthesis, no prosthesis dislocation, or periprosthetic infection during follow-up. Knee ROM, KSS function score, and KSS clinical score were significantly improved at 1 week after operation and at last follow-up when compared with preoperative ones (P < 0.05), but no significant difference was shown between at 1 week and at last follow-up (P > 0.05). Oxford mobile-bearing bipolar prosthesis UKA is an effective method to treat single compartmental knee osteoarthritis, with the advantages of less trauma, earlier rehabilitation exercise, near physiological state in joint function, and less risk of complications.

  10. Does location of patellofemoral chondral lesion influence outcome after Oxford medial compartmental knee arthroplasty?

    PubMed

    Konan, S; Haddad, F S

    2016-10-01

    Medial unicompartmental knee arthroplasty (UKA) is associated with successful outcomes in carefully selected patient cohorts. We hypothesised that severity and location of patellofemoral cartilage lesions significantly influences functional outcome after Oxford medial compartmental knee arthroplasty. We reviewed 100 consecutive UKAs at minimum eight-year follow-up (96 to 132). A single surgeon performed all procedures. Patients were selected based on clinical and plain radiographic assessment. All patients had end-stage medial compartment osteoarthritis (OA) with sparing of the lateral compartment and intact anterior cruciate ligaments. None of the patients had end-stage patellofemoral OA, but patients with anterior knee pain or partial thickness chondral loss were not excluded. There were 57 male and 43 female patients. The mean age at surgery was 69 years (41 to 82). At surgery the joint was carefully inspected for patellofemoral chondral loss and this was documented based on severity of cartilage loss (0 to 4 Outerbridge grading) and topographic location (medial, lateral, central, and superior or inferior). Functional scores collected included Oxford Knee Score (OKS), patient satisfaction scale and University College Hospital (UCH) knee score. Intraclass correlation was used to compare chondral damage to outcomes. All patients documented significant improvement in pain and improved functional scores at mid-term follow-up. There were four revisions (mean 2.9 years, 2 to 4; standard deviation (sd) 0.9) in this cohort, three for tibial loosening and one for femoral loosening. There was one infection that was treated with debridement and insert exchange. The mean OKS improved from 23.2 (sd 7.1) to 39.1 (sd 6.9); p < 0.001. The cohort with central and lateral grade 3 patellofemoral OA documented lower mean satisfaction with pain (90, sd 11.8) and function (87.5, sd 10.3) on the patient satisfaction scale. On the UCH scale, patients reported significantly decreased

  11. Does location of patellofemoral chondral lesion influence outcome after Oxford medial compartmental knee arthroplasty?

    PubMed Central

    Konan, S.; Haddad, F. S.

    2016-01-01

    Aims Medial unicompartmental knee arthroplasty (UKA) is associated with successful outcomes in carefully selected patient cohorts. We hypothesised that severity and location of patellofemoral cartilage lesions significantly influences functional outcome after Oxford medial compartmental knee arthroplasty. Patients and Methods We reviewed 100 consecutive UKAs at minimum eight-year follow-up (96 to 132). A single surgeon performed all procedures. Patients were selected based on clinical and plain radiographic assessment. All patients had end-stage medial compartment osteoarthritis (OA) with sparing of the lateral compartment and intact anterior cruciate ligaments. None of the patients had end-stage patellofemoral OA, but patients with anterior knee pain or partial thickness chondral loss were not excluded. There were 57 male and 43 female patients. The mean age at surgery was 69 years (41 to 82). At surgery the joint was carefully inspected for patellofemoral chondral loss and this was documented based on severity of cartilage loss (0 to 4 Outerbridge grading) and topographic location (medial, lateral, central, and superior or inferior). Functional scores collected included Oxford Knee Score (OKS), patient satisfaction scale and University College Hospital (UCH) knee score. Intraclass correlation was used to compare chondral damage to outcomes. Results All patients documented significant improvement in pain and improved functional scores at mid-term follow-up. There were four revisions (mean 2.9 years, 2 to 4; standard deviation (sd) 0.9) in this cohort, three for tibial loosening and one for femoral loosening. There was one infection that was treated with debridement and insert exchange. The mean OKS improved from 23.2 (sd 7.1) to 39.1 (sd 6.9); p < 0.001. The cohort with central and lateral grade 3 patellofemoral OA documented lower mean satisfaction with pain (90, sd 11.8) and function (87.5, sd 10.3) on the patient satisfaction scale. On the UCH scale, patients

  12. Structural localization and origin of compartmentalized fluid flow, Comstock lode, Virginia City, Nevada

    Berger, B.R.; Tingley, J.V.; Drew, L.J.

    2003-01-01

    Bonanza-grade orebodies in epithermal-style mineral deposits characteristically occur as discrete zones within spatially more extensive fault and/or fracture systems. Empirically, the segregation of such systems into compartments of higher and lower permeability appears to be a key process necessary for high-grade ore formation and, most commonly, it is such concentrations of metals that make an epithermal vein district world class. In the world-class silver- and gold-producing Comstock mining district, Nevada, several lines of evidence lead to the conclusion that the Comstock lode is localized in an extensional stepover between right-lateral fault zones. This evidence includes fault geometries, kinematic indicators of slip, the hydraulic connectivity of faults as demonstrated by veins and dikes along faults, and the opening of a normal-fault-bounded, asymmetric basin between two parallel and overlapping northwest-striking, lateral- to lateral-oblique-slip fault zones. During basin opening, thick, generally subeconomic, banded quartz-adularia veins were deposited in the normal fault zone, the Comstock fault, and along one of the bounding lateral fault zones, the Silver City fault. As deformation continued, the intrusion of dikes and small plugs into the hanging wall of the Comstock fault zone may have impeded the ability of the stepover to accommodate displacement on the bounding strike-slip faults through extension within the stepover. A transient period of transpressional deformation of the Comstock fault zone ensued, and the early-stage veins were deformed through boudinaging and hydraulic fragmentation, fault-motion inversion, and high- and low-angle axial rotations of segments of the fault planes and some fault-bounded wedges. This deformation led to the formation of spatially restricted compartments of high vertical permeability and hydraulic connectivity and low lateral hydraulic connectivity. Bonanza orebodies were formed in the compartmentalized zones of

  13. The kinase domain of CK1 enzymes contains the localization cue essential for compartmentalized signaling at the spindle pole.

    PubMed

    Elmore, Zachary C; Guillen, Rodrigo X; Gould, Kathleen L

    2018-05-09

    CK1 protein kinases contribute to multiple biological processes, but how they are tailored to function in compartmentalized signaling events is largely unknown. Hhp1 and Hhp2 (Hhp1/2) are the soluble CK1 family members in Schizosaccharomyces pombe. One of their functions is to inhibit the septation initiation network (SIN) during a mitotic checkpoint arrest. The SIN is assembled by Sid4 at spindle pole bodies (SPBs), and though Hhp1/2 co-localize there, it is not known how they are targeted there nor if their SPB localization is required for SIN inhibition. Here, we establish that Hhp1/2 localize throughout the cell cycle to SPBs, as well as to the nucleus, cell tips, and division site. We find that their catalytic domains but not enzymatic function are used for SPB targeting and that this targeting strategy is conserved in human CK1δ/ε localization to centrosomes. Further, we pinpoint amino acids in the Hhp1 catalytic domain required for SPB interaction; mutation of these residues disrupts Hhp1 association with the core SPB protein Ppc89, and the inhibition of cytokinesis in the setting of spindle stress. Taken together, we have defined a molecular mechanism used by CK1 enzymes to target to a specific cellular locale for compartmentalized signaling.

  14. Cellular compartmentation follows rules: The Schnepf theorem, its consequences and exceptions: A biological membrane separates a plasmatic from a non-plasmatic phase.

    PubMed

    Moog, Daniel; Maier, Uwe G

    2017-08-01

    Is the spatial organization of membranes and compartments within cells subjected to any rules? Cellular compartmentation differs between prokaryotic and eukaryotic life, because it is present to a high degree only in eukaryotes. In 1964, Prof. Eberhard Schnepf formulated the compartmentation rule (Schnepf theorem), which posits that a biological membrane, the main physical structure responsible for cellular compartmentation, usually separates a plasmatic form a non-plasmatic phase. Here we review and re-investigate the Schnepf theorem by applying the theorem to different cellular structures, from bacterial cells to eukaryotes with their organelles and compartments. In conclusion, we can confirm the general correctness of the Schnepf theorem, noting explicit exceptions only in special cases such as endosymbiosis and parasitism. © 2017 WILEY Periodicals, Inc.

  15. Is the Dissociative Experiences Scale able to identify detachment and compartmentalization symptoms? Factor structure of the Dissociative Experiences Scale in a large sample of psychiatric and nonpsychiatric subjects.

    PubMed

    Mazzotti, Eva; Farina, Benedetto; Imperatori, Claudio; Mansutti, Federica; Prunetti, Elena; Speranza, Anna Maria; Barbaranelli, Claudio

    2016-01-01

    In this study, we explored the ability of the Dissociative Experiences Scale (DES) to catch detachment and compartmentalization symptoms. The DES factor structure was evaluated in 768 psychiatric patients (546 women and 222 men) and in 2,403 subjects enrolled in nonpsychiatric settings (1,857 women and 546 men). All participants were administered the Italian version of DES. Twenty senior psychiatric experts in the treatment of dissociative symptoms independently assessed the DES items and categorized each of them as follows: "C" for compartmentalization, "D" for detachment, and "NC" for noncongruence with either C or D. Confirmatory factor analysis supported the three-factor structure of DES in both clinical and nonclinical samples and its invariance across the two groups. Moreover, factor analyses results overlapped with those from the expert classification procedure. Our results showed that DES can be used as a valid instrument for clinicians to assess the frequency of different types of dissociative experiences including detachment and compartmentalization.

  16. Computer Modeling of Sand Transport on Mars Using a Compart-Mentalized Fluids Algorithm (CFA)

    NASA Technical Reports Server (NTRS)

    Marshall, J.; Stratton, D.

    1999-01-01

    of sand comminution on Mars. A multiple-grain transport model using just the equations of grain motion describing lift and drag is impossible to develop owing to stochastic effects --the very effects we wish to model. Also, unless we were to employ supercomputing techniques and extremely complex computer codes that could deal with millions of grains simultaneously, it would also be difficult to model grain transport if we attempted to consider every grain in motion. No existing computer models were found that satisfactorily used the equations of motion to arrive at transport flux numbers for the different populations of saltation and reptation. Modeling all the grains in a transport system was an intractable problem within our resources, and thus we developed what we believe to be a new modeling approach to simulating grain transport. The CFA deals with grain populations, but considers them to belong to various compartmentalized fluid units in the boundary layer. In this way, the model circumvents the multigrain problem by dealing primarily with the consequences of grain transport --momentum transfer between air and grains, which is the physical essence of a dynamic grain-fluid mixture. We thus chose to model the aeolian transport process as a superposition of fluids. These fluids include the air as well as particle populations of various properties. The prime property distinguishing these fluids is upward and downward grain motion. In a normal saltation trajectory, a grain's downwind velocity increases with time, so a rising grain will have a smaller downwind velocity than a failing grain. Because of this disparity in rising and falling grain proper-ties, it seemed appropriate to track these as two separate grain populations within the same physical space. The air itself can be considered a separate fluid superimposed within and interacting with the various grain-cloud "fluids". Additional informaiton is contained in the original.

  17. Hybrid Molecular Structure of the Giant Protease Tripeptidyl Peptidase II

    PubMed Central

    Chuang, Crystal K.; Rockel, Beate; Seyit, Gönül; Walian, Peter J.; Schönegge, Anne–Marie; Peters, Jürgen; Zwart, Petrus H.; Baumeister, Wolfgang; Jap, Bing K.

    2010-01-01

    Tripeptidyl peptidase II (TPP II) is the largest known eukaryotic protease (6MDa). It is believed to act downstream of the 26S proteasome cleaving tripeptides from the N– termini of longer peptides and it is implicated in numerous cellular processes. Here we report the structure of Drosophila TPP II determined by a hybrid approach: The structure of the dimer was solved by x–ray crystallography and docked into the three– dimensional map of the holocomplex obtained by single-particle cryo-electron microscopy. The resulting structure reveals the compartmentalization of the active sites inside a system of chambers and suggests the existence of a molecular ruler determining the size of the cleavage products. Furthermore, the structure suggests a model for activation of TPP II involving the relocation of a flexible loop and a repositioning of the active–site serine, coupling it to holocomplex assembly and active site sequestration. PMID:20676100

  18. Compartmental and noncompartmental modeling of ¹³C-lycopene absorption, isomerization, and distribution kinetics in healthy adults.

    PubMed

    Moran, Nancy E; Cichon, Morgan J; Riedl, Kenneth M; Grainger, Elizabeth M; Schwartz, Steven J; Novotny, Janet A; Erdman, John W; Clinton, Steven K

    2015-12-01

    Lycopene, which is a red carotenoid in tomatoes, has been hypothesized to mediate disease-preventive effects associated with tomato consumption. Lycopene is consumed primarily as the all-trans geometric isomer in foods, whereas human plasma and tissues show greater proportions of cis isomers. With the use of compartmental modeling and stable isotope technology, we determined whether endogenous all-trans-to-cis-lycopene isomerization or isomeric-bioavailability differences underlie the greater proportion of lycopene cis isomers in human tissues than in tomato foods. Healthy men (n = 4) and women (n = 4) consumed (13)C-lycopene (10.2 mg; 82% all-trans and 18% cis), and plasma was collected over 28 d. Unlabeled and (13)C-labeled total lycopene and lycopene-isomer plasma concentrations, which were measured with the use of high-performance liquid chromatography-mass spectrometry, were fit to a 7-compartment model. Subjects absorbed a mean ± SEM of 23% ± 6% of the lycopene. The proportion of plasma cis-(13)C-lycopene isomers increased over time, and all-trans had a shorter half-life than that of cis isomers (5.3 ± 0.3 and 8.8 ± 0.6 d, respectively; P < 0.001) and an earlier time to reach maximal plasma concentration than that of cis isomers (28 ± 7 and 48 ± 9 h, respectively). A compartmental model that allowed for interindividual differences in cis- and all-trans-lycopene bioavailability and endogenous trans-to-cis-lycopene isomerization was predictive of plasma (13)C and unlabeled cis- and all-trans-lycopene concentrations. Although the bioavailability of cis (24.5% ± 6%) and all-trans (23.2% ± 8%) isomers did not differ, endogenous isomerization (0.97 ± 0.25 μmol/d in the fast-turnover tissue lycopene pool) drove tissue and plasma isomeric profiles. (13)C-Lycopene combined with physiologic compartmental modeling provides a strategy for following complex in vivo metabolic processes in humans and reveals that postabsorptive trans-to-cis-lycopene isomerization

  19. Compartmental and noncompartmental modeling of 13C-lycopene absorption, isomerization, and distribution kinetics in healthy adults123

    PubMed Central

    Moran, Nancy E; Cichon, Morgan J; Riedl, Kenneth M; Grainger, Elizabeth M; Schwartz, Steven J; Novotny, Janet A; Erdman, John W; Clinton, Steven K

    2015-01-01

    Background: Lycopene, which is a red carotenoid in tomatoes, has been hypothesized to mediate disease-preventive effects associated with tomato consumption. Lycopene is consumed primarily as the all-trans geometric isomer in foods, whereas human plasma and tissues show greater proportions of cis isomers. Objective: With the use of compartmental modeling and stable isotope technology, we determined whether endogenous all-trans-to-cis-lycopene isomerization or isomeric-bioavailability differences underlie the greater proportion of lycopene cis isomers in human tissues than in tomato foods. Design: Healthy men (n = 4) and women (n = 4) consumed 13C-lycopene (10.2 mg; 82% all-trans and 18% cis), and plasma was collected over 28 d. Unlabeled and 13C-labeled total lycopene and lycopene-isomer plasma concentrations, which were measured with the use of high-performance liquid chromatography–mass spectrometry, were fit to a 7-compartment model. Results: Subjects absorbed a mean ± SEM of 23% ± 6% of the lycopene. The proportion of plasma cis-13C-lycopene isomers increased over time, and all-trans had a shorter half-life than that of cis isomers (5.3 ± 0.3 and 8.8 ± 0.6 d, respectively; P < 0.001) and an earlier time to reach maximal plasma concentration than that of cis isomers (28 ± 7 and 48 ± 9 h, respectively). A compartmental model that allowed for interindividual differences in cis- and all-trans-lycopene bioavailability and endogenous trans-to-cis-lycopene isomerization was predictive of plasma 13C and unlabeled cis- and all-trans-lycopene concentrations. Although the bioavailability of cis (24.5% ± 6%) and all-trans (23.2% ± 8%) isomers did not differ, endogenous isomerization (0.97 ± 0.25 μmol/d in the fast-turnover tissue lycopene pool) drove tissue and plasma isomeric profiles. Conclusion: 13C-Lycopene combined with physiologic compartmental modeling provides a strategy for following complex in vivo metabolic processes in humans and reveals that

  20. The cellular and compartmental profile of mouse retinal glycolysis, tricarboxylic acid cycle, oxidative phosphorylation, and ~P transferring kinases

    PubMed Central

    Rueda, Elda M.; Johnson, Jerry E.; Giddabasappa, Anand; Swaroop, Anand; Brooks, Matthew J.; Sigel, Irena; Chaney, Shawnta Y.

    2016-01-01

    Purpose The homeostatic regulation of cellular ATP is achieved by the coordinated activity of ATP utilization, synthesis, and buffering. Glucose is the major substrate for ATP synthesis through glycolysis and oxidative phosphorylation (OXPHOS), whereas intermediary metabolism through the tricarboxylic acid (TCA) cycle utilizes non-glucose-derived monocarboxylates, amino acids, and alpha ketoacids to support mitochondrial ATP and GTP synthesis. Cellular ATP is buffered by specialized equilibrium-driven high-energy phosphate (~P) transferring kinases. Our goals were twofold: 1) to characterize the gene expression, protein expression, and activity of key synthesizing and regulating enzymes of energy metabolism in the whole mouse retina, retinal compartments, and/or cells and 2) to provide an integrative analysis of the results related to function. Methods mRNA expression data of energy-related genes were extracted from our whole retinal Affymetrix microarray data. Fixed-frozen retinas from adult C57BL/6N mice were used for immunohistochemistry, laser scanning confocal microscopy, and enzymatic histochemistry. The immunoreactivity levels of well-characterized antibodies, for all major retinal cells and their compartments, were obtained using our established semiquantitative confocal and imaging techniques. Quantitative cytochrome oxidase (COX) and lactate dehydrogenase (LDH) activity was determined histochemically. Results The Affymetrix data revealed varied gene expression patterns of the ATP synthesizing and regulating enzymes found in the muscle, liver, and brain. Confocal studies showed differential cellular and compartmental distribution of isozymes involved in glucose, glutamate, glutamine, lactate, and creatine metabolism. The pattern and intensity of the antibodies and of the COX and LDH activity showed the high capacity of photoreceptors for aerobic glycolysis and OXPHOS. Competition assays with pyruvate revealed that LDH-5 was localized in the photoreceptor

  1. The cellular and compartmental profile of mouse retinal glycolysis, tricarboxylic acid cycle, oxidative phosphorylation, and ~P transferring kinases.

    PubMed

    Rueda, Elda M; Johnson, Jerry E; Giddabasappa, Anand; Swaroop, Anand; Brooks, Matthew J; Sigel, Irena; Chaney, Shawnta Y; Fox, Donald A

    2016-01-01

    The homeostatic regulation of cellular ATP is achieved by the coordinated activity of ATP utilization, synthesis, and buffering. Glucose is the major substrate for ATP synthesis through glycolysis and oxidative phosphorylation (OXPHOS), whereas intermediary metabolism through the tricarboxylic acid (TCA) cycle utilizes non-glucose-derived monocarboxylates, amino acids, and alpha ketoacids to support mitochondrial ATP and GTP synthesis. Cellular ATP is buffered by specialized equilibrium-driven high-energy phosphate (~P) transferring kinases. Our goals were twofold: 1) to characterize the gene expression, protein expression, and activity of key synthesizing and regulating enzymes of energy metabolism in the whole mouse retina, retinal compartments, and/or cells and 2) to provide an integrative analysis of the results related to function. mRNA expression data of energy-related genes were extracted from our whole retinal Affymetrix microarray data. Fixed-frozen retinas from adult C57BL/6N mice were used for immunohistochemistry, laser scanning confocal microscopy, and enzymatic histochemistry. The immunoreactivity levels of well-characterized antibodies, for all major retinal cells and their compartments, were obtained using our established semiquantitative confocal and imaging techniques. Quantitative cytochrome oxidase (COX) and lactate dehydrogenase (LDH) activity was determined histochemically. The Affymetrix data revealed varied gene expression patterns of the ATP synthesizing and regulating enzymes found in the muscle, liver, and brain. Confocal studies showed differential cellular and compartmental distribution of isozymes involved in glucose, glutamate, glutamine, lactate, and creatine metabolism. The pattern and intensity of the antibodies and of the COX and LDH activity showed the high capacity of photoreceptors for aerobic glycolysis and OXPHOS. Competition assays with pyruvate revealed that LDH-5 was localized in the photoreceptor inner segments. The

  2. Human Immunodeficiency Viruses Appear Compartmentalized to the Female Genital Tract in Cross-Sectional Analyses but Genital Lineages Do Not Persist Over Time

    PubMed Central

    Bull, Marta E.; Heath, Laura M.; McKernan-Mullin, Jennifer L.; Kraft, Kelli M.; Acevedo, Luis; Hitti, Jane E.; Cohn, Susan E.; Tapia, Kenneth A.; Holte, Sarah E.; Dragavon, Joan A.; Coombs, Robert W.; Mullins, James I.; Frenkel, Lisa M.

    2013-01-01

    Background. Whether unique human immunodeficiency type 1 (HIV) genotypes occur in the genital tract is important for vaccine development and management of drug resistant viruses. Multiple cross-sectional studies suggest HIV is compartmentalized within the female genital tract. We hypothesize that bursts of HIV replication and/or proliferation of infected cells captured in cross-sectional analyses drive compartmentalization but over time genital-specific viral lineages do not form; rather viruses mix between genital tract and blood. Methods. Eight women with ongoing HIV replication were studied during a period of 1.5 to 4.5 years. Multiple viral sequences were derived by single-genome amplification of the HIV C2-V5 region of env from genital secretions and blood plasma. Maximum likelihood phylogenies were evaluated for compartmentalization using 4 statistical tests. Results. In cross-sectional analyses compartmentalization of genital from blood viruses was detected in three of eight women by all tests; this was associated with tissue specific clades containing multiple monotypic sequences. In longitudinal analysis, the tissues-specific clades did not persist to form viral lineages. Rather, across women, HIV lineages were comprised of both genital tract and blood sequences. Conclusions. The observation of genital-specific HIV clades only in cross-sectional analysis and an absence of genital-specific lineages in longitudinal analyses suggest a dynamic interchange of HIV variants between the female genital tract and blood. PMID:23315326

  3. Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time.

    PubMed

    Bull, Marta E; Heath, Laura M; McKernan-Mullin, Jennifer L; Kraft, Kelli M; Acevedo, Luis; Hitti, Jane E; Cohn, Susan E; Tapia, Kenneth A; Holte, Sarah E; Dragavon, Joan A; Coombs, Robert W; Mullins, James I; Frenkel, Lisa M

    2013-04-15

    Whether unique human immunodeficiency type 1 (HIV) genotypes occur in the genital tract is important for vaccine development and management of drug resistant viruses. Multiple cross-sectional studies suggest HIV is compartmentalized within the female genital tract. We hypothesize that bursts of HIV replication and/or proliferation of infected cells captured in cross-sectional analyses drive compartmentalization but over time genital-specific viral lineages do not form; rather viruses mix between genital tract and blood. Eight women with ongoing HIV replication were studied during a period of 1.5 to 4.5 years. Multiple viral sequences were derived by single-genome amplification of the HIV C2-V5 region of env from genital secretions and blood plasma. Maximum likelihood phylogenies were evaluated for compartmentalization using 4 statistical tests. In cross-sectional analyses compartmentalization of genital from blood viruses was detected in three of eight women by all tests; this was associated with tissue specific clades containing multiple monotypic sequences. In longitudinal analysis, the tissues-specific clades did not persist to form viral lineages. Rather, across women, HIV lineages were comprised of both genital tract and blood sequences. The observation of genital-specific HIV clades only in cross-sectional analysis and an absence of genital-specific lineages in longitudinal analyses suggest a dynamic interchange of HIV variants between the female genital tract and blood.

  4. On the contributions of photorespiration and compartmentation to the contrasting intramolecular 2H profiles of C3 and C4 plant sugars

    Youping Zhou; Benli Zhang; Hilary Stuart-Williams; Kliti Grice; Charles H. Hocart; Arthur Gessler; Zachary E. Kayler; Graham D. Farquhar

    2018-01-01

    Compartmentation of C4 photosynthetic biochemistry into bundle sheath (BS) and mesophyll (M) cells, and photorespiration in C3 plants is predicted to have hydrogen isotopic consequences for metabolites at both molecular and site-specific levels. Molecular-level evidence was recently reported (Zhou et al., 2016), but...

  5. Selection of ribozymes that catalyse multiple-turnover Diels–Alder cycloadditions by using in vitro compartmentalization

    PubMed Central

    Agresti, Jeremy J.; Kelly, Bernard T.; Jäschke, Andres; Griffiths, Andrew D.

    2005-01-01

    In vitro compartmentalization (IVC) has previously been used to evolve protein enzymes. Here, we demonstrate how IVC can be applied to select RNA enzymes (ribozymes) for a property that has previously been unselectable: true intermolecular catalysis. Libraries containing 1011 ribozyme genes are compartmentalized in the aqueous droplets of a water-in-oil emulsion, such that most droplets contain no more than one gene, and transcribed in situ. By coencapsulating the gene, RNA, and the substrates/products of the catalyzed reaction, ribozymes can be selected for all enzymatic properties: substrate recognition, product formation, rate acceleration, and turnover. Here we exploit the complementarity of IVC with systematic evolution of ligands by exponential enrichment (SELEX), which allows selection of larger libraries (≥1015) and for very small rate accelerations (kcat/kuncat) but only selects for intramolecular single-turnover reactions. We selected ≈1014 random RNAs for Diels–Alderase activity with five rounds of SELEX, then six to nine rounds with IVC. All selected ribozymes catalyzed the Diels–Alder reaction in a truly bimolecular fashion and with multiple turnover. Nearly all ribozymes selected by using eleven rounds of SELEX alone contain a common catalytic motif. Selecting with SELEX then IVC gave ribozymes with significant sequence variations in this catalytic motif and ribozymes with completely novel motifs. Interestingly, the catalytic properties of all of the selected ribozymes were quite similar. The ribozymes are strongly product inhibited, consistent with the Diels–Alder transition state closely resembling the product. More efficient Diels–Alderases may need to catalyze a second reaction that transforms the product and prevents product inhibition. PMID:16260754

  6. Compartmental profile of solids content in modified anaerobic inclining-baffled reactor treating recycled paper mill effluent

    NASA Astrophysics Data System (ADS)

    Zwain, Haider M.; Marshdi, Qosai Sahib; Murshedi, Kareem Radii Obaid; Dahlan, Irvan

    2017-10-01

    Recycled paper mill effluent (RPME) contains high concentrations of organic matters and total solids, and therefore requires proper treatment prior to discharge. There is a lack of experimental data available on the biodegradation of solids contents of RPME and digested sludge in anaerobic reactors. In this study, the treatment of RPME was studied using five compartments modified anaerobic inclining-baffled reactor (MAI-BR). The compartmental profiles of TSS, VSS, TDS and lignin contents, and floc size were investigated at different influent chemical oxygen demand concentration (CODin) from 1,000 to 4,000 mg/L, and hydraulic retention time (HRT) from 3 to 1 days (corresponding to organic loading rate (OLR) from 0.33 to 4 g/L day). The results showed that the contents of TSS, VSS and lignin were the highest at Compartment 1 (14,818-32,130 mg/L), (6,772-20,548 mg/L) and (7-227 mg/L), and gradually decreased towards Compartment 5 (627-8,518 mg/L), (281-6,145 mg/L) and (7-22 mg/L), respectively. Conversely, the content of TDS was low at Compartment 1 (508-712 mg/L) and slightly increased towards Compartment 5 (531-836 mg/L). Throughout 126 days, the floc size at Compartmental 1 was increased from 104 to 731 µm, similarly for other compartments. These results concluded that Compartment 1 played a major role in the operation of MAI-BR treating RPME.

  7. [Correlation of medial compartmental joint line elevation with femorotibial angle correction and clinical function after unicompartmental arthroplasty].

    PubMed

    Zhang, Zhan-Feng; Wang, Dan; Min, Ji-Kang

    2017-04-25

    To study the correlation of postoperative femorotibial angle with medial compartmental joint line elevation after unicompartmental arthroplasty(UKA), as well as the correlation of joint line elevation with the clinical function by measuring radiological joint line. A retrospective study of 56 patients from July 2012 to August 2015 was performed. The mean body mass index (BMI) was 23.5 (ranged, 18.3 to 30.1). The standing anteroposterior radiographs of these patients were assessed both pre-and post-operatively, and the knee function was evaluated according to HSS grading. The correlation between postoperative femorotibial angle(FTA) and joint line elevation was analyzed as well as the correlation between joint line elevation and the clinical function. The mean medial joint line elevation was (2.2±2.0) mm(ranged, -3.3 to 7.0 mm), and the mean FTA correction was (2.3±3.0)°(ranged, -4.5° to 9.6°). The mean follow-up period was 12.2 months. There was a significant correlation between in joint line elevation and FTA correction( P <0.05), while there was no significant correlation between joint line elevation and the clinical function( P >0.05). There was a significant correlation between medial compartmental joint line elevation and FTA correction after UKA, and the proximal tibial osteotomy was critical during the procedure. There was no significant correlation between joint line elevation and the clinical function, which may be related to the design of UKA prosthesis.

  8. Lipid Droplet-Associated Proteins (LDAPs) Are Required for the Dynamic Regulation of Neutral Lipid Compartmentation in Plant Cells1

    PubMed Central

    Park, Sunjung; Wu, Peng

    2016-01-01

    Eukaryotic cells compartmentalize neutral lipids into organelles called lipid droplets (LDs), and while much is known about the role of LDs in storing triacylglycerols in seeds, their biogenesis and function in nonseed tissues are poorly understood. Recently, we identified a class of plant-specific, lipid droplet-associated proteins (LDAPs) that are abundant components of LDs in nonseed cell types. Here, we characterized the three LDAPs in Arabidopsis (Arabidopsis thaliana) to gain insight to their targeting, assembly, and influence on LD function and dynamics. While all three LDAPs targeted specifically to the LD surface, truncation analysis of LDAP3 revealed that essentially the entire protein was required for LD localization. The association of LDAP3 with LDs was detergent sensitive, but the protein bound with similar affinity to synthetic liposomes of various phospholipid compositions, suggesting that other factors contributed to targeting specificity. Investigation of LD dynamics in leaves revealed that LD abundance was modulated during the diurnal cycle, and characterization of LDAP misexpression mutants indicated that all three LDAPs were important for this process. LD abundance was increased significantly during abiotic stress, and characterization of mutant lines revealed that LDAP1 and LDAP3 were required for the proper induction of LDs during heat and cold temperature stress, respectively. Furthermore, LDAP1 was required for proper neutral lipid compartmentalization and triacylglycerol degradation during postgerminative growth. Taken together, these studies reveal that LDAPs are required for the maintenance and regulation of LDs in plant cells and perform nonredundant functions in various physiological contexts, including stress response and postgerminative growth. PMID:26896396

  9. A compartmental model of uranium in human hair for protracted ingestion of natural uranium in drinking water.

    PubMed

    Li, W B; Karpas, Z; Salonen, L; Kurttio, P; Muikku, M; Wahl, W; Höllriegl, V; Hoeschen, C; Oeh, U

    2009-06-01

    To predict uranium in human hair due to chronic exposure through drinking water, a compartment representing human hair was added into the uranium biokinetic model developed by the International Commission on Radiological Protection (ICRP). The hair compartmental model was used to predict uranium excretion in human hair as a bioassay indicator due to elevated uranium intakes. Two excretion pathways, one starting from the compartment of plasma and the other from the compartment of intermediate turnover soft tissue, are assumed to transfer uranium to the compartment of hair. The transfer rate was determined from reported uranium contents in urine and in hair, taking into account the hair growth rate of 0.1 g d(-1). The fractional absorption in the gastrointestinal tract of 0.6% was found to fit best to describe the measured uranium levels among the users of drilled wells in Finland. The ingestion dose coefficient for (238)U, which includes its progeny of (234)Th, (234m)Pa, and (234)Pa, was calculated equal to 1.3 x 10(-8) Sv Bq(-1) according to the hair compartmental model. This estimate is smaller than the value of 4.5 x 10(-8) Sv Bq(-1) published by ICRP for the members of the public. In this new model, excretion of uranium through urine is better represented when excretion to the hair compartment is accounted for and hair analysis can provide a means for assessing the internal body burden of uranium. The model is applicable for chronic exposure as well as for an acute exposure incident. In the latter case, the hair sample can be collected and analyzed even several days after the incident, whereas urinalysis requires sample collection shortly after the exposure. The model developed in this study applies to ingestion intakes of uranium.

  10. A hydrophobic ionic liquid compartmentalized sampling/labeling and its separation techniques in polydimethylsiloxane microchip capillary electrophoresis.

    PubMed

    Quan, Hong Hua; Li, Ming; Huang, Yan; Hahn, Jong Hoon

    2017-01-01

    This paper demonstrates a novel compartmentalized sampling/labeling method and its separation techniques using a hydrophobic ionic liquid (IL)-1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)-imidate (BmimNTf 2 )-as the immiscible phase, which is capable of minimizing signal losses during microchip capillary electrophoresis (MCE). The MCE device consists of a silica tube connected to a straight polydimethylsiloxane (PDMS) separation channel. Poly(diallyldimethylammonium chloride) (PDDAC) was coated on the inner surface of channel to ease the introduction of IL plugs and enhance the IL wetting on the PDMS surface for sample releasing. Electroosmotic flow (EOF)-based sample compartmentalization was carried out through a sequenced injection into sampling tubes with the following order: leading IL plug/sample segment/terminal IL plug. The movement of the sample segment was easily controlled by applying an electrical voltage across both ends of the chip without a sample volume change. This approach effectively prevented analyte diffusion before injection into MCE channels. When the sample segment was manipulated to the PDDAC-modified PDMS channel, the sample plug then was released from isolation under EOF while IL plugs adsorbed onto channel surfaces owing to strong adhesion. A mixture of flavin adenine nucleotides (FAD) and flavin mononucleotides (FMN) was successfully separated on a 2.5 cm long separation channel, for which the theoretical numbers of plates were 15 000 and 17 000, respectively. The obtained peak intensity was increased 6.3-fold over the corresponding value from conventional electrokinetic injection with the same sampling time. Furthermore, based on the compartmented sample segment serving as an interim reactor, an on-chip fluorescence labeling is demonstrated. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Differential compartmentalization of Streptococcus pyogenes virulence factors and host protein binding properties as a mechanism for host adaptation.

    PubMed

    Kilsgård, Ola; Karlsson, Christofer; Malmström, Erik; Malmström, Johan

    2016-11-01

    Streptococcus pyogenes is an important human pathogen responsible for substantial morbidity and mortality worldwide. Although S. pyogenes is a strictly human pathogen with no other known animal reservoir, several murine infection models exist to explore different aspects of the bacterial pathogenesis. Inoculating mice with wild-type S. pyogenes strains can result in the generation of new bacterial phenotypes that are hypervirulent compared to the original inoculum. In this study, we used a serial mass spectrometry based proteomics strategy to investigate if these hypervirulent strains have an altered distribution of virulence proteins across the intracellular, surface associated and secreted bacterial compartments and if any change in compartmentalization can alter the protein-protein interaction network between bacteria and host proteins. Quantitative analysis of the S. pyogenes surface and secreted proteomes revealed that animal passaged strains are associated with significantly higher amount of virulence factors on the bacterial surface and in the media. This altered virulence factor compartmentalization results in increased binding of several mouse plasma proteins to the bacterial surface, a trend that was consistent for mouse plasma from several different mouse strains. In general, both the wild-type strain and animal passaged strain were capable of binding high amounts of human plasma proteins. However, compared to the non-passaged strains, the animal passaged strains displayed an increased ability to bind mouse plasma proteins, in particular for M protein binders, indicating that the increased affinity for mouse blood plasma proteins is a consequence of host adaptation of this pathogen to a new host. In conclusion, plotting the total amount of virulence factors against the total amount of plasma proteins associated to the bacterial surface could clearly separate out animal passaged strains from wild type strains indicating a virulence model that could

  12. Rational design of thermostability in bacterial 1,3-1,4-β-glucanases through spatial compartmentalization of mutational hotspots.

    PubMed

    Niu, Chengtuo; Zhu, Linjiang; Xu, Xin; Li, Qi

    2017-02-01

    Higher thermostability is required for 1,3-1,4-β-glucanase to maintain high activity under harsh conditions in the brewing and animal feed industries. In this study, a comprehensive and comparative analysis of thermostability in bacterial β-glucanases was conducted through a method named spatial compartmentalization of mutational hotspots (SCMH), which combined alignment of homologous protein sequences, spatial compartmentalization, and molecular dynamic (MD) simulation. The overall/local flexibility of six homologous β-glucanases was calculated by MD simulation and linearly fitted with enzyme optimal enzymatic temperatures. The calcium region was predicted to be the crucial region for thermostability of bacterial 1,3-1,4-β-glucanases, and optimization of four residue sites in this region by iterative saturation mutagenesis greatly increased the thermostability of a mesophilic β-glucanase (BglT) from Bacillus terquilensis. The E46P/S43E/H205P/S40E mutant showed a 20 °C increase in optimal enzymatic temperature and a 13.8 °C rise in protein melting temperature (T m ) compared to wild-type BglT. Its half-life values at 60 and 70 °C were 3.86-fold and 7.13-fold higher than those of wild-type BglT. The specific activity of E46P/S43E/H205P/S40E mutant was increased by 64.4 %, while its stability under acidic environment was improved. The rational design strategy used in this study might be applied to improve the thermostability of other industrial enzymes.

  13. Compartmentalization of HIV-1 within the female genital tract is due to monotypic and low-diversity variants not distinct viral populations.

    PubMed

    Bull, Marta; Learn, Gerald; Genowati, Indira; McKernan, Jennifer; Hitti, Jane; Lockhart, David; Tapia, Kenneth; Holte, Sarah; Dragavon, Joan; Coombs, Robert; Mullins, James; Frenkel, Lisa

    2009-09-22

    Compartmentalization of HIV-1 between the genital tract and blood was noted in half of 57 women included in 12 studies primarily using cell-free virus. To further understand differences between genital tract and blood viruses of women with chronic HIV-1 infection cell-free and cell-associated virus populations were sequenced from these tissues, reasoning that integrated viral DNA includes variants archived from earlier in infection, and provides a greater array of genotypes for comparisons. Multiple sequences from single-genome-amplification of HIV-1 RNA and DNA from the genital tract and blood of each woman were compared in a cross-sectional study. Maximum likelihood phylogenies were evaluated for evidence of compartmentalization using four statistical tests. Genital tract and blood HIV-1 appears compartmentalized in 7/13 women by >/=2 statistical analyses. These subjects' phylograms were characterized by low diversity genital-specific viral clades interspersed between clades containing both genital and blood sequences. Many of the genital-specific clades contained monotypic HIV-1 sequences. In 2/7 women, HIV-1 populations were significantly compartmentalized across all four statistical tests; both had low diversity genital tract-only clades. Collapsing monotypic variants into a single sequence diminished the prevalence and extent of compartmentalization. Viral sequences did not demonstrate tissue-specific signature amino acid residues, differential immune selection, or co-receptor usage. In women with chronic HIV-1 infection multiple identical sequences suggest proliferation of HIV-1-infected cells, and low diversity tissue-specific phylogenetic clades are consistent with bursts of viral replication. These monotypic and tissue-specific viruses provide statistical support for compartmentalization of HIV-1 between the female genital tract and blood. However, the intermingling of these clades with clades comprised of both genital and blood sequences and the absence

  14. Droplet Microfluidics for Compartmentalized Cell Lysis and Extension of DNA from Single-Cells

    NASA Astrophysics Data System (ADS)

    Zimny, Philip; Juncker, David; Reisner, Walter

    Current single cell DNA analysis methods suffer from (i) bias introduced by the need for molecular amplification and (ii) limited ability to sequence repetitive elements, resulting in (iii) an inability to obtain information regarding long range genomic features. Recent efforts to circumvent these limitations rely on techniques for sensing single molecules of DNA extracted from single-cells. Here we demonstrate a droplet microfluidic approach for encapsulation and biochemical processing of single-cells inside alginate microparticles. In our approach, single-cells are first packaged inside the alginate microparticles followed by cell lysis, DNA purification, and labeling steps performed off-chip inside this microparticle system. The alginate microparticles are then introduced inside a micro/nanofluidic system where the alginate is broken down via a chelating buffer, releasing long DNA molecules which are then extended inside nanofluidic channels for analysis via standard mapping protocols.

  15. Metabolic Plasticity and Inter-Compartmental Interactions in Rice Metabolism: An Analysis from Reaction Deletion Study.

    PubMed

    Shaw, Rahul; Kundu, Sudip

    2015-01-01

    More than 20% of the total caloric intake of human population comes from rice. The expression of rice genes and hence, the concentration of enzymatic proteins might vary due to several biotic and abiotic stresses. It in turn, can influence the overall metabolism and survivability of rice plant. Thus, understanding the rice cellular metabolism, its plasticity and potential readjustments under different perturbations can help rice biotechnologists to design efficient rice cultivars. Here, using the flux balance analysis (FBA) method, with the help of in-silico reaction deletion strategy, we study the metabolic plasticity of genome-scale metabolic model of rice leaf. A set of 131 reactions, essential for the production of primary biomass precursors is identified; deletion of any of them can inhibit the overall biomass production. Usability Index (IU) for the rest of the reactions are estimated and based on this parameter, they are classified into three categories-maximally-favourable, quasi-favourable and unfavourable for the primary biomass production. The lower value of 1 - IU of a reaction suggests that the cell cannot easily bypass it for biomass production. While some of the alternative paths are energetically equally efficient, others demand for higher photon. The variations in (i) ATP/NADPH ratio, (ii) exchange of metabolites through chloroplastic transporters and (iii) total biomass production are also presented here. Mutual metabolic dependencies of different cellular compartments are also demonstrated.

  16. Lipid droplet-associated proteins (LDAPs) are involved in the compartmentalization of lipophilic compounds in plant cells

    PubMed Central

    Gidda, Satinder K; Watt, Samantha C; Collins-Silva, Jillian; Kilaru, Aruna; Arondel, Vincent; Yurchenko, Olga; Horn, Patrick J; James, Christopher N; Shintani, David; Ohlrogge, John B; Chapman, Kent D; Mullen, Robert T; Dyer, John M

    2013-01-01

    While lipid droplets have traditionally been considered as inert sites for the storage of triacylglycerols and sterol esters, they are now recognized as dynamic and functionally diverse organelles involved in energy homeostasis, lipid signaling, and stress responses. Unlike most other organelles, lipid droplets are delineated by a half-unit membrane whose protein constituents are poorly understood, except in the specialized case of oleosins, which are associated with seed lipid droplets. Recently, we identified a new class of lipid-droplet associated proteins called LDAPs that localize specifically to the lipid droplet surface within plant cells and share extensive sequence similarity with the small rubber particle proteins (SRPPs) found in rubber-accumulating plants. Here, we provide additional evidence for a role of LDAPs in lipid accumulation in oil-rich fruit tissues, and further explore the functional relationships between LDAPs and SRPPs. In addition, we propose that the larger LDAP/SRPP protein family plays important roles in the compartmentalization of lipophilic compounds, including triacylglycerols and polyisoprenoids, into lipid droplets within plant cells. Potential roles in lipid droplet biogenesis and function of these proteins also are discussed. PMID:24305619

  17. Prenatal HIV testing: the compartmentalization of women's sexual risk exposure and the return of the maternal fetal conflict.

    PubMed

    Kelly, Kristin; Hampson, Sarah Cote; Huff, Jamie

    2012-01-01

    The purpose of the researchers in this study was to investigate how women who were being tested for HIV during their pregnancies were evaluating, conceptualizing, and negotiating their risk of infection. The study included two focus groups and 20 in-depth interviews with 30 patients, ages 17-38 years, from diverse ethnic/racial, social, and economic backgrounds. Qualitative analyses of the interview transcripts revealed support for the idea that pregnant women have a responsibility to minimize risks to their fetus, with all interviewees describing actions to minimize those risks while pregnant. Two sub-themes emerged that were related to the presence of differences in how interviewees conceptualized risk depending on the type of risk being discussed. In the case of diet and lifestyle influences, interviewees framed their health and the health of the fetus as connected. In contrast, when the issue of HIV risk and testing was raised, the interviewees described the risk of HIV to themselves and their fetuses as separate concerns and, with few exceptions, reported no effort to reduce the risk of becoming infected while pregnant (beyond consenting to HIV screening while receiving prenatal care). Findings suggest the importance of developing HIV prevention messages that counter the compartmentalization of risk during pregnancy.

  18. Familiarity with a vocal category biases the compartmental expression of Arc/Arg3.1 in core auditory cortex.

    PubMed

    Ivanova, Tamara N; Gross, Christina; Mappus, Rudolph C; Kwon, Yong Jun; Bassell, Gary J; Liu, Robert C

    2017-12-01

    Learning to recognize a stimulus category requires experience with its many natural variations. However, the mechanisms that allow a category's sensorineural representation to be updated after experiencing new exemplars are not well understood, particularly at the molecular level. Here we investigate how a natural vocal category induces expression in the auditory system of a key synaptic plasticity effector immediate early gene, Arc/Arg3.1 , which is required for memory consolidation. We use the ultrasonic communication system between mouse pups and adult females to study whether prior familiarity with pup vocalizations alters how Arc is engaged in the core auditory cortex after playback of novel exemplars from the pup vocal category. A computerized, 3D surface-assisted cellular compartmental analysis, validated against manual cell counts, demonstrates significant changes in the recruitment of neurons expressing Arc in pup-experienced animals (mothers and virgin females "cocaring" for pups) compared with pup-inexperienced animals (pup-naïve virgins), especially when listening to more familiar, natural calls compared to less familiar but similarly recognized tonal model calls. Our data support the hypothesis that the kinetics of Arc induction to refine cortical representations of sensory categories is sensitive to the familiarity of the sensory experience. © 2017 Ivanova et al.; Published by Cold Spring Harbor Laboratory Press.

  19. Combining a Complex Network Approach and a SEIR Compartmental Model to link Fast Spreading of Infectious Diseases with Climate Change

    NASA Astrophysics Data System (ADS)

    Brenner, F.; Hoffmann, P.; Marwan, N.

    2016-12-01

    Infectious diseases are a major threat to human health. The spreading of airborne diseases has become fast and hard to predict. Global air travelling created a network which allows a pathogen to migrate worldwide in only a few days. Pandemics of SARS (2002/03) and H1N1 (2009) have impressively shown the epidemiological danger in a strongly connected world. In this study we simulate the outbreak of an airborne infectious disease that is directly transmitted from human to human. We use a regular Susceptible-Infected-Recovered (SIR) model and a modified Susceptible-Exposed-Infected-Recovered (SEIR) compartmental approach with the basis of a complex network built by global air traffic data (from openflights.org). Local Disease propagation is modeled with a global population dataset (from SEDAC and MaxMind) and parameterizations of human behavior regarding mobility, contacts and awareness. As a final component we combine the worldwide outbreak simulation with daily averaged climate data from WATCH-Forcing-Data-ERA-Interim (WFDEI) and Coupled Model Intercomparison Project Phase 5 (CMIP5). Here we focus on Influenza-like illnesses (ILI), whose transmission rate has a dependency on relative humidity and temperature. Even small changes in relative humidity are sufficient to trigger significant differences in the global outbreak behavior. Apart from the direct effect of climate change on the transmission of airborne diseases, there are indirect ramifications that alter spreading patterns. For example seasonal changing human mobility is influenced by climate settings.

  20. Two-compartmental population balance modeling of a pulsed spray fluidized bed granulation based on computational fluid dynamics (CFD) analysis.

    PubMed

    Liu, Huolong; Li, Mingzhong

    2014-11-20

    In this work a two-compartmental population balance model (TCPBM) was proposed to model a pulsed top-spray fluidized bed granulation. The proposed TCPBM considered the spatially heterogeneous granulation mechanisms of the granule growth by dividing the granulator into two perfectly mixed zones of the wetting compartment and drying compartment, in which the aggregation mechanism was assumed in the wetting compartment and the breakage mechanism was considered in the drying compartment. The sizes of the wetting and drying compartments were constant in the TCPBM, in which 30% of the bed was the wetting compartment and 70% of the bed was the drying compartment. The exchange rate of particles between the wetting and drying compartments was determined by the details of the flow properties and distribution of particles predicted by the computational fluid dynamics (CFD) simulation. The experimental validation has shown that the proposed TCPBM can predict evolution of the granule size and distribution within the granulator under different binder spray operating conditions accurately. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Inter-compartmental transport of organophosphate and pyrethroid pesticides in South China: implications for a regional risk assessment.

    PubMed

    Li, Huizhen; Wei, Yanli; Lydy, Michael J; You, Jing

    2014-07-01

    The dynamic flux of an organophosphate and four pyrethroid pesticides was determined in an air-(soil)-water-sediment system based on monitoring data from Guangzhou, China. The total air-water flux, including air-water gaseous exchange and atmospheric deposition, showed deposition from air to water for chlorpyrifos, bifenthrin and cypermethrin, but volatilization for lambda-cyhalothrin and permethrin. The transport of the pesticides from overlying water to sediment suggested that sediment acted as a sink for the pesticides. Additionally, distinct annual atmospheric depositional fluxes between legacy and current-use pesticides suggested the role of consumer usage in their transport throughout the system. Finally, pesticide toxicity was estimated from annual air-water-sediment flux within an urban stream in Guangzhou. A dynamic flux-based risk assessment indicated that inter-compartmental transport of chlorpyrifos decreased its atmospheric exposure, but had little influence on its aquatic toxicity. Instead, water-to-sediment transport of pyrethroids increased their sediment toxicity, which was supported by previously reported toxicity data. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Using Cluster Analysis to Compartmentalize a Large Managed Wetland Based on Physical, Biological, and Climatic Geospatial Attributes.

    PubMed

    Hahus, Ian; Migliaccio, Kati; Douglas-Mankin, Kyle; Klarenberg, Geraldine; Muñoz-Carpena, Rafael

    2018-04-27

    Hierarchical and partitional cluster analyses were used to compartmentalize Water Conservation Area 1, a managed wetland within the Arthur R. Marshall Loxahatchee National Wildlife Refuge in southeast Florida, USA, based on physical, biological, and climatic geospatial attributes. Single, complete, average, and Ward's linkages were tested during the hierarchical cluster analyses, with average linkage providing the best results. In general, the partitional method, partitioning around medoids, found clusters that were more evenly sized and more spatially aggregated than those resulting from the hierarchical analyses. However, hierarchical analysis appeared to be better suited to identify outlier regions that were significantly different from other areas. The clusters identified by geospatial attributes were similar to clusters developed for the interior marsh in a separate study using water quality attributes, suggesting that similar factors have influenced variations in both the set of physical, biological, and climatic attributes selected in this study and water quality parameters. However, geospatial data allowed further subdivision of several interior marsh clusters identified from the water quality data, potentially indicating zones with important differences in function. Identification of these zones can be useful to managers and modelers by informing the distribution of monitoring equipment and personnel as well as delineating regions that may respond similarly to future changes in management or climate.

  3. Role of cellular compartmentalization in the trophic transfer of mercury species in a freshwater plant-crustacean food chain.

    PubMed

    Beauvais-Flück, Rebecca; Chaumot, Arnaud; Gimbert, Frédéric; Quéau, Hervé; Geffard, Olivier; Slaveykova, Vera I; Cosio, Claudia

    2016-12-15

    Mercury (Hg) represents an important risk for human health through the food webs contamination. Macrophytes bioaccumulate Hg and play a role in Hg transfer to food webs in shallow aquatic ecosystems. Nevertheless, the compartmentalization of Hg within macrophytes, notably major accumulation in the cell wall and its impact on trophic transfer to primary consumers are overlooked. The present work focusses on the trophic transfer of inorganic Hg (IHg) and monomethyl-Hg (MMHg) from the intracellular and cell wall compartments of the macrophyte Elodea nuttallii - considered a good candidate for phytoremediation - to the crustacean Gammarus fossarum. The results demonstrated that Hg accumulated in both compartments was trophically bioavailable to gammarids. Besides IHg from both compartments were similarly transferred to G. fossarum, while for MMHg, uptake rates were ∼2.5-fold higher in G. fossarum fed with the cell wall vs the intracellular compartment. During the depuration phase, Hg concentrations in G. fossarum varied insignificantly suggesting that both IHg and MMHg were strongly bound to biological ligands in the crustacean. Our data imply that cell walls have to be considered as an important source of Hg to consumers in freshwater food webs when developing procedures for enhancing aquatic environment protection during phytoremediation programs. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction

    SciT

    Wang, Yingchun; Yang, Feng; Fu, Yi

    Abstract - Brain development and spinal cord regeneration require neurite sprouting and growth cone navigation in response to extension and collapsing factors present in the extracellular environment. These external guidance cues control neurite growth cone extension and retraction processes through intracellular protein phosphorylation of numerous cytoskeletal, adhesion, and polarity complex signaling proteins. However, the complex kinase/substrate signaling networks that mediate neuritogenesis have not been investigated. Here, we compare the neurite phosphoproteome under growth and retraction conditions using neurite purification methodology combined with mass spectrometry. More than 4000 non-redundant phosphorylation sites from 1883 proteins have been annotated and mapped to signalingmore » pathways that control kinase/phosphatase networks, cytoskeleton remodeling, and axon/dendrite specification. Comprehensive informatics and functional studies revealed a compartmentalized ERK activation/deactivation cytoskeletal switch that governs neurite growth and retraction, respectively. Our findings provide the first system-wide analysis of the phosphoprotein signaling networks that enable neurite growth and retraction and reveal an important molecular switch that governs neuritogenesis.« less

  5. A computational analysis of the impact of the transient genetic imbalance on compartmentalized gene expression during sporulation in Bacillus subtilis.

    PubMed

    Iber, Dagmar

    2006-06-30

    Sporulation in Bacillus subtilis serves as paradigm for the development of two different cell types (mother cell and prespore) from a single cell. Differential gene expression is achieved by restricting the activation of the key transcription factor sigmaF to the smaller prespore. By use of a combination of mathematical and experimental techniques we have recently shown that the volume difference determines cell fate and that the accumulation of the phosphatase SpoIIE on the asymmetrically placed septum is sufficient for prespore-specific sigmaF activation. Since compartmentalized gene expression is still obtained when SpoIIE cannot accumulate on the septum a number of alternative mechanisms have been proposed. These mechanisms focus on the difference in gene content between mother cell and prespore immediately after septation. Here the computational model is employed to show that under physiological conditions the transient genetic imbalance is unlikely to affect the septation-dependent release of sigmaF. The duration of the transient genetic imbalance is too short for the degradation of SpoIIAB to have an impact on the release of sigmaF. Moreover, the existence of an elusive IIE inhibitor, which has been proposed to become depleted in the prespore because of the transient genetic imbalance, is shown to be inconsistent with available experimental data. We conclude that the volume difference between the two compartments is the main determinant of cell fate.

  6. Is the Dissociative Experiences Scale able to identify detachment and compartmentalization symptoms? Factor structure of the Dissociative Experiences Scale in a large sample of psychiatric and nonpsychiatric subjects

    PubMed Central

    Mazzotti, Eva; Farina, Benedetto; Imperatori, Claudio; Mansutti, Federica; Prunetti, Elena; Speranza, Anna Maria; Barbaranelli, Claudio

    2016-01-01

    Background In this study, we explored the ability of the Dissociative Experiences Scale (DES) to catch detachment and compartmentalization symptoms. Participants and methods The DES factor structure was evaluated in 768 psychiatric patients (546 women and 222 men) and in 2,403 subjects enrolled in nonpsychiatric settings (1,857 women and 546 men). All participants were administered the Italian version of DES. Twenty senior psychiatric experts in the treatment of dissociative symptoms independently assessed the DES items and categorized each of them as follows: “C” for compartmentalization, “D” for detachment, and “NC” for noncongruence with either C or D. Results Confirmatory factor analysis supported the three-factor structure of DES in both clinical and nonclinical samples and its invariance across the two groups. Moreover, factor analyses results overlapped with those from the expert classification procedure. Conclusion Our results showed that DES can be used as a valid instrument for clinicians to assess the frequency of different types of dissociative experiences including detachment and compartmentalization. PMID:27350746

  7. Combined Recirculatory-compartmental Population Pharmacokinetic Modeling of Arterial and Venous Plasma S(+) and R(-) Ketamine Concentrations.

    PubMed

    Henthorn, Thomas K; Avram, Michael J; Dahan, Albert; Gustafsson, Lars L; Persson, Jan; Krejcie, Tom C; Olofsen, Erik

    2018-05-16

    The pharmacokinetics of infused drugs have been modeled without regard for recirculatory or mixing kinetics. We used a unique ketamine dataset with simultaneous arterial and venous blood sampling, during and after separate S(+) and R(-) ketamine infusions, to develop a simplified recirculatory model of arterial and venous plasma drug concentrations. S(+) or R(-) ketamine was infused over 30 min on two occasions to 10 healthy male volunteers. Frequent, simultaneous arterial and forearm venous blood samples were obtained for up to 11 h. A multicompartmental pharmacokinetic model with front-end arterial mixing and venous blood components was developed using nonlinear mixed effects analyses. A three-compartment base pharmacokinetic model with additional arterial mixing and arm venous compartments and with shared S(+)/R(-) distribution kinetics proved superior to standard compartmental modeling approaches. Total pharmacokinetic flow was estimated to be 7.59 ± 0.36 l/min (mean ± standard error of the estimate), and S(+) and R(-) elimination clearances were 1.23 ± 0.04 and 1.06 ± 0.03 l/min, respectively. The arm-tissue link rate constant was 0.18 ± 0.01 min and the fraction of arm blood flow estimated to exchange with arm tissue was 0.04 ± 0.01. Arterial drug concentrations measured during drug infusion have two kinetically distinct components: partially or lung-mixed drug and fully mixed-recirculated drug. Front-end kinetics suggest the partially mixed concentration is proportional to the ratio of infusion rate and total pharmacokinetic flow. This simplified modeling approach could lead to more generalizable models for target-controlled infusions and improved methods for analyzing pharmacokinetic-pharmacodynamic data.

  8. Compartmentalized self-replication (CSR) selection of Thermococcus litoralis Sh1B DNA polymerase for diminished uracil binding.

    PubMed

    Tubeleviciute, Agne; Skirgaila, Remigijus

    2010-08-01

    The thermostable archaeal DNA polymerase Sh1B from Thermococcus litoralis has a typical uracil-binding pocket, which in nature plays an essential role in preventing the accumulation of mutations caused by cytosine deamination to uracil and subsequent G-C base pair transition to A-T during the genomic DNA replication. The uracil-binding pocket recognizes and binds uracil base in a template strand trapping the polymerase. Since DNA replication stops, the repair systems have a chance to correct the promutagenic event. Archaeal family B DNA polymerases are employed in various PCR applications. Contrary to nature, in PCR the uracil-binding property of archaeal polymerases is disadvantageous and results in decreased DNA amplification yields and lowered sensitivity. Furthermore, in diagnostics qPCR, RT-qPCR and end-point PCR are performed using dNTP mixtures, where dTTP is partially or fully replaced by dUTP. Uracil-DNA glycosylase treatment and subsequent heating of the samples is used to degrade the DNA containing uracil and prevent carryover contamination, which is the main concern in diagnostic laboratories. A thermostable archaeal DNA polymerase with the abolished uracil binding would be a highly desirable and commercially interesting product. An attempt to disable uracil binding in DNA polymerase Sh1B from T. litoralis by generating site-specific mutants did not yield satisfactory results. However, a combination of random mutagenesis of the whole polymerase gene and compartmentalized self-replication was successfully used to select variants of thermostable Sh1B polymerase capable of performing PCR with dUTP instead of dTTP.

  9. A comparative evaluation of two decompression procedures for technical diving using inflammatory responses: compartmental versus ratio deco.

    PubMed

    Spisni, Enzo; Marabotti, Claudio; De Fazio, Luigia; Valerii, Maria Chiara; Cavazza, Elena; Brambilla, Stefano; Hoxha, Klarida; L'Abbate, Antonio; Longobardi, Pasquale

    2017-03-01

    The aim of this study was to compare two decompression procedures commonly adopted by technical divers: the ZH-L16 algorithm modified by 30/85 gradient factors (compartmental decompression model, CDM) versus the 'ratio decompression strategy' (RDS). The comparison was based on an analysis of changes in diver circulating inflammatory profiles caused by decompression from a single dive. Fifty-one technical divers performed a single trimix dive to 50 metres' sea water (msw) for 25 minutes followed by enriched air (EAN50) and oxygen decompression. Twenty-three divers decompressed according to a CDM schedule and 28 divers decompressed according to a RDS schedule. Peripheral blood for detection of inflammatory markers was collected before and 90 min after diving. Venous gas emboli were measured 30 min after diving using 2D echocardiography. Matched groups of 23 recreational divers (dive to 30 msw; 25 min) and 25 swimmers were also enrolled as control groups to assess the effects of decompression from a standard air dive or of exercise alone on the inflammatory profile. Echocardiography at the single 30 min observation post dive showed no significant differences between the two decompression procedures. Divers adopting the RDS showed a worsening of post-dive inflammatory profile compared to the CDM group, with significant increases in circulating chemokines CCL2 (P = 0.001) and CCL5 (P = 0.006) levels. There was no increase in chemokines following the CDM decompression. The air scuba group also showed a statistically significant increase in CCL2 (P < 0.001) and CCL5 (P = 0.003) levels post dive. No cases of decompression sickness occurred. The ratio deco strategy did not confer any benefit in terms of bubbles but showed the disadvantage of increased decompression-associated secretion of inflammatory chemokines involved in the development of vascular damage.

  10. Development of reservoir facies and porosity-permeability compartmentalization in middle Mississippian Salem Limestone, eastern margin of the Illinois Basin

    SciT

    Ahmad, N.; Keith, B.D.; Thompson, T.A.

    Shoal facies of the Salem Limestone in south-central Indiana are composed of (1) bryozoan- and echinoderm-rich (85-95%) grainstones, and (3) foraminiferal-echinodermal grainstones. Microfacies and bedform analyses indicate that deposition took place under tidal conditions where sporadic storm events mobilized the entire sand body. Strong, primarily unidirectional currents, abundant sediment supply, and rapid burial resulted in thick, massive deposits in the Salem shoal. In this hydraulic regime, shape and specific gravity determined the distribution of echinoderm grains relative to heavier bryozoan grains. The relative amount of echinoderms controlled the development of early syntaxial rim cement, which preserved porosity during early compaction.more » A significant amount of calcium carbonate ({approximately}58%) filled the micropores within the echinoderm grains before the intergranular cement could form. Areas such as toes of avalanche forests, where intermediate amounts of echinoderms are mixed with other grains, have greater porosity and permeability. Numerous stylolites also occur throughout the Salem grainstones. Variations in microfacies composition and bedforms are grouped into architectural packages that compartmentalize the porosity and permeability and form micro-to scale macroscale heterogeneities. The basal channel architectural package studied exhibits porosity-permeability compartments orthogonal to the overlying channel-fill sandwave package. In an analogous petroleum reservoir this can result in poor reservoir performance during primary and enhanced recovery leaving behind significant amounts of unrecovered mobile oil. Higher porosity and permeability at the base of a package due to the presence of toesets of a certain grain composition can result in poor sweep efficiency for enhanced recovery.« less

  11. Combined Proteomic and Transcriptomic Interrogation of the Venom Gland of Conus geographus Uncovers Novel Components and Functional Compartmentalization*

    PubMed Central

    Safavi-Hemami, Helena; Hu, Hao; Gorasia, Dhana G.; Bandyopadhyay, Pradip K.; Veith, Paul D.; Young, Neil D.; Reynolds, Eric C.; Yandell, Mark; Olivera, Baldomero M.; Purcell, Anthony W.

    2014-01-01

    Cone snails are highly successful marine predators that use complex venoms to capture prey. At any given time, hundreds of toxins (conotoxins) are synthesized in the secretory epithelial cells of the venom gland, a long and convoluted organ that can measure 4 times the length of the snail's body. In recent years a number of studies have begun to unveil the transcriptomic, proteomic and peptidomic complexity of the venom and venom glands of a number of cone snail species. By using a combination of DIGE, bottom-up proteomics and next-generation transcriptome sequencing the present study identifies proteins involved in envenomation and conotoxin maturation, significantly extending the repertoire of known (poly)peptides expressed in the venom gland of these remarkable animals. We interrogate the molecular and proteomic composition of different sections of the venom glands of 3 specimens of the fish hunter Conus geographus and demonstrate regional variations in gene expression and protein abundance. DIGE analysis identified 1204 gel spots of which 157 showed significant regional differences in abundance as determined by biological variation analysis. Proteomic interrogation identified 342 unique proteins including those that exhibited greatest fold change. The majority of these proteins also exhibited significant changes in their mRNA expression levels validating the reliability of the experimental approach. Transcriptome sequencing further revealed a yet unknown genetic diversity of several venom gland components. Interestingly, abundant proteins that potentially form part of the injected venom mixture, such as echotoxins, phospholipase A2 and con-ikots-ikots, classified into distinct expression clusters with expression peaking in different parts of the gland. Our findings significantly enhance the known repertoire of venom gland polypeptides and provide molecular and biochemical evidence for the compartmentalization of this organ into distinct functional entities

  12. Extrachromosomal Nucleolus-Like Compartmentalization by a Plasmid-Borne Ribosomal RNA Operon and Its Role in Nucleoid Compaction.

    PubMed

    Mata Martin, Carmen; Sun, Zhe; Zhou, Yan Ning; Jin, Ding Jun

    2018-01-01

    In the fast-growing Escherichia coli cells, RNA polymerase (RNAP) molecules are concentrated and form foci at clusters of ribosomal RNA (rRNA) operons resembling eukaryotic nucleolus. The bacterial nucleolus-like organization, spatially compartmentalized at the surface of the compact bacterial chromosome (nucleoid), serves as transcription factories for rRNA synthesis and ribosome biogenesis, which influences the organization of the nucleoid. Unlike wild type that has seven rRNA operons in the genome in a mutant that has six (Δ6 rrn ) rRNA operons deleted in the genome, there are no apparent transcription foci and the nucleoid becomes uncompacted, indicating that formation of RNAP foci requires multiple copies of rRNA operons clustered in space and is critical for nucleoid compaction. It has not been determined, however, whether a multicopy plasmid-borne rRNA operon (p rrnB ) could substitute the multiple chromosomal rRNA operons for the organization of the bacterial nucleolus-like structure in the mutants of Δ6 rrn and Δ7 rrn that has all seven rRNA operons deleted in the genome. We hypothesized that extrachromosomal nucleolus-like structures are similarly organized and functional in trans from p rrnB in these mutants. In this report, using multicolor images of three-dimensional superresolution Structured Illumination Microscopy (3D-SIM), we determined the distributions of both RNAP and NusB that are a transcription factor involved in rRNA synthesis and ribosome biogenesis, p rrnB clustering, and nucleoid structure in these two mutants in response to environmental cues. Our results found that the extrachromosomal nucleolus-like organization tends to be spatially located at the poles of the mutant cells. In addition, formation of RNAP foci at the extrachromosomal nucleolus-like structure condenses the nucleoid, supporting the idea that active transcription at the nucleolus-like organization is a driving force in nucleoid compaction.

  13. EphA2/Ephrin-A1 Mediate Corneal Epithelial Cell Compartmentalization via ADAM10 Regulation of EGFR Signaling.

    PubMed

    Kaplan, Nihal; Ventrella, Rosa; Peng, Han; Pal-Ghosh, Sonali; Arvanitis, Constadina; Rappoport, Joshua Z; Mitchell, Brian J; Stepp, Mary Ann; Lavker, Robert M; Getsios, Spiro

    2018-01-01

    Progenitor cells of the limbal epithelium reside in a discrete area peripheral to the more differentiated corneal epithelium and maintain tissue homeostasis. What regulates the limbal-corneal epithelial boundary is a major unanswered question. Ephrin-A1 ligand is enriched in the limbal epithelium, whereas EphA2 receptor is concentrated in the corneal epithelium. This reciprocal pattern led us to assess the role of ephrin-A1 and EphA2 in limbal-corneal epithelial boundary organization. EphA2-expressing corneal epithelial cells engineered to express ephrin-A1 were used to study boundary formation in vitro in a manner that mimicked the relative abundance of these juxtamembrane signaling proteins in the limbal and corneal epithelium in vivo. Interaction of these two distinct cell populations following initial seeding into discrete culture compartments was assessed by live cell imaging. Immunofluoresence and immunoblotting was used to evaluate the contribution of downstream growth factor signaling and cell-cell adhesion systems to boundary formation at sites of heterotypic contact between ephrin-A1 and EphA2 expressing cells. Ephrin-A1-expressing cells impeded and reversed the migration of EphA2-expressing corneal epithelial cells upon heterotypic contact formation leading to coordinated migration of the two cell populations in the direction of an ephrin-A1-expressing leading front. Genetic silencing and pharmacologic inhibitor studies demonstrated that the ability of ephrin-A1 to direct migration of EphA2-expressing cells depended on an a disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) and epidermal growth factor receptor (EGFR) signaling pathway that limited E-cadherin-mediated adhesion at heterotypic boundaries. Ephrin-A1/EphA2 signaling complexes play a key role in limbal-corneal epithelial compartmentalization and the response of these tissues to injury.

  14. EphA2/Ephrin-A1 Mediate Corneal Epithelial Cell Compartmentalization via ADAM10 Regulation of EGFR Signaling

    PubMed Central

    Kaplan, Nihal; Ventrella, Rosa; Peng, Han; Pal-Ghosh, Sonali; Arvanitis, Constadina; Rappoport, Joshua Z.; Mitchell, Brian J.; Stepp, Mary Ann; Lavker, Robert M.

    2018-01-01

    Purpose Progenitor cells of the limbal epithelium reside in a discrete area peripheral to the more differentiated corneal epithelium and maintain tissue homeostasis. What regulates the limbal–corneal epithelial boundary is a major unanswered question. Ephrin-A1 ligand is enriched in the limbal epithelium, whereas EphA2 receptor is concentrated in the corneal epithelium. This reciprocal pattern led us to assess the role of ephrin-A1 and EphA2 in limbal–corneal epithelial boundary organization. Methods EphA2-expressing corneal epithelial cells engineered to express ephrin-A1 were used to study boundary formation in vitro in a manner that mimicked the relative abundance of these juxtamembrane signaling proteins in the limbal and corneal epithelium in vivo. Interaction of these two distinct cell populations following initial seeding into discrete culture compartments was assessed by live cell imaging. Immunofluoresence and immunoblotting was used to evaluate the contribution of downstream growth factor signaling and cell–cell adhesion systems to boundary formation at sites of heterotypic contact between ephrin-A1 and EphA2 expressing cells. Results Ephrin-A1–expressing cells impeded and reversed the migration of EphA2-expressing corneal epithelial cells upon heterotypic contact formation leading to coordinated migration of the two cell populations in the direction of an ephrin-A1–expressing leading front. Genetic silencing and pharmacologic inhibitor studies demonstrated that the ability of ephrin-A1 to direct migration of EphA2-expressing cells depended on an a disintegrin and metalloproteinase domain-containing protein 10 (ADAM10) and epidermal growth factor receptor (EGFR) signaling pathway that limited E-cadherin–mediated adhesion at heterotypic boundaries. Conclusions Ephrin-A1/EphA2 signaling complexes play a key role in limbal–corneal epithelial compartmentalization and the response of these tissues to injury. PMID:29351356

  15. Laser Capture Microdissection Assessment of Virus Compartmentalization in the Central Nervous Systems of Macaques Infected with Neurovirulent Simian Immunodeficiency Virus

    PubMed Central

    Matsuda, Kenta; Brown, Charles R.; Foley, Brian; Goeken, Robert; Whitted, Sonya; Dang, Que; Wu, Fan; Plishka, Ronald; Buckler-White, Alicia

    2013-01-01

    Nonhuman primate-simian immunodeficiency virus (SIV) models are powerful tools for studying the pathogenesis of human immunodeficiency virus type 1 (HIV-1) in the brain. Our laboratory recently isolated a neuropathogenic viral swarm, SIVsmH804E, a derivative of SIVsmE543-3, which was the result of sequential intravenous passages of viruses isolated from the brains of rhesus macaques with SIV encephalitis. Animals infected with SIVsmH804E or its precursor (SIVsmH783Br) developed SIV meningitis and/or encephalitis at high frequencies. Since we observed macaques with a combination of meningitis and encephalitis, as well as animals in which meningitis or encephalitis was the dominant component, we hypothesized that distinct mechanisms could be driving the two pathological states. Therefore, we assessed viral populations in the meninges and the brain parenchyma by laser capture microdissection. Viral RNAs were isolated from representative areas of the meninges, brain parenchyma, terminal plasma, and cerebrospinal fluid (CSF) and from the inoculum, and the SIV envelope fragment was amplified by PCR. Phylogenetic analysis of envelope sequences from the conventional progressors revealed compartmentalization of viral populations between the meninges and the parenchyma. In one of these animals, viral populations in meninges were closely related to those from CSF and shared signature truncations in the cytoplasmic domain of gp41, consistent with a common origin. Apart from magnetic resonance imaging (MRI) and positron-emission tomography (PET) imaging, CSF is the most accessible assess to the central nervous system for HIV-1-infected patients. However, our results suggest that the virus in the CSF may not always be representative of viral populations in the brain and that caution should be applied in extrapolating between the properties of viruses in these two compartments. PMID:23720733

  16. Gait analysis of patients with an off-the-shelf total knee replacement versus customized bi-compartmental knee replacement.

    PubMed

    Wang, Henry; Foster, Jonathan; Franksen, Natasha; Estes, Jill; Rolston, Lindsey

    2018-04-01

    Newer TKR designs have been introduced to the market with the aim of overcoming common sizing problems with older TKR designs. Furthermore, since a sizable percentage of patients with OA present with disease limited to the medial/lateral knee compartment in addition to the patellofemoral joint, for whom, a customized bi-compartmental knee replacement (BKR) is available as a treatment option. To date, there is very little information regarding knee strength and mechanics during gait for patients implanted with these modern TKR and BKR designs. The purpose of the study was to evaluate knee strength and mechanics during walking for patients with either a modern off the shelf TKR or a customized BKR and compare these findings to a cohort of healthy controls. Twelve healthy controls, eight BKR, and nine TKR patients participated in the study. Maximal isometric knee strength was evaluated. 3D kinematic and kinetic analyses were conducted for level walking. The TKR knee exhibited less peak extensor torque when compared to, both the BKR and control limbs (p < 0.05). The TKR knee had less extensor moment at stance than both the BKR and control knees (p < 0.05). Both the BKR and control knees displayed larger internal rotation at stance than that of the TKR knee (p < 0.05). This study suggests that, for patients that exhibit isolated OA of the tibiofemoral joint, using a customized BKR implant is a viable treatment option and may contribute to superior mechanical advantages.

  17. The role of extracellular conductivity profiles in compartmental models for neurons: particulars for layer 5 pyramidal cells.

    PubMed

    Wang, Kai; Riera, Jorge; Enjieu-Kadji, Herve; Kawashima, Ryuta

    2013-07-01

    With the rapid increase in the number of technologies aimed at observing electric activity inside the brain, scientists have felt the urge to create proper links between intracellular- and extracellular-based experimental approaches. Biophysical models at both physical scales have been formalized under assumptions that impede the creation of such links. In this work, we address this issue by proposing a multicompartment model that allows the introduction of complex extracellular and intracellular resistivity profiles. This model accounts for the geometrical and electrotonic properties of any type of neuron through the combination of four devices: the integrator, the propagator, the 3D connector, and the collector. In particular, we applied this framework to model the tufted pyramidal cells of layer 5 (PCL5) in the neocortex. Our model was able to reproduce the decay and delay curves of backpropagating action potentials (APs) in this type of cell with better agreement with experimental data. We used the voltage drops of the extracellular resistances at each compartment to approximate the local field potentials generated by a PCL5 located in close proximity to linear microelectrode arrays. Based on the voltage drops produced by backpropagating APs, we were able to estimate the current multipolar moments generated by a PCL5. By adding external current sources in parallel to the extracellular resistances, we were able to create a sensitivity profile of PCL5 to electric current injections from nearby microelectrodes. In our model for PCL5, the kinetics and spatial profile of each ionic current were determined based on a literature survey, and the geometrical properties of these cells were evaluated experimentally. We concluded that the inclusion of the extracellular space in the compartmental models of neurons as an extra electrotonic medium is crucial for the accurate simulation of both the propagation of the electric potentials along the neuronal dendrites and the

  18. Role of Compartmentalization on HiF-1α Degradation Dynamics during Changing Oxygen Conditions: A Computational Approach

    PubMed Central

    Bedessem, Baptiste; Stéphanou, Angélique

    2014-01-01

    HiF-1α is the central protein driving the cellular response to hypoxia. Its accumulation in cancer cells is linked to the appearance of chemoresistant and aggressive tumor phenotypes. As a consequence, understanding the regulation of HiF-1α dynamics is a major issue to design new anti-cancer therapies. In this paper, we propose a model of the hypoxia pathway, involving HiF-1α and its inhibitor pVHL. Based on data from the literature, we made the hypothesis that the regulation of HiF-1α involves two compartments (nucleus and cytoplasm) and a constitutive shuttle of the pVHL protein between them. We first show that this model captures correctly the main features of HiF-1α dynamics, including the bi-exponential degradation profile in normoxia, the kinetics of induction in hypoxia, and the switch-like accumulation. Second, we simulated the effects of a hypoxia/reoxygenation event, and show that it generates a strong instability of HiF-1α. The protein concentration rapidly increases 3 hours after the reoxygenation, and exhibits an oscillating pattern. This effect vanishes if we do not consider compartmentalization of HiF-1α. This result can explain various counter-intuitive observations about the specific molecular and cellular response to the reoxygenation process. Third, we simulated the HiF-1α dynamics in the tumor case. We considered different types of mutations associated with tumorigenesis, and we compared their consequences on HiF-1α dynamics. Then, we tested different therapeutics strategies. We show that a therapeutic decrease of HiF-1α nuclear level is not always correlated with an attenuation of reoxygenation-induced instabilities. Thus, it appears that the design of anti-HiF-1α therapies have to take into account these two aspects to maximize their efficiency. PMID:25338163

  19. Distinct physiological effects of β1- and β2-adrenoceptors in mouse ventricular myocytes: insights from a compartmentalized mathematical model.

    PubMed

    Rozier, Kelvin; Bondarenko, Vladimir E

    2017-05-01

    The β 1 - and β 2 -adrenergic signaling systems play different roles in the functioning of cardiac cells. Experimental data show that the activation of the β 1 -adrenergic signaling system produces significant inotropic, lusitropic, and chronotropic effects in the heart, whereas the effects of the β 2 -adrenergic signaling system is less apparent. In this paper, a comprehensive compartmentalized experimentally based mathematical model of the combined β 1 - and β 2 -adrenergic signaling systems in mouse ventricular myocytes is developed to simulate the experimental findings and make testable predictions of the behavior of the cardiac cells under different physiological conditions. Simulations describe the dynamics of major signaling molecules in different subcellular compartments; kinetics and magnitudes of phosphorylation of ion channels, transporters, and Ca 2+ handling proteins; modifications of action potential shape and duration; and [Ca 2+ ] i and [Na + ] i dynamics upon stimulation of β 1 - and β 2 -adrenergic receptors (β 1 - and β 2 -ARs). The model reveals physiological conditions when β 2 -ARs do not produce significant physiological effects and when their effects can be measured experimentally. Simulations demonstrated that stimulation of β 2 -ARs with isoproterenol caused a marked increase in the magnitude of the L-type Ca 2+ current, [Ca 2+ ] i transient, and phosphorylation of phospholamban only upon additional application of pertussis toxin or inhibition of phosphodiesterases of type 3 and 4. The model also made testable predictions of the changes in magnitudes of [Ca 2+ ] i and [Na + ] i fluxes, the rate of decay of [Na + ] i concentration upon both combined and separate stimulation of β 1 - and β 2 -ARs, and the contribution of phosphorylation of PKA targets to the changes in the action potential and [Ca 2+ ] i transient. Copyright © 2017 the American Physiological Society.

  20. Correlation of near-infrared spectroscopy and direct pressure monitoring in an acute porcine compartmental syndrome model.

    PubMed

    Cathcart, Curtis C; Shuler, Michael S; Freedman, Brett A; Reno, Lisa R; Budsberg, Steven C

    2014-06-01

    To correlate near-infrared spectroscopy (NIRS) and the tibial intracompartmental perfusion pressure (TIPP) in an acute limb compartmental syndrome. Landrace swine were subdivided into 2 groups: plasma infusion (n = 16) and blunt trauma plus plasma infusion (n = 15). NIRS sensors were placed over the craniolateral muscle compartment of proximal both tibiae. Albumin infusion elevated tibial intracompartmental pressures (TICP). Time-synchronized measures of systolic, diastolic, and mean arterial pressures, TICP, and percent oxygenation from each leg were collected. For the blunt trauma group, trauma was induced by dropping a 2-kg weight 30 times from 100 cm directly on the muscle compartment. For each group, a repeated-measures analysis of variance model was used to test differences in the TICP, TIPP, and oxygenation values. Pearson correlations were calculated between TICP and oxygenation and between TIPP and oxygenation. Both models created reproducible increases in TICP and decreases in TIPP. Trauma did not alter TICP, TIPP, or percent oxygenation in the model. NIRS was able to detect significant changes in tissue oxygenation at all the same time points. NIRS was able to detect decreased oxygenation at every TIPP decrease and subsequent increase after fasciotomies. An increase in percent oxygenation was seen in all cases once fasciotomy was performed and TICP was reduced. NIRS provided a sensitive measure correlating to both an increase and decrease in TICP and TIPP, respectively, in this infusion model. The addition of blunt trauma to the model did not alter the correlations of NIRS values with TICP and TIPP. Fasciotomy produced a rebound in oxygenation values.

  1. Human biokinetic data and a new compartmental model of zirconium--a tracer study with enriched stable isotopes.

    PubMed

    Greiter, Matthias B; Giussani, Augusto; Höllriegl, Vera; Li, Wei Bo; Oeh, Uwe

    2011-09-01

    Biokinetic models describing the uptake, distribution and excretion of trace elements are an essential tool in nutrition, toxicology, or internal dosimetry of radionuclides. Zirconium, especially its radioisotope (95)Zr, is relevant to radiation protection due to its production in uranium fission and neutron activation of nuclear fuel cladding material. We present a comprehensive set of human data from a tracer study with stable isotopes of zirconium. The data are used to refine a biokinetic model of zirconium. Six female and seven male healthy adult volunteers participated in the study. It includes 16 complete double tracer investigations with oral ingestion and intravenous injection, and seven supplemental investigations. Tracer concentrations were measured in blood plasma and urine collected up to 100 d after tracer administration. The four data sets (two chemical tracer forms in plasma and urine) each encompass 105-240 measured concentration values above detection limits. Total fractional absorption of ingested zirconium was found to be 0.001 for zirconium in citrate-buffered drinking solution and 0.007 for zirconium oxalate solution. Biokinetic models were developed based on the linear first-order kinetic compartmental model approach used by the International Commission on Radiological Protection (ICRP). The main differences of the optimized systemic model of zirconium to the current ICRP model are (1) recycling into the transfer compartment made necessary by the observed tracer clearance from plasma, (2) different parameters related to fractional absorption for each form of the ingested tracer, and (3) a physiologically based excretion pathway to urine. The study considerably expands the knowledge on the biokinetics of zirconium, which was until now dominated by data from animal studies. The proposed systemic model improves the existing ICRP model, yet is based on the same principles and fits well into the ICRP radiation protection approach. Copyright © 2011

  2. Comparison of linear and nonlinear implementation of the compartmental tissue uptake model for dynamic contrast-enhanced MRI.

    PubMed

    Kallehauge, Jesper F; Sourbron, Steven; Irving, Benjamin; Tanderup, Kari; Schnabel, Julia A; Chappell, Michael A

    2017-06-01

    Fitting tracer kinetic models using linear methods is much faster than using their nonlinear counterparts, although this comes often at the expense of reduced accuracy and precision. The aim of this study was to derive and compare the performance of the linear compartmental tissue uptake (CTU) model with its nonlinear version with respect to their percentage error and precision. The linear and nonlinear CTU models were initially compared using simulations with varying noise and temporal sampling. Subsequently, the clinical applicability of the linear model was demonstrated on 14 patients with locally advanced cervical cancer examined with dynamic contrast-enhanced magnetic resonance imaging. Simulations revealed equal percentage error and precision when noise was within clinical achievable ranges (contrast-to-noise ratio >10). The linear method was significantly faster than the nonlinear method, with a minimum speedup of around 230 across all tested sampling rates. Clinical analysis revealed that parameters estimated using the linear and nonlinear CTU model were highly correlated (ρ ≥ 0.95). The linear CTU model is computationally more efficient and more stable against temporal downsampling, whereas the nonlinear method is more robust to variations in noise. The two methods may be used interchangeably within clinical achievable ranges of temporal sampling and noise. Magn Reson Med 77:2414-2423, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

  3. The V-ATPase subunit A is essential for salt tolerance through participating in vacuolar Na+ compartmentalization in Salicornia europaea.

    PubMed

    Lv, Sulian; Jiang, Ping; Tai, Fang; Wang, Duoliya; Feng, Juanjuan; Fan, Pengxiang; Bao, Hexigeduleng; Li, Yinxin

    2017-12-01

    The V-ATPase subunit A participates in vacuolar Na + compartmentalization in Salicornia europaea regulating V-ATPase and V-PPase activities. Na + sequestration into the vacuole is an efficient strategy in response to salinity in many halophytes. However, it is not yet fully understood how this process is achieved. Particularly, the role of vacuolar H + -ATPase (V-ATPase) in this process is controversial. Our previous proteomic investigation in the euhalophyte Salicornia europaea L. found a significant increase of the abundance of V-ATPase subunit A under salinity. Here, the gene encoding this subunit named SeVHA-A was characterized, and its role in salt tolerance was demonstrated by RNAi directed downregulation in suspension-cultured cells of S. europaea. The transcripts of genes encoding vacuolar H + -PPase (V-PPase) and vacuolar Na + /H + antiporter (SeNHX1) also decreased significantly in the RNAi cells. Knockdown of SeVHA-A resulted in a reduction in both V-ATPase and vacuolar H + -PPase (V-PPase) activities. Accordingly, the SeVHA-A-RNAi cells showed increased vacuolar pH and decreased cell viability under different NaCl concentrations. Further Na + staining showed the reduced vacuolar Na + sequestration in RNAi cells. Taken together, our results evidenced that SeVHA-A participates in vacuolar Na + sequestration regulating V-ATPase and V-PPase activities and thereby vacuolar pH in S. europaea. The possible mechanisms underlying the reduction of vacuolar V-PPase activity in SeVHA-A-RNAi cells were also discussed.

  4. BASS II

    2014-02-14

    ISS038-E-047576 (14 Feb. 2014) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, works with the Burning and Suppression of Solids (BASS-II) experiment in the Microgravity Science Glovebox (MSG) located in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  5. BASS II

    2014-02-14

    ISS038-E-047582 (14 Feb. 2014) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, works with the Burning and Suppression of Solids (BASS-II) experiment in the Microgravity Science Glovebox (MSG) located in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  6. Subcellular compartmentalization of Cd and Zn in two bivalves. I. Significance of metal-sensitive fractions (MSF) and biologically detoxified metal (BDM)

    Wallace, W.G.; Lee, B.-G.; Luoma, S.N.

    2003-01-01

    Many aspects of metal accumulation in aquatic invertebrates (i.e. toxicity, tolerance and trophic transfer) can be understood by examining the subcellular partitioning of accumulated metal. In this paper, we use a compartmentalization approach to interpret the significance of metal, species and size dependence in the subcellular partitioning of Cd and Zn in the bivalves Macoma balthica and Potamocorbula amurensis. Of special interest is the compartmentalization of metal as metal-sensitive fractions (MSF) (i.e. organelles and heat-sensitive proteins, termed 'enzymes' hereafter) and biologically detoxified metal (BDM) (i.e. metallothioneins [MT] and metal-rich granules [MRG]). Clams from San Francisco Bay, CA, were exposed for 14 d to seawater (20??? salinity) containing 3.5 ??g l-1 Cd and 20.5 ??g l-1 Zn, including 109Cd and 65Zn as radiotracers. Uptake was followed by 21 d of depuration. The subcellular partitioning of metal within clams was examined following exposure and loss. P. amurensis accumulated ???22x more Cd and ???2x more Zn than M. balthica. MT played an important role in the storage of Cd in P. amurensis, while organelles were the major site of Zn accumulation. In M. balthica, Cd and Zn partitioned similarly, although the pathway of detoxification was metal-specific (MRG for Cd; MRG and MT for Zn). Upon loss, M. balthica depurated ???40% of Cd with Zn being retained; P. amurensis retained Cd and depurated Zn (???40%). During efflux, Cd and Zn concentrations in the MSF compartment of both clams declined with metal either being lost from the animal or being transferred to the BDM compartment. Subcellular compartmentalization was also size-dependent, with the importance of BDM increasing with clam size; MSF decreased accordingly. We hypothesized that progressive retention of metal as BDM (i.e. MRG) with age may lead to size dependency of metal concentrations often observed in some populations of M. balthica.

  7. Compartmentalizing the embryo

    PubMed Central

    Ile, Kristina E.; Renault, Andrew D.

    2013-01-01

    Lipid phosphate phosphatases (LPPs) are a class of enzymes that can dephosphorylate a number of lysophopholipids in vitro. Analysis of knockouts of LPP family members has demonstrated striking but diverse developmental roles for these enzymes. LPP3 is required for mouse vascular development while the Drosophila LPPs Wunen (Wun) and Wunen2 (Wun2) are required during embryogenesis for germ cell migration and survival. In a recent publication we examined if these fly LPPs have further developmental roles and found that Wun is required for proper tracheal formation. In particular we highlight a role for Wun in septate junction mediated barrier function in the tracheal system. In this paper we discuss further the possible mechanisms by which LPPs may influence barrier activity. PMID:23221483

  8. Golgi Compartmentation and Identity

    PubMed Central

    Papanikou, Effrosyni; Glick, Benjamin S.

    2014-01-01

    Recent work supports the idea that cisternae of the Golgi apparatus can be assigned to three classes, which correspond to discrete stages of cisternal maturation. Each stage has a unique pattern of membrane traffic. At the first stage, cisternae form in association with the ER at multifunctional membrane assembly stations. At the second stage, cisternae synthesize carbohydrates while exchanging material via COPI vesicles. At the third stage, cisternae of the trans-Golgi network segregate into domains and produce transport carriers with the aid of specific lipids and the actin cytoskeleton. These processes are coordinated by cascades of Rab and Arf/Arl GTPases. PMID:24840895

  9. Double-input compartmental modeling and spectral analysis for the quantification of positron emission tomography data in oncology

    NASA Astrophysics Data System (ADS)

    Tomasi, G.; Kimberley, S.; Rosso, L.; Aboagye, E.; Turkheimer, F.

    2012-04-01

    In positron emission tomography (PET) studies involving organs different from the brain, ignoring the metabolite contribution to the tissue time-activity curves (TAC), as in the standard single-input (SI) models, may compromise the accuracy of the estimated parameters. We employed here double-input (DI) compartmental modeling (CM), previously used for [11C]thymidine, and a novel DI spectral analysis (SA) approach on the tracers 5-[18F]fluorouracil (5-[18F]FU) and [18F]fluorothymidine ([18F]FLT). CM and SA were performed initially with a SI approach using the parent plasma TAC as an input function. These methods were then employed using a DI approach with the metabolite plasma TAC as an additional input function. Regions of interest (ROIs) corresponding to healthy liver, kidneys and liver metastases for 5-[18F]FU and to tumor, vertebra and liver for [18F]FLT were analyzed. For 5-[18F]FU, the improvement of the fit quality with the DI approaches was remarkable; in CM, the Akaike information criterion (AIC) always selected the DI over the SI model. Volume of distribution estimates obtained with DI CM and DI SA were in excellent agreement, for both parent 5-[18F]FU (R2 = 0.91) and metabolite [18F]FBAL (R2 = 0.99). For [18F]FLT, the DI methods provided notable improvements but less substantial than for 5-[18F]FU due to the lower rate of metabolism of [18F]FLT. On the basis of the AIC values, agreement between [18F]FLT Ki estimated with the SI and DI models was good (R2 = 0.75) for the ROIs where the metabolite contribution was negligible, indicating that the additional input did not bias the parent tracer only-related estimates. When the AIC suggested a substantial contribution of the metabolite [18F]FLT-glucuronide, on the other hand, the change in the parent tracer only-related parameters was significant (R2 = 0.33 for Ki). Our results indicated that improvements of DI over SI approaches can range from moderate to substantial and are more significant for tracers with

  10. Double-input compartmental modeling and spectral analysis for the quantification of positron emission tomography data in oncology.

    PubMed

    Tomasi, G; Kimberley, S; Rosso, L; Aboagye, E; Turkheimer, F

    2012-04-07

    In positron emission tomography (PET) studies involving organs different from the brain, ignoring the metabolite contribution to the tissue time-activity curves (TAC), as in the standard single-input (SI) models, may compromise the accuracy of the estimated parameters. We employed here double-input (DI) compartmental modeling (CM), previously used for [¹¹C]thymidine, and a novel DI spectral analysis (SA) approach on the tracers 5-[¹⁸F]fluorouracil (5-[¹⁸F]FU) and [¹⁸F]fluorothymidine ([¹⁸F]FLT). CM and SA were performed initially with a SI approach using the parent plasma TAC as an input function. These methods were then employed using a DI approach with the metabolite plasma TAC as an additional input function. Regions of interest (ROIs) corresponding to healthy liver, kidneys and liver metastases for 5-[¹⁸F]FU and to tumor, vertebra and liver for [¹⁸F]FLT were analyzed. For 5-[¹⁸F]FU, the improvement of the fit quality with the DI approaches was remarkable; in CM, the Akaike information criterion (AIC) always selected the DI over the SI model. Volume of distribution estimates obtained with DI CM and DI SA were in excellent agreement, for both parent 5-[¹⁸F]FU (R(2) = 0.91) and metabolite [¹⁸F]FBAL (R(2) = 0.99). For [¹⁸F]FLT, the DI methods provided notable improvements but less substantial than for 5-[¹⁸F]FU due to the lower rate of metabolism of [¹⁸F]FLT. On the basis of the AIC values, agreement between [¹⁸F]FLT K(i) estimated with the SI and DI models was good (R² = 0.75) for the ROIs where the metabolite contribution was negligible, indicating that the additional input did not bias the parent tracer only-related estimates. When the AIC suggested a substantial contribution of the metabolite [¹⁸F]FLT-glucuronide, on the other hand, the change in the parent tracer only-related parameters was significant (R² = 0.33 for K(i)). Our results indicated that improvements of DI over SI approaches can range from moderate to

  11. HIV-1 tropism testing in subjects achieving undetectable HIV-1 RNA: diagnostic accuracy, viral evolution and compartmentalization.

    PubMed

    Pou, Christian; Codoñer, Francisco M; Thielen, Alexander; Bellido, Rocío; Pérez-Álvarez, Susana; Cabrera, Cecilia; Dalmau, Judith; Curriu, Marta; Lie, Yolanda; Noguera-Julian, Marc; Puig, Jordi; Martínez-Picado, Javier; Blanco, Julià; Coakley, Eoin; Däumer, Martin; Clotet, Bonaventura; Paredes, Roger

    2013-01-01

    Technically, HIV-1 tropism can be evaluated in plasma or peripheral blood mononuclear cells (PBMCs). However, only tropism testing of plasma HIV-1 has been validated as a tool to predict virological response to CCR5 antagonists in clinical trials. The preferable tropism testing strategy in subjects with undetectable HIV-1 viremia, in whom plasma tropism testing is not feasible, remains uncertain. We designed a proof-of-concept study including 30 chronically HIV-1-infected individuals who achieved HIV-1 RNA <50 copies/mL during at least 2 years after first-line ART initiation. First, we determined the diagnostic accuracy of 454 and population sequencing of gp120 V3-loops in plasma and PBMCs, as well as of MT-2 assays before ART initiation. The Enhanced Sensitivity Trofile Assay (ESTA) was used as the technical reference standard. 454 sequencing of plasma viruses provided the highest agreement with ESTA. The accuracy of 454 sequencing decreased in PBMCs due to reduced specificity. Population sequencing in plasma and PBMCs was slightly less accurate than plasma 454 sequencing, being less sensitive but more specific. MT-2 assays had low sensitivity but 100% specificity. Then, we used optimized 454 sequence data to investigate viral evolution in PBMCs during viremia suppression and only found evolution of R5 viruses in one subject. No de novo CXCR4-using HIV-1 production was observed over time. Finally, Slatkin-Maddison tests suggested that plasma and cell-associated V3 forms were sometimes compartmentalized. The absence of tropism shifts during viremia suppression suggests that, when available, testing of stored plasma samples is generally safe and informative, provided that HIV-1 suppression is maintained. Tropism testing in PBMCs may not necessarily produce equivalent biological results to plasma, because the structure of viral populations and the diagnostic performance of tropism assays may sometimes vary between compartments. Thereby, proviral DNA tropism testing

  12. Analytical solutions to compartmental indoor air quality models with application to environmental tobacco smoke concentrations measured in a house.

    PubMed

    Ott, Wayne R; Klepeis, Neil E; Switzer, Paul

    2003-08-01

    This paper derives the analytical solutions to multi-compartment indoor air quality models for predicting indoor air pollutant concentrations in the home and evaluates the solutions using experimental measurements in the rooms of a single-story residence. The model uses Laplace transform methods to solve the mass balance equations for two interconnected compartments, obtaining analytical solutions that can be applied without a computer. Environmental tobacco smoke (ETS) sources such as the cigarette typically emit pollutants for relatively short times (7-11 min) and are represented mathematically by a "rectangular" source emission time function, or approximated by a short-duration source called an "impulse" time function. Other time-varying indoor sources also can be represented by Laplace transforms. The two-compartment model is more complicated than the single-compartment model and has more parameters, including the cigarette or combustion source emission rate as a function of time, room volumes, compartmental air change rates, and interzonal air flow factors expressed as dimensionless ratios. This paper provides analytical solutions for the impulse, step (Heaviside), and rectangular source emission time functions. It evaluates the indoor model in an unoccupied two-bedroom home using cigars and cigarettes as sources with continuous measurements of carbon monoxide (CO), respirable suspended particles (RSP), and particulate polycyclic aromatic hydrocarbons (PPAH). Fine particle mass concentrations (RSP or PM3.5) are measured using real-time monitors. In our experiments, simultaneous measurements of concentrations at three heights in a bedroom confirm an important assumption of the model-spatial uniformity of mixing. The parameter values of the two-compartment model were obtained using a "grid search" optimization method, and the predicted solutions agreed well with the measured concentration time series in the rooms of the home. The door and window positions in

  13. Compartmentalized cAMP Signaling Associated With Lipid Raft and Non-raft Membrane Domains in Adult Ventricular Myocytes.

    PubMed

    Agarwal, Shailesh R; Gratwohl, Jackson; Cozad, Mia; Yang, Pei-Chi; Clancy, Colleen E; Harvey, Robert D

    2018-01-01

    Aim: Confining cAMP production to discrete subcellular locations makes it possible for this ubiquitous second messenger to elicit unique functional responses. Yet, factors that determine how and where the production of this diffusible signaling molecule occurs are incompletely understood. The fluid mosaic model originally proposed that signal transduction occurs through random interactions between proteins diffusing freely throughout the plasma membrane. However, it is now known that the movement of membrane proteins is restricted, suggesting that the plasma membrane is segregated into distinct microdomains where different signaling proteins can be concentrated. In this study, we examined what role lipid raft and non-raft membrane domains play in compartmentation of cAMP signaling in adult ventricular myocytes. Methods and Results: The freely diffusible fluorescence resonance energy transfer-based biosensor Epac2-camps was used to measure global cytosolic cAMP responses, while versions of the probe targeted to lipid raft (Epac2-MyrPalm) and non-raft (Epac2-CAAX) domains were used to monitor local cAMP production near the plasma membrane. We found that β-adrenergic receptors, which are expressed in lipid raft and non-raft domains, produce cAMP responses near the plasma membrane that are distinctly different from those produced by E-type prostaglandin receptors, which are expressed exclusively in non-raft domains. We also found that there are differences in basal cAMP levels associated with lipid raft and non-raft domains, and that this can be explained by differences in basal adenylyl cyclase activity associated with each of these membrane environments. In addition, we found evidence that phosphodiesterases 2, 3, and 4 work together in regulating cAMP activity associated with both lipid raft and non-raft domains, while phosphodiesterase 3 plays a more prominent role in the bulk cytoplasmic compartment. Conclusion: These results suggest that different membrane

  14. Photosystem II

    James Barber

    2017-12-09

    James Barber, Ernst Chain Professor of Biochemistry at Imperial College, London, gives a BSA Distinguished Lecture titled, "The Structure and Function of Photosystem II: The Water-Splitting Enzyme of Photosynthesis."

  15. The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features

    PubMed Central

    Kamke, Janine; Rinke, Christian; Schwientek, Patrick; Mavromatis, Kostas; Ivanova, Natalia; Sczyrba, Alexander; Woyke, Tanja; Hentschel, Ute

    2014-01-01

    The candidate phylum Poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that Poribacteria form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake. PMID:24498082

  16. Co-infected C57BL/6 mice mount appropriately polarized and compartmentalized cytokine responses to Litomosoides sigmodontis and Leishmania major but disease progression is altered.

    PubMed

    Lamb, T J; Graham, A L; Le Goff, L; Allen, J E

    2005-09-01

    This study examines the capacity of the mammalian host to fully compartmentalize the response to infection with type 1 vs. type 2 inducing organisms that infect different sites in the body. For this purpose, C57BL/6 mice were infected with the rodent filarial nematode Litomosoides sigmodontis followed by footpad infection with the protozoan parasite Leishmania major. In this host, nematode infection is established in the thoracic cavity but no microfilariae circulate in the bloodstream. We utilized quantitative ELISPOT analysis of IL-4 and IFN-gamma producing cells to assess cytokine bias and response magnitude in the lymph nodes draining the sites of infection as well as more systemic responses in the spleen and serum. Contrary to other systems where co-infection has a major impact on bias, cytokine ratios were unaltered in either local lymph node. The most notable effect of co-infection was an unexpected increase in the magnitude of the IFN-gamma response to L. major in mice previously infected with L. sigmodontis. Further, lesion development was significantly delayed in these mice. Thus, despite the ability of the immune system to appropriately compartmentalize the immune response, interactions between responses at distinct infection sites can alter disease progression.

  17. Mechanisms of salt tolerance in habanero pepper plants (Capsicum chinense Jacq.): Proline accumulation, ions dynamics and sodium root-shoot partition and compartmentation

    PubMed Central

    Bojórquez-Quintal, Emanuel; Velarde-Buendía, Ana; Ku-González, Ángela; Carillo-Pech, Mildred; Ortega-Camacho, Daniela; Echevarría-Machado, Ileana; Pottosin, Igor; Martínez-Estévez, Manuel

    2014-01-01

    Despite its economic relevance, little is known about salt tolerance mechanisms in pepper plants. To address this question, we compared differences in responses to NaCl in two Capsicum chinense varieties: Rex (tolerant) and Chichen-Itza (sensitive). Under salt stress (150 mM NaCl over 7 days) roots of Rex variety accumulated 50 times more compatible solutes such as proline compared to Chichen-Itza. Mineral analysis indicated that Na+ is restricted to roots by preventing its transport to leaves. Fluorescence analysis suggested an efficient Na+ compartmentalization in vacuole-like structures and in small intracellular compartments in roots of Rex variety. At the same time, Na+ in Chichen-Itza plants was compartmentalized in the apoplast, suggesting substantial Na+ extrusion. Rex variety was found to retain more K+ in its roots under salt stress according to a mineral analysis and microelectrode ion flux estimation (MIFE). Vanadate-sensitive H+ efflux was higher in Chichen-Itza variety plants, suggesting a higher activity of the plasma membrane H+-ATPase, which fuels the extrusion of Na+, and, possibly, also the re-uptake of K+. Our results suggest a combination of stress tolerance mechanisms, in order to alleviate the salt-induced injury. Furthermore, Na+ extrusion to apoplast does not appear to be an efficient strategy for salt tolerance in pepper plants. PMID:25429292

  18. Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model1[C][W][OPEN

    PubMed Central

    Simons, Margaret; Saha, Rajib; Amiour, Nardjis; Kumar, Akhil; Guillard, Lenaïg; Clément, Gilles; Miquel, Martine; Li, Zhenni; Mouille, Gregory; Lea, Peter J.; Hirel, Bertrand; Maranas, Costas D.

    2014-01-01

    Maize (Zea mays) is an important C4 plant due to its widespread use as a cereal and energy crop. A second-generation genome-scale metabolic model for the maize leaf was created to capture C4 carbon fixation and investigate nitrogen (N) assimilation by modeling the interactions between the bundle sheath and mesophyll cells. The model contains gene-protein-reaction relationships, elemental and charge-balanced reactions, and incorporates experimental evidence pertaining to the biomass composition, compartmentalization, and flux constraints. Condition-specific biomass descriptions were introduced that account for amino acids, fatty acids, soluble sugars, proteins, chlorophyll, lignocellulose, and nucleic acids as experimentally measured biomass constituents. Compartmentalization of the model is based on proteomic/transcriptomic data and literature evidence. With the incorporation of information from the MetaCrop and MaizeCyc databases, this updated model spans 5,824 genes, 8,525 reactions, and 9,153 metabolites, an increase of approximately 4 times the size of the earlier iRS1563 model. Transcriptomic and proteomic data have also been used to introduce regulatory constraints in the model to simulate an N-limited condition and mutants deficient in glutamine synthetase, gln1-3 and gln1-4. Model-predicted results achieved 90% accuracy when comparing the wild type grown under an N-complete condition with the wild type grown under an N-deficient condition. PMID:25248718

  19. Mechanisms of salt tolerance in habanero pepper plants (Capsicum chinense Jacq.): Proline accumulation, ions dynamics and sodium root-shoot partition and compartmentation.

    PubMed

    Bojórquez-Quintal, Emanuel; Velarde-Buendía, Ana; Ku-González, Angela; Carillo-Pech, Mildred; Ortega-Camacho, Daniela; Echevarría-Machado, Ileana; Pottosin, Igor; Martínez-Estévez, Manuel

    2014-01-01

    Despite its economic relevance, little is known about salt tolerance mechanisms in pepper plants. To address this question, we compared differences in responses to NaCl in two Capsicum chinense varieties: Rex (tolerant) and Chichen-Itza (sensitive). Under salt stress (150 mM NaCl over 7 days) roots of Rex variety accumulated 50 times more compatible solutes such as proline compared to Chichen-Itza. Mineral analysis indicated that Na(+) is restricted to roots by preventing its transport to leaves. Fluorescence analysis suggested an efficient Na(+) compartmentalization in vacuole-like structures and in small intracellular compartments in roots of Rex variety. At the same time, Na(+) in Chichen-Itza plants was compartmentalized in the apoplast, suggesting substantial Na(+) extrusion. Rex variety was found to retain more K(+) in its roots under salt stress according to a mineral analysis and microelectrode ion flux estimation (MIFE). Vanadate-sensitive H(+) efflux was higher in Chichen-Itza variety plants, suggesting a higher activity of the plasma membrane H(+)-ATPase, which fuels the extrusion of Na(+), and, possibly, also the re-uptake of K(+). Our results suggest a combination of stress tolerance mechanisms, in order to alleviate the salt-induced injury. Furthermore, Na(+) extrusion to apoplast does not appear to be an efficient strategy for salt tolerance in pepper plants.

  20. Inhibition of Glutathione Biosynthesis Alters Compartmental Redox Status and the Thiol Proteome in Organogenesis-Stage Rat Conceptuses

    PubMed Central

    Harris, Craig; Shuster, Daniel Z.; Gomez, Rosaicela Roman; Sant, Karilyn E.; Reed, Matthew S.; Pohl, Jan; Hansen, Jason M.

    2013-01-01

    significant net oxidation was seen in the BSO-treated AF compartment after 6 hr. Biotinylated iodoacetamide (BIAM) labeling of proteins revealed the significant thiol-oxidation of many EMB proteins following BSO treatment. Quantitative changes in the thiol proteome, associated with developmentally-relevant pathways, were detected using isotope coded affinity tag (ICAT) labeling and mass spectroscopy. Adaptive pathways were selectively enriched with increased concentrations of proteins involved in mRNA processing (splicesome) and mRNA stabilization (glycolysis, GAPDH), as well as, protein synthesis (aminoacyl-tRNA) and protein folding (antigen processing, Hsp70, protein disulfide isomerase). These results show the ability of chemical and environmental modulators to selectively alter compartmental intracellular and extracellular GSH and Cys concentrations and change their corresponding Eh within the intact viable conceptus. The altered Eh were also of sufficient magnitude to alter the redox proteome and change relative protein concentrations suggesting that the mechanistic links through which environmental factors inform and regulate developmental signaling pathways may be discovered using systems developmental biology techniques. PMID:23736079

  1. Inhibition of glutathione biosynthesis alters compartmental redox status and the thiol proteome in organogenesis-stage rat conceptuses.

    PubMed

    Harris, Craig; Shuster, Daniel Z; Roman Gomez, Rosaicela; Sant, Karilyn E; Reed, Matthew S; Pohl, Jan; Hansen, Jason M

    2013-10-01

    oxidation was seen in the BSO-treated AF compartment after 6 h. Biotinylated iodoacetamide (BIAM) labeling of proteins revealed the significant thiol oxidation of many EMB proteins following BSO treatment. Quantitative changes in the thiol proteome, associated with developmentally relevant pathways, were detected using isotope coded affinity tag (ICAT) labeling and mass spectroscopy. Adaptive pathways were selectively enriched with increased concentrations of proteins involved in mRNA processing (splicesome) and mRNA stabilization (glycolysis, GAPDH), as well as protein synthesis (aminoacyl-tRNA) and protein folding (antigen processing, Hsp70, protein disulfide isomerase). These results show the ability of chemical and environmental modulators to selectively alter compartmental intracellular and extracellular GSH and Cys concentrations and change their corresponding E(h) within the intact viable conceptus. The altered E(h) were also of sufficient magnitude to alter the redox proteome and change relative protein concentrations, suggesting that the mechanistic links through which environmental factors inform and regulate developmental signaling pathways may be discovered using systems developmental biology techniques. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. FAQs II

    ERIC Educational Resources Information Center

    Kezar, Adrianna; Frank, Vikki; Lester, Jaime; Yang, Hannah

    2008-01-01

    In their paper entitled "Why should postsecondary institutions consider partnering to offer (Individual Development Accounts (IDAs)?" the authors reviewed frequently asked questions they encountered from higher education professionals about IDAs, but as their research continued so did the questions. FAQ II has more in-depth questions and…

  3. Quantitative analysis of [99mTc]C2A-GST distribution in the area at risk after myocardial ischemia and reperfusion using a compartmental model.

    PubMed

    Audi, Said; Poellmann, Michael; Zhu, Xiaoguang; Li, Zhixin; Zhao, Ming

    2007-11-01

    It was recently demonstrated that the radiolabeled C2A domain of synaptotagmin I accumulates avidly in the area at risk after ischemia and reperfusion. The objective was to quantitatively characterize the dynamic uptake of radiolabeled C2A in normal and ischemically injured myocardia using a compartmental model. To induce acute myocardial infarction, the left descending coronary artery was ligated for 18 min, followed by reperfusion. [99mTc]C2A-GST or its inactivated form, [99mTc]C2A-GST-NHS, was injected intravenously at 2 h after reperfusion. A group of four rats was sacrificed at 10, 30, 60 and 180 after injection. Uptake of [99mTc]C2A-GST and [99mTc]C2A-GST-NHS in the area at risk and in the normal myocardium were determined by gamma counting. A compartmental model was developed to quantitatively interpret myocardial uptake kinetic data. The model consists of two physical spaces (vascular space and tissue space), with plasma activity as input. The model allows for [99mTc]C2A-GST and [99mTc]C2A-GST-NHS diffusion between vascular and tissue spaces, as well as for [99mTc]C2A-GST sequestration in vascular and tissue spaces via specific binding. [99mTc]C2A-GST uptake in the area at risk was significantly higher than that for [99mTc]C2A-GST-NHS at all time points. The compartmental model separated [99mTc]C2A-GST uptake in the area at risk due to passive retention from that due to specific binding. The maximum amount of [99mTc]C2A-GST that could be sequestered in the area at risk due to specific binding was estimated at a total of 0.048 nmol/g tissue. The rate of [99mTc]C2A-GST sequestration within the tissue space of the area at risk was 0.012 ml/min. Modeling results also revealed that the diffusion rate of radiotracer between vascular and tissue spaces is the limiting factor of [99mTc]C2A-GST sequestration within the tissue space of the area at risk. [99mTc]C2A-GST is sequestered in the ischemically injured myocardium in a well-defined dynamic profile. Model

  4. PORT II

    NASA Technical Reports Server (NTRS)

    Muniz, Beau

    2009-01-01

    One unique project that the Prototype lab worked on was PORT I (Post-landing Orion Recovery Test). PORT is designed to test and develop the system and components needed to recover the Orion capsule once it splashes down in the ocean. PORT II is designated as a follow up to PORT I that will utilize a mock up pressure vessel that is spatially compar able to the final Orion capsule.

  5. BORE II

    SciT

    Bore II, co-developed by Berkeley Lab researchers Frank Hale, Chin-Fu Tsang, and Christine Doughty, provides vital information for solving water quality and supply problems and for improving remediation of contaminated sites. Termed "hydrophysical logging," this technology is based on the concept of measuring repeated depth profiles of fluid electric conductivity in a borehole that is pumping. As fluid enters the wellbore, its distinct electric conductivity causes peaks in the conductivity log that grow and migrate upward with time. Analysis of the evolution of the peaks enables characterization of groundwater flow distribution more quickly, more cost effectively, and with higher resolutionmore » than ever before. Combining the unique interpretation software Bore II with advanced downhole instrumentation (the hydrophysical logging tool), the method quantifies inflow and outflow locations, their associated flow rates, and the basic water quality parameters of the associated formation waters (e.g., pH, oxidation-reduction potential, temperature). In addition, when applied in conjunction with downhole fluid sampling, Bore II makes possible a complete assessment of contaminant concentration within groundwater.« less

  6. Development of In Vitro-In Vivo Correlation/Relationship Modeling Approaches for Immediate Release Formulations Using Compartmental Dynamic Dissolution Data from “Golem”: A Novel Apparatus

    PubMed Central

    Tuszyński, Paweł K.; Polak, Sebastian; Jachowicz, Renata; Mendyk, Aleksander; Dohnal, Jiří

    2015-01-01

    Different batches of atorvastatin, represented by two immediate release formulation designs, were studied using a novel dynamic dissolution apparatus, simulating stomach and small intestine. A universal dissolution method was employed which simulated the physiology of human gastrointestinal tract, including the precise chyme transit behavior and biorelevant conditions. The multicompartmental dissolution data allowed direct observation and qualitative discrimination of the differences resulting from highly pH dependent dissolution behavior of the tested batches. Further evaluation of results was performed using IVIVC/IVIVR development. While satisfactory correlation could not be achieved using a conventional deconvolution based-model, promising results were obtained through the use of a nonconventional approach exploiting the complex compartmental dissolution data. PMID:26120580

  7. Development and Evaluation of a Compartmental Picture Archiving and Communications System Model for Integration and Visualization of Multidisciplinary Biomedical Data to Facilitate Student Learning in an Integrative Health Clinic

    ERIC Educational Resources Information Center

    Chow, Meyrick; Chan, Lawrence

    2010-01-01

    Information technology (IT) has the potential to improve the clinical learning environment. The extent to which IT enhances or detracts from healthcare professionals' role performance can be expected to affect both student learning and patient outcomes. This study evaluated nursing students' satisfaction with a novel compartmental Picture…

  8. IP-10 and MIG are compartmentalized at the site of disease during pleural and meningeal tuberculosis and are decreased after antituberculosis treatment.

    PubMed

    Yang, Qianting; Cai, Yi; Zhao, Wei; Wu, Fan; Zhang, Mingxia; Luo, Kai; Zhang, Yan; Liu, Haiying; Zhou, Boping; Kornfeld, Hardy; Chen, Xinchun

    2014-12-01

    The diagnosis of active tuberculosis (TB) disease remains a challenge, especially in high-burden settings. Cytokines and chemokines are important in the pathogenesis of TB. Here we investigate the usefulness of circulating and compartmentalized cytokines/chemokines for diagnosis of TB. The levels of multiple cytokines/chemokines in plasma, pleural fluid (PF), and cerebrospinal fluid (CSF) were determined by Luminex liquid array-based multiplexed immunoassays. Three of 26 cytokines/chemokines in plasma were significantly different between TB and latent tuberculosis infection (LTBI). Among them, IP-10 and MIG had the highest diagnostic values, with an area under the receiver operating characteristic curve (ROC AUC) of 0.92 for IP-10 and 0.86 for MIG for distinguishing TB from LTBI. However, IP-10 and MIG levels in plasma were not different between TB and non-TB lung disease. In contrast, compartmentalized IP-10 and MIG in the PF and CSF showed promising diagnostic values in discriminating TB and non-TB pleural effusion (AUC = 0.87 for IP-10 and 0.93 for MIG), as well as TB meningitis and non-TB meningitis (AUC = 0.9 for IP-10 and 0.95 for MIG). A longitudinal study showed that the plasma levels of IP-10, MIG, granulocyte colony-stimulating factor (G-CSF), and gamma interferon (IFN-γ) decreased, while the levels of MCP-1/CCL2 and eotaxin-1/CCL11 increased, after successful treatment of TB. Our findings provide a practical methodology for discriminating active TB from LTBI by sequential IFN-γ release assays (IGRAs) and plasma IP-10 testing, while increased IP-10 and MIG at the site of infection (PF or CSF) can be used as a marker for distinguishing pleural effusion and meningitis caused by TB from those of non-TB origins. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  9. Work-Related Pain in Extrinsic Finger Extensor Musculature of Instrumentalists Is Associated with Intracellular pH Compartmentation during Exercise

    PubMed Central

    Moreno-Torres, Angel; Rosset-Llobet, Jaume; Pujol, Jesus; Fàbregas, Sílvia; Gonzalez-de-Suso, Jose-Manuel

    2010-01-01

    Background Although non-specific pain in the upper limb muscles of workers engaged in mild repetitive tasks is a common occupational health problem, much is unknown about the associated structural and biochemical changes. In this study, we compared the muscle energy metabolism of the extrinsic finger extensor musculature in instrumentalists suffering from work-related pain with that of healthy control instrumentalists using non-invasive phosphorus magnetic resonance spectroscopy (31P-MRS). We hypothesize that the affected muscles will show alterations related with an impaired energy metabolism. Methodology/Principal Findings We studied 19 volunteer instrumentalists (11 subjects with work-related pain affecting the extrinsic finger extensor musculature and 8 healthy controls). We used 31P-MRS to find deviations from the expected metabolic response to exercise in phosphocreatine (PCr), inorganic phosphate (Pi), Pi/PCr ratio and intracellular pH kinetics. We observed a reduced finger extensor exercise tolerance in instrumentalists with myalgia, an intracellular pH compartmentation in the form of neutral and acid compartments, as detected by Pi peak splitting in 31P-MRS spectra, predominantly in myalgic muscles, and a strong association of this pattern with the condition. Conclusions/Significance Work-related pain in the finger extrinsic extensor muscles is associated with intracellular pH compartmentation during exercise, non-invasively detectable by 31P-MRS and consistent with the simultaneous energy production by oxidative metabolism and glycolysis. We speculate that a deficit in energy production by oxidative pathways may exist in the affected muscles. Two possible explanations for this would be the partial and/or local reduction of blood supply and the reduction of the muscle oxidative capacity itself. PMID:20161738

  10. Compartmentalized oxidative stress in dopaminergic cell death induced by pesticides and complex I inhibitors: Distinct roles of superoxide anion and superoxide dismutases

    PubMed Central

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely; Pickett, Chillian; Sumin, Li; Jones, Jocelyn; Chen, Han; Webb, Brian; Choi, Jae; Zhou, You; Zimmerman, Matthew C.; Franco, Rodrigo

    2013-01-01

    The loss of dopaminergic neurons induced by the parkinsonian toxins paraquat, rotenone and 1-methyl-4-phenylpyridinium (MPP+) is associated with oxidative stress. However, controversial reports exist regarding the source/compartmentalization of reactive oxygen species (ROS) generation and its exact role in cell death. We aimed to determine in detail the role of superoxide anion (O2•−), oxidative stress and their subcellular compartmentalization in dopaminergic cell death induced by parkinsonian toxins. Oxidative stress and ROS formation was determined in the cytosol, intermembrane (IMS) and mitochondrial matrix compartments, using dihydroethidine derivatives, the redox sensor roGFP, as well as electron paramagnetic resonance spectroscopy. Paraquat induced an increase in ROS and oxidative stress in both the cytosol and mitochondrial matrix prior to cell death. MPP+ and rotenone primarily induced an increase in ROS and oxidative stress in the mitochondrial matrix. No oxidative stress was detected at the level of the IMS. In contrast to previous studies, overexpression of manganese superoxide dismutase (MnSOD) or copper/zinc SOD (CuZnSOD) had no effect on ROS steady state levels, lipid peroxidation, loss of mitochondrial membrane potential (ΔΨm) and dopaminergic cell death induced by MPP+ or rotenone. In contrast, paraquat-induced oxidative stress and cell death were selectively reduced by MnSOD overexpression, but not by CuZnSOD or manganese-porphyrins. However, MnSOD also failed to prevent ΔΨm loss. Finally, paraquat, but not MPP+ or rotenone, induced the transcriptional activation the redox-sensitive antioxidant response elements (ARE) and nuclear factor kappa-B (NF-κB). These results demonstrate a selective role of mitochondrial O2•− in dopaminergic cell death induced by paraquat, and show that toxicity induced by the complex I inhibitors rotenone and MPP+ does not depend directly on mitochondrial O2•− formation. PMID:23602909

  11. Test-retest reliability of automated whole body and compartmental muscle volume measurements on a wide bore 3T MR system.

    PubMed

    Thomas, Marianna S; Newman, David; Leinhard, Olof Dahlqvist; Kasmai, Bahman; Greenwood, Richard; Malcolm, Paul N; Karlsson, Anette; Rosander, Johannes; Borga, Magnus; Toms, Andoni P

    2014-09-01

    To measure the test-retest reproducibility of an automated system for quantifying whole body and compartmental muscle volumes using wide bore 3 T MRI. Thirty volunteers stratified by body mass index underwent whole body 3 T MRI, two-point Dixon sequences, on two separate occasions. Water-fat separation was performed, with automated segmentation of whole body, torso, upper and lower leg volumes, and manually segmented lower leg muscle volumes. Mean automated total body muscle volume was 19·32 L (SD9·1) and 19·28 L (SD9·12) for first and second acquisitions (Intraclass correlation coefficient (ICC) = 1·0, 95% level of agreement -0·32-0·2 L). ICC for all automated test-retest muscle volumes were almost perfect (0·99-1·0) with 95% levels of agreement 1.8-6.6% of mean volume. Automated muscle volume measurements correlate closely with manual quantification (right lower leg: manual 1·68 L (2SD0·6) compared to automated 1·64 L (2SD 0·6), left lower leg: manual 1·69 L (2SD 0·64) compared to automated 1·63 L (SD0·61), correlation coefficients for automated and manual segmentation were 0·94-0·96). Fully automated whole body and compartmental muscle volume quantification can be achieved rapidly on a 3 T wide bore system with very low margins of error, excellent test-retest reliability and excellent correlation to manual segmentation in the lower leg. Sarcopaenia is an important reversible complication of a number of diseases. Manual quantification of muscle volume is time-consuming and expensive. Muscles can be imaged using in and out of phase MRI. Automated atlas-based segmentation can identify muscle groups. Automated muscle volume segmentation is reproducible and can replace manual measurements.

  12. Determination of Glucose Utilization Rates in Cultured Astrocytes and Neurons with [14C]deoxyglucose: Progress, Pitfalls, and Discovery of Intracellular Glucose Compartmentation.

    PubMed

    Dienel, Gerald A; Cruz, Nancy F; Sokoloff, Louis; Driscoll, Bernard F

    2017-01-01

    2-Deoxy-D-[ 14 C]glucose ([ 14 C]DG) is commonly used to determine local glucose utilization rates (CMR glc ) in living brain and to estimate CMR glc in cultured brain cells as rates of [ 14 C]DG phosphorylation. Phosphorylation rates of [ 14 C]DG and its metabolizable fluorescent analog, 2-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-2-deoxyglucose (2-NBDG), however, do not take into account differences in the kinetics of transport and metabolism of [ 14 C]DG or 2-NBDG and glucose in neuronal and astrocytic cells in cultures or in single cells in brain tissue, and conclusions drawn from these data may, therefore, not be correct. As a first step toward the goal of quantitative determination of CMR glc in astrocytes and neurons in cultures, the steady-state intracellular-to-extracellular concentration ratios (distribution spaces) for glucose and [ 14 C]DG were determined in cultured striatal neurons and astrocytes as functions of extracellular glucose concentration. Unexpectedly, the glucose distribution spaces rose during extreme hypoglycemia, exceeding 1.0 in astrocytes, whereas the [ 14 C]DG distribution space fell at the lowest glucose levels. Calculated CMR glc was greatly overestimated in hypoglycemic and normoglycemic cells because the intracellular glucose concentrations were too high. Determination of the distribution space for [ 14 C]glucose revealed compartmentation of intracellular glucose in astrocytes, and probably, also in neurons. A smaller metabolic pool is readily accessible to hexokinase and communicates with extracellular glucose, whereas the larger pool is sequestered from hexokinase activity. A new experimental approach using double-labeled assays with DG and glucose is suggested to avoid the limitations imposed by glucose compartmentation on metabolic assays.

  13. Functional compartmentalization of Rad9 and Hus1 reveals diverse assembly of the 9‐1‐1 complex components during the DNA damage response in Leishmania

    PubMed Central

    Damasceno, Jeziel D.; Obonaga, Ricardo; Santos, Elaine V.; Scott, Alan; McCulloch, Richard

    2016-01-01

    Summary The Rad9‐Rad1‐Hus1 (9‐1‐1) complex is a key component in the coordination of DNA damage sensing, cell cycle progression and DNA repair pathways in eukaryotic cells. This PCNA‐related trimer is loaded onto RPA‐coated single stranded DNA and interacts with ATR kinase to mediate effective checkpoint signaling to halt the cell cycle and to promote DNA repair. Beyond these core activities, mounting evidence suggests that a broader range of functions can be provided by 9‐1‐1 structural diversification. The protozoan parasite Leishmania is an early‐branching eukaryote with a remarkably plastic genome, which hints at peculiar genome maintenance mechanisms. Here, we investigated the existence of homologs of the 9‐1‐1 complex subunits in L. major and found that LmRad9 and LmRad1 associate with chromatin in response to replication stress and form a complex in vivo with LmHus1. Similar to LmHus1, LmRad9 participates in telomere homeostasis and in the response to both replication stress and double strand breaks. However, LmRad9 and LmHus1‐deficient cells present markedly opposite phenotypes, which suggest their functional compartmentalization. We show that some of the cellular pool of LmRad9 forms an alternative complex and that some of LmHus1 exists as a monomer. We propose that the diverse assembly of the Leishmania 9‐1‐1 subunits mediates functional compartmentalization, which has a direct impact on the response to genotoxic stress. PMID:27301589

  14. APOLLO II

    SciT

    Sanchez, R.; Mondot, J.; Stankovski, Z.

    1988-11-01

    APOLLO II is a new, multigroup transport code under development at the Commissariat a l'Energie Atomique. The code has a modular structure and uses sophisticated software for data structuralization, dynamic memory management, data storage, and user macrolanguage. This paper gives an overview of the main methods used in the code for (a) multidimensional collision probability calculations, (b) leakage calculations, and (c) homogenization procedures. Numerical examples are given to demonstrate the potential of the modular structure of the code and the novel multilevel flat-flux representation used in the calculation of the collision probabilities.

  15. Cell- and ligand-specific dephosphorylation of acid hydrolases: evidence that the mannose 6-phosphatase is controlled by compartmentalization

    PubMed Central

    1991-01-01

    Mouse L cells that possess the cation-independent mannose 6-phosphate (Man 6-P)/insulin-like growth factor (IGF) II receptor change the extent to which they dephosphorylate endocytosed acid hydrolases in response to serum (Einstein, R., and C. A. Gabel. 1989. J. Cell Biol. 109:1037-1046). To investigate the mechanism by which dephosphorylation competence is regulated, the dephosphorylation of individual acid hydrolases was studied in Man 6-P/IGF II receptor-positive and - deficient cell lines. 125I-labeled Man 6-P-containing acid hydrolases were proteolytically processed but remained phosphorylated when endocytosed by receptor-positive L cells maintained in the absence of serum; after the addition of serum, however, the cell-associated hydrolases were dephosphorylated. Individual hydrolases were dephosphorylated at distinct rates and to different extents. In contrast, the same hydrolases were dephosphorylated equally and completely after entry into Man 6-P/IGF II receptor-positive Chinese hamster ovary (CHO) cells. The dephosphorylation competence of Man 6- P/IGF II receptor-deficient mouse J774 cells was more limited. beta- Glucuronidase produced by these cells underwent a limited dephosphorylation in transit to lysosomes such that diphosphorylated oligosaccharides were converted to monophosphorylated species. The overall quantity of phosphorylated oligosaccharides associated with the enzyme, however, did not decrease within the lysosomal compartment. Likewise, beta-glucuronidase was not dephosphorylated when introduced into J774 cells via Fc receptor-mediated endocytosis. The CHO and J774 cell lysosomes, therefore, display opposite extremes with respect to their capacity to dephosphorylate acid hydrolases; within CHO cell lysosomes acid hydrolases are rapidly and efficiently dephosphorylated, but within J774 cell lysosomes the same acid hydrolases remain phosphorylated. This difference in processing indicates that lysosomes themselves exist in a dephosphorylation

  16. Biokinetic modelling development and analysis of arsenic dissolution into the gastrointestinal tract using SAAM II

    NASA Astrophysics Data System (ADS)

    Perama, Yasmin Mohd Idris; Siong, Khoo Kok

    2018-04-01

    A mathematical model comprising 8 compartments were designed to describe the kinetic dissolution of arsenic (As) from water leach purification (WLP) waste samples ingested into the gastrointestinal system. A totally reengineered software system named Simulation, Analysis and Modelling II (SAAM II) was employed to aid in the experimental design and data analysis. As a powerful tool that creates, simulate and analyze data accurately and rapidly, SAAM II computationally creates a system of ordinary differential equations according to the specified compartmental model structure and simulates the solutions based upon the parameter and model inputs provided. The experimental design of in vitro DIN approach was applied to create an artificial gastric and gastrointestinal fluids. These synthetic fluids assay were produced to determine the concentrations of As ingested into the gastrointestinal tract. The model outputs were created based upon the experimental inputs and the recommended fractional transfer rates parameter. As a result, the measured and predicted As concentrations in gastric fluids were much similar against the time of study. In contrast, the concentrations of As in the gastrointestinal fluids were only similar during the first hour and eventually started decreasing until the fifth hours of study between the measured and predicted values. This is due to the loss of As through the fractional transfer rates of q2 compartment to corresponding compartments of q3 and q5 which are involved with excretion and distribution to the whole body, respectively. The model outputs obtained after best fit to the data were influenced significantly by the fractional transfer rates between each compartment. Therefore, a series of compartmental model created with the association of fractional transfer rates parameter with the aid of SAAM II provides better estimation that simulate the kinetic behavior of As ingested into the gastrointestinal system.

  17. Cytoplasmic localization of Hug1p, a negative regulator of the MEC1 pathway, coincides with the compartmentalization of Rnr2p–Rnr4p

    SciT

    Ainsworth, William B.; Hughes, Bridget Todd; Au, Wei Chun

    2013-10-04

    Highlights: •Hug1p overexpression sensitizes wild-type cells to DNA damage and hydroxyurea (HU). •Expression of Hug1p in response to HU treatment is delayed relative to Rnr3p. •MEC1 pathway genes are required for cytoplasmic localization of Hug1p. •Hug1p subcellular compartmentalization to the cytoplasm coincides with Rnr2p–Rnr4p. -- Abstract: The evolutionarily conserved MEC1 checkpoint pathway mediates cell cycle arrest and induction of genes including the RNR (Ribonucleotide reductase) genes and HUG1 (Hydroxyurea, ultraviolet, and gamma radiation) in response to DNA damage and replication arrest. Rnr complex activity is in part controlled by cytoplasmic localization of the Rnr2p–Rnr4p subunits and inactivation of negative regulatorsmore » Sml1p and Dif1p upon DNA damage and hydroxyurea (HU) treatment. We previously showed that a deletion of HUG1 rescues lethality of mec1Δ and suppresses dun1Δ strains. In this study, multiple approaches demonstrate the regulatory response of Hug1p to DNA damage and HU treatment and support its role as a negative effector of the MEC1 pathway. Consistent with our hypothesis, wild-type cells are sensitive to DNA damage and HU when HUG1 is overexpressed. A Hug1 polyclonal antiserum reveals that HUG1 encodes a protein in budding yeast and its MEC1-dependent expression is delayed compared to the rapid induction of Rnr3p in response to HU treatment. Cell biology and subcellular fractionation experiments show localization of Hug1p-GFP to the cytoplasm upon HU treatment. The cytoplasmic localization of Hug1p-GFP is dependent on MEC1 pathway genes and coincides with the cytoplasmic localization of Rnr2p–Rnr4p. Taken together, the genetic interactions, gene expression, and localization studies support a novel role for Hug1p as a negative regulator of the MEC1 checkpoint response through its compartmentalization with Rnr2p–Rnr4p.« less

  18. A Simple Plasma Retinol Isotope Ratio Method for Estimating β-Carotene Relative Bioefficacy in Humans: Validation with the Use of Model-Based Compartmental Analysis.

    PubMed

    Ford, Jennifer Lynn; Green, Joanne Balmer; Lietz, Georg; Oxley, Anthony; Green, Michael H

    2017-09-01

    Background: Provitamin A carotenoids are an important source of dietary vitamin A for many populations. Thus, accurate and simple methods for estimating carotenoid bioefficacy are needed to evaluate the vitamin A value of test solutions and plant sources. β-Carotene bioefficacy is often estimated from the ratio of the areas under plasma isotope response curves after subjects ingest labeled β-carotene and a labeled retinyl acetate reference dose [isotope reference method (IRM)], but to our knowledge, the method has not yet been evaluated for accuracy. Objectives: Our objectives were to develop and test a physiologically based compartmental model that includes both absorptive and postabsorptive β-carotene bioconversion and to use the model to evaluate the accuracy of the IRM and a simple plasma retinol isotope ratio [(RIR), labeled β-carotene-derived retinol/labeled reference-dose-derived retinol in one plasma sample] for estimating relative bioefficacy. Methods: We used model-based compartmental analysis (Simulation, Analysis and Modeling software) to develop and apply a model that provided known values for β-carotene bioefficacy. Theoretical data for 10 subjects were generated by the model and used to determine bioefficacy by RIR and IRM; predictions were compared with known values. We also applied RIR and IRM to previously published data. Results: Plasma RIR accurately predicted β-carotene relative bioefficacy at 14 d or later. IRM also accurately predicted bioefficacy by 14 d, except that, when there was substantial postabsorptive bioconversion, IRM underestimated bioefficacy. Based on our model, 1-d predictions of relative bioefficacy include absorptive plus a portion of early postabsorptive conversion. Conclusion: The plasma RIR is a simple tracer method that accurately predicts β-carotene relative bioefficacy based on analysis of one blood sample obtained at ≥14 d after co-ingestion of labeled β-carotene and retinyl acetate. The method also provides

  19. Specific binding of [(18)F]fluoroethyl-harmol to monoamine oxidase A in rat brain cryostat sections, and compartmental analysis of binding in living brain.

    PubMed

    Maschauer, Simone; Haller, Adelina; Riss, Patrick J; Kuwert, Torsten; Prante, Olaf; Cumming, Paul

    2015-12-01

    We investigated [(18)F]fluoroethyl-harmol ([(18)F]FEH) as a reversible and selective ligand for positron emission tomography (PET) studies of monoamine oxidase A (MAO-A). Binding of [(18)F]FEH in rat brain cryostat sections indicated high affinity (KD = 3 nM), and density (Bmax; 600 pmol/g). The plasma free fraction was 45%, and untransformed parent constituted only 13% of plasma radioactivity at 10 min after injection. Compartmental analysis of PET recordings in pargyline-treated rats showed high permeability to brain (K1; 0.32 mL/g/min) and slow washout (k2; 0.024/min), resulting in a uniformly high equilibrium distribution volume (VD; 20 mL/g). Using this VD to estimate unbound ligand in brain of untreated rats, the binding potential ranged from 4.2 in cerebellum to 7.2 in thalamus. We also calculated maps of rats receiving [(18)F]FEH at a range of specific activities, and then estimated saturation binding parameters in the living brain. In thalamus, striatum and frontal cortex KD was globally close to 300 nM and Bmax was close to 1600 pmol/g; the 100-fold discrepancy in affinity suggests a very low free fraction for [(18)F]FEH in the living brain. Based on a synthesis of findings, we calculate the endogenous dopamine concentration to be 0.4 μM in the striatal compartment containing MAO-A, thus unlikely to exert competition against [(18)F]FEH binding in vivo. In summary, [(18)F]FEH has good properties for the detection of MAO-A in the rat brain by PET, and may present logistic advantages for clinical research at centers lacking a medical cyclotron. We made a compartmental analysis of [(18)F]fluoroethylharmol ([(18)F]FEH) binding to monoamine oxidase A (MAO-A) in living rat brain and estimated the saturation binding parameters from the binding potential (BPND). The Bmax was of comparable magnitude to that in vitro, but with apparent affinity (300 nM), it was 100-fold lower in vivo. PET imaging with [(18) F]FEH is well suited for quantitation of MAO-A in living

  20. Spectral Clustering Predicts Tumor Tissue Heterogeneity Using Dynamic 18F-FDG PET: A Complement to the Standard Compartmental Modeling Approach.

    PubMed

    Katiyar, Prateek; Divine, Mathew R; Kohlhofer, Ursula; Quintanilla-Martinez, Leticia; Schölkopf, Bernhard; Pichler, Bernd J; Disselhorst, Jonathan A

    2017-04-01

    In this study, we described and validated an unsupervised segmentation algorithm for the assessment of tumor heterogeneity using dynamic 18 F-FDG PET. The aim of our study was to objectively evaluate the proposed method and make comparisons with compartmental modeling parametric maps and SUV segmentations using simulations of clinically relevant tumor tissue types. Methods: An irreversible 2-tissue-compartmental model was implemented to simulate clinical and preclinical 18 F-FDG PET time-activity curves using population-based arterial input functions (80 clinical and 12 preclinical) and the kinetic parameter values of 3 tumor tissue types. The simulated time-activity curves were corrupted with different levels of noise and used to calculate the tissue-type misclassification errors of spectral clustering (SC), parametric maps, and SUV segmentation. The utility of the inverse noise variance- and Laplacian score-derived frame weighting schemes before SC was also investigated. Finally, the SC scheme with the best results was tested on a dynamic 18 F-FDG measurement of a mouse bearing subcutaneous colon cancer and validated using histology. Results: In the preclinical setup, the inverse noise variance-weighted SC exhibited the lowest misclassification errors (8.09%-28.53%) at all noise levels in contrast to the Laplacian score-weighted SC (16.12%-31.23%), unweighted SC (25.73%-40.03%), parametric maps (28.02%-61.45%), and SUV (45.49%-45.63%) segmentation. The classification efficacy of both weighted SC schemes in the clinical case was comparable to the unweighted SC. When applied to the dynamic 18 F-FDG measurement of colon cancer, the proposed algorithm accurately identified densely vascularized regions from the rest of the tumor. In addition, the segmented regions and clusterwise average time-activity curves showed excellent correlation with the tumor histology. Conclusion: The promising results of SC mark its position as a robust tool for quantification of tumor

  1. A compartmentalized phosphoinositide signaling axis at cilia is regulated by INPP5E to maintain cilia and promote Sonic Hedgehog medulloblastoma.

    PubMed

    Conduit, S E; Ramaswamy, V; Remke, M; Watkins, D N; Wainwright, B J; Taylor, M D; Mitchell, C A; Dyson, J M

    2017-10-26

    Sonic Hedgehog (SHH) signaling at primary cilia drives the proliferation and progression of a subset of medulloblastomas, the most common malignant paediatric brain tumor. Severe side effects associated with conventional treatments and resistance to targeted therapies has led to the need for new strategies. SHH signaling is dependent on primary cilia for signal transduction suggesting the potential for cilia destabilizing mechanisms as a therapeutic target. INPP5E is an inositol polyphosphate 5-phosphatase that hydrolyses PtdIns(4,5)P 2 and more potently, the phosphoinositide (PI) 3-kinase product PtdIns(3,4,5)P 3 . INPP5E promotes SHH signaling during embryonic development via PtdIns(4,5)P 2 hydrolysis at cilia, that in turn regulates the cilia recruitment of the SHH suppressor GPR161. However, the role INPP5E plays in cancer is unknown and the contribution of PI3-kinase signaling to cilia function is little characterized. Here, we reveal INPP5E promotes SHH signaling in SHH medulloblastoma by negatively regulating a cilia-compartmentalized PI3-kinase signaling axis that maintains primary cilia on tumor cells. Conditional deletion of Inpp5e in a murine model of constitutively active Smoothened-driven medulloblastoma slowed tumor progression, suppressed cell proliferation, reduced SHH signaling and promoted tumor cell cilia loss. PtdIns(3,4,5)P 3 , its effector pAKT and the target pGSK3β, which when non-phosphorylated promotes cilia assembly/stability, localized to tumor cell cilia. The number of PtdIns(3,4,5)P 3 /pAKT/pGSK3β-positive cilia was increased in cultured Inpp5e-null tumor cells relative to controls. PI3-kinase inhibition or expression of wild-type, but not catalytically inactive HA-INPP5E partially rescued cilia loss in Inpp5e-null tumor cells in vitro. INPP5E mRNA and copy number were reduced in human SHH medulloblastoma compared to other molecular subtypes and consistent with the murine model, reduced INPP5E was associated with improved overall

  2. Compartmental modeling with nitrogen-15 to determine effects of degree of fat saturation on intraruminal N recycling.

    PubMed

    Oldick, B S; Firkins, J L; Kohn, R A

    2000-09-01

    Two- and three-compartment models were developed to describe N kinetics within the rumen using three Holstein heifers and one nonlactating Holstein cow fitted with ruminal and duodenal cannulas. A 4 x 4 Latin square design included a control diet containing no supplemental fat and diets containing 4.85% of diet dry matter as partially hydrogenated tallow (iodine value = 13), tallow (iodine value = 51), or animal-vegetable fat (iodine value = 110). Effects of fat on intraruminal N recycling and relationships between intraruminal N recycling and ruminal protozoa concentration or the efficiency of microbial protein synthesis were determined. A pulse dose of 15(NH4)2SO4 was introduced into the ruminal NH3 N pool, and samples were taken over time from the ruminal NH3 N and nonammonia N pools. For the three-compartment model, precipitates of nonammonia N after trichloroacetic acid and ethanol extraction were defined as slowly turning over nonammonia N; rapidly turning over nonammonia N was determined by difference. Curves of 15N enrichment were fit to models with two (NH3 N and nonammonia N) or three (NH3 N, rapidly turning over nonammonia N, and slowly turning over nonammonia N) compartments using the software SAAM II. Because the three-compartment model did not remove a small systematic bias or improve the fit of the data, the two-compartment model was used to provide measurements of intraruminal N recycling. Intraruminal NH3 N recycling (45% for control) decreased linearly as fat unsaturation increased (50.2, 43.0, and 41.7% for partially hydrogenated tallow, tallow, and animal-vegetable fat, respectively). Intraruminal nitrogen recycling was not correlated with efficiency of microbial protein synthesis or ruminal protozoa counts.

  3. Interaction of singlet oxygen with bovine serum albumin and the role of the protein nano-compartmentalization.

    PubMed

    Giménez, Rodrigo E; Vargová, Veronika; Rey, Valentina; Turbay, M Beatriz Espeche; Abatedaga, Inés; Morán Vieyra, Faustino E; Paz Zanini, Verónica I; Mecchia Ortiz, Juan H; Katz, Néstor E; Ostatná, Veronika; Borsarelli, Claudio D

    2016-05-01

    Singlet molecular oxygen ((1)O2) contributes to protein damage triggering biophysical and biochemical changes that can be related with aging and oxidative stress. Serum albumins, such as bovine serum albumin (BSA), are abundant proteins in blood plasma with different biological functions. This paper presents a kinetic and spectroscopic study of the (1)O2-mediated oxidation of BSA using the tris(2,2'-bipyridine)ruthenium(II) cation [Ru(bpy)3](2+) as sensitizer. BSA quenches efficiently (1)O2 with a total (chemical+physical interaction) rate constant kt(BSA)=7.3(±0.4)×10(8)M(-1)s(-1), where the chemical pathway represented 37% of the interaction. This efficient quenching by BSA indicates the participation of several reactive residues. MALDI-TOF MS analysis of intact BSA confirmed that after oxidation by (1)O2, the mass protein increased the equivalent of 13 oxygen atoms. Time-resolved emission spectra analysis of BSA established that Trp residues were oxidized to N'-formylkynurenine, being the solvent-accessible W134 preferentially oxidized by (1)O2 as compared with the buried W213. MS confirmed oxidation of at least two Tyr residues to form dihydroxyphenylalanine, with a global reactivity towards (1)O2 six-times lower than for Trp residues. Despite the lack of MS evidences, kinetic and chemical analysis also suggested that residues other than Trp and Tyr, e.g. Met, must react with (1)O2. Modeling of the 3D-structure of BSA indicated that the oxidation pattern involves a random distribution of (1)O2 into BSA; allowing also the interaction of (1)O2 with buried residues by its diffusion from the bulk solvent through interconnected internal hydrophilic and hydrophobic grooves. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Compartmentalized self-replication under fast PCR cycling conditions yields Taq DNA polymerase mutants with increased DNA-binding affinity and blood resistance.

    PubMed

    Arezi, Bahram; McKinney, Nancy; Hansen, Connie; Cayouette, Michelle; Fox, Jeffrey; Chen, Keith; Lapira, Jennifer; Hamilton, Sarah; Hogrefe, Holly

    2014-01-01

    Faster-cycling PCR formulations, protocols, and instruments have been developed to address the need for increased throughput and shorter turn-around times for PCR-based assays. Although run times can be cut by up to 50%, shorter cycle times have been correlated with lower detection sensitivity and increased variability. To address these concerns, we applied Compartmentalized Self Replication (CSR) to evolve faster-cycling mutants of Taq DNA polymerase. After five rounds of selection using progressively shorter PCR extension times, individual mutations identified in the fastest-cycling clones were randomly combined using ligation-based multi-site mutagenesis. The best-performing combinatorial mutants exhibit 35- to 90-fold higher affinity (lower Kd ) for primed template and a moderate (2-fold) increase in extension rate compared to wild-type Taq. Further characterization revealed that CSR-selected mutations provide increased resistance to inhibitors, and most notably, enable direct amplification from up to 65% whole blood. We discuss the contribution of individual mutations to fast-cycling and blood-resistant phenotypes.

  5. Understanding the drug release mechanism from a montmorillonite matrix and its binary mixture with a hydrophilic polymer using a compartmental modelling approach

    NASA Astrophysics Data System (ADS)

    Choiri, S.; Ainurofiq, A.

    2018-03-01

    Drug release from a montmorillonite (MMT) matrix is a complex mechanism controlled by swelling mechanism of MMT and an interaction of drug and MMT. The aim of this research was to explain a suitable model of the drug release mechanism from MMT and its binary mixture with a hydrophilic polymer in the controlled release formulation based on a compartmental modelling approach. Theophylline was used as a drug model and incorporated into MMT and a binary mixture with hydroxyl propyl methyl cellulose (HPMC) as a hydrophilic polymer, by a kneading method. The dissolution test was performed and the modelling of drug release was assisted by a WinSAAM software. A 2 model was purposed based on the swelling capability and basal spacing of MMT compartments. The model evaluation was carried out to goodness of fit and statistical parameters and models were validated by a cross-validation technique. The drug release from MMT matrix regulated by a burst release mechanism of unloaded drug, swelling ability, basal spacing of MMT compartment, and equilibrium between basal spacing and swelling compartments. Furthermore, the addition of HPMC in MMT system altered the presence of swelling compartment and equilibrium between swelling and basal spacing compartment systems. In addition, a hydrophilic polymer reduced the burst release mechanism of unloaded drug.

  6. The amino-terminal hydrophilic region of the vacuolar transporter Avt3p is dispensable for the vacuolar amino acid compartmentalization of Schizosaccharomyces pombe.

    PubMed

    Kawano-Kawada, Miyuki; Chardwiriyapreecha, Soracom; Manabe, Kunio; Sekito, Takayuki; Akiyama, Koichi; Takegawa, Kaoru; Kakinuma, Yoshimi

    2016-12-01

    Avt3p, a vacuolar amino acid exporter (656 amino acid residues) that is important for vacuolar amino acid compartmentalization as well as spore formation in Schizosaccharomyces pombe, has an extremely long hydrophilic region (approximately 290 amino acid residues) at its N-terminus. Because known functional domains have not been found in this region, its functional role was examined with a deletion mutant avt3 (∆1-270) expressed in S. pombe avt3∆ cells. The deletion of this region did not affect its intracellular localization or vacuolar contents of basic amino acids as well as neutral ones. The defect of avt3Δ cells in spore formation was rescued by the expression of avt3 + but was not completely rescued by the expression of avt3 (∆1-270) . The N-terminal region is thus dispensable for the function of Avt3p as an amino acid exporter, but it is likely to be involved in the role of Avt3p under nutritional starvation conditions.

  7. Compartmental analysis of [11C]flumazenil kinetics for the estimation of ligand transport rate and receptor distribution using positron emission tomography.

    PubMed

    Koeppe, R A; Holthoff, V A; Frey, K A; Kilbourn, M R; Kuhl, D E

    1991-09-01

    The in vivo kinetic behavior of [11C]flumazenil ([11C]FMZ), a non-subtype-specific central benzodiazepine antagonist, is characterized using compartmental analysis with the aim of producing an optimized data acquisition protocol and tracer kinetic model configuration for the assessment of [11C]FMZ binding to benzodiazepine receptors (BZRs) in human brain. The approach presented is simple, requiring only a single radioligand injection. Dynamic positron emission tomography data were acquired on 18 normal volunteers using a 60- to 90-min sequence of scans and were analyzed with model configurations that included a three-compartment, four-parameter model, a three-compartment, three-parameter model, with a fixed value for free plus nonspecific binding; and a two-compartment, two-parameter model. Statistical analysis indicated that a four-parameter model did not yield significantly better fits than a three-parameter model. Goodness of fit was improved for three- versus two-parameter configurations in regions with low receptor density, but not in regions with moderate to high receptor density. Thus, a two-compartment, two-parameter configuration was found to adequately describe the kinetic behavior of [11C]FMZ in human brain, with stable estimates of the model parameters obtainable from as little as 20-30 min of data. Pixel-by-pixel analysis yields functional images of transport rate (K1) and ligand distribution volume (DV"), and thus provides independent estimates of ligand delivery and BZR binding.

  8. In vitro digestion of short-dough biscuits enriched in proteins and/or fibres, using a multi-compartmental and dynamic system (1): viscosity measurement and prediction.

    PubMed

    Villemejane, C; Wahl, R; Aymard, P; Denis, S; Michon, C

    2015-09-01

    The effects of biscuit composition on the viscosity generated during digestion were investigated. A control biscuit, one with proteins, one with fibres, and one with both proteins and fibres were digested under the same conditions, using the TNO intestinal model (TIM-1). The TIM-1 is a multi-compartmental and dynamic in vitro system, simulating digestion in the upper tract (stomach and small intestine) of healthy adult humans. Digesta were collected at different times, in the different compartments of the TIM-1 (stomach, duodenum, jejunum and ileum) and viscosity was measured with a dynamic rheometer. Results showed a marked effect of biscuit composition on chyme viscosity. Highest viscosity was obtained with biscuits containing viscous soluble fibres, followed by those enriched in both proteins and fibres, then by protein-enriched and control biscuits. The viscosity was maintained throughout the gut up to the ileal compartment. A prediction of the evolution of the chyme viscosity in each compartment of the TIM-1 was built, based on model curves describing the evolution of the viscosity as a function of biscuit concentration, and on dilution factors measured by spectrophotometry on a blank digestion. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. A physiologically required G protein-coupled receptor (GPCR)-regulator of G protein signaling (RGS) interaction that compartmentalizes RGS activity.

    PubMed

    Croft, Wayne; Hill, Claire; McCann, Eilish; Bond, Michael; Esparza-Franco, Manuel; Bennett, Jeannette; Rand, David; Davey, John; Ladds, Graham

    2013-09-20

    G protein-coupled receptors (GPCRs) can interact with regulator of G protein signaling (RGS) proteins. However, the effects of such interactions on signal transduction and their physiological relevance have been largely undetermined. Ligand-bound GPCRs initiate by promoting exchange of GDP for GTP on the Gα subunit of heterotrimeric G proteins. Signaling is terminated by hydrolysis of GTP to GDP through intrinsic GTPase activity of the Gα subunit, a reaction catalyzed by RGS proteins. Using yeast as a tool to study GPCR signaling in isolation, we define an interaction between the cognate GPCR (Mam2) and RGS (Rgs1), mapping the interaction domains. This reaction tethers Rgs1 at the plasma membrane and is essential for physiological signaling response. In vivo quantitative data inform the development of a kinetic model of the GTPase cycle, which extends previous attempts by including GPCR-RGS interactions. In vivo and in silico data confirm that GPCR-RGS interactions can impose an additional layer of regulation through mediating RGS subcellular localization to compartmentalize RGS activity within a cell, thus highlighting their importance as potential targets to modulate GPCR signaling pathways.

  10. Rapid and Quantitative Detection of Vibrio parahemolyticus by the Mixed-Dye-Based Loop-Mediated Isothermal Amplification Assay on a Self-Priming Compartmentalization Microfluidic Chip.

    PubMed

    Pang, Bo; Ding, Xiong; Wang, Guoping; Zhao, Chao; Xu, Yanan; Fu, Kaiyue; Sun, Jingjing; Song, Xiuling; Wu, Wenshuai; Liu, Yushen; Song, Qi; Hu, Jiumei; Li, Juan; Mu, Ying

    2017-12-27

    Vibrio parahemolyticus (VP) mostly isolated from aquatic products is one of the major causes of bacterial food-poisoning events worldwide, which could be reduced using a promising on-site detection method. Herein, a rapid and quantitative method for VP detection was developed by applying a mixed-dye-loaded loop-mediated isothermal amplification (LAMP) assay on a self-priming compartmentalization (SPC) microfluidic chip, termed on-chip mixed-dye-based LAMP (CMD-LAMP). In comparison to conventional approaches, CMD-LAMP was advantageous on the limit of detection, which reached down to 1 × 10 3 CFU/mL in food-contaminated samples without the pre-enrichment of bacteria. Additionally, as a result of the use of a mixed dye and SPC chip, the quantitative result could be easily acquired, avoiding the requirement of sophisticated instruments and tedious operation. Also, CMD-LAMP was rapid and cost-effective. Conclusively, CMD-LAMP has great potential in realizing the on-site quantitative analysis of VP for food safety.

  11. 31P-Nuclear Magnetic Resonance Determination of Phosphate Compartmentation in Leaves of Reproductive Soybeans (Glycine max L.) as Affected by Phosphate Nutrition 1

    PubMed Central

    Lauer, Michael J.; Blevins, Dale G.; Sierzputowska-Gracz, Hanna

    1989-01-01

    Most leaf phosphorus is remobilized to the seed during reproductive development in soybean. We determined, using 31P-NMR, the effect phosphorus remobilization has on vacuolar inorganic phosphate pool size in soybean (Glycine max [L.] Merr.) leaves with respect to phosphorus nutrition and plant development. Phosphate compartmentation between cytoplasmic and vacuolar pools was observed and followed in intact tissue grown hydroponically, at the R2, R4, and R6 growth stages. As phosphorus in the nutrient solution decreased from 0.45 to 0.05 millimolar, the vacuolar phosphate peak became less prominent relative to cytoplasmic phosphate and hexose monophosphate peaks. At a nutrient phosphate concentration of 0.05 millimolar, the vacuolar phosphate peak was not detectable. At higher levels of nutrient phosphate, as plants progressed from the R2 to the R6 growth stage, the vacuolar phosphate peak was the first to disappear, suggesting that storage phosphate was remobilized to a greater extent than metabolic phosphate. Under suboptimal phosphate nutrition (≤ 0.20 millimolar), the hexose monophosphate and cytoplasmic phosphate peaks declined earlier in reproductive development than when phosphate was present in optimal amounts. Under low phosphate concentrations (0.05 millimolar) cytoplasmic phosphate was greatly reduced. Carbon metabolism was coincidently disrupted under low phosphate nutrition as shown by the appearance of large, prominent starch grains in the leaves. Cytoplasmic phosphate, and leaf carbon metabolism dependent on it, are buffered by vacuolar phosphate until late stages of reproductive growth. Images Figure 4 PMID:16666705

  12. Neuroglial metabolic compartmentation underlying leptin deficiency in the obese ob/ob mice as detected by magnetic resonance imaging and spectroscopy methods

    PubMed Central

    Delgado, Teresa C; Violante, Inês R; Nieto-Charques, Laura; Cerdán, Sebastián

    2011-01-01

    Manganese-Enhanced Magnetic Resonance Imaging (MEMRI), 1H and 13C High-Resolution-Magic Angle Spinning (HR-MAS) Spectroscopy, and genomic approaches were used to compare cerebral activation and neuronal and glial oxidative metabolism in ad libitum fed C57BL6/J leptin-deficient, genetically obese ob/ob mice. T1-weighted Magnetic Resonance Images across the hypothalamic Arcuate and the Ventromedial nuclei were acquired kinetically after manganese infusion. Neuroglial compartmentation was investigated in hypothalamic biopsies after intraperitoneal injections of [1-13C]glucose or [2-13C]acetate. Total RNA was extracted to determine the effects of leptin deficiency in the expression of representative genes coding for regulatory enzymes of hypothalamic energy pathways and glutamatergic neurotransmission. Manganese-Enhanced Magnetic Resonance Imaging revealed enhanced cerebral activation in the hypothalamic Arcuate and Ventromedial nuclei of the ob/ob mice. 13C HR-MAS analysis showed increased 13C accumulation in the hypothalamic glutamate and glutamine carbons of ob/ob mice after the administration of [1-13C]glucose, a primarily neuronal substrate. Hypothalamic expression of the genes coding for glucokinase, phosphofructokinase, pyruvate dehydrogenase, and glutamine synthase was not significantly altered while pyruvate kinase expression was slightly upregulated. In conclusion, leptin deficiency associated with obesity led to increased cerebral activation in the hypothalamic Arcuate and Ventromedial nuclei, concomitant with significant increases in neuronal oxidative metabolism and glutamatergic neurotransmission. PMID:21971349

  13. Genetic characterization of human immunodeficiency virus type 1 in blood and genital secretions: evidence for viral compartmentalization and selection during sexual transmission.

    PubMed

    Zhu, T; Wang, N; Carr, A; Nam, D S; Moor-Jankowski, R; Cooper, D A; Ho, D D

    1996-05-01

    To explore the mechanism of sexual transmission of human immunodeficiency virus type 1 (HIV-1), we compared HIV-1 gp120 sequences in longitudinal samples from five acute seroconvertors with those from their corresponding sexual partners (transmitters). We used a quantitative homoduplex tracking assay to compare the overall genetic composition of HIV-1 quasispecies in each transmission pair and to track the transmitted viruses during the acute and asymptomatic stages of HIV-1 infection. In the chronically infected transmitters, HIV-1 variants in genital secretions differed from those in blood and variants in cells differed from those in cell-free plasma, indicating remarkable sequence heterogeneity in these subjects as well as compartmentalization of the virus in different bodily sites. Conversely, two of five seroconvertors had only a few related variants and three of five harbored only one viral population, indicating that in these subjects the transmitted viruses were typically homogeneous. Transmitted viruses were evident in the donor's seminal plasma (one of five cases) and even more so in their seminal cells (three of five cases), suggesting that both cell-associated and cell-free viruses can be transmitted. In every pair studied, the transmitted variant(s) represents only a minor population in the semen of the corresponding transmitter, thereby providing evidence that HIV-1 selection indeed occurs during sexual transmission.

  14. First extensive microscopic study of butternut defense mechanisms following inoculation with the canker pathogen Ophiognomonia clavigignenti-juglandacearum reveals compartmentalization of tissue damage.

    PubMed

    Rioux, Danny; Blais, Martine; Nadeau-Thibodeau, Nicholas; Lagacé, Marie; DesRochers, Pierre; Klimaszewska, Krystyna; Bernier, Louis

    2018-05-11

    Ophiognomonia clavigignenti-juglandacearum (Oc-j) endangers the survival of butternut (Juglans cinerea) throughout its native range. While screening for disease resistance, we found that artificial inoculations of 48 butternut seedlings with Oc-j induced the expression of external symptoms, but only after a period of dormancy. Before dormancy, compartmentalized tissues such as necrophylactic periderms (NPs) and xylem reaction zones (RZs) contributed to limiting pathogen invasion. Phenols were regularly detected in RZs, often in continuity with NPs during wound closure, and confocal microscopy revealed their presence in parenchyma cells, vessel plugs and cell walls. Vessels were blocked with tyloses and gels, particularly those present in RZs. Suberin was also detected in cells formed over the affected xylem by the callus at the inoculation point, in a few tylosis walls, and in longitudinal tubes that formed near NPs. Following dormancy, in all inoculated seedlings but one, defensive barriers were breached by Oc-j and then additional ones were produced in response to this new invasion. The results of this histopathological study indicate that trees inoculated in selection programs to test butternut canker resistance should go through at least one period of dormancy and that asymptomatic individuals should be dissected to better assess how they defend themselves against Oc-j.

  15. Kinetic modelling of passive transport and active efflux of a fluoroquinolone across Caco-2 cells using a compartmental approach in NONMEM.

    PubMed

    González-Alvarez, I; Fernández-Teruel, C; Garrigues, T M; Casabo, V G; Ruiz-García, A; Bermejo, M

    2005-12-01

    The purpose was to develop a general mathematical model for estimating passive permeability and efflux transport parameters from in vitro cell culture experiments. The procedure is applicable for linear and non-linear transport of drug with time, <10 or >10% of drug transport, negligible or relevant back flow, and would allow the adequate correction in the case of relevant mass balance problems. A compartmental kinetic approach was used and the transport barriers were described quantitatively in terms of apical and basolateral clearances. The method can be applied when sink conditions are not achieved and it allows the evaluation of the location of the transporter and its binding site. In this work it was possible to demonstrate, from a functional point of view, the higher efflux capacity of the TC7 clone and to identify the apical membrane as the main resistance for the xenobiotic transport. This methodology can be extremely useful as a complementary tool for molecular biology approaches in order to establish meaningful hypotheses about transport mechanisms.

  16. Building America Case Study: Apartment Compartmentalization with an Aerosol-Based Sealing Process - Queens, NY; Technology Solutions for New and Existing Homes, Energy Efficiency & Renewable Energy (EERE)

    SciT

    None

    2015-07-01

    Air sealing of building enclosures is a difficult and time-consuming process. Current methods in new construction require laborers to physically locate small and sometimes large holes in multiple assemblies and then manually seal each of them. The innovation demonstrated under this research study was the automated air sealing and compartmentalization of buildings through the use of an aerosolized sealant, developed by the Western Cooling Efficiency Center at University of California Davis.CARB sought to demonstrate this new technology application in a multifamily building in Queens, NY. The effectiveness of the sealing process was evaluated by three methods: air leakage testing ofmore » overall apartment before and after sealing, point-source testing of individual leaks, and pressure measurements in the walls of the target apartment during sealing. Aerosolized sealing was successful by several measures in this study. Many individual leaks that are labor-intensive to address separately were well sealed by the aerosol particles. In addition, many diffuse leaks that are difficult to identify and treat were also sealed. The aerosol-based sealing process resulted in an average reduction of 71% in air leakage across three apartments and an average apartment airtightness of 0.08 CFM50/SF of enclosure area.« less

  17. Compartmentalization of immune responses in human tuberculosis: few CD8+ effector T cells but elevated levels of FoxP3+ regulatory t cells in the granulomatous lesions.

    PubMed

    Rahman, Sayma; Gudetta, Berhanu; Fink, Joshua; Granath, Anna; Ashenafi, Senait; Aseffa, Abraham; Derbew, Milliard; Svensson, Mattias; Andersson, Jan; Brighenti, Susanna Grundström

    2009-06-01

    Immune responses were assessed at the single-cell level in lymph nodes from children with tuberculous lymphadenitis. Tuberculosis infection was associated with tissue remodeling of lymph nodes as well as altered cellular composition. Granulomas were significantly enriched with CD68+ macrophages expressing the M. tuberculosis complex-specific protein antigen MPT64 and inducible nitric oxide synthase. There was a significant increase in CD8+ cytolytic T cells surrounding the granuloma; however, CD8+ T cells expressed low levels of the cytolytic and antimicrobial effector molecules perforin and granulysin in the granulomatous lesions. Quantitative real-time mRNA analysis revealed that interferon-gamma, tumor necrosis factor-alpha, and interleukin-17 were not up-regulated in infected lymph nodes, but there was a significant induction of both transforming growth factor-beta and interleukin-13. In addition, granulomas contained an increased number of CD4+FoxP3+ T cells co-expressing the immunoregulatory cytotoxic T-lymphocyte antigen-4 and glucocorticoid-induced tumor necrosis factor receptor molecules. Low numbers of CD8+ T cells in the lesions correlated with high levels of transforming growth factor-beta and FoxP3+ regulatory T cells, suggesting active immunosuppression at the local infection site. Compartmentalization and skewing of the immune response toward a regulatory phenotype may result in an uncoordinated effector T-cell response that reduces granule-mediated killing of M. tuberculosis-infected cells and subsequent disease control.

  18. Parasagittal compartmentation of cerebellar mossy fibers as revealed by the patterned expression of vesicular glutamate transporters VGLUT1 and VGLUT2.

    PubMed

    Gebre, Samrawit A; Reeber, Stacey L; Sillitoe, Roy V

    2012-04-01

    The cerebellum receives sensory signals from spinocerebellar (lower limbs) and dorsal column nuclei (upper limbs) mossy fibers. In the cerebellum, mossy fibers terminate in bands that are topographically aligned with stripes of Purkinje cells. While much is known about the molecular heterogeneity of Purkinje cell stripes, little is known about whether mossy fiber compartments have distinct molecular profiles. Here, we show that the vesicular glutamate transporters VGLUT1 and VGLUT2, which mediate glutamate uptake into synaptic vesicles of excitatory neurons, are expressed in complementary bands of mossy fibers in the adult mouse cerebellum. Using a combination of immunohistochemistry and anterograde tracing, we found heavy VGLUT2 and weak VGLUT1 expression in bands of spinocerebellar mossy fibers. The adjacent bands, which are in part comprised of dorsal column nuclei mossy fibers, strongly express VGLUT1 and weakly express VGLUT2. Simultaneous injections of fluorescent tracers into the dorsal column nuclei and lower thoracic-upper lumbar spinal cord revealed that upper and lower limb sensory pathways innervate adjacent VGLUT1/VGLUT2 parasagittal bands. In summary, we demonstrate that VGLUT1 and VGLUT2 are differentially expressed by dorsal column nuclei and spinocerebellar mossy fibers, which project to complementary cerebellar bands and respect common compartmental boundaries in the adult mouse cerebellum.

  19. Red blood cells donate electrons to methylene blue mediated chemical reduction of methemoglobin compartmentalized in liposomes in blood.

    PubMed

    Sakai, Hiromi; Li, Bing; Lim, Wei Lee; Iga, Yumika

    2014-07-16

    Electron-energy-rich coenzymes in cells, NADH and NADPH, are re-energized repeatedly through the Embden-Meyerhof and pentose-phosphate glycolytic pathways, respectively. This study demonstrates extraction of their electron energies in red blood cells (RBCs) for in vivo extracellular chemical reactions using an electron mediator shuttling across the biomembrane. Hemoglobin-vesicles (HbVs) are an artificial oxygen carrier encapsulating purified and concentrated Hb solution in liposomes. Because of the absence of a metHb-reducing enzymatic system in HbV, HbO2 gradually autoxidizes to form metHb. Wistar rats received HbV suspension (10 mL/kg body weight) intravenously. At the metHb level of around 50%, methylene blue [MB(+); 3,7-bis(dimethylamino)phenothiazinium chloride] was injected. The level of metHb quickly decreased to around 16% in 40 min, remaining for more than 5 h. In vitro mixing of HbV/MB(+) with RBCs recreated the in vivo metHb reduction, but not with plasma. NAD(P)H levels in RBCs decreased after metHb reduction. The addition of glucose facilitated metHb reduction. Liposome-encapsulated NAD(P)H, a model of RBC, reduced metHb in HbV in the presence of MB(+). These results indicate that (i) NAD(P)H in RBCs reacts with MB(+) to convert it to leukomethylene blue (MBH); (ii) MB(+) and MBH shuttle freely between RBC and HbV across the hydrophobic lipid membranes; and (iii) MBH is transferred into HbV and reduces metHb in HbV. Four other electron mediators with appropriate redox potentials appeared to be as effective as MB(+) was, indicating the possibility for further optimization of electron mediators. We established an indirect enzymatic metHb reducing system for HbV using unlimited endogenous electrons created in RBCs in combination with an effective electron mediator that prolongs the functional lifespan of HbV in blood circulation.

  20. The Synthesis and Origin of the Pectic Polysaccharide Rhamnogalacturonan II – Insights from Nucleotide Sugar Formation and Diversity

    PubMed Central

    Bar-Peled, Maor; Urbanowicz, Breeanna R.; O’Neill, Malcolm A.

    2012-01-01

    There is compelling evidence showing that the structurally complex pectic polysaccharide rhamnogalacturonan II (RG-II) exists in the primary cell wall as a borate cross-linked dimer and that this dimer is required for the assembly of a functional wall and for normal plant growth and development. The results of several studies have also established that RG-II structure and cross-linking is conserved in vascular plants and that RG-II likely appeared early in the evolution of land plants. Two features that distinguish RG-II from other plant polysaccharides are that RG-II is composed of 13 different glycoses linked to each other by up to 22 different glycosidic linkages and that RG-II is the only polysaccharide known to contain both apiose and aceric acid. Thus, one key event in land plant evolution was the emergence of genes encoding nucleotide sugar biosynthetic enzymes that generate the activated forms of apiose and aceric acid required for RG-II synthesis. Many of the genes involved in the generation of the nucleotide sugars used for RG-II synthesis have been functionally characterized. By contrast, only one glycosyltransferase involved in the assembly of RG-II has been identified. Here we provide an overview of the formation of the activated sugars required for RG-II synthesis and point to the possible cellular and metabolic processes that could be involved in assembling and controlling the formation of a borate cross-linked RG-II molecule. We discuss how nucleotide sugar synthesis is compartmentalized and how this may control the flux of precursors to facilitate and regulate the formation of RG-II. PMID:22639675

  1. Compartmentalized, functional role of angiogenin during spotted fever group rickettsia-induced endothelial barrier dysfunction: evidence of possible mediation by host tRNA-derived small noncoding RNAs

    PubMed Central

    2013-01-01

    vivo. We also have provided direct evidence that rickettsial infection sensitizes human ECs to the translocation of exogenous ANG in a compartmentalized pattern at different times post-infection. Typically, exogenous ANG translocates into the nucleus at 24 hrs and to the cytoplasm at 72 hrs post-infection. The ANG cytoplasmic translocation enhances phosphorylation and destabilization of VE-cadherin and attenuates endothelial barrier function. Of note, deep sequencing analysis detected tRFs, mostly derived from the 5'-halves of host tRNAs, that are induced by ANG. Northern hybridization validates the two most abundantly cloned tRFs derived from tRNA-ValGTG and tRNA-GlyGCC, in both mouse tissues and human cells. Bioinformatics analysis predicted that these tRFs may interact with transcripts associated with the endothelial barrier, the host cell inflammatory response, and autophagy. Conclusions Our data provide new insight into the role of compartmentalized ANG during SFG rickettsioses, and highlight its possible mediation through tRFs. PMID:23800282

  2. Regulation of Sterol Content in Membranes by Subcellular Compartmentation of Steryl-Esters Accumulating in a Sterol-Overproducing Tobacco Mutant.

    PubMed Central

    Gondet, L.; Bronner, R.; Benveniste, P.

    1994-01-01

    The study of sterol overproduction in tissues of LAB 1-4 mutant tobacco (Nicotiana tabacum L. cv Xanthi) (P. Maillot-Vernier, H. Schaller, P. Benveniste, G. Belliard [1989] Biochem Biophys Res Commun 165: 125-130) over several generations showed that the overproduction phenotype is stable in calli, with a 10-fold stimulation of sterol content when compared with wild-type calli. However, leaves of LAB 1-4 plants obtained after two steps of self-fertilization were characterized by a mere 3-fold stimulation, whereas calli obtained from these plants retained a typical sterol-overproducing mutant phenotype (i.e. a 10-fold increase of sterol content). These results suggest that the expression of the LAB 1-4 phenotype is dependent on the differentiation state of cells. Most of the sterols accumulating in the mutant tissues were present as steryl-esters, which were minor species in wild-type tissues. Subcellular fractionation showed that in both mutant and wild-type tissues, free sterols were associated mainly with microsomal membranes. In contrast, the bulk of steryl-esters present in mutant tissues was found in the soluble fraction of cells. Numerous lipid droplets were detected in the hyaloplasm of LAB 1-4 cells by cytochemical and cytological techniques. After isolation, these lipid granules were shown to contain steryl-esters. These results show that the overproduced sterols of mutant tissues accumulate as steryl-esters in hyaloplasmic bodies. The esterification process thus allows regulation of the amount of free sterols in membranes by subcellular compartmentation. PMID:12232218

  3. Dynamic phenotypic restructuring of the CD4 and CD8 T-cell subsets with age in healthy humans: a compartmental model analysis.

    PubMed

    Jackola, D R; Hallgren, H M

    1998-11-16

    In healthy humans, phenotypic restructuring occurs with age within the CD3+ T-lymphocyte complement. This is characterized by a non-linear decrease of the percentage of 'naive' (CD45RA+) cells and a corresponding non-linear increase of the percentage of 'memory' (CD45R0+) cells among both the CD4+ and CD8+ T-cell subsets. We devised a simple compartmental model to study the age-dependent kinetics of phenotypic restructuring. We also derived differential equations whose parameters determined yearly gains minus losses of the percentage and absolute numbers of circulating naive cells, yearly gains minus losses of the percentage and absolute numbers of circulating memory cells, and the yearly rate of conversion of naive to memory cells. Solutions of these evaluative differential equations demonstrate the following: (1) the memory cell complement 'resides' within its compartment for a longer time than the naive cell complement within its compartment for both CD4 and CD8 cells; (2) the average, annual 'turnover rate' is the same for CD4 and CD8 naive cells. In contrast, the average, annual 'turnover rate' for memory CD8 cells is 1.5 times that of memory CD4 cells; (3) the average, annual conversion rate of CD4 naive cells to memory cells is twice that of the CD8 conversion rate; (4) a transition in dynamic restructuring occurs during the third decade of life that is due to these differences in turnover and conversion rates, between and from naive to memory cells.

  4. Full-length cellular β-secretase has a trimeric subunit stoichiometry, and its sulfur-rich transmembrane interaction site modulates cytosolic copper compartmentalization.

    PubMed

    Liebsch, Filip; Aurousseau, Mark R P; Bethge, Tobias; McGuire, Hugo; Scolari, Silvia; Herrmann, Andreas; Blunck, Rikard; Bowie, Derek; Multhaup, Gerd

    2017-08-11

    The β-secretase (BACE1) initiates processing of the amyloid precursor protein (APP) into Aβ peptides, which have been implicated as central players in the pathology of Alzheimer disease. BACE1 has been described as a copper-binding protein and its oligomeric state as being monomeric, dimeric, and/or multimeric, but the native cellular stoichiometry has remained elusive. Here, by using single-molecule fluorescence and in vitro cross-linking experiments with photo-activatable unnatural amino acids, we show that full-length BACE1, independently of its subcellular localization, exists as trimers in human cells. We found that trimerization requires the BACE1 transmembrane sequences (TMSs) and cytoplasmic domains, with residues Ala 463 and Cys 466 buried within the trimer interface of the sulfur-rich core of the TMSs. Our 3D model predicts that the sulfur-rich core of the trimeric BACE1 TMS is accessible to metal ions, but copper ions did not trigger trimerization. The results of functional assays of endogenous BACE1 suggest that it has a role in intracellular copper compartmentalization by transferring cytosolic copper to intracellular compartments, while leaving the overall cellular copper concentration unaltered. Adding to existing physiological models, our results provide novel insight into the atypical interactions between copper and BACE1 and into its non-enzymatic activities. In conclusion, therapeutic Alzheimer disease prevention strategies aimed at decreasing BACE1 protein levels should be regarded with caution, because adverse effects in copper homeostasis may occur. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Compartmentalized beta subunit distribution determines characteristics and ethanol sensitivity of somatic, dendritic, and terminal large-conductance calcium-activated potassium channels in the rat central nervous system.

    PubMed

    Wynne, P M; Puig, S I; Martin, G E; Treistman, S N

    2009-06-01

    Neurons are highly differentiated and polarized cells, whose various functions depend upon the compartmentalization of ion channels. The rat hypothalamic-neurohypophysial system (HNS), in which cell bodies and dendrites reside in the hypothalamus, physically separated from their nerve terminals in the neurohypophysis, provides a particularly powerful preparation in which to study the distribution and regional properties of ion channel proteins. Using electrophysiological and immunohistochemical techniques, we characterized the large-conductance calcium-activated potassium (BK) channel in each of the three primary compartments (soma, dendrite, and terminal) of HNS neurons. We found that dendritic BK channels, in common with somatic channels but in contrast to nerve terminal channels, are insensitive to iberiotoxin. Furthermore, analysis of dendritic BK channel gating kinetics indicates that they, like somatic channels, have fast activation kinetics, in contrast to the slow gating of terminal channels. Dendritic and somatic channels are also more sensitive to calcium and have a greater conductance than terminal channels. Finally, although terminal BK channels are highly potentiated by ethanol, somatic and dendritic channels are insensitive to the drug. The biophysical and pharmacological properties of somatic and dendritic versus nerve terminal channels are consistent with the characteristics of exogenously expressed alphabeta1 versus alphabeta4 channels, respectively. Therefore, one possible explanation for our findings is a selective distribution of auxiliary beta1 subunits to the somatic and dendritic compartments and beta4 to the terminal compartment. This hypothesis is supported immunohistochemically by the appearance of distinct punctate beta1 or beta4 channel clusters in the membrane of somatic and dendritic or nerve terminal compartments, respectively.

  6. Activity and subcellular compartmentalization of peroxisome proliferator-activated receptor alpha are altered by the centrosome-associated protein CAP350.

    PubMed

    Patel, Hansa; Truant, Ray; Rachubinski, Richard A; Capone, John P

    2005-01-01

    Peroxisome proliferator-activated nuclear hormone receptors (PPAR) are ligand-activated transcription factors that play pivotal roles in governing metabolic homeostasis and cell growth. PPARs are primarily in the nucleus but, under certain circumstances, can be found in the cytoplasm. We show here that PPAR(alpha) interacts with the centrosome-associated protein CAP350. CAP350 also interacts with PPAR(delta), PPAR(gamma) and liver-X-receptor alpha, but not with the 9-cis retinoic acid receptor, RXR(alpha). Immunofluorescence analysis indicated that PPAR(alpha) is diffusely distributed in the nucleus and excluded from the cytoplasm. However, in the presence of coexpressed CAP350, PPAR(alpha) colocalizes with CAP350 to discrete nuclear foci and to the centrosome, perinuclear region and intermediate filaments. In contrast, the subcellular distribution of RXR(alpha) or of thyroid hormone receptor alpha was not altered by coexpression of CAP350. An amino-terminal fragment of CAP350 was localized exclusively to nuclear foci and was sufficient to recruit PPAR(alpha) to these sites. Mutation of the single putative nuclear hormone receptor interacting signature motif LXXLL present in this fragment had no effect on its subnuclear localization but abrogated recruitment of PPAR(alpha) to nuclear foci. Surprisingly, mutation of the LXXLL motif in this CAP350 subfragment did not prevent its binding to PPAR(alpha) in vitro, suggesting that this motif serves some function other than PPAR(alpha) binding in recruiting PPAR(alpha) to nuclear spots. CAP350 inhibited PPAR(alpha)-mediated transactivation in an LXXLL-dependent manner, suggesting that CAP350 represses PPAR(alpha) function. Our findings implicate CAP350 in a dynamic process that recruits PPAR(alpha) to discrete nuclear and cytoplasmic compartments and suggest that altered intracellular compartmentalization represents a regulatory process that modulates PPAR function.

  7. Functional restoration of HCV-specific CD8 T cells by PD-1 blockade is defined by PD-1 expression and compartmentalization.

    PubMed

    Nakamoto, Nobuhiro; Kaplan, David E; Coleclough, Jennifer; Li, Yun; Valiga, Mary E; Kaminski, Mary; Shaked, Abraham; Olthoff, Kim; Gostick, Emma; Price, David A; Freeman, Gordon J; Wherry, E John; Chang, Kyong-Mi

    2008-06-01

    The immunoinhibitory receptor programmed death-1 (PD-1) is up-regulated on dysfunctional virus-specific CD8 T cells during chronic viral infections, and blockade of PD-1/PD-ligand (PD-L) interactions can restore their function. As hepatitis C virus (HCV) persists in the liver with immune-mediated disease pathogenesis, we examined the role of PD-1/PD-L pathway in antigen-specific CD8 T-cell dysfunction in the liver and blood of HCV-infected patients. PD-1 expression and function of circulating CD8 T cells specific for HCV, Epstein-Barr virus, and influenza virus were examined ex vivo and following antigenic stimulation in vitro in patients with acute, chronic, and resolved HCV infection using class I tetramers and flow cytometry. Intrahepatic CD8 T cells were examined from liver explants of chronically HCV-infected transplant recipients. Intrahepatic HCV-specific CD8 T cells from chronically HCV-infected patients were highly PD-1 positive, profoundly dysfunctional, and unexpectedly refractory to PD-1/PD-L blockade, contrasting from circulating PD-1-intermediate HCV-specific CD8 T cells with responsiveness to PD-1/PD-L blockade. This intrahepatic functional impairment was HCV-specific and directly associated with the level of PD-1 expression. Highly PD-1-positive intrahepatic CD8 T cells were more phenotypically exhausted with increased cytotoxic T-lymphocyte antigen 4 and reduced CD28 and CD127 expression, suggesting that active antigen-specific stimulation in the liver induces a profound functional exhaustion not reversible by PD-1/PD-L blockade alone. HCV-specific CD8 T-cell dysfunction and responsiveness to PD-1/PD-L blockade are defined by their PD-1 expression and compartmentalization. These findings provide new and clinically relevant insight to differential antigen-specific CD8 T-cell exhaustion and their functional restoration.

  8. Small Diameter Bomb Increment II (SDB II)

    DTIC Science & Technology

    2015-12-01

    Selected Acquisition Report ( SAR ) RCS: DD-A&T(Q&A)823-439 Small Diameter Bomb Increment II (SDB II) As of FY 2017 President’s Budget Defense...Acquisition Management Information Retrieval (DAMIR) March 23, 2016 16:19:13 UNCLASSIFIED SDB II December 2015 SAR March 23, 2016 16:19:13 UNCLASSIFIED...Document OSD - Office of the Secretary of Defense O&S - Operating and Support PAUC - Program Acquisition Unit Cost SDB II December 2015 SAR March 23

  9. The role of glutamine and other alternate substrates as energy sources in the fetal rat lung type II cell.

    PubMed

    Fox, R E; Hopkins, I B; Cabacungan, E T; Tildon, J T

    1996-07-01

    Glucose has been thought to be the primary substrate for energy metabolism in the developing lung; however, alternate substrates are used for energy metabolism in other organs. To examine the role of alternate substrates in the lung, we measured rates of oxidation of glutamine, glucose, lactate, and 3-hydroxybutyrate in type II pneumocytes isolated from d 19 fetal rat lungs by measuring the production of 14CO2 from labeled substrates. Glutamine had a rate of 24.36 +/- 4.51 nmol 14CO2 produced/ h/mg of protein (mean +/- SEM), whereas lactate had a significantly higher rate, 40.29 +/- 4.42. 3-Hydroxybutyrate had a rate of 14.91 +/- 1.93. The rate of glucose oxidation was 2.13 +/- 0.36, significantly lower than that of glutamine. To examine the interactions of substrates normally found in the intracellular milieu, we measured the effect of unlabeled substrates as competitors on labeled substrate. This identifies multiple metabolic compartments of energy metabolism. Glucose, but not lactate, inhibited the oxidation of glutamine, suggesting a compartmentation of tricarboxylic acid cycle activity, rather than simple dilution by glucose. Glucose and lactate had reciprocal inhibition. Our data suggest at least two separate compartments in the type II cells for substrate oxidation, one for glutamine metabolism and a second for glucose metabolism. In summary, we have documented that glutamine and other alternate substrates are oxidized preferentially over glucose for energy metabolism in the d 19 fetal rat lung type II pneumocyte. In addition, we have delineated some of the compartmentation that occurs within the developing type II cell, which may determine how these substrates are used.

  10. Localization of a bacterial group II intron-encoded protein in eukaryotic nuclear splicing-related cell compartments.

    PubMed

    Nisa-Martínez, Rafael; Laporte, Philippe; Jiménez-Zurdo, José Ignacio; Frugier, Florian; Crespi, Martin; Toro, Nicolás

    2013-01-01

    Some bacterial group II introns are widely used for genetic engineering in bacteria, because they can be reprogrammed to insert into the desired DNA target sites. There is considerable interest in developing this group II intron gene targeting technology for use in eukaryotes, but nuclear genomes present several obstacles to the use of this approach. The nuclear genomes of eukaryotes do not contain group II introns, but these introns are thought to have been the progenitors of nuclear spliceosomal introns. We investigated the expression and subcellular localization of the bacterial RmInt1 group II intron-encoded protein (IEP) in Arabidopsis thaliana protoplasts. Following the expression of translational fusions of the wild-type protein and several mutant variants with EGFP, the full-length IEP was found exclusively in the nucleolus, whereas the maturase domain alone targeted EGFP to nuclear speckles. The distribution of the bacterial RmInt1 IEP in plant cell protoplasts suggests that the compartmentalization of eukaryotic cells into nucleus and cytoplasm does not prevent group II introns from invading the host genome. Furthermore, the trafficking of the IEP between the nucleolus and the speckles upon maturase inactivation is consistent with the hypothesis that the spliceosomal machinery evolved from group II introns.

  11. Localization of a Bacterial Group II Intron-Encoded Protein in Eukaryotic Nuclear Splicing-Related Cell Compartments

    PubMed Central

    Nisa-Martínez, Rafael; Laporte, Philippe; Jiménez-Zurdo, José Ignacio; Frugier, Florian; Crespi, Martin; Toro, Nicolás

    2013-01-01

    Some bacterial group II introns are widely used for genetic engineering in bacteria, because they can be reprogrammed to insert into the desired DNA target sites. There is considerable interest in developing this group II intron gene targeting technology for use in eukaryotes, but nuclear genomes present several obstacles to the use of this approach. The nuclear genomes of eukaryotes do not contain group II introns, but these introns are thought to have been the progenitors of nuclear spliceosomal introns. We investigated the expression and subcellular localization of the bacterial RmInt1 group II intron-encoded protein (IEP) in Arabidopsis thaliana protoplasts. Following the expression of translational fusions of the wild-type protein and several mutant variants with EGFP, the full-length IEP was found exclusively in the nucleolus, whereas the maturase domain alone targeted EGFP to nuclear speckles. The distribution of the bacterial RmInt1 IEP in plant cell protoplasts suggests that the compartmentalization of eukaryotic cells into nucleus and cytoplasm does not prevent group II introns from invading the host genome. Furthermore, the trafficking of the IEP between the nucleolus and the speckles upon maturase inactivation is consistent with the hypothesis that the spliceosomal machinery evolved from group II introns. PMID:24391881

  12. Selection Dynamics in Transient Compartmentalization

    NASA Astrophysics Data System (ADS)

    Blokhuis, Alex; Lacoste, David; Nghe, Philippe; Peliti, Luca

    2018-04-01

    Transient compartments have been recently shown to be able to maintain functional replicators in the context of prebiotic studies. Here, we show that a broad class of selection dynamics is able to achieve this goal. We identify two key parameters, the relative amplification of nonactive replicators (parasites) and the size of compartments. These parameters account for competition and diversity, and the results are relevant to similar multilevel selection problems, such as those found in virus-host ecology and trait group selection.

  13. Cellular compartmentalization of secondary metabolism

    Fungal secondary metabolism is often considered apart from the essential housekeeping functions of the cell. However, there are clear links between fundamental cellular metabolism and the biochemical pathways leading to secondary metabolite synthesis. Besides utilizing key biochemical precursors sh...

  14. Compartmentalization of decay in trees

    Alex L. Shigo

    1985-01-01

    Trees have a spectacular survival record. Over a period of more than 400 million years they have evolved as the tallest, most massive and longest-lived organisms ever to inhabit the earth. Yet trees lack a means of defense that almost every animal has: trees cannot move away from destructive forces. Because they cannot move, all types of living and nonliving enemies—...

  15. Ultra-Short-Term Reproducibility of Speckle-Noise Freed Fluid and Tissue Compartmentalization of the Choroid Analyzed by Standard OCT.

    PubMed

    Maloca, Peter; Gyger, Cyrill; Schoetzau, Andreas; Hasler, Pascal W

    2015-11-01

    We measured reproducibility of speckle-noise freed fluid and tissue compartmentalization of the choroid (choroidal angiography and tissue characterization). This study included 26 eyes of 13 healthy females: 13 were used for repeated measurements and 13 were used for side comparison. A semiautomated algorithm removed speckle-noise with structure preservation. Intraclass correlation (ICC), with respect to reproducibility of the method, showed an ICC for choroidal fluid inner space analysis (FISA) of 95.15% (90.01-98.24). The ICC of tissue inner space analysis (TISA) was 99.75% (99.47-99.91). The total choroid ratio (TCR), calculated from volumes of tissue to vessels, showed an ICC of 88.84% (78.28-95.82). Comparison of eyes (left to right) showed a difference for FISA of 0.033 (95% confidence interval [CI] -0.0018-0.0680, P = 0.063), TISA -0.118 (CI -0.2373-0.0023, P = 0.055), and TCR -0.590 (CI -0.9047 to -0.2754, P = 0.004). The ICC for FISA and TISA showed a trend in the difference comparing left and right eyes; however, TCR showed a significant difference between the eyes in the measured area ( P < 0.001). Mean overall FISA was 0.58 mm 3 (range, 0.25-0.98 mm 3 , SD = 0.14). Mean TISA was 3.45 mm 3 (range, 2.38-5.0 mm 3 , SD 0.072). Mean TCR was 6.13 (overall range, 3.93-10.2, SD = 1.34). Differences in choroidal layers between subjects were found mainly due to alterations in choroidal tissue. Reproducibility of speckle-noise freed choroidal angiography appeared excellent. Speckle noise is a granular "noise" that appears in a wide range of medical imaging methods as ultrasonography, magnetic resonance, computer tomography, or optical coherence tomography (OCT). Findings from basic science about speckle noise were translated into a novel, medical image postprocessing application that can separate signal from speckle noise with structure preservation with high reproducibility and enhance medical imaging.

  16. The compartmentalized inflammatory response in the multiple sclerosis brain is composed of tissue-resident CD8+ T lymphocytes and B cells.

    PubMed

    Machado-Santos, Joana; Saji, Etsuji; Tröscher, Anna R; Paunovic, Manuela; Liblau, Roland; Gabriely, Galina; Bien, Christian G; Bauer, Jan; Lassmann, Hans

    2018-06-04

    Multiple sclerosis is an inflammatory demyelinating disease in which active demyelination and neurodegeneration are associated with lymphocyte infiltrates in the brain. However, so far little is known regarding the phenotype and function of these infiltrating lymphocyte populations. In this study, we performed an in-depth phenotypic characterization of T and B cell infiltrates in a large set of multiple sclerosis cases with different disease and lesion stages and compared the findings with those seen in inflammatory, non-inflammatory and normal human controls. In multiple sclerosis lesions, we found a dominance of CD8+ T cells and a prominent contribution of CD20+ B cells in all disease courses and lesion stages, including acute multiple sclerosis cases with very short disease duration, while CD4+ T cells were sparse. A dominance of CD8+ T cells was also seen in other inflammatory controls, such as Rasmussen's encephalitis and viral encephalitis, but the contribution of B cells in these diseases was modest. Phenotypic analysis of the CD8+ T cells suggested that part of the infiltrating cells in active lesions proliferate, show an activated cytotoxic phenotype and are in part destroyed by apoptosis. Further characterization of the remaining cells suggest that CD8+ T cells acquire features of tissue-resident memory cells, which may be focally reactivated in active lesions of acute, relapsing and progressive multiple sclerosis, while B cells, at least in part, gradually transform into plasma cells. The loss of surface molecules involved in the egress of leucocytes from inflamed tissue, such as S1P1 or CCR7, and the upregulation of CD103 expression may be responsible for the compartmentalization of the inflammatory response in established lesions. Similar phenotypic changes of tissue-infiltrating CD8+ T cells were also seen in Rasmussen's encephalitis. Our data underline the potential importance of CD8+ T lymphocytes and B cells in the inflammatory response in

  17. Functional restoration of HCV-specific CD8 T-cells by PD1 blockade is defined by PD1 expression and compartmentalization

    PubMed Central

    Nakamoto, Nobuhiro; Kaplan, David E.; Coleclough, Jennifer; Li, Yun; Kaminski, Mary; Shaked, Abraham; Olthoff, Kim; Gostick, Emma; Price, David A.; Freeman, Gordon J.; Wherry, E. John; Chang, Kyong-Mi

    2008-01-01

    Background & Aims The immuno-inhibitory receptor Programmed Death-1 (PD-1) is upregulated on dysfunctional virus-specific CD8 T-cells during chronic viral infections and blockade of PD-1:PD-ligand (PD-L) interactions can restore their function. As hepatitis C virus (HCV) persists in the liver with immune-mediated disease pathogenesis, we examined the role of PD1/PD-L pathway in antigen-specific CD8 T-cell dysfunction in the liver and blood of HCV-infected patients. Methods PD-1 expression and function of circulating CD8 T-cells specific for HCV, EBV and Flu were examined ex vivo and following antigenic stimulation in vitro in patients with acute, chronic and resolved HCV infection using class I tetramers and flow cytometry. Intrahepatic CD8 T-cells were examined from liver explants of chronically HCV-infected transplant recipients. Results Intrahepatic HCV-specific CD8 T-cells from chronically HCV-infected patients were highly PD-1-positive, profoundly dysfunctional and unexpectedly refractory to PD-1:PD-L blockade, contrasting from circulating PD-1-intermediate HCV-specific CD8 T-cells with responsiveness to PD-1:PD-L blockade. This intrahepatic functional impairment was HCV-specific and directly associated with the level of PD-1 expression. Highly PD-1-positive intrahepatic CD8 T-cells were more phenotypically exhausted with increased cytotoxic T-lymphocyte antigen 4 (CTLA-4) and reduced CD28 and CD127 expression, suggesting that active antigen-specific stimulation in the liver induces a profound functional exhaustion not reversible by PD-1:PD-L blockade alone. Conclusion HCV-specific CD8 T-cell dysfunction and responsiveness to PD-1:PD-L blockade are defined by their PD-1 expression and compartmentalization. These findings provide new and clinically relevant insight to differential antigen-specific CD8 T-cell exhaustion and their functional restoration. PMID:18549878

  18. Ultra–Short-Term Reproducibility of Speckle-Noise Freed Fluid and Tissue Compartmentalization of the Choroid Analyzed by Standard OCT

    PubMed Central

    Maloca, Peter; Gyger, Cyrill; Schoetzau, Andreas; Hasler, Pascal W.

    2015-01-01

    Purpose We measured reproducibility of speckle-noise freed fluid and tissue compartmentalization of the choroid (choroidal angiography and tissue characterization). Methods This study included 26 eyes of 13 healthy females: 13 were used for repeated measurements and 13 were used for side comparison. A semiautomated algorithm removed speckle-noise with structure preservation. Results Intraclass correlation (ICC), with respect to reproducibility of the method, showed an ICC for choroidal fluid inner space analysis (FISA) of 95.15% (90.01–98.24). The ICC of tissue inner space analysis (TISA) was 99.75% (99.47–99.91). The total choroid ratio (TCR), calculated from volumes of tissue to vessels, showed an ICC of 88.84% (78.28–95.82). Comparison of eyes (left to right) showed a difference for FISA of 0.033 (95% confidence interval [CI] −0.0018–0.0680, P = 0.063), TISA −0.118 (CI −0.2373–0.0023, P = 0.055), and TCR −0.590 (CI −0.9047 to −0.2754, P = 0.004). The ICC for FISA and TISA showed a trend in the difference comparing left and right eyes; however, TCR showed a significant difference between the eyes in the measured area (P < 0.001). Mean overall FISA was 0.58 mm3 (range, 0.25–0.98 mm3, SD = 0.14). Mean TISA was 3.45 mm3 (range, 2.38–5.0 mm3, SD 0.072). Mean TCR was 6.13 (overall range, 3.93–10.2, SD = 1.34). Conclusions Differences in choroidal layers between subjects were found mainly due to alterations in choroidal tissue. Reproducibility of speckle-noise freed choroidal angiography appeared excellent. Translational Relevance Speckle noise is a granular “noise” that appears in a wide range of medical imaging methods as ultrasonography, magnetic resonance, computer tomography, or optical coherence tomography (OCT). Findings from basic science about speckle noise were translated into a novel, medical image postprocessing application that can separate signal from speckle noise with structure preservation with high reproducibility and

  19. The health, poverty, and financial consequences of a cigarette price increase among 500 million male smokers in 13 middle income countries: compartmental model study

    PubMed Central

    2018-01-01

    Abstract Objective To examine the impact of a 50% increase in market prices of cigarettes on health, poverty, and financial protection. Design Compartmental model study. Setting 13 middle income countries, totalling two billion men. Participants 500 million male smokers. Main outcome measures Life years gained, averted treatment costs, number of men avoiding catastrophic healthcare expenditures and poverty, and additional tax revenue by income group. Results A 50% increase in cigarette prices would lead to about 450 million years of life gained across the 13 countries from smoking cessation, with half of these in China. Across all countries, men in the bottom income group (poorest 20% of the population) would gain 6.7 times more life years than men in the top income group (richest 20% of the population; 155 v 23 million). The average life years gained from cessation for each smoker in the bottom income group was 5.1 times that of the top group (1.46 v 0.23 years). Of the $157bn (£113bn; €127bn) in averted treatment costs, the bottom income group would avert 4.6 times more costs than the top income group ($46bn v $10bn). About 15.5 million men would avoid catastrophic health expenditures in a subset of seven countries without universal health coverage. As result, 8.8 million men, half of them in the bottom income group, would avoid falling below the World Bank definition of extreme poverty. These 8.8 million men constitute 2.4% of people living in extreme poverty in these countries. In contrast, the top income group would pay twice as much as the bottom income group of the $122bn additional tax collected. Overall, the bottom income group would get 31% of the life years saved and 29% each of the averted disease costs and averted catastrophic health expenditures, while paying only 10% of the additional taxes. Conclusions Higher prices of cigarettes provide more health and financial gains to the poorest 20% than to the richest 20% of the population. Higher excise

  20. BASS-II Experiment

    2014-08-02

    Image taken on card 8 during BASS-II flame test session with reduced O2 partial pressure. Session conducted on GMT 213. The Burning and Suppression of Solids - II (BASS-II) investigation examines the burning and extinction characteristics of a wide variety of fuel samples in microgravity. The BASS-II experiment will guide strategies for materials flammability screening for use in spacecraft as well as provide valuable data on solid fuel burning behavior in microgravity. BASS-II results contribute to the combustion computational models used in the design of fire detection and suppression systems in microgravity and on Earth.

  1. Type II universal spacetimes

    NASA Astrophysics Data System (ADS)

    Hervik, S.; Málek, T.; Pravda, V.; Pravdová, A.

    2015-12-01

    We study type II universal metrics of the Lorentzian signature. These metrics simultaneously solve vacuum field equations of all theories of gravitation with the Lagrangian being a polynomial curvature invariant constructed from the metric, the Riemann tensor and its covariant derivatives of an arbitrary order. We provide examples of type II universal metrics for all composite number dimensions. On the other hand, we have no examples for prime number dimensions and we prove the non-existence of type II universal spacetimes in five dimensions. We also present type II vacuum solutions of selected classes of gravitational theories, such as Lovelock, quadratic and L({{Riemann}}) gravities.

  2. Small Diameter Bomb Increment II (SDB II)

    DTIC Science & Technology

    2013-12-01

    in 2013: Electromagnetic Environments and Effects and Hazards of Electromagnetic Radiation to Ordnance . Reliability Growth Testing started in June...unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 SDB II December 2013 SAR April 16, 2014 17:24:29...Framework EMC - Electromagnetic Compatibility EMI - Electromagnetic Interference GESP - GIG Enterprise Service Profiles GIG - Global Information Grid i.e

  3. ASDIR-II. Volume II. Program Description

    DTIC Science & Technology

    1975-01-01

    in ASDIR. INPUT: Engine description, gas properties and case definition (See ASDIR-II, Volume I, User’s Manual). OIWPUT: Primarily the information...conditions Special surface cooling flow conditions Exhaust system surface properties The predictions provided by the progi un for the combination of a...nonattenuated by the atmosphere Optional exhaust system information which can be requested from the program is: Internal fluid flow properties Surface

  4. Multiple endocrine neoplasia (MEN) II

    MedlinePlus

    Sipple syndrome; MEN II; Pheochromocytoma - MEN II; Thyroid cancer - pheochromocytoma; Parathyroid cancer - pheochromocytoma ... The cause of MEN II is a defect in a gene called RET. This defect causes many tumors to appear in the same ...

  5. SAGE II V7

    Atmospheric Science Data Center

    2017-09-06

    ... The series of Stratospheric Aerosol and Gas Experiments (SAGE I, II, and III) are satellite-based solar occultation ... significantly more shortwave radiation than previously thought. Clouds in a Clear Sky Scientists have detected a nearly ...

  6. Digital optical computer II

    NASA Astrophysics Data System (ADS)

    Guilfoyle, Peter S.; Stone, Richard V.

    1991-12-01

    OptiComp is currently completing a 32-bit, fully programmable digital optical computer (DOC II) that is designed to operate in a UNIX environment running RISC microcode. OptiComp's DOC II architecture is focused toward parallel microcode implementation where data is input in a dual rail format. By exploiting the physical principals inherent to optics (speed and low power consumption), an architectural balance of optical interconnects and software code efficiency can be achieved including high fan-in and fan-out. OptiComp's DOC II program is jointly sponsored by the Office of Naval Research (ONR), the Strategic Defense Initiative Office (SDIO), NASA space station group and Rome Laboratory (USAF). This paper not only describes the motivational basis behind DOC II but also provides an optical overview and architectural summary of the device that allows the emulation of any digital instruction set.

  7. Proton Improvement Plan II

    SciT

    Fermilab

    Fermilab's Proton Improvement Plan II will generate the world’s most powerful high-energy neutrino beam for the international Deep Underground Neutrino Experiment and position Fermilab as the world leader in accelerator-based neutrino research.

  8. Factor II assay

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/003674.htm Factor II assay To use the sharing features on ... M. is also a founding member of Hi-Ethics and subscribes to the principles of the Health ...

  9. Nsls-II Boster

    NASA Astrophysics Data System (ADS)

    Gurov, S. M.; Akimov, A. V.; Akimov, V. E.; Anashin, V. V.; Anchugov, O. V.; Baranov, G. N.; Batrakov, A. M.; Belikov, O. V.; Bekhtenev, E. A.; Blum, E.; Bulatov, A. V.; Burenkov, D. B.; Cheblakov, P. B.; Chernyakin, A. D.; Cheskidov, V. G.; Churkin, I. N.; Davidsavier, M.; Derbenev, A. A.; Erokhin, A. I.; Fliller, R. P.; Fulkerson, M.; Gorchakov, K. M.; Ganetis, G.; Gao, F.; Gurov, D. S.; Hseuh, H.; Hu, Y.; Johanson, M.; Kadyrov, R. A.; Karnaev, S. E.; Karpov, G. V.; Kiselev, V. A.; Kobets, V. V.; Konstantinov, V. M.; Kolmogorov, V. V.; Korepanov, A. A.; Kramer, S.; Krasnov, A. A.; Kremnev, A. A.; Kuper, E. A.; Kuzminykh, V. S.; Levichev, E. B.; Li, Y.; Long, J. De; Makeev, A. V.; Mamkin, V. R.; Medvedko, A. S.; Meshkov, O. I.; Nefedov, N. B.; Neyfeld, V. V.; Okunev, I. N.; Ozaki, S.; Padrazo, D.; Petrov, V. V.; Petrichenkov, M. V.; Philipchenko, A. V.; Polyansky, A. V.; Pureskin, D. N.; Rakhimov, A. R.; Rose, J.; Ruvinskiy, S. I.; Rybitskaya, T. V.; Sazonov, N. V.; Schegolev, L. M.; Semenov, A. M.; Semenov, E. P.; Senkov, D. V.; Serdakov, L. E.; Serednyakov, S. S.; Shaftan, T. V.; Sharma, S.; Shichkov, D. S.; Shiyankov, S. V.; Shvedov, D. A.; Simonov, E. A.; Singh, O.; Sinyatkin, S. V.; Smaluk, V. V.; Sukhanov, A. V.; Tian, Y.; Tsukanova, L. A.; Vakhrushev, R. V.; Vobly, P. D.; Utkin, A. V.; Wang, G.; Wahl, W.; Willeke, F.; Yaminov, K. R.; Yong, H.; Zhuravlev, A.; Zuhoski, P.

    The National Synchrotron Light Source II is a third generation light source, which was constructed at Brookhaven National Laboratory. This project includes a highly-optimized 3 GeV electron storage ring, linac preinjector, and full-energy synchrotron injector. Budker Institute of Nuclear Physics built and delivered the booster for NSLS-II. The commissioning of the booster was successfully completed. This paper reviews fulfilled work by participants.

  10. Real-time dynamics of RNA Polymerase II clustering in live human cells

    NASA Astrophysics Data System (ADS)

    Cisse, Ibrahim

    2014-03-01

    Transcription is the first step in the central dogma of molecular biology, when genetic information encoded on DNA is made into messenger RNA. How this fundamental process occurs within living cells (in vivo) is poorly understood,[1] despite extensive biochemical characterizations with isolated biomolecules (in vitro). For high-order organisms, like humans, transcription is reported to be spatially compartmentalized in nuclear foci consisting of clusters of RNA Polymerase II, the enzyme responsible for synthesizing all messenger RNAs. However, little is known of when these foci assemble or their relative stability. We developed an approach based on photo-activation localization microscopy (PALM) combined with a temporal correlation analysis, which we refer to as tcPALM. The tcPALM method enables the real-time characterization of biomolecular spatiotemporal organization, with single-molecule sensitivity, directly in living cells.[2] Using tcPALM, we observed that RNA Polymerase II clusters form transiently, with an average lifetime of 5.1 (+/- 0.4) seconds. Stimuli affecting transcription regulation yielded orders of magnitude changes in the dynamics of the polymerase clusters, implying that clustering is regulated and plays a role in the cells ability to effect rapid response to external signals. Our results suggest that the transient crowding of enzymes may aid in rate-limiting steps of genome regulation.

  11. Carnitine palmitoyltransferase II deficiency

    PubMed Central

    Roe, C R.; Yang, B-Z; Brunengraber, H; Roe, D S.; Wallace, M; Garritson, B K.

    2008-01-01

    Background: Carnitine palmitoyltransferase II (CPT II) deficiency is an important cause of recurrent rhabdomyolysis in children and adults. Current treatment includes dietary fat restriction, with increased carbohydrate intake and exercise restriction to avoid muscle pain and rhabdomyolysis. Methods: CPT II enzyme assay, DNA mutation analysis, quantitative analysis of acylcarnitines in blood and cultured fibroblasts, urinary organic acids, the standardized 36-item Short-Form Health Status survey (SF-36) version 2, and bioelectric impedance for body fat composition. Diet treatment with triheptanoin at 30% to 35% of total daily caloric intake was used for all patients. Results: Seven patients with CPT II deficiency were studied from 7 to 61 months on the triheptanoin (anaplerotic) diet. Five had previous episodes of rhabdomyolysis requiring hospitalizations and muscle pain on exertion prior to the diet (two younger patients had not had rhabdomyolysis). While on the diet, only two patients experienced mild muscle pain with exercise. During short periods of noncompliance, two patients experienced rhabdomyolysis with exercise. None experienced rhabdomyolysis or hospitalizations while on the diet. All patients returned to normal physical activities including strenuous sports. Exercise restriction was eliminated. Previously abnormal SF-36 physical composite scores returned to normal levels that persisted for the duration of the therapy in all five symptomatic patients. Conclusions: The triheptanoin diet seems to be an effective therapy for adult-onset carnitine palmitoyltransferase II deficiency. GLOSSARY ALT = alanine aminotransferase; AST = aspartate aminotransferase; ATP = adenosine triphosphate; BHP = β-hydroxypentanoate; BKP = β-ketopentanoate; BKP-CoA = β-ketopentanoyl–coenzyme A; BUN = blood urea nitrogen; CAC = citric acid cycle; CoA = coenzyme A; CPK = creatine phosphokinase; CPT II = carnitine palmitoyltransferase II; LDL = low-density lipoprotein; MCT

  12. Collaborative Research to Optimize Warfighter Nutrition II (CROWN II)

    DTIC Science & Technology

    2016-09-01

    Award Number: W81XWH-14-1-0335 TITLE: Collaborative Research to Optimize Warfighter Nutrition II (CROWN II) PRINCIPAL INVESTIGATOR: Jennifer C...2016 4. TITLE AND SUBTITLE Collaborative Research to Optimize Warfighter Nutrition II (CROWN II) 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-14-1...has been forged between USARIEM and Pennington Biomedical Research Center (PBRC) since 1988. Objective: CROWN II conducts research in nutrition

  13. Mod II engine performance

    NASA Technical Reports Server (NTRS)

    Richey, Albert E.; Huang, Shyan-Cherng

    1987-01-01

    The testing of a prototype of an automotive Stirling engine, the Mod II, is discussed. The Mod II is a one-piece cast block with a V-4 single-crankshaft configuration and an annular regenerator/cooler design. The initial testing of Mod II concentrated on the basic engine, with auxiliaries driven by power sources external to the engine. The performance of the engine was tested at 720 C set temperature and 820 C tube temperature. At 720 C, it is observed that the power deficiency is speed dependent and linear, with a weak pressure dependency, and at 820 C, the power deficiency is speed and pressure dependent. The effects of buoyancy and nozzle spray pattern on the heater temperature spread are investigated. The characterization of the oil pump and the operating cycle and temperature spread tests are proposed for further evaluation of the engine.

  14. About APPLE II Operation

    NASA Astrophysics Data System (ADS)

    Schmidt, T.; Zimoch, D.

    2007-01-01

    The operation of an APPLE II based undulator beamline with all its polarization states (linear horizontal and vertical, circular and elliptical, and continous variation of the linear vector) requires an effective description allowing an automated calculation of gap and shift parameter as function of energy and operation mode. The extension of the linear polarization range from 0 to 180° requires 4 shiftable magnet arrrays, permitting use of the APU (adjustable phase undulator) concept. Studies for a pure fixed gap APPLE II for the SLS revealed surprising symmetries between circular and linear polarization modes allowing for simplified operation. A semi-analytical model covering all types of APPLE II and its implementation will be presented.

  15. SAGE II Ozone Analysis

    NASA Technical Reports Server (NTRS)

    Cunnold, Derek; Wang, Ray

    2002-01-01

    Publications from 1999-2002 describing research funded by the SAGE II contract to Dr. Cunnold and Dr. Wang are listed below. Our most recent accomplishments include a detailed analysis of the quality of SAGE II, v6.1, ozone measurements below 20 km altitude (Wang et al., 2002 and Kar et al., 2002) and an analysis of the consistency between SAGE upper stratospheric ozone trends and model predictions with emphasis on hemispheric asymmetry (Li et al., 2001). Abstracts of the 11 papers are attached.

  16. The Position of the Patella and Extensor Mechanism Affects Intraoperative Compartmental Loads During Total Knee Arthroplasty: A Pilot Study Using Intraoperative Sensing to Guide Soft Tissue Balance.

    PubMed

    Schnaser, Erik; Lee, Yuo-yu; Boettner, Friedrich; Gonzalez Della Valle, Alejandro

    2015-08-01

    The achievement of a well-balanced total knee arthroplasty is necessary for long-term success. We hypothesize that the dislocation of the patella during surgery affects the distribution of loads in the medial and lateral compartments. Intraoperative load sensors were used to record medial and lateral compartment loads in 56 well-balanced TKAs. Loads were recorded in full extension, relaxed extension, at 45 and 90° of flexion at full gravity-assisted flexion, with the patella in four different positions: dislocated (everted and not), located, and located and secured with two retinacular sutures. The loads in the lateral compartment in flexion were higher with a dislocated patella than with a located patella (P<0.001). A lateralized extensor mechanism artificially increases in the lateral compartment loads in flexion during TKA surgery. Instruments that allow intraoperative soft tissue balance with the patella in a physiologic position are more likely to replicate postoperative compartment loads. II (prospective comparative study). Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Building Trades II.

    ERIC Educational Resources Information Center

    Hamlin, Larry

    This packet contains a curriculum guide, a set of lesson plans, a student manual, and a competency test packet for the Building Trades II course, the second year of a 2-year, 2-unit (350 hour) preemployment program for students in grades 11-12. This technical course is designed to develop the basic skills associated with builders. An additional…

  18. Project 1946: Phase II

    DTIC Science & Technology

    2010-07-01

    History (Project 1946 - Phase II),” for the National Intelligence Council. The views, opinions, and findings should not be construed as representing...29 Section 1: Senior Leadership  Foreign Assistance  Officer Corps  Saddam‘s Personality ...45 Section 3: Personal Interactions with Saddam  Senior Leadership

  19. Dissecting Diversity Part II

    ERIC Educational Resources Information Center

    Matthews, Frank

    2005-01-01

    This article presents "Dissecting Diversity, Part II," the conclusion of a wide-ranging two-part roundtable discussion on diversity in higher education. The participants were as follows: Lezli Baskerville, J.D., President and CEO of the National Association for Equal Opportunity (NAFEO); Dr. Gerald E. Gipp, Executive Director of the…

  20. Instant Insanity II

    ERIC Educational Resources Information Center

    Richmond, Tom; Young, Aaron

    2013-01-01

    "Instant Insanity II" is a sliding mechanical puzzle whose solution requires the special alignment of 16 colored tiles. We count the number of solutions of the puzzle's classic challenge and show that the more difficult ultimate challenge has, up to row permutation, exactly two solutions, and further show that no…

  1. UNISIST II: Special Report.

    ERIC Educational Resources Information Center

    Hattery, Lowell H., Ed.

    1979-01-01

    The major part of this report of the Intergovernmental Conference on Scientific and Technical Information (UNISIST II), held in Paris May 28-June 1, 1979, focuses on three sets of recommendations which were unanimously approved after combining the recommendations proposed by various groups and blocs: (1) recommendations to the United Nations…

  2. Periodontics II: Course Proposal.

    ERIC Educational Resources Information Center

    Dordick, Bruce

    A proposal is presented for Periodontics II, a course offered at the Community College of Philadelphia to give the dental hygiene/assisting student an understanding of the disease states of the periodontium and their treatment. A standardized course proposal cover form is given, followed by a statement of purpose for the course, a list of major…

  3. Combined experimental and theoretical studies on selective sensing of zinc and pyrophosphate ions by rational design of compartmental chemosensor probe: Dual sensing behaviour via secondary recognition approach and cell imaging studies.

    PubMed

    Mawai, Kiran; Nathani, Sandip; Roy, Partha; Singh, U P; Ghosh, Kaushik

    2018-05-08

    A compartmental chemosensor probe HL has been designed and synthesized for the selective recognition of zinc ions over other transition metal ions via fluorescence "ON" strategy. The chemosensing behaviour of HL was demonstrated through fluorescence, absorption and NMR spectroscopic techniques. The molecular structure of the zinc complex derived from HL was determined by X-ray crystallography. A probable mechanism of this selective sensing behavior was described on the basis of spectroscopic results and theoretical studies by density functional theory (DFT). The biological applicability of the chemosensor HL was examined via cell imaging on HeLa cells. The HL-zinc complex served as a secondary fluorescent probe responding to the pyrophosphate anion specifically over other anions. The fluorescence enhancement of HL in association with Zn2+ ions was quenched in the presence of pyrophosphate (PPi). Thus, a dual response was established based on "OFF-ON-OFF" strategy for detection of both cation and anion. This phenomenon was utilized in the construction of a "INHIBIT" logic gate.

  4. Increase of chromium tolerance in Scenedesmus acutus after sulfur starvation: Chromium uptake and compartmentalization in two strains with different sensitivities to Cr(VI).

    PubMed

    Marieschi, M; Gorbi, G; Zanni, C; Sardella, A; Torelli, A

    2015-10-01

    In photosynthetic organisms sulfate constitutes the main sulfur source for the biosynthesis of GSH and its precursor Cys. Hence, sulfur availability can modulate the capacity to cope with environmental stresses, a phenomenon known as SIR/SED (Sulfur Induced Resistance or Sulfur Enhanced Defence). Since chromate may compete for sulfate transport into the cells, in this study chromium accumulation and tolerance were investigated in relation to sulfur availability in two strains of the unicellular green alga Scenedesmus acutus with different Cr-sensitivities. Paradoxically, sulfur deprivation has been demonstrated to induce a transient increase of Cr-tolerance in both strains. Sulfur deprivation is known to enhance the sulfate uptake/assimilation pathway leading to important consequences on Cr-tolerance: (i) reduced chromate uptake due to the induction of high affinity sulfate transporters (ii) higher production of cysteine and GSH which can play a role both through the formation of unsoluble complexes and their sequestration in inert compartments. To investigate the role of the above mentioned mechanisms, Cr accumulation in total cells and in different cell compartments (cell wall, membranes, soluble and miscellaneous fractions) was analyzed in both sulfur-starved and unstarved cells. Both strains mainly accumulated chromium in the soluble fraction, but the uptake was higher in the wild-type. In this type a short period of sulfur starvation before Cr(VI) treatment lowered chromium accumulation to the level observed in the unstarved Cr-tolerant strain, in which Cr uptake seems instead less influenced by S-starvation, since no significant decrease was observed. The increase in Cr-tolerance following S-starvation seems thus to rely on different mechanisms in the two strains, suggesting the induction of a mechanism constitutively active in the Cr-tolerant strain, maybe a high affinity sulfate transporter also in the wild-type. Changes observed in the cell wall and

  5. TARN II project

    SciT

    Katayama, T.

    On the basis of the achievement of the accelerator studies at present TARN, it is decided to construct the new ring TARN II which will be operated as an accumulator, accelerator, cooler and stretcher. It has the maximum magnetic rigidity of 7 Txm corresponding to the proton energy 1.3 GeV and the ring diameter is around 23 m. Light and heavy ions from the SF cyclotron will be injected and accelerated to the working energy where the ring will be operated as a desired mode, for example a cooler ring mode. At the cooler ring operation, the strong cooling devicesmore » such as stochastic and electron beam coolings will work together with the internal gas jet target for the precise nuclear experiments. TARN II is currently under the contruction with the schedule of completion in 1986. In this paper general features of the project are presented.« less

  6. Where is Population II?

    NASA Astrophysics Data System (ADS)

    Mould, J.; Bianchini, F.; Forbes, Duncan A.; Reichardt, C. L.

    2018-03-01

    The use of roman numerals for stellar populations represents a classification approach to galaxy formation which is now well behind us. Nevertheless, the concept of a pristine generation of stars, followed by a protogalactic era, and finally the mainstream stellar population is a plausible starting point for testing our physical understanding of early star formation. This will be observationally driven as never before in the coming decade. In this paper, we search out observational tests of an idealised coeval and homogeneous distribution of population II stars. We examine the spatial distribution of quasars, globular clusters, and the integrated free electron density of the intergalactic medium, in order to test the assumption of homogeneity. Any real inhomogeneity implies a population II that is not coeval.

  7. What is LAMPF II

    SciT

    Thiessen, H.A.

    1982-08-01

    The present conception of LAMPF II is a high-intensity 16-GeV synchrotron injected by the LAMPF 800-MeV H/sup -/ beam. The proton beam will be used to make secondary beams of neutrinos, muons, pions, kaons, antiprotons, and hyperons more intense than those of any existing or proposed accelerator. For example, by taking maximum advantage of a thick target, modern beam optics, and the LAMPF II proton beam, it will be possible to make a negative muon beam with nearly 100% duty factor and nearly 100 times the flux of the existing Stopped Muon Channel (SMC). Because the unique features of themore » proposed machine are most applicable to beams of the same momentum as LAMPF (that is, < 2 GeV/c), it may be possible to use most of the experimental areas and some of the auxiliary equipment, including spectrometers, with the new accelerator. The complete facility will provide improved technology for many areas of physics already available at LAMPF and will allow expansion of medium-energy physics to include kaons, antiprotons, and hyperons. When LAMPF II comes on line in 1990 LAMPF will have been operational for 18 years and a major upgrade such as this proposal will be reasonable and prudent.« less

  8. Operation Everest II

    PubMed Central

    2010-01-01

    Abstract Wagner, Peter D. Operation Everest II. High Alt. Med. Biol. 11:111–119, 2010.—In October 1985, 25 years ago, 8 subjects and 27 investigators met at the United States Army Research Institute for Environmental Medicine (USARIEM) altitude chambers in Natick, Massachusetts, to study human responses to a simulated 40-day ascent of Mt. Everest, termed Operation Everest II (OE II). Led by Charlie Houston, John Sutton, and Allen Cymerman, these investigators conducted a large number of investigations across several organ systems as the subjects were gradually decompressed over 40 days to the Everest summit equivalent. There the subjects reached a \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland,xspace}\\usepackage{amsmath,amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6} \\begin{document} \\begin{align*} \\dot{\\rm V}{\\sc O}_2{\\rm max} \\end{align*} \\end{document} of 15.3 mL/kg/min (28% of initial sea-level values) at 100 W and arterial Po2 and Pco2 of ∼28 and ∼10 mm Hg, respectively. Cardiac function resisted hypoxia, but the lungs could not: ventilation–perfusion inequality and O2 diffusion limitation reduced arterial oxygenation considerably. Pulmonary vascular resistance was increased, was not reversible after short-term hyperoxia, but was reduced during exercise. Skeletal muscle atrophy occurred, but muscle structure and function were otherwise remarkably unaffected. Neurological deficits (cognition and memory) persisted after return to sea level, more so in those with high hypoxic ventilatory responsiveness, with motor function essentially spared. Nine percent body weight loss (despite an unrestricted diet) was mainly (67%) from muscle and exceeded the 2% predicted from energy intake–expenditure balance. Some immunological and lipid metabolic changes occurred, of uncertain

  9. Average [O II] nebular emission associated with Mg II absorbers: dependence on Fe II absorption

    NASA Astrophysics Data System (ADS)

    Joshi, Ravi; Srianand, Raghunathan; Petitjean, Patrick; Noterdaeme, Pasquier

    2018-05-01

    We investigate the effect of Fe II equivalent width (W2600) and fibre size on the average luminosity of [O II] λλ3727, 3729 nebular emission associated with Mg II absorbers (at 0.55 ≤ z ≤ 1.3) in the composite spectra of quasars obtained with 3 and 2 arcsec fibres in the Sloan Digital Sky Survey. We confirm the presence of strong correlations between [O II] luminosity (L_{[O II]}) and equivalent width (W2796) and redshift of Mg II absorbers. However, we show L_{[O II]} and average luminosity surface density suffer from fibre size effects. More importantly, for a given fibre size, the average L_{[O II]} strongly depends on the equivalent width of Fe II absorption lines and found to be higher for Mg II absorbers with R ≡W2600/W2796 ≥ 0.5. In fact, we show the observed strong correlations of L_{[O II]} with W2796 and z of Mg II absorbers are mainly driven by such systems. Direct [O II] detections also confirm the link between L_{[O II]} and R. Therefore, one has to pay attention to the fibre losses and dependence of redshift evolution of Mg II absorbers on W2600 before using them as a luminosity unbiased probe of global star formation rate density. We show that the [O II] nebular emission detected in the stacked spectrum is not dominated by few direct detections (i.e. detections ≥3σ significant level). On an average, the systems with R ≥ 0.5 and W2796 ≥ 2 Å are more reddened, showing colour excess E(B - V) ˜ 0.02, with respect to the systems with R < 0.5 and most likely trace the high H I column density systems.

  10. START II Frame Work

    DTIC Science & Technology

    1992-04-01

    Colonel Richard J. Barringer , USAF The Industrial College of the Armed Forces National Defense University Fort McNair, Washington, D.C. 20319-6000 93...Executive Research Project A94 START II Frame Work Lieutenant Colonel Donald E. Belche U.S. Air Force Faculty Research Advisor Colonel Richard J. Barringer ...1,659 - 3,456 0.48 Bombers 0.11 x 4,208 = 463 - 1,100 = 0.42 Total 9,064 2,248 - 5,956 = 0.38 charts 12 and 13 28 CHART 14 U.§ IA~aI ULA QC TU R AFTER 5

  11. Delta II Mars Pathfinder

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Final preparations for lift off of the DELTA II Mars Pathfinder Rocket are shown. Activities include loading the liquid oxygen, completing the construction of the Rover, and placing the Rover into the Lander. After the countdown, important visual events include the launch of the Delta Rocket, burnout and separation of the three Solid Rocket Boosters, and the main engine cutoff. The cutoff of the main engine marks the beginning of the second stage engine. After the completion of the second stage, the third stage engine ignites and then cuts off. Once the third stage engine cuts off spacecraft separation occurs.

  12. MULTIMEDIA ENVIRONMENTAL DISTRIBUTION OF TOXICS (MEND-TOX): PART II, SOFTWARE IMPLEMENTATION AND CASE STUDIES

    EPA Science Inventory

    An integrated hybrid spatial-compartmental simulator is presented for analyzing the dynamic distribution of chemicals in the multimedia environment. Information obtained from such analysis, which includes temporal chemical concentration profiles in various media, mass distribu...

  13. Human autoantibody to topoisomerase II.

    PubMed

    Hoffmann, A; Heck, M M; Bordwell, B J; Rothfield, N F; Earnshaw, W C

    1989-02-01

    The rheumatic diseases are characterized by the production of autoantibodies that are usually directed against components of the cell nucleus. In this communication, we describe autoantibodies that recognize DNA topoisomerase II (anti-topoII) present in the serum of a patient with systemic lupus erythematosus. Several lines of evidence indicate that this antibody recognizes topoisomerase II. First, it binds to the native enzyme in soluble extracts prepared from isolated chromosomes and effectively depletes such extracts of active enzyme. Second, the serum binds to topoisomerase II in immunoblots of mitotic chromosomes and chromosome scaffolds. Finally, the antiserum binds strongly to a fusion protein encoded by a cloned cDNA and expressed in Escherichia coli that (based on immunological evidence) represents the carboxy-terminal portion of chicken topoisomerase II. Autoantibodies such as the one described here may provide useful reagents for the study of human topoisomerase II.

  14. Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

    PubMed Central

    Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix

    2012-01-01

    Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we generated temporal DNA occupancy profiles by RNA polymerase II (Pol II) as well as profiles of the histone modifications H3K4me3 and H3K36me3. We used these data to quantify the relationships of phases and amplitudes between different marks. We found that rhythmic Pol II recruitment at promoters rather than rhythmic transition from paused to productive elongation underlies diurnal gene transcription, a conclusion further supported by modeling. Moreover, Pol II occupancy preceded mRNA accumulation by 3 hours, consistent with mRNA half-lives. Both methylation marks showed that the epigenetic landscape is highly dynamic and globally remodeled during the 24-hour cycle. While promoters of transcribed genes had tri-methylated H3K4 even at their trough activity times, tri-methylation levels reached their peak, on average, 1 hour after Pol II. Meanwhile, rhythms in tri-methylation of H3K36 lagged transcription by 3 hours. Finally, modeling profiles of Pol II occupancy and mRNA accumulation identified three classes of genes: one showing rhythmicity both in transcriptional and mRNA accumulation, a second class with rhythmic transcription but flat mRNA levels, and a third with constant transcription but rhythmic mRNAs. The latter class emphasizes widespread temporally gated posttranscriptional regulation in the mouse liver. PMID:23209382

  15. NSLS II Vacuum System

    SciT

    Ferreira, M.; Doom, L.; Hseuh, H.

    2009-09-13

    National Synchrotron Light Source II, being constructed at Brookhaven, is a 3-GeV, 500 mA, 3rd generation synchrotron radiation facility with ultra low emittance electron beams. The storage ring vacuum system has a circumference of 792 m and consists of over 250 vacuum chambers with a simulated average operating pressure of less than 1 x 10{sup -9} mbar. A summary of the update design of the vacuum system including girder supports of the chambers, gauges, vacuum pumps, bellows, beam position monitors and simulation of the average pressure will be shown. A brief description of the techniques and procedures for cleaning andmore » mounting the chambers are given.« less

  16. Effect of Cu(II), Cd(II) and Zn(II) on Pb(II) biosorption by algae Gelidium-derived materials.

    PubMed

    Vilar, Vítor J P; Botelho, Cidália M S; Boaventura, Rui A R

    2008-06-15

    Biosorption of Pb(II), Cu(II), Cd(II) and Zn(II) from binary metal solutions onto the algae Gelidium sesquipedale, an algal industrial waste and a waste-based composite material was investigated at pH 5.3, in a batch system. Binary Pb(II)/Cu(II), Pb(II)/Cd(II) and Pb(II)/Zn(II) solutions have been tested. For the same equilibrium concentrations of both metal ions (1 mmol l(-1)), approximately 66, 85 and 86% of the total uptake capacity of the biosorbents is taken by lead ions in the systems Pb(II)/Cu(II), Pb(II)/Cd(II) and Pb(II)/Zn(II), respectively. Two-metal results were fitted to a discrete and a continuous model, showing the inhibition of the primary metal biosorption by the co-cation. The model parameters suggest that Cd(II) and Zn(II) have the same decreasing effect on the Pb(II) uptake capacity. The uptake of Pb(II) was highly sensitive to the presence of Cu(II). From the discrete model it was possible to obtain the Langmuir affinity constant for Pb(II) biosorption. The presence of the co-cations decreases the apparent affinity of Pb(II). The experimental results were successfully fitted by the continuous model, at different pH values, for each biosorbent. The following sequence for the equilibrium affinity constants was found: Pb>Cu>Cd approximately Zn.

  17. Solar Type II Radio Bursts and IP Type II Events

    NASA Technical Reports Server (NTRS)

    Cane, H. V.; Erickson, W. C.

    2005-01-01

    We have examined radio data from the WAVES experiment on the Wind spacecraft in conjunction with ground-based data in order to investigate the relationship between the shocks responsible for metric type II radio bursts and the shocks in front of coronal mass ejections (CMEs). The bow shocks of fast, large CMEs are strong interplanetary (IP) shocks, and the associated radio emissions often consist of single broad bands starting below approx. 4 MHz; such emissions were previously called IP type II events. In contrast, metric type II bursts are usually narrowbanded and display two harmonically related bands. In addition to displaying complete dynamic spectra for a number of events, we also analyze the 135 WAVES 1 - 14 MHz slow-drift time periods in 2001-2003. We find that most of the periods contain multiple phenomena, which we divide into three groups: metric type II extensions, IP type II events, and blobs and bands. About half of the WAVES listings include probable extensions of metric type II radio bursts, but in more than half of these events, there were also other slow-drift features. In the 3 yr study period, there were 31 IP type II events; these were associated with the very fastest CMEs. The most common form of activity in the WAVES events, blobs and bands in the frequency range between 1 and 8 MHz, fall below an envelope consistent with the early signatures of an IP type II event. However, most of this activity lasts only a few tens of minutes, whereas IP type II events last for many hours. In this study we find many examples in the radio data of two shock-like phenomena with different characteristics that occur simultaneously in the metric and decametric/hectometric bands, and no clear example of a metric type II burst that extends continuously down in frequency to become an IP type II event. The simplest interpretation is that metric type II bursts, unlike IP type II events, are not caused by shocks driven in front of CMEs.

  18. National Synchrotron Light Source II

    Steve Dierker

    2017-12-09

    The National Synchrotron Light Source II (NSLS-II) at the U.S. Department of Energy's Brookhaven National Laboratory is a proposed new state-of-the-art medium energy storage ring designed to deliver world-leading brightness and flux with top-off operation

  19. Mastracchio during BASS II Setup

    2014-02-12

    ISS038-E-046381 (12 Feb. 2014) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, sets up the Microgravity Science Glovebox (MSG) for the Burning and Suppression of Solids (BASS-II) experiment in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  20. Hopkins during BASS II Setup

    2014-02-12

    ISS038-E-046393 (12 Feb. 2014) --- NASA astronaut Mike Hopkins, Expedition 38 flight engineer, sets up the Microgravity Science Glovebox (MSG) for the Burning and Suppression of Solids (BASS-II) experiment in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  1. Technology II: Implementation Planning Guide.

    ERIC Educational Resources Information Center

    California Community Colleges, Sacramento. Office of the Chancellor.

    The California Community Colleges (CCC) are facing a number of challenges, including the explosive use of the Internet, the digital divide, the need for integrating technology into teaching and learning, the impact of Tidal Wave II, and the need to ensure that technology is accessible to persons with disabilities. The CCCs' Technology II Strategic…

  2. PARIS II: DESIGNING GREENER SOLVENTS

    EPA Science Inventory

    PARIS II (the program for assisting the replacement of industrial solvents, version II), developed at the USEPA, is a unique software tool that can be used for customizing the design of replacement solvents and for the formulation of new solvents. This program helps users avoid ...

  3. Mastracchio during BASS II Setup

    2014-02-12

    ISS038-E-046387 (12 Feb. 2014) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, sets up the Microgravity Science Glovebox (MSG) for the Burning and Suppression of Solids (BASS-II) experiment in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  4. Hopkins during BASS II Setup

    2014-02-12

    ISS038-E-046394 (12 Feb. 2014) --- NASA astronaut Mike Hopkins, Expedition 38 flight engineer, sets up the Microgravity Science Glovebox (MSG) for the Burning and Suppression of Solids (BASS-II) experiment in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  5. Mastracchio during BASS II Setup

    2014-02-12

    ISS038-E-046391 (12 Feb. 2014) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, sets up the Microgravity Science Glovebox (MSG) for the Burning and Suppression of Solids (BASS-II) experiment in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  6. Compartmentalization, resource allocation, and wood quality

    Kevin T. Smith

    2015-01-01

    The concept of a trade-off of tree resources between growth and defense is readily grasped. The most detailed development of the concept is for the growth-differentiation balance hypothesis that predicts that resources for normal growth and primary metabolism are diverted to support plant defense and secondary or stress metabolism. This hypothesis has been applied to...

  7. RNA Polymerase II Elongation Control

    PubMed Central

    Zhou, Qiang; Li, Tiandao; Price, David H.

    2014-01-01

    Regulation of the elongation phase of transcription by RNA Polymerase II (Pol II) is utilized extensively to generate the pattern of mRNAs needed to specify cell types and to respond to environmental changes. After Pol II initiates, negative elongation factors cause it to pause in a promoter proximal position. These polymerases are poised to respond to the positive transcription elongation factor, P-TEFb, and then enter productive elongation only under the appropriate set of signals to generate full length properly processed mRNAs. Recent global analyses of Pol II and elongation factors, mechanisms that regulate P-TEFb involving the 7SK snRNP, factors that control both the negative and positive elongation properties of Pol II and the mRNA processing events that are coupled with elongation are discussed. PMID:22404626

  8. Use of a "Super-child" Approach to Assess the Vitamin A Equivalence of Moringa oleifera Leaves, Develop a Compartmental Model for Vitamin A Kinetics, and Estimate Vitamin A Total Body Stores in Young Mexican Children.

    PubMed

    Lopez-Teros, Veronica; Ford, Jennifer Lynn; Green, Michael H; Tang, Guangwen; Grusak, Michael A; Quihui-Cota, Luis; Muzhingi, Tawanda; Paz-Cassini, Mariela; Astiazaran-Garcia, Humberto

    2017-12-01

    Background: Worldwide, an estimated 250 million children <5 y old are vitamin A (VA) deficient. In Mexico, despite ongoing efforts to reduce VA deficiency, it remains an important public health problem; thus, food-based interventions that increase the availability and consumption of provitamin A-rich foods should be considered. Objective: The objectives were to assess the VA equivalence of 2 H-labeled Moringa oleifera (MO) leaves and to estimate both total body stores (TBS) of VA and plasma retinol kinetics in young Mexican children. Methods: β-Carotene was intrinsically labeled by growing MO plants in a 2 H 2 O nutrient solution. Fifteen well-nourished children (17-35 mo old) consumed puréed MO leaves (1 mg β-carotene) and a reference dose of [ 13 C 10 ]retinyl acetate (1 mg) in oil. Blood (2 samples/child) was collected 10 times (2 or 3 children each time) over 35 d. The bioefficacy of MO leaves was calculated from areas under the composite "super-child" plasma isotope response curves, and MO VA equivalence was estimated through the use of these values; a compartmental model was developed to predict VA TBS and retinol kinetics through the use of composite plasma [ 13 C 10 ]retinol data. TBS were also estimated with isotope dilution. Results: The relative bioefficacy of β-carotene retinol activity equivalents from MO was 28%; VA equivalence was 3.3:1 by weight (0.56 μmol retinol:1 μmol β-carotene). Kinetics of plasma retinol indicate more rapid plasma appearance and turnover and more extensive recycling in these children than are observed in adults. Model-predicted mean TBS (823 μmol) was similar to values predicted using a retinol isotope dilution equation applied to data from 3 to 6 d after dosing (mean ± SD: 832 ± 176 μmol; n = 7). Conclusions: The super-child approach can be used to estimate population carotenoid bioefficacy and VA equivalence, VA status, and parameters of retinol metabolism from a composite data set. Our results provide initial

  9. Rhizobium etli asparaginase II

    PubMed Central

    Huerta-Saquero, Alejandro; Evangelista-Martínez, Zahaed; Moreno-Enriquez, Angélica; Perez-Rueda, Ernesto

    2013-01-01

    Bacterial l-asparaginase has been a universal component of therapies for childhood acute lymphoblastic leukemia since the 1970s. Two principal enzymes derived from Escherichia coli and Erwinia chrysanthemi are the only options clinically approved to date. We recently reported a study of recombinant l-asparaginase (AnsA) from Rhizobium etli and described an increasing type of AnsA family members. Sequence analysis revealed four conserved motifs with notable differences with respect to the conserved regions of amino acid sequences of type I and type II l-asparaginases, particularly in comparison with therapeutic enzymes from E. coli and E. chrysanthemi. These differences suggested a distinct immunological specificity. Here, we report an in silico analysis that revealed immunogenic determinants of AnsA. Also, we used an extensive approach to compare the crystal structures of E. coli and E. chrysantemi asparaginases with a computational model of AnsA and identified immunogenic epitopes. A three-dimensional model of AsnA revealed, as expected based on sequence dissimilarities, completely different folding and different immunogenic epitopes. This approach could be very useful in transcending the problem of immunogenicity in two major ways: by chemical modifications of epitopes to reduce drug immunogenicity, and by site-directed mutagenesis of amino acid residues to diminish immunogenicity without reduction of enzymatic activity. PMID:22895060

  10. Delta II - SIRTF

    2003-03-06

    The Space Infrared Telescope Facility (SIRTF) is rotated to a vertical position in the clean room of Building AE today following its arrival from the Lockheed Martin plant in Sunnyvale, Calif. Final preparations for its launch aboard a Delta II rocket will now commence. SIRTF will obtain images and spectra by detecting the infrared energy, or heat, radiated by objects in space between wavelengths of 3 and 180 microns (1 micron is one-millionth of a meter). Most of this infrared radiation is blocked by the Earth's atmosphere and cannot be observed from the ground. Consisting of an 0.85-meter telescope and three cryogenically cooled science instruments, SIRTF is one of NASA's largest infrared telescopes to be launched. Its highly sensitive instruments will give a unique view of the Universe and peer into regions of space that are hidden from optical telescopes on the ground or orbiting telescopes such as the Hubble Space Telescope. SIRTF is scheduled for launch April 15 at 4:34:07 a.m. EDT from Launch Complex 17-B, Cape Canaveral Air Force Station.

  11. Delta II - SIRTF

    2003-03-06

    The Space Infrared Telescope Facility (SIRTF) is uncovered in the clean room of Building AE to permit workers access to the spacecraft to begin final preparations for its launch aboard a Delta II rocket. The observatory was shipped to Florida from the Lockheed Martin plant in Sunnyvale, Calif. SIRTF will obtain images and spectra by detecting the infrared energy, or heat, radiated by objects in space between wavelengths of 3 and 180 microns (1 micron is one-millionth of a meter). Most of this infrared radiation is blocked by the Earth's atmosphere and cannot be observed from the ground. Consisting of an 0.85-meter telescope and three cryogenically cooled science instruments, SIRTF is one of NASA's largest infrared telescopes to be launched. Its highly sensitive instruments will give a unique view of the Universe and peer into regions of space that are hidden from optical telescopes on the ground or orbiting telescopes such as the Hubble Space Telescope. SIRTF is scheduled for launch April 15 at 4:34:07 a.m. EDT from Launch Complex 17-B, Cape Canaveral Air Force Station.

  12. Delta II - SIRTF

    2003-03-06

    The Space Infrared Telescope Facility (SIRTF) arrived at Building AE today to begin final preparations for its launch aboard a Delta II rocket. The observatory was shipped to Florida from the Lockheed Martin plant in Sunnyvale, Calif. SIRTF will obtain images and spectra by detecting the infrared energy, or heat, radiated by objects in space between wavelengths of 3 and 180 microns (1 micron is one-millionth of a meter). Most of this infrared radiation is blocked by the Earth's atmosphere and cannot be observed from the ground. Consisting of an 0.85-meter telescope and three cryogenically cooled science instruments, SIRTF is one of NASA's largest infrared telescopes to be launched. Its highly sensitive instruments will give a unique view of the Universe and peer into regions of space that are hidden from optical telescopes on the ground or orbiting telescopes such as the Hubble Space Telescope. SIRTF is scheduled for launch April 15 at 4:34:07 a.m. EDT from Launch Complex 17-B, Cape Canaveral Air Force Station.

  13. Airborne Laser Hydrography II

    NASA Astrophysics Data System (ADS)

    Philpot, W.; Wozencraft, J.

    2016-02-01

    In 1985, Dr. Gary Guenther assembled the text, "Airborne Laser Hydrography" which quickly became a heavily used manual and guide for any and all scientists and engineers involved with airborne lidar bathymetry (ALB). It was a remarkable book that captured a snapshot of the state of the art of ALB and included historical developments, theoretical and modeling efforts as well as design characteristics and constraints, ending with accuracy assessment and a discussion of design tradeoffs. Known familiarly as the "Blue Book" it served the community remarkably well for many years. At 30 years of age, it is still a valued reference, but unavoidably dated in a field that has developed rapidly and nonstop over the intervening years. It is time for an update. The new text is attempt by the ALB community to update and expand upon Guenther's text. Like the original, Blue Book II reviews the historical developments in ALB, extending them into the 21st century, considers basic environmental water optical properties, theoretical developments, data processing and performance evaluation. All have progressed dramatically in the past 30 years. This paper presents an outline of the new book, a description of the contents, with emphasis on the theoretical models of the lidar waveform and its propagation through, and interaction with the water.

  14. A family of acetato-diphenoxo triply bridged dimetallic Zn(II)Ln(III) complexes: SMM behavior and luminescent properties.

    PubMed

    Oyarzabal, Itziar; Artetxe, Beñat; Rodríguez-Diéguez, Antonio; García, JoséÁngel; Seco, José Manuel; Colacio, Enrique

    2016-06-21

    Eleven dimetallic Zn(II)-Ln(III) complexes of the general formula [Zn(µ-L)(µ-OAc)Ln(NO3)2]·CH3CN (Ln(III) = Pr (1), Nd (2), Sm (3), Eu (4), Gd (5), Tb (6), Dy (7), Ho (8), Er (9), Tm (10), Yb (11)) have been prepared in a one-pot reaction from the compartmental ligand N,N'-dimethyl-N,N'-bis(2-hydroxy-3-formyl-5-bromo-benzyl)ethylenediamine (H2L). In all these complexes, the Zn(II) ions occupy the internal N2O2 site whereas the Ln(III) ions show preference for the O4 external site. Both metallic ions are bridged by an acetate bridge, giving rise to triple mixed diphenoxido/acetate bridged Zn(II)Ln(III) compounds. The Nd, Dy, Er and Yb complexes exhibit field induced single-ion magnet (SIM) behaviour, with Ueff values ranging from 14.12 to 41.55 K. The Er complex shows two relaxation processes, but only the second relaxation process with an energy barrier of 21.0 K has been characterized. The chromophoric L(2-) ligand is able to act as an "antenna" group, sensitizing the near-infrared (NIR) Nd(III) and Yb(III)-based luminescence in complexes 2 and 11 and therefore, both compounds can be considered as magneto-luminescent materials. In addition, the Sm(III), Eu(III) and Tb(III) derivatives exhibit characteristic emissions in the visible region.

  15. Retrovirus Epidemiology Donor Study-II (REDS-II)

    ClinicalTrials.gov

    2016-04-14

    Acquired Immunodeficiency Syndrome; Blood Donors; Blood Transfusion; HIV Infections; HIV-1; HIV-2; HTLV-I; HTLV-II; Retroviridae Infections; Hepatitis, Viral, Human; Hepatitis B; Hepacivirus; West Nile Virus

  16. BASS-II Hardware Repair

    2014-03-27

    ISS039-E-005726 (27 March 2014) --- Expedition 39 Flight Engineer Rick Mastracchio performs inflight maintenance on an experiment called Burning and Suppression of Solids (BASS)-II. The investigation examines the burning and extinction characteristics of a wide variety of fuel samples in microgravity. The BASS-II experiment will guide strategies for materials flammability screening for use in spacecraft as well as provide valuable data on solid fuel burning behavior in microgravity. BASS-II results contribute to the combustion computational models used in the design of fire detection and suppression systems in microgravity and on Earth.

  17. Dinuclear complexes containing linear M-F-M [M = Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II), Cd(II)] bridges: trends in structures, antiferromagnetic superexchange interactions, and spectroscopic properties.

    PubMed

    Reger, Daniel L; Pascui, Andrea E; Smith, Mark D; Jezierska, Julia; Ozarowski, Andrew

    2012-11-05

    The reaction of M(BF(4))(2)·xH(2)O, where M is Fe(II), Co(II), Ni(II), Cu(II), Zn(II), and Cd(II), with the new ditopic ligand m-bis[bis(3,5-dimethyl-1-pyrazolyl)methyl]benzene (L(m)*) leads to the formation of monofluoride-bridged dinuclear metallacycles of the formula [M(2)(μ-F)(μ-L(m)*)(2)](BF(4))(3). The analogous manganese(II) species, [Mn(2)(μ-F)(μ-L(m)*)(2)](ClO(4))(3), was isolated starting with Mn(ClO(4))(2)·6H(2)O using NaBF(4) as the source of the bridging fluoride. In all of these complexes, the geometry around the metal centers is trigonal bipyramidal, and the fluoride bridges are linear. The (1)H, (13)C, and (19)F NMR spectra of the zinc(II) and cadmium(II) compounds and the (113)Cd NMR of the cadmium(II) compound indicate that the metallacycles retain their structure in acetonitrile and acetone solution. The compounds with M = Mn(II), Fe(II), Co(II), Ni(II), and Cu(II) are antiferromagnetically coupled, although the magnitude of the coupling increases dramatically with the metal as one moves to the right across the periodic table: Mn(II) (-6.7 cm(-1)) < Fe(II) (-16.3 cm(-1)) < Co(II) (-24.1 cm(-1)) < Ni(II) (-39.0 cm(-1)) ≪ Cu(II) (-322 cm(-1)). High-field EPR spectra of the copper(II) complexes were interpreted using the coupled-spin Hamiltonian with g(x) = 2.150, g(y) = 2.329, g(z) = 2.010, D = 0.173 cm(-1), and E = 0.089 cm(-1). Interpretation of the EPR spectra of the iron(II) and manganese(II) complexes required the spin Hamiltonian using the noncoupled spin operators of two metal ions. The values g(x) = 2.26, g(y) = 2.29, g(z) = 1.99, J = -16.0 cm(-1), D(1) = -9.89 cm(-1), and D(12) = -0.065 cm(-1) were obtained for the iron(II) complex and g(x) = g(y) = g(z) = 2.00, D(1) = -0.3254 cm(-1), E(1) = -0.0153, J = -6.7 cm(-1), and D(12) = 0.0302 cm(-1) were found for the manganese(II) complex. Density functional theory (DFT) calculations of the exchange integrals and the zero-field splitting on manganese(II) and iron(II) ions were performed

  18. Integrated Procurement Management System, Version II

    NASA Technical Reports Server (NTRS)

    Collier, L. J.

    1985-01-01

    Integrated Procurement Management System, Version II (IPMS II) is online/ batch system for collecting developing, managing and disseminating procurementrelated data at NASA Johnson Space Center. Portions of IPMS II adaptable to other procurement situations.

  19. GeoGIS : phase II.

    DOT National Transportation Integrated Search

    2009-12-01

    A new web-based geotechnical Geographic Information System (GeoGIS) was developed and tested for the Alabama Department of Transportation (ALDOT) during Phase II of this research project. This web-based system stores geotechnical information about tr...

  20. Tier II Forms and Instructions

    EPA Pesticide Factsheets

    Facilities must comply with the new requirements on the Tier II emergency and hazardous chemical inventory form starting reporting year 2013, which is due by March 1, 2014. Some states may have specific requirements for reporting and submission.

  1. Konstantinov effect in helium II

    NASA Astrophysics Data System (ADS)

    Melnikovsky, L. A.

    2008-04-01

    The reflection of first and second sound waves by a rigid flat wall in helium II is considered. A nontrivial dependence of the reflection coefficients on the angle of incidence is obtained. Sound conversion is predicted at oblique incidence.

  2. Transition probabilities of Br II

    NASA Technical Reports Server (NTRS)

    Bengtson, R. D.; Miller, M. H.

    1976-01-01

    Absolute transition probabilities of the three most prominent visible Br II lines are measured in emission. Results compare well with Coulomb approximations and with line strengths extrapolated from trends in homologous atoms.

  3. A Bomber Fighter Duel (II)

    DTIC Science & Technology

    1949-07-25

    RAND 1 RESEARCH MEMORANDUM c: . A BOMBER FIGHTER DUEL (II) David Blackwell and Max Shiffiaan HM-193 • 25 July 1949 Copy No./c^JZ. . Thi...II) David Blackwell and Max Shiffman 0. Summary. This memorandum completes the study’of the fighteir- bomber duel described in RM-l65i» The... duel is one in which a fighter fires a single rocket burst at a bomber, which has limited ammunition, and defends itself by intermittent firing. It

  4. Mastracchio during BASS II Setup

    2014-02-12

    ISS038-E-046385 (12 Feb. 2014) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, uses a computer while setting up the Microgravity Science Glovebox (MSG) for the Burning and Suppression of Solids (BASS-II) experiment in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  5. Mu2e-II Injection from PIP-II

    SciT

    Neuffer, David

    We discuss injection of 800 MeV proton beam from PIP-II into the production target for Mu2e-II, assuming a targeting and μ production scenario similar to mu2e. The incoming beam trajectory must be modified from the mu2e parameters to match the focusing fields. Adding a vertical deflection at injection enables the injected beam to reach the target. Other differences from the mu2e system must be considered, including changes in the target structure, the radiation shielding and beam dump/absorber. H- beam should be stripped to p+. Other variations are discussed.

  6. EBR-II Data Digitization

    SciT

    Yoon, Su-Jong; Rabiti, Cristian; Sackett, John

    2014-08-01

    1. Objectives To produce a validation database out of those recorded signals it will be necessary also to identify the documents need to reconstruct the status of reactor at the time of the beginning of the recordings. This should comprehends the core loading specification (assemblies type and location and burn-up) along with this data the assemblies drawings and the core drawings will be identified. The first task of the project will be identify the location of the sensors, with respect the reactor plant layout, and the physical quantities recorded by the Experimental Breeder Reactor-II (EBR-II) data acquisition system. This firstmore » task will allow guiding and prioritizing the selection of drawings needed to numerically reproduce those signals. 1.1 Scopes and Deliverables The deliverables of this project are the list of sensors in EBR-II system, the identification of storing location of those sensors, identification of a core isotopic composition at the moment of the start of system recording. Information of the sensors in EBR-II reactor system was summarized from the EBR-II system design descriptions listed in Section 1.2.« less

  7. The II Zw 40 Supernebula

    NASA Astrophysics Data System (ADS)

    Leitherer, C.; Byler, N.; Lee, J. C.; Levesque, E. M.

    2017-11-01

    We obtained HST COS G140L spectroscopy of the enigmatic nearby blue compact dwarf galaxy II Zw 40. The galaxy hosts a nuclear super star cluster with a luminosity 10 times that of 30 Doradus, the most powerful giant HII region in the Local Group. The super star cluster has been suggested to be the ionizing source of a ”supernebula” detected via its free-free radiation in the radio. The physical conditions, however, are much more complex, as demonstrated by the detection of the nebular He II and the mid-infrared line of [O IV] 25.9. These lines are unlikely to be related to hot stars and require a different powering source. II Zw 40 shares many similarities with the related blue compact dwarfs NGC 5253 and Henize 2-10. However, II Zw 40’s UV spectrum is unique in terms of the exceptional strength of He II 1640, O III 1663 and CIII 1909. We determined reddening, age, and the stellar initial mass function and perform a comparison with the local benchmark 30 Doradus. Photoionization modeling is used to determine the origin of the nebular lines as due to stellar ionization, shocks, or powering by a black hole.

  8. Coordination of N,O-donor appended Schiff base ligand (H2L1) towards Zinc(II) in presence of pseudohalides: Syntheses, crystal structures, photoluminescence, antimicrobial activities and Hirshfeld surfaces

    NASA Astrophysics Data System (ADS)

    Majumdar, Dhrubajyoti; Biswas, Jayanta Kumar; Mondal, Monojit; Surendra Babu, M. S.; Metre, Ramesh K.; Das, Sourav; Bankura, Kalipada; Mishra, Dipankar

    2018-03-01

    A series of dinuclear Zn(II) complexes [Zn2 (L1) (CH3OH)2(SCN) (OAc)](1), [Zn2 (L1) (CH3OH)2(N3)2](2) and [Zn2 (L1) (Cl)2(CH3OH)]·CH3OH (3) have been synthesized by the reaction of compartmental Schiff base ligand (H2L1) [N,N‧-Bis(3-ethoxysalicylidenimino)-1,3-diaminopropane] with Zn(OAc)2·2H2O in presence of coligand like KSCN, NaN3 and NaCl respectively. X-ray diffraction analysis revealed that all the complexes are neutral and possess a 4-membered Zn2 (μ2-O)2 ring fastened by the unified coordination action of a doubly deprotonated ligand. In addition, solid state structure of the complexes display extensive intermolecular interaction which has been supported theoretically by Hirshfeld surface analysis with 2D Fingerprint plots. The synthesized Zn(II) metal complexes observed enhancement of luminescence emission compared to the parent Schiff base due to emanating ligand based intraligand (π→π∗) fluorescence. Additionally, Zn(II) metal complexes exhibited considerable antimicrobial potency against some important Gram +ve and Gram -ve bacteria.

  9. Type-II Dirac photons

    NASA Astrophysics Data System (ADS)

    Wang, Hai-Xiao; Chen, Yige; Hang, Zhi Hong; Kee, Hae-Young; Jiang, Jian-Hua

    2017-09-01

    The Dirac equation for relativistic electron waves is the parent model for Weyl and Majorana fermions as well as topological insulators. Simulation of Dirac physics in three-dimensional photonic crystals, though fundamentally important for topological phenomena at optical frequencies, encounters the challenge of synthesis of both Kramers double degeneracy and parity inversion. Here we show how type-II Dirac points—exotic Dirac relativistic waves yet to be discovered—are robustly realized through the nonsymmorphic screw symmetry. The emergent type-II Dirac points carry nontrivial topology and are the mother states of type-II Weyl points. The proposed all-dielectric architecture enables robust cavity states at photonic-crystal—air interfaces and anomalous refraction, with very low energy dissipation.

  10. Analysis of Magnetic Anisotropy and the Role of Magnetic Dilution in Triggering Single-Molecule Magnet (SMM) Behavior in a Family of CoII YIII Dinuclear Complexes with Easy-Plane Anisotropy.

    PubMed

    Palacios, María A; Nehrkorn, Joscha; Suturina, Elizaveta A; Ruiz, Eliseo; Gómez-Coca, Silvia; Holldack, Karsten; Schnegg, Alexander; Krzystek, Jurek; Moreno, José M; Colacio, Enrique

    2017-08-25

    Three new closely related Co II Y III complexes of general formula [Co(μ-L)(μ-X)Y(NO 3 ) 2 ] (X - =NO 3 - 1, benzoate 2, or 9-anthracenecarboxylato 3) have been prepared with the compartmental ligand N,N',N''-trimethyl-N,N''-bis(2-hydroxy-3-methoxy-5-methylbenzyl)diethylenetriamine (H 2 L). In these complexes, Co II and Y III are triply bridged by two phenoxide groups belonging to the di-deprotonated ligand (L 2- ) and one ancillary anion X - . The change of the ancillary bridging group connecting Co II and Y III ions induces small differences in the trigonally distorted CoN 3 O 3 coordination sphere with a concomitant tuning of the magnetic anisotropy and intermolecular interactions. Direct current magnetic, high-frequency and -field EPR (HFEPR), frequency domain Fourier transform THz electron paramagnetic resonance (FD-FT THz-EPR) measurements, and ab initio theoretical calculations demonstrate that Co II ions in compounds 1-3 have large and positive D values (≈50 cm -1 ), which decrease with increasing the distortion of the pseudo-octahedral Co II coordination sphere. Dynamic ac magnetic susceptibility measurements indicate that compound 1 exhibits field-induced single-molecule magnet (SMM) behavior, whereas compounds 2 and 3 only display this behavior when they are magnetically diluted with diamagnetic Zn II (Zn/Co=10:1). In view of this, it is always advisable to use magnetically diluted complexes, in which intermolecular interactions and quantum tunneling of magnetism (QTM) would be at least partly suppressed, so that "hidden single-ion magnet (SIM)" behavior could emerge. Field- and temperature-dependence of the relaxation times indicate the prevalence of the Raman process in all these complexes above approximately 3 K. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Propulsion Systems for Aircraft. Aerospace Education II. Instructional Unit II.

    ERIC Educational Resources Information Center

    Elmer, James D.

    This curriculum guide accompanies another publication in the Aerospace Education II series entitled "Propulsion Systems for Aircraft." The guide includes specific guidelines for teachers on each chapter in the textbook. Suggestions are included for objectives (traditional and behavioral), suggested outline, orientation, suggested key…

  12. Administrative Plans. STIP II (Skill Training Improvement Programs Round II).

    ERIC Educational Resources Information Center

    Los Angeles Community Coll. District, CA.

    Personnel policies, job responsibilities, and accounting procedures are summarized for the Los Angeles Community College District's Skill Training Improvement Programs (STIP II). This report first cites references to the established personnel and affirmative action procedures governing the program and then presents an organizational chart for the…

  13. 40 CFR Table II-1 to Subpart II of... - Emission Factors

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Emission Factors II Table II-1 to Subpart II of Part 98 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) MANDATORY GREENHOUSE GAS REPORTING Industrial Wastewater Treatment Pt. 98, Subpt. II, Table II-1...

  14. 40 CFR Table II-1 to Subpart II of... - Emission Factors

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Emission Factors II Table II-1 to Subpart II of Part 98 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) MANDATORY GREENHOUSE GAS REPORTING Industrial Wastewater Treatment Pt. 98, Subpt. II, Table II-1...

  15. Military Aerospace. Aerospace Education II.

    ERIC Educational Resources Information Center

    Smith, J. C.

    This book is a revised publication in the series on Aerospace Education II. It describes the employment of aerospace forces, their methods of operation, and some of the weapons and equipment used in combat and combat support activities. The first chapter describes some of the national objectives and policies served by the Air Force in peace and…

  16. Psychiatric Aide II. Instructor's Guide.

    ERIC Educational Resources Information Center

    Heimericks, Belinda K.

    This instructor's guide is for a Psychiatric Aide II course intended to provide Psychiatric Aids Is who have demonstrated expertise in giving basic nursing care to the mentally ill with more advanced nursing interventions and techniques. (It is assumed that all nursing care the aides provide is under the direction of a Registered Nurse.)…

  17. Recent results from DORIS II

    SciT

    Bloom, E.D.

    1985-01-01

    This report contains a brief review of recent results from the ARGUS and Crystal Ball experiments at DORIS II, concentrating on UPSILON(1S) and UPSILON(2S) spectroscopy with a short foray into ..gamma gamma.. physics. 18 refs., 10 figs.

  18. TREC Initiative with Cheshire II.

    ERIC Educational Resources Information Center

    Larson, Ray R.

    2001-01-01

    Describes the University of California at Berkeley's participation in the TREC (Text Retrieval Conference) interactive track experiments. Highlights include results of searches on two systems, Cheshire II and ZPRISE; system design goals and implementation; precision and recall results; search questions by topic and system; and results of…

  19. Teaching Statistics with Minitab II.

    ERIC Educational Resources Information Center

    Ryan, T. A., Jr.; And Others

    Minitab is a statistical computing system which uses simple language, produces clear output, and keeps track of bookkeeping automatically. Error checking with English diagnostics and inclusion of several default options help to facilitate use of the system by students. Minitab II is an improved and expanded version of the original Minitab which…

  20. Type-II Weyl semimetals.

    PubMed

    Soluyanov, Alexey A; Gresch, Dominik; Wang, Zhijun; Wu, QuanSheng; Troyer, Matthias; Dai, Xi; Bernevig, B Andrei

    2015-11-26

    Fermions--elementary particles such as electrons--are classified as Dirac, Majorana or Weyl. Majorana and Weyl fermions had not been observed experimentally until the recent discovery of condensed matter systems such as topological superconductors and semimetals, in which they arise as low-energy excitations. Here we propose the existence of a previously overlooked type of Weyl fermion that emerges at the boundary between electron and hole pockets in a new phase of matter. This particle was missed by Weyl because it breaks the stringent Lorentz symmetry in high-energy physics. Lorentz invariance, however, is not present in condensed matter physics, and by generalizing the Dirac equation, we find the new type of Weyl fermion. In particular, whereas Weyl semimetals--materials hosting Weyl fermions--were previously thought to have standard Weyl points with a point-like Fermi surface (which we refer to as type-I), we discover a type-II Weyl point, which is still a protected crossing, but appears at the contact of electron and hole pockets in type-II Weyl semimetals. We predict that WTe2 is an example of a topological semimetal hosting the new particle as a low-energy excitation around such a type-II Weyl point. The existence of type-II Weyl points in WTe2 means that many of its physical properties are very different to those of standard Weyl semimetals with point-like Fermi surfaces.

  1. 40 K Fastrac II Test

    NASA Technical Reports Server (NTRS)

    1997-01-01

    A 40 K Fastrac II duration test performed at Marshall Test Stand 116. The purpose of this test was to gauge the length of time between contact of TEA (Triethylenealuminum) and LOX (liquid oxygen) as an ignitor for the Fastrac engine.

  2. Case 22:Type II diabetes

    Diabetes mellitus is characterized by elevated blood glucose levels. It is composed of two types depending on the pathogenesis. Type I diabetes is characterized by insulin deficiency and usually has its onset during childhood or teenage years. This is also called ketosis-prone diabetes. Type II diab...

  3. National Synchrotron Light Source II

    Hill, John; Dooryhee, Eric; Wilkins, Stuart; Miller, Lisa; Chu, Yong

    2018-01-16

    NSLS-II is a synchrotron light source helping researchers explore solutions to the grand energy challenges faced by the nation, and open up new regimes of scientific discovery that will pave the way to discoveries in physics, chemistry, and biology — advances that will ultimately enhance national security and help drive the development of abundant, safe, and clean energy technologies.

  4. Application Programming in AWIPS II

    NASA Technical Reports Server (NTRS)

    Smit, Matt; McGrath, Kevin; Burks, Jason; Carcione, Brian

    2012-01-01

    Since its inception almost 8 years ago, NASA's Short-term Prediction Research and Transition (SPoRT) Center has integrated NASA data into the National Weather Service's decision support system (DSS) the Advanced Weather Interactive Processing System (AWIPS). SPoRT has, in some instances, had to shape and transform data sets into various formats and manipulate configurations to visualize them in AWIPS. With the advent of the next generation of DSS, AWIPS II, developers will be able to develop their own plugins to handle any type of data. Raytheon is developing AWIPS II to be a more extensible package written mainly in Java, and built around a Service Oriented Architecture. A plugin architecture will allow users to install their own code modules, and (if all the rules have been properly followed) they will work hand-in-hand with AWIPS II as if it were originally built in. Users can bring in new datasets with existing plugins, tweak plugins to handle a nuance or desired new functionality, or create an entirely new visualization layout for a new dataset. SPoRT is developing plugins to ensure its existing NASA data will be ready for AWIPS II when it is delivered, and to prepare for the future of new instruments on upcoming satellites.

  5. The Impact of IMPACT II.

    ERIC Educational Resources Information Center

    Mann, Dale

    IMPACT II is a teacher-to-teacher networking program designed to improve teaching in New York City schools. Teachers who have been working on new ideas that need more refinement are eligible for $300 grants offered to program developers. Teachers who would like to adopt ideas previously developed by the program may receive $200 as replicator…

  6. Adsorption of Pb(II), Cu(II), Cd(II), Zn(II), Ni(II), Fe(II), and As(V) on bacterially produced metal sulfides.

    PubMed

    Jong, Tony; Parry, David L

    2004-07-01

    The adsorption of Pb(II), Cu(II), Cd(II), Zn(II), Ni(II), Fe(II) and As(V) onto bacterially produced metal sulfide (BPMS) material was investigated using a batch equilibrium method. It was found that the sulfide material had adsorptive properties comparable with those of other adsorbents with respect to the specific uptake of a range of metals and, the levels to which dissolved metal concentrations in solution can be reduced. The percentage of adsorption increased with increasing pH and adsorbent dose, but decreased with increasing initial dissolved metal concentration. The pH of the solution was the most important parameter controlling adsorption of Cd(II), Cu(II), Fe(II), Ni(II), Pb(II), Zn(II), and As(V) by BPMS. The adsorption data were successfully modeled using the Langmuir adsorption isotherm. Desorption experiments showed that the reversibility of adsorption was low, suggesting high-affinity adsorption governed by chemisorption. The mechanism of adsorption for the divalent metals was thought to be the formation of strong, inner-sphere complexes involving surface hydroxyl groups. However, the mechanism for the adsorption of As(V) by BPMS appears to be distinct from that of surface hydroxyl exchange. These results have important implications to the management of metal sulfide sludge produced by bacterial sulfate reduction.

  7. Type II Supernova Spectral Diversity. II. Spectroscopic and Photometric Correlations

    NASA Astrophysics Data System (ADS)

    Gutiérrez, Claudia P.; Anderson, Joseph P.; Hamuy, Mario; González-Gaitan, Santiago; Galbany, Lluis; Dessart, Luc; Stritzinger, Maximilian D.; Phillips, Mark M.; Morrell, Nidia; Folatelli, Gastón

    2017-11-01

    We present an analysis of observed trends and correlations between a large range of spectral and photometric parameters of more than 100 type II supernovae (SNe II), during the photospheric phase. We define a common epoch for all SNe of 50 days post-explosion, where the majority of the sample is likely to be under similar physical conditions. Several correlation matrices are produced to search for interesting trends between more than 30 distinct light-curve and spectral properties that characterize the diversity of SNe II. Overall, SNe with higher expansion velocities are brighter, have more rapidly declining light curves, shorter plateau durations, and higher 56Ni masses. Using a larger sample than previous studies, we argue that “Pd”—the plateau duration from the transition of the initial to “plateau” decline rates to the end of the “plateau”—is a better indicator of the hydrogen envelope mass than the traditionally used optically thick phase duration (OPTd: explosion epoch to end of plateau). This argument is supported by the fact that Pd also correlates with s 3, the light-curve decline rate at late times: lower Pd values correlate with larger s 3 decline rates. Large s 3 decline rates are likely related to lower envelope masses, which enables gamma-ray escape. We also find a significant anticorrelation between Pd and s 2 (the plateau decline rate), confirming the long standing hypothesis that faster declining SNe II (SNe IIL) are the result of explosions with lower hydrogen envelope masses and therefore have shorter Pd values. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile; and the Gemini Observatory, Cerro Pachon, Chile (Gemini Program GS- 2008B-Q-56). Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile (ESO Programs 076.A-0156, 078.D-0048, 080.A-0516, and 082.A-0526).

  8. Binding Selectivity of Methanobactin from Methylosinus trichosporium OB3b for Copper(I), Silver(I), Zinc(II), Nickel(II), Cobalt(II), Manganese(II), Lead(II), and Iron(II)

    NASA Astrophysics Data System (ADS)

    McCabe, Jacob W.; Vangala, Rajpal; Angel, Laurence A.

    2017-12-01

    Methanobactin (Mb) from Methylosinus trichosporium OB3b is a member of a class of metal binding peptides identified in methanotrophic bacteria. Mb will selectively bind and reduce Cu(II) to Cu(I), and is thought to mediate the acquisition of the copper cofactor for the enzyme methane monooxygenase. These copper chelating properties of Mb make it potentially useful as a chelating agent for treatment of diseases where copper plays a role including Wilson's disease, cancers, and neurodegenerative diseases. Utilizing traveling wave ion mobility-mass spectrometry (TWIMS), the competition for the Mb copper binding site from Ag(I), Pb(II), Co(II), Fe(II), Mn(II), Ni(II), and Zn(II) has been determined by a series of metal ion titrations, pH titrations, and metal ion displacement titrations. The TWIMS analyses allowed for the explicit identification and quantification of all the individual Mb species present during the titrations and measured their collision cross-sections and collision-induced dissociation patterns. The results showed Ag(I) and Ni(II) could irreversibly bind to Mb and not be effectively displaced by Cu(I), whereas Ag(I) could also partially displace Cu(I) from the Mb complex. At pH ≈ 6.5, the Mb binding selectivity follows the order Ag(I)≈Cu(I)>Ni(II)≈Zn(II)>Co(II)>>Mn(II)≈Pb(II)>Fe(II), and at pH 7.5 to 10.4 the order is Ag(I)>Cu(I)>Ni(II)>Co(II)>Zn(II)>Mn(II)≈Pb(II)>Fe(II). Breakdown curves of the disulfide reduced Cu(I) and Ag(I) complexes showed a correlation existed between their relative stability and their compact folded structure indicated by their CCS. Fluorescence spectroscopy, which allowed the determination of the binding constant, compared well with the TWIMS analyses, with the exception of the Ni(II) complex. [Figure not available: see fulltext.

  9. Binding Selectivity of Methanobactin from Methylosinus trichosporium OB3b for Copper(I), Silver(I), Zinc(II), Nickel(II), Cobalt(II), Manganese(II), Lead(II), and Iron(II).

    PubMed

    McCabe, Jacob W; Vangala, Rajpal; Angel, Laurence A

    2017-12-01

    Methanobactin (Mb) from Methylosinus trichosporium OB3b is a member of a class of metal binding peptides identified in methanotrophic bacteria. Mb will selectively bind and reduce Cu(II) to Cu(I), and is thought to mediate the acquisition of the copper cofactor for the enzyme methane monooxygenase. These copper chelating properties of Mb make it potentially useful as a chelating agent for treatment of diseases where copper plays a role including Wilson's disease, cancers, and neurodegenerative diseases. Utilizing traveling wave ion mobility-mass spectrometry (TWIMS), the competition for the Mb copper binding site from Ag(I), Pb(II), Co(II), Fe(II), Mn(II), Ni(II), and Zn(II) has been determined by a series of metal ion titrations, pH titrations, and metal ion displacement titrations. The TWIMS analyses allowed for the explicit identification and quantification of all the individual Mb species present during the titrations and measured their collision cross-sections and collision-induced dissociation patterns. The results showed Ag(I) and Ni(II) could irreversibly bind to Mb and not be effectively displaced by Cu(I), whereas Ag(I) could also partially displace Cu(I) from the Mb complex. At pH ≈ 6.5, the Mb binding selectivity follows the order Ag(I)≈Cu(I)>Ni(II)≈Zn(II)>Co(II)>Mn(II)≈Pb(II)>Fe(II), and at pH 7.5 to 10.4 the order is Ag(I)>Cu(I)>Ni(II)>Co(II)>Zn(II)>Mn(II)≈Pb(II)>Fe(II). Breakdown curves of the disulfide reduced Cu(I) and Ag(I) complexes showed a correlation existed between their relative stability and their compact folded structure indicated by their CCS. Fluorescence spectroscopy, which allowed the determination of the binding constant, compared well with the TWIMS analyses, with the exception of the Ni(II) complex. Graphical abstract ᅟ.

  10. Three series of heterometallic NiII-LnIII Schiff base complexes: synthesis, crystal structures and magnetic characterization.

    PubMed

    Jiang, Lin; Liu, Yue; Liu, Xin; Tian, Jinlei; Yan, Shiping

    2017-09-26

    Three series of Ni II -Ln III complexes were synthesized with the general formulae [(μ 3 -CO 3 ) 2 {Ni(HL)(CH 3 -CH 2 OH)Ln(CH 3 COO)} 2 ]·2CH 3 CH 2 OH (1-6) (Ln = Tb (1), Dy (2), Ho (3), Er (4), Tm (5), Yb (6); H 3 L = N,N'-bis(3-methoxysalicylidene)-1,3-diamino-2-prop-anol), [Ni(HL)Ln(dbm) 3 ]·CH 3 OH 2 ·2CH 2 Cl 2 (7-10) (Ln = Tb (7), Eu (8), Gd (9), Ho (10); Hdbm = 1,3-diphenyl-1,3-propanedione) and [Ni(HL)(H 2 O)(tfa)Ln(hfac) 2 ] (11-15) (Ln = Tb (11), Dy (12), Eu (13), Gd (14), Ho (15); Hhfac = 1,1,1,5,5,5-hexafluoropentane-2,4-dione, tfa - = trifluoroacetate) using compartmental Schiff base ligands in conjunction with auxiliary ligands. For the NiLn series, the tetranuclear structure could be considered as two Ni II -Ln III dinuclear subunits bridged by two carbonates derived from atmospheric carbon dioxide. The Ln III ions of complexes 1-6 were octa-coordinated with distorted triangular dodecahedral geometry, while the Ln III ions of the dinuclear complexes 7-15 were nona-coordinated with distorted muffin geometry. The magnetic properties of the three series complexes were studied using dc and ac magnetic measurements. For the Ni II -Gd III complexes, the dc magnetic susceptibility measurements suggested the existence of the anticipated ferromagnetic interaction between Ni II and Gd III ions. The fitting of the χ M T vs. T data processed by PHI software provided the parameters g = 2.08 (J = +0.87 cm -1 ) for 9 and g = 2.02 (J = +1.83 cm -1 ) for 14. The interaction exchange was magneto-structurally correlated to the Ni-O-Gd angle (α) and Ni(μ-O)Gd dihedral angle (β). With an applied dc field, complexes 1 (Tb), 2 (Dy), 7 (Tb) and 12 (Dy) exhibited single magnetic relaxation with SMM parameters of U eff /k = 13.60 K, 11.52 K, 7.69 K and 5.14 K, respectively. Analysis of the Cole-Cole plots for complexes 2 and 7 suggested that a single relaxation process was mainly involved in the relaxation process, with α values in the range of 0.37-0.17 and 0

  11. TAF(II)250: a transcription toolbox.

    PubMed

    Wassarman, D A; Sauer, F

    2001-08-01

    Activation of RNA-polymerase-II-dependent transcription involves conversion of signals provided by gene-specific activator proteins into the synthesis of messenger RNA. This conversion requires dynamic structural changes in chromatin and assembly of general transcription factors (GTFs) and RNA polymerase II at core promoter sequence elements surrounding the transcription start site of genes. One hallmark of transcriptional activation is the interaction of DNA-bound activators with coactivators such as the TATA-box binding protein (TBP)-associated factors (TAF(II)s) within the GTF TFIID. TAF(II)250 possesses a variety of activities that are likely to contribute to the initial steps of RNA polymerase II transcription. TAF(II)250 is a scaffold for assembly of other TAF(II)s and TBP into TFIID, TAF(II)250 binds activators to recruit TFIID to particular promoters, TAF(II)250 regulates binding of TBP to DNA, TAF(II)250 binds core promoter initiator elements, TAF(II)250 binds acetylated lysine residues in core histones, and TAF(II)250 possesses protein kinase, ubiquitin-activating/conjugating and acetylase activities that modify histones and GTFs. We speculate that these activities achieve two goals--(1) they aid in positioning and stabilizing TFIID at particular promoters, and (2) they alter chromatin structure at the promoter to allow assembly of GTFs--and we propose a model for how TAF(II)250 converts activation signals into active transcription.

  12. PERMEABILITY OF BACTERIAL SPORES II.

    PubMed Central

    Gerhardt, Philipp; Black, S. H.

    1961-01-01

    Gerhardt, Philipp (University of Michigan, Ann Arbor) and S. H. Black. Permeability of bacterial spores. II. Molecular variables affecting solute permeation. J. Bacteriol. 82:750–760. 1961.—More than 100 compounds were tested for their uptake by dormant spores of a bacillus. The extent of penetration was found to be dependent on at least three molecular properties: (i) The dissociation of electrolytes usually resulted in high or low uptake predictable from their charge. (ii) Lipid insolubility restricted permeation of small molecules. (iii) The molecular weight of unsubstituted glycol and sugar polymers exponentially limited penetration to eventual exclusion at mol wt above 160,000. The results were plotted as a generalized curve, calculations from which permitted an interpretation that the effective spore surface contains pores varying in diameter from 10 to 200 A. PMID:13897940

  13. Belle II silicon vertex detector

    NASA Astrophysics Data System (ADS)

    Adamczyk, K.; Aihara, H.; Angelini, C.; Aziz, T.; Babu, V.; Bacher, S.; Bahinipati, S.; Barberio, E.; Baroncelli, Ti.; Baroncelli, To.; Basith, A. K.; Batignani, G.; Bauer, A.; Behera, P. K.; Bergauer, T.; Bettarini, S.; Bhuyan, B.; Bilka, T.; Bosi, F.; Bosisio, L.; Bozek, A.; Buchsteiner, F.; Casarosa, G.; Ceccanti, M.; Červenkov, D.; Chendvankar, S. R.; Dash, N.; Divekar, S. T.; Doležal, Z.; Dutta, D.; Enami, K.; Forti, F.; Friedl, M.; Hara, K.; Higuchi, T.; Horiguchi, T.; Irmler, C.; Ishikawa, A.; Jeon, H. B.; Joo, C. W.; Kandra, J.; Kang, K. H.; Kato, E.; Kawasaki, T.; Kodyš, P.; Kohriki, T.; Koike, S.; Kolwalkar, M. M.; Kvasnička, P.; Lanceri, L.; Lettenbicher, J.; Maki, M.; Mammini, P.; Mayekar, S. N.; Mohanty, G. B.; Mohanty, S.; Morii, T.; Nakamura, K. R.; Natkaniec, Z.; Negishi, K.; Nisar, N. K.; Onuki, Y.; Ostrowicz, W.; Paladino, A.; Paoloni, E.; Park, H.; Pilo, F.; Profeti, A.; Rashevskaya, I.; Rao, K. K.; Rizzo, G.; Rozanska, M.; Sandilya, S.; Sasaki, J.; Sato, N.; Schultschik, S.; Schwanda, C.; Seino, Y.; Shimizu, N.; Stypula, J.; Suzuki, J.; Tanaka, S.; Tanida, K.; Taylor, G. N.; Thalmeier, R.; Thomas, R.; Tsuboyama, T.; Uozumi, S.; Urquijo, P.; Vitale, L.; Volpi, M.; Watanuki, S.; Watson, I. J.; Webb, J.; Wiechczynski, J.; Williams, S.; Würkner, B.; Yamamoto, H.; Yin, H.; Yoshinobu, T.; Belle II SVD Collaboration

    2016-09-01

    The Belle II experiment at the SuperKEKB collider in Japan is designed to indirectly probe new physics using approximately 50 times the data recorded by its predecessor. An accurate determination of the decay-point position of subatomic particles such as beauty and charm hadrons as well as a precise measurement of low-momentum charged particles will play a key role in this pursuit. These will be accomplished by an inner tracking device comprising two layers of pixelated silicon detector and four layers of silicon vertex detector based on double-sided microstrip sensors. We describe herein the design, prototyping and construction efforts of the Belle-II silicon vertex detector.

  14. DCERP Annual Technical Report II

    DTIC Science & Technology

    2009-05-01

    information among the various DCERP partners . Research and monitoring activities during Phase II of DCERP are currently planned for 4 years (until...this information to improve scheduling of amphibious maneuvers in the NRE. Preliminary analysis of MCBCL air quality data indicated an increasing...2008 at the three MCBCL sites exceeded current National Ambient Air Quality Standards. Experimental results show that salt marshes bordering the

  15. ADIEM II end terminal for concrete barrier

    DOT National Transportation Integrated Search

    2001-03-01

    On September 9, 1997, an ADIEM II (Advanced Dynamic Impact Extension Module) was installed on Interstate 5 near Salem, Oregon. The ADIEM II offered a redirecting, energy-absorbing crash cushion and end treatment for portable and permanent protection ...

  16. Genetics Home Reference: carnitine palmitoyltransferase II deficiency

    MedlinePlus

    ... Zierz S. Muscle carnitine palmitoyltransferase II deficiency: clinical and molecular genetic features and diagnostic aspects. Arch Neurol. 2005 Jan; ... K, Hermann T, Zierz S. Carnitine palmitoyltransferase II deficiency: molecular and biochemical analysis of 32 ... Bulletins Genetics Home Reference Celebrates Its ...

  17. Testing the Gossamer Albatross II

    NASA Technical Reports Server (NTRS)

    1980-01-01

    The Gossamer Albatross II is seen here during a test flight at NASA's Dryden Flight Research Center, Edwards, California. The original Gossamer Albatross is best known for completing the first completely human powered flight across the English Channel on June 12, 1979. The Albatross II was the backup craft for the Channel flight. It was fitted with a small battery-powered electric motor and flight instruments for the NASA research program in low-speed flight. NASA completed its flight testing of the Gossamer Albatross II and began analysis of the results in April, 1980. During the six week program, 17 actual data gathering flights and 10 other flights were flown here as part of the joint NASA Langley/Dryden flight research program. The lightweight craft, carrying a miniaturized instrumentation system, was flown in three configurations; using human power, with a small electric motor, and towed with the propeller removed. Results from the program contributed to data on the unusual aerodynamic, performance, stability, and control characteristics of large, lightweight aircraft that fly at slow speeds for application to future high altitude aircraft. The Albatross' design and research data contributed to numerous later high altitude projects, including the Pathfinder.

  18. Synthesis, spectral, thermal and antimicrobial studies on cobalt(II), nickel(II), copper(II), zinc(II) and palladium(II) complexes containing thiosemicarbazone ligand

    NASA Astrophysics Data System (ADS)

    El-Sawaf, Ayman K.; El-Essawy, Farag; Nassar, Amal A.; El-Samanody, El-Sayed A.

    2018-04-01

    The coordination characteristic of new N4-morpholinyl isatin-3-thiosemicarbazone (HL) towards Co(II), Ni(II), Cu(II), Zn(II) and Pd(II) has been studies. The structures of the complexes were described by elemental analyses, molar conductivity, magnetic, thermal and spectral (IR, UV-Vis, 1H and 13C NMR and ESR) studies. On the basis of analytical and spectral studies the ligand behaves as monobasic tridentate ONS donor forming two five membered rings towards cobalt, copper and palladium and afforded complexes of the kind [M(L)X], (Mdbnd Co, Cu or Pd; Xdbnd Cl, Br or OAc). Whereas the ligand bound to NiCl2 as neutral tridentate ONS donor and with ZnCl2 as neutral bidentate NS donor. The newly synthesized thiosemicarbazone ligand and some of its complexes were examined for antimicrobial activity against 2 gram negative bacterial strains (Escherichia coli Pseudomonas and aeruginosa), 2 gram positive bacterial strains (Streptococcus pneumoniae and Staphylococcus aureus)} and two Pathogenic fungi (Aspergillus fumigatus and Candida albicans). All metal complexes possess higher antimicrobial activity comparing with the free thiosemicarbazone ligand. The high potent activities of the complexes may arise from the coordination and chelation, which tends to make metal complexes act as more controlling and potent antimicrobial agents, thus hindering the growing of the microorganisms. The antimicrobial results also show that copper bromide complex is better antimicrobial agent as compared to the Schiff base and its metal complexes.

  19. Macrocyclic receptor showing extremely high Sr(II)/Ca(II) and Pb(II)/Ca(II) selectivities with potential application in chelation treatment of metal intoxication.

    PubMed

    Ferreirós-Martínez, Raquel; Esteban-Gómez, David; Tóth, Éva; de Blas, Andrés; Platas-Iglesias, Carlos; Rodríguez-Blas, Teresa

    2011-04-18

    Herein we report a detailed investigation of the complexation properties of the macrocyclic decadentate receptor N,N'-Bis[(6-carboxy-2-pyridil)methyl]-4,13-diaza-18-crown-6 (H(2)bp18c6) toward different divalent metal ions [Zn(II), Cd(II), Pb(II), Sr(II), and Ca(II)] in aqueous solution. We have found that this ligand is especially suited for the complexation of large metal ions such as Sr(II) and Pb(II), which results in very high Pb(II)/Ca(II) and Pb(II)/Zn(II) selectivities (in fact, higher than those found for ligands widely used for the treatment of lead poisoning such as ethylenediaminetetraacetic acid (edta)), as well as in the highest Sr(II)/Ca(II) selectivity reported so far. These results have been rationalized on the basis of the structure of the complexes. X-ray crystal diffraction, (1)H and (13)C NMR spectroscopy, as well as theoretical calculations at the density functional theory (B3LYP) level have been performed. Our results indicate that for large metal ions such as Pb(II) and Sr(II) the most stable conformation is Δ(δλδ)(δλδ), while for Ca(II) our calculations predict the Δ(λδλ)(λδλ) form being the most stable one. The selectivity that bp18c6(2-) shows for Sr(II) over Ca(II) can be attributed to a better fit between the large Sr(II) ions and the relatively large crown fragment of the ligand. The X-ray crystal structure of the Pb(II) complex shows that the Δ(δλδ)(δλδ) conformation observed in solution is also maintained in the solid state. The Pb(II) ion is endocyclically coordinated, being directly bound to the 10 donor atoms of the ligand. The bond distances to the donor atoms of the pendant arms (2.55-2.60 Å) are substantially shorter than those between the metal ion and the donor atoms of the crown moiety (2.92-3.04 Å). This is a typical situation observed for the so-called hemidirected compounds, in which the Pb(II) lone pair is stereochemically active. The X-ray structures of the Zn(II) and Cd(II) complexes show that

  20. Spectroscopic and mycological studies of Co(II), Ni(II) and Cu(II) complexes with 4-aminoantipyrine derivative

    NASA Astrophysics Data System (ADS)

    Sharma, Amit Kumar; Chandra, Sulekh

    2011-10-01

    Complexes of the type [M(L)X 2], where M = Co(II), Ni(II) and Cu(II), have been synthesized with novel NO-donor Schiff's base ligand, 1,4-diformylpiperazine bis(4-imino-2,3-dimethyl-1-phenyl-3-pyrazolin-5-one) which is obtained by the acid catalyzed condensation of 1,4-diformylpiperazine with 4-aminoantipyrine. The elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, UV, NMR, mass and EPR studies of the compounds led to the conclusion that the ligand acts as tetradentate chelate. The Schiff's base ligand forms hexacoordinated complexes having octahedral geometry for Ni(II) and tetragonal geometry for Co(II) and Cu(II) complexes. The mycological studies of the compounds were examined against the several opportunistic pathogens, i.e., Alternaria brassicae, Aspergillus niger and Fusarium oxysporum. The Cu(II) complexes were found to have most fungicidal behavior.

  1. The complete nucleotide sequences of the 5 genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data.

    PubMed

    Greiner, Stephan; Wang, Xi; Herrmann, Reinhold G; Rauwolf, Uwe; Mayer, Klaus; Haberer, Georg; Meurer, Jörg

    2008-09-01

    A unique combination of genetic features and a rich stock of information make the flowering plant genus Oenothera an appealing model to explore the molecular basis of speciation processes including nucleus-organelle coevolution. From representative species, we have recently reported complete nucleotide sequences of the 5 basic and genetically distinguishable plastid chromosomes of subsection Oenothera (I-V). In nature, Oenothera plastid genomes are associated with 6 distinct, either homozygous or heterozygous, diploid nuclear genotypes of the 3 basic genomes A, B, or C. Artificially produced plastome-genome combinations that do not occur naturally often display interspecific plastome-genome incompatibility (PGI). In this study, we compare formal genetic data available from all 30 plastome-genome combinations with sequence differences between the plastomes to uncover potential determinants for interspecific PGI. Consistent with an active role in speciation, a remarkable number of genes have high Ka/Ks ratios. Different from the Solanacean cybrid model Atropa/tobacco, RNA editing seems not to be relevant for PGIs in Oenothera. However, predominantly sequence polymorphisms in intergenic segments are proposed as possible sources for PGI. A single locus, the bidirectional promoter region between psbB and clpP, is suggested to contribute to compartmental PGI in the interspecific AB hybrid containing plastome I (AB-I), consistent with its perturbed photosystem II activity.

  2. Synthesis of tin (II) oxide from tin (II) oxohydroxide

    NASA Astrophysics Data System (ADS)

    Kuznetsova, Svetlana; Lisitsa, Konstantin

    2017-11-01

    Sufficiently limited use of tin (II) oxide is associated with the difficulties of its preparation without impurities of tin (IV) oxide. Understanding the cause of the oxidation process will make it possible to develop methods for obtaining SnO without impurities. The influence of ammonium chloride concentration in the suspension on the oxide composition was investigated. The temperature of oxidation (400 °C) on the air and temperature decomposition in the argon (350 °C) of Sn6O4(OH)4 in the solid phase were determined by the thermal analysis method. The decomposition temperature of the oxyhydroxide in the suspension of ammonium chloride does not exceed 100 °C. An increase in the content of ammonium chloride in an aqueous solution leads to an increase i n the solubility of oxohydroxide and leads to an increase in pH. The suspensions of Sn6O4(OH)4 were subjected to heat treatment on a sand bath and under microwave irradiation. Samples of tin oxide were obtained. The quantitative composition of the mixture of tin oxides was determined. The research also highlights emphasizes that the oxidation of tin (II) to tin (IV) is associated with the dissolved oxygen content in the suspension.

  3. PEP-II Hardware Reliability

    SciT

    Allen, C. W.

    2005-04-28

    Hardware reliability takes on special importance in large accelerator facilities intended to work as factories; i.e., when they are expected to deliver design performance for extended periods of time. The PEP-II B-Factory at SLAC is such a facility. In this paper, we summarize PEP-II reliability statistics from the first four years of production running. The four running periods extended from January 12 through October 31, 2000, from February 4, 2001 through June 30, 2002, from November 15, 2002 through June 30, 2003, and from September 9, 2003 through July 31, 2004. These four periods are designated Runs 1, 2, 3,more » and 4 in the discussion and tables presented in the paper. The first four runs encompassed 30,359 hours. During this time, PEP-II was delivering luminosity to the BaBar detector 57.9 percent of the time. In addition, 5.3 percent of the time was used for scheduled dedicated machine development work, and 4.5 percent was scheduled off for maintenance, installations, or safety checks. Injection and tuning accounted for 19.9 percent. The remaining 12.4 percent was lost due to malfunctions. During this time period, a total of 9701 malfunctions were reported, but most did not interrupt the running program. The unscheduled down time, a total of 3883 hours, was attributed to 1724 of these malfunctions. Mean Time to Fail (MTTF) and Mean Time to Repair (MTTR) are presented for each of the major subsystems, and long-term availability trends are discussed.« less

  4. Structural alteration of hexagonal birnessite by aqueous Mn(II): Impacts on Ni(II) sorption

    SciT

    Lefkowitz, Joshua P.; Elzinga, Evert J.

    We studied the impacts of aqueous Mn(II) (1 mM) on the sorption of Ni(II) (200 μM) by hexagonal birnessite (0.1 g L- 1) at pH 6.5 and 7.5 with batch experiments and XRD, ATR-FTIR and Ni K-edge EXAFS analyses. In the absence of Mn(II)aq, sorbed Ni(II) was coordinated predominantly as triple corner-sharing complexes at layer vacancies at both pH values. Introduction of Mn(II)aq into Ni(II)-birnessite suspensions at pH 6.5 caused Ni(II) desorption and led to the formation of edge-sharing Ni(II) complexes. This was attributed to competitive displacement of Ni(II) from layer vacancies by either Mn(II) or by Mn(III) formed throughmore » interfacial Mn(II)-Mn(IV) comproportionation, and/or incorporation of Ni(II) into the birnessite lattice promoted by Mn(II)-catalyzed recrystallization of the sorbent. Similar to Mn(II)aq, the presence of HEPES or MES caused the formation of edge-sharing Ni(II) sorption complexes in Ni(II)-birnessite suspensions, which was attributed to partial reduction of the sorbent by the buffers. At pH 7.5, interaction with aqueous Mn(II) caused reductive transformation of birnessite into secondary feitknechtite that incorporated Ni(II), enhancing removal of Ni(II) from solution. These results demonstrate that reductive alteration of phyllomanganates may significantly affect the speciation and solubility of Ni(II) in anoxic and suboxic environments.« less

  5. Delta II JPSS-1 Rollback

    2017-11-13

    At Vandenberg Air Force Base in California, the gantry rolls back at Space Launch Complex 2 in preparation for the liftoff of the Joint Polar Satellite System-1, or JPSS-1, spacecraft. The United Launch Alliance Delta II rocket now is poised to boost the satellite to a polar orbit. Built by Ball Aerospace and Technologies Corp. of Boulder, Colorado, JPSS is the first in a series four next-generation environmental satellites in a collaborative program between NOAA and NASA. The satellite is scheduled to liftoff at 1:47 a.m. PST (4:47 a.m. EST), on Nov. 14, 2017.

  6. Manganese(II), iron(II), cobalt(II), and copper(II) complexes of an extended inherently chiral tris-bipyridyl cage.

    PubMed

    Perkins, David F; Lindoy, Leonard F; McAuley, Alexander; Meehan, George V; Turner, Peter

    2006-01-17

    Manganese(II), iron(II), cobalt(II), and copper(II) derivatives of two inherently chiral, Tris(bipyridyl) cages (L and L') of type [ML]-(PF(6))(2)(solvent)(n) and [FeL'](ClO(4))(2) are reported, where L is the hexa-tertiary butyl-substituted derivative of L'. These products were obtained by using the free cage and metal template procedures; the latter involved the reductive amination of the respective Tris-dialdehyde precursor complexes of iron(II), cobalt(II), or nickel(II). Electrochemical, EPR, and NMR studies have been used to probe the nature of the individual complexes. X-ray structures of the manganese(II), iron(II), and copper(II) complexes of L and the iron(II) complex of L' are presented; these are compared with the previously reported structures of the corresponding nickel(II) complex and metal-free cage (L). In each complex the metal cation occupies the cage's central cavity and is coordinated to six nitrogens from the three bipyridyl groups. The cations [MnL](2+) and [FeL](2+) are isostructural but both exhibit a different arrangement of the bound cage to that observed in the corresponding nickel(II) and copper(II) complexes. The latter have an exo-exo arrangement of the bridgehead nitrogen lone pairs, with the metal inducing a triple helical twist that extends approximately 22 A along the axial length of each complex. In contrast, [MnL](2+) and [FeL](2+) have their terminal nitrogen lone pairs directed endo, causing a significant change in the configuration of the bound ligand. In [FeL'](2+), the cage has both bridgehead nitrogen lone pairs orientated exo. Semiempirical calculations indicate that the observed endo-endo and exo-exo arrangements are of comparable energy.

  7. Solid Phase Extraction of Trace Al(III), Fe(II), Co(II), Cu(II), Cd(II) and Pb(II) Ions in Beverages on Functionalized Polymer Microspheres Prior to Flame Atomic Absorption Spectrometric Determinations.

    PubMed

    Berber, Hale; Alpdogan, Güzin

    2017-01-01

    In this study, poly(glycidyl methacrylate-methyl methacrylate-divinylbenzene) was synthesized in the form of microspheres, and then functionalized by 2-aminobenzothiazole ligand. The sorption properties of these functionalized microspheres were investigated for separation, preconcentration and determination of Al(III), Fe(II), Co(II), Cu(II), Cd(II) and Pb(II) ions using flame atomic absorption spectrometry. The optimum pH values for quantitative sorption were 2 - 4, 5 - 8, 6 - 8, 4 - 6, 2 - 6 and 2 - 3 for Al(III), Fe(II), Co(II), Cu(II), Cd(II) and Pb(II), respectively, and also the highest sorption capacity of the functionalized microspheres was found to be for Cu(II) with the value of 1.87 mmol g -1 . The detection limits (3σ; N = 6) obtained for the studied metals in the optimal conditions were observed in the range of 0.26 - 2.20 μg L -1 . The proposed method was successfully applied to different beverage samples for the determination of Al(III), Fe(II), Co(II), Cu(II), Cd(II) and Pb(II) ions, with the relative standard deviation of <3.7%.

  8. Image-derived and arterial blood sampled input functions for quantitative PET imaging of the angiotensin II subtype 1 receptor in the kidney

    SciT

    Feng, Tao; Tsui, Benjamin M. W.; Li, Xin

    Purpose: The radioligand {sup 11}C-KR31173 has been introduced for positron emission tomography (PET) imaging of the angiotensin II subtype 1 receptor in the kidney in vivo. To study the biokinetics of {sup 11}C-KR31173 with a compartmental model, the input function is needed. Collection and analysis of arterial blood samples are the established approach to obtain the input function but they are not feasible in patients with renal diseases. The goal of this study was to develop a quantitative technique that can provide an accurate image-derived input function (ID-IF) to replace the conventional invasive arterial sampling and test the method inmore » pigs with the goal of translation into human studies. Methods: The experimental animals were injected with [{sup 11}C]KR31173 and scanned up to 90 min with dynamic PET. Arterial blood samples were collected for the artery derived input function (AD-IF) and used as a gold standard for ID-IF. Before PET, magnetic resonance angiography of the kidneys was obtained to provide the anatomical information required for derivation of the recovery coefficients in the abdominal aorta, a requirement for partial volume correction of the ID-IF. Different image reconstruction methods, filtered back projection (FBP) and ordered subset expectation maximization (OS-EM), were investigated for the best trade-off between bias and variance of the ID-IF. The effects of kidney uptakes on the quantitative accuracy of ID-IF were also studied. Biological variables such as red blood cell binding and radioligand metabolism were also taken into consideration. A single blood sample was used for calibration in the later phase of the input function. Results: In the first 2 min after injection, the OS-EM based ID-IF was found to be biased, and the bias was found to be induced by the kidney uptake. No such bias was found with the FBP based image reconstruction method. However, the OS-EM based image reconstruction was found to reduce variance in the

  9. Diet History Questionnaire II FAQs | EGRP/DCCPS/NCI/NIH

    Cancer.gov

    Answers to general questions about the Diet History Questionnaire II (DHQ II), as well as those related to DHQ II administration, validation, scanning, nutrient estimates, calculations, DHQ II modification, data quality, and more.

  10. Stability of the human respiratory control system. II. Analysis of a three-dimensional delay state-space model.

    PubMed

    Batzel, J J; Tran, H T

    2000-07-01

    A number of mathematical models of the human respiratory control system have been developed since 1940 to study a wide range of features of this complex system. Among them, periodic breathing (including Cheyne-Stokes respiration and apneustic breathing) is a collection of regular but involuntary breathing patterns that have important medical implications. The hypothesis that periodic breathing is the result of delay in the feedback signals to the respiratory control system has been studied since the work of Grodins et al. in the early 1950's [1]. The purpose of this paper is to study the stability characteristics of a feedback control system of five differential equations with delays in both the state and control variables presented by Khoo et al. [4] in 1991 for modeling human respiration. The paper is divided in two parts. Part I studies a simplified mathematical model of two nonlinear state equations modeling arterial partial pressures of O2 and CO2 and a peripheral controller. Analysis was done on this model to illuminate the effect of delay on the stability. It shows that delay dependent stability is affected by the controller gain, compartmental volumes and the manner in which changes in the ventilation rate is produced (i.e., by deeper breathing or faster breathing). In addition, numerical simulations were performed to validate analytical results. Part II extends the model in Part I to include both peripheral and central controllers. This, however, necessitates the introduction of a third state equation modeling CO2 levels in the brain. In addition to analytical studies on delay dependent stability, it shows that the decreased cardiac output (and hence increased delay) resulting from the congestive heart condition can induce instability at certain control gain levels. These analytical results were also confirmed by numerical simulations.

  11. BNL ATF II beamlines design

    SciT

    Fedurin, M.; Jing, Y.; Stratakis, D.

    The Brookhaven National Laboratory. Accelerator Test Facility (BNL ATF) is currently undergoing a major upgrade (ATF-II). Together with a new location and much improved facilities, the ATF will see an upgrade in its major capabilities: electron beam energy and quality and CO 2 laser power. The electron beam energy will be increased in stages, first to 100-150 MeV followed by a further increase to 500 MeV. Combined with the planned increase in CO 2 laser power (from 1-100 TW), the ATF-II will be a powerful tool for Advanced Accelerator research. A high-brightness electron beam, produced by a photocathode gun, willmore » be accelerated and optionally delivered to multiple beamlines. Besides the energy range (up to a possible 500 MeV in the final stage) the electron beam can be tailored to each experiment with options such as: small transverse beam size (<10 um), short bunch length (<100 fsec) and, combined short and small bunch options. This report gives a detailed overview of the ATFII capabilities and beamlines configuration.« less

  12. The SRC-II process

    NASA Astrophysics Data System (ADS)

    Schmid, B. K.; Jackson, D. M.

    1981-03-01

    The Solvent Refined Coal (SRC-II) process which produces low-sulfur distillate fuel oil from coal is discussed. The process dissolves coal in a process-derived solvent at elevated temperature and pressure in the presence of hydrogen, separates the undissolved mineral residue, then recovers the original solvent by vacuum distillation. The distillate fuel oil produced is for use largely as a nonpolluting fuel for generating electrical power and steam and is expected to be competitive with petroleum fuels during the 1980s. During this period, the SRC-II fuel oil is expected to be attractive compared with combustion of coal with flue gas desulfurization in U.S. East Coast oil-burning power plants, as well as in small and medium-sized industrial boilers. The substantial quantities of methane, light hydrocarbons and naphtha produced by the process have value as feedstocks for preparation of pipeline gas, ethylene and high-octane unleaded gasoline, and can replace petroleum fractions in many applications. The liquid and gas products from a future large-scale plant, such as the 6000 t/day plant planned for Morgantown, West Virginia, are expected to have an overall selling price of $4.25 to $4.75/GJ.

  13. THE SPECTRUM OF Fe II

    SciT

    Nave, Gillian; Johansson, Sveneric, E-mail: gillian.nave@nist.gov

    2013-01-15

    The spectrum of singly ionized iron (Fe II) has been recorded using high-resolution Fourier transform (FT) and grating spectroscopy over the wavelength range 900 A to 5.5 {mu}m. The spectra were observed in high-current continuous and pulsed hollow cathode discharges using FT spectrometers at the Kitt Peak National Observatory, Tucson, AZ and Imperial College, London and with the 10.7 m Normal Incidence Spectrograph at the National Institute of Standards and Technology. Roughly 12,900 lines were classified using 1027 energy levels of Fe II that were optimized to measured wavenumbers. The wavenumber uncertainties of lines in the FT spectra range frommore » 10{sup -4} cm{sup -1} for strong lines around 4 {mu}m to 0.05 cm{sup -1} for weaker lines around 1500 A. The wavelength uncertainty of lines in the grating spectra is 0.005 A. The ionization energy of (130,655.4 {+-} 0.4) cm{sup -1} was estimated from the 3d{sup 6}({sup 5}D)5g and 3d{sup 6}({sup 5}D)6h levels.« less

  14. Quiet High Speed Fan II (QHSF II): Final Report

    NASA Technical Reports Server (NTRS)

    Kontos, Karen; Weir, Don; Ross, Dave

    2012-01-01

    This report details the aerodynamic, mechanical, structural design and fabrication of a Honey Engines Quiet High Speed Fan II (lower hub/tip ratio and higher specific flow than the Baseline I fan). This fan/nacelle system incorporates features such as advanced forward sweep and an advanced integrated fan/fan exit guide vane design that provides for the following characteristics: (1) Reduced noise at supersonic tip speeds, in comparison to current state-of-the-art fan technology; (2) Improved aeroelastic stability within the anticipated operating envelope; and (3) Aerodynamic performance consistent with current state-of-the-art fan technology. This fan was fabricated by Honeywell and tested in the NASA Glenn 9- by 15-Ft Low Speed Wind Tunnel for aerodynamic, aeromechanical, and acoustic performance.

  15. Synthesis, spectroscopic characterization, thermal analysis and electrical conductivity studies of Mg(II), Ca(II), Sr(II) and Ba(II) vitamin B2 complexes

    NASA Astrophysics Data System (ADS)

    Refat, Moamen S.; Moussa, Mohamed A. A.; Mohamed, Soha F.

    2011-05-01

    Riboflavin (RF) complexes of Mg(II), Ca(II), Sr(II) and Ba(II) were successfully synthesized. Structures of metal complexes obtained were confirmed and characterized by elemental analysis, molar conductance, and infrared spectra. DC electrical conductivity measurements indicated that the alkaline earth metal (II) complexes of RF ligand are non-electrolytes. Elemental analysis of chelates suggest that the metal(II) ligand ratio is 1:2 with structure formula as [M(RF) 2( X) 2]· nH 2O. Infrared assignments clearly show that RF ligand coordinated as a bidentate feature through azomethine nitrogen of pyrazine ring and C dbnd O of pyrimidine-2,4-dione. Thermal analyses of Mg(II), Ca(II), Sr(II) and Ba(II) complexes were investigated using (TG/DSC) under atmospheric nitrogen between 30 and 800 °C. The surface morphology of the complexes was studied by SEM. The electrical conductivities of RF and its metal complexes were also measured with DC electrical conductivity in the temperature range from room to 483 K.

  16. Synthesis, spectroscopic characterization, first order nonlinear optical properties and DFT calculations of novel Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) complexes with 1,3-diphenyl-4-phenylazo-5-pyrazolone ligand

    NASA Astrophysics Data System (ADS)

    Abdel-Latif, Samir A.; Mohamed, Adel A.

    2018-02-01

    Novel Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) metal ions with 1,3-diphenyl-4-phenylazo-5-pyrazolone (L) have been prepared and characterized using different analytical and spectroscopic techniques. 1:1 Complexes of Mn(II), Co(II) and Zn(II) are distorted octahedral whereas Ni(II) complex is square planar and Cu(II) is distorted trigonal bipyramid. 1:2 Complexes of Mn(II), Co(II), Cu(II) and Zn(II) are distorted trigonal bipyramid whereas Ni(II) complex is distorted tetrahedral. All complexes behave as non-ionic in dimethyl formamide (DMF). The electronic structure and nonlinear optical parameters (NLO) of the complexes were investigated theoretically at the B3LYP/GEN level of theory. Molecular stability and bond strengths have been investigated by applying natural bond orbital (NBO) analysis. The geometries of the studied complexes are non-planner. DFT calculations have been also carried out to calculate the global properties; hardness (η), global softness (S) and electronegativity (χ). The calculated small energy gap between HOMO and LUMO energies shows that the charge transfer occurs within the complexes. The total static dipole moment (μtot), the mean polarizability (<α>), the anisotropy of the polarizability (Δα) and the mean first-order hyperpolarizability (<β>) were calculated and compared with urea as a reference material. The complexes show implying optical properties.

  17. Shark class II invariant chain reveals ancient conserved relationships with cathepsins and MHC class II.

    PubMed

    Criscitiello, Michael F; Ohta, Yuko; Graham, Matthew D; Eubanks, Jeannine O; Chen, Patricia L; Flajnik, Martin F

    2012-03-01

    The invariant chain (Ii) is the critical third chain required for the MHC class II heterodimer to be properly guided through the cell, loaded with peptide, and expressed on the surface of antigen presenting cells. Here, we report the isolation of the nurse shark Ii gene, and the comparative analysis of Ii splice variants, expression, genomic organization, predicted structure, and function throughout vertebrate evolution. Alternative splicing to yield Ii with and without the putative protease-protective, thyroglobulin-like domain is as ancient as the MHC-based adaptive immune system, as our analyses in shark and lizard further show conservation of this mechanism in all vertebrate classes except bony fish. Remarkable coordinate expression of Ii and class II was found in shark tissues. Conserved Ii residues and cathepsin L orthologs suggest their long co-evolution in the antigen presentation pathway, and genomic analyses suggest 450 million years of conserved Ii exon/intron structure. Other than an extended linker preceding the thyroglobulin-like domain in cartilaginous fish, the Ii gene and protein are predicted to have largely similar physiology from shark to man. Duplicated Ii genes found only in teleosts appear to have become sub-functionalized, as one form is predicted to play the same role as that mediated by Ii mRNA alternative splicing in all other vertebrate classes. No Ii homologs or potential ancestors of any of the functional Ii domains were found in the jawless fish or lower chordates. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Chelation of Cu(II), Zn(II), and Fe(II) by tannin constituents of selected edible nuts.

    PubMed

    Karamać, Magdalena

    2009-12-22

    The tannin fractions isolated from hazelnuts, walnuts and almonds were characterised by colorimetric assays and by an SE-HPLC technique. The complexation of Cu(II) and Zn(II) was determined by the reaction with tetramethylmurexide, whereas for Fe(II), ferrozine was employed. The walnut tannins exhibited a significantly weaker reaction with the vanillin/HCl reagent than hazelnut and almond tannins, but the protein precipitation capacity of the walnut fraction was high. The SE-HPLC chromatogram of the tannin fraction from hazelnuts revealed the presence of oligomers with higher molecular weights compared to that of almonds. Copper ions were most effectively chelated by the constituents of the tannin fractions of hazelnuts, walnuts and almonds. At a 0.2 mg/assay addition level, the walnut tannins complexed almost 100% Cu(II). The Fe(II) complexation capacities of the tannin fractions of walnuts and hazelnuts were weaker in comparison to that of the almond tannin fraction, which at a 2.5 mg/assay addition level, bound Fe(II) by approximately 90%. The capacity to chelate Zn(II) was quite varied for the different nut tannin fractions: almond tannins bound as much as 84% Zn(II), whereas the value for walnut tannins was only 8.7%; and for hazelnut tannins, no Zn(II) chelation took place at the levels tested.

  19. Chelation of Cu(II), Zn(II), and Fe(II) by Tannin Constituents of Selected Edible Nuts

    PubMed Central

    Karamać, Magdalena

    2009-01-01

    The tannin fractions isolated from hazelnuts, walnuts and almonds were characterised by colorimetric assays and by an SE-HPLC technique. The complexation of Cu(II) and Zn(II) was determined by the reaction with tetramethylmurexide, whereas for Fe(II), ferrozine was employed. The walnut tannins exhibited a significantly weaker reaction with the vanillin/HCl reagent than hazelnut and almond tannins, but the protein precipitation capacity of the walnut fraction was high. The SE-HPLC chromatogram of the tannin fraction from hazelnuts revealed the presence of oligomers with higher molecular weights compared to that of almonds. Copper ions were most effectively chelated by the constituents of the tannin fractions of hazelnuts, walnuts and almonds. At a 0.2 mg/assay addition level, the walnut tannins complexed almost 100% Cu(II). The Fe(II) complexation capacities of the tannin fractions of walnuts and hazelnuts were weaker in comparison to that of the almond tannin fraction, which at a 2.5 mg/assay addition level, bound Fe(II) by ~90%. The capacity to chelate Zn(II) was quite varied for the different nut tannin fractions: almond tannins bound as much as 84% Zn(II), whereas the value for walnut tannins was only 8.7%; and for hazelnut tannins, no Zn(II) chelation took place at the levels tested. PMID:20054482

  20. Porous cellulosic adsorbent for the removal of Cd (II), Pb(II) and Cu(II) ions from aqueous media

    NASA Astrophysics Data System (ADS)

    Barsbay, Murat; Kavaklı, Pınar Akkaş; Tilki, Serhad; Kavaklı, Cengiz; Güven, Olgun

    2018-01-01

    The main objective of this work is to prepare a renewable cellulosic adsorbent by γ-initiated grafting of poly(glycidyl methacrylate) (PGMA) from cellulose substrate and subsequent modification of PGMA with chelating species, iminodiacetic acid (IDA), for Cd (II), Pb(II) and Cu(II) removal from aqueous media. Modification of PGMA grafted cellulose with IDA in aqueous solution under mild conditions has proceeded efficiently to yield a natural-based and effective porous adsorbent with well-defined properties as provided by the controlled polymerization technique, namely RAFT, applied during the radiation-induced graft copolymerization step and with sufficient degree of IDA immobilization as confirmed by XPS, FTIR, contact angle measurements and elemental analysis. In order to examine the Cd (II), Pb(II) and Cu(II) removing performance of the resulting adsorbent, batch experiments were carried out by ICP-MS. The adsorption capacities were determined as 53.4 mg Cd(II)/g polymer, 52.0 mg Pb(II)/g polymer and 69.6 mg Cu(II)/g polymer at initial feed concentration of 250 ppm, showing the promising potential of the natural-based adsorbent to steadily and efficiently chemisorb toxic metal ions.

  1. Electrochemical, spectroscopic, and photophysical properties of structurally diverse polyazine-bridged Ru(II),Pt(II) and Os(II),Ru(II),Pt(II) supramolecular motifs.

    PubMed

    Knoll, Jessica D; Arachchige, Shamindri M; Wang, Guangbin; Rangan, Krishnan; Miao, Ran; Higgins, Samantha L H; Okyere, Benjamin; Zhao, Meihua; Croasdale, Paul; Magruder, Katherine; Sinclair, Brian; Wall, Candace; Brewer, Karen J

    2011-09-19

    Five new tetrametallic supramolecules of the motif [{(TL)(2)M(dpp)}(2)Ru(BL)PtCl(2)](6+) and three new trimetallic light absorbers [{(TL)(2)M(dpp)}(2)Ru(BL)](6+) (TL = bpy = 2,2'-bipyridine or phen = 1,10-phenanthroline; M = Ru(II) or Os(II); BL = dpp = 2,3-bis(2-pyridyl)pyrazine, dpq = 2,3-bis(2-pyridyl)quinoxaline, or bpm = 2,2'-bipyrimidine) were synthesized and their redox, spectroscopic, and photophysical properties investigated. The tetrametallic complexes couple a Pt(II)-based reactive metal center to Ru and/or Os light absorbers through two different polyazine BL to provide structural diversity and interesting resultant properties. The redox potential of the M(II/III) couple is modulated by M variation, with the terminal Ru(II/III) occurring at 1.58-1.61 V and terminal Os(II/III) couples at 1.07-1.18 V versus Ag/AgCl. [{(TL)(2)M(dpp)}(2)Ru(BL)](PF(6))(6) display terminal M(dπ)-based highest occupied molecular orbitals (HOMOs) with the dpp(π*)-based lowest unoccupied molecular orbital (LUMO) energy relatively unaffected by the nature of BL. The coupling of Pt to the BL results in orbital inversion with localization of the LUMO on the remote BL in the tetrametallic complexes, providing a lowest energy charge separated (CS) state with an oxidized terminal Ru or Os and spatially separated reduced BL. The complexes [{(TL)(2)M(dpp)}(2)Ru(BL)](6+) and [{(TL)(2)M(dpp)}(2)Ru(BL)PtCl(2)](6+) efficiently absorb light throughout the UV and visible regions with intense metal-to-ligand charge transfer (MLCT) transitions in the visible at about 540 nm (M = Ru) and 560 nm (M = Os) (ε ≈ 33,000-42,000 M(-1) cm(-1)) and direct excitation to the spin-forbidden (3)MLCT excited state in the Os complexes about 720 nm. All the trimetallic and tetrametallic Ru-based supramolecular systems emit from the terminal Ru(dπ)→dpp(π*) (3)MLCT state, λ(max)(em) ≈ 750 nm. The tetrametallic systems display complex excited state dynamics with quenching of the (3)MLCT emission at

  2. Bacterial group II introns: not just splicing.

    PubMed

    Toro, Nicolás; Jiménez-Zurdo, José Ignacio; García-Rodríguez, Fernando Manuel

    2007-04-01

    Group II introns are both catalytic RNAs (ribozymes) and mobile retroelements that were discovered almost 14 years ago. It has been suggested that eukaryotic mRNA introns might have originated from the group II introns present in the alphaproteobacterial progenitor of the mitochondria. Bacterial group II introns are of considerable interest not only because of their evolutionary significance, but also because they could potentially be used as tools for genetic manipulation in biotechnology and for gene therapy. This review summarizes what is known about the splicing mechanisms and mobility of bacterial group II introns, and describes the recent development of group II intron-based gene-targetting methods. Bacterial group II intron diversity, evolutionary relationships, and behaviour in bacteria are also discussed.

  3. Elaboration of a Highly Porous RuII,II Analogue of HKUST-1.

    PubMed

    Zhang, Wenhua; Freitag, Kerstin; Wannapaiboon, Suttipong; Schneider, Christian; Epp, Konstantin; Kieslich, Gregor; Fischer, Roland A

    2016-12-19

    When the dinuclear Ru II,II precursor [Ru 2 (OOCCH 3 ) 4 ] is employed under redox-inert conditions, a Ru II,II analogue of HKUST-1 was successfully prepared and characterized as a phase-pure microcrystalline powder. X-ray absorption near-edge spectroscopy confirms the oxidation state of the Ru centers of the paddle-wheel nodes in the framework. The porosity of 1371 m 2 /mmol of Ru II,II -HKUST-1 exceeds that of the parent compound HKUST1 (1049 m 2 / mmol).

  4. Delta II SIRTF MST Rollback

    2003-08-24

    The mobile service tower is rolled back at Launch Pad 17-B, Cape Canaveral Air Force Station, to reveal NASA's Space Infrared Telescope Facility (SIRTF) ready for launch aboard a Delta II Heavy launch vehicle. Liftoff is scheduled for Aug. 25 at 1:35:39 a.m. EDT. SIRTF will obtain images and spectra by detecting the infrared energy, or heat, radiated by objects in space. Consisting of a 0.85-meter telescope and three cryogenically cooled science instruments, SIRTF will be the largest infrared telescope ever launched into space. It is the fourth and final element in NASA’s family of orbiting “Great Observatories.” Its highly sensitive instruments will give a unique view of the Universe and peer into regions of space that are hidden from optical telescopes.

  5. LIPIDS OF SARCINA LUTEA II.

    PubMed Central

    Albro, Phillip W.; Huston, Charles K.

    1964-01-01

    Albro, Phillip W. (Ft. Detrick, Frederick, Md.), and Charles K. Huston. Lipids of Sarcina lutea. II. Hydrocarbon content of the lipid extracts. J. Bacteriol. 88:981–986. 1964.—The hydrocarbon fraction from Sarcina lutea lipid extracts was characterized by a combination of thin-layer and gas-liquid chromatography and infrared spectroscopy. A total of 37 components were observed by gas-liquid chromatography of this material. A breakdown of the components into classes indicated a composition consisting of 88.9% n-saturates, 1.2% monoenes, 2.1% dienes, 5.0% trienes, and 0.6% branched-saturates. Less than 0.1% of the hydrocarbon material was aromatic. No attempt was made in this study to relate the composition to either origin or function in the cell. PMID:14222808

  6. Inhibitory effects of nitrite on the reactions of bovine carbonic anhydrase II with CO2 and bicarbonate consistent with zinc-bound nitrite.

    PubMed

    Nielsen, Per M; Fago, Angela

    2015-08-01

    Carbonic anhydrase (CA) is a zinc enzyme that catalyzes hydration of carbon dioxide (CO2) and dehydration of bicarbonate in red blood cells, thus facilitating CO2 transport and excretion. Bovine CA II may also react with nitrite to generate nitric oxide, although nitrite is a known inhibitor of the CO2 hydration reaction. To address the potential in vivo interference of these reactions and the nature of nitrite binding to the enzyme, we here investigate the inhibitory effect of 10-30 mM nitrite on Michaelis-Menten kinetics of CO2 hydration and bicarbonate dehydration by stopped-flow spectroscopy. Our data show that nitrite significantly affects the apparent dissociation constant KM for CO2 (11 mM) and bicarbonate (221 mM), and the turnover number kcat for the CO2 hydration (1.467 × 10(6) s(-1)) but not for the bicarbonate dehydration (7.927 × 10(5) s(-1)). These effects demonstrate mixed and competitive inhibition for the reaction with CO2 and bicarbonate, respectively, and are consistent with nitrite binding to the active site zinc. The high apparent dissociation constant found here for CO2, bicarbonate and nitrite (16-120 mM) are all overall consistent with published data and reveal a large capacity of free enzyme available for binding each of the three substrates at their in vivo levels, with little or no significant interference among reactions. The low affinity of the enzyme for nitrite suggests that the in vivo interaction between red blood cell CA II and nitrite requires compartmentalization at the anion exchanger protein of the red cell membrane to be physiologically relevant. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Telemetry Tests Of The Advanced Receiver II

    NASA Technical Reports Server (NTRS)

    Hinedi, Sami M.; Bevan, Roland P.; Marina, Miguel

    1993-01-01

    Report describes telemetry tests of Advanced Receiver II (ARX-II): digital radio receiving subsystem operating on intermediate-frequency output of another receiving subsystem called "multimission receiver" (MMR), detecting carrier, subcarrier, and data-symbol signals transmitted by spacecraft, and extracts Doppler information from signals. Analysis of data shows performance of MMR/ARX-II system comparable and sometimes superior to performances of Blk-III/BPA and Blk-III/SDA/SSA systems.

  8. The Type II Supernova Mechanism

    NASA Astrophysics Data System (ADS)

    Bruenn, Stephen W.

    1996-05-01

    Supernova 1987A has confirmed the basic core collapse paradigm for Type-II supernovae by the detection of electron antineutrinos in the Kamiokande II and IMB experiments several hours prior to the first optical sighting. Furthermore, the evidence of large-scale mixing and overturn in the debris of SN1987A indicates that hydrodynamic instabilities occurred early on in the evolution of the remnant and have played a crucial role in the explosion mechanism itself. Despite these important clues, and many years of theoretical and numerical investigation of increasing sophistication, the core collapse explosion mechanism is still not well understood. I review the status of the currently favored scenario, which is the transfer of energy from hot material at small radii to cooler material in the region further out behind the stalled shock by a combination of neutrino flow and hydrodynamic instabilities. The nature and role of these hydrodynamic instabilities is explored in detail on the basis of linear perturbation analyses and multidimensional hydrodynamic simulations. Neutrino flow is shown to have an inhibiting effect on convection in the region immediately below the neutrinosphere. Farther in, material is likely to be semiconvective for several hundred milliseconds, but stable thereafter. Convection in the neutrino heated-layer outside the neutrinosphere and below the shock front is found to help but by no means guarantee and explosion. General relativistic effects are shown to be deleterious for neutrino heated explosions. The role of the progenitor structure is discussed on the basis of two distinct but representative examples. Finally, the importance of several neutrino processes not incorporated in current calculations is assessed.

  9. 18F-Alfatide II and 18F-FDG Dual Tracer Dynamic PET for Parametric, Early Prediction of Tumor Response to Therapy

    PubMed Central

    Guo, Jinxia; Guo, Ning; Lang, Lixin; Kiesewetter, Dale O.; Xie, Qingguo; Li, Quanzheng; Eden, Henry S.; Niu, Gang; Chen, Xiaoyuan

    2014-01-01

    analysis in tumors showed significant decreases. For Abraxane therapy of MDA-MB-435 tumors, significant decrease was only observed with 18F-Alfatide II Bp value from kinetic analysis but not 18F-FDG influx. Conclusion The parameters fitted with compartmental modeling from the dual tracer dynamic imaging are consistent with those from single tracer imaging, substantiating the feasibility of this methodology. Even though no significant differences in tumor size were found until 5 days after doxorubicin treatment started, at day 3 there were already substantial differences in 18F-Alfatide II Bp and 18F-FDG influx rate. Dual tracer imaging can measure 18F-Alfatide II Bp value and 18F-FDG influx simultaneously to evaluate tumor angiogenesis and metabolism. Such changes are known to precede anatomical changes, and thus parametric imaging may offer the promise of early prediction of therapy response. PMID:24232871

  10. (18)F-alfatide II and (18)F-FDG dual-tracer dynamic PET for parametric, early prediction of tumor response to therapy.

    PubMed

    Guo, Jinxia; Guo, Ning; Lang, Lixin; Kiesewetter, Dale O; Xie, Qingguo; Li, Quanzheng; Eden, Henry S; Niu, Gang; Chen, Xiaoyuan

    2014-01-01

    or (18)F-FDG were observed, both (18)F-alfatide II Bp and (18)F-FDG influx from kinetic analysis in tumors showed significant decreases. For therapy of MDA-MB-435 tumors with paclitaxel protein-bound particles, a significant decrease was observed only with (18)F-alfatide II Bp value from kinetic analysis but not (18)F-FDG influx. The parameters fitted with compartmental modeling from the dual-tracer dynamic imaging are consistent with those from single-tracer imaging, substantiating the feasibility of this methodology. Even though no significant differences in tumor size were found until 5 d after doxorubicin treatment started, at day 3 there were already substantial differences in (18)F-alfatide II Bp and (18)F-FDG influx rate. Dual-tracer imaging can measure (18)F-alfatide II Bp value and (18)F-FDG influx simultaneously to evaluate tumor angiogenesis and metabolism. Such changes are known to precede anatomic changes, and thus parametric imaging may offer the promise of early prediction of therapy response.

  11. A phase II study of radioimmunotherapy with intraventricular 131 I-3F8 for medulloblastoma.

    PubMed

    Kramer, Kim; Pandit-Taskar, Neeta; Humm, John L; Zanzonico, Pat B; Haque, Sofia; Dunkel, Ira J; Wolden, Suzanne L; Donzelli, Maria; Goldman, Debra A; Lewis, Jason S; Lyashchenko, Serge K; Khakoo, Yasmin; Carrasquillo, Jorge A; Souweidane, Mark M; Greenfield, Jeffrey P; Lyden, David; De Braganca, Kevin D; Gilheeney, Stephen W; Larson, Steven M; Cheung, Nai-Kong V

    2018-01-01

    High-risk and recurrent medulloblastoma (MB) is associated with significant mortality. The murine monoclonal antibody 3F8 targets the cell-surface disialoganglioside GD2 on MB. We tested the efficacy, toxicity, and dosimetry of compartmental radioimmunotherapy (cRIT) with intraventricular 131 I-labeled 3F8 in patients with MB on a phase II clinical trial. Patients with histopathologically confirmed high-risk or recurrent MB were eligible for cRIT. After determining adequate cerebrospinal fluid (CSF) flow, patients received 2 mCi (where Ci is Curie) 124 I-3F8 or 131 I-3F8 with nuclear imaging for dosimetry, followed by up to four therapeutic (10 mCi/dose) 131 I-3F8 injections. Dosimetry estimates were based on serial CSF and blood samplings over 48 hr plus region-of-interest analyses on serial imaging scans. Disease evaluation included pre- and posttherapy brain/spine magnetic resonance imaging approximately every 3 months for the first year after treatment, and every 6-12 months thereafter. Forty-three patients received a total of 167 injections; 42 patients were evaluable for outcome. No treatment-related deaths occurred. Toxicities related to drug administration included acute bradycardia with somnolence, headache, fatigue, and CSF pleocytosis consistent with chemical meningitis and dystonic reaction. Total CSF absorbed dose was 1,453 cGy (where Gy is Gray; 350.0-2,784). Median overall survival from first dose of cRIT was 24.9 months (95% confidence interval [CI]:16.3-55.8). Patients treated in radiographic and cytologic remission were at a lower risk of death compared to patients with radiographically measurable disease (hazard ratio: 0.40, 95% CI: 0.18-0.88, P = 0.024). cRIT with 131 I-3F8 is safe, has favorable dosimetry to CSF, and when added to salvage therapy using conventional modalities, may have clinical utility in maintaining remission in high-risk or recurrent MB. © 2017 Wiley Periodicals, Inc.

  12. Angiotensin II in Refractory Septic Shock.

    PubMed

    Antonucci, Elio; Gleeson, Patrick J; Annoni, Filippo; Agosta, Sara; Orlando, Sergio; Taccone, Fabio Silvio; Velissaris, Dimitrios; Scolletta, Sabino

    2017-05-01

    Refractory septic shock is defined as persistently low mean arterial blood pressure despite volume resuscitation and titrated vasopressors/inotropes in patients with a proven or suspected infection and concomitant organ dysfunction. Its management typically requires high doses of catecholamines, which can induce significant adverse effects such as ischemia and arrhythmias. Angiotensin II (Ang II), a key product of the renin-angiotensin-aldosterone system, is a vasopressor agent that could be used in conjunction with other vasopressors to stabilize critically ill patients during refractory septic shock, and reduce catecholamine requirements. However, very few clinical data are available to support Ang II administration in this setting. Here, we review the current literature on this topic to better understand the role of Ang II administration during refractory septic shock, differentiating experimental from clinical studies. We also consider the potential role of exogenous Ang II administration in specific organ dysfunction and possible pitfalls with Ang II in sepsis. Various issues remain unresolved and future studies should investigate important topics such as: the optimal dose and timing of Ang II administration, a comparison between Ang II and the other vasopressors (epinephrine; vasopressin), and Ang II effects on microcirculation.

  13. Structural, spectroscopic and thermal characterization of 2-tert-butylaminomethylpyridine-6-carboxylic acid methylester and its Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and UO(2)(II) complexes.

    PubMed

    Mohamed, Gehad G; El-Gamel, Nadia E A

    2005-04-01

    Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and UO(2)(II) complexes with the ligand 2-tert-butylaminomethylpyridine-6-carboxylic acid methylester (HL(2)) have been prepared and characterized by elemental analyses, molar conductance, magnetic moment, thermal analysis and spectral data. 1:1 M:HL(2) complexes, with the general formula [M(HL(2))X(2)].nH(2)O (where M = Co(II) (X = Cl, n = 0), Ni(II) (X = Cl, n = 3), Cu(II) (grey colour, X = AcO, n = 1), Cu(II) (yellow colour, X = Cl, n = 0) and Zn(II) (X = Br, n = 0). In addition, the Fe(III) and UO(2)(II) complexes of the type 1:2 M:HL(2) and with the formulae [Fe(L(2))(2)]Cl and [UO(2)(HL(2))(2)](NO(3))(2) are prepared. From the IR data, it is seen that HL(2) ligand behaves as a terdentate ligand coordinated to the metal ions via the pyridyl N, carboxylate O and protonated NH group; except the Fe(III) complex, it coordinates via the deprotonated NH group. This is supported by the molar conductance data, which show that all the complexes are non-electrolytes, while the Fe(III) and UO(2)(II) complexes are 1:1 electrolytes. IR and H1-NMR spectral studies suggest a similar behaviour of the Zn(II) complex in solid and solution states. From the solid reflectance spectral data and magnetic moment measurements, the complexes have a trigonal bipyramidal (Co(II), Ni(II), Cu(II) and Zn(II) complexes) and octahedral (Fe(III), UO(2)(II) complexes) geometrical structures. The thermal behaviour of the complexes is studied and the different dynamic parameters are calculated applying Coats-Redfern equation.

  14. Free metal ion depletion by "Good's" buffers. III. N-(2-acetamido)iminodiacetic acid, 2:1 complexes with zinc(II), cobalt(II), nickel(II), and copper(II); amide deprotonation by Zn(II), Co(II), and Cu(II).

    PubMed

    Lance, E A; Rhodes, C W; Nakon, R

    1983-09-01

    Potentiometric, visible, infrared, electron spin, and nuclear magnetic resonance studies of the complexation of N-(2-acetamido)iminodiacetic acid (H2ADA) by Ca(II), Mg(II), Mn(II), Zn(II), Co(II), Ni(II), and Cu(II) are reported. Ca(II) and Mg(II) were found not to form 2:1 ADA2- to M(II) complexes, while Mn(II), Cu(II), Ni(II), Zn(II), and Co(II) did form 2:1 metal chelates at or below physiological pH values. Co(II) and Zn(II), but not Cu(II), were found to induce stepwise deprotonation of the amide groups to form [M(H-1ADA)4-(2)]. Formation (affinity) constants for the various metal complexes are reported, and the probable structures of the various metal chelates in solution are discussed on the basis of various spectral data.

  15. MHC class II expression in lung cancer.

    PubMed

    He, Yayi; Rozeboom, Leslie; Rivard, Christopher J; Ellison, Kim; Dziadziuszko, Rafal; Yu, Hui; Zhou, Caicun; Hirsch, Fred R

    2017-10-01

    Immunotherapy is an exciting development in lung cancer research. In this study we described major histocompatibility complex (MHC) Class II protein expression in lung cancer cell lines and patient tissues. We studied MHC Class II (DP, DQ, DR) (CR3/43, Abcam) protein expression in 55 non-small cell lung cancer (NSCLC) cell lines, 42 small cell lung cancer (SCLC) cell lines and 278 lung cancer patient tissues by immunohistochemistry (IHC). Seven (12.7%) NSCLC cell lines were positive for MHC Class II. No SCLC cell lines were found to be MHC Class II positive. We assessed 139 lung cancer samples available in the Hirsch Lab for MHC Class II. There was no positive MHC Class II staining on SCLC tumor cells. MHC Class II expression on TILs in SCLC was significantly lower than that on TILs in NSCLC (P<0.001). MHC Class II was also assessed in an additional 139 NSCLC tumor tissues from Medical University of Gdansk, Poland. Patients with positive staining of MHC Class II on TILs had longer regression-free survival (RFS) and overall survival (OS) than those whose TILs were MHC Class II negative (2.980 years, 95% CI 1.628-4.332 vs. 1.050 years, 95% CI 0.556-1.554, P=0.028) (3.230 years, 95% CI 2.617-3.843 vs. 1.390 years, 95% CI 0.629-2.151, P=0.014). MHC Class II was expressed both in NSCLC cell lines and tissues. However, MHC Class II was not detected in SCLC cell lines or tissue tumor cells. MHC Class II expression was lower on SCLC TILs than on NSCLC TILs. Loss of expression of MHC Class II on SCLC tumor cells and reduced expression on SCLC TILs may be a means of escaping anti-cancer immunity. Higher MHC Class II expression on TILs was correlated with better prognosis in patients with NSCLC. Copyright © 2017. Published by Elsevier B.V.

  16. Competitive adsorption of copper(II), cadmium(II), lead(II) and zinc(II) onto basic oxygen furnace slag.

    PubMed

    Xue, Yongjie; Hou, Haobo; Zhu, Shujing

    2009-02-15

    Polluted and contaminated water can often contain more than one heavy metal species. It is possible that the behavior of a particular metal species in a solution system will be affected by the presence of other metals. In this study, we have investigated the adsorption of Cd(II), Cu(II), Pb(II), and Zn(II) onto basic oxygen furnace slag (BOF slag) in single- and multi-element solution systems as a function of pH and concentration, in a background solution of 0.01M NaNO(3). In adsorption edge experiments, the pH was varied from 2.0 to 13.0 with total metal concentration 0.84mM in the single element system and 0.21mM each of Cd(II), Cu(II), Pb(II), and Zn(II) in the multi-element system. The value of pH(50) (the pH at which 50% adsorption occurs) was found to follow the sequence Zn>Cu>Pb>Cd in single-element systems, but Pb>Cu>Zn>Cd in the multi-element system. Adsorption isotherms at pH 6.0 in the multi-element systems showed that there is competition among various metals for adsorption sites on BOF slag. The adsorption and potentiometric titrations data for various slag-metal systems were modeled using an extended constant-capacitance surface complexation model that assumed an ion-exchange process below pH 6.5 and the formation of inner-sphere surface complexes at higher pH. Inner-sphere complexation was more dominant for the Cu(II), Pb(II) and Zn(II) systems.

  17. Angiotensin II-mediated microvascular thrombosis

    PubMed Central

    Senchenkova, Elena Y.; Russell, Janice; Almeida-Paula, Lidiana D.; Harding, Joseph W.; Granger, D. Neil

    2010-01-01

    Hypertension is associated with an increased risk of thrombosis that appears to involve an interaction between the renin-angiotensin system and hemostasis. In this study we determined whether angiotensin II-mediatedthrombosis occurs in arterioles and/or venules, and assessed the involvement of type-1 (AT1), type-2 (AT2) and type 4 (AT4) angiotensin II receptors, as well as receptors for endothelin-1 (ET-1) and bradykinin (BK-1, BK-2) in angiotensin II-enhanced microvascular thrombosis. Thrombus development in mouse cremaster microvessels was quantified after light/dye injury using the time of onset of the thrombus and time to blood flow cessation. Wild type and AT1-receptor deficient mice were implanted with an angiotensin II-loaded Alzet pump for 2 wks. Angiotensin II administration in both wild type and AT1-receptor deficient mice significantly accelerated thrombosis in arterioles. Genetic deficiency and pharmacological antagonism of AT1-receptors did not alter the thrombosis response to angiotensin II. Isolated murine platelets aggregated in response to low (pM), but not high (nM), concentrations of angiotensin II. The platelet aggregation response to angiotensin II was dependent on AT1-receptors. Antagonism of AT2-receptors in vivo significantly prolonged the onset of angiotensin II enhanced thrombosis, while an AT4-receptor antagonist prolonged the time to flow cessation. Selective antagonism of either ET-1 or BK-1 receptors largely prevented both the onset and flow cessation responses to chronic angiotensin II infusion. Our findings indicate that angiotensin II-induced hypertension is accompanied by enhanced thrombosis in arterioles and this response is mediated by a mechanism that involves AT2, AT4, BK-1 and ET-1 receptor-mediated signaling. PMID:20975035

  18. Composition, Characterization and Antibacterial activity of Mn(II), Co(II),Ni(II), Cu(II) Zn(II) and Cd(II) mixed ligand complexes Schiff base derived from Trimethoprim with 8-Hydroxy quinoline

    NASA Astrophysics Data System (ADS)

    Numan, Ahmed T.; Atiyah, Eman M.; Al-Shemary, Rehab K.; Ulrazzaq, Sahira S. Abd

    2018-05-01

    New Schiff base ligand 2-((4-amino-5-(3, 4, 5-trimethoxybenzyl) pyrimidin-2-ylimino) (phenyl)methyl)benzoic acid] = [HL] was synthesized using microwave irradiation trimethoprim and 2-benzoyl benzoic acid. Mixed ligand complexes of Mn((II), Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) are reacted in ethanol with Schiff base ligand [HL] and 8-hydroxyquinoline [HQ] then reacted with metal salts in ethanol as a solvent in (1:1:1) ratio. The ligand [HL] is characterized by FTIR, UV-Vis, melting point, elemental microanalysis (C.H.N), 1H-NMR, 13C-NMR, and mass spectra. The mixed ligand complexes are characterized by infrared spectra, electronic spectra, (C.H.N), melting point, atomic absorption, molar conductance and magnetic moment measurements. These measurements indicate that the ligand [HL] coordinates with metal (II) ion in a tridentate manner through the oxygen and nitrogen atoms of the ligand, octahedral structures are suggested for these complexes. Antibacterial activity of the ligands [HL], [HQ] and their complexes are studied against (gram positive) and (gram negative) bacteria.

  19. Preschool Racial Attitude Measure II (PRAM II): Technical Report #1: 1970-71 Standardization Study.

    ERIC Educational Resources Information Center

    Williams, John E.

    This report provides detailed technical information concerning the Preschool Racial Attitude Measure II (PRAM II) a method for assessing the attitudes of pre-literate children toward light- and dark-skinned individuals. Several major changes were involved in the PRAM II revision: (1) the length was doubled, (2) the general artistic quality of the…

  20. 40 CFR Table II-2 to Subpart II - Collection Efficiencies of Anaerobic Processes

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Collection Efficiencies of Anaerobic Processes II Table II-2 to Subpart II Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) MANDATORY GREENHOUSE GAS REPORTING Industrial Wastewater Treatment Pt. 98...

  1. 40 CFR Table II-2 to Subpart II - Collection Efficiencies of Anaerobic Processes

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Collection Efficiencies of Anaerobic Processes II Table II-2 to Subpart II Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) MANDATORY GREENHOUSE GAS REPORTING Industrial Wastewater Treatment Pt. 98...

  2. World War II Homefront: A Historiography.

    ERIC Educational Resources Information Center

    Winkler, Allan M.

    2002-01-01

    Highlights the scholarship that exists on the World War II homefront covering topics such as World War II as a good war, Franklin D. Roosevelt, economic policy, propaganda, status of women and women's employment, the role of African Americans, racial violence, and the Japanese American experience. (CMK)

  3. Mastracchio works with BASS-II

    2014-02-18

    ISS038-E-053250 (18 Feb. 2014) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, works with the Burning and Suppression of Solids (BASS-II) experiment in the Microgravity Science Glovebox (MSG) located in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  4. Oral Assessment Kit, Levels II & III. Draft.

    ERIC Educational Resources Information Center

    Agrelo-Gonzalez, Maria; And Others

    The assessment packet includes a series of oral tests to help develop speaking as an integral part of second language instruction at levels II and III. It contains: 8 mini-tests for use at level II; 9 mini-tests for use at level III; a rating scale and score sheet masters for evaluating performance on these tests; and a collection of suggested…

  5. Biology II Curriculum Guide. Bulletin 1820.

    ERIC Educational Resources Information Center

    Louisiana State Dept. of Education, Baton Rouge. Div. of Academic Programs.

    In 1986, the Louisiana State Board of Elementary and Secondary Education requested that an advanced course in Biology II be developed. The resulting curriculum guide contains grade appropriate goals, skills, and competencies; suggested activities; suggested materials of instruction; and minimum time allotments for instruction. Biology II is a…

  6. World War II Memorial Learning Activities.

    ERIC Educational Resources Information Center

    Tennessee State Dept. of Education, Nashville.

    These learning activities can help students get the most out of a visit to the Tennessee World War II Memorial, a group of ten pylons located in Nashville (Tennessee). Each pylon contains informational text about the events of World War II. The ten pylons are listed as: (1) "Pylon E-1--Terror: America Enters the War against Fascism, June…

  7. Mastracchio works with BASS-II

    2014-02-18

    ISS038-E-053251 (18 Feb. 2014) --- NASA astronaut Rick Mastracchio, Expedition 38 flight engineer, works with the Burning and Suppression of Solids (BASS-II) experiment in the Microgravity Science Glovebox (MSG) located in the Destiny laboratory of the International Space Station. BASS-II explores how different substances burn in microgravity with benefits for combustion on Earth and fire safety in space.

  8. World War II: A Technology Lesson Plan.

    ERIC Educational Resources Information Center

    Hagar, Suzy

    1990-01-01

    Presents a class activity on the history, causes, and consequences of World War II. Focuses on the development and deployment of the atomic bomb. Utilizes a Video Encyclopedia Program for historical background. Divides the class into groups that are responsible for researching and preparing a videotape on a World War II topic. (RW)

  9. TEMPEST II--A NEUTRON THERMALIZATION CODE

    SciT

    Shudde, R.H.; Dyer, J.

    The TEMPEST II neutron thermalization code in Fortran for IBM 709 or 7090 calculates thermal neutron flux spectra based upon the Wigner-Wilkins equation, the Wilkins equation, or the Maxwellian distribution. When a neutron spectrum is obtained, TEMPEST II provides microscopic and macroscopic cross section averages over that spectrum. Equations used by the code and sample input and output data are given. (auth)

  10. SAMS-II Requirements and Operations

    NASA Technical Reports Server (NTRS)

    Wald, Lawrence W.

    1998-01-01

    The Space Acceleration Measurements System (SAMS) II is the primary instrument for the measurement, storage, and communication of the microgravity environment aboard the International Space Station (ISS). SAMS-II is being developed by the NASA Lewis Research Center Microgravity Science Division to primarily support the Office of Life and Microgravity Science and Applications (OLMSA) Microgravity Science and Applications Division (MSAD) payloads aboard the ISS. The SAMS-II is currently in the test and verification phase at NASA LeRC, prior to its first hardware delivery scheduled for July 1998. This paper will provide an overview of the SAMS-II instrument, including the system requirements and topology, physical and electrical characteristics, and the Concept of Operations for SAMS-II aboard the ISS.

  11. Aldosterone response to angiotensin II during hypoxemia

    SciT

    Colice, G.L.; Ramirez, G.

    1986-07-01

    Exercise stimulates the renin-angiotensin-aldosterone system (RAAS). However, increases in plasma aldosterone concentrations (PAC) are suppressed when exercise is performed at high altitude or under hypoxemic conditions. As the angiotensin-II response to high-altitude exercise is normal, it is speculated that an inhibitor, discharged during hypoxemia, acted to suppress angiotensin-II-mediated aldosterone release. A study was conducted to test this hypothesis, taking into account the measurement of the aldosterone response to exogenous angiotensin II during normoxemia and hypoxemia. It was found that the dose-response curve of PAC to angiotensin II was not significantly inhibited by the considered model of hypoxemia. The hypoxemia-mediated releasemore » of an angiotensin II inhibitor does, therefore, not explain the previous observations of PAC suppression during hypoxemic exercise. 28 references.« less

  12. Reoperative Cardiac Surgery - Part II.

    PubMed

    Tribble, Curtis G

    2018-04-10

    The preparation for a reoperative cardiac surgical case was covered in Part I of this two part review [Tribble 2018]. Part II will cover primarily intraoperative strategies and techniques.  As noted in Part I, there has been surprisingly little written about the strategies and techniques of reoperative cardiac surgery. Thus, the goal of this two-part review is to collect and collate some of the lessons, abjurations, and tenets related to reoperative cardiac surgery that may be valuable to cardiac surgeons, especially those in training or early in their careers.Some time-honored admonitions that can apply to all complex operations, often enunciated by "old salts," bear repeating:•  Everything matters. Nothing is neutral.•  Some say that a "life or death" decision is made, on average, every 10 seconds during cardiac surgery. •  If something can go wrong, presume that it will.•  If it seems absolutely impossible for something to go wrong, it will anyway, at least some of the time.•  When something does go wrong, it generally does so all at once.•  If what you are doing is working, keep on doing it. If it ain't working, do something else.

  13. Multi-metals column adsorption of lead(II), cadmium(II) and manganese(II) onto natural bentonite clay.

    PubMed

    Alexander, Jock Asanja; Surajudeen, Abdulsalam; Aliyu, El-Nafaty Usman; Omeiza, Aroke Umar; Zaini, Muhammad Abbas Ahmad

    2017-10-01

    The present work was aimed at evaluating the multi-metals column adsorption of lead(II), cadmium(II) and manganese(II) ions onto natural bentonite. The bentonite clay adsorbent was characterized for physical and chemical properties using X-ray diffraction, X-ray fluorescence, Brunauer-Emmett-Teller surface area and cation exchange capacity. The column performance was evaluated using adsorbent bed height of 5.0 cm, with varying influent concentrations (10 mg/L and 50 mg/L) and flow rates (1.4 mL/min and 2.4 mL/min). The result shows that the breakthrough time for all metal ions ranged from 50 to 480 minutes. The maximum adsorption capacity was obtained at initial concentration of 10 mg/L and flow rate of 1.4 mL/min, with 2.22 mg/g of lead(II), 1.71 mg/g of cadmium(II) and 0.37 mg/g of manganese(II). The order of metal ions removal by natural bentonite is lead(II) > cadmium(II) > manganese(II). The sorption performance and the dynamic behaviour of the column were predicted using Adams-Bohart, Thomas, and Yoon-Nelson models. The linear regression analysis demonstrated that the Thomas and Yoon-Nelson models fitted well with the column adsorption data for all metal ions. The natural bentonite was effective for the treatment of wastewater laden with mul